Table of contents for issues of Journal of Computational Chemistry

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Volume 18, Number 12, September, 1997
Volume 28, Number 16, December, 2007
Volume 29, Number 11, August, 2008
Volume 30, Number 3, February, 2009
Volume 30, Number 11, August, 2009
Volume 30, Number 12, September, 2009
Volume 30, Number 16, December, 2009
Volume 31, Number 1, January 15, 2010
Volume 31, Number 2, January 30, 2010
Volume 31, Number 3, February, 2010
Volume 31, Number 4, March, 2010
Volume 31, Number 5, April 15, 2010
Volume 31, Number 6, April 30, 2010
Volume 31, Number 7, May, 2010
Volume 31, Number 8, June, 2010
Volume 31, Number 9, July 15, 2010
Volume 31, Number 10, July 30, 2010
Volume 31, Number 11, August, 2010
Volume 31, Number 12, September, 2010
Volume 31, Number 13, October, 2010
Volume 31, Number 14, November 15, 2010
Volume 31, Number 15, November 30, 2010
Volume 31, Number 16, December, 2010
Volume 32, Number 1, January 15, 2011
Volume 32, Number 2, January 30, 2011
Volume 32, Number 3, February, 2011
Volume 32, Number 4, March, 2011
Volume 32, Number 5, April 15, 2011
Volume 32, Number 6, April 30, 2011
Volume 32, Number 7, May, 2011
Volume 32, Number 8, June, 2011
Volume 32, Number 9, July 15, 2011
Volume 32, Number 10, July 30, 2011
Volume 32, Number 11, August, 2011
Volume 32, Number 12, September, 2011
Volume 32, Number 13, October, 2011
Volume 32, Number 14, November 15, 2011
Volume 32, Number 15, November 30, 2011
Volume 32, Number 16, December, 2011
Volume 33, Number 1, January 5, 2012
Volume 33, Number 2, January 15, 2012
Volume 33, Number 3, January 30, 2012
Volume 33, Number 4, February 5, 2012
Volume 33, Number 5, February 15, 2012
Volume 33, Number 6, March 5, 2012
Volume 33, Number 7, March 15, 2012
Volume 33, Number 8, March 30, 2012
Volume 33, Number 9, April 5, 2012
Volume 33, Number 10, April 15, 2012
Volume 33, Number 11, April 30, 2012
Volume 33, Number 12, May 5, 2012
Volume 33, Number 13, May 15, 2012
Volume 33, Number 14, May 30, 2012
Volume 33, Number 15, June 5, 2012
Volume 33, Number 16, June 15, 2012
Volume 33, Number 17, June 30, 2012
Volume 33, Number 18, July 5, 2012
Volume 33, Number 19, July 15, 2012
Volume 33, Number 20, July 30, 2012
Volume 33, Number 21, August 5, 2012
Volume 33, Number 22, August 15, 2012
Volume 33, Number 23, September 5, 2012
Volume 33, Number 24, September 15, 2012
Volume 33, Number 25, September 30, 2012
Volume 33, Number 26, October 5, 2012
Volume 33, Number 27, October 15, 2012
Volume 33, Number 28, October 30, 2012
Volume 33, Number 29, November 5, 2012
Volume 33, Number 30, November 15, 2012
Volume 33, Number 31, December 5, 2012
Volume 33, Number 32, December 15, 2012
Volume 34, Number 1, January 5, 2013
Volume 34, Number 2, January 15, 2013
Volume 34, Number 3, January 30, 2013
Volume 34, Number 4, February 5, 2013
Volume 34, Number 5, February 15, 2013
Volume 34, Number 6, March 5, 2013
Volume 34, Number 7, March 15, 2013
Volume 34, Number 8, March 30, 2013
Volume 34, Number 9, April 5, 2013
Volume 34, Number 10, April 5, 2013
Volume 34, Number 11, April 30, 2013
Volume 34, Number 12, May 5, 2013
Volume 34, Number 13, May 15, 2013
Volume 34, Number 14, May 30, 2013
Volume 34, Number 15, June 5, 2013
Volume 34, Number 16, June 15, 2013
Volume 34, Number 17, June 30, 2013
Volume 34, Number 18, July 5, 2013
Volume 34, Number 19, July 15, 2013
Volume 34, Number 20, July 30, 2013
Volume 34, Number 21, August 5, 2013
Volume 34, Number 22, August 15, 2013
Volume 34, Number 23, September 5, 2013
Volume 34, Number 24, September 15, 2013
Volume 34, Number 25, September 30, 2013
Volume 34, Number 26, October 5, 2013
Volume 34, Number 27, October 15, 2013
Volume 34, Number 28, October 30, 2013
Volume 34, Number 29, November 5, 2013
Volume 34, Number 30, November 15, 2013
Volume 34, Number 31, December 5, 2013
Volume 34, Number 32, December 15, 2013
Volume 35, Number 1, January 5, 2014
Volume 35, Number 2, January 15, 2014
Volume 35, Number 3, January 30, 2014
Volume 35, Number 4, February 5, 2014
Volume 35, Number 5, February 15, 2014
Volume 35, Number 6, March 5, 2014
Volume 35, Number 7, March 15, 2014
Volume 35, Number 8, March 30, 2014
Volume 35, Number 9, April 5, 2014
Volume 35, Number 10, April 15, 2014
Volume 35, Number 11, April 30, 2014
Volume 35, Number 12, May 5, 2014
Volume 35, Number 13, May 15, 2014
Volume 35, Number 14, May 30, 2014
Volume 35, Number 15, June 5, 2014
Volume 35, Number 16, June 15, 2014
Volume 35, Number 17, June 30, 2014
Volume 35, Number 18, July 5, 2014
Volume 35, Number 19, July 15, 2014
Volume 35, Number 20, July 30, 2014
Volume 35, Number 21, August 5, 2014
Volume 35, Number 22, August 15, 2014
Volume 35, Number 23, September 5, 2014
Volume 35, Number 24, September 15, 2014
Volume 35, Number 25, September 30, 2014
Volume 35, Number 26, October 5, 2014
Volume 35, Number 27, October 15, 2014
Volume 35, Number 28, October 30, 2014
Volume 35, Number 29, November 5, 2014
Volume 35, Number 30, November 15, 2014
Volume 35, Number 31, December 5, 2014
Volume 35, Number 32, December 15, 2014
Volume 36, Number 1, January 5, 2015
Volume 36, Number 2, January 15, 2015
Volume 36, Number 3, January 30, 2015
Volume 36, Number 4, February 5, 2015
Volume 36, Number 5, February 15, 2015
Volume 36, Number 6, March 5, 2015
Volume 36, Number 7, March 15, 2015
Volume 36, Number 8, March 30, 2015
Volume 36, Number 9, April 5, 2015
Volume 36, Number 10, April 15, 2015
Volume 36, Number 11, April 30, 2015
Volume 36, Number 12, May 5, 2015
Volume 36, Number 13, May 15, 2015
Volume 36, Number 14, May 30, 2015
Volume 36, Number 15, June 5, 2015
Volume 36, Number 16, June 15, 2015
Volume 36, Number 17, June 30, 2015
Volume 36, Number 18, July 5, 2015
Volume 36, Number 19, July 15, 2015
Volume 36, Number 20, July 30, 2015
Volume 36, Number 21, August 5, 2015
Volume 36, Number 22, August 15, 2015
Volume 36, Number 23, September 5, 2015
Volume 36, Number 24, September 15, 2015
Volume 36, Number 25, September 30, 2015
Volume 36, Number 26, October 5, 2015
Volume 36, Number 27, October 15, 2015
Volume 36, Number 28, October 30, 2015
Volume 36, Number 29, November 5, 2015
Volume 36, Number 30, November 15, 2015
Volume 36, Number 31, December 5, 2015
Volume 36, Number 32, December 15, 2015
Volume 37, Number 1, January 5, 2016
Volume 37, Number 2, January 15, 2016
Volume 37, Number 3, January 30, 2016
Volume 37, Number 4, February 5, 2016
Volume 37, Number 5, February 15, 2016
Volume 37, Number 6, March 5, 2016
Volume 37, Number 7, March 15, 2016
Volume 37, Number 8, March 30, 2016
Volume 37, Number 9, April 5, 2016
Volume 37, Number 10, April 15, 2016
Volume 37, Number 11, April 30, 2016
Volume 37, Number 12, May 5, 2016
Volume 37, Number 13, May 15, 2016
Volume 37, Number 14, May 30, 2016
Volume 37, Number 15, June 5, 2016
Volume 37, Number 16, June 15, 2016
Volume 37, Number 17, June 30, 2016
Volume 37, Number 18, July 5, 2016
Volume 37, Number 19, July 15, 2016
Volume 37, Number 20, July 30, 2016
Volume 37, Number 21, August 05, 2016
Volume 37, Number 22, August 15, 2016
Volume 37, Number 23, September 5, 2016
Volume 37, Number 24, September 15, 2016
Volume 37, Number 25, September 30, 2016
Volume 37, Number 26, October 5, 2016
Volume 37, Number 27, October 15, 2016
Volume 37, Number 28, October 30, 2016
Volume 37, Number 29, November 5, 2016
Volume 37, Number 30, November 15, 2016
Volume 37, Number 31, December 5, 2016
Volume 37, Number 32, December 15, 2016
Volume 38, Number 1, January 05, 2017
Volume 38, Number 2, January 15, 2017
Volume 38, Number 3, January 30, 2017
Volume 38, Number 4, February 5, 2017
Volume 38, Number 5, February 15, 2017
Volume 38, Number 6, March 5, 2017
Volume 38, Number 7, March 15, 2017
Volume 38, Number 8, March 30, 2017
Volume 38, Number 9, April 5, 2017
Volume 38, Number 10, April 15, 2017
Volume 38, Number 11, April 30, 2017
Volume 38, Number 12, May 5, 2017
Volume 38, Number 13, May 15, 2017
Volume 38, Number 14, May 30, 2017
Volume 38, Number 15, June 5, 2017
Volume 38, Number 16, June 15, 2017
Volume 38, Number 17, June 30, 2017
Volume 38, Number 18, July 5, 2017
Volume 38, Number 19, July 15, 2017
Volume 38, Number 20, July 30, 2017
Volume 38, Number 21, August 5, 2017
Volume 38, Number 22, August 15, 2017
Volume 38, Number 23, September 5, 2017
Volume 38, Number 24, September 15, 2017
Volume 38, Number 25, September 30, 2017
Volume 38, Number 26, October 5, 2017
Volume 38, Number 27, October 15, 2017
Volume 38, Number 28, October 30, 2017
Volume 38, Number 29, November 5, 2017
Volume 38, Number 30, November 15, 2017
Volume 38, Number 31, December 5, 2017
Volume 38, Number 32, December 15, 2017
Volume 39, Number 1, January 5, 2018
Volume 39, Number 2, January 15, 2018
Volume 39, Number 3, January 30, 2018
Volume 39, Number 4, February 5, 2018
Volume 39, Number 5, February 15, 2018
Volume 39, Number 6, March 5, 2018
Volume 39, Number 7, March 15, 2018
Volume 39, Number 8, March 30, 2018
Volume 39, Number 9, April 5, 2018


Journal of Computational Chemistry
Volume 18, Number 12, September, 1997

     Gábor I. Csonka and   
             Nam Anh Nguyen and   
István Kolossváry   Simple tests for density functional
                                  methods  . . . . . . . . . . . . . . . . 1534--1545


Journal of Computational Chemistry
Volume 28, Number 16, December, 2007

                D. Heringer and   
              T. A. Niehaus and   
                   M. Wanko and   
                 Th. Frauenheim   Analytical excited state forces for the
                                  time-dependent density-functional
                                  tight-binding method . . . . . . . . . . 2589--2601


Journal of Computational Chemistry
Volume 29, Number 11, August, 2008

            Laban Bondesson and   
              Elias Rudberg and   
                     Yi Luo and   
                  Pawe\l Sa\lek   Basis set dependence of solute--solvent
                                  interaction energy of benzene in water:
                                  a HF/DFT study . . . . . . . . . . . . . 1725--1732


Journal of Computational Chemistry
Volume 30, Number 3, February, 2009

              Lingchun Song and   
              Jinshuai Song and   
                  Yirong Mo and   
                         Wei Wu   An efficient algorithm for energy
                                  gradients and orbital optimization in
                                  valence bond theory  . . . . . . . . . . 399--406

Journal of Computational Chemistry
Volume 30, Number 11, August, 2009

                Mengen Chen and   
                       Wei Yang   On-the-path random walk sampling for
                                  efficient optimization of minimum
                                  free-energy path . . . . . . . . . . . . 1649--1653

Journal of Computational Chemistry
Volume 30, Number 12, September, 2009

                 Xinli Song and   
                   Jicun Li and   
                    Hua Hou and   
                   Baoshan Wang   Extensive theoretical studies of a new
                                  energetic material:
                                  Tetrazino-tetrazine-tetraoxide (TTTO)    1816--1820

Journal of Computational Chemistry
Volume 30, Number 16, December, 2009

J. Oscar C. Jiménez-Halla and   
              Eduard Matito and   
    Lluís Blancafort and   
            Juvencio Robles and   
                  Miquel Sol\`a   Tuning aromaticity in trigonal alkaline
                                  earth metal clusters and their alkali
                                  metal salts  . . . . . . . . . . . . . . 2764--2776


Journal of Computational Chemistry
Volume 31, Number 1, January 15, 2010

           Halvor S. Hansen and   
   Philippe H. Hünenberger   Using the local elevation method to
                                  construct optimized umbrella sampling
                                  potentials: Calculation of the relative
                                  free energies and interconversion
                                  barriers of glucopyranose ring
                                  conformers in water  . . . . . . . . . . 1--23
                    Lili Xi and   
                    Juan Du and   
                  Shuyan Li and   
                Jiazhong Li and   
              Huanxiang Liu and   
                    Xiaojun Yao   A combined molecular modeling study on
                                  gelatinases and their potent inhibitors  24--42
                    Ming-Der Su   A computational study of photochemical
                                  isomerization reactions of thiophenes    43--56
                  In-Ho Lee and   
             Seung-Yeon Kim and   
                   Jooyoung Lee   Dynamic folding pathway models of the
                                  villin headpiece subdomain (HP-36)
                                  structure  . . . . . . . . . . . . . . . 57--65
         Reza Sharifi Sedeh and   
                 Mark Bathe and   
        Klaus-Jürgen Bathe   The subspace iteration method in protein
                                  normal mode analysis . . . . . . . . . . 66--74
            Tamar Ansbacher and   
    Hemant Kumar Srivastava and   
           Jan M. L. Martin and   
                  Avital Shurki   Can DFT methods correctly and
                                  efficiently predict the coordination
                                  number of copper(I) complexes? A case
                                  study  . . . . . . . . . . . . . . . . . 75--83
            Igor Zilberberg and   
                Sergey Ruzankin   Paired orbitals for different spins
                                  equations  . . . . . . . . . . . . . . . 84--89
                 Maja Parac and   
               Markus Doerr and   
         Christel M. Marian and   
                   Walter Thiel   QM/MM calculation of solvent effects on
                                  absorption spectra of guanine  . . . . . 90--106
               Hajime Torii and   
                 Masaki Yoshida   Properties of halogen atoms for
                                  representing intermolecular
                                  electrostatic interactions related to
                                  halogen bonding and their substituent
                                  effects  . . . . . . . . . . . . . . . . 107--116
             Imran S. Haque and   
                 Vijay S. Pande   PAPER --- accelerating parallel
                                  evaluations of ROCS  . . . . . . . . . . 117--132
               Evgeny Krissinel   Crystal contacts as nature's docking
                                  solutions  . . . . . . . . . . . . . . . 133--143
          Roman I. Zubatyuk and   
                Leonid Gorb and   
           Oleg V. Shishkin and   
                   Mo Qasim and   
              Jerzy Leszczynski   Exploration of density functional
                                  methods for one-electron reduction
                                  potential of nitrobenzenes . . . . . . . 144--150
           Traci Strohecker and   
                Herschel Rabitz   Quantum control implemented as
                                  combinatorial optimization . . . . . . . 151--153
              Bong Hyun Boo and   
                     Suk Im and   
                    Sungyul Lee   Ab initio and DFT studies of the thermal
                                  rearrangement of
                                  trimethylsilyl(methyl)silylene:
                                  Remarkable rearrangements of silicon
                                  intermediates  . . . . . . . . . . . . . 154--163
   Francisco J. Prado-Prado and   
        Florencio M. Ubeira and   
            Fernanda Borges and   
Humberto González-Díaz   Unified QSAR & network-based
                                  computational chemistry approach to
                                  antimicrobials. II. Multiple distance
                                  and triadic census analysis of
                                  antiparasitic drugs complex networks . . 164--173
Alfonso T. García-Sosa and   
       Csaba Hetényi and   
                      Uko Maran   Drug efficiency indices for improvement
                                  of molecular docking scoring functions   174--184
Marie-Céline van Severen and   
      Christophe Gourlaouen and   
                Olivier Parisel   Application of the topological analysis
                                  of the electronic localization function
                                  to archetypical [Pb(II)L$_n$ ]$^p$
                                  complexes: the bonding of Pb$^{2+}$
                                  revisited  . . . . . . . . . . . . . . . 185--194
              Yin-Feng Wang and   
                  Zhi-Ru Li and   
                      Di Wu and   
             Chia-Chung Sun and   
                   Feng-Long Gu   Excess electron is trapped in a large
                                  single molecular cage C$_{60}$F$_{60}$   195--203
          Alexey K. Shaytan and   
           Victor A. Ivanov and   
      Konstantin V. Shaitan and   
             Alexei R. Khokhlov   Free energy profiles of amino acid side
                                  chain analogs near water-vapor interface
                                  obtained via MD simulations  . . . . . . 204--216
                  Yu-yen Ou and   
                Shu-an Chen and   
             M. Michael Gromiha   Prediction of membrane spanning segments
                                  and topology in $ \beta $-barrel
                                  membrane proteins at better accuracy . . 217--223
        Francesco Aquilante and   
               Luca De Vico and   
       Nicolas Ferré and   
             Giovanni Ghigo and   
    Per-åke Malmqvist and   
      Pavel Neogrády and   
      Thomas Bondo Pedersen and   
    Michal Pito\unák and   
              Markus Reiher and   
         Björn O. Roos and   
 Luis Serrano-Andrés and   
             Miroslav Urban and   
            Valera Veryazov and   
                   Roland Lindh   MOLCAS 7: the Next Generation  . . . . . 224--247

Journal of Computational Chemistry
Volume 31, Number 2, January 30, 2010

       Viwat Vchirawongkwin and   
          Andreas B. Pribil and   
                  Bernd M. Rode   Ab initio quantum mechanical charge
                                  field study of hydrated bicarbonate ion:
                                  Structural and dynamical properties  . . 249--257
            Hsin-Tsung Chen and   
             Jee-Gong Chang and   
                Shin-Pon Ju and   
                  Hui-Lung Chen   First-principle calculations on CO
                                  oxidation catalyzed by a gold
                                  nanoparticle . . . . . . . . . . . . . . 258--265
           Priyanka Prakash and   
  Ramasubbu Sankararamakrishnan   Force field dependence of phospholipid
                                  headgroup and acyl chain properties:
                                  Comparative molecular dynamics
                                  simulations of DMPC bilayers . . . . . . 266--277
           S. Sikander Azam and   
          Len Herald V. Lim and   
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Hydrated germanium (II): Irregular
                                  structural and dynamical properties
                                  revealed by a quantum mechanical charge
                                  field molecular dynamics study . . . . . 278--285
                  S. Jalili and   
                     M. Akhavan   Molecular dynamics simulation study of
                                  association in trifluoroethanol/water
                                  mixtures . . . . . . . . . . . . . . . . 286--294
              Lionello Pogliani   Model of twelve properties of a set of
                                  organic solvents with graph-theoretical
                                  and/or experimental parameters . . . . . 295--307
       Johan Strümpfer and   
                Kevin J. Naidoo   Computing free energy hypersurfaces for
                                  anisotropic intermolecular associations  308--316
           Irina S. Moreira and   
         Pedro A. Fernandes and   
                 Maria J. Ramos   Protein--protein docking dealing with
                                  the unknown  . . . . . . . . . . . . . . 317--342
                   Carlo Canepa   A stationary-wave model of enzyme
                                  catalysis  . . . . . . . . . . . . . . . 343--350
                     Qi Dai and   
               Xiaoqing Liu and   
                   Lihua Li and   
                  Yuhua Yao and   
                    Bin Han and   
                        Lei Zhu   Using Gaussian model to improve
                                  biological sequence comparison . . . . . 351--361
                     Bin Li and   
               Tian-Shu Chu and   
                      Ke-Li Han   Non-Born--Oppenheimer dynamics
                                  calculations using the coherent
                                  switching with decay of mixing method    362--370
               Zhongqiao Hu and   
                  Jianwen Jiang   Assessment of biomolecular force fields
                                  for molecular dynamics simulations in a
                                  protein crystal  . . . . . . . . . . . . 371--380
          Andrey A. Toropov and   
           Alla P. Toropova and   
           Emilio Benfenati and   
         Danuta Leszczynska and   
              Jerzy Leszczynski   SMILES-based optimal descriptors: QSAR
                                  analysis of fullerene-based HIV-1 PR
                                  inhibitors by means of balance of
                                  correlations . . . . . . . . . . . . . . 381--392
                 Shihai Yan and   
                Sunwoo Kang and   
           Tomoyuki Hayashi and   
              Shaul Mukamel and   
                   Jin Yong Lee   Computational studies on electron and
                                  proton transfer in phenol-imidazole-base
                                  triads . . . . . . . . . . . . . . . . . 393--402
                  Hui Zhang and   
             Gui-Ling Zhang and   
               Jing-Yao Liu and   
                   Miao Sun and   
                     Bo Liu and   
                    Ze-Sheng Li   Theoretical study and rate constants
                                  calculation for the reactions of SiH$_3$
                                  radical with SiH$_3$CH$_3$ and SiH$_2$
                                  (CH$_3$ )$_2$  . . . . . . . . . . . . . 403--411
    Christos Christodouleas and   
          Demetrios Xenides and   
              Theodore E. Simos   Trends of the bonding effect on the
                                  performance of DFT methods in electric
                                  properties calculations: a pattern
                                  recognition and metric space approach on
                                  some XY$_2$ (X = O, S and Y = H, O, F,
                                  S, Cl) molecules . . . . . . . . . . . . 412--420
                A. V. Larin and   
           G. M. Zhidomirov and   
            D. N. Trubnikov and   
              D. P. Vercauteren   Ion-exchanged binuclear Ca$_2$O$_x$
                                  clusters, $ x = 1 $--4, as active sites
                                  of selective oxidation over MOR and FAU
                                  zeolites . . . . . . . . . . . . . . . . 421--430
      Athanassios C. Tsipis and   
        Ioannis G. Depastas and   
  Efstathios E. Karagiannis and   
         Constantinos A. Tsipis   Diagnosis of magnetoresponsive aromatic
                                  and antiaromatic zones in three-membered
                                  rings of $d$- and $f$-block elements . . 431--446
            Tsutomu Ikegami and   
            Toyokazu Ishida and   
          Dmitri G. Fedorov and   
              Kazuo Kitaura and   
             Yuichi Inadomi and   
              Hiroaki Umeda and   
            Mitsuo Yokokawa and   
              Satoshi Sekiguchi   Fragment molecular orbital study of the
                                  electronic excitations in the
                                  photosynthetic reaction center of
                                  Blastochloris viridis  . . . . . . . . . 447--454
                 Oleg Trott and   
                Arthur J. Olson   AutoDock Vina: Improving the speed and
                                  accuracy of docking with a new scoring
                                  function, efficient optimization, and
                                  multithreading . . . . . . . . . . . . . 455--461

Journal of Computational Chemistry
Volume 31, Number 3, February, 2010

                Rekik Najeh and   
             Ghalla Houcine and   
           Henryk T. Flakus and   
        Magdalena Jablonska and   
                   Oujia Brahim   Experimental and theoretical study of
                                  the polarized infrared spectra of the
                                  hydrogen bond in 3-thiophenic acid
                                  crystal  . . . . . . . . . . . . . . . . 463--475
           Daniel K. W. Mok and   
               Foo-Tim Chau and   
           Edmond P. F. Lee and   
                   John M. Dyke   High-level ab initio calculations on
                                  HGeCl and the equilibrium geometry of
                                  the $ {\rm \tilde {A}}^1 {\rm A}' $
                                  state derived from Franck--Condon
                                  analysis of the single-vibronic-level
                                  emission spectra of HGeCl and DGeCl  . . 476--491
                   Peng Cui and   
                    Jian Wu and   
              Guiqing Zhang and   
                Russell J. Boyd   A simple representation of energy matrix
                                  elements in terms of symmetry-invariant
                                  bases  . . . . . . . . . . . . . . . . . 492--496
            Masahiro Sekiya and   
               Takeshi Noro and   
            Toshikatsu Koga and   
                 Shiro L. Saito   Relativistic correlating basis sets for
                                  $_{57}$La and $_{89}$Ac  . . . . . . . . 497--499
          Mohamad Akbar Ali and   
                   B. Rajakumar   Rate coefficients for the reaction of OH
                                  with CF$_3$CH$_2$CH$_3$ (HFC-263fb)
                                  between 200 and 400 K: ab initio, DFT,
                                  and transition state theory calculations 500--509
                Yue-Meng Ji and   
                Fenglei Cao and   
                    Hui Gao and   
                Xiangzhi Li and   
               Cunyuan Zhao and   
               Chengyong Su and   
               Jing-Yao Liu and   
                    Ze-Sheng Li   On the kinetic mechanism of the hydrogen
                                  abstraction reactions of the hydroxyl
                                  radical with CH$_3$CF$_2$Cl and
                                  CH$_3$CFCl$_2$: a dual level direct
                                  dynamics study . . . . . . . . . . . . . 510--519
 Jesús Gálvez and   
                Antonio Guirado   A theoretical study of topomerization of
                                  imine systems: Inversion, rotation or
                                  mixed mechanisms?  . . . . . . . . . . . 520--531
                 Yong Zhang and   
                  Wenhua Xu and   
                 Qiming Sun and   
                  Wenli Zou and   
                    Wenjian Liu   Excited states of OsO$_4$: a
                                  comprehensive time-dependent
                                  relativistic density functional theory
                                  study  . . . . . . . . . . . . . . . . . 532--551
        Angelika Baranowska and   
              Andrzej J. Sadlej   Polarized basis sets for accurate
                                  calculations of static and dynamic
                                  electric properties of molecules . . . . 552--560
     Pieter M. S. Hendrickx and   
          Francisco Corzana and   
         Stefaan Depraetere and   
      Dirk A. Tourwé and   
             Koen Augustyns and   
         José C. Martins   The use of time-averaged $^3$J$_{HH}$
                                  restrained molecular dynamics (tar-MD)
                                  simulations for the conformational
                                  analysis of five-membered ring systems:
                                  Methodology and applications . . . . . . 561--572
             Wolfgang Quapp and   
                   Alraune Zech   Transition state theory with Tsallis
                                  statistics . . . . . . . . . . . . . . . 573--585
                   Feng Fan and   
               Jiagao Cheng and   
                   Zhong Li and   
                Xiaoyong Xu and   
                    Xuhong Qian   Novel dimer based descriptors with
                                  solvational computation for QSAR study
                                  of oxadiazoylbenzoyl-ureas as novel
                                  insect-growth regulators . . . . . . . . 586--591
             Dong-Sheng Cao and   
              Yi-Zeng Liang and   
               Qing-Song Xu and   
               Hong-Dong Li and   
                      Xian Chen   A new strategy of outlier detection for
                                  QSAR/QSPR  . . . . . . . . . . . . . . . 592--602
                 Youn Jo Ko and   
                      Won Ho Jo   Chloride ion conduction without water
                                  coordination in the pore of ClC protein  603--611
     Michael Gilleßen and   
            Richard Dronskowski   A combinatorial study of inverse Heusler
                                  alloys by first-principles computational
                                  methods  . . . . . . . . . . . . . . . . 612--619
             Jory Z. Ruscio and   
           Nicolas L. Fawzi and   
             Teresa Head-Gordon   How hot? Systematic convergence of the
                                  replica exchange method using multiple
                                  reservoirs . . . . . . . . . . . . . . . 620--627
                    Tao Liu and   
                Bao-Hui Xia and   
           Qing-Chuan Zheng and   
                   Xin Zhou and   
             Qing-Jiang Pan and   
                Hong-Xing Zhang   DFT/TD-DFT investigation on Ir(III)
                                  complexes with $N$-heterocyclic carbene
                                  ligands: Geometries, electronic
                                  structures, absorption, and
                                  phosphorescence properties . . . . . . . 628--638
                T. G. A. Youngs   Aten --- an application for the
                                  creation, editing, and visualization of
                                  coordinates for glasses, liquids,
                                  crystals, and molecules  . . . . . . . . 639--648
     Thierry Schüpbach and   
              Vincent Zoete and   
 Brice Tsakam-Sotché and   
              Olivier Michielin   Fourier transform convolution integrals
                                  applied to generalized Born molecular
                                  volume . . . . . . . . . . . . . . . . . 649--659
                   Udo Feldkamp   CANADA: Designing nucleic acid sequences
                                  for nanobiotechnology applications . . . 660--663

Journal of Computational Chemistry
Volume 31, Number 4, March, 2010

          Sebastian Schlund and   
Eline M. Basílio Janke and   
                Klaus Weisz and   
                   Bernd Engels   Predicting the tautomeric equilibrium of
                                  acetylacetone in solution. I. The right
                                  answer for the wrong reason? . . . . . . 665--670
          K. Vanommeslaeghe and   
                 E. Hatcher and   
                 C. Acharya and   
                   S. Kundu and   
                   S. Zhong and   
                    J. Shim and   
                  E. Darian and   
                 O. Guvench and   
                   P. Lopes and   
                I. Vorobyov and   
            A. D. Mackerell Jr.   CHARMM general force field: a force
                                  field for drug-like molecules compatible
                                  with the CHARMM all-atom additive
                                  biological force fields  . . . . . . . . 671--690
        Ramu Anandakrishnan and   
             Alexey V. Onufriev   An $ N \log N $ approximation based on
                                  the natural organization of biomolecules
                                  for speeding up the computation of long
                                  range interactions . . . . . . . . . . . 691--706
             Santiago Vilar and   
               Joel Karpiak and   
               Stefano Costanzi   Ligand and structure-based models for
                                  the prediction of ligand-receptor
                                  affinities and virtual screenings:
                                  Development and application to the $
                                  \beta_2 $-adrenergic receptor  . . . . . 707--720
             Selina C. Wang and   
              Peter A. Beal and   
               Dean J. Tantillo   Covalent hydration energies for purine
                                  analogs by quantum chemical methods  . . 721--725
            Julien Maupetit and   
        Philippe Derreumaux and   
          Pierre Tufféry   A fast method for large-scale De Novo
                                  peptide and miniprotein structure
                                  prediction . . . . . . . . . . . . . . . 726--738
           Nilesh R. Tawari and   
               Mariam S. Degani   Pharmacophore mapping and electronic
                                  feature analysis for a series of
                                  nitroaromatic compounds with
                                  antitubercular activity  . . . . . . . . 739--751
                Hanbing Rao and   
                  Zerong Li and   
               Xiangyuan Li and   
                 Xiaohua Ma and   
             Choongyong Ung and   
                      Hu Li and   
               Xianghui Liu and   
                    Yuzong Chen   Identification of small molecule
                                  aggregators from large compound
                                  libraries by support vector machines . . 752--763
    Vill\Ho K. Pálfi and   
          András Perczel   Stability of the hydration layer of
                                  tropocollagen: a  QM study . . . . . . . 764--777
                     Hui Li and   
          Dmitri G. Fedorov and   
             Takeshi Nagata and   
              Kazuo Kitaura and   
              Jan H. Jensen and   
                 Mark S. Gordon   Energy gradients in combined fragment
                                  molecular orbital and polarizable
                                  continuum model (FMO/PCM) calculation    778--790
             Katsumi Murata and   
               Naoya Nagata and   
             Isao Nakanishi and   
                  Kazuo Kitaura   Ligand shape emerges in solvent dipole
                                  ordering region at ligand binding site
                                  of protein . . . . . . . . . . . . . . . 791--796
            Giulio Rastelli and   
            Alberto Del Rio and   
      Gianluca Degliesposti and   
                  Miriam Sgobba   Fast and accurate predictions of binding
                                  free energies using MM-PBSA and MM-GBSA  797--810
Jean-François Truchon and   
           Anthony Nicholls and   
            J. Andrew Grant and   
            Radu I. Iftimie and   
             Beno\^\it Roux and   
           Christopher I. Bayly   Using electronic polarization from the
                                  internal continuum (EPIC) for
                                  intermolecular interactions  . . . . . . 811--824
               Laibin Zhang and   
                 Huifang Li and   
                   Jilai Li and   
               Xiaohua Chen and   
                     Yuxiang Bu   Absorption and fluorescence emission
                                  spectroscopic characters of
                                  naphtho-homologated yy-DNA bases and
                                  effect of methanol solution and base
                                  pairing  . . . . . . . . . . . . . . . . 825--836
            Samuel Genheden and   
                       Ulf Ryde   How to obtain statistically converged
                                  MM/GBSA results  . . . . . . . . . . . . 837--846
                  Ling Wang and   
                Boris Stumm and   
                 Volkhard Helms   Graph-theoretical identification of
                                  dissociation pathways on free energy
                                  landscapes of biomolecular interaction   847--854
                  Yves Noel and   
            Philippe D'arco and   
       Raffaella Demichelis and   
 Claudio M. Zicovich-Wilson and   
                 Roberto Dovesi   On the use of symmetry in the ab initio
                                  quantum mechanical simulation of
                                  nanotubes and related materials  . . . . 855--862
               Guang Tao Yu and   
                   Wei Chen and   
               Feng Long Gu and   
                    Yuriko Aoki   Theoretical study on nonlinear optical
                                  properties of the Li$^+$
                                  [calix[4]pyrrole]Li$^-$ dimer, trimer
                                  and its polymer with diffuse excess
                                  electrons  . . . . . . . . . . . . . . . 863--870
              Xiaoyan Zheng and   
                 Xueye Wang and   
                Shanfeng Yi and   
              Nuanqing Wang and   
                   Yueming Peng   Density functional theory study of the
                                  free and tetraprotonated spheroidal
                                  macrotricyclic ligands and the complexes
                                  with halide anions: F$^-$, Cl$^-$,
                                  Br$^-$ . . . . . . . . . . . . . . . . . 871--881
    Alejandro Speck Planche and   
       Marcus Tulius Scotti and   
Vicente de Paulo Emerenciano and   
América García López and   
Enrique Molina Pérez and   
                Eugenio Uriarte   Designing novel antitrypanosomal agents
                                  from a mixed graph-theoretical
                                  substructural approach . . . . . . . . . 882--894
             Michael Springborg   Book review: \booktitleComputational
                                  Chemistry Workbook, by Thomas Heine,
                                  Jan-Ole Joswig, and Achim Gelessus,
                                  Wiley-VCH Verlag GmbH & Co. KGaA,
                                  Weinheim, 2009, 250 pp. ISBN-10
                                  3-527-32442-9  . . . . . . . . . . . . . 895--896

Journal of Computational Chemistry
Volume 31, Number 5, April 15, 2010

                Hwanho Choi and   
               Hongsuk Kang and   
                  Hwangseo Park   New angle-dependent potential energy
                                  function for backbone--backbone hydrogen
                                  bond in protein--protein interactions    897--903
          Benjamin D. Allen and   
                Stephen L. Mayo   An efficient algorithm for multistate
                                  protein design based on FASTER . . . . . 904--916
            Mercedes Alonso and   
       Bernardo Herradón   A universal scale of aromaticity for $
                                  \pi $-organic compounds  . . . . . . . . 917--928
     Behnam Assadollahzadeh and   
        Sascha Schäfer and   
            Peter Schwerdtfeger   Electronic properties for small tin
                                  clusters Sn$_n$ ($ n \leq 20 $ ) from
                                  density functional theory and the
                                  convergence toward the solid state . . . 929--937
                   Chao Gao and   
              Hua-Qing Yang and   
                    Jian Xu and   
                   Song Qin and   
                   Chang-Wei Hu   Theoretical study on the gas-phase
                                  reaction mechanism between rhodium
                                  monoxide and methane for methanol
                                  production . . . . . . . . . . . . . . . 938--953
                  Yu Takano and   
                Haruki Nakamura   Electronic structures of heme $a$ of
                                  cytochrome $c$ oxidase in the redox
                                  states --- charge density migration to
                                  the propionate groups of heme $a$  . . . 954--962
      Richard Kramer Campen and   
               James D. Kubicki   Interaction energy and the shift in OH
                                  stretch frequency on hydrogen bonding
                                  for the H$_2$O $ \rightarrow $ H$_2$O,
                                  CH$_3$OH $ \rightarrow $ H$_2$O, and
                                  H$_2$O $ \rightarrow $ CH$_3$OH dimers   963--972
                Jiazhong Li and   
                  Shuyan Li and   
                 Beilei Lei and   
              Huanxiang Liu and   
                Xiaojun Yao and   
                Mancang Liu and   
                Paola Gramatica   A new strategy to improve the predictive
                                  ability of the local lazy regression and
                                  its application to the QSAR study of
                                  melanin-concentrating hormone receptor 1
                                  antagonists  . . . . . . . . . . . . . . 973--985
            Zheng Guo Huang and   
                     Lei Yu and   
                     Yu Mei Dai   An ab initio potential energy surface
                                  and vibrational energy levels of ZnH$_2$ 986--993
                 An Ghysels and   
   Veronique Van Speybroeck and   
              Ewald Pauwels and   
                Saron Catak and   
          Bernard R. Brooks and   
           Dimitri Van Neck and   
               Michel Waroquier   Comparative study of various normal mode
                                  analysis techniques based on partial
                                  Hessians . . . . . . . . . . . . . . . . 994--1007
           Jason P. Holland and   
              Jennifer C. Green   Evaluation of exchange-correlation
                                  functionals for time-dependent density
                                  functional theory calculations on metal
                                  complexes  . . . . . . . . . . . . . . . 1008--1014
                 Bogdan Lev and   
                  Rui Zhang and   
Aurélien de la Lande and   
             Dennis Salahub and   
               Sergei Yu Noskov   The QM--MM interface for CHARMM--deMon   1015--1023
       Karmen Condic-Jurkic and   
              Hendrik Zipse and   
                 David M. Smith   A compound QM/MM procedure: Comparative
                                  performance on a pyruvate formate-lyase
                                  model system . . . . . . . . . . . . . . 1024--1035
           Chang-Sheng Wang and   
                Chang-Liang Sun   Investigation on the individual
                                  contributions of N H\dottedbondO C and C
                                  H\dottedbondO C interactions to the
                                  binding energies of $ \beta $-sheet
                                  models . . . . . . . . . . . . . . . . . 1036--1044
                 Yu-Hua Yao and   
                     Qi Dai and   
                    Ling Li and   
                Xu-Ying Nan and   
                 Ping-An He and   
                 Yao-Zhou Zhang   Similarity/dissimilarity studies of
                                  protein sequences based on a new $2$D
                                  graphical representation . . . . . . . . 1045--1052
           Vincent Tognetti and   
            Pascal Le Floch and   
                    Carlo Adamo   How the choice of a computational model
                                  could rule the chemical interpretation:
                                  the Ni(II) catalyzed ethylene
                                  dimerization as a case study . . . . . . 1053--1062
                 Noel Ferro and   
                  Thomas Bredow   Assessment of quantum-chemical methods
                                  for electronic properties and geometry
                                  of signaling biomolecules  . . . . . . . 1063--1079
               Yury N. Vorobjev   Blind docking method combining search of
                                  low-resolution binding sites with ligand
                                  pose refinement by molecular
                                  dynamics-based global optimization . . . 1080--1092
           Michal Brylinski and   
               Jeffrey Skolnick   Q-Dock$^{LHM}$: Low-resolution
                                  refinement for ligand comparative
                                  modeling . . . . . . . . . . . . . . . . 1093--1105
             Simone Marsili and   
 Giorgio Federico Signorini and   
            Riccardo Chelli and   
             Massimo Marchi and   
                 Piero Procacci   ORAC: a molecular dynamics simulation
                                  program to explore free energy surfaces
                                  in biomolecular systems at the atomistic
                                  level  . . . . . . . . . . . . . . . . . 1106--1116

Journal of Computational Chemistry
Volume 31, Number 6, April 30, 2010

                David Poger and   
   Wilfred F. Van Gunsteren and   
                   Alan E. Mark   A new force field for simulating
                                  phosphatidylcholine bilayers . . . . . . 1117--1125
                 Jingyu Sun and   
                Yizhen Tang and   
                    Hao Sun and   
                Xiujuan Jia and   
                 Xiumei Pan and   
                  Rongshun Wang   Theoretical and kinetic study of the H +
                                  C$_2$H$_5$CN reaction  . . . . . . . . . 1126--1134
              Jens Kleesiek and   
                Andrew E. Torda   RNA secondary structure prediction using
                                  a self-consistent mean field approach    1135--1142
         Urszula Koz\lowska and   
                  Adam Liwo and   
             Harold A. Scheraga   Determination of side-chain-rotamer and
                                  side-chain and backbone
                                  virtual-bond-stretching potentials of
                                  mean force from AM1 energy surfaces of
                                  terminally-blocked amino-acid residues,
                                  for coarse-grained simulations of
                                  protein structure and folding. I. The
                                  method . . . . . . . . . . . . . . . . . 1143--1153
         Urszula Koz\lowska and   
          Gia G. Maisuradze and   
                  Adam Liwo and   
             Harold A. Scheraga   Determination of side-chain-rotamer and
                                  side-chain and backbone
                                  virtual-bond-stretching potentials of
                                  mean force from AM1 energy surfaces of
                                  terminally-blocked amino-acid residues,
                                  for coarse-grained simulations of
                                  protein structure and folding. II.
                                  Results, comparison with statistical
                                  potentials, and implementation in the
                                  UNRES force field  . . . . . . . . . . . 1154--1167
                 Ryota Jono and   
           Yuusuke Watanabe and   
            Kentaro Shimizu and   
                   Tohru Terada   Multicanonical ab inito QM/MM molecular
                                  dynamics simulation of a peptide in an
                                  aqueous environment  . . . . . . . . . . 1168--1175
        Angelika Baranowska and   
 Krzysztof Z. \L\kaczkowski and   
              Andrzej J. Sadlej   Model studies of the optical rotation,
                                  and theoretical determination of its
                                  sign for $ \beta $-pinene and trans
                                  -pinane  . . . . . . . . . . . . . . . . 1176--1181
           K. Senthil Kumar and   
                Archita Patnaik   Intramolecular electronic communication
                                  in a dimethylaminoazobenzene--fullerene
                                  C$_{60}$ dyad: an experimental and
                                  TD-DFT study . . . . . . . . . . . . . . 1182--1194
          Len Herald V. Lim and   
          Andreas B. Pribil and   
        Andreas E. Ellmerer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Temperature dependence of structure and
                                  dynamics of the hydrated Ca$^{2+}$ ion
                                  according to ab initio quantum
                                  mechanical charge field and classical
                                  molecular dynamics . . . . . . . . . . . 1195--1200
               Xiaoqi Zheng and   
                    Chun Li and   
                       Jun Wang   An information-theoretic approach to the
                                  prediction of protein structural class   1201--1206
                 Maria Safi and   
                 Ryan H. Lilien   Restricted dead-end elimination: Protein
                                  redesign with a bounded number of
                                  residue mutations  . . . . . . . . . . . 1207--1215
                     Hao Wu and   
             Alana Canfield and   
        Jhashanath Adhikari and   
                 Shuanghong Huo   Quantum mechanical studies on model $
                                  \alpha $-pleated sheets  . . . . . . . . 1216--1223
        Kenneth W. Borrelli and   
           Benjamin Cossins and   
                 Victor Guallar   Exploring hierarchical refinement
                                  techniques for induced fit docking with
                                  protein and ligand flexibility . . . . . 1224--1235
       Gráinne Black and   
                 John M. Simmie   Barrier heights for H-atom abstraction
                                  by H\.O$_2$ from $n$-butanol --- a
                                  simple yet exacting test for model
                                  chemistries? . . . . . . . . . . . . . . 1236--1248
              Xue-Gang Yang and   
                     Wei Lv and   
               Yu-Zong Chen and   
                       Ying Xue   In silico prediction and screening of $
                                  \gamma $-secretase inhibitors by
                                  molecular descriptors and machine
                                  learning methods . . . . . . . . . . . . 1249--1258
                Ahmed Mehdi and   
              Legesse Adane and   
            Dhilon S. Patel and   
             Prasad V. Bharatam   Electronic structure and reactivity of
                                  guanylthiourea: a quantum chemical study 1259--1267
              Peter Eastman and   
                 Vijay S. Pande   Efficient nonbonded interactions for
                                  molecular dynamics on a graphics
                                  processing unit  . . . . . . . . . . . . 1268--1272
                 Anne Lopes and   
    Marcel Schmidt Am Busch and   
                Thomas Simonson   Computational design of protein--ligand
                                  binding: Modifying the specificity of
                                  asparaginyl-tRNA synthetase  . . . . . . 1273--1286
             Norio Takenaka and   
           Yoshiyuki Koyano and   
          Yukinori Nakagawa and   
               Masataka Nagaoka   An optimum strategy for solution
                                  chemistry using semiempirical molecular
                                  orbital method: Importance of
                                  description of charge distribution . . . 1287--1296
         Chérif F. Matta   How dependent are molecular and atomic
                                  properties on the electronic structure
                                  method? Comparison of Hartree--Fock,
                                  DFT, and MP2 on a biologically relevant
                                  set of molecules . . . . . . . . . . . . 1297--1311
                  N. Yousfi and   
            M. Sekkal-Rahal and   
                  A. Sayede and   
                  M. Springborg   Relaxed energetic maps of $ \kappa
                                  $-carrabiose: a  DFT study . . . . . . . 1312--1320
J. J. Borrás-Almenar and   
           S. Cardona-Serra and   
        J. M. Clemente-Juan and   
                E. Coronado and   
                A. V. Palii and   
               B. S. Tsukerblat   MVPACK: a package to calculate energy
                                  levels and magnetic properties of high
                                  nuclearity mixed valence clusters  . . . 1321--1332
        Andrzej J. Rzepiela and   
       Lars V. Schäfer and   
               Nicolae Goga and   
        H. Jelger Risselada and   
           Alex H. De Vries and   
             Siewert J. Marrink   Reconstruction of atomistic details from
                                  coarse-grained structures  . . . . . . . 1333--1343
                      Anonymous   Journal of Computational Chemistry,
                                  Volume 31, Number 2, January 30, 2010    1344--1344
                      Anonymous   Computing free energy hypersurfaces for
                                  anisotropic intermolecular associations  

Journal of Computational Chemistry
Volume 31, Number 7, May, 2010

           Trevor Cickovski and   
         Santanu Chatterjee and   
               Jacob Wenger and   
       Christopher R. Sweet and   
      Jesús A. Izaguirre   MDLab: a molecular dynamics simulation
                                  prototyping environment  . . . . . . . . 1345--1356
            Hisashi Okumura and   
          Emilio Gallicchio and   
                 Ronald M. Levy   Conformational populations of
                                  ligand-sized molecules by replica
                                  exchange molecular dynamics and
                                  temperature reweighting  . . . . . . . . 1357--1367
              Changjun Chen and   
                        Yi Xiao   Accurate free energy calculation along
                                  optimized paths  . . . . . . . . . . . . 1368--1375
                      Na Qi and   
             Rong-Zhen Liao and   
                Jian-Guo Yu and   
                 Ruo-Zhuang Liu   DFT study of the asymmetric nitroaldol
                                  (Henry) reaction catalyzed by a
                                  dinuclear Zn complex . . . . . . . . . . 1376--1384
                    Tianshu Chu   Quantum mechanics and quasiclassical
                                  study of the H/D + FO $ \rightarrow $
                                  OH/OD + F, HF/DF + O reactions: Chemical
                                  stereodynamics . . . . . . . . . . . . . 1385--1396
                 Wen-Zuo Li and   
              Jian-Bo Cheng and   
              Qing-Zhong Li and   
                Bao-An Gong and   
                  Jia-Zhong Sun   Theoretical study on HBO$^+$ and HOB$^+$
                                  cations using multiconfiguration
                                  second-order perturbation theory . . . . 1397--1401
          Edyta Ma\lolepsza and   
             Birgit Strodel and   
                Mey Khalili and   
           Semen Trygubenko and   
           Szilard N. Fejer and   
                 David J. Wales   Symmetrization of the AMBER and CHARMM
                                  force fields . . . . . . . . . . . . . . 1402--1409
             Xiao-Nan Jiang and   
            Chang-Liang Sun and   
               Chang-Sheng Wang   A scheme for rapid prediction of
                                  cooperativity in hydrogen bond chains of
                                  formamides, acetamides, and
                                  $N$-methylformamides . . . . . . . . . . 1410--1420
                    Yena Qu and   
                    Kehe Su and   
                   Xin Wang and   
                    Yan Liu and   
              Qingfeng Zeng and   
               Laifei Cheng and   
                   Litong Zhang   Reaction pathways of propene pyrolysis   1421--1442
          Amir Abbas Rafati and   
 Sayed Majid Hashemianzadeh and   
   Zabiollah Bolboli Nojini and   
               Negin Naghshineh   Canonical Monte Carlo simulation of
                                  adsorption of O$_2$ and N$_2$ mixture on
                                  single walled carbon nanotube at
                                  different temperatures and pressures . . 1443--1449
         Rungtiwa Chidthong and   
                Supa Hannongbua   Excited state properties, fluorescence
                                  energies, and lifetimes of a
                                  poly(fluorene-phenylene), based on
                                  TD-DFT investigation . . . . . . . . . . 1450--1457
              Xiaoyan Zheng and   
                 Xueye Wang and   
                Shanfeng Yi and   
              Nuanqing Wang and   
                   Yueming Peng   Density functional theory study of
                                  calix[4]arene-$N$-azacrown-5,
                                  calix[4]arene-$N$-phenyl-azacrown-5, and
                                  their complexes with alkali-metal
                                  cations: Na$^+$, K$^+$, and Rb$^+$ . . . 1458--1468
                Ville Weijo and   
   Maharavo Randrianarivony and   
           Helmut Harbrecht and   
                  Luca Frediani   Wavelet formulation of the polarizable
                                  continuum model  . . . . . . . . . . . . 1469--1477
                    Lin Zhu and   
                   Jie Yang and   
            Jiang-Ning Song and   
              Kuo-Chen Chou and   
                  Hong-Bin Shen   Improving the accuracy of predicting
                                  disulfide connectivity by feature
                                  selection  . . . . . . . . . . . . . . . 1478--1485
               Lj. Miljacic and   
                    D. E. Ellis   Radial-template approach for accurate
                                  density representation in computational
                                  quantum theory . . . . . . . . . . . . . 1486--1494
           J. M. C. Marques and   
           A. A. C. C. Pais and   
                    P. E. Abreu   Generation and characterization of
                                  low-energy structures in atomic clusters 1495--1503
             Viktor Bezugly and   
              Pawel Wielgus and   
            Miroslav Kohout and   
                Frank R. Wagner   Electron localizability indicators
                                  ELI--D and ELIA for highly correlated
                                  wavefunctions of homonuclear dimers. I.
                                  Li$_2$, Be$_2$, B$_2$, and C$_2$ . . . . 1504--1519
                Yizhen Tang and   
                 Jingyu Sun and   
                Xiujuan Jia and   
                    Hao Sun and   
                 Xiumei Pan and   
                  Rongshun Wang   Mechanistic and kinetic investigations
                                  of N$_2$H$_4$ + OH reaction  . . . . . . 1520--1527
             Thomas A. Manz and   
                 David S. Sholl   A dimensionless reaction coordinate for
                                  quantifying the lateness of transition
                                  states . . . . . . . . . . . . . . . . . 1528--1541
              Artur Gertych and   
                    Jacek Koput   Ab initio prediction of the structure
                                  and vibration-rotation spectroscopic
                                  properties of Na$_2$OH and K$_2$OH . . . 1542--1549
         Alexey Aleksandrov and   
                Thomas Simonson   A molecular mechanics model for imatinib
                                  and imatinib:kinase binding  . . . . . . 1550--1560
                     Pu Liu and   
     Dimitris K. Agrafiotis and   
            Douglas L. Theobald   Fast determination of the optimal
                                  rotational matrix for macromolecular
                                  superpositions . . . . . . . . . . . . . 1561--1563
                  Hendrik Heinz   Computational screening of biomolecular
                                  adsorption and self-assembly on
                                  nanoscale surfaces . . . . . . . . . . . 1564--1568

Journal of Computational Chemistry
Volume 31, Number 8, June, 2010

            Clara D. Christ and   
               Alan E. Mark and   
       Wilfred F. van Gunsteren   Basic ingredients of free energy
                                  calculations: a review . . . . . . . . . 1569--1582
        Asbjòrn Holt and   
         Jonas Boström and   
      Gunnar Karlström and   
                   Roland Lindh   A NEMO potential that includes the
                                  dipole--quadrupole and
                                  quadrupole--quadrupole polarizability    1583--1591
                 Ying Xiong and   
                 Junjun Liu and   
              Guang-Fu Yang and   
                 Chang-Guo Zhan   Computational determination of
                                  fundamental pathway and activation
                                  barriers for acetohydroxyacid
                                  synthase-catalyzed condensation
                                  reactions of $ \alpha $-keto acids . . . 1592--1602
        Elsa Sanchez-Garcia and   
               Markus Doerr and   
                   Walter Thiel   QM/MM study of the absorption spectra of
                                  DsRed.M1 chromophores  . . . . . . . . . 1603--1612
             Michael Wessel and   
            Richard Dronskowski   A first-principles study on the
                                  existence and structures of the lighter
                                  alkaline-earth pernitrides . . . . . . . 1613--1617
             Xian-Yong Pang and   
                   Bin Xing and   
                 Li-Qin Xue and   
                 Gui-Chang Wang   Selective oxidation of styrene on an
                                  oxygen-adsorbed Cu(111): a comparison
                                  with Au(111) . . . . . . . . . . . . . . 1618--1624
            Stephen D. Bond and   
   Jehanzeb Hameed Chaudhry and   
                Eric C. Cyr and   
                  Luke N. Olson   A first-order system least-squares
                                  finite element method for the
                                  Poisson--Boltzmann equation  . . . . . . 1625--1635
              Nathan Schmid and   
       Mathias Bötschi and   
       Wilfred F. Van Gunsteren   A GPU solvent--solvent interaction
                                  calculation accelerator for biomolecular
                                  simulations using the GROMOS software    1636--1643
          Maciej Maciejczyk and   
          Aleksandar Spasic and   
                  Adam Liwo and   
             Harold A. Scheraga   Coarse-grained model of nucleic acid
                                  bases  . . . . . . . . . . . . . . . . . 1644--1655
            Nitin Wadnerkar and   
         Vijayanand Kalamse and   
                 Ajay Chaudhari   Hydrogen uptake capacity of C$_2$H$_4$Sc
                                  and its ions: a density functional study 1656--1661
              Qing-Zhong Li and   
                    Xu Dong and   
                    Bo Jing and   
                 Wen-Zuo Li and   
              Jian-Bo Cheng and   
                Bao-An Gong and   
                      Zhi-Wu Yu   A new unconventional halogen bond
                                  C\bondX\dottedbondH\bondM between HCCX
                                  (X = Cl and Br) and HMH (M = Be and Mg):
                                  an ab initio study . . . . . . . . . . . 1662--1669
                   G. Cilpa and   
         M. T. Hyvönen and   
              A. Koivuniemi and   
                 M.-L. Riekkola   Atomistic insight into
                                  chondroitin-6-sulfate glycosaminoglycan
                                  chain through quantum mechanics
                                  calculations and molecular dynamics
                                  simulation . . . . . . . . . . . . . . . 1670--1680
                  J. W. Liu and   
                      Z. F. Liu   Thermal dissociation of tripropylamine
                                  as the first step in the growth of
                                  carbon nanotubes inside AlPO$_4$-5
                                  channels . . . . . . . . . . . . . . . . 1681--1688
                   Jun Wang and   
                        Ray Luo   Assessment of linear finite-difference
                                  Poisson--Boltzmann solvers . . . . . . . 1689--1698
               Hiroshi Takeuchi   Global minimum geometries of acetylene
                                  clusters (HCCH)$_n$ with $ n \leq 55 $
                                  obtained by a heuristic method combined
                                  with geometrical perturbations . . . . . 1699--1706
           Polina Georgieva and   
                     Fahmi Himo   Quantum chemical modeling of enzymatic
                                  reactions: the case of histone lysine
                                  methyltransferase  . . . . . . . . . . . 1707--1714
                 Li-Hua Gan and   
            Jian-Qiang Zhao and   
                        Qun Hui   Nonclassical fullerenes with a heptagon
                                  violating the pentagon adjacency penalty
                                  rule . . . . . . . . . . . . . . . . . . 1715--1721
         J. Santeri Puranen and   
            Mikko J. Vainio and   
                Mark S. Johnson   Accurate conformation-dependent
                                  molecular electrostatic potentials for
                                  high-throughput in silico drug discovery 1722--1732
            Marcin Makowski and   
           Jacek Korchowiec and   
               Feng Long Gu and   
                    Yuriko Aoki   Describing electron correlation effects
                                  in the framework of the elongation
                                  method --- Elongation-MP2: Formalism,
                                  implementation and efficiency  . . . . . 1733--1740
               Julien Preat and   
Francisco Rodríguez-Ropero and   
                Juan Torras and   
              Oscar Bertran and   
                David Zanuy and   
           Carlos Alemán   Parameterization of the torsional
                                  potential for calix[4]arene-substituted
                                  poly(thiophene)s . . . . . . . . . . . . 1741--1751
                   Yibo Lei and   
               Bingbing Suo and   
                Yusheng Dou and   
                 Yubin Wang and   
                     Zhenyi Wen   New implementations of MRCI in
                                  semiempirical frameworks . . . . . . . . 1752--1758
               Guang-Yue Li and   
             Guang-Jiu Zhao and   
                 Yu-Hui Liu and   
                  Ke-Li Han and   
                   Guo-Zhong He   TD--DFT study on the sensing mechanism
                                  of a fluorescent chemosensor for
                                  fluoride: Excited-state proton transfer  1759--1765
                   Lei Chen and   
               Ziliang Qian and   
                 Kaiyan Fen and   
                     Yudong Cai   Prediction of interactiveness between
                                  small molecules and enzymes by combining
                                  gene ontology and compound similarity    1766--1776
         Anna Maria Ferrari and   
       Bartolomeo Civalleri and   
                 Roberto Dovesi   Ab initio periodic study of the
                                  conformational behavior of glycine
                                  helical homopeptides . . . . . . . . . . 1777--1784
 Chinapong Kritayakornupong and   
       Viwat Vchirawongkwin and   
                  Bernd M. Rode   An ab initio quantum mechanical charge
                                  field molecular dynamics simulation of a
                                  dilute aqueous HCl solution  . . . . . . 1785--1792
            W. H. Eugen Schwarz   Book review: \booktitleThe Periodic
                                  Table: Its Story and Its Significance,
                                  by Eric R. Scerri, ISBN-13:
                                  978-0-19-530573-9  . . . . . . . . . . . 1793--1794

Journal of Computational Chemistry
Volume 31, Number 9, July 15, 2010

                 Weiyu Song and   
                  Jing Wang and   
                  Jian Meng and   
                     Zhijian Wu   Half metallic properties of LaSrVMoO$_6$ 1795--1798
            Sergei Grudinin and   
                 Stephane Redon   Practical modeling of molecular systems
                                  with symmetries  . . . . . . . . . . . . 1799--1814
              Santanab Giri and   
          Debesh Ranjan Roy and   
                 Soma Duley and   
        Arindam Chakraborty and   
 Ramakrishnan Parthasarathi and   
            Munusamy Elango and   
         Ramadoss Vijayaraj and   
     Venkatesan Subramanian and   
               Rafael Islas and   
             Gabriel Merino and   
         Pratim Kumar Chattaraj   Bonding, aromaticity, and structure of
                                  trigonal dianion metal clusters  . . . . 1815--1821
                 Chunzhi Ai and   
                     Yan Li and   
               Yonghua Wang and   
                     Wei Li and   
                Peipei Dong and   
                 Guangbo Ge and   
                      Ling Yang   Investigation of binding features:
                                  Effects on the interaction between
                                  CYP2A6 and inhibitors  . . . . . . . . . 1822--1831
             Milan Randi\'c and   
           Toma\vz Pisanski and   
            Marjana Novi\vc and   
              Dejan Plav\vsi\'c   Novel graph distance matrix  . . . . . . 1832--1841
   Benjamí Martorell and   
                Anna Clotet and   
                 Jordi Fraxedas   A first principle study of the
                                  structural, vibrational and electronic
                                  properties of tetrathiafulvalene
                                  adsorbed on Ag(110) and Au(110) surfaces 1842--1852
                Timm Lankau and   
                    Chin-Hui Yu   A model study of the efficiency of the
                                  Asp--His--Ser triad  . . . . . . . . . . 1853--1859
          Richard P. Muller and   
            Ann E. Mattsson and   
              Curtis L. Janssen   Calculation of chemical reaction
                                  energies using the AM05 density
                                  functional . . . . . . . . . . . . . . . 1860--1863
               Elad Project and   
            Esther Nachliel and   
                Menachem Gutman   Force field-dependant structural
                                  divergence revealed during long time
                                  simulations of Calbindin d9k . . . . . . 1864--1872
              Janne Pesonen and   
       Krister O. E. Henriksson   Polymer conformations in internal
                                  (polyspherical) coordinates  . . . . . . 1873--1881
   Krister O. E. Henriksson and   
                  Janne Pesonen   Polymer dynamics in torsion space  . . . 1882--1888
         Roman Affentranger and   
                   Xavier Daura   Polypeptide folding on a
                                  conformational-space network: Dependence
                                  of network topology on the structural
                                  discretization procedure . . . . . . . . 1889--1903
                 Erjun Zhao and   
               Jinping Wang and   
                  Jian Meng and   
                     Zhijian Wu   Phase stability and mechanical
                                  properties of rhenium borides by
                                  first-principles calculations  . . . . . 1904--1910
               Jan Fuhrmann and   
        Alexander Rurainski and   
          Hans-Peter Lenhof and   
                   Dirk Neumann   A new Lamarckian genetic algorithm for
                                  flexible ligand-receptor docking . . . . 1911--1918
                Tim Geppert and   
           Ewgenij Proschak and   
              Gisbert Schneider   Protein-protein docking by
                                  shape-complementarity and property
                                  matching . . . . . . . . . . . . . . . . 1919--1928
                  Efrat Noy and   
                Amiram Goldblum   Flexible protein-protein docking based
                                  on Best-First search algorithm . . . . . 1929--1943

Journal of Computational Chemistry
Volume 31, Number 10, July 30, 2010

           Potjaman Poolmee and   
                Supa Hannongbua   Investigation of excited-state
                                  properties of fluorene--thiophene
                                  oligomers by the SAC--CI theoretical
                                  approach . . . . . . . . . . . . . . . . 1945--1955
                Jingheng Wu and   
                   Juan Mei and   
                Sixiang Wen and   
                 Siyan Liao and   
                Jincan Chen and   
                      Yong Shen   A self-adaptive genetic
                                  algorithm-artificial neural network
                                  algorithm with leave-one-out cross
                                  validation for descriptor selection in
                                  QSAR study . . . . . . . . . . . . . . . 1956--1968
        John T. Tsalavoutis and   
             Michael P. Sigalas   Density functional investigation and
                                  bonding analysis of pentacoordinated
                                  iron complexes with mixed cyano and
                                  carbonyl ligands . . . . . . . . . . . . 1969--1978
                Suchaya Pongsai   Combination of the Metropolis Monte
                                  Carlo and Lattice Statics method for
                                  geometry optimization of H-(Al)-ZSM-5    1979--1985
Júlio C. S. da Silva and   
            Roberta P. Dias and   
       Wagner B. de Almeida and   
               Willian R. Rocha   DFT study of the full catalytic cycle
                                  for the propene hydroformylation
                                  catalyzed by a heterobimetallic
                                  HPt(SnCl$_3$ )(PH$_3$ )$_2$ model
                                  catalyst . . . . . . . . . . . . . . . . 1986--2000
                 Prasenjit Seal   Carbondioxide rare-gas systems:
                                  Sensitivity of basis sets and
                                  double-hybrid density functionals  . . . 2001--2007
               Philip Brown and   
       Christopher J. Woods and   
       Simon McIntosh-Smith and   
             Frederick R. Manby   A massively multicore parallelization of
                                  the Kohn--Sham energy gradients  . . . . 2008--2013
                 Huameng Li and   
                   Chenglong Li   Multiple ligand simultaneous docking:
                                  Orchestrated dancing of ligands in
                                  binding sites of protein . . . . . . . . 2014--2022
                 Cui-Yu Niu and   
                  Jiao Jiao and   
                   Bin Xing and   
             Gui-Chang Wang and   
                     Xian-He Bu   Reaction mechanism of methanol
                                  decomposition on Pt-based model
                                  catalysts: a theoretical study . . . . . 2023--2037
              Zheng-Wang Qu and   
                        Hui Zhu   Do anionic titanium dioxide
                                  nano-clusters reach bulk band gap? A
                                  density functional theory study  . . . . 2038--2045
          Hasan Pa\vsali\'c and   
 Adélia J. A. Aquino and   
              Daniel Tunega and   
           Georg Haberhauer and   
         Martin H. Gerzabek and   
           Herbert C. Georg and   
          Tatiane F. Moraes and   
            Kaline Coutinho and   
              Sylvio Canuto and   
                   Hans Lischka   Thermodynamic stability of
                                  hydrogen-bonded systems in polar and
                                  nonpolar environments  . . . . . . . . . 2046--2055
                Shu-Hui Yin and   
                 Yufang Liu and   
                  Wei Zhang and   
              Ming-Xing Guo and   
                      Peng Song   Time-dependent density functional theory
                                  study on the hydrogen bonding-induced
                                  twisted intramolecular charge-transfer
                                  excited states of 2-(4'-$N$,
                                  $N$-dimethylaminophenyl)imidazo[4,5-b]pyridine 2056--2062
                   Xiao Zhu and   
               Peter Koenig and   
           Michael Hoffmann and   
              Arun Yethiraj and   
                      Qiang Cui   Establishing effective simulation
                                  protocols for $ \beta $- and $ \alpha $
                                  /$ \beta $-peptides. III. Molecular
                                  mechanical model for acyclic $ \beta
                                  $-amino acids  . . . . . . . . . . . . . 2063--2077
Károly Németh and   
           Matt Challacombe and   
          Michel Van Veenendaal   The choice of internal coordinates in
                                  complex chemical systems . . . . . . . . 2078--2086

Journal of Computational Chemistry
Volume 31, Number 11, August, 2010

                Udo Schnupf and   
              J. L. Willett and   
                Frank A. Momany   27 ps DFT molecular dynamics simulation
                                  of $ \alpha $-maltose: a reduced basis
                                  set study  . . . . . . . . . . . . . . . 2087--2097
               Li-Dong Gong and   
                 Zhong-Zhi Yang   Investigation of the molecular surface
                                  area and volume: Defined and calculated
                                  by the molecular face theory . . . . . . 2098--2108
                     Xun Li and   
                     Yan Li and   
               Tiejun Cheng and   
                 Zhihai Liu and   
                   Renxiao Wang   Evaluation of the performance of four
                                  molecular docking programs on a diverse
                                  set of protein-ligand complexes  . . . . 2109--2125
                Jia-Feng Yu and   
                       Xiao Sun   Reannotation of protein-coding genes
                                  based on an improved graphical
                                  representation of DNA sequence . . . . . 2126--2135
                 Ping-An He and   
             Yan-Ping Zhang and   
                 Yu-Hua Yao and   
                 Yi-Fa Tang and   
                    Xu-Ying Nan   The graphical representation of protein
                                  sequences based on the physicochemical
                                  properties and its applications  . . . . 2136--2142
              Xiaoyan Zheng and   
                 Xueye Wang and   
                  Keqi Shen and   
              Nuanqing Wang and   
                   Yueming Peng   Molecular design of a ``molecular
                                  syringe'' mimic for metal cations using
                                  a 1,3-alternate calix[4]arene cavity . . 2143--2156
                   Rui Wang and   
                     Ce Hao and   
                    Peng Li and   
              Ning-Ning Wei and   
               Jingwen Chen and   
                    Jieshan Qiu   Time-dependent density functional theory
                                  study on the electronic excited-state
                                  hydrogen-bonding dynamics of
                                  4-aminophthalimide (4AP) in aqueous
                                  solution: 4AP and 4AP--(H$_2$O)$_{1, 2}$
                                  clusters . . . . . . . . . . . . . . . . 2157--2163
               Xiangqian Hu and   
                     Hao Hu and   
           David N. Beratan and   
                    Weitao Yang   A gradient-directed Monte Carlo approach
                                  for protein design . . . . . . . . . . . 2164--2168
            Maarten G. Wolf and   
            Martin Hoefling and   
Camilo Aponte-Santamaría and   
     Helmut Grubmüller and   
                Gerrit Groenhof   \tt g\_membed: Efficient insertion of a
                                  membrane protein into an equilibrated
                                  lipid bilayer with minimal perturbation  2169--2174
                   Yuko Ito and   
             Mitsunori Ikeguchi   Structural fluctuation and concerted
                                  motions in F$_1$-ATPase: a molecular
                                  dynamics study . . . . . . . . . . . . . 2175--2185
                Kenta Hongo and   
                Ryo Maezono and   
                  Kenichi Miura   Random number generators tested on
                                  quantum Monte Carlo simulations  . . . . 2186--2194
   Ramon Carbó-Dorca and   
               Luz Dary Mercado   Commentaries on quantum similarity (1):
                                  Density gradient quantum similarity  . . 2195--2212
      Jakub Kaminský and   
                 Ivan Raich and   
Kate\vrina Tom\vcáková and   
                    Petr Bou\vr   Conformational behavior of simple
                                  furanosides studied by optical rotation  2213--2224
                Hajime Muta and   
               Noriaki Hirayama   Alpha sphere filter method: Application
                                  of pseudomolecular descriptors in
                                  virtual screening of $2$D chemical
                                  structures . . . . . . . . . . . . . . . 2225--2232

Journal of Computational Chemistry
Volume 31, Number 12, September, 2010

                Bisheng Tan and   
                Rufang Peng and   
                  Hongbo Li and   
                     Bo Jin and   
                 Shijin Chu and   
                   Xinping Long   Theoretical investigation of an
                                  energetic fullerene derivative . . . . . 2233--2237
                Xian-Hui Wu and   
                Guo-Lin Zou and   
               Jun-Min Quan and   
                    Yun-Dong Wu   A theoretical study on the catalytic
                                  mechanism of Mus musculus adenosine
                                  deaminase  . . . . . . . . . . . . . . . 2238--2247
                    Yong Wu and   
                     Lu Jin and   
                   Ying Xue and   
                  Ik-Mo Lee and   
                 Chan Kyung Kim   Mechanisms of norbornadiene dimerization
                                  to Binor-S using cationic Co$^I$,
                                  Rh$^I$, and Ir$^I$ catalysts . . . . . . 2248--2257
              Chin-Hung Lai and   
                    Pi-Tai Chou   A computational study on the capability
                                  of borane-cyclic boryl anion adducts to
                                  act as hydrogen atom donors  . . . . . . 2258--2262
               Xiu-Juan Jia and   
                You-Jun Liu and   
                Jing-Yu Sun and   
                    Hao Sun and   
                  Fang Wang and   
               Zhong-Min Su and   
                Xiu-Mei Pan and   
                 Rong-Shun Wang   Computational studies on the mechanism
                                  and kinetics of Cl reaction with
                                  C$_2$H$_5$I  . . . . . . . . . . . . . . 2263--2272
             Viktor Bezugly and   
              Pawel Wielgus and   
            Miroslav Kohout and   
                Frank R. Wagner   Electron localizability indicators
                                  ELI--D and ELIA for highly correlated
                                  wavefunctions of homonuclear dimers. II.
                                  N$_2$, O$_2$, F$_2$, and Ne$_2$  . . . . 2273--2285
                 Stijn Fias and   
            Sofie Van Damme and   
               Patrick Bultinck   Multidimensionality of delocalization
                                  indices and nucleus-independent chemical
                                  shifts in polycyclic aromatic
                                  hydrocarbons II: Proof of further
                                  nonlocality  . . . . . . . . . . . . . . 2286--2293
       Milan On\vcák and   
       Detlef Schröder and   
         Petr Slaví\vcek   Theoretical study of the microhydration
                                  of mononuclear and dinuclear uranium(VI)
                                  species derived from solvolysis of
                                  uranyl nitrate in water  . . . . . . . . 2294--2306
           Benjamin Waldher and   
               Jadwiga Kuta and   
                Samuel Chen and   
                Neil Henson and   
                Aurora E. Clark   ForceFit: a code to fit classical force
                                  fields to quantum mechanical potential
                                  energy surfaces  . . . . . . . . . . . . 2307--2316
                 Hisashi Ishida   Branch migration of Holliday junction in
                                  RuvA tetramer complex studied by
                                  umbrella sampling simulation using a
                                  path-search algorithm  . . . . . . . . . 2317--2329
                   Xiao Zhu and   
     Alexander D. Mackerell Jr.   Polarizable empirical force field for
                                  sulfur-containing compounds based on the
                                  classical Drude oscillator model . . . . 2330--2341
               Shuchi Nagar and   
                  Achintya Saha   Modeling of diarylalkyl-imidazole and
                                  diarylalkyl-triazole derivatives as
                                  potent aromatase inhibitors for
                                  treatment of hormone-dependent cancer    2342--2353
        Vali Zare-shahabadi and   
            Fatemeh Abbasitabar   Application of ant colony optimization
                                  in development of models for prediction
                                  of anti-HIV-1 activity of HEPT
                                  derivatives  . . . . . . . . . . . . . . 2354--2362
                   Peng Tao and   
           H. Bernhard Schlegel   A toolkit to assist ONIOM calculations   2363--2369

Journal of Computational Chemistry
Volume 31, Number 13, October, 2010

          Sadegh Salehzadeh and   
                    Mehdi Bayat   Theoretical studies on the structure and
                                  protonation of Cu(II) complexes of a
                                  series of tripodal aliphatic
                                  tetraamines: Good correlations with the
                                  experimental data  . . . . . . . . . . . 2371--2380
              Hiroaki Umeda and   
             Yuichi Inadomi and   
            Toshio Watanabe and   
                  Toru Yagi and   
         Takayoshi Ishimoto and   
            Tsutomu Ikegami and   
              Hiroto Tadano and   
            Tetsuya Sakurai and   
                Umpei Nagashima   Parallel Fock matrix construction with
                                  distributed shared memory model for the
                                  FMO--MO method . . . . . . . . . . . . . 2381--2388
             David Casanova and   
               Pere Alemany and   
               Santiago Alvarez   Symmetry measures of the electron
                                  density  . . . . . . . . . . . . . . . . 2389--2404
          Anuja P. Rahalkar and   
             Michio Katouda and   
          Shridhar R. Gadre and   
                 Shigeru Nagase   Molecular tailoring approach in
                                  conjunction with MP2 and Ri-MP2 codes: a
                                  comparison with fragment molecular
                                  orbital method . . . . . . . . . . . . . 2405--2418
               Zhixiong Lin and   
                 Haiyan Liu and   
       Wilfred F. van Gunsteren   Using one-step perturbation to predict
                                  the effect of changing force-field
                                  parameters on the simulated folding
                                  equilibrium of a $ \beta $-peptide in
                                  solution . . . . . . . . . . . . . . . . 2419--2427
              Gregory Scott and   
                Martin Gruebele   Solving the low dimensional Smoluchowski
                                  equation with a singular value basis set 2428--2433
     Cédric Grauffel and   
            Roland H. Stote and   
               Annick Dejaegere   Force field parameters for the
                                  simulation of modified histone tails . . 2434--2451
      R. Carbó-Dorca and   
               E. Besalú   Communications on quantum similarity
                                  (2): a geometric discussion on
                                  holographic electron density theorem and
                                  confined quantum similarity measures . . 2452--2462
 Santhosh Kannan Venkatesan and   
          Anil Kumar Shukla and   
             Vikash Kumar Dubey   Molecular docking studies of selected
                                  tricyclic and quinone derivatives on
                                  trypanothione reductase of Leishmania
                                  infantum . . . . . . . . . . . . . . . . 2463--2475
            Bulumoni Kalita and   
                 Ramesh C. Deka   Adsorption of CO on oxygen preadsorbed
                                  neutral and charged gas phase Pd$_4$
                                  clusters: a density functional study . . 2476--2482
                Kiyull Yang and   
             Young Hee Park and   
             Soo Gyeong Cho and   
              Hai Whang Lee and   
             Chan Kyung Kim and   
                   Hyun-Joo Koo   Theoretical studies on the formation
                                  mechanism and explosive performance of
                                  nitro-substituted 1,3,5-triazines  . . . 2483--2492
P. González-Navarrete and   
                  L. Gracia and   
               M. Calatayud and   
               J. AndréS   Density functional theory study of the
                                  oxidation of methanol to formaldehyde on
                                  a hydrated vanadia cluster . . . . . . . 2493--2501
               Xuewei Jiang and   
              Changjun Chen and   
                        Yi Xiao   Improvements of network approach for
                                  analysis of the folding free-energy
                                  surface of peptides and proteins . . . . 2502--2509
       Antoni Aguilar-Mogas and   
      Xavier Giménez and   
             Josep Maria Bofill   Implementation of an algorithm based on
                                  the Runge--Kutta--Fehlberg technique and
                                  the potential energy as a reaction
                                  coordinate to locate intrinsic reaction
                                  paths  . . . . . . . . . . . . . . . . . 2510--2525
             Wolfgang Quapp and   
             Josep Maria Bofill   A comment to the nudged elastic band
                                  method . . . . . . . . . . . . . . . . . 2526--2531

Journal of Computational Chemistry
Volume 31, Number 14, November 15, 2010

                Haiying Liu and   
               Xiaohua Chen and   
                     Yuxiang Bu   Redox-induced configuration conversion
                                  for thioacetamide dimer can function as
                                  a molecular switch . . . . . . . . . . . 2533--2539
            Jianwen A. Feng and   
            Garland R. Marshall   SKATE: a docking program that decouples
                                  systematic sampling from scoring . . . . 2540--2554
            Slawomir Berski and   
           Zdzislaw Latajka and   
            Agnieszka J. Gordon   Ab initio and Quantum Chemical Topology
                                  studies on the isomerization of HONO to
                                  HNO$_2$. Effect of the basis set in QCT  2555--2567
          Kathrin Götz and   
              Florian Meier and   
                Carlo Gatti and   
      Asbjörn M. Burow and   
               Marek Sierka and   
              Joachim Sauer and   
                   Martin Kaupp   Modeling environmental effects on charge
                                  density distributions in polar
                                  organometallics: Validation of embedded
                                  cluster models for the methyl lithium
                                  crystal  . . . . . . . . . . . . . . . . 2568--2576
               Jianguo Qian and   
                     Fuji Zhang   Counting the cyclocized polyphenacenes   2577--2584
                 Cun-Xi Liu and   
               Hai-Xia Wang and   
                 Ze-Rong Li and   
             Chong-Wen Zhou and   
               Han-Bing Rao and   
                  Xiang-Yuan Li   Accurate prediction of enthalpies of
                                  formation for a large set of organic
                                  compounds  . . . . . . . . . . . . . . . 2585--2592
                Per Larsson and   
                   Erik Lindahl   A high-performance parallel-generalized
                                  Born implementation enabled by tabulated
                                  interaction rescaling  . . . . . . . . . 2593--2600
          Ramin M. Abolfath and   
                  Thomas Brabec   DNA-backbone radio resistivity induced
                                  by spin blockade effect  . . . . . . . . 2601--2606
           Fahrettin Gogtas and   
               Rukiye Tutuk and   
                 Mustafa Kurban   Time-dependent quantum study of H($^2$S)
                                  $+$ FO($^2 \Pi $ ) $ \rightarrow $
                                  OH($^2 \Pi $ ) $+$ F($^2$P) reaction on
                                  the 1$^3$A' and 1$^3$A'' states  . . . . 2607--2611
             Alice Borghini and   
               Paolo Crotti and   
             Daniele Pietra and   
             Lucilla Favero and   
            Anna Maria Bianucci   Chemical reactivity predictions: Use of
                                  data mining techniques for analyzing
                                  regioselective azidolysis of epoxides    2612--2619
        Jörg Von Appen and   
               Bernhard Eck and   
            Richard Dronskowski   A density-functional study of the phase
                                  diagram of cementite-type (Fe,Mn)$_3$C
                                  at absolute zero temperature . . . . . . 2620--2627
           Yoshiyuki Koyano and   
             Norio Takenaka and   
          Yukinori Nakagawa and   
               Masataka Nagaoka   An optimum strategy for solution
                                  chemistry using semiempirical molecular
                                  orbital method. II. Primary importance
                                  of reproducing electrostatic interaction
                                  in the QM/MM framework . . . . . . . . . 2628--2641
Esteban Vöhringer-Martinez and   
    Alejandro Toro-Labbé   The role of water in the proton transfer
                                  reaction mechanism in tryptophan . . . . 2642--2649
               Shu-Wei Tang and   
             Jing-Dong Feng and   
              Yong-Qing Qiu and   
                    Hao Sun and   
               Feng-Di Wang and   
             Ying-Fei Chang and   
                 Rong-Shun Wang   Electronic structures and nonlinear
                                  optical properties of highly deformed
                                  halofullerenes C$_{3v}$ C$_{60}$F$_{18}$
                                  and D$_{3d}$ C$_{60}$Cl$_{30}$ . . . . . 2650--2657
                   Mihaly Mezei   Simulaid: a simulation facilitator and
                                  analysis program . . . . . . . . . . . . 2658--2668
              Oscar Bertran and   
              S. B. Trickey and   
                    Juan Torras   Incorporation of deMon2k as a new
                                  parallel quantum mechanical code for the
                                  PUPIL system . . . . . . . . . . . . . . 2669--2676

Journal of Computational Chemistry
Volume 31, Number 15, November 30, 2010

Christopher J. R. Illingworth and   
              Paul D. Scott and   
         Kevin E. B. Parkes and   
       Christopher R. Snell and   
        Matthew P. Campbell and   
        Christopher A. Reynolds   Connectivity and binding-site
                                  recognition: Applications relevant to
                                  drug design  . . . . . . . . . . . . . . 2677--2688
        Sree V. Chintapalli and   
                Boon K. Yew and   
Christopher J. R. Illingworth and   
         Graham J. G. Upton and   
           Philip J. Reeves and   
         Kevin E. B. Parkes and   
       Christopher R. Snell and   
        Christopher A. Reynolds   Closed loop folding units from
                                  structural alignments: Experimental
                                  foldons revisited  . . . . . . . . . . . 2689--2701
           Dennis M. Elking and   
              Lalith Perera and   
                Robert Duke and   
              Thomas Darden and   
                Lee G. Pedersen   Atomic forces for geometry-dependent
                                  point multipole and Gaussian multipole
                                  models . . . . . . . . . . . . . . . . . 2702--2713
             Katsumi Murata and   
               Naoya Nagata and   
             Isao Nakanishi and   
                  Kazuo Kitaura   SDOVS: a solvent dipole ordering-based
                                  method for virtual screening . . . . . . 2714--2722
          Pedro A. Valiente and   
           Alejandro Gil L. and   
           Paulo R. Batista and   
       Ernesto R. Caffarena and   
                 Tirso Pons and   
              Pedro G. Pascutti   New parameterization approaches of the
                                  LIE method to improve free energy
                                  calculations of PlmII-inhibitors
                                  complexes  . . . . . . . . . . . . . . . 2723--2734
             Marcos Mandado and   
M. Natália D. S. Cordeiro   On the stability of metal--aminoacid
                                  complexes in water based on
                                  water--ligand exchange reactions and
                                  electronic properties: Detailed study on
                                  iron--glycine hexacoordinated complexes  2735--2745
                   Eri Sano and   
                  Weihua Li and   
                Hitomi Yuki and   
                  Xinli Liu and   
            Tomomi Furihata and   
            Kaoru Kobayashi and   
                  Kan Chiba and   
                Saburo Neya and   
                  Tyuji Hoshino   Mechanism of the decrease in catalytic
                                  activity of human cytochrome P450 2C9
                                  polymorphic variants investigated by
                                  computational analysis . . . . . . . . . 2746--2758
               Tzong-Yi Lee and   
          Justin Bo-Kai Hsu and   
               Feng-Mao Lin and   
              Wen-Chi Chang and   
              Po-Chiang Hsu and   
                 Hsien-Da Huang   $N$-Ace: Using solvent accessibility and
                                  physicochemical properties to identify
                                  protein $N$-acetylation sites  . . . . . 2759--2771
                  Hao Zhang and   
                 Yun-Hong Zhang   Ab initio investigation on the
                                  ion-associated species and process in
                                  Mg(NO$_3$ )$_2$ solution . . . . . . . . 2772--2782
                    Juan Du and   
                    Lili Xi and   
                 Beilei Lei and   
                    Jing Lu and   
                Jiazhong Li and   
              Huanxiang Liu and   
                    Xiaojun Yao   Structure-based quantitative
                                  structure-activity relationship studies
                                  of checkpoint kinase 1 inhibitors  . . . 2783--2793
                  Hui Zhang and   
             Gui-Ling Zhang and   
               Jing-Yao Liu and   
                   Miao Sun and   
                     Bo Liu and   
                    Ze-Sheng Li   Theoretical studies on the reactions
                                  CH$_3$SCH$_3$ with OH, CF$_3$, and
                                  CH$_3$ radicals  . . . . . . . . . . . . 2794--2803
                Qi Liang Lu and   
                 Li Li Chen and   
               Jian Guo Wan and   
                 Guang Hou Wang   First principles studies on the
                                  interaction of O$_2$ with X@Al$_{12}$ (X
                                  = Al$^-$, P$^+$, C, Si) clusters . . . . 2804--2809
         Volker Hähnke and   
              Matthias Rupp and   
             Mireille Krier and   
         Friedrich Rippmann and   
              Gisbert Schneider   Pharmacophore alignment search tool:
                                  Influence of canonical atom labeling on
                                  similarity searching . . . . . . . . . . 2810--2826

Journal of Computational Chemistry
Volume 31, Number 16, December, 2010

                   Emilia L. Wu   Coriolis coupling and nonadiabaticity in
                                  chemical reaction dynamics . . . . . . . 2827--2835
     Dimitrios N. Garbounis and   
      Athanassios C. Tsipis and   
         Constantinos A. Tsipis   Structural, electronic, bonding,
                                  magnetic, and optical properties of
                                  bimetallic [Ru$_n$Au$_m$ ]$^{0 / +}$ ($
                                  n + m \leq 3 $ ) clusters  . . . . . . . 2836--2852
              Ning-Ning Wei and   
                     Ce Hao and   
                Zhilong Xiu and   
               Jingwen Chen and   
                    Jieshan Qiu   Time-dependent density functional theory
                                  study on excited-state dihydrogen
                                  bonding OH\dottedbondHGe of the
                                  dihydrogen-bonded
                                  phenol-triethylgermanium complex . . . . 2853--2858
                   Huan Rui and   
                      Wonpil Im   Protegrin-1 orientation and
                                  physicochemical properties in membrane
                                  bilayers studied by potential of mean
                                  force calculations . . . . . . . . . . . 2859--2867
             Bernhard Knapp and   
              Nadja Lederer and   
             Ulrich Omasits and   
             Wolfgang Schreiner   vmdICE: a plug-in for rapid evaluation
                                  of molecular dynamics simulations using
                                  VMD  . . . . . . . . . . . . . . . . . . 2868--2873
               Neetha Mohan and   
  Kunduchi P. Vijayalakshmi and   
               Nobuaki Koga and   
        Cherumuttathu H. Suresh   Comparison of aromatic NH\dottedbond$
                                  \pi $, OH\dottedbond$ \pi $, and
                                  CH\dottedbond$ \pi $ interactions of
                                  alanine using MP2, CCSD, and DFT methods 2874--2882
                 Erjun Zhao and   
               Jinping Wang and   
                     Zhijian Wu   Structural stability and phase
                                  transition in OsC and RuC  . . . . . . . 2883--2888
           Stewart N. Weiss and   
                 Lulu Huang and   
                      Lou Massa   A generalized higher order kernel energy
                                  approximation method . . . . . . . . . . 2889--2899
              Seungsoo Hahn and   
              Orr Ashenberg and   
           Gevorg Grigoryan and   
                 Amy E. Keating   Identifying and reducing error in
                                  cluster-expansion approximations of
                                  protein energies . . . . . . . . . . . . 2900--2914
             Young Kee Kang and   
                 Byung Jin Byun   Assessment of density functionals with
                                  long-range and/or empirical dispersion
                                  corrections for conformational energy
                                  calculations of peptides . . . . . . . . 2915--2923
                Shinji Aono and   
                   Shigeki Kato   Proton transfer in phenol--amine
                                  complexes: Phenol electronic effects on
                                  free energy profile in solution  . . . . 2924--2931
       Benedict M. Sattelle and   
                  Andrew Almond   Less is more when simulating unsulfated
                                  glycosaminoglycan 3D-structure:
                                  Comparison of GLYCAM06/TIP3P,
                                  PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P
                                  predictions with experiment  . . . . . . 2932--2947
                   Anik Sen and   
              Bishwajit Ganguly   What is the minimum number of water
                                  molecules required to dissolve a
                                  potassium chloride molecule? . . . . . . 2948--2954
            Maria L. Sushko and   
            Peter V. Sushko and   
          Igor V. Abarenkov and   
           Alexander L. Shluger   QM/MM method for metal--organic
                                  interfaces . . . . . . . . . . . . . . . 2955--2966
            Claudia Steffen and   
               Klaus Thomas and   
                 Uwe Huniar and   
              Arnim Hellweg and   
              Oliver Rubner and   
              Alexander Schroer   TmoleX --- a graphical user interface
                                  for TURBOMOLE  . . . . . . . . . . . . . 2967--2970


Journal of Computational Chemistry
Volume 32, Number 1, January 15, 2011

            Subrata Mahanta and   
           Bijan Kumar Paul and   
      Rupashree Balia Singh and   
                Nikhil Guchhait   Inequivalence of substitution pairs in
                                  hydroxynaphthaldehyde: a theoretical
                                  measurement by intramolecular hydrogen
                                  bond strength, aromaticity, and
                                  excited-state intramolecular proton
                                  transfer reaction  . . . . . . . . . . . 1--14
                  Qiang Hao and   
        Andrew C. Simmonett and   
            Yukio Yamaguchi and   
                De-Cai Fang and   
          Henry F. Schaefer III   From acetylene complexes to vinylidene
                                  structures: The GeC$_2$H$_2$ system  . . 15--22
                 Oz Sharabi and   
               Chen Yanover and   
               Ayelet Dekel and   
               Julia M. Shifman   Optimizing energy functions for
                                  protein--protein interface design  . . . 23--32
              Yongbing Zhao and   
                    Jingfa Xiao   Homology modeling and molecular dynamics
                                  simulation studies of human type 1 3$
                                  \beta $-hydroxysteroid dehydrogenase:
                                  Toward the understanding of cofactor
                                  specificity  . . . . . . . . . . . . . . 33--42
                  Jon Baker and   
             Krzysztof Wolinski   Isomerization of stilbene using enforced
                                  geometry optimization  . . . . . . . . . 43--53
            Eric J. Bylaska and   
           Kiril Tsemekhman and   
             Scott B. Baden and   
              John H. Weare and   
                 Hannes Jonsson   Parallel implementation of $ \gamma
                                  $-point pseudopotential plane-wave DFT
                                  with exact exchange  . . . . . . . . . . 54--69
              Shih-Hau Chiu and   
             Chien-Chi Chen and   
              Gwo-Fang Yuan and   
                    Thy-Hou Lin   Deriving the phylogenetic information
                                  from some physicochemical properties of
                                  protein sequences computed . . . . . . . 70--80
          Annalisa Bordogna and   
         Alessandro Pandini and   
                   Laura Bonati   Predicting the accuracy of
                                  protein--ligand docking on homology
                                  models . . . . . . . . . . . . . . . . . 81--98
            A. M. Tokmachev and   
                 R. Dronskowski   Hydrogen-bond networks in finite ice
                                  nanotubes  . . . . . . . . . . . . . . . 99--105
           Guillaume Launay and   
                Thomas Simonson   A large decoy set of protein--protein
                                  complexes produced by flexible docking   106--120
       Mohammad Alaghemandi and   
            Joachim Schulte and   
Frédéric Leroy and   
 Florian Müller-Plathe and   
           Michael C. Böhm   Correlation between thermal conductivity
                                  and bond length alternation in carbon
                                  nanotubes: a combined reverse
                                  nonequilibrium molecular dynamics ---
                                  crystal orbital analysis . . . . . . . . 121--133
                Conrad Shyu and   
              F. Marty Ytreberg   Accurate estimation of solvation free
                                  energy using polynomial fitting
                                  techniques . . . . . . . . . . . . . . . 134--141
              Qingyong Meng and   
                 Ming-Bao Huang   A CAS study on S-loss and O-loss
                                  dissociation mechanisms of the SO$_2^+$
                                  ion in the C, D, and E states  . . . . . 142--151
                 Chaoyang Zhang   Shape and size effects in $ \pi $--$ \pi
                                  $ interactions: Face-to-face dimers  . . 152--160
                 Jae In Kim and   
                 Sungsoo Na and   
                      Kilho Eom   Domain decomposition-based structural
                                  condensation of large protein structures
                                  for understanding their conformational
                                  dynamics . . . . . . . . . . . . . . . . 161--169
            Joseph N. Zadeh and   
        Conrad D. Steenberg and   
             Justin S. Bois and   
             Brian R. Wolfe and   
         Marshall B. Pierce and   
               Asif R. Khan and   
            Robert M. Dirks and   
                Niles A. Pierce   NUPACK: Analysis and design of nucleic
                                  acid systems . . . . . . . . . . . . . . 170--173
          Abdul-Rahman Allouche   Gabedit --- a graphical user interface
                                  for computational chemistry softwares    174--182
              Gerald R. Kneller   Comment on ``Fast determination of the
                                  optimal rotational matrix for
                                  macromolecular superpositions'' [J.
                                  Comp. Chem. \bf 31, 1561 (2010)] . . . . 183--184
                     Pu Liu and   
     Dimitris K. Agrafiotis and   
            Douglas L. Theobald   Rapid communication reply to comment on:
                                  ``Fast determination of the optimal
                                  rotational matrix for macromolecular
                                  superpositions'' . . . . . . . . . . . . 185--186

Journal of Computational Chemistry
Volume 32, Number 2, January 30, 2011

            Samuel Genheden and   
                       Ulf Ryde   A comparison of different initialization
                                  protocols to obtain statistically
                                  independent molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 187--195
            Juan R. Perilla and   
           Oliver Beckstein and   
       Elizabeth J. Denning and   
                Thomas B. Woolf   Computing ensembles of transitions from
                                  stable states: Dynamic importance
                                  sampling . . . . . . . . . . . . . . . . 196--209
            John W. Raymond and   
        Daniel D. Holsworth and   
                  Mehran Jalaie   The flexible alignment of molecular
                                  structures using simulated annealing
                                  with weighted Lagrangian multipliers . . 210--217
                Wen-Zhi Yao and   
                  Da-Zhi Li and   
                     Si-Dian Li   Bridging gold: B-Au-B
                                  three-center--two-electron bonds in
                                  electron-deficient B$_2$Au$_n^{- / 0}$
                                  ($ n = 1 $, $3$, $5$ ) and mixed
                                  analogues  . . . . . . . . . . . . . . . 218--225
          Kathy L. Phillips and   
         Stanley I. Sandler and   
                    Pei C. Chiu   A method to calculate the one-electron
                                  reduction potentials for nitroaromatic
                                  compounds based on gas-phase quantum
                                  mechanics  . . . . . . . . . . . . . . . 226--239
           Blandine Courcot and   
              Adam J. Bridgeman   Optimization of a molecular mechanics
                                  force field for polyoxometalates based
                                  on a genetic algorithm . . . . . . . . . 240--247
                   Peng Bao and   
                  Zhong-Heng Yu   New procedure to evaluate aromaticity at
                                  the density functional theory,
                                  Hartree--Fock, and post-self-consistent
                                  field levels . . . . . . . . . . . . . . 248--259
                  Suyong Re and   
               Takashi Imai and   
               Jaewoon Jung and   
           Seiichiro Ten-No and   
                    Yuji Sugita   Geometrically associative yet
                                  electronically dissociative character in
                                  the transition state of enzymatic
                                  reversible phosphorylation . . . . . . . 260--270
              Dongsheng Zou and   
                Zhongshi He and   
                Jingyuan He and   
                     Yuxian Xia   Supersecondary structure prediction
                                  using Chou's pseudo amino acid
                                  composition  . . . . . . . . . . . . . . 271--278
    Massimiliano Bartolomei and   
     Estela Carmona-Novillo and   
  Marta I. Hernández and   
José Campos-Martínez and   
Ramón Hernández-Lamoneda   Long-range interaction for dimers of
                                  atmospheric interest: dispersion,
                                  induction and electrostatic
                                  contributions for O$_2$O$_2$, N$_2$N$_2$
                                  and O$_2$N$_2$ . . . . . . . . . . . . . 279--290
        A. Otero-de-la-Roza and   
     Víctor Luaña   A fast and accurate algorithm for QTAIM
                                  integration in solids  . . . . . . . . . 291--305
              Daniel Tunega and   
                      Ali Zaoui   Understanding of bonding and mechanical
                                  characteristics of cementitious mineral
                                  tobermorite from first principles  . . . 306--314
          Carmen J. Calzado and   
                  A. Monari and   
                 S. Evangelisti   Heisenberg behavior of some
                                  carbon-beryllium compounds: How well
                                  truncated-CI approaches work . . . . . . 315--324
      Uttam Sinha Mahapatra and   
        Sudip Chattopadhyay and   
             Rajat K. Chaudhuri   Second-order state-specific
                                  multireference Mòller--Plesset
                                  perturbation theory: Application to
                                  energy surfaces of diimide, ethylene,
                                  butadiene, and cyclobutadiene  . . . . . 325--337
              Shu-Ling Chen and   
              Dong-Xia Zhao and   
                 Zhong-Zhi Yang   An estimation method of binding free
                                  energy in terms of ABEEM$ \sigma \pi $
                                  /MM and continuum electrostatics fused
                                  into LIE method  . . . . . . . . . . . . 338--348
                Chewook Lee and   
                     Sihyun Ham   Characterizing amyloid-beta protein
                                  misfolding from molecular dynamics
                                  simulations with explicit water  . . . . 349--355
Luká\vs Bu\vcinský and   
       Stanislav Biskupi\vc and   
             Michal Il\vcin and   
    Vladimír Luke\vs and   
                 Viliam Laurinc   Relativistic effects in HgHe and HgXe
                                  CCSD(T) ground state potential curves.
                                  Low-density viscosity simulations of
                                  Hg:Xe mixture  . . . . . . . . . . . . . 356--367
           Richard Lonsdale and   
           Jeremy N. Harvey and   
         Frederick R. Manby and   
           Adrian J. Mulholland   Comment on ``A stationary-wave model of
                                  enzyme catalysis'' by Carlo Canepa . . . 368--369
                   Carlo Canepa   Reply to the comment on ``A
                                  stationary-wave model of enzyme
                                  catalysis''  . . . . . . . . . . . . . . 370--371
J. Oscar C. Jiménez-Halla and   
              Eduard Matito and   
    Lluís Blancafort and   
            Juvencio Robles and   
                  Miquel Sol\`a   Erratum: ``Tuning aromaticity in
                                  trigonal alkaline earth metal clusters
                                  and their alkali metal salts'' . . . . . 372--373
                      Anonymous   Tuning aromaticity in trigonal alkaline
                                  earth metal clusters and their alkali
                                  metal salts  . . . . . . . . . . . . . . 

Journal of Computational Chemistry
Volume 32, Number 3, February, 2011

              Brad A. Bauer and   
            Joseph E. Davis and   
             Michela Taufer and   
                  Sandeep Patel   Molecular dynamics simulations of
                                  aqueous ions at the liquid--vapor
                                  interface accelerated using graphics
                                  processors . . . . . . . . . . . . . . . 375--385
          Wouter Heyndrickx and   
             Pedro Salvador and   
           Patrick Bultinck and   
              Miquel Sol\`a and   
                  Eduard Matito   Performance of 3D-space-based
                                  atoms-in-molecules methods for
                                  electronic delocalization aromaticity
                                  indices  . . . . . . . . . . . . . . . . 386--395
           Artem B. Mamonov and   
                  Xin Zhang and   
            Daniel M. Zuckerman   Rapid sampling of all-atom peptides
                                  using a library-based polymer-growth
                                  approach . . . . . . . . . . . . . . . . 396--405
                  Yuan Miao and   
                 Xueye Wang and   
                    Xin Jin and   
                    Ling Yi and   
                    Cuihuan Ren   Density functional theory study of a
                                  molecular allosteric switch for
                                  2,2'-bipyridyl-3,3'-15-crown-5 . . . . . 406--415
                    Bo Yang and   
                 Yanyan Zhu and   
                   Yan Wang and   
                   Guangju Chen   Interaction identification of Zif268 and
                                  TATA$_{ZF}$ proteins with GC-/AT-rich
                                  DNA sequence: a theoretical study  . . . 416--428
        Matthew A. Addicoat and   
           Gregory F. Metha and   
                     Tak W. Kee   Density functional theory investigation
                                  of Cu(I)- and Cu(II)-curcumin complexes  429--438
            Joseph N. Zadeh and   
             Brian R. Wolfe and   
                Niles A. Pierce   Nucleic acid sequence design via
                                  efficient ensemble defect optimization   439--452
           Omololu Akin-Ojo and   
                      Feng Wang   The quest for the best nonpolarizable
                                  water model from the adaptive force
                                  matching method  . . . . . . . . . . . . 453--462
     Ahmed Mutanabbi Abdula and   
           Reema Abu Khalaf and   
        Mohammad S. Mubarak and   
                Mutasem O. Taha   Discovery of new $ \beta $-
                                  D-galactosidase inhibitors via
                                  pharmacophore modeling and QSAR analysis
                                  followed by in silico screening  . . . . 463--482
              Burak Alakent and   
                Sena Baskan and   
                  Pemra Doruker   Effect of ligand binding on the
                                  intraminimum dynamics of proteins  . . . 483--496
    Andres Jaramillo-Botero and   
                  Julius Su and   
                      An Qi and   
         William A. Goddard III   Large-scale, long-term nonadiabatic
                                  electron molecular dynamics for
                                  describing material properties and
                                  phenomena in extreme environments  . . . 497--512
           Timothy H. Click and   
                 Aibing Liu and   
             George A. Kaminski   Quality of random number generators
                                  significantly affects results of Monte
                                  Carlo simulations for organic and
                                  biological systems . . . . . . . . . . . 513--524
         Aravindhan Ganesan and   
                  Feng Wang and   
                 Chantal Falzon   Intramolecular interactions of
                                  L-phenylalanine: Valence ionization
                                  spectra and orbital momentum
                                  distributions of its fragment molecules  525--535
               Dorota Latek and   
               Andrzej Kolinski   CABS-NMR --- de novo tool for rapid
                                  global fold determination from chemical
                                  shifts, residual dipolar couplings and
                                  sparse methyl-methyl NOEs  . . . . . . . 536--544
                Wenwei Zhao and   
                Yihong Ding and   
                     Qiying Xia   Time-dependent density functional theory
                                  study on the absorption spectrum of
                                  Coumarin 102 and its hydrogen-bonded
                                  complexes  . . . . . . . . . . . . . . . 545--553

Journal of Computational Chemistry
Volume 32, Number 4, March, 2011

           Jagdish C. Patra and   
                   Boon H. Chua   Artificial neural network-based drug
                                  design for diabetes mellitus using
                                  flavonoids . . . . . . . . . . . . . . . 555--567
        Dariusz Plewczynski and   
      Micha\l \La\.zniewski and   
       Marcin Von Grotthuss and   
          Leszek Rychlewski and   
             Krzysztof Ginalski   VoteDock: Consensus docking method for
                                  prediction of protein--ligand
                                  interactions . . . . . . . . . . . . . . 568--581
   Ramon Carbó-Dorca and   
        Emili Besalú and   
               Luz Dary Mercado   Communications on quantum similarity,
                                  part 3: a geometric-quantum similarity
                                  molecular superposition algorithm  . . . 582--599
        Christian C. Gruber and   
             Jürgen Pleiss   Systematic benchmarking of large
                                  molecular dynamics simulations employing
                                  GROMACS on massive multiprocessing
                                  facilities . . . . . . . . . . . . . . . 600--606
         David Curcó and   
                David Zanuy and   
              Ruth Nussinov and   
           Carlos Alemán   A simulation strategy for the atomistic
                                  modeling of flexible molecules
                                  covalently tethered to rigid surfaces:
                                  Application to peptides  . . . . . . . . 607--619
      Athanassios C. Tsipis and   
         Alexandros V. Stalikas   Structural, electronic, and
                                  magnetoresponsive properties of
                                  triangular lanthanide clusters and their
                                  free-standing nitrides . . . . . . . . . 620--638
           Arthur N. Mayeno and   
       Jonathan L. Robinson and   
                  Brad Reisfeld   Rapid estimation of activation
                                  enthalpies for cytochrome-P450-mediated
                                  hydroxylations . . . . . . . . . . . . . 639--657
               Shu-Wei Tang and   
             Jing-Dong Feng and   
              Yong-Qing Qiu and   
                    Hao Sun and   
               Feng-Di Wang and   
               Zhong-Min Su and   
             Ying-Fei Chang and   
                 Rong-Shun Wang   Thermochemical stabilities, electronic
                                  structures, and optical properties of
                                  C$_{56}$X$_{10}$ (X = H, F, and Cl)
                                  fullerene compounds  . . . . . . . . . . 658--667
               Guang-Yue Li and   
             Guang-Jiu Zhao and   
                  Ke-Li Han and   
                   Guo-Zhong He   A TD-DFT study on the
                                  cyanide-chemosensing mechanism of
                                  8-formyl-7-hydroxycoumarin . . . . . . . 668--674
                    Chun Li and   
                    Hong Ma and   
                  Yang Zhou and   
               Xiaolei Wang and   
                   Xiaoqi Zheng   Similarity analysis of DNA sequences
                                  based on the weighted pseudo-entropy . . 675--680
               Juan M. Ruiz and   
           R. Joshua Mulder and   
Célia Fonseca Guerra and   
        F. Matthias Bickelhaupt   Steric effects on alkyl cation
                                  affinities of maingroup-element hydrides 681--688
                  T. Zoboki and   
                       I. Mayer   Extremely localized nonorthogonal
                                  orbitals by the pairing theorem  . . . . 689--695
               Zahid Rashid and   
             Joop H. van Lenthe   Generation of Kekulé valence structures
                                  and the corresponding valence bond wave
                                  function . . . . . . . . . . . . . . . . 696--708
             Matthew S. Lin and   
             Teresa Head-Gordon   Reliable protein structure refinement
                                  using a physical energy function . . . . 709--717
               Andrzej T. Kowal   Ab initio molecular geometry and
                                  anharmonic vibrational spectra of
                                  thiourea and thiourea-$ d_4 $  . . . . . 718--729
                      Shih-I Lu   Computational study of static first
                                  hyperpolarizability of donor--acceptor
                                  substituted (E)-benzaldehyde
                                  phenylhydrazone  . . . . . . . . . . . . 730--736
              Zongling Ding and   
                  Jun Jiang and   
             Huaizhong Xing and   
                  Haibo Shu and   
                Ruibin Dong and   
            Xiaoshuang Chen and   
                         Wei Lu   Transport properties of graphene
                                  nanoribbon-based molecular devices . . . 737--741
        Dariusz Plewczynski and   
      Micha\l \La\'zniewski and   
         Rafa\l Augustyniak and   
             Krzysztof Ginalski   Can we trust docking results? Evaluation
                                  of seven commonly used programs on
                                  PDBbind database . . . . . . . . . . . . 742--755
                  Duan Chen and   
                  Zhan Chen and   
              Changjun Chen and   
                Weihua Geng and   
                    Guo-Wei Wei   MIBPB: a software package for
                                  electrostatic analysis . . . . . . . . . 756--770

Journal of Computational Chemistry
Volume 32, Number 5, April 15, 2011

             Chang-Bin Shao and   
                    Lin Jin and   
                   Yi-Hong Ding   A theoretical survey on the structures,
                                  energetics, and isomerization pathways
                                  of the B$_5$O radical  . . . . . . . . . 771--777
                 Kenji Hori and   
             Toru Yamaguchi and   
                 Keita Uezu and   
             Michinori Sumimoto   A free-energy perturbation method based
                                  on Monte Carlo simulations using quantum
                                  mechanical calculations (QM/MC/FEP
                                  method): Application to highly
                                  solvent-dependent reactions  . . . . . . 778--786
               Pralay Mitra and   
                    Debnath Pal   Using correlated parameters for improved
                                  ranking of protein--protein docking
                                  decoys . . . . . . . . . . . . . . . . . 787--796
        Hossein Farrokhpour and   
            Zainab Mombeini and   
           Mansoor Namazian and   
              Michelle L. Coote   Intermolecular potential energy surface
                                  for CS$_2$ dimer . . . . . . . . . . . . 797--809
                   Kay Hamacher   Efficient quantification of the
                                  importance of contacts for the dynamical
                                  stability of proteins  . . . . . . . . . 810--815
            Adam D. Swetnam and   
               Michael P. Allen   Improving the Wang--Landau algorithm for
                                  polymers and proteins  . . . . . . . . . 816--821
        Eric A. C. Bushnell and   
              Edvin Erdtman and   
                Jorge Llano and   
           Leif A. Eriksson and   
                 James W. Gauld   The first branching point in porphyrin
                                  biosynthesis: a systematic docking,
                                  molecular dynamics and quantum
                                  mechanical/molecular mechanical study of
                                  substrate binding and mechanism of
                                  uroporphyrinogen-III decarboxylase . . . 822--834
                    C. Weng and   
              J. Kouvetakis and   
            A. V. G. Chizmeshya   A novel predictive model for formation
                                  enthalpies of Si and Ge hydrides with
                                  propane- and butane-like structures  . . 835--853
          Ramkumar Rajamani and   
                Yen-Lin Lin and   
                      Jiali Gao   The opsin shift and mechanism of
                                  spectral tuning in rhodopsin . . . . . . 854--865
                Tingjun Hou and   
                Junmei Wang and   
                 Youyong Li and   
                       Wei Wang   Assessing the performance of the
                                  molecular mechanics/Poisson Boltzmann
                                  surface area and molecular
                                  mechanics/generalized Born surface area
                                  methods. II. The accuracy of ranking
                                  poses generated from docking . . . . . . 866--877
                    Bin Lin and   
          B. Montgomery Pettitt   Electrostatic solvation free energy of
                                  amino acid side chain analogs:
                                  Implications for the validity of
                                  electrostatic linear response in water   878--885
          Syed Tarique Moin and   
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Structure and dynamics of methanol in
                                  water: a quantum mechanical charge field
                                  molecular dynamics study . . . . . . . . 886--892
           Goutam Mukherjee and   
              Niladri Patra and   
           Poranjyoti Barua and   
                     B. Jayaram   A fast empirical GAFF compatible partial
                                  atomic charge assignment scheme for
                                  modeling interactions of small molecules
                                  with biomolecular targets  . . . . . . . 893--907
                    H. Reis and   
                  O. Loboda and   
            A. Avramopoulos and   
         M. G. Papadopoulos and   
                 B. Kirtman and   
                 J. M. Luis and   
                   R. Zale\'sny   Electronic and vibrational linear and
                                  nonlinear polarizabilities of
                                  Li@C$_{60}$ and [Li@C$_{60}$ ]$^+$ . . . 908--914
             J. M. Villalba and   
              A. J. Barbero and   
             R. Diaz-Sierra and   
                 E. Arribas and   
      M. J. Garcia-Meseguer and   
          F. Garcia-Sevilla and   
           M. Garcia-Moreno and   
       J. A. Vidal De Labra and   
                       R. Varon   Computerized evaluation of mean
                                  residence times in multicompartmental
                                  linear system and pharmacokinetics . . . 915--931
             Takuya Okamoto and   
               Kenta Yamada and   
           Yoshiyuki Koyano and   
               Toshio Asada and   
               Nobuaki Koga and   
               Masataka Nagaoka   A minimal implementation of the
                                  AMBER--GAUSSIAN interface for ab initio
                                  QM/MM-MD simulation  . . . . . . . . . . 932--942
             Gui-Xiang Wang and   
              Xue-Dong Gong and   
                    Yan Liu and   
               Hong-Chen Du and   
               Xiao-Juan Xu and   
                   He-Ming Xiao   Looking for high energy density
                                  compounds applicable for propellant
                                  among the derivatives of DPO with N$_3$,
                                  ONO$_2$, and NNO$_2$ groups  . . . . . . 943--952
                    Yang Li and   
             Xiao-Nan Jiang and   
               Chang-Sheng Wang   Rapid evaluation of the binding energies
                                  in hydrogen-bonded amide--thymine and
                                  amide--uracil dimers in gas phase  . . . 953--966
                    Yue Shi and   
                Chuanjie Wu and   
              Jay W. Ponder and   
                     Pengyu Ren   Multipole electrostatics in hydration
                                  free energy calculations . . . . . . . . 967--977
                Andreas Uhe and   
           Sebastian Kozuch and   
                    Sason Shaik   Automatic analysis of computed catalytic
                                  cycles . . . . . . . . . . . . . . . . . 978--985

Journal of Computational Chemistry
Volume 32, Number 6, April 30, 2011

                    Jie Luo and   
                Xiujuan Jia and   
                   Yang Gao and   
                Guicai Song and   
                   Yanbo Yu and   
              Rongshun Wang and   
                     Xiumei Pan   Theoretical study on the kinetics of OH
                                  radical reactions with CH$_3$OOH and
                                  CH$_3$CH$_2$OOH  . . . . . . . . . . . . 987--997
           Halvor S. Hansen and   
   Philippe H. Hünenberger   A reoptimized GROMOS force field for
                                  hexopyranose-based carbohydrates
                                  accounting for the relative free
                                  energies of ring conformers, anomers,
                                  epimers, hydroxymethyl rotamers, and
                                  glycosidic linkage conformers  . . . . . 998--1032
                 Xiao-Na Li and   
                Zhi-Jian Wu and   
                  Xi-Yan Li and   
             Hong-Jie Zhang and   
                  Xiao-Juan Liu   Theoretical study on phosphorescence
                                  efficiency and color tuning from orange
                                  to blue-green of Ir(III) complexes based
                                  on substituted
                                  2-phenylimidazo[1,2-a]pyridine ligand    1033--1042
          Ivan I. Vorontsov and   
                Osamu Miyashita   Crystal molecular dynamics simulations
                                  to speed up MM/PB(GB)SA evaluation of
                                  binding free energies of di-mannose
                                  deoxy analogs with P51G-m4-Cyanovirin-N  1043--1053
             Piotr De Silva and   
               Jacek Korchowiec   Energy partitioning scheme based on
                                  self-consistent method for subsystems:
                                  Populational space approach  . . . . . . 1054--1064
              Wen-Fei Huang and   
               P. Raghunath and   
                      M. C. Lin   Computational study on the reactions of
                                  H$_2$O$_2$ on TiO$_2$ anatase (101) and
                                  rutile (110) surfaces  . . . . . . . . . 1065--1081
         Gerhard König and   
                 Stefan Boresch   Non-Boltzmann sampling and Bennett's
                                  acceptance ratio method: How to profit
                                  from bending the rules . . . . . . . . . 1082--1090
                Xianfeng Li and   
               Robert A. Latour   The temperature intervals with global
                                  exchange of replicas empirical
                                  accelerated sampling method: Parameter
                                  sensitivity and extension to a complex
                                  molecular system . . . . . . . . . . . . 1091--1100
             Jee-Gong Chang and   
            Hsin-Tsung Chen and   
                Shin-Pon Ju and   
          Ching-Sheng Chang and   
               Meng-Hsiung Weng   Adsorption and dissociation of NH$_3$ on
                                  clean and hydroxylated TiO$_2$ rutile
                                  (110) surfaces: a computational study    1101--1112
                  Francesco Rao   Protein inherent structures by different
                                  minimization strategies  . . . . . . . . 1113--1116
               Marcel Swart and   
              Miquel Sol\`a and   
        F. Matthias Bickelhaupt   Inter- and intramolecular dispersion
                                  interactions . . . . . . . . . . . . . . 1117--1127
                  Adam Tuer and   
           Serguei Krouglov and   
              Richard Cisek and   
            Danielle Tokarz and   
              Virginijus Barzda   Three-dimensional visualization of the
                                  first hyperpolarizability tensor . . . . 1128--1134
            Steven Lettieri and   
           Artem B. Mamonov and   
            Daniel M. Zuckerman   Extending fragment-based free energy
                                  calculations with library Monte Carlo
                                  simulation: Annealing in interaction
                                  space  . . . . . . . . . . . . . . . . . 1135--1143
         Jhon Zapata-Rivera and   
              Rosa Caballol and   
              Carmen J. Calzado   Electronic structure and relative
                                  stability of 1:1 Cu-O$_2$ adducts from
                                  difference-dedicated configuration
                                  interaction calculations . . . . . . . . 1144--1158
                 Huifang Li and   
               Laibin Zhang and   
                     Li Han and   
                Wenming Sun and   
                     Yuxiang Bu   Internucleotide $J$-couplings and
                                  chemical shifts of the
                                  N\bondH\dottedbondN hydrogen-bonds in
                                  the radiation-damaged guanine-cytosine
                                  base pairs . . . . . . . . . . . . . . . 1159--1169
                Meiyan Wang and   
                  Lin Cheng and   
               Jinping Wang and   
                     Zhijian Wu   Mechanism of methylacetylene
                                  bisselenation catalyzed by palladium
                                  complex from density functional study    1170--1177
       Aurelien De La Lande and   
          Dennis R. Salahub and   
          Jacques Maddaluno and   
            Anthony Scemama and   
               Julien Pilme and   
            Olivier Parisel and   
              Helene Gerard and   
            Michel Caffarel and   
           Jean-Philip Piquemal   Spin-driven activation of dioxygen in
                                  various metalloenzymes and their
                                  inspired models  . . . . . . . . . . . . 1178--1182
             Michele Seeber and   
             Angelo Felline and   
         Francesco Raimondi and   
              Stefanie Muff and   
               Ran Friedman and   
              Francesco Rao and   
            Amedeo Caflisch and   
              Francesca Fanelli   Wordom: a user-friendly program for the
                                  analysis of molecular structures,
                                  trajectories, and free energy surfaces   1183--1194
      Christoph van Wüllen   Shared-memory parallelization of the
                                  TURBOMOLE programs AOFORCE, ESCF, and
                                  EGRAD: How to quickly parallelize legacy
                                  code . . . . . . . . . . . . . . . . . . 1195--1201
          Barbara Collignon and   
              Roland Schulz and   
            Jeremy C. Smith and   
                  Jerome Baudry   Task-parallel message passing interface
                                  implementation of Autodock4 for docking
                                  of very large databases of compounds
                                  using high-performance super-computers   1202--1209

Journal of Computational Chemistry
Volume 32, Number 7, May, 2011

                  Shuyan Li and   
                    Lili Xi and   
                Jiazhong Li and   
               Chengqi Wang and   
                 Beilei Lei and   
                 Yulin Shen and   
              Huanxiang Liu and   
                Xiaojun Yao and   
                        Biao Li   In silico prediction of deleterious
                                  single amino acid polymorphisms from
                                  amino acid sequence  . . . . . . . . . . 1211--1216
 Adélia J. A. Aquino and   
         Dana Nachtigallova and   
                Pavel Hobza and   
          Donald G. Truhlar and   
       Christof Hättig and   
                   Hans Lischka   The charge-transfer states in a stacked
                                  nucleobase dimer complex: a benchmark
                                  study  . . . . . . . . . . . . . . . . . 1217--1227
          Tsuyoshi Terakawa and   
             Tomoshi Kameda and   
                   Shoji Takada   On easy implementation of a variant of
                                  the replica exchange with solute
                                  tempering in GROMACS . . . . . . . . . . 1228--1234
                Hongping Li and   
                  Shuhui Lv and   
               Xiaojuan Liu and   
                      Jian Meng   First-principles investigation of A-B
                                  intersite charge transfer and correlated
                                  electrical and magnetic properties in
                                  BiCu$_3$Fe$_4$O$_{12}$ . . . . . . . . . 1235--1240
  Efstathios E. Karagiannis and   
      Christos E. Kefalidis and   
       Ioanna Petrakopoulou and   
         Constantinos A. Tsipis   Density functional study of structural,
                                  electronic, and optical properties of
                                  small bimetallic ruthenium-copper
                                  clusters . . . . . . . . . . . . . . . . 1241--1261
       Zsófia Szalay and   
          János Rohonczy   Fast calculation of DNMR spectra on
                                  CUDA-enabled graphics card . . . . . . . 1262--1270
               Li-Zhen Zhao and   
               Wan-Sheng Su and   
                 Wen-Cai Lu and   
                 C. Z. Wang and   
                       K. M. Ho   Competitive diamond-like and endohedral
                                  fullerene structures of Si$_{70}$  . . . 1271--1278
                   Yang Liu and   
                       Huai Sun   Electronic ground states and vibrational
                                  frequency shifts of diatomic ligands in
                                  heme adducts . . . . . . . . . . . . . . 1279--1285
               Jinzen Ikebe and   
               Koji Umezawa and   
           Narutoshi Kamiya and   
          Takanori Sugihara and   
         Yasushige Yonezawa and   
                  Yu Takano and   
            Haruki Nakamura and   
                   Junichi Higo   Theory for trivial trajectory
                                  parallelization of multicanonical
                                  molecular dynamics and application to a
                                  polypeptide in water . . . . . . . . . . 1286--1297
                  Chong Han and   
               Shi-Shen Yan and   
               Xue-Ling Lin and   
                 Shu-Jun Hu and   
              Ming-Wen Zhao and   
                Xin-Xin Yao and   
               Yan-Xue Chen and   
                Guo-Lei Liu and   
                   Liang-Mo Mei   Effect of native defects and Co doping
                                  on ferromagnetism in HfO$_2$:
                                  First-principles calculations  . . . . . 1298--1302
            Stefan Bruckner and   
                 Stefan Boresch   Efficiency of alchemical free energy
                                  simulations. I. A practical comparison
                                  of the exponential formula,
                                  thermodynamic integration, and Bennett's
                                  acceptance ratio method  . . . . . . . . 1303--1319
            Stefan Bruckner and   
                 Stefan Boresch   Efficiency of alchemical free energy
                                  simulations. II. Improvements for
                                  thermodynamic integration  . . . . . . . 1320--1333
               Albert H. Ng and   
            Christopher D. Snow   Polarizable protein packing  . . . . . . 1334--1344
               Hiroshi Takeuchi   A theoretical investigation on optimal
                                  structures of ethane clusters
                                  (C$_2$H$_6$ )$_n$ with $ n \leq 25 $ and
                                  their building-up principle  . . . . . . 1345--1352
            Yoshitake Sakae and   
          Tomoyuki Hiroyasu and   
             Mitsunori Miki and   
                   Yuko Okamoto   Protein structure predictions by
                                  parallel simulated annealing molecular
                                  dynamics using genetic crossover . . . . 1353--1360
              Jun-Xian Chen and   
              Chang Kon Kim and   
              Hai Whang Lee and   
                   Ying Xue and   
                 Chan Kyung Kim   Reexamination of the $ \pi $-bond
                                  strengths within H$_2$C\doublebondXH$_n$
                                  systems: a theoretical study . . . . . . 1361--1367
             P. O. Fedichev and   
           E. G. Getmantsev and   
                L. I. Menshikov   $ O(N \log N) $ continuous
                                  electrostatics method for fast
                                  calculation of solvation energies of
                                  biomolecules . . . . . . . . . . . . . . 1368--1376
      Johannes M. Dieterich and   
                   Bernd Hartke   Composition-induced structural
                                  transitions in mixed Lennard-Jones
                                  clusters: Global reparametrization and
                                  optimization . . . . . . . . . . . . . . 1377--1385
                Eduard S. Fomin   Consideration of data load time on
                                  modern processors for the Verlet table
                                  and linked-cell algorithms . . . . . . . 1386--1399
              Nicolas Sapay and   
              D. Peter Tieleman   Combination of the CHARMM27 force field
                                  with united-atom lipid force fields  . . 1400--1410
       Emanuel H. Rubensson and   
                  Elias Rudberg   Bringing about matrix sparsity in
                                  linear-scaling electronic structure
                                  calculations . . . . . . . . . . . . . . 1411--1423
                    Felix Hanke   Sensitivity analysis and uncertainty
                                  calculation for dispersion corrected
                                  density functional theory  . . . . . . . 1424--1430
             Allyn R. Brice and   
                Brian N. Dominy   Analyzing the robustness of the MM/PBSA
                                  free energy calculation method:
                                  Application to DNA conformational
                                  transitions  . . . . . . . . . . . . . . 1431--1440
       Justyna Dominikowska and   
                Marcin Palusiak   Cyclooctatetraene dianion --- an
                                  artifact?  . . . . . . . . . . . . . . . 1441--1448
                 Nan-Nan Wu and   
              Chao-Zheng He and   
               Xue-Mei Duan and   
                   Jing-Yao Liu   Theoretical mechanistic study on the
                                  reaction of CN radical with HNCN . . . . 1449--1455
              Stefan Grimme and   
            Stephan Ehrlich and   
                   Lars Goerigk   Effect of the damping function in
                                  dispersion corrected density functional
                                  theory . . . . . . . . . . . . . . . . . 1456--1465
                   Chun Wei Yap   PaDEL-descriptor: an open source
                                  software to calculate molecular
                                  descriptors and fingerprints . . . . . . 1466--1474
Hossein Ali Karimi-Varzaneh and   
                Hu-Jun Qian and   
                Xiaoyu Chen and   
              Paola Carbone and   
     Florian Müller-Plathe   IBIsCO: a molecular dynamics simulation
                                  package for coarse-grained simulation    1475--1487
                 Samir Unni and   
                 Yong Huang and   
           Robert M. Hanson and   
             Malcolm Tobias and   
            Sriram Krishnan and   
              Wilfred W. Li and   
            Jens E. Nielsen and   
                Nathan A. Baker   Web servers and services for
                                  electrostatics calculations with APBS
                                  and PDB2PQR  . . . . . . . . . . . . . . 1488--1491

Journal of Computational Chemistry
Volume 32, Number 8, June, 2011

              Thomas M. Gilbert   Testing the ONIOM G2R3 model against
                                  donor--acceptor dissociation energies of
                                  group 13--15 complexes: Accuracy
                                  comparable to CCSD(T)/aug-CC-pVTZ at a
                                  fraction of the resource cost  . . . . . 1493--1499
              Zheng-Wang Qu and   
                    Hui Zhu and   
                   Volkhard May   Vibrational spectral signatures of
                                  peptide secondary structures:
                                  $N$-methylation and side chain hydrogen
                                  bond in cyclosporin A  . . . . . . . . . 1500--1518
          Joshua A. Plumley and   
               J. J. Dannenberg   A comparison of the behavior of
                                  functional/basis set combinations for
                                  hydrogen-bonding in the water dimer with
                                  emphasis on basis set superposition
                                  error  . . . . . . . . . . . . . . . . . 1519--1527
            Slawomir Berski and   
           Zdzislaw Latajka and   
            Agnieszka J. Gordon   Electron localization function and
                                  electron localizability indicator
                                  applied to study the bonding in the
                                  peroxynitrous acid HOONO . . . . . . . . 1528--1540
            Stephen M. Long and   
               Tran T. Tran and   
                Peter Adams and   
                Paul Darwen and   
                 Mark L. Smythe   Conformational searching using a
                                  population-based incremental learning
                                  algorithm  . . . . . . . . . . . . . . . 1541--1549
   Stéphanie Halbert and   
   Carine Clavaguéra and   
                   Guy Bouchoux   The shape of gaseous $n$-butylbenzene:
                                  Assessment of computational methods and
                                  comparison with experiments  . . . . . . 1550--1560
          Dieter Ghillemijn and   
           Patrick Bultinck and   
           Dimitri Van Neck and   
                  Paul W. Ayers   A self-consistent Hirshfeld method for
                                  the atom in the molecule based on
                                  minimization of information loss . . . . 1561--1567
       Thanisorn Yakhanthip and   
     Siriporn Jungsuttiwong and   
       Supawadee Namuangruk and   
              Nawee Kungwan and   
            Vinich Promarak and   
        Taweesak Sudyoadsuk and   
             Palita Kochpradist   Theoretical investigation of novel
                                  carbazole-fluorene based D-$ \pi $-A
                                  conjugated organic dyes as
                                  dye-sensitizer in dye-sensitized solar
                                  cells (DSCs) . . . . . . . . . . . . . . 1568--1576
                      Le Yu and   
                  Wensheng Bian   Extensive theoretical study on
                                  electronically excited states and
                                  predissociation mechanisms of sulfur
                                  monoxide including spin--orbit coupling  1577--1588
          Svetlana Artemova and   
            Sergei Grudinin and   
                 Stephane Redon   Fast construction of assembly trees for
                                  molecular graphs . . . . . . . . . . . . 1589--1598
            Stefano Pelloni and   
        Raphaël Carion and   
    Vincent Liégeois and   
               Paolo Lazzeretti   The ring current model of the
                                  pentaprismane molecule . . . . . . . . . 1599--1611
                Jianxiu Guo and   
                   Nini Rao and   
             Guangxiong Liu and   
                  Yong Yang and   
                      Gang Wang   Predicting protein folding rates using
                                  the concept of Chou's pseudo amino acid
                                  composition  . . . . . . . . . . . . . . 1612--1617
         Volker Hähnke and   
          Alexander Klenner and   
         Friedrich Rippmann and   
              Gisbert Schneider   Pharmacophore alignment search tool:
                                  Influence of the third dimension on
                                  text-based similarity searching  . . . . 1618--1634
         Volker Hähnke and   
              Gisbert Schneider   Pharmacophore alignment search tool:
                                  Influence of scoring systems on
                                  text-based similarity searching  . . . . 1635--1647
           Daniel K. W. Mok and   
           Edmond P. F. Lee and   
               Foo-Tim Chau and   
                   John M. Dyke   Franck--Condon simulation of the
                                  photoelectron spectrum of AsCl$_2$ and
                                  the photodetachment spectrum of AsCl
                                  employing UCCSD(T)-F12a potential energy
                                  functions: IE and EA of AsCl$_2$ . . . . 1648--1660
             Tatsuya Ohyama and   
            Masato Hayakawa and   
             Shin Nishikawa and   
                Noriyuki Kurita   Specific interactions between lactose
                                  repressor protein and DNA affected by
                                  ligand binding: Ab initio molecular
                                  orbital calculations . . . . . . . . . . 1661--1670
            Yao-Yuan Chuang and   
                 Sheng-Min Chen   Infinite basis set extrapolation for
                                  double hybrid density functional theory
                                  1: Effect of applying various
                                  extrapolation functions  . . . . . . . . 1671--1679
                Shide Liang and   
                 Yaoqi Zhou and   
               Nick Grishin and   
              Daron M. Standley   Protein side chain modeling with
                                  orientation-dependent atomic force
                                  fields derived by series expansions  . . 1680--1686
                Hongmei Liu and   
              Zhenzhen Zhao and   
                   Nan Wang and   
                     Cui Yu and   
                   Jianwei Zhao   Can the transition from tunneling to
                                  hopping in molecular junctions be
                                  predicted by theoretical calculation?    1687--1693
                    Sen Lin and   
                    Daiqian Xie   New ab initio potential energy surfaces
                                  for both the ground (\~X$^1$A') and
                                  excited (Ã$^1$A'') electronic states of
                                  HSiCl and the absorption and emission
                                  spectra of HSiCl/DSiCl . . . . . . . . . 1694--1702
           Blandine Courcot and   
              Adam J. Bridgeman   Optimization of a molecular mechanics
                                  force field for type-II polyoxometalates
                                  focussing on electrostatic interactions:
                                  a case study . . . . . . . . . . . . . . 1703--1710
            Nicole Legenski and   
             Chenggang Zhou and   
              Qingfan Zhang and   
                     Bo Han and   
                 Jinping Wu and   
                 Liang Chen and   
              Hansong Cheng and   
               Robert C. Forrey   Force fields for metallic clusters and
                                  nanoparticles  . . . . . . . . . . . . . 1711--1720
              Pawe\l Szarek and   
              Ludwik Komorowski   Modeling the electron density kernels    1721--1724
    Mohammednoor Altarawneh and   
       Ala'A H. Al-Muhtaseb and   
      Bogdan Z. Dlugogorski and   
            Eric M. Kennedy and   
                 John C. Mackie   Rate constants for hydrogen abstraction
                                  reactions by the hydroperoxyl radical
                                  from methanol, ethenol, acetaldehyde,
                                  toluene, and phenol  . . . . . . . . . . 1725--1733
          Ch. Bheema Lingam and   
             K. Ramesh Babu and   
            Surya P. Tewari and   
               G. Vaitheeswaran   Structural, electronic, bonding, and
                                  elastic properties of NH$_3$BH$_3$: a
                                  density functional study . . . . . . . . 1734--1742
       Hannes G. Wallnoefer and   
             Klaus R. Liedl and   
                     Thomas Fox   A challenging system: Free energy
                                  prediction for factor Xa . . . . . . . . 1743--1752
              Zongling Ding and   
                  Jun Jiang and   
             Huaizhong Xing and   
                  Haibo Shu and   
                  Yan Huang and   
            Xiaoshuang Chen and   
                         Wei Lu   The finite-size effect on the transport
                                  properties in edge-modified graphene
                                  nanoribbon-based molecular devices . . . 1753--1759
             Chaoyang Zhang and   
               Xiaolin Wang and   
                   Mingfei Zhou   Isomers and isomerization reactions of
                                  four nitro derivatives of methane  . . . 1760--1768
            Daniel Sheppard and   
               Graeme Henkelman   Paths to which the nudged elastic band
                                  converges  . . . . . . . . . . . . . . . 1769--1771
             Wolfgang Quapp and   
             Josep Maria Bofill   Reply to the comment by Sheppard and
                                  Henkelman on the nudged elastic band
                                  method . . . . . . . . . . . . . . . . . 1772--1773

Journal of Computational Chemistry
Volume 32, Number 9, July 15, 2011

            M. De La Pierre and   
                 R. Orlando and   
                 L. Maschio and   
                    K. Doll and   
                P. Ugliengo and   
                      R. Dovesi   Performance of six functionals (LDA,
                                  PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in
                                  the simulation of vibrational and
                                  dielectric properties of crystalline
                                  compounds. The case of forsterite
                                  Mg$_2$SiO$_4$  . . . . . . . . . . . . . 1775--1784
            Moshe Goldstein and   
                Erick Fredj and   
                R. Benny Gerber   A new hybrid algorithm for finding the
                                  lowest minima of potential surfaces:
                                  Approach and application to peptides . . 1785--1800
             Denise Steiner and   
          Chris Oostenbrink and   
  François Diederich and   
       Martina Zürcher and   
       Wilfred F. van Gunsteren   Calculation of binding free energies of
                                  inhibitors to plasmepsin II  . . . . . . 1801--1812
            Nasr Y. M. Omar and   
       Noorsaadah A. Rahman and   
            Sharifuddin Md Zain   Enantioselective organocatalytic
                                  Diels--Alder reactions: a density
                                  functional theory and kinetic isotope
                                  effects study  . . . . . . . . . . . . . 1813--1823
            Igor Ying Zhang and   
                Jianming Wu and   
                     Yi Luo and   
                         Xin Xu   Accurate bond dissociation enthalpies by
                                  using doubly hybrid XYG3 functional  . . 1824--1838
         Doreen Mollenhauer and   
              Johannes Flob and   
        Hans-Ulrich Reissig and   
            Elena Voloshina and   
                   Beate Paulus   Accurate quantum-chemical description of
                                  gold complexes with pyridine and its
                                  derivatives  . . . . . . . . . . . . . . 1839--1845
                 Zhiwei Liu and   
              Alexey Teslja and   
           Vojislava Pophristic   An ab initio molecular orbital study of
                                  intramolecular hydrogen bonding in
                                  ortho-substituted arylamides:
                                  Implications for the parameterization of
                                  molecular mechanics force fields . . . . 1846--1858
               Jongtaek Kim and   
                Eunjung Yoo and   
               Sukbok Chang and   
                   Yoon Sup Lee   Electronic and chelation effects on the
                                  unusual C2-methylation of
                                  $N$-(para-substituted)phenylaziridines
                                  with lithium organocuprates  . . . . . . 1859--1868
          Fabrice Avaltroni and   
           Clemence Corminboeuf   Efficiency of random search procedures
                                  along the silicon cluster series: Si$_n$
                                  ($ n = 5 $--$ 10 $, $ 15 $, and $ 20 $ ) 1869--1875
Francisco Rodríguez-Ropero and   
                  Marco Fioroni   Effect of Na$^+$, Mg$^{2+}$, and
                                  Zn$^{2+}$ chlorides on the structural
                                  and thermodynamic properties of
                                  water/$n$-heptane interfaces . . . . . . 1876--1886
    \.Zaneta Czy\.znikowska and   
            Wojciech Bartkowiak   Physical origins of the stability of
                                  aromatic amino acid core ring-polycyclic
                                  hydrocarbon complexes: a
                                  post-Hartree--Fock and density
                                  functional study . . . . . . . . . . . . 1887--1895
               Chi-Shiun Wu and   
                    Ming-Der Su   A computational study of the
                                  reactivities of four-membered heavy
                                  carbene systems  . . . . . . . . . . . . 1896--1906
               Shao-Yong Lu and   
             Yong-Jun Jiang and   
                    Jing Lv and   
               Jian-Wei Zou and   
                   Tian-Xing Wu   Role of bridging water molecules in
                                  GSK3$ \beta $-inhibitor complexes:
                                  Insights from QM/MM, MD, and molecular
                                  docking studies  . . . . . . . . . . . . 1907--1918
          Djurre H. De Jong and   
       Lars V. Schäfer and   
           Alex H. De Vries and   
         Siewert J. Marrink and   
     Herman J. C. Berendsen and   
         Helmut Grubmüller   Determining equilibrium constants for
                                  dimerization reactions from molecular
                                  dynamics simulations . . . . . . . . . . 1919--1928
       Elizabeth J. Denning and   
         U. Deva Priyakumar and   
            Lennart Nilsson and   
     Alexander D. Mackerell Jr.   Impact of 2'-hydroxyl sampling on the
                                  conformational properties of RNA: Update
                                  of the CHARMM all-atom additive force
                                  field for RNA  . . . . . . . . . . . . . 1929--1943
                Abdel Laoui and   
             Valery R. Polyakov   Web services as applications'
                                  integration tool: QikProp case study . . 1944--1951
  Pieter Van der Weeën and   
             Jan M. Baetens and   
               Bernard De Baets   Design and parameterization of a
                                  stochastic cellular automaton describing
                                  a chemical reaction  . . . . . . . . . . 1952--1961
          Manjaly J. Ajitha and   
        Cherumuttathu H. Suresh   Role of stereoelectronic features of
                                  imine and enamine in (S)-proline
                                  catalyzed Mannich reaction of
                                  acetaldehyde: an in silico study . . . . 1962--1970
                 Wenlan Liu and   
             Volker Settels and   
      Philipp H. P. Harbach and   
              Andreas Dreuw and   
           Reinhold F. Fink and   
                   Bernd Engels   Assessment of TD-DFT- and TD-HF-based
                                  approaches for the prediction of exciton
                                  coupling parameters, potential energy
                                  curves, and electronic characters of
                                  electronically excited aggregates  . . . 1971--1981
  Volodymyr P. Sergiievskyi and   
         Wolfgang Hackbusch and   
               Maxim V. Fedorov   Multigrid solver for the reference
                                  interaction site model of molecular
                                  liquids theory . . . . . . . . . . . . . 1982--1992
     Evgeniy Yu. Pankratyev and   
         Artur R. Tulyabaev and   
            Leonard M. Khalilov   How reliable are GIAO calculations of
                                  $^1$H and $^{13}$C NMR chemical shifts?
                                  A statistical analysis and empirical
                                  corrections at DFT (PBE/3z) level  . . . 1993--1997
                    Eliseo Ruiz   Exchange coupling constants using
                                  density functional theory: Long-range
                                  corrected functionals  . . . . . . . . . 1998--2004
                Guangtao Yu and   
                Xu-Ri Huang and   
                   Wei Chen and   
                 Chia-Chung Sun   Alkali metal atom-aromatic ring: a novel
                                  interaction mode realizes large first
                                  hyperpolarizabilities of M@AR (M = Li,
                                  Na, and K, AR = pyrrole, indole,
                                  thiophene, and benzene)  . . . . . . . . 2005--2011
              Yin-Feng Wang and   
                   Wei Chen and   
               Guang-Tao Yu and   
                  Zhi-Ru Li and   
                      Di Wu and   
                 Chia-Chung Sun   Evolution of lone pair of excess
                                  electrons inside molecular cages with
                                  the deformation of the cage in $ e_2 $
                                  @C$_{60}$F$_{60}$ systems  . . . . . . . 2012--2021
          Darren J. Simpson and   
              Thomas Bredow and   
           Anand P. Chandra and   
      Giuseppe P. Cavallaro and   
               Andrea R. Gerson   The effect of iron and copper impurities
                                  on the wettability of sphalerite (110)
                                  surface  . . . . . . . . . . . . . . . . 2022--2030
            Mark J. Abraham and   
                 Jill E. Gready   Optimization of parameters for molecular
                                  dynamics simulation using smooth
                                  particle-mesh Ewald in GROMACS 4.5 . . . 2031--2040
                Mark J. Abraham   Performance enhancements for GROMACS
                                  nonbonded interactions on BlueGene . . . 2041--2046
              Sanliang Ling and   
                Maciej Gutowski   SSC: a tool for constructing libraries
                                  for systematic screening of conformers   2047--2054

Journal of Computational Chemistry
Volume 32, Number 10, July 30, 2011

              Zhaowei Huang and   
                    Hui Sun and   
                Houyu Zhang and   
                   Yue Wang and   
                         Fei Li   $ \pi $--$ \pi $ interaction of
                                  quinacridone derivatives . . . . . . . . 2055--2063
          Alexey I. Baranov and   
                Miroslav Kohout   Electron localization and delocalization
                                  indices for solids . . . . . . . . . . . 2064--2076
             Lalitha Selvam and   
             Fang Fang Chen and   
                      Feng Wang   Methylation of zebularine investigated
                                  using density functional theory
                                  calculations . . . . . . . . . . . . . . 2077--2083
               Jens Smiatek and   
                  Andreas Heuer   Calculation of free energy landscapes: a
                                  histogram reweighted metadynamics
                                  approach . . . . . . . . . . . . . . . . 2084--2096
              R. S. Rathore and   
                  P. Aparoy and   
                P. Reddanna and   
              A. K. Kondapi and   
                  M. Rami Reddy   Minimum MD simulation length required to
                                  achieve reliable results in free energy
                                  perturbation calculations: Case study of
                                  relative binding free energies of
                                  fructose-1,6-bisphosphatase inhibitors   2097--2103
Juan M. Ramírez-Anguita and   
\`Angels González-Lafont and   
           José M. Lluch   Variational transition-state theory
                                  study of the rate constant of the DMS$
                                  \cdot $OH scavenging reaction by O$_2$   2104--2118
            Hadley A. Iliff and   
             Diane L. Lynch and   
       Evangelia Kotsikorou and   
             Patricia H. Reggio   Parameterization of Org27569: an
                                  allosteric modulator of the cannabinoid
                                  CB$_1$G protein-coupled receptor . . . . 2119--2126
                 Peng Zhang and   
                   Peng Bao and   
                      Jiali Gao   Dipole preserving and polarization
                                  consistent charges . . . . . . . . . . . 2127--2139
           Steven K. Burger and   
                  Paul W. Ayers   Empirical prediction of protein $ p K_a
                                  $ values with residue mutation . . . . . 2140--2148
 Aurélien Grosdidier and   
              Vincent Zoete and   
              Olivier Michielin   Fast docking using the CHARMM force
                                  field with EADock DSS  . . . . . . . . . 2149--2159
    Stephanie B. A. De Beer and   
         Alice GlÄttli and   
           Johannes Hutzler and   
       Nico P. E. Vermeulen and   
              Chris Oostenbrink   Molecular dynamics simulations and free
                                  energy calculations on the enzyme
                                  4-hydroxyphenylpyruvate dioxygenase  . . 2160--2169
        Manoj K. Kesharwani and   
              Bishwajit Ganguly   Probing the structural and electronic
                                  effects to stabilize nonplanar forms of
                                  thioamide derivatives: a computational
                                  study  . . . . . . . . . . . . . . . . . 2170--2176
Frédéric Labat and   
             Claude Pouchan and   
                Carlo Adamo and   
            Gustavo E. Scuseria   Role of nonlocal exchange in molecular
                                  crystals: the case of two proton-ordered
                                  phases of ice  . . . . . . . . . . . . . 2177--2185
         Alexander M. Silva and   
              Itamar Borges Jr.   How to find an optimum cluster size
                                  through topological site properties:
                                  MoS$_x$ model clusters . . . . . . . . . 2186--2194
         Liudmila Sviatenko and   
            Olexandr Isayev and   
                Leonid Gorb and   
               Frances Hill and   
              Jerzy Leszczynski   Toward robust computational
                                  electrochemical predicting the
                                  environmental fate of organic pollutants 2195--2203
Raghuvir R. S. Pissurlenkar and   
           Vijay M. Khedkar and   
      Radhakrishnan P. Iyer and   
              Evans C. Coutinho   Ensemble QSAR: a  QSAR method based on
                                  conformational ensembles and metric
                                  descriptors  . . . . . . . . . . . . . . 2204--2218
               Flavio Forti and   
            Leonardo Boechi and   
            Dario A. Estrin and   
               Marcelo A. Marti   Comparing and combining implicit ligand
                                  sampling with multiple steered molecular
                                  dynamics to study ligand migration
                                  processes in heme proteins . . . . . . . 2219--2231
          Matthew G. Seetin and   
               David H. Mathews   Automated RNA tertiary structure
                                  prediction from secondary structure and
                                  low-resolution restraints  . . . . . . . 2232--2244
          Christoph Grebner and   
            Johannes Becker and   
        Svetlana Stepanenko and   
                   Bernd Engels   Efficiency of tabu-search-based
                                  conformational search algorithms . . . . 2245--2253
         Victor M. Anisimov and   
           Claudio N. Cavasotto   Quantum mechanical binding free energy
                                  calculation for phosphopeptide
                                  inhibitors of the Lck SH2 domain . . . . 2254--2263
              Yutaka Uejima and   
         Tomoharu Terashima and   
                    Ryo Maezono   Acceleration of a QM/MM-QMC simulation
                                  using GPU  . . . . . . . . . . . . . . . 2264--2272
            Trent E. Balius and   
          Sudipto Mukherjee and   
                Robert C. Rizzo   Implementation and evaluation of a
                                  docking-rescoring method using molecular
                                  footprint comparisons  . . . . . . . . . 2273--2289
               Zhixiong Lin and   
   Wilfred F. Van Gunsteren and   
                     Haiyan Liu   Conformational state-specific free
                                  energy differences by one-step
                                  perturbation: Protein secondary
                                  structure preferences of the GROMOS 43A1
                                  and 53A6 force fields  . . . . . . . . . 2290--2297
                 Weihua Zhu and   
             Chenchen Zhang and   
                    Tao Wei and   
                    Heming Xiao   Computational study of energetic
                                  nitrogen-rich derivatives of 1,1'- and
                                  5,5'-bridged ditetrazoles  . . . . . . . 2298--2312
          Karl A. Wilkinson and   
              Paul Sherwood and   
            Martyn F. Guest and   
                Kevin J. Naidoo   Acceleration of the GAMESS-UK electronic
                                  structure package on graphical
                                  processing units . . . . . . . . . . . . 2313--2318
     Naveen Michaud-Agrawal and   
       Elizabeth J. Denning and   
            Thomas B. Woolf and   
               Oliver Beckstein   MDAnalysis: a toolkit for the analysis
                                  of molecular dynamics simulations  . . . 2319--2327
         Christoph R. Jacob and   
             S. Maya Beyhan and   
               Rosa E. Bulo and   
André Severo Pereira Gomes and   
       Andreas W. Götz and   
             Karin Kiewisch and   
              Jetze Sikkema and   
                 Lucas Visscher   PyADF --- a scripting framework for
                                  multiscale quantum chemistry . . . . . . 2328--2338

Journal of Computational Chemistry
Volume 32, Number 11, August, 2011

             Marie L. Laury and   
            Scott E. Boesch and   
                  Ian Haken and   
               Pankaj Sinha and   
           Ralph A. Wheeler and   
               Angela K. Wilson   Harmonic vibrational frequencies: Scale
                                  factors for pure, hybrid, hybrid meta,
                                  and double-hybrid functionals in
                                  conjunction with correlation consistent
                                  basis sets . . . . . . . . . . . . . . . 2339--2347
                Yuhang Wang and   
           Jason A. Wallace and   
            Peter H. Koenig and   
                   Jana K. Shen   Molecular dynamics simulations of ionic
                                  and nonionic surfactant micelles with a
                                  generalized Born implicit-solvent model  2348--2358
              Vincent Zoete and   
          Michel A. Cuendet and   
 Aurélien Grosdidier and   
              Olivier Michielin   SwissParam: a fast force field
                                  generation tool for small organic
                                  molecules  . . . . . . . . . . . . . . . 2359--2368
             Robert J. Petrella   A versatile method for systematic
                                  conformational searches: Application to
                                  CheY . . . . . . . . . . . . . . . . . . 2369--2385
          Partha Pratim Roy and   
            Simona Kovarich and   
                Paola Gramatica   QSAR model reproducibility and
                                  applicability: a case study of rate
                                  constants of hydroxyl radical reaction
                                  models applied to polybrominated
                                  diphenyl ethers and (benzo-)triazoles    2386--2396
             Pablo A. Denis and   
              Federico Iribarne   On the applicability of cluster models
                                  to study the chemical reactivity of
                                  carbon nanotubes . . . . . . . . . . . . 2397--2403
                          Vikas   He molecular ion in a strong
                                  time-dependent magnetic field: a
                                  current-density functional study . . . . 2404--2413
             Yi-Hsing Chung and   
          Arvin Huang-Te Li and   
                  Sheng D. Chao   Computer simulation of trifluoromethane
                                  properties with ab initio force field    2414--2421
        Cina Foroutan-Nejad and   
           Shant Shahbazian and   
              Ferran Feixas and   
     Parviz Rashidi-Ranjbar and   
                  Miquel Sol\`a   A dissected ring current model for
                                  assessing magnetic aromaticity: a
                                  general approach for both organic and
                                  inorganic rings  . . . . . . . . . . . . 2422--2431
              Qing-Zhong Li and   
              Jun-Ling Zhao and   
                    Bo Jing and   
                     Ran Li and   
                 Wen-Zuo Li and   
                  Jian-Bo Cheng   The structure, properties, and nature of
                                  HArF--HOX (X = F, Cl, Br) complex: an ab
                                  initio study and an unusual short
                                  hydrogen bond  . . . . . . . . . . . . . 2432--2440
                 Luc Roumen and   
              Bram Van Hoof and   
              Koen Pieterse and   
        Peter A. J. Hilbers and   
        Erica M. G. Custers and   
                 Ralf Plate and   
           Marcel De Gooyer and   
        Ilona P. E. Beugels and   
         Judith M. A. Emmen and   
                Dirk Leysen and   
            Jos F. M. Smits and   
     Harry C. J. Ottenheijm and   
              J. J. Rob Hermans   Application of a ligand-based
                                  theoretical approach to derive
                                  conversion paths and ligand
                                  conformations in CYP11B2-mediated
                                  aldosterone formation  . . . . . . . . . 2441--2448
             Stefan Boresch and   
                Stefan Bruckner   Avoiding the van der Waals endpoint
                                  problem using serial atomic insertion    2449--2458
             Alexander V. Larin   Point atomic multipole moments for
                                  simulation of electrostatic potential
                                  and field in all-siliceous zeolites  . . 2459--2473
                   Qun Jing and   
                Hai-Bin Cao and   
                Gui-Xian Ge and   
               Yuan Xu Wang and   
               Hong-Xia Yan and   
              Zi-Ying Zhang and   
                     Yun-Hu Liu   Giant magnetic moment of the core-shell
                                  Co$_{13}$ @Mn$_{20}$ clusters:
                                  First-principles calculations  . . . . . 2474--2478
        Hossein Farrokhpour and   
                  Fariman Fathi   Theoretical study of valance
                                  photoelectron spectra of hypoxanthine,
                                  xanthine, and caffeine using direct
                                  symmetry-adapted cluster/configuration
                                  interaction methodology  . . . . . . . . 2479--2491
          Rafa\l A. Bachorz and   
        Florian A. Bischoff and   
    Andreas Glöß and   
       Christof Hättig and   
     Sebastian Höfener and   
                Wim Klopper and   
                   David P. Tew   The MP2-F12 method in the T URBOMOLE
                                  program package  . . . . . . . . . . . . 2492--2513

Journal of Computational Chemistry
Volume 32, Number 12, September, 2011

             Ali Nekouzadeh and   
                     Yoram Rudy   Three-residue loop closure in proteins:
                                  a new kinematic method reveals a locus
                                  of connected loop conformations  . . . . 2515--2525
               Chaim Dryzun and   
                  Amir Zait and   
                    David Avnir   Quantitative symmetry and chirality ---
                                  a fast computational algorithm for large
                                  structures: Proteins, macromolecules,
                                  nanotubes, and unit cells  . . . . . . . 2526--2538
                    Bo Liao and   
                Benyou Liao and   
                  Xinguo Lu and   
                        Zhi Cao   A novel graphical representation of
                                  protein sequences and its application    2539--2544
                 Futing Xia and   
                        Hua Zhu   Alkaline hydrolysis of ethylene
                                  phosphate: an ab initio study by
                                  supermolecule model and polarizable
                                  continuum approach . . . . . . . . . . . 2545--2554
                Han-Ying Wu and   
                Wan-Fei Cai and   
                 Lai-Cai Li and   
                An-Min Tian and   
                  Ning-Bew Wong   Theoretical study on the ring-opening
                                  isomerization reaction mechanism of the
                                  ring isomers of N$_8$H$_8$ . . . . . . . 2555--2563
          Mahmoud A. A. Ibrahim   Molecular mechanical study of halogen
                                  bonding in drug discovery  . . . . . . . 2564--2574
               Florian Fink and   
            Jochen Hochrein and   
           Vincent Wolowski and   
               Rainer Merkl and   
               Wolfram Gronwald   PROCOS: Computational analysis of
                                  protein--protein complexes . . . . . . . 2575--2586
                   Zheng Fu and   
                     Xue Li and   
            Kenneth M. Merz Jr.   Accurate assessment of the strain energy
                                  in a protein-bound drug using QM/MM
                                  X-ray refinement and converged quantum
                                  chemistry  . . . . . . . . . . . . . . . 2587--2597
           Changsheng Zhang and   
                      Luhua Lai   SDOCK: a global protein-protein docking
                                  program using stepwise force-field
                                  potentials . . . . . . . . . . . . . . . 2598--2612
             David Robinson and   
         Nicholas A. Besley and   
                Paul O'Shea and   
              Jonathan D. Hirst   Water order profiles on
                                  phospholipid/cholesterol membrane
                                  bilayer surfaces . . . . . . . . . . . . 2613--2618
           Arne Lüchow and   
               René Petz   Single electron densities: a new tool to
                                  analyze molecular wavefunctions  . . . . 2619--2626
        Adriana Pietropaolo and   
          Davide Branduardi and   
        Massimiliano Bonomi and   
             Michele Parrinello   A chirality-based metrics for
                                  free-energy calculations in biomolecular
                                  systems  . . . . . . . . . . . . . . . . 2627--2637
Elisabet Gregori-Puigjané and   
           Rut Garriga-Sust and   
                  Jordi Mestres   Indexing molecules with chemical graph
                                  identifiers  . . . . . . . . . . . . . . 2638--2646
       Konstantin V. Klenin and   
             Frank Tristram and   
                Timo Strunk and   
                Wolfgang Wenzel   Derivatives of molecular surface area
                                  and volume: Simple and exact analytical
                                  formulas . . . . . . . . . . . . . . . . 2647--2653
 Luís Pinto Da Silva and   
 Joaquim C. G. Esteves Da Silva   Theoretical modulation of the color of
                                  light emitted by firefly oxyluciferin    2654--2663
             Michel Masella and   
              Daniel Borgis and   
              Philippe Cuniasse   Combining a polarizable force-field and
                                  a coarse-grained polarizable solvent
                                  model. II. Accounting for hydrophobic
                                  effects  . . . . . . . . . . . . . . . . 2664--2678
                 Rini Gupta and   
               Amalendu Chandra   Nonideality in diffusion of ionic and
                                  neutral solutes and hydrogen bond
                                  dynamics in dimethyl
                                  sulfoxide--chloroform mixtures of
                                  varying composition  . . . . . . . . . . 2679--2689
          Giovanni Granucci and   
               Maurizio Persico   Gradients for configuration interaction
                                  energies with spin-orbit coupling in a
                                  semiempirical framework  . . . . . . . . 2690--2696
                 R. S. Dias and   
                   P. Linse and   
               A. A. C. C. Pais   Stepwise disproportionation in
                                  polyelectrolyte complexes  . . . . . . . 2697--2707
       Ala'a H. Al-Muhtaseb and   
    Mohammednoor Altarawneh and   
      Mansour H. Almatarneh and   
         Raymond A. Poirier and   
                Niveen W. Assaf   Theoretical study on the unimolecular
                                  decomposition of thiophenol  . . . . . . 2708--2715
                  Ka-un Lao and   
                    Chin-hui Yu   A computational study of unique
                                  properties of pillar$ [n] $ quinones:
                                  Self-assembly to tubular structures and
                                  potential applications as electron
                                  acceptors and anion recognizers  . . . . 2716--2726
             A. P. Toropova and   
              A. A. Toropov and   
               E. Benfenati and   
                    G. Gini and   
             D. Leszczynska and   
                 J. Leszczynski   CORAL: Quantitative structure--activity
                                  relationship models for estimating
                                  toxicity of organic compounds in rats    2727--2733
            Maciej D\lugosz and   
         Pawe\l Zieli\'nski and   
                 Joanna Trylska   Brownian dynamics simulations on CPU and
                                  GPU with BD\_BOX . . . . . . . . . . . . 2734--2744

Journal of Computational Chemistry
Volume 32, Number 13, October, 2011

                 Peipei Han and   
                    Kehe Su and   
                    Yan Liu and   
                 Yanli Wang and   
                   Xin Wang and   
              Qingfeng Zeng and   
               Laifei Cheng and   
                   Litong Zhang   Reaction rate of propene pyrolysis . . . 2745--2755
             Michio Katouda and   
           Masato Kobayashi and   
               Hiromi Nakai and   
                 Shigeru Nagase   Two-level hierarchical parallelization
                                  of second-order Mòller--Plesset
                                  perturbation calculations in
                                  divide-and-conquer method  . . . . . . . 2756--2764
                    Yang Li and   
               Chang-Sheng Wang   Rapid evaluation of the binding energies
                                  between peptide amide and DNA base . . . 2765--2773
             Tomonaga Ozawa and   
             Kosuke Okazaki and   
                  Kazuo Kitaura   Importance of CH/$ \pi $ hydrogen bonds
                                  in recognition of the core motif in
                                  proline-recognition domains: An ab
                                  initio fragment molecular orbital study  2774--2782
                   Pei-Kun Yang   Discrepancy in the near-solute electric
                                  dipole moment calculated from the
                                  electric field . . . . . . . . . . . . . 2783--2799
                    Juan Du and   
                 Huijun Sun and   
                    Lili Xi and   
                Jiazhong Li and   
                  Ying Yang and   
              Huanxiang Liu and   
                    Xiaojun Yao   Molecular modeling study of checkpoint
                                  kinase 1 inhibitors by multiple docking
                                  strategies and prime/MM--GBSA
                                  calculation  . . . . . . . . . . . . . . 2800--2809
            Hironori Kokubo and   
           Toshimasa Tanaka and   
                   Yuko Okamoto   Ab initio prediction of protein--ligand
                                  binding structures by replica-exchange
                                  umbrella sampling simulations  . . . . . 2810--2821
            Giovanni Micera and   
               Eugenio Garribba   Is the spin-orbit coupling important in
                                  the prediction of the $^{51}$V hyperfine
                                  coupling constants of V$^{IV}$O$^{2+}$
                                  species? ORCA versus Gaussian
                                  performance and biological applications  2822--2835
           Jonah Z. Vilseck and   
  Somisetti V. Sambasivarao and   
                Orlando Acevedo   Optimal scaling factors for CM1 and CM3
                                  atomic charges in RM1-based aqueous
                                  simulations  . . . . . . . . . . . . . . 2836--2842
               Shunzhou Wan and   
               Peter V. Coveney   Molecular dynamics simulation reveals
                                  structural and thermodynamic features of
                                  kinase activation by cancer mutations
                                  within the epidermal growth factor
                                  receptor . . . . . . . . . . . . . . . . 2843--2852
           Janus J. Eriksen and   
Jógvan Magnus H. Olsen and   
           K\kestutis Aidas and   
           Hans Ågren and   
          Kurt V. Mikkelsen and   
                 Jacob Kongsted   Computational protocols for prediction
                                  of solute NMR relative chemical shifts.
                                  A case study of L-tryptophan in aqueous
                                  solution . . . . . . . . . . . . . . . . 2853--2864
          Svetlana Artemova and   
            Sergei Grudinin and   
                 Stephane Redon   A comparison of neighbor search
                                  algorithms for large rigid molecules . . 2865--2877
            Nathanael Weill and   
     Christopher R. Corbeil and   
       Joris W. De Schutter and   
             Nicolas Moitessier   Toward a computational tool predicting
                                  the stereochemical outcome of asymmetric
                                  reactions: Development of the molecular
                                  mechanics-based program ACE and
                                  application to asymmetric epoxidation
                                  reactions  . . . . . . . . . . . . . . . 2878--2889
              Yung-Fou Chen and   
               J. J. Dannenberg   The effect of polarization on multiple
                                  hydrogen-bond formation in models of
                                  self-assembling materials  . . . . . . . 2890--2895
             Xiao Wei Sheng and   
              Lukasz Mentel and   
          Oleg V. Gritsenko and   
             Evert Jan Baerends   Counterpoise correction is not useful
                                  for short and van der Waals distances
                                  but may be useful at long range  . . . . 2896--2901
               Taro Udagawa and   
                    Shogo Sakai   Ab initio molecular dynamics of
                                  protonated water clusters by integrated
                                  multicenter molecular-orbital method . . 2902--2908
         Jennifer L. Knight and   
          Charles L. Brooks III   Surveying implicit solvent models for
                                  estimating small molecule absolute
                                  hydration free energies  . . . . . . . . 2909--2923
           Matthieu Chavent and   
              Antoine Vanel and   
                   Alex Tek and   
                 Bruno Levy and   
              Sophie Robert and   
               Bruno Raffin and   
                    Marc Baaden   GPU-accelerated atom and dynamic bond
                                  visualization using hyperballs: a
                                  unified algorithm for balls, sticks, and
                                  hyperboloids . . . . . . . . . . . . . . 2924--2935
              Reed B. Jacob and   
           Casey W. Bullock and   
               Tim Andersen and   
               Owen M. McDougal   DockoMatic: Automated peptide analog
                                  creation for high throughput virtual
                                  screening  . . . . . . . . . . . . . . . 2936--2941
                   Bing Xia and   
               Zheng-Fu Tai and   
                Yu-Cheng Gu and   
               Bang-Jing Li and   
              Li-Sheng Ding and   
                       Yan Zhou   MyMolDB: a micromolecular database
                                  solution with open source and free
                                  components . . . . . . . . . . . . . . . 2942--2948

Journal of Computational Chemistry
Volume 32, Number 14, November 15, 2011

             Robin Chaudret and   
                Nohad Gresh and   
            Olivier Parisel and   
           Jean-Philip Piquemal   Many-body exchange-repulsion in
                                  polarizable molecular mechanics. I.
                                  orbital-based approximations and
                                  applications to hydrated metal cation
                                  complexes  . . . . . . . . . . . . . . . 2949--2957
            Narayan Ganesan and   
              Brad A. Bauer and   
           Timothy R. Lucas and   
              Sandeep Patel and   
                 Michela Taufer   Structural, dynamic, and electrostatic
                                  properties of fully hydrated DMPC
                                  bilayers from molecular dynamics
                                  simulations accelerated with graphical
                                  processing units (GPUs)  . . . . . . . . 2958--2973
               G. L. Gutsev and   
          C. A. Weatherford and   
                 K. Pradhan and   
                        P. Jena   Density functional study of neutral and
                                  anionic AlO$_n$ and ScO$_n$ with high
                                  oxygen content . . . . . . . . . . . . . 2974--2982
             Davide Ravelli and   
              Daniele Dondi and   
           Maurizio Fagnoni and   
              Angelo Albini and   
               Alessandro Bagno   Predicting the UV spectrum of
                                  polyoxometalates by TD-DFT . . . . . . . 2983--2987
             Wojciech Plazinski   Molecular basis of calcium binding by
                                  polyguluronate chains. Revising the
                                  egg-box model  . . . . . . . . . . . . . 2988--2995
         Milind M. Deshmukh and   
       Libero J. Bartolotti and   
              Shridhar R. Gadre   Intramolecular hydrogen bond energy and
                                  cooperative interactions in $ \alpha $-,
                                  $ \beta $-, and $ \gamma $-cyclodextrin
                                  conformers . . . . . . . . . . . . . . . 2996--3004
           Urban Bor\vstnik and   
         Benjamin T. Miller and   
          Bernard R. Brooks and   
          Du\vsanka Jane\vzi\vc   The distributed diagonal force
                                  decomposition method for parallelizing
                                  molecular dynamics simulations . . . . . 3005--3013
              Mark A. Olson and   
        Sidhartha Chaudhury and   
                 Michael S. Lee   Comparison between self-guided Langevin
                                  dynamics and molecular dynamics
                                  simulations for structure refinement of
                                  protein loop conformations . . . . . . . 3014--3022
                  Paul Mach and   
                  Patrice Koehl   Geometric measures of large
                                  biomolecules: Surface, volume, and
                                  pockets  . . . . . . . . . . . . . . . . 3023--3038
Pablo García-Risueño and   
            Pablo Echenique and   
                   J. L. Alonso   Exact and efficient calculation of
                                  Lagrange multipliers in biological
                                  polymers with constrained bond lengths
                                  and bond angles: Proteins and nucleic
                                  acids as example cases . . . . . . . . . 3039--3046
            Kenichi Dedachi and   
           Tatsuya Hirakawa and   
               Seiya Fujita and   
   Mahmud Tareq Hassan Khan and   
            Ingebrigt Sylte and   
                Noriyuki Kurita   Specific interactions and binding free
                                  energies between thermolysin and
                                  dipeptides: Molecular simulations
                                  combined with ab initio molecular
                                  orbital and classical vibrational
                                  analysis . . . . . . . . . . . . . . . . 3047--3057
                Chuang Miao and   
                       Ying Shi   Reconsideration on hydrogen bond
                                  strengthening or cleavage of
                                  photoexcited coumarin 102 in aqueous
                                  solvent: a DFT/TDDFT study . . . . . . . 3058--3061
         Michinori Sumimoto and   
            Yukio Kawashima and   
           Daisuke Yokogawa and   
                 Kenji Hori and   
               Hitoshi Fujimoto   Theoretical study on the molecular
                                  structures of X-, $ \alpha $-, and $
                                  \beta $-types of lithium phthalocyanine
                                  dimer  . . . . . . . . . . . . . . . . . 3062--3067
              Feng-Chao Cui and   
             Xiao-Liang Pan and   
                    Wei Liu and   
                   Jing-Yao Liu   Elucidation of the methyl transfer
                                  mechanism catalyzed by chalcone
                                  O-methyltransferase: a density
                                  functional study . . . . . . . . . . . . 3068--3074
                  Zhinan Ma and   
               Wensheng Cai and   
                  Xueguang Shao   Impact of different potentials on the
                                  structures and energies of clusters  . . 3075--3080
             Taichi Inagaki and   
           Takeshi Yamamoto and   
                   Shigeki Kato   Proton-coupled electron transfer of the
                                  phenoxyl/phenol couple: Effect of
                                  Hartree--Fock exchange on transition
                                  structures . . . . . . . . . . . . . . . 3081--3091
               Kenta Yamada and   
           Yoshiyuki Koyano and   
             Takuya Okamoto and   
               Toshio Asada and   
               Nobuaki Koga and   
               Masataka Nagaoka   Toward a new approach for determination
                                  of solute's charge distribution to
                                  analyze interatomic electrostatic
                                  interactions in quantum
                                  mechanical/molecular mechanical
                                  simulations  . . . . . . . . . . . . . . 3092--3104
          Alessandra Manzin and   
          Oriano Bottauscio and   
     Domenico Patrizio Ansalone   Application of the thin-shell
                                  formulation to the numerical modeling of
                                  Stern layer in biomolecular
                                  electrostatics . . . . . . . . . . . . . 3105--3113
                   Robert Ponec   Bond indices in solids: Extended
                                  analytical model . . . . . . . . . . . . 3114--3121
            Chang-wen Zhang and   
                   Fu-bao Zheng   First-principles prediction on
                                  electronic and magnetic properties of
                                  hydrogenated AlN nanosheets  . . . . . . 3122--3128
           Alexander Baldes and   
                Wim Klopper and   
       Ján \vSimunek and   
                 Jozef Noga and   
                Florian Weigend   Acceleration of self-consistent-field
                                  convergence by combining conventional
                                  diagonalization and a
                                  diagonalization-free procedure . . . . . 3129--3134
                 Sunhwan Jo and   
              Kevin C. Song and   
            Heather Desaire and   
 Alexander D. MacKerell Jr. and   
                      Wonpil Im   Glycan reader: Automated sugar
                                  identification and simulation
                                  preparation for carbohydrates and
                                  glycoproteins  . . . . . . . . . . . . . 3135--3141

Journal of Computational Chemistry
Volume 32, Number 15, November 30, 2011

           Blandine Courcot and   
              Adam J. Bridgeman   Modeling the interactions between
                                  polyoxometalates and their environment   3143--3153
         Safwat Abdel-Azeim and   
                     Xin Li and   
              Lung Wa Chung and   
                 Keiji Morokuma   Zinc--Homocysteine binding in
                                  cobalamin-dependent methionine synthase
                                  and its role in the substrate
                                  activation: DFT, ONIOM, and QM/MM
                                  molecular dynamics studies . . . . . . . 3154--3167
           Hanna Kjær and   
        Stephan P. A. Sauer and   
                 Jacob Kongsted   The coupling constant polarizability and
                                  hyperpolarizabilty of $^1$J (NH) in
                                  $N$-methylacetamide, and its application
                                  for the multipole spin--spin coupling
                                  constant polarizability/reaction field
                                  approach to solvation  . . . . . . . . . 3168--3174
              Jenn-Huei Lii and   
               Fu-Xing Liao and   
                   Ching-Han Hu   Accurate prediction of the enthalpies of
                                  formation for xanthophylls . . . . . . . 3175--3187
                   Beisi Xu and   
                 Hujun Shen and   
                   Xiao Zhu and   
                      Guohui Li   Fast and accurate computation schemes
                                  for evaluating vibrational entropy of
                                  proteins . . . . . . . . . . . . . . . . 3188--3193
      Alexios Grigoropoulos and   
             Robert K. Szilagyi   In silico evaluation of proposed
                                  biosynthetic pathways for the unique
                                  dithiolate ligand of the H-cluster of
                                  [FeFe]-hydrogenase . . . . . . . . . . . 3194--3206
            David Kozlowski and   
            Julien Pilmé   New insights in quantum chemical
                                  topology studies using numerical
                                  grid-based analyses  . . . . . . . . . . 3207--3217
                  Shuo Chai and   
                Shu-Hao Wen and   
              Jin-Dou Huang and   
                      Ke-Li Han   Density functional theory study on
                                  electron and hole transport properties
                                  of organic pentacene derivatives with
                                  electron-withdrawing substituent . . . . 3218--3225
             Woong-Hee Shin and   
                    Lim Heo and   
                 Juyong Lee and   
                   Junsu Ko and   
                 Chaok Seok and   
                   Jooyoung Lee   LigDockCSA: Protein--ligand docking
                                  using conformational space annealing . . 3226--3232
                Zhao-Hui Qi and   
                    Ling Li and   
                    Xiao-Qin Qi   Using Huffman coding method to visualize
                                  and analyze DNA sequences  . . . . . . . 3233--3240
                     Jie Xu and   
                   Lei Wang and   
                Luoxin Wang and   
               Xiaolin Shen and   
                      Weilin Xu   QSPR study of Setschenow constants of
                                  organic compounds using MLR, ANN, and
                                  SVM analyses . . . . . . . . . . . . . . 3241--3252
        Thomas Steinbrecher and   
                InSuk Joung and   
                  David A. Case   Soft-core potentials in thermodynamic
                                  integration: Comparing one- and two-step
                                  transformations  . . . . . . . . . . . . 3253--3263
           Fengting T. Wang and   
                   Lei Chen and   
           Chuanjin J. Tian and   
                   Yan Meng and   
            Zhigang G. Wang and   
            Ruiqin Q. Zhang and   
            Mingxing X. Jin and   
                 Ping Zhang and   
                  Dajun J. Ding   Interactions between free radicals and a
                                  graphene fragment: Physical versus
                                  chemical bonding, charge transfer, and
                                  deformation  . . . . . . . . . . . . . . 3264--3268
              Jong-Won Song and   
               Daoling Peng and   
                 Kimihiko Hirao   A semiempirical long-range corrected
                                  exchange correlation functional
                                  including a short-range Gaussian
                                  attenuation (LCgau-B97)  . . . . . . . . 3269--3275
                   Keju Sun and   
           Masanori Kohyama and   
              Shingo Tanaka and   
                   Seiji Takeda   A theoretical study of CO adsorption on
                                  gold by Hückel theory and density
                                  functional theory calculations . . . . . 3276--3282
           Dennis M. Elking and   
              Lalith Perera and   
                Robert Duke and   
              Thomas Darden and   
                Lee G. Pedersen   A finite field method for calculating
                                  molecular polarizability tensors for
                                  arbitrary multipole rank . . . . . . . . 3283--3295
               Qingzhong Li and   
                     Ran Li and   
                 Zhenbo Liu and   
                  Wenzuo Li and   
                   Jianbo Cheng   Interplay between halogen bond and
                                  lithium bond in MCN--LiCN--XCCH (M = H,
                                  Li, and Na; X = Cl, Br, and I) complex:
                                  The enhancement of halogen bond by a
                                  lithium bond . . . . . . . . . . . . . . 3296--3303
                  Jon Baker and   
             Krzysztof Wolinski   An efficient parallel algorithm for the
                                  calculation of unrestricted canonical
                                  MP2 energies . . . . . . . . . . . . . . 3304--3312
                  Jing Wang and   
                  Jian Meng and   
                     Zhijian Wu   Theoretical insights on the electron
                                  doping and Curie temperature in La-doped
                                  Sr$_2$CrWO$_6$ . . . . . . . . . . . . . 3313--3318
       Anurag Prakash Sunda and   
              Arun Venkatnathan   Molecular dynamics simulations of
                                  triflic acid and triflate ion/water
                                  mixtures: a proton conducting
                                  electrolytic component in fuel cells . . 3319--3328
            M. N. Bannerman and   
                 R. Sargant and   
                         L. Lue   DynamO: a free $ O(N) $ general
                                  event-driven molecular dynamics
                                  simulator  . . . . . . . . . . . . . . . 3329--3338

Journal of Computational Chemistry
Volume 32, Number 16, December, 2011

                 Yang Zhong and   
              Brad A. Bauer and   
                  Sandeep Patel   Solvation properties of $N$-acetyl-$
                                  \beta $-glucosamine: Molecular dynamics
                                  study incorporating electrostatic
                                  polarization . . . . . . . . . . . . . . 3339--3353
                 C. Izanloo and   
             G. A. Parsafar and   
                H. Abroshan and   
                  H. Akbarzadeh   Denaturation of Drew--Dickerson DNA in a
                                  high salt concentration medium:
                                  Molecular dynamics simulations . . . . . 3354--3361
      András Czajlik and   
        Ilona Hudáky and   
          András Perczel   Local protein backbone folds determined
                                  by calculated NMR chemical shifts  . . . 3362--3382
Júlio C. S. Da Silva and   
               Willian R. Rocha   C\bondH bond activation of methane in
                                  aqueous solution: a hybrid quantum
                                  mechanical/effective fragment potential
                                  study  . . . . . . . . . . . . . . . . . 3383--3392
                     Qi Dai and   
                      Li Wu and   
                       Lihua Li   Improving protein structural class
                                  prediction using novel combined sequence
                                  information and predicted secondary
                                  structural features  . . . . . . . . . . 3393--3398
                Kuan-Yu Yeh and   
               Michael J. Janik   Density functional theory-based
                                  electrochemical models for the oxygen
                                  reduction reaction: Comparison of
                                  modeling approaches for electric field
                                  and solvent effects  . . . . . . . . . . 3399--3408
                Ren-Jie Lin and   
               Soonmin Jang and   
              Chen-Chang Wu and   
                Ya-Ling Liu and   
                    Feng-Yin Li   Site specificity of OH $ \alpha $-H
                                  abstraction reaction for a $ \beta
                                  $-hairpin peptide: an ab initio study    3409--3422
         Jennifer L. Knight and   
          Charles L. Brooks III   Applying efficient implicit nongeometric
                                  constraints in alchemical free energy
                                  simulations  . . . . . . . . . . . . . . 3423--3432
                 Simon Leis and   
               Martin Zacharias   Efficient inclusion of receptor
                                  flexibility in grid-based
                                  protein--ligand docking* . . . . . . . . 3433--3439
              Hua-Qing Yang and   
               Chang-Wei Hu and   
                   Chao Gao and   
              Meng-Yao Yang and   
               Fang-Ming Li and   
                 Cai-Qin Li and   
                  Xiang-Yuan Li   Theoretical study on the gas-phase
                                  reaction mechanism between palladium
                                  monoxide and methane . . . . . . . . . . 3440--3455
                Jan Meisner and   
           Judith B. Rommel and   
          Johannes Kästner   Kinetic isotope effects calculated with
                                  the instanton method . . . . . . . . . . 3456--3463
     Léonard Jaillet and   
         Francesc J. Corcho and   
Juan-Jesús Pérez and   
             Juan Cortés   Randomized tree construction algorithm
                                  to explore energy landscapes . . . . . . 3464--3474
                Yu-Fang Liu and   
               Da-Peng Yang and   
                De-Heng Shi and   
                   Jin-Feng Sun   A TD-DFT study on the hydrogen bonding
                                  of three esculetin complexes in
                                  electronically excited states:
                                  Strengthening and weakening  . . . . . . 3475--3484
       Diederik Vanfleteren and   
          Dieter Ghillemijn and   
           Dimitri Van Neck and   
           Patrick Bultinck and   
           Michel Waroquier and   
                  Paul W. Ayers   Fast density matrix-based partitioning
                                  of the energy over the atoms in a
                                  molecule consistent with the hirshfeld-I
                                  partitioning of the electron density . . 3485--3496
             Maria Jadraque and   
               Margarita Martin   Charge-transfer processes in the
                                  assembly of Si$_n$ O$_m$ neutral
                                  clusters . . . . . . . . . . . . . . . . 3497--3504
                Junmei Wang and   
                    Tingjun Hou   Application of molecular dynamics
                                  simulations in molecular property
                                  prediction II: Diffusion coefficient . . 3505--3519
                  Boran Han and   
                    Yujun Zheng   Nonadiabatic quantum dynamics in
                                  O($^3$P) + H$_2$ $ \rightarrow $ OH + H:
                                  a revisited study  . . . . . . . . . . . 3520--3525


Journal of Computational Chemistry
Volume 33, Number 1, January 5, 2012

                       A. Laref   Tight-binding molecular dynamics
                                  simulation of ZnSe liquid within the
                                  local environment dependence . . . . . . 1--10
               Chengqi Wang and   
                    Lili Xi and   
                  Shuyan Li and   
              Huanxiang Liu and   
                    Xiaojun Yao   A sequence-based computational model for
                                  the prediction of the solvent accessible
                                  surface area for $ \alpha $-helix and $
                                  \beta $-barrel transmembrane residues    11--17
                Xiang Po Du and   
             Veng Cheong Lo and   
                   Yuan Xu Wang   The effect of structure and phase
                                  transformation on the mechanical
                                  properties of Re$_2$N and the stability
                                  of Mn$_2$N . . . . . . . . . . . . . . . 18--24
          Floris P. Buelens and   
         Helmut Grubmüller   Linear-scaling soft-core scheme for
                                  alchemical free energy calculations  . . 25--33
            Hongjiang Zhang and   
          Jean-Paul Malrieu and   
                   Haibo Ma and   
                        Jing Ma   Implementation of renormalized excitonic
                                  method at ab initio level  . . . . . . . 34--43
         Uppula Purushotham and   
                Dolly Vijay and   
             G. Narahari Sastry   A computational investigation and the
                                  conformational analysis of dimers,
                                  anions, cations, and zwitterions of
                                  L-phenylalanine  . . . . . . . . . . . . 44--59
              Yusuke Ootani and   
              Tetsuya Taketsugu   Ab initio molecular dynamics approach to
                                  tunneling splitting in polyatomic
                                  molecules  . . . . . . . . . . . . . . . 60--65
                    Li Wang and   
                  Yanjie Li and   
                Hongqing He and   
                  Jinglai Zhang   Hydrogen abstraction reactions of OH
                                  radicals with CH$_3$CH$_2$CH$_2$Cl and
                                  CH$_3$CHClCH$_3$: a mechanistic and
                                  kinetic study  . . . . . . . . . . . . . 66--75
                   Pedro Gonnet   Pairwise Verlet lists: Combining cell
                                  lists and Verlet lists to improve memory
                                  locality and parallelism . . . . . . . . 76--81
                Hongping Li and   
                  Shuhui Lv and   
                  Yijia Bai and   
                 Yanjie Xia and   
               Xiaojuan Liu and   
                      Jian Meng   First-principle investigation of
                                  magnetic coupling mechanism in
                                  hypothesized A-site-ordered perovskite
                                  YMn$_3$Sc$_4$O$_{12}$  . . . . . . . . . 82--87
                  Yu Li Yan and   
                   Yuan Xu Wang   Electronic structure and low temperature
                                  thermoelectric properties of
                                  In$_{24}$M$_8$O$_{48}$ (M = Ge$^{4+}$,
                                  Sn$^{4+}$, Ti$^{4+}$, and Zr$^{4+}$ )    88--92
                Xu-Geng Guo and   
             Jing-Lai Zhang and   
                      Yuan Zhao   Ab initio characterization of size
                                  dependence of electronic spectra for
                                  linear anionic carbon clusters C$_n^-$
                                  ($ n = 4 $--$ 17 $ ) . . . . . . . . . . 93--102
               Chi-Shiun Wu and   
                    Ming-Der Su   Theoretical investigations of the
                                  reactivities of four-membered
                                  N-heterocyclic carbene analogues of the
                                  group 13 elements  . . . . . . . . . . . 103--111
           Andreas Orthaber and   
           Alexander F. Sax and   
           Kevin A. Francesconi   Oxygen versus sulfur: Structure and
                                  reactivity of substituted arsine oxides
                                  and arsine sulfides  . . . . . . . . . . 112--117

Journal of Computational Chemistry
Volume 33, Number 2, January 15, 2012

           Kiumars Shahrokh and   
               Anita Orendt and   
             Garold S. Yost and   
         Thomas E. Cheatham III   Quantum mechanically derived
                                  AMBER-compatible heme parameters for
                                  various states of the cytochrome P450
                                  catalytic cycle  . . . . . . . . . . . . 119--133
           Benjamin Helmich and   
                   Marek Sierka   Similarity recognition of molecular
                                  structures by optimal atomic matching
                                  and rotational superposition . . . . . . 134--140
           Timothy R. Lucas and   
              Brad A. Bauer and   
            Joseph E. Davis and   
                  Sandeep Patel   Molecular dynamics simulation of
                                  hydrated DPPC monolayers using charge
                                  equilibration force fields . . . . . . . 141--152
                  Qi-Shi Du and   
                 Si-Yu Long and   
             Jian-Zong Meng and   
                    Ri-Bo Huang   Empirical formulation and
                                  parameterization of cation--$ \pi $
                                  interactions for protein modeling  . . . 153--162
                Lingli Tang and   
                 Linwei Sai and   
                 Jijun Zhao and   
                    Ruifeng Qiu   A topological method for global
                                  optimization of clusters: Application to
                                  (TiO$_2$ )$_n$ ($ n = 1 $--$6$ ) . . . . 163--169
            Nitin Wadnerkar and   
         Vijayanand Kalamse and   
              Shyi-Long Lee and   
                 Ajay Chaudhari   Verification of DFT-predicted hydrogen
                                  storage capacity of VC$_3$H$_3$ complex
                                  using molecular dynamics simulations . . 170--174
   Sermsiri Chaiwongwattana and   
           Mayuree Phonyiem and   
       Viwat Vchirawongkwin and   
       Supakit Prueksaaroon and   
               Kritsana Sagarik   Dynamics and mechanism of structural
                                  diffusion in linear hydrogen bond  . . . 175--188
        Joseph D. Yesselman and   
            Daniel J. Price and   
         Jennifer L. Knight and   
          Charles L. Brooks III   MATCH: an atom-typing toolset for
                                  molecular mechanics force fields . . . . 189--202
                  Hui Zhang and   
                   Liu Yang and   
               Jing-Yao Liu and   
                    Ze-Sheng Li   Theoretical study on the reaction CX$_3$
                                  + SiH(CH$_3$ )$_3$ (X = H, F)  . . . . . 203--210
                    Nana Ma and   
              Chunguang Liu and   
               Yongqing Qiu and   
                Shiling Sun and   
                    Zhongmin Su   Theoretical investigation on
                                  redox-switchable second-order nonlinear
                                  optical responses of push--pull
                                  Cp*CoEt$_2$C$_2$B$_4$H$_3$-expanded
                                  (metallo)porphyrins  . . . . . . . . . . 211--219
               Jie Ying Gao and   
            Cheng Hua Zhang and   
               Mei Ming Luo and   
             Chan Kyung Kim and   
                    Wei Chu and   
                       Ying Xue   Mechanism for the reaction of 2-naphthol
                                  with N-methyl-N-phenyl-hydrazine
                                  suggested by the density functional
                                  theory investigations  . . . . . . . . . 220--230
               Jia-Nan Wang and   
              Hong-Liang Xu and   
               Shi-Ling Sun and   
                   Ting Gao and   
                Hong-Zhi Li and   
                     Hui Li and   
                   Zhong-Min Su   An effective method for accurate
                                  prediction of the first
                                  hyperpolarizability of alkalides . . . . 231--236
             Wolf-D. Ihlenfeldt   Letters to the editor: Comment on the
                                  paper ``Indexing molecules with chemical
                                  graph identifiers' by Elisabeth
                                  Gregori-Puigjané, Rut Garriga-Sust, and
                                  Jordi Mestres  . . . . . . . . . . . . . 237--237
Elisabet Gregori-Puigjané and   
           Rut Garriga-Sust and   
                  Jordi Mestres   Letters to the Editor: Response to the
                                  comment by Wolf Ihlenfeldt on the paper
                                  ``Indexing molecules with chemical graph
                                  identifiers''  . . . . . . . . . . . . . 238--238

Journal of Computational Chemistry
Volume 33, Number 3, January 30, 2012

          Hirofumi Fujimoto and   
             Mariko Higuchi and   
               Manabu Koike and   
               Hirotaka Ode and   
             Miroslav Pinak and   
        Juraj Kotulic Bunta and   
           Toshiyuki Nemoto and   
            Takashi Sakudoh and   
                Naoko Honda and   
            Hideaki Maekawa and   
              Kimiaki Saito and   
                  Kozo Tsuchida   A possible overestimation of the effect
                                  of acetylation on lysine residues in KQ
                                  mutant analysis  . . . . . . . . . . . . 239--246
Jean-Marie Ducéré and   
              Anne Hemeryck and   
             Alain Est\`eve and   
      Mehdi Djafari Rouhani and   
              Georges Landa and   
     Philippe Ménini and   
               Cyril Tropis and   
     André Maisonnat and   
                 Pierre Fau and   
                 Bruno Chaudret   A computational chemist approach to gas
                                  sensors: Modeling the response of
                                  SnO$_2$ to CO, O$_2$, and H$_2$O Gases   247--258
              Eshel Faraggi and   
                  Tuo Zhang and   
               Yuedong Yang and   
              Lukasz Kurgan and   
                     Yaoqi Zhou   SPINE X: Improving protein secondary
                                  structure prediction by multistep
                                  learning coupled with prediction of
                                  solvent accessible surface area and
                                  backbone torsion angles  . . . . . . . . 259--267
            Steven Lettieri and   
            Daniel M. Zuckerman   Accelerating molecular Monte Carlo
                                  simulations using distance and
                                  orientation-dependent energy tables:
                                  Tuning from atomistic accuracy to
                                  smoothed ``coarse-grained'' models . . . 268--275
             Shantanu Kadam and   
                    Kumar Vanka   A new approximate method for the
                                  stochastic simulation of chemical
                                  systems: the representative reaction
                                  approach . . . . . . . . . . . . . . . . 276--285
              Takaharu Mori and   
              Fumiko Ogushi and   
                    Yuji Sugita   Analysis of lipid surface area in
                                  protein--membrane systems combining
                                  Voronoi tessellation and Monte Carlo
                                  integration methods  . . . . . . . . . . 286--293
          V. Ruiz de Angulo and   
           J. Cortés and   
                    J. M. Porta   Rigid-CLL: Avoiding constant-distance
                                  computations in cell linked-lists
                                  algorithms . . . . . . . . . . . . . . . 294--300
                     Xue Li and   
                   Zheng Fu and   
            Kenneth M. Merz Jr.   QM/MM refinement and analysis of protein
                                  bound retinoic acid  . . . . . . . . . . 301--310
              Xiao-Jing Liu and   
               Ian Hamilton and   
         Robert P. Krawczyk and   
            Peter Schwerdtfeger   The stability of small helical gold
                                  nanorods: a relativistic density
                                  functional study . . . . . . . . . . . . 311--318
          Yulia N. Kalugina and   
       Victor N. Cherepanov and   
        Mikhail A. Buldakov and   
 Natalia Zvereva-Loëte and   
                 Vincent Boudon   Theoretical investigation of the
                                  ethylene dimer: Interaction energy and
                                  dipole moment  . . . . . . . . . . . . . 319--330
                 Kyu Il Lee and   
                 Sunhwan Jo and   
                   Huan Rui and   
            Bernhard Egwolf and   
             Beno\^\it Roux and   
          Richard W. Pastor and   
                      Wonpil Im   Software News and Updates: Web interface
                                  for Brownian dynamics simulation of ion
                                  transport and its applications to
                                  beta-barrel pores  . . . . . . . . . . . 331--339
      Anna-Pitschna E. Kunz and   
            Jane R. Allison and   
             Daan P. Geerke and   
          Bruno A. C. Horta and   
Philippe H. Hünenberger and   
            Sereina Riniker and   
              Nathan Schmid and   
       Wilfred F. van Gunsteren   Software News and Updates: New
                                  functionalities in the GROMOS
                                  biomolecular simulation software . . . . 340--353
            Laban Bondesson and   
              Elias Rudberg and   
                     Yi Luo and   
                  Pawe\l Sa\lek   Erratum: ``Basis set dependence of
                                  solute--solvent interaction energy of
                                  benzene in water: a HF/DFT study'' . . . 354--354

Journal of Computational Chemistry
Volume 33, Number 4, February 5, 2012

          Michael Honigmann and   
          Robert J. Buenker and   
         Heinz-Peter Liebermann   Complex configuration interaction
                                  calculations of the cross section for
                                  the dissociative electron attachment
                                  process $ e^- $ + F$_2$ $ \rightarrow $
                                  F $ \rightarrow $ F + F$^-$ using the
                                  complex basis function method  . . . . . 355--362
            Katharina Meier and   
               Walter Thiel and   
       Wilfred F. van Gunsteren   On the effect of a variation of the
                                  force field, spatial boundary condition
                                  and size of the QM region in QM/MM MD
                                  simulations  . . . . . . . . . . . . . . 363--378
                    Cui Liu and   
              Dong-Xia Zhao and   
                 Zhong-Zhi Yang   Direct evaluation of individual hydrogen
                                  bond energy in situ in intra- and
                                  intermolecular multiple hydrogen bonds
                                  system . . . . . . . . . . . . . . . . . 379--390
         Andrew J. Logsdail and   
                   Z. Y. Li and   
                Roy L. Johnston   Development and optimization of a novel
                                  genetic algorithm for identifying
                                  nanoclusters from scanning transmission
                                  electron microscopy images . . . . . . . 391--400
                        Feng Yu   Ab initio direct classical trajectory
                                  investigation on the S$_N$2 reaction of
                                  F$^-$ with NH$_2$F: Nonstatistical
                                  central barrier recrossing dynamics  . . 401--405
                Marcus Lundberg   Understanding cross-boundary events in
                                  ONIOM QM:QM' calculations  . . . . . . . 406--415
          Gennady L. Gutsev and   
     Charles A. Weatherford and   
           Lewis E. Johnson and   
                Purusottam Jena   Structure and properties of the aluminum
                                  borates Al(BO$_2$ )$_n$ and Al(BO$_2$
                                  )$_n^-$, ($ n = 1 $--$4$ ) . . . . . . . 416--424
                  Sudip Pan and   
              Santanab Giri and   
            Pratim K. Chattaraj   A computational study on the hydrogen
                                  adsorption capacity of various
                                  lithium-doped boron hydrides . . . . . . 425--434
  Alexandra Vardi-Kilshtain and   
                 Asaf Azuri and   
               Dan Thomas Major   Path-integral calculations of heavy atom
                                  kinetic isotope effects in condensed
                                  phase reactions using higher-order
                                  Trotter factorizations . . . . . . . . . 435--441
           J. M. C. Marques and   
           A. A. C. C. Pais and   
                    P. E. Abreu   On the use of big-bang method to
                                  generate low-energy structures of atomic
                                  clusters modeled with pair potentials of
                                  different ranges . . . . . . . . . . . . 442--452
              Fangqiang Zhu and   
                 Gerhard Hummer   Convergence and error estimation in free
                                  energy calculations using the weighted
                                  histogram analysis method  . . . . . . . 453--465
                  Wei Quan Tian   Modeling nonlinear optics of nanosystems
                                  with sum-over-states model . . . . . . . 466--470
          Francois Berenger and   
             Rojan Shrestha and   
                  Yong Zhou and   
            David Simoncini and   
                Kam Y. J. Zhang   Software News and Updates: Durandal:
                                  Fast exact clustering of protein decoys  471--474

Journal of Computational Chemistry
Volume 33, Number 5, February 15, 2012

              Francesco Rao and   
                 Martin Spichty   Thermodynamics and kinetics of
                                  large-time-step molecular dynamics . . . 475--483
                 Bu-Tong Li and   
                  Lu-Lin Li and   
                    Hai-Shun Wu   Theoretical calculation about the
                                  valence and Rydberg excited states of
                                  hydrogen cyanide . . . . . . . . . . . . 484--489
                Wenming Sun and   
                 Yuxiang Bu and   
                    Yixuan Wang   Interaction and protection mechanism
                                  between li@C$_{60}$ and nucleic acid
                                  bases (NABs): Performance of PM6-DH2 on
                                  noncovalent interaction of NABs-Li@C60   490--501
          Fabrice Avaltroni and   
           Clemence Corminboeuf   Identifying clusters as low-lying minima
                                  --- efficiency of stochastic and genetic
                                  algorithms using inexpensive electronic
                                  structure levels . . . . . . . . . . . . 502--508
    Israel Fernández and   
        F. Matthias Bickelhaupt   Alder-ene reaction: Aromaticity and
                                  activation-strain analysis . . . . . . . 509--516
                  Shuming Zhang   A reliable and efficient first
                                  principles-based method for predicting
                                  pK$_a$ values. III. Adding explicit
                                  water molecules: Can the theoretical
                                  slope be reproduced and pK$_a$ values
                                  predicted more accurately? . . . . . . . 517--526
                 Weiwei Xue and   
              Huanxiang Liu and   
                    Xiaojun Yao   Molecular mechanism of HIV-1
                                  integrase--vDNA interactions and strand
                                  transfer inhibitor action: a molecular
                                  modeling perspective . . . . . . . . . . 527--536
                   Hua Dong and   
               Bo-Zhen Chen and   
             Ming-Bao Huang and   
                   Roland Lindh   The Bergman cyclizations of the enediyne
                                  and its N-substituted analogs using
                                  multiconfigurational second-order
                                  perturbation theory  . . . . . . . . . . 537--549
             Shuntaro Chiba and   
               Yuich Harano and   
                Roland Roth and   
         Masahiro Kinoshita and   
                 Minoru Sakurai   Evaluation of protein-ligand binding
                                  free energy focused on its entropic
                                  components . . . . . . . . . . . . . . . 550--560
           Stefano Costanzi and   
                 Santiago Vilar   In Silico screening for agonists and
                                  blockers of the $ \beta_2 $ adrenergic
                                  receptor: Implications of inactive and
                                  activated state structures . . . . . . . 561--572
                Tim Geppert and   
               Felix Reisen and   
                Max Pillong and   
         Volker Hähnke and   
            Yusuf Tanrikulu and   
          Christian P. Koch and   
           Anna Maria Perna and   
      Tatiana Batista Perez and   
            Petra Schneider and   
              Gisbert Schneider   Virtual screening for compounds that
                                  mimic protein--protein interface
                                  epitopes . . . . . . . . . . . . . . . . 573--579
                    Tian Lu and   
                     Feiwu Chen   Software News and Updates: Multiwfn: a
                                  multifunctional wavefunction analyzer    580--592
                D. Heringer and   
              T. A. Niehaus and   
                   M. Wanko and   
                 Th. Frauenheim   Erratum: ``Analytical excited state
                                  forces for the time-dependent
                                  density-functional tight-binding
                                  method'' [J. Comp. Chem. \bf 28, 2589]   593--593

Journal of Computational Chemistry
Volume 33, Number 6, March 5, 2012

               Jun-Xi Liang and   
              Zhi-Yuan Geng and   
                Yong-Cheng Wang   Density functional study of S$_N$2
                                  substitution reactions for CH$_3$Cl +
                                  CX$^1$X$^{2 \bullet -}$ (X$^1$ X$^2$ =
                                  HH, HF, HCl, HBr, HI, FF, ClCl, BrBr,
                                  and II)  . . . . . . . . . . . . . . . . 595--606
           Florent Barbault and   
         François Maurel   Is inhibition process better described
                                  with MD(QM/MM) simulations? The case of
                                  urokinase type plasminogen activator
                                  inhibitors . . . . . . . . . . . . . . . 607--616
         Milind M. Deshmukh and   
              Shigeyoshi Sakaki   Two-step evaluation of binding energy
                                  and potential energy surface of van der
                                  Waals complexes  . . . . . . . . . . . . 617--628
       Soumya Ganguly Neogi and   
               Pinaki Chaudhury   Structure and spectroscopy of
                                  water-fluoride microclusters: a combined
                                  genetic algorithm and DFT-based study    629--639
               Niels Hansen and   
            Jo\vzica Dolenc and   
            Matthias Knecht and   
            Sereina Riniker and   
       Wilfred F. van Gunsteren   Assessment of enveloping distribution
                                  sampling to calculate relative free
                                  enthalpies of binding for eight
                                  netropsin--DNA duplex complexes in
                                  aqueous solution . . . . . . . . . . . . 640--651
                M. Kaukonen and   
                  A. Gulans and   
                    P. Havu and   
                   E. Kauppinen   Lennard-Jones parameters for small
                                  diameter carbon nanotubes and water for
                                  molecular mechanics simulations from van
                                  der Waals density functional
                                  calculations . . . . . . . . . . . . . . 652--658
                    Cen Gao and   
           J. Martin Herold and   
                  Dmitri Kireev   Assessment of free energy predictors for
                                  ligand binding to a methyllysine histone
                                  code reader  . . . . . . . . . . . . . . 659--665
                Jinliang Li and   
              Zhenzhen Zhao and   
                     Cui Yu and   
                Hongbo Wang and   
                   Jianwei Zhao   Theoretical investigation on the
                                  transportation behavior of molecular
                                  wires with redox reaction  . . . . . . . 666--672
                   A. Laref and   
                   S. Laref and   
                   S. Bin-Omran   Electronic structure, X-ray absorption,
                                  and optical spectroscopy of LaCoO$_3$ in
                                  the ground-state and excited-states  . . 673--684
                  Hui Zhang and   
                   Yang Liu and   
               Jing-Yao Liu and   
                    Ze-Sheng Li   Theoretical study and rate constants
                                  calculation for the reactions X +
                                  CF$_3$CH$_2$OCF$_3$ (X = F, Cl, Br)  . . 685--690
       Jan \vRezá\vc and   
             Kevin E. Riley and   
                    Pavel Hobza   Evaluation of the performance of
                                  post-Hartree--Fock methods in terms of
                                  intermolecular distance in noncovalent
                                  complexes  . . . . . . . . . . . . . . . 691--694
            Katrin Tonigold and   
                Axel Groß   Dispersive interactions in water
                                  bilayers at metallic surfaces: a
                                  comparison of the PBE and RPBE
                                  functional including semiempirical
                                  dispersion corrections . . . . . . . . . 695--701
                    M. Randi\'c   Very Efficient Search for Protein
                                  Alignment --- VESPA  . . . . . . . . . . 702--707
             Sergio Rampino and   
        Noelia Faginas Lago and   
           Antonio Lagan\`a and   
 Fermin Huarte-Larrañaga   Software News and Updates: An extension
                                  of the grid empowered molecular
                                  simulator to quantum reactive scattering 708--714

Journal of Computational Chemistry
Volume 33, Number 7, March 15, 2012

              Wenjing Zhang and   
                 Yanyan Zhu and   
                Donghui Wei and   
                 Mingsheng Tang   Reviews: Mechanisms of the cascade
                                  synthesis of substituted
                                  4-amino-1,2,4-triazol-3-one from huisgen
                                  zwitterion and aldehyde hydrazone: a DFT
                                  study  . . . . . . . . . . . . . . . . . 715--722
        Michael E. Lasinski and   
          Nichols A. Romero and   
             Shawn T. Brown and   
         Jean-Philippe Blaudeau   Recent performance improvements to the
                                  DFT and TDDFT in GAMESS  . . . . . . . . 723--731
        Abolghasem Beheshti and   
              Siavash Riahi and   
      Mohammad Reza Ganjali and   
                 Parviz Norouzi   Highlighting and trying to overcome a
                                  serious drawback with QSPR studies; data
                                  collection in different experimental
                                  conditions (mixed-QSPR)  . . . . . . . . 732--747
           J. Andrés and   
                  S. Berski and   
              L. R. Domingo and   
   P. González-Navarrete   Nature of the ring-closure process along
                                  the rearrangement of
                                  octa-1,3,5,7-tetraene to
                                  cycloocta-1,3,5-triene from the
                                  perspective of the electron localization
                                  function and catastrophe theory  . . . . 748--756
             Franziska Hess and   
              Attila Farkas and   
           Ari P. Seitsonen and   
                   Herbert Over   ``First-Principles'' kinetic Monte Carlo
                                  simulations revisited: CO oxidation over
                                  RuO$_2$(110) . . . . . . . . . . . . . . 757--766
Vladimír Sládek and   
    Vladimír Luke\vs and   
             Michal Il\vcin and   
           Stanislav Biskupi\vc   Ab initio calculation of structure and
                                  transport properties of He\ldotsX (X =
                                  Zn, Cd, Hg) van der Waals complexes  . . 767--778
           Mäel Bosson and   
           Caroline Richard and   
               Antoine Plet and   
            Sergei Grudinin and   
                 Stephane Redon   Interactive quantum chemistry: a
                                  divide-and-conquer ASED-MO method  . . . 779--790
            Sampath Koppole and   
               Michael Schaefer   A discriminative Ramachandran potential
                                  of mean force aimed at minimizing
                                  secondary structure bias . . . . . . . . 791--799
              Truong Ba Tai and   
                Minh Tho Nguyen   Electronic structure and thermochemical
                                  properties of silicon-doped lithium
                                  clusters Li$_n$Si$^{0 \slash +}$, $ n =
                                  1 $--$8$: New insights on their
                                  stability  . . . . . . . . . . . . . . . 800--809
            Philipp Plessow and   
                Florian Weigend   Software News and Updates: Seminumerical
                                  calculation of the Hartree--Fock
                                  exchange matrix: Application to
                                  two-component procedures and efficient
                                  evaluation of local hybrid density
                                  functionals  . . . . . . . . . . . . . . 810--816

Journal of Computational Chemistry
Volume 33, Number 8, March 30, 2012

                  Jiande Gu and   
                  Jing Wang and   
                Yaoming Xie and   
          Jerzy Leszczynski and   
          Henry F. Schaefer III   Structural and electronic property
                                  responses to the arsenic/phosphorus
                                  exchange in GC-related DNA of the
                                  $B$-form . . . . . . . . . . . . . . . . 817--821
            Alessandro Erba and   
                  Cesare Pisani   Evaluation of the electron momentum
                                  density of crystalline systems from ab
                                  initio linear combination of atomic
                                  orbitals calculations  . . . . . . . . . 822--831
               Yury N. Vorobjev   Potential of mean force of water--proton
                                  bath and molecular dynamic simulation of
                                  proteins at constant pH  . . . . . . . . 832--842
      Debashree Chakraborty and   
               Amalendu Chandra   Voids and necks in liquid ammonia and
                                  their roles in diffusion of ions of
                                  varying size . . . . . . . . . . . . . . 843--852
       Barbara Logan Mooney and   
    L. René Corrales and   
                Aurora E. Clark   MoleculaRnetworks: an integrated graph
                                  theoretic and data mining tool to
                                  explore solvent organization in
                                  molecular simulation . . . . . . . . . . 853--860
               Cai-Hua Zhou and   
                     Xiang Zhao   Chemically modified fullerene
                                  derivatives as photosensitizers in
                                  photodynamic therapy: a first-principles
                                  study  . . . . . . . . . . . . . . . . . 861--867
                  Ying Zhao and   
          Antonio De Nicola and   
        Toshihiro Kawakatsu and   
                Giuseppe Milano   Software News and Updates: Hybrid
                                  particle-field molecular dynamics
                                  simulations: Parallelization and
                                  benchmarks . . . . . . . . . . . . . . . 868--880
              Arnim Hellweg and   
        Michael Diedenhofen and   
                     Uwe Huniar   Software News and Updates: \tt
                                  thermocalc --- a poor man's approach to
                                  computational thermochemistry  . . . . . 881--886
          R. Thomas Ullmann and   
            G. Matthias Ullmann   Software News and Updates: GMCT: a Monte
                                  Carlo simulation package for
                                  macromolecular receptors . . . . . . . . 887--900
André A. S. T. Ribeiro and   
       Ricardo B. de Alencastro   Software News and Updates: Mixed Monte
                                  Carlo/molecular dynamics simulations in
                                  explicit solvent . . . . . . . . . . . . 901--905
            Ilya A. Balabin and   
               Xiangqian Hu and   
               David N. Beratan   Software News and Updates: Exploring
                                  biological electron transfer pathway
                                  dynamics with the Pathways Plugin for
                                  VMD  . . . . . . . . . . . . . . . . . . 906--910
           J. H. van Lenthe and   
          H. B. Broer-Braam and   
                      Z. Rashid   Letters to the Editor: On the efficiency
                                  of VBSCF algorithms, a comment on ``An
                                  efficient algorithm for energy gradients
                                  and orbital optimization in valence bond
                                  theory'' . . . . . . . . . . . . . . . . 911--913
                     Wei Wu and   
                      Yirong Mo   Letters to the Editor: Reply to comment
                                  on the paper ``An Efficient Algorithm
                                  for Energy Gradients and Orbital
                                  Optimization in Valence Bond Theory''    914--915

Journal of Computational Chemistry
Volume 33, Number 9, April 5, 2012

        Gleb Y. Solomentsev and   
           Niall J. English and   
               Damian A. Mooney   Effects of external electromagnetic
                                  fields on the conformational sampling of
                                  a short alanine peptide  . . . . . . . . 917--923
                Kazuhiro Ishida   Fourier transform general formula for
                                  systematic potentials  . . . . . . . . . 924--936
        Olga Bezkorovaynaya and   
         Alexander Lukyanov and   
                Kurt Kremer and   
                Christine Peter   Multiscale simulation of small peptides:
                                  Consistent conformational sampling in
                                  atomistic and coarse-grained models  . . 937--949
             Jeffrey S. Tan and   
   Stephan X. M. Boerrigter and   
        Raymond P. Scaringe and   
              Kenneth R. Morris   Core-shell potential-derived point
                                  charges  . . . . . . . . . . . . . . . . 950--957
        Gustavo L. C. Moura and   
               Alfredo M. Simas   Quantum molecular mechanics --- a
                                  noniterative procedure for the fast ab
                                  initio calculation of closed shell
                                  systems  . . . . . . . . . . . . . . . . 958--969
              P. Nuno Palma and   
Maria João Bonifácio and   
        Ana Isabel Loureiro and   
Patrício Soares-da-Silva   Computation of the binding affinities of
                                  catechol-O-methyltransferase inhibitors:
                                  Multisubstate relative free energy
                                  calculations . . . . . . . . . . . . . . 970--986
          Ch. Bheema Lingam and   
             K. Ramesh Babu and   
            Surya P. Tewari and   
               G. Vaitheeswaran   Density functional study of
                                  electronic,bonding, and vibrational
                                  properties of Ca(NH$_2$BH$_3$ )$_2$  . . 987--997
               Shi-Bao Wang and   
          Arvin Huang-Te Li and   
                  Sheng D. Chao   Liquid properties of dimethyl ether from
                                  molecular dynamics simulations using ab
                                  initio force fields  . . . . . . . . . . 998--1003
              Hannes Kopitz and   
          Daniel A. Cashman and   
    Stefania Pfeiffer-Marek and   
                  Holger Gohlke   Influence of the solvent representation
                                  on vibrational entropy calculations:
                                  Generalized Born versus
                                  distance-dependent dielectric model  . . 1004--1013

Journal of Computational Chemistry
Volume 33, Number 10, April 15, 2012

        Valentina Cantatore and   
          Giovanni Granucci and   
               Maurizio Persico   Stochastic model for photoinduced
                                  anisotropy . . . . . . . . . . . . . . . 1015--1022
           K. V. Turcheniuk and   
                 A. B. Rozhenko   $ (\sigma^3, \lambda^5) $-phosphoranes
                                  versus $ (\sigma^3, \lambda^3)
                                  $-thiaphosphiranes: Quantum chemical
                                  investigation of products of
                                  phosphaalkene sulfurization  . . . . . . 1023--1028
              Antonio Ricci and   
                Andrea Brancale   Density functional theory calculation of
                                  cyclic carboxylic phosphorus mixed
                                  anhydrides as possible intermediates in
                                  biochemical reactions: Implications for
                                  the Pro-Tide approach  . . . . . . . . . 1029--1037
                     Qi Cao and   
                  Jing Wang and   
             Zhao-Shuo Tian and   
               Zai-Feng Xie and   
                    Fu-Quan Bai   Theoretical investigation on the
                                  photophysical properties of
                                  N-heterocyclic carbene iridium (III)
                                  complexes (fpmb)$_x$ Ir(bptz)$_{3 - x}$
                                  ($ x = 1 $--$2$ )  . . . . . . . . . . . 1038--1046
           Sambath Baskaran and   
       Masilamani Tamizmani and   
  Thanigachalam Mahalakshmi and   
          Chinnappan Sivasankar   A [Fe(CB$_6$ )] platform for binding of
                                  small molecules: Insights from DFT
                                  calculations . . . . . . . . . . . . . . 1047--1054
                Ivo Cacelli and   
           Antonella Cimoli and   
      Paolo Roberto Livotto and   
             Giacomo Prampolini   An automated approach for the
                                  parameterization of accurate
                                  intermolecular force-fields: Pyridine as
                                  a case study . . . . . . . . . . . . . . 1055--1067
       Emmanuel N. Koukaras and   
       Aristides D. Zdetsis and   
      Panaghiotis Karamanis and   
             Claude Pouchan and   
       Aggelos Avramopoulos and   
        Manthos G. Papadopoulos   Structural and static electric response
                                  properties of highly symmetric lithiated
                                  silicon cages: Theoretical predictions   1068--1079
Martin Dra\vcínský and   
                    Petr Bou\vr   Vibrational averaging of the chemical
                                  shift in crystalline $ \alpha $-glycine  1080--1089

Journal of Computational Chemistry
Volume 33, Number 11, April 30, 2012

 Angelo Domenico Quartarolo and   
     Sandro Giuseppe Chiodo and   
                     Nino Russo   A TDDFT investigation of bay substituted
                                  perylenediimides: Absorption and
                                  intersystem crossing . . . . . . . . . . 1091--1100
              Riguang Zhang and   
                 Luzhi Song and   
                Baojun Wang and   
                       Zhong Li   A density functional theory
                                  investigation on the mechanism and
                                  kinetics of dimethyl carbonate formation
                                  on Cu$_2$O catalyst  . . . . . . . . . . 1101--1110
             Milan Randi\'c and   
        Damir Vuki\vcevi\'c and   
       Alexandru T. Balaban and   
            Marjan Vra\vcko and   
              Dejan Plav\vsi\'c   Conjugated circuits currents in
                                  hexabenzocoronene and its derivatives
                                  formed by joining proximal carbons . . . 1111--1122
        Robert A. Evarestov and   
              Andrei V. Bandura   First-principles calculations on the
                                  four phases of BaTiO$_3$ . . . . . . . . 1123--1130
            Asit K. Chandra and   
Thér\`ese Zeegers-Huyskens   A theoretical investigation of the
                                  interaction between substituted carbonyl
                                  derivatives and water: Open or cyclic
                                  complexes? . . . . . . . . . . . . . . . 1131--1141
           Timothy H. Click and   
        Sergei Y. Ponomarev and   
             George A. Kaminski   Importance of electrostatic
                                  polarizability in calculating cysteine
                                  acidity constants and copper(I) binding
                                  energy of \em Bacillus subtilis CopZ . . 1142--1151
    Alexander H. Boschitsch and   
               Pavel V. Danilov   Formulation of a new and simple
                                  nonuniform size-modified
                                  Poisson--Boltzmann description . . . . . 1152--1164

Journal of Computational Chemistry
Volume 33, Number 12, May 5, 2012

               Supriya Saha and   
                Sougata Pal and   
              Pranab Sarkar and   
                 A. L. Rosa and   
                 Th. Frauenheim   A complete set of self-consistent charge
                                  density-functional tight-binding
                                  parametrization of zinc chalcogenides
                                  (ZnX; X = O, S, Se, and Te)  . . . . . . 1165--1178
          Paulius Mikulskis and   
            Samuel Genheden and   
             Karin Wichmann and   
                       Ulf Ryde   A semiempirical approach to
                                  ligand-binding affinities: Dependence on
                                  the Hamiltonian and corrections  . . . . 1179--1189
           Patrick Laflamme and   
         Alexandre Beaudoin and   
            Thomas Chapaton and   
               Claude Spino and   
                 Armand Soldera   Simulated infrared spectra of triflic
                                  acid during proton dissociation  . . . . 1190--1196
  Tibor András Rokob and   
Lubomír Rulí\vsek   Curvature correction for microiterative
                                  optimizations with QM/MM electronic
                                  embedding  . . . . . . . . . . . . . . . 1197--1206
           René Pool and   
               Jaap Heringa and   
            Martin Hoefling and   
              Roland Schulz and   
            Jeremy C. Smith and   
              K. Anton Feenstra   Software News and Updates: Enabling
                                  grand-canonical Monte Carlo: Extending
                                  the flexibility of GROMACS through the
                                  GromPy Python interface module . . . . . 1207--1214
             Markus Wagener and   
             Jacob de Vlieg and   
              Sander B. Nabuurs   Software News and Updates: Flexible
                                  protein-ligand docking using the Fleksy
                                  protocol . . . . . . . . . . . . . . . . 1215--1217
             A. P. Toropova and   
              A. A. Toropov and   
                A. Lombardo and   
             A. Roncaglioni and   
               E. Benfenati and   
                        G. Gini   Software News and Updates: Coral: QSAR
                                  models for acute toxicity in fathead
                                  minnow (\em Pimephales promelas) . . . . 1218--1223

Journal of Computational Chemistry
Volume 33, Number 13, May 15, 2012

                     You Lu and   
              Zhenggang Lan and   
                   Walter Thiel   Monomeric adenine decay dynamics
                                  influenced by the DNA environment  . . . 1225--1235
      Marta González and   
Roi Álvarez Rodríguez and   
        Maria Magdalena Cid and   
      Carlos Silva López   A stepwise retro-imino-ene as a key step
                                  in the mechanism of allene formation via
                                  the Crabbé acetylene homologation . . . . 1236--1239
       Nicolás Otero and   
                 Marcos Mandado   Chemical reactivity in the framework of
                                  pair density functional theories . . . . 1240--1251
               Deok-Soo Kim and   
              Joonghyun Ryu and   
                Hayong Shin and   
                  Youngsong Cho   Beta-decomposition for the volume and
                                  area of the union of three-dimensional
                                  balls and their offsets  . . . . . . . . 1252--1273
              Jyh Shing Lin and   
                 Shao-Yu Lu and   
              Po-Jung Tseng and   
                   Wen-Chi Chou   Temperature dependence of vibrational
                                  modes of CH$_3$CC$_{(ads)}$ and
                                  I$_{(ads)}$ coadsorbed on Ag(111): ab
                                  initio molecular dynamics approach . . . 1274--1283

Journal of Computational Chemistry
Volume 33, Number 14, May 30, 2012

      Uttam Sinha Mahapatra and   
            Sudip Chattopadhyay   Diagnosis of the performance of the
                                  state-specific multireference
                                  coupled-cluster method with different
                                  truncation schemes . . . . . . . . . . . 1285--1303
             Peter Deglmann and   
                 Stephan Schenk   Thermodynamics of chemical reactions
                                  with COSMO-RS: the extreme case of
                                  charge separation or recombination . . . 1304--1320
                 Yanli Zeng and   
                    Min Zhu and   
                 Xiaoyan Li and   
               Shijun Zheng and   
                  Lingpeng Meng   Assessment of intermolecular
                                  interactions at three sites of the
                                  arylalkyne in phenylacetylene-containing
                                  lithium-bonded complexes: ab initio and
                                  QTAIM studies  . . . . . . . . . . . . . 1321--1327
               Guosheng Shi and   
                Yihong Ding and   
                   Haiping Fang   Unexpectedly strong anion--$ \pi $
                                  interactions on the graphene flakes  . . 1328--1337
         Thiago C. F. Gomes and   
                  Munir S. Skaf   Software News and Updates:
                                  Cellulose-Builder: a toolkit for
                                  building crystalline structures of
                                  cellulose  . . . . . . . . . . . . . . . 1338--1346

Journal of Computational Chemistry
Volume 33, Number 15, June 5, 2012

                        Feng Yu   Assessment of ab initio MP2 and density
                                  functionals for characterizing the
                                  potential energy profiles of the S$_N$2
                                  reactions at N center  . . . . . . . . . 1347--1352
              Shanshan Tang and   
                 Jingping Zhang   Design of donors with broad absorption
                                  regions and suitable frontier molecular
                                  orbitals to match typical acceptors via
                                  substitution on
                                  oligo(thienylenevinylene) toward solar
                                  cells  . . . . . . . . . . . . . . . . . 1353--1363
     Jennifer M. Kashmirian and   
             Alfred Uhlherr and   
                 Alan Dorin and   
                 David G. Green   Molecular dynamics extended for
                                  fluctuating networks: Application to
                                  water  . . . . . . . . . . . . . . . . . 1364--1373
                     Ye Mei and   
                 Yong L. Li and   
                  Juan Zeng and   
               John Z. H. Zhang   Electrostatic polarization is critical
                                  for the strong binding in
                                  streptavidin-biotin system . . . . . . . 1374--1382
               David J. Huggins   Benchmarking the thermodynamic analysis
                                  of water molecules around a model beta
                                  sheet  . . . . . . . . . . . . . . . . . 1383--1392
             William B. Sherman   Software News and Updates: HolT Hunter:
                                  Software for identifying and
                                  characterizing low-strain DNA Holliday
                                  triangles  . . . . . . . . . . . . . . . 1393--1405

Journal of Computational Chemistry
Volume 33, Number 16, June 15, 2012

         Jhon Zapata-Rivera and   
              Rosa Caballol and   
              Carmen J. Calzado   The role of macrocyclic ligands in the
                                  peroxo/superoxo nature of Ni--O$_2$
                                  biomimetic complexes . . . . . . . . . . 1407--1415
                Chang G. Ji and   
               John Z. H. Zhang   Effect of interprotein polarization on
                                  protein--protein binding energy  . . . . 1416--1420
                    Anan Wu and   
                         Xin Xu   DCMB that combines divide-and-conquer
                                  and mixed-basis set methods for accurate
                                  geometry optimizations, total energies,
                                  and vibrational frequencies of large
                                  molecules  . . . . . . . . . . . . . . . 1421--1432
                  Shuhui Lv and   
               Xiaojuan Liu and   
                Hongping Li and   
                    Lin Han and   
            Zhongchang Wang and   
                      Jian Meng   Insulator--metal transition driven by
                                  pressure and B-site disorder in double
                                  perovskite La$_2$CoMnO$_6$ . . . . . . . 1433--1439
Christopher J. R. Illingworth and   
        Sree V. Chintipalli and   
        Stefano A. Serapian and   
           Andrew D. Miller and   
             Vaclav Veverka and   
               Mark D. Carr and   
        Christopher A. Reynolds   The statistical significance of selected
                                  sense--antisense peptide interactions    1440--1447
                   Hao Tang and   
                    Zhuo Li and   
               Yu-Hong Yang and   
                  Ying Zhao and   
                 Su-Qin Wan and   
               Hui-Ling Liu and   
                    Xu-Ri Huang   Comparison of the FeO$^{2+}$ and
                                  FeS$^{2+}$ complexes in the cyanide and
                                  isocyanide ligand environment for
                                  methane hydroxylation  . . . . . . . . . 1448--1457
           Pradip K. Biswas and   
          Nadeem A. Vellore and   
           Jeremy A. Yancey and   
          Tugba G. Kucukkal and   
              Galen Collier and   
          Bernard R. Brooks and   
           Steven J. Stuart and   
               Robert A. Latour   Simulation of multiphase systems
                                  utilizing independent force fields to
                                  control intraphase and interphase
                                  behavior . . . . . . . . . . . . . . . . 1458--1466

Journal of Computational Chemistry
Volume 33, Number 17, June 30, 2012

             Denise Steiner and   
          Chris Oostenbrink and   
       Wilfred F. van Gunsteren   Calculation of the relative free energy
                                  of oxidation of azurin at pH 5 and pH 9  1467--1477
             Sergey Gusarov and   
      Bhalchandra S. Pujari and   
               Andriy Kovalenko   Efficient treatment of solvation shells
                                  in $3$D molecular theory of solvation    1478--1494
               Alexander F. Sax   Localization of molecular orbitals on
                                  fragments  . . . . . . . . . . . . . . . 1495--1510
                 Pablo A. Denis   Interaction between alkyl radicals and
                                  single wall carbon nanotubes . . . . . . 1511--1516
     Siriporn Jungsuttiwong and   
       Thanisorn Yakhanthip and   
          Yaowarat Surakhot and   
         Janeeya Khunchalee and   
        Taweesak Sudyoadsuk and   
            Vinich Promarak and   
              Nawee Kungwan and   
           Supawadee Namuangruk   The effect of conjugated spacer on novel
                                  carbazole derivatives for dye-sensitized
                                  solar cells: Density functional
                                  theory/time-dependent density functional
                                  theory study . . . . . . . . . . . . . . 1517--1523
                      Anonymous   Retracted: ``Prediction of
                                  posttranslational modification sites
                                  from sequences with kernel methods'' by
                                  Xiaobo Wang, Yongcui Wang, Yingjie Tian,
                                  Xiaojian Shao, Ling-Yun Wu, and Naiyang
                                  Deng, published online on 21 April 2010  1524--1524

Journal of Computational Chemistry
Volume 33, Number 18, July 5, 2012

              David Gfeller and   
          Olivier Michielin and   
                  Vincent Zoete   Expanding molecular modeling and design
                                  tools to non-natural sidechains  . . . . 1525--1535
       Daniel J. Sindhikara and   
              Norio Yoshida and   
                   Fumio Hirata   Placevent: an algorithm for prediction
                                  of explicit solvent atom distribution
                                  --- application to HIV-1 protease and
                                  F-ATP synthase . . . . . . . . . . . . . 1536--1543
             Volker Settels and   
                 Wenlan Liu and   
                Jens Pflaum and   
           Reinhold F. Fink and   
                   Bernd Engels   Comparison of the electronic structure
                                  of different perylene-based
                                  dye-aggregates . . . . . . . . . . . . . 1544--1553
          Andrei V. Bandura and   
            Robert A. Evarestov   First-principles calculations on
                                  thermodynamic properties of BaTiO$_3$
                                  rhombohedral phase . . . . . . . . . . . 1554--1563
                  Keda Yang and   
                   Jiaye Su and   
                    Hongxia Guo   GPU accelerated numerical simulations of
                                  viscoelastic phase separation model  . . 1564--1571
              Jussi Lehtola and   
               Mikko Hakala and   
                 Arto Sakko and   
Keijo Hämäläinen   Software News and Updates: ERKALE --- a
                                  flexible program package for X-ray
                                  properties of atoms and molecules  . . . 1572--1585

Journal of Computational Chemistry
Volume 33, Number 19, July 15, 2012

                  Jing Wang and   
                  Jiande Gu and   
              Jerzy Leszczynski   The electronic spectra and the H-bonding
                                  pattern of the sulfur and selenium
                                  substituted guanines . . . . . . . . . . 1587--1593
          Robert J. Buenker and   
         Heinz-Peter Liebermann   Ab initio study of the positronation of
                                  the CaO and SrO molecules including
                                  calculation of annihilation rates  . . . 1594--1602
         Tomasz Bere\'zniak and   
        Andres Jäschke and   
            Jeremy C. Smith and   
                    Petra Imhof   Stereoselection in the Diels--Alderase
                                  ribozyme: a molecular dynamics study . . 1603--1614
              John Kendrick and   
         Frank J. J. Leusen and   
              Marcus A. Neumann   Empirical van der Waals corrections to
                                  solid-state density functional theory:
                                  Iodine and phosphorous containing
                                  molecular crystals . . . . . . . . . . . 1615--1622
           Chiara Panosetti and   
                Werner A. Hofer   Adsorption of metadiiodobenzene on
                                  Cu(110): a theoretical study . . . . . . 1623--1631
           Semen O. Yesylevskyy   Software News and Updates: Pteros: Fast
                                  and easy to use open-source C++ library
                                  for molecular analysis . . . . . . . . . 1632--1636
         R. Jeffrey Largent and   
           William F. Polik and   
                  J. R. Schmidt   Software News and Updates: Symmetrizer:
                                  Algorithmic determination of point
                                  groups in nearly symmetric molecules . . 1637--1642
        Benjamin P. Roberts and   
          Gustavo M. Seabra and   
         Adrian E. Roitberg and   
            Kenneth M. Merz and   
               Erik Deumens and   
                Juan Torras and   
              Samuel B. Trickey   Software News and Updates: Commentary:
                                  Comment on ``A minimal implementation of
                                  the AMBER--GAUSSIAN interface for Ab
                                  Initio QM/MM-MD simulation'' . . . . . . 1643--1644

Journal of Computational Chemistry
Volume 33, Number 20, July 30, 2012

             Daniel W. Kulp and   
      Sabareesh Subramaniam and   
            Jason E. Donald and   
          Brett T. Hannigan and   
        Benjamin K. Mueller and   
           Gevorg Grigoryan and   
               Alessandro Senes   Structural informatics, modeling, and
                                  design with an open-source Molecular
                                  Software Library (MSL) . . . . . . . . . 1645--1661
               Hyun Woo Kim and   
                 Young Min Rhee   Molecule-specific determination of
                                  atomic polarizabilities with the
                                  polarizable atomic multipole model . . . 1662--1672
           Christian Kramer and   
               Peter Gedeck and   
                  Markus Meuwly   Atomic multipoles: Electrostatic
                                  potential fit, local reference axis
                                  systems, and conformational dependence   1673--1688
      Christos E. Kefalidis and   
         Constantinos A. Tsipis   DFT study of the mechanism of
                                  hydroamination of ethylene with ammonia
                                  catalyzed by diplatinum(II) complexes:
                                  Inner- or outer-sphere?  . . . . . . . . 1689--1700
                Xue-Fang Yu and   
            Shohei Yamazaki and   
              Tetsuya Taketsugu   Theoretical study of the excited-state
                                  double proton transfer in the
                                  (3-methyl-7-azaindole)-(7-azaindole)
                                  heterodimer  . . . . . . . . . . . . . . 1701--1708
         Wojciech Plazinski and   
                  Mateusz Drach   The dynamics of the calcium-induced
                                  chain--chain association in the
                                  polyuronate systems  . . . . . . . . . . 1709--1715

Journal of Computational Chemistry
Volume 33, Number 21, August 5, 2012

                Pieter Chys and   
            Pablo Chacón   Spinor product computations for protein
                                  conformations  . . . . . . . . . . . . . 1717--1729
                Jens Antony and   
                  Stefan Grimme   Fully ab initio protein-ligand
                                  interaction energies with dispersion
                                  corrected density functional theory  . . 1730--1739
               Nikhil Taxak and   
          Prashant V. Desai and   
              Bhargav Patel and   
           Michael Mohutsky and   
    Valentine J. Klimkowski and   
               Vijay Gombar and   
             Prasad V. Bharatam   Metabolic-intermediate complex formation
                                  with cytochrome P450: Theoretical
                                  studies in elucidating the reaction
                                  pathway for the generation of reactive
                                  nitroso intermediate . . . . . . . . . . 1740--1747
             Zahra Tabookht and   
        Xavier López and   
              Coen de Graaf and   
    Nathalie Guihéry and   
              Nicolas Suaud and   
                  Nadia Benamor   Rationalization of the behavior of M$_2$
                                  (CH$_3$CS$_2$ )$_4$I (M = Ni, Pt) chains
                                  at room temperature from periodic
                                  density functional theory and ab initio
                                  cluster calculations . . . . . . . . . . 1748--1761
                   D. Koley and   
                  E. Arunan and   
                S. Ramakrishnan   Computational investigations on covalent
                                  dimerization/oligomerization of
                                  polyacenes: Is it relevant to soot
                                  formation? . . . . . . . . . . . . . . . 1762--1772
              Hongfang Yang and   
               Qisheng Song and   
                 Xinyu Song and   
                     Yuxiang Bu   Multi-zinc-expanded graphene patches:
                                  Tetraradical versus diradical character  1773--1780

Journal of Computational Chemistry
Volume 33, Number 22, August 15, 2012

                 Weihua Zhu and   
                 Qingli Yan and   
                 Jinshan Li and   
                 Bibo Cheng and   
                Yuling Shao and   
                 Xuelan Xia and   
                    Heming Xiao   Prediction of the properties and
                                  thermodynamics of formation for
                                  energetic nitrogen-rich salts composed
                                  of triaminoguanidinium cation and
                                  5-nitroiminotetrazolate-based anions . . 1781--1789
                    Hui Liu and   
                  Fang Wang and   
             Gui-Xiang Wang and   
                  Xue-Dong Gong   Theoretical investigations on structure,
                                  density, detonation properties, and
                                  sensitivity of the derivatives of PYX    1790--1796
              Andreas Dreuw and   
        Matthias A. Polkehn and   
              Robert Binder and   
           Alexander Heckel and   
             Stefan Knippenberg   Computational design of improved
                                  two-photon active caging compounds based
                                  on nitrodibenzofuran . . . . . . . . . . 1797--1805
    Massimiliano Bartolomei and   
            Fernando Pirani and   
           Antonio Lagan\`a and   
                Andrea Lombardi   A full dimensional grid empowered
                                  simulation of the CO$_2$ + CO$_2$
                                  processes  . . . . . . . . . . . . . . . 1806--1819
                  Fang Wang and   
               Hong-Chen Du and   
                    Hui Liu and   
                  Xue-Dong Gong   Density functional theory study of
                                  high-pressure effect on crystalline
                                  4,4',6,6'-tetra(azido)hydrazo-1,3,5-triazine 1820--1830
             Luis F. Pacios and   
Cristina Gómez-Casado and   
        Leticia Tordesillas and   
     Arantxa Palacín and   
  Rosa Sánchez-Monge and   
    Araceli Díaz-Perales   Computational study of ligand binding in
                                  lipid transfer proteins: Structures,
                                  interfaces, and free energies of
                                  protein-lipid complexes  . . . . . . . . 1831--1844

Journal of Computational Chemistry
Volume 33, Number 23, September 5, 2012

           Hanna Kjær and   
           Monia R. Nielsen and   
          Gabriel I. Pagola and   
           Marta B. Ferraro and   
           Paolo Lazzeretti and   
            Stephan P. A. Sauer   Nuclear magnetic resonance $J$ coupling
                                  constant polarizabilities of hydrogen
                                  peroxide: a basis set and correlation
                                  study  . . . . . . . . . . . . . . . . . 1845--1853
                Guangfen Wu and   
                Mingli Yang and   
                 Xingyu Guo and   
                    Jinlan Wang   Comparative DFT study of N$_2$ and no
                                  adsorption on vanadium clusters V$_n$ ($
                                  n = 2 $--$ 13 $ )  . . . . . . . . . . . 1854--1861
                  Qunyan Wu and   
               Chunmei Deng and   
                  Qian Peng and   
                 Yingli Niu and   
                  Zhigang Shuai   Quantum chemical insights into the
                                  aggregation induced emission phenomena:
                                  a QM/MM study for pyrazine derivatives   1862--1869
                 Yulei Guan and   
                     Bolun Yang   Kinetics for the hydrogen-abstraction of
                                  CH$_4$ with NO$_2$ . . . . . . . . . . . 1870--1879
          Theresa J. Foster and   
 Alexander D. MacKerell Jr. and   
                  Olgun Guvench   Balancing target flexibility and target
                                  denaturation in computational
                                  fragment-based inhibitor discovery . . . 1880--1891
              Malin Uppsten and   
                     Bo Durbeej   Quantum chemical comparison of vertical,
                                  adiabatic, and $0$--$0$ excitation
                                  energies: The PYP and GFP chromophores   1892--1901
              A. A. Toropov and   
             A. P. Toropova and   
              B. F. Rasulev and   
               E. Benfenati and   
                    G. Gini and   
             D. Leszczynska and   
                 J. Leszczynski   Software News and Updates: Coral: QSPR
                                  modeling of rate constants of reactions
                                  between organic aromatic pollutants and
                                  hydroxyl radical . . . . . . . . . . . . 1902--1906
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 23 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 23 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 24, September 15, 2012

          Bruno A. C. Horta and   
               Zhixiong Lin and   
                  Wei Huang and   
            Sereina Riniker and   
   Wilfred F. van Gunsteren and   
   Philippe H. Hünenberger   Reoptimized interaction parameters for
                                  the peptide-backbone model compound
                                  N-methylacetamide in the GROMOS force
                                  field: Influence on the folding
                                  properties of two beta-peptides in
                                  methanol . . . . . . . . . . . . . . . . 1907--1917
           Paola Antoniotti and   
             Elena Bottizzo and   
            Stefano Borocci and   
             Maria Giordani and   
             Felice Grandinetti   Gas-phase reactions of SiH$_n^+$ ($ n =
                                  1, 2 $ ) with NF$_3$: a computational
                                  investigation on the detailed
                                  mechanistic aspects  . . . . . . . . . . 1918--1926
                Tae-Rae Kim and   
                  Sangho Oh and   
        Joshua SungWoo Yang and   
               Sanghyuk Lee and   
               Seokmin Shin and   
                    Jinhyuk Lee   A simplified homology-model builder
                                  toward highly protein-like structures:
                                  an inspection of restraining potentials  1927--1935
                Vinzenz Bachler   A quantum chemical calculation on
                                  Fe(CO)$_5$ revealing the operation of
                                  the Dewar--Chatt--Duncanson model  . . . 1936--1947
Conchín Meliá and   
              Silvia Ferrer and   
             Vicent Moliner and   
Iñaki Tuñón and   
            Juan Bertrán   Computational study on hydrolysis of
                                  cefotaxime in gas phase and in aqueous
                                  solution . . . . . . . . . . . . . . . . 1948--1959
                   Chuan Li and   
                     Lin Li and   
                  Jie Zhang and   
                    Emil Alexov   Software News and Updates: Highly
                                  efficient and exact method for
                                  parallelization of grid-based algorithms
                                  and its implementation in DelPhi . . . . 1960--1966
       Kameron R. Jorgensen and   
               Angela K. Wilson   Letters to the Editor: Comment on the
                                  paper ``Extensive Theoretical Studies of
                                  a New Energetic Material:
                                  Tetrazino-Tetrazine-Tetraoxide (TTTO)''
                                  by Xinli Song, Jicun Li, Hua Hou, and
                                  Baoshan Wang . . . . . . . . . . . . . . 1967--1968
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 24 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 24 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 25, September 30, 2012

                   Lu Zhang and   
       Daniel-Adriano Silva and   
                 YiJing Yan and   
                    Xuhui Huang   Force field development for cofactors in
                                  the photosystem II . . . . . . . . . . . 1969--1980
            Nail A. Gumerov and   
          Konstantin Berlin and   
              David Fushman and   
              Ramani Duraiswami   A hierarchical algorithm for fast Debye
                                  summation with applications to small
                                  angle scattering . . . . . . . . . . . . 1981--1996
              Vishal Maingi and   
               Vaibhav Jain and   
         Prasad V. Bharatam and   
                Prabal K. Maiti   Dendrimer building toolkit: Model
                                  building and characterization of various
                                  dendrimer architectures  . . . . . . . . 1997--2011
           Janus J. Eriksen and   
        Stephan P. A. Sauer and   
          Kurt V. Mikkelsen and   
         Hans J. Aa. Jensen and   
                 Jacob Kongsted   On the importance of excited state
                                  dynamic response electron correlation in
                                  polarizable embedding methods  . . . . . 2012--2022
             Werner Reckien and   
           Florian Janetzko and   
      Michael F. Peintinger and   
                  Thomas Bredow   Implementation of empirical dispersion
                                  corrections to density functional theory
                                  for periodic systems . . . . . . . . . . 2023--2031
            Brent R. Wilson and   
         Nathan J. DeYonker and   
               Angela K. Wilson   Prediction of hydrocarbon enthalpies of
                                  formation by various thermochemical
                                  schemes  . . . . . . . . . . . . . . . . 2032--2042
              Konrad Hinsen and   
            Eric Pellegrini and   
         S\lawomir Stachura and   
              Gerald R. Kneller   Software News and Updates: n Moldyn 3:
                                  Using task farming for a parallel
                                  spectroscopy-oriented analysis of
                                  molecular dynamics simulations . . . . . 2043--2048
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 25 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 25 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 26, October 5, 2012

         Otello M. Roscioni and   
           Edmond P. F. Lee and   
                   John M. Dyke   Development and testing of a compact
                                  basis set for use in effective core
                                  potential calculations on rhodium
                                  complexes  . . . . . . . . . . . . . . . 2049--2057
             V. N. Glushkov and   
                     X. Assfeld   On orthogonality constrained multiple
                                  core-hole states and optimized effective
                                  potential method . . . . . . . . . . . . 2058--2066
                 Tobias Schwabe   Accurate and fast treatment of large
                                  molecular systems: Assessment of CEPA
                                  and pCCSD within the local pair natural
                                  orbital approximation  . . . . . . . . . 2067--2072
        Pradeep R. Varadwaj and   
            Arpita Varadwaj and   
            Gilles H. Peslherbe   An electronic structure theory
                                  investigation of the physical chemistry
                                  of the intermolecular complexes of
                                  cyclopropenylidene with hydrogen halides 2073--2082
                   F. Rabilloud   Structure and stability of coinage metal
                                  fluoride and chloride clusters
                                  (M$_n$F$_n$ and M$_n$Cl$_n$, M = Cu, Ag,
                                  or Au; $ n = 1 $--$6$ )  . . . . . . . . 2083--2091
            Zden\uek Futera and   
            James A. Platts and   
              Jaroslav V. Burda   Binding of piano-stool Ru(II) complexes
                                  to DNA; QM/MM study  . . . . . . . . . . 2092--2101
                  C. Wessel and   
                 C. Reimann and   
             A. Müller and   
                   D. Weber and   
                   M. Lerch and   
                 T. Ressler and   
                  T. Bredow and   
                 R. Dronskowski   Electronic structure and thermodynamics
                                  of V$_2$O$_3$ polymorphs . . . . . . . . 2102--2107
            Katharina Meier and   
              Nathan Schmid and   
       Wilfred F. van Gunsteren   Interfacing the GROMOS (bio)molecular
                                  simulation software to quantum-chemical
                                  program packages . . . . . . . . . . . . 2108--2117
 Luís Pinto da Silva and   
 Joaquim C. G. Esteves da Silva   Density functional theory study of
                                  1,2-dioxetanone decomposition in
                                  condensed phase  . . . . . . . . . . . . 2118--2123
 Daniel Roca-Sanjuán and   
            Marcus Lundberg and   
         David A. Mazziotti and   
                   Roland Lindh   Letters to the Editor: Comment on
                                  ``Density functional theory study of
                                  1,2-dioxetanone decomposition in
                                  condensed phase''  . . . . . . . . . . . 2124--2126
 Luís Pinto da Silva and   
 Joaquim C. G. Esteves da Silva   Letters to the Editor: Response to
                                  ``Comment on density functional theory
                                  study of 1,2-dioxetanone decomposition
                                  in condensed phase'' . . . . . . . . . . 2127--2130
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 26 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 26 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 27, October 15, 2012

             Patrick Marais and   
             Julian Kenwood and   
    Keegan Carruthers Smith and   
         Michelle M. Kuttel and   
                     James Gain   Efficient compression of molecular
                                  dynamics trajectory files  . . . . . . . 2131--2141
                Wenping Guo and   
                    Anan Wu and   
            Igor Ying Zhang and   
                         Xin Xu   XO: an extended ONIOM method for
                                  accurate and efficient modeling of large
                                  systems  . . . . . . . . . . . . . . . . 2142--2160
         Ruairidh S. Hunter and   
               Tanja van Mourik   DNA base stacking: the stacked
                                  uracil/uracil and thymine/thymine minima 2161--2172
              Sergey P. Gavrish   Approximate expressions and the
                                  relationship between pyramidalization
                                  (out-of-plane deformation)
                                  characteristics of trigonal centers  . . 2173--2179
 Mario Ulises Delgado-Jaime and   
                  Serena DeBeer   Software News and Updates: Expedited
                                  analysis of DFT outputs: Introducing
                                  moanalyzer . . . . . . . . . . . . . . . 2180--2185
             Thomas Weymuth and   
             Moritz P. Haag and   
             Karin Kiewisch and   
               Sandra Luber and   
             Stephan Schenk and   
         Christoph R. Jacob and   
            Carmen Herrmann and   
        Johannes Neugebauer and   
                  Markus Reiher   Software News and Updates: \sc MoViPac:
                                  Vibrational spectroscopy with a robust
                                  meta-program for massively parallel
                                  standard and inverse calculations  . . . 2186--2198
                 Janez Konc and   
           Matja\vz Depolli and   
               Roman Trobec and   
                Kati Rozman and   
          Du\vsanka Jane\vzi\vc   Software News and Updates:
                                  Parallel-ProBiS: Fast parallel algorithm
                                  for local structural comparison of
                                  protein structures and binding sites . . 2199--2203
           Giovanni Garberoglio   Software News and Updates: OBGMX: a
                                  Web-based generator of GROMACS
                                  topologies for molecular and periodic
                                  systems using the universal force field  2204--2208
          Edyta Ma\lolepsza and   
             Birgit Strodel and   
                Mey Khalili and   
           Semen Trygubenko and   
              Szilard Fejer and   
             Joanne M. Carr and   
                 David J. Wales   Erratum: ``Symmetrization of the AMBER
                                  and CHARMM force fields'' [J. Comp.
                                  Chem. \bf 31, 1402]  . . . . . . . . . . 2209--2209
             Shuntaro Chiba and   
              Yuichi Harano and   
                Roland Roth and   
         Masahiro Kinoshita and   
                 Minoru Sakurai   Errata: ``Evaluation of protein-ligand
                                  binding free energy focused on its
                                  entropic components'' [J. Comp. Chem.
                                  \bf 33, 550--560]  . . . . . . . . . . . 2210--2210
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 27 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 27 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 28, October 30, 2012

           Chanda-Malis Ouk and   
 Natalia Zvereva-Loëte and   
            Yohann Scribano and   
Béatrice Bussery-Honvault   Transition state theory thermal rate
                                  constants and RRKM-based branching
                                  ratios for the N($^2$D) + CH$_4$
                                  reaction based on multi-state and
                                  multi-reference ab initio calculations
                                  of interest for the Titan's chemistry    2211--2224
            Maarten G. Wolf and   
                Gerrit Groenhof   Evaluating nonpolarizable nucleic acid
                                  force fields: a systematic comparison of
                                  the nucleobases hydration free energies
                                  and chloroform-to-water partition
                                  coefficients . . . . . . . . . . . . . . 2225--2232
          Jan P. Götze and   
              Claudio Greco and   
            Roland Mitri\'c and   
Vlasta Bona\vci\'c-Koutecký and   
                Peter Saalfrank   BLUF hydrogen network dynamics and
                                  UV/Vis spectra: a combined molecular
                                  dynamics and quantum chemical study  . . 2233--2242
                  Jian Wang and   
                    Yu Wang and   
                Jesus M. Ugalde   Electron-pair density decomposition for
                                  core--valence separable systems  . . . . 2243--2249
                 An Ghysels and   
         Benjamin T. Miller and   
        Frank C. Pickard IV and   
              Bernard R. Brooks   Comparing normal modes across different
                                  models and scales: Hessian reduction
                                  versus coarse-graining . . . . . . . . . 2250--2275
            Roberto Orlando and   
        Massimo Delle Piane and   
                Ian J. Bush and   
             Piero Ugliengo and   
           Matteo Ferrabone and   
                 Roberto Dovesi   Software News and Updates: a new
                                  massively parallel version of CRYSTAL
                                  for large systems on high performance
                                  computing architectures  . . . . . . . . 2276--2284
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 28 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 28 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 29, November 5, 2012

            Orsolya Gereben and   
   László Pusztai   RMC\_POT: a computer code for reverse
                                  Monte Carlo modeling the structure of
                                  disordered systems containing molecules
                                  of arbitrary complexity  . . . . . . . . 2285--2291
             Diego Paschoal and   
           Bruna L. Marcial and   
       Juliana Fedoce Lopes and   
       Wagner B. De Almeida and   
     Hélio F. Dos Santos   The role of the basis set and the level
                                  of quantum mechanical theory in the
                                  prediction of the structure and
                                  reactivity of cisplatin  . . . . . . . . 2292--2302
                M. V. Vener and   
              A. N. Egorova and   
             A. V. Churakov and   
                V. G. Tsirelson   Intermolecular hydrogen bond energies in
                                  crystals evaluated using electron
                                  density properties: DFT computations
                                  with periodic boundary conditions  . . . 2303--2309
      Ji\vrí Kessler and   
              Milan Jakubek and   
    Bohumil Dolenský and   
                    Petr Bou\vr   Binding energies of five molecular
                                  pincers calculated by explicit and
                                  implicit solvent models  . . . . . . . . 2310--2317
      Athanassios C. Tsipis and   
       Dimitrios N. Gkarmpounis   Probing the electronic structure,
                                  chemical bonding, and excitation spectra
                                  of [CuE]$^{+ / 0 / -}$ (E = 14 group
                                  element) diatomics employing DFT and ab
                                  initio methods . . . . . . . . . . . . . 2318--2331
            Emanuele Coccia and   
               Leonardo Guidoni   Quantum Monte Carlo study of the retinal
                                  minimal model C$_5$H$_6$NH$_2^+$ . . . . 2332--2339
        Sushil Kumar Mishra and   
                 Johan Sund and   
         Johan Åqvist and   
                Jaroslav Ko\vca   Computational prediction of
                                  monosaccharide binding free energies to
                                  lectins with linear interaction energy
                                  models . . . . . . . . . . . . . . . . . 2340--2350
    Siegfried Höfinger and   
            Angela Acocella and   
              Sergiu C. Pop and   
               Tetsu Narumi and   
              Kenji Yasuoka and   
                  Titus Beu and   
             Francesco Zerbetto   GPU-accelerated computation of electron
                                  transfer . . . . . . . . . . . . . . . . 2351--2356
             Damien Farrell and   
              Jens Erik Nielsen   Software News and Updates: DataPipeline:
                                  Automated importing and fitting of large
                                  amounts of biophysical data  . . . . . . 2357--2362
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 29 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 29 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 30, November 15, 2012

                 Frank Weinhold   Natural bond orbital analysis: a
                                  critical overview of relationships to
                                  alternative bonding perspectives . . . . 2363--2379
             Marie L. Laury and   
         Matthew J. Carlson and   
               Angela K. Wilson   Vibrational frequency scale factors for
                                  density functional theory and the
                                  polarization consistent basis sets . . . 2380--2387
                 Ity Sharma and   
             George A. Kaminski   Calculating pK$_a$ values for
                                  substituted phenols and hydration
                                  energies for other compounds with the
                                  first-order fuzzy-border continuum
                                  solvation model  . . . . . . . . . . . . 2388--2399
Patricio González-Navarrete and   
            Luis R. Domingo and   
         Juan Andrés and   
            Slawomir Berski and   
                  Bernard Silvi   Electronic fluxes during Diels--Alder
                                  reactions involving 1,2-benzoquinones:
                                  mechanistic insights from the analysis
                                  of electron localization function and
                                  catastrophe theory . . . . . . . . . . . 2400--2411
          Ilia A. Solov'yov and   
    Alexander V. Yakubovich and   
          Pavel V. Nikolaev and   
             Ilya Volkovets and   
            Andrey V. Solov'yov   MesoBioNano explorer --- a universal
                                  program for multiscale computer
                                  simulations of complex molecular
                                  structure and dynamics . . . . . . . . . 2412--2439
                 Frank Weinhold   Software News and Updates: Natural bond
                                  critical point analysis: Quantitative
                                  relationships between natural bond
                                  orbital-based and QTAIM-based
                                  topological descriptors of chemical
                                  bonding  . . . . . . . . . . . . . . . . 2440--2449
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 30 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 30 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 31, December 5, 2012

                   Wenbo Yu and   
                  Xibing He and   
       Kenno Vanommeslaeghe and   
     Alexander D. MacKerell Jr.   Extension of the CHARMM general force
                                  field to sulfonyl-containing compounds
                                  and its utility in biomolecular
                                  simulations  . . . . . . . . . . . . . . 2451--2468
                  Shuming Zhang   A reliable and efficient first
                                  principles-based method for predicting
                                  pK$_a$ values. 4. organic bases  . . . . 2469--2482
            Michael D. Tyka and   
               Kenneth Jung and   
                    David Baker   Efficient sampling of protein
                                  conformational space using fast loop
                                  building and batch minimization on
                                  highly parallel computers  . . . . . . . 2483--2491
        Abu Md. Asaduzzaman and   
       Guy A. G. Chappellaz and   
            Georg Schreckenbach   Relationship between dye--iodine binding
                                  and cell voltage in dye-sensitized solar
                                  cells: a quantum-mechanical look . . . . 2492--2497
                 Bu-Tong Li and   
               Zi-Zhang Wei and   
                    Hai-Shun Wu   The valence and Rydberg excited states
                                  of CH$_2$: a theoretical exploration . . 2498--2503
             Johannes Flick and   
             Frank Tristram and   
                Wolfgang Wenzel   Modeling loop backbone flexibility in
                                  receptor-ligand docking simulations  . . 2504--2515
                Yunqing Han and   
               Tianxiang Li and   
                     Kozo Saito   Comprehensive method based on model free
                                  method and IKP method for evaluating
                                  kinetic parameters of solid state
                                  reactions  . . . . . . . . . . . . . . . 2516--2525
                 David Vega and   
               Yosslen Aray and   
  Jesús Rodríguez   Software News and Updates: C library for
                                  topological study of the electronic
                                  charge density . . . . . . . . . . . . . 2526--2531
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 31 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 31 . . . . i--ii

Journal of Computational Chemistry
Volume 33, Number 32, December 15, 2012

         David Ferro-Costas and   
       Nicolás Otero and   
        Ana M. Graña and   
            Ricardo A. Mosquera   A QTAIM-based energy partitioning for
                                  understanding the physical origin of
                                  conformational preferences: Application
                                  to the Z effect in
                                  O\doublebondC\bondX\bondR and related
                                  units  . . . . . . . . . . . . . . . . . 2533--2543
          Yulia N. Kalugina and   
        Mikhail A. Buldakov and   
           Victor N. Cherepanov   Static hyperpolarizability of the van
                                  der Waals complex CH$_4$N$_2$  . . . . . 2544--2553
        Lennart Heinzerling and   
               Robert Klein and   
                 Matthias Rarey   Fast force field-based optimization of
                                  protein--ligand complexes with graphics
                                  processor  . . . . . . . . . . . . . . . 2554--2565
            Daniel P. Oehme and   
      Robert T. C. Brownlee and   
             David J. D. Wilson   Effect of atomic charge, solvation,
                                  entropy, and ligand protonation state on
                                  MM-PB(GB)SA binding energies of HIV
                                  protease . . . . . . . . . . . . . . . . 2566--2580
             Mohamed Hacene and   
      Ani Anciaux-Sedrakian and   
            Xavier Rozanska and   
                Diego Klahr and   
             Thomas Guignon and   
           Paul Fleurat-Lessard   Accelerating VASP electronic structure
                                  calculations using graphic processing
                                  units  . . . . . . . . . . . . . . . . . 2581--2589
           Amanda G. Riojas and   
             Joshua R. John and   
          T. Gavin Williams and   
               Angela K. Wilson   Proton affinities of
                                  deoxyribonucleosides via the ONIOM-ccCA
                                  methodology  . . . . . . . . . . . . . . 2590--2601
                  T. Strunk and   
                    M. Wolf and   
                   M. Brieg and   
                  K. Klenin and   
                  A. Biewer and   
                F. Tristram and   
                   M. Ernst and   
               P. J. Kleine and   
                N. Heilmann and   
                  I. Kondov and   
                      W. Wenzel   Software News and Updates: SIMONA 1.0:
                                  an efficient and versatile framework for
                                  stochastic simulations of molecular and
                                  nanoscale systems  . . . . . . . . . . . 2602--2613
                Jianxiu Guo and   
                   Nini Rao and   
             Guangxiong Liu and   
                  Yong Yang and   
                      Gang Wang   Retracted: Predicting protein folding
                                  rates using the concept of Chou's pseudo
                                  amino acid composition . . . . . . . . . 2614--2614
                      Anonymous   Cover Image: Inside Cover, Volume 33,
                                  Issue 32 . . . . . . . . . . . . . . . . iii--iv
                      Anonymous   Cover Image, Volume 33, Issue 32 . . . . i--ii


Journal of Computational Chemistry
Volume 34, Number 1, January 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 1  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 1  . . . . . . . . . . . . . . . . iii--iv
      Charles L. Brooks III and   
             Masahiro Ehara and   
            Gernot Frenking and   
             Peter R. Schreiner   Editorials: New paint and a new engine   1--1
                Mark Pinsky and   
                  Amir Zait and   
             Maayan Bonjack and   
                    David Avnir   Continuous symmetry analyses: C$_{nv}$
                                  and D$_n$ measures of molecules,
                                  complexes, and proteins  . . . . . . . . 2--9
               Susanne Pape and   
        Franziska Hoffgaard and   
            Mirjam Dür and   
                   Kay Hamacher   Distance dependency and minimum amino
                                  acid alphabets for decoy scoring
                                  potentials . . . . . . . . . . . . . . . 10--20
                Toru Matsui and   
          Yasutaka Kitagawa and   
          Mitsutaka Okumura and   
           Yasuteru Shigeta and   
              Shigeyoshi Sakaki   Consistent scheme for computing standard
                                  hydrogen electrode and redox potentials  21--26
           Andriy Samsonyuk and   
             Christoph Scheurer   Configuration space partitioning and
                                  matrix buildup scaling for the
                                  vibrational configuration interaction
                                  method . . . . . . . . . . . . . . . . . 27--37
              Jinshuai Song and   
               Zhenhua Chen and   
                Sason Shaik and   
                         Wei Wu   An efficient algorithm for complete
                                  active space valence bond
                                  self-consistent field calculation  . . . 38--48
                  J. Drujon and   
                    Y. Carissan   Pseudopotentials for hybridized carbon
                                  atoms  . . . . . . . . . . . . . . . . . 49--59
                   Jin Yang and   
         Paul J. Dauenhauer and   
         Ashwin Ramasubramaniam   The role of water in the adsorption of
                                  oxygenated aromatics on Pt and Pd  . . . 60--66
                     Yu Liu and   
                   Lei Zhao and   
                  Wentao Li and   
                Dongyu Zhao and   
                  Miao Song and   
                 Yongliang Yang   FIPSDock: a new molecular docking
                                  technique driven by fully informed swarm
                                  optimization algorithm . . . . . . . . . 67--75

Journal of Computational Chemistry
Volume 34, Number 2, January 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 2  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 2  . . . . . . . . . . . . . . . . iii--iv
                 Milan Randi\'c   Very efficient search for nucleotide
                                  alignments . . . . . . . . . . . . . . . 77--82
              Yutaka Uejima and   
                    Ryo Maezono   GPGPU for orbital function evaluation
                                  with a new updating scheme . . . . . . . 83--94
                Yutong Zhao and   
              Fu Kit Sheong and   
                   Jian Sun and   
               Pedro Sander and   
                    Xuhui Huang   A fast parallel clustering algorithm for
                                  molecular simulation trajectories  . . . 95--104
                  Paul Mach and   
                  Patrice Koehl   An analytical method for computing
                                  atomic contact areas in biomolecules . . 105--120
                   Yuan Liu and   
                 Jijun Zhao and   
                  Fengyu Li and   
                 Zhongfang Chen   Appropriate description of
                                  intermolecular interactions in the
                                  methane hydrates: an assessment of DFT
                                  methods  . . . . . . . . . . . . . . . . 121--131
           Yannick G. Spill and   
          Guillaume Bouvier and   
                 Michael Nilges   A convective replica-exchange method for
                                  sampling new energy basins . . . . . . . 132--140
        Eric A. C. Bushnell and   
                 James W. Gauld   An assessment of pure, hybrid, meta, and
                                  hybrid-meta GGA density functional
                                  theory methods for open-shell systems:
                                  the case of the nonheme iron enzyme
                                  8R--LOX  . . . . . . . . . . . . . . . . 141--148
               Kenta Yamada and   
                   Nobuaki Koga   Variationally determined electronic
                                  states for the theoretical analysis of
                                  intramolecular interaction. II.
                                  Qualitative nature of the P\bondO bond
                                  in phosphine oxides  . . . . . . . . . . 149--161

Journal of Computational Chemistry
Volume 34, Number 3, January 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 3  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 3  . . . . . . . . . . . . . . . . iii--iv
                 Yang Zhong and   
                  Sandeep Patel   Binding structures of tri-N-acetyl-$
                                  \beta $-glucosamine in hen egg white
                                  lysozyme using molecular dynamics with a
                                  polarizable force field  . . . . . . . . 163--174
        Robert A. Evarestov and   
          Andrei V. Bandura and   
              Dmitrii D. Kuruch   BaTiO$_3$-based nanolayers and
                                  nanotubes: First-principles calculations 175--186
  Joakim P. M. Jämbeck and   
            Francesca Mocci and   
    Alexander P. Lyubartsev and   
                Aatto Laaksonen   Partial atomic charges and their impact
                                  on the free energy of solvation  . . . . 187--197
           Hiroshi Watanabe and   
             Marcus Elstner and   
            Thomas Steinbrecher   Rotamer decomposition and protein
                                  dynamics: Efficiently analyzing dihedral
                                  populations from molecular dynamics  . . 198--205
            Pavel M. Polestshuk   Accurate integration over atomic regions
                                  bounded by zero-flux surfaces  . . . . . 206--219
        Christopher Pfleger and   
        Sebastian Radestock and   
              Elena Schmidt and   
                  Holger Gohlke   Global and local indices for
                                  characterizing biomolecular flexibility
                                  and rigidity . . . . . . . . . . . . . . 220--233
             Josep M. Porta and   
         Léonard Jaillet   Exploring the energy landscapes of
                                  flexible molecular loops using
                                  higher-dimensional continuation  . . . . 234--244
             Elijah Roberts and   
              John E. Stone and   
          Zaida Luthey-Schulten   Lattice microbes: High-performance
                                  stochastic simulation method for the
                                  reaction-diffusion master equation . . . 245--255
Christopher J. R. Illingworth and   
        Sree V. Chintapalli and   
        Stefano A. Serapian and   
           Andrew D. Miller and   
             Vaclav Veverka and   
               Mark D. Carr and   
        Christopher A. Reynolds   Erratum: The statistical significance of
                                  selected sense--antisense peptide
                                  interactions [J. Comp. Chem. \bf 33,
                                  1440--1447]  . . . . . . . . . . . . . . 256--256
           Paola Antoniotti and   
             Elena Bottizzo and   
            Stefano Borocci and   
             Maria Giordani and   
             Felice Grandinetti   Erratum: Gas-phase reactions of
                                  SiH$_n^+$ ($ n = 1, 2 $ ) with NF$_3$: a
                                  computational investigation on the
                                  detailed mechanistic aspects [J. Comp.
                                  Chem. 33, 1918--1926]  . . . . . . . . . 257--257

Journal of Computational Chemistry
Volume 34, Number 4, February 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 4  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 4  . . . . . . . . . . . . . . . . iii--iv
         Stephen J. Barigye and   
       Yovani Marrero-Ponce and   
Yoan Martínez-López and   
          Francisco Torrens and   
Luis Manuel Artiles-Martínez and   
      Ricardo W. Pino-Urias and   
 Oscar Martínez-Santiago   Relations frequency hypermatrices in
                                  mutual, conditional and joint
                                  entropy-based information indices  . . . 259--274
Angelika Baranowska-\L\kaczkowska and   
     Berta Fernández and   
               Robert Zale\'sny   New basis sets for the evaluation of
                                  interaction-induced electric properties
                                  in hydrogen-bonded complexes . . . . . . 275--283
                    Li Yang and   
             Alauddin Ahmed and   
             Stanley I. Sandler   Comparison of two simulation methods to
                                  compute solvation free energies and
                                  partition coefficients . . . . . . . . . 284--293
         \Lukasz Pi\kEko\'s and   
         Mariusz Pawe\l Mitoraj   Theoretical description of
                                  dihydrogen/hydride and trihydride
                                  molybdocene complexes: an insight from
                                  static and molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 294--304
              Hongguang Liu and   
                   Jin Yong Lee   Electric field assisted oxygen removal
                                  from the basal plane of the graphitic
                                  material . . . . . . . . . . . . . . . . 305--310
            Sheng-You Huang and   
                    Xiaoqin Zou   A nonredundant structure dataset for
                                  benchmarking protein-RNA computational
                                  docking  . . . . . . . . . . . . . . . . 311--318
         Alexander V. Popov and   
           Yury N. Vorobjev and   
              Dmitry O. Zharkov   Software News and Updates: MDTRA: a
                                  molecular dynamics trajectory analyzer
                                  with a graphical user interface  . . . . 319--325
             Xuchang Ouyang and   
                  Shuo Zhou and   
           Chinh Tran To Su and   
                   Zemei Ge and   
                  Runtao Li and   
                Chee Keong Kwoh   Software News and Updates: CovalentDock:
                                  Automated covalent docking with
                                  parameterized covalent linkage energy
                                  estimation and molecular geometry
                                  constraints  . . . . . . . . . . . . . . 326--336

Journal of Computational Chemistry
Volume 34, Number 5, February 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 5  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 5  . . . . . . . . . . . . . . . . iii--iv
           Pawe\l Ma\lyszek and   
                    Jacek Koput   Accurate Ab initio potential energy
                                  surface and vibration-rotation energy
                                  levels of hydrogen peroxide  . . . . . . 337--345
            Alessandro Erba and   
           Matteo Ferrabone and   
            Roberto Orlando and   
                 Roberto Dovesi   Accurate dynamical structure factors
                                  from ab initio lattice dynamics: the
                                  case of crystalline silicon  . . . . . . 346--354
             Gonzalo Astray and   
      Juan F. Gálvez and   
             Juan C. Mejuto and   
            Oscar A. Moldes and   
                   Iago Montoya   Esters flash point prediction using
                                  artificial neural networks . . . . . . . 355--359
                Hongmei Liu and   
                Hongbo Wang and   
               Jianwei Zhao and   
                 Manabu Kiguchi   Molecular rectification in triangularly
                                  shaped graphene nanoribbons  . . . . . . 360--365
      Ji\vrí Kessler and   
Martin Dra\vcínský and   
                    Petr Bou\vr   Parallel variable selection of molecular
                                  dynamics clusters as a tool for
                                  calculation of spectroscopic properties  366--371
                 Binju Wang and   
                     Zexing Cao   How water molecules modulate the
                                  hydration of CO$_2$ in water solution:
                                  Insight from the cluster-continuum model
                                  calculations . . . . . . . . . . . . . . 372--378
             Raman K. Singh and   
                  Takao Tsuneda   Reaction energetics on long-range
                                  corrected density functional theory:
                                  Diels--Alder reactions . . . . . . . . . 379--386
               Zhixiong Lin and   
       Wilfred F. van Gunsteren   On the choice of a reference state for
                                  one-step perturbation calculations
                                  between polar and nonpolar molecules in
                                  a polar environment  . . . . . . . . . . 387--393
             Shantanu Kadam and   
                    Kumar Vanka   Solving the problem of negative
                                  populations in approximate accelerated
                                  stochastic simulations using the
                                  representative reaction approach . . . . 394--404
      Danny E. P. Vanpoucke and   
           Patrick Bultinck and   
           Isabel Van Driessche   Extending Hirshfeld-I to bulk and
                                  periodic materials . . . . . . . . . . . 405--417
                 Thomas A. Manz   Letters to the Editor: Comment on
                                  ``Extending Hirshfeld-I to bulk and
                                  periodic materials'' . . . . . . . . . . 418--421
      Danny E. P. Vanpoucke and   
       Isabel Van Driessche and   
               Patrick Bultinck   Letters to the Editor: Reply to `Comment
                                  on ``Extending Hirshfeld-I to bulk and
                                  periodic materials'''  . . . . . . . . . 422--427

Journal of Computational Chemistry
Volume 34, Number 6, March 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 6  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 6  . . . . . . . . . . . . . . . . iii--iv
               Louis P. Lee and   
             Daniel J. Cole and   
              Mike C. Payne and   
          Chris-Kriton Skylaris   Natural bond orbital analysis in the
                                  ONETEP code: Applications to large
                                  protein systems  . . . . . . . . . . . . 429--444
             Mohsen Chitsaz and   
                Stephen L. Mayo   GRID: a high-resolution protein
                                  structure refinement algorithm . . . . . 445--450
      Michael F. Peintinger and   
     Daniel Vilela Oliveira and   
                  Thomas Bredow   Consistent Gaussian basis sets of
                                  triple-zeta valence with polarization
                                  quality for solid-state calculations . . 451--459
         János Pipek and   
                   Szilvia Nagy   An economic prediction of refinement
                                  coefficients in wavelet-based adaptive
                                  methods for electron structure
                                  calculations . . . . . . . . . . . . . . 460--465
                  Jack Yang and   
                 Mark P. Waller   Revealing noncovalent interactions in
                                  quantum crystallography: Taurine
                                  revisited  . . . . . . . . . . . . . . . 466--470
       Soumya Ganguly Neogi and   
               Pinaki Chaudhury   Structure and spectroscopic aspects of
                                  water-halide ion clusters: a study based
                                  on a conjunction of stochastic and
                                  quantum chemical methods . . . . . . . . 471--491
           Maël Bosson and   
            Sergei Grudinin and   
                 Stephane Redon   Block-adaptive quantum mechanics: an
                                  adaptive divide-and-conquer approach to
                                  interactive quantum chemistry  . . . . . 492--504
        Jorge M. C. Marques and   
           Francisco B. Pereira   A detailed investigation on the global
                                  minimum structures of mixed rare-gas
                                  clusters: Geometry, energetics, and site
                                  occupancy  . . . . . . . . . . . . . . . 505--517
           David D. Jenkins and   
            Jason B. Harris and   
        Elizabeth E. Howell and   
            Robert J. Hinde and   
                  Jerome Baudry   Software News and Updates: STAAR:
                                  Statistical analysis of aromatic rings   518--522

Journal of Computational Chemistry
Volume 34, Number 7, March 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 7  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 7  . . . . . . . . . . . . . . . . iii--iv
          Ananth P. Kaushik and   
                Paulette Clancy   Solvent-driven symmetry of
                                  self-assembled nanocrystal superlattices
                                  --- a computational study  . . . . . . . 523--532
         Vladimir V. Rybkin and   
           Anton O. Simakov and   
      Vebjòrn Bakken and   
                Simen Reine and   
     Thomas Kjærgaard and   
            Trygve Helgaker and   
                  Einar Uggerud   Insights into the dynamics of
                                  evaporation and proton migration in
                                  protonated water clusters from
                                  large-scale Born--Oppenheimer direct
                                  dynamics . . . . . . . . . . . . . . . . 533--544
                  Maggie Ng and   
           Daniel K. W. Mok and   
           Edmond P. F. Lee and   
                   John M. Dyke   Rate coefficients of the CF$_3$CHFCF$_3$
                                  $+$ H $ \rightarrow $ CF$_3$CFCF$_3$ $+$
                                  H$_2$ reaction at different temperatures
                                  calculated by transition state theory
                                  with ab initio and DFT reaction paths    545--557
           Shelley A. Smith and   
              Karen E. Hand and   
            Melissa L. Love and   
                 Glake Hill and   
                David H. Magers   Conventional strain energies of
                                  azetidine and phosphetane: Can density
                                  functional theory yield reliable
                                  results? . . . . . . . . . . . . . . . . 558--565
               Jia-Nan Wang and   
               Jun-Ling Jin and   
                   Yun Geng and   
               Shi-Ling Sun and   
              Hong-Liang Xu and   
                Ying-Hua Lu and   
                   Zhong-Min Su   An accurate and efficient method to
                                  predict the electronic excitation
                                  energies of BODIPY fluorescent dyes  . . 566--575
   Bradley Scott Perrin Jr. and   
               Shuqiang Niu and   
                 Toshiko Ichiye   Calculating standard reduction
                                  potentials of [4Fe--4S] proteins . . . . 576--582
              Mingyue Zheng and   
                 Yanlian Li and   
                 Bing Xiong and   
             Hualiang Jiang and   
                  Jingkang Shen   Water PMF for predicting the properties
                                  of water molecules in protein binding
                                  site . . . . . . . . . . . . . . . . . . 583--592
                Jihyun Shim and   
                   Xiao Zhu and   
             Robert B. Best and   
     Alexander D. MacKerell Jr.   (Ala)$_4$ -X-(Ala)$_4$ as a model system
                                  for the optimization of the $\chi_1$ and
                                  $\chi_2$ amino acid side-chain dihedral
                                  empirical force field parameters . . . . 593--603
                    Yuye He and   
              Chin Yee Liew and   
               Nitin Sharma and   
              Sze Kwang Woo and   
               Yi Ting Chau and   
                   Chun Wei Yap   Software News and Updates:
                                  PaDEL-DDPredictor: Open-source software
                                  for PD-PK-T prediction . . . . . . . . . 604--610

Journal of Computational Chemistry
Volume 34, Number 8, March 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 8  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 8  . . . . . . . . . . . . . . . . iii--iv
    Marcus V. P. dos Santos and   
          Eduardo C. Aguiar and   
João Bosco P. da Silva and   
               Ricardo L. Longo   PICVib: an accurate, fast, and simple
                                  procedure to investigate selected
                                  vibrational modes at high theoretical
                                  levels . . . . . . . . . . . . . . . . . 611--621
             Satoru G. Itoh and   
                Hisashi Okumura   Coulomb replica-exchange method:
                                  Handling electrostatic attractive and
                                  repulsive forces for biomolecules  . . . 622--639
                    Ning Ma and   
             Ying-Hua Chung and   
            Arjan van der Vaart   Free energy simulation of helical
                                  transitions  . . . . . . . . . . . . . . 640--645
            Goran Kovacevic and   
             Aleksandar Sabljic   Theoretical study on the mechanism and
                                  kinetics of addition of hydroxyl
                                  radicals to fluorobenzene  . . . . . . . 646--655
       Drahomír Hnyk and   
      Elambalassery G. Jayasree   Cationic Closo-carboranes 2. Do computed
                                  $^{11}$B and $^{13}$C NMR chemical
                                  shifts support their experimental
                                  availability?  . . . . . . . . . . . . . 656--661
                Soumen Saha and   
    Rituparna Bhattacharjee and   
                 Ram Kinkar Roy   Hardness potential derivatives and their
                                  relation to Fukui indices  . . . . . . . 662--672
            Jian-Dong Zhang and   
                 Shu-Jin Li and   
                    Fu-Ming Tao   Ab initio calculations of the Ar--ethane
                                  intermolecular potential energy surface
                                  using bond function basis sets . . . . . 673--680
       Juan I. Rodríguez   An efficient method for computing the
                                  QTAIM topology of a scalar field: the
                                  electron density case  . . . . . . . . . 681--686
           Dennis G. Thomas and   
                Jaehun Chun and   
                  Zhan Chen and   
                 Guowei Wei and   
                Nathan A. Baker   Parameterization of a geometric flow
                                  implicit solvation model . . . . . . . . 687--695
        Halina Szaty\lowicz and   
       Tadeusz M. Krygowski and   
Célia Fonseca Guerra and   
        F. Matthias Bickelhaupt   Complexes of 4-substituted phenolates
                                  with HF and HCN: Energy decomposition
                                  and electronic structure analyses of
                                  hydrogen bonding . . . . . . . . . . . . 696--705

Journal of Computational Chemistry
Volume 34, Number 9, April 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 9  . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 9  . . . . . . . . . . . . . . . . iii--iv
        Florent Réal and   
              Michael Trumm and   
      Bernd Schimmelpfennig and   
             Michel Masella and   
          Valérie Vallet   Further insights in the ability of
                                  classical nonadditive potentials to
                                  model actinide ion--water interactions   707--719
                 David Casanova   Efficient implementation of restricted
                                  active space configuration interaction
                                  with the hole and particle approximation 720--730
              Olga Yuzlenko and   
               Themis Lazaridis   Membrane protein native state
                                  discrimination by implicit membrane
                                  models . . . . . . . . . . . . . . . . . 731--738
               Jin Yu Xiang and   
                  Jay W. Ponder   A valence bond model for aqueous Cu(II)
                                  and Zn(II) ions in the AMOEBA
                                  polarizable force field  . . . . . . . . 739--749
         Marcin Nowosielski and   
            Marcin Hoffmann and   
                Aneta Kuron and   
Ma\lgorzata Korycka-Machala and   
              Jaros\law Dziadek   The MM2QM tool for combining docking,
                                  molecular dynamics, molecular mechanics,
                                  and quantum mechanics  . . . . . . . . . 750--756
              Jia-Lin Chang and   
           Cyong-Huei Huang and   
             Sue-Chang Chen and   
              Tsung-Hao Yin and   
                  Yi-Tsung Chen   An analytical approach for computing
                                  Franck--Condon integrals of harmonic
                                  oscillators with arbitrary dimensions    757--765
       Ramon Carbó-Dorca   Notes on quantitative
                                  structure--property relationships
                                  (QSPR), part 3: Density functions origin
                                  shift as a source of quantum QSPR
                                  algorithms in molecular spaces . . . . . 766--779
            Ignacio Viciano and   
            Slawomir Berski and   
        Sergio Martí and   
             Juan Andrés   New insight into the electronic
                                  structure of iron(IV)-oxo porphyrin
                                  compound I. A quantum chemical
                                  topological analysis . . . . . . . . . . 780--789
            Nikola Minovski and   
              Andrej Perdih and   
              Marjana Novic and   
                   Tom Solmajer   Cluster-based molecular docking study
                                  for in silico identification of novel
                                  6-fluoroquinolones as potential
                                  inhibitors against mycobacterium
                                  tuberculosis . . . . . . . . . . . . . . 790--801

Journal of Computational Chemistry
Volume 34, Number 10, April 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 10 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 10 . . . . . . . . . . . . . . . . iii--iv
             Ardita Shkurti and   
                 Mario Orsi and   
               Enrico Macii and   
              Elisa Ficarra and   
               Andrea Acquaviva   Acceleration of coarse grain molecular
                                  dynamics on GPU architectures  . . . . . 803--818
Angelika Baranowska-\L\kaczkowska and   
        Wojciech Bartkowiak and   
      Robert W. Góra and   
           Filip Paw\lowski and   
               Robert Zale\'sny   On the performance of
                                  long-range-corrected density functional
                                  theory and reduced-size polarized
                                  LPol-$n$ basis sets in computations of
                                  electric dipole (hyper)polarizabilities
                                  of $ \pi $-conjugated molecules  . . . . 819--826
            Ole Schütt and   
              Daniel Sebastiani   Spectroscopic fingerprints of toroidal
                                  nuclear quantum delocalization via ab
                                  initio path integral simulations . . . . 827--835
            Thomas Simonson and   
            Priyadarshi Satpati   Simulating GTP:Mg and GDP:Mg with a
                                  simple force field: a structural and
                                  thermodynamic analysis . . . . . . . . . 836--846
                  Juan Zeng and   
                  LiLi Duan and   
           John Z. H. Zhang and   
                         Ye Mei   A numerically stable restrained
                                  electrostatic potential charge fitting
                                  method . . . . . . . . . . . . . . . . . 847--853
        György G. Ferenczy   Calculation of wave-functions with
                                  frozen orbitals in mixed quantum
                                  mechanics/molecular mechanics methods.
                                  Part I. Application of the Huzinaga
                                  equation . . . . . . . . . . . . . . . . 854--861
        György G. Ferenczy   Calculation of wave-functions with
                                  frozen orbitals in mixed quantum
                                  mechanics/molecular mechanics methods.
                                  II. Application of the local basis
                                  equation . . . . . . . . . . . . . . . . 862--869
          Andranik Kazaryan and   
             Evert Jan Baerends   Assessment of density functional methods
                                  for reaction energetics:
                                  Iridium-catalyzed water oxidation as
                                  case study . . . . . . . . . . . . . . . 870--878
               Yoonjoo Choi and   
           Karl E. Griswold and   
           Chris Bailey-Kellogg   Structure-based redesign of proteins for
                                  minimal T-cell epitope content . . . . . 879--891

Journal of Computational Chemistry
Volume 34, Number 11, April 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 11 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 11 . . . . . . . . . . . . . . . . iii--iv
         Jennifer L. Knight and   
        Joseph D. Yesselman and   
          Charles L. Brooks III   Assessing the quality of absolute
                                  hydration free energies among
                                  CHARMM-compatible ligand
                                  parameterization schemes . . . . . . . . 893--903
          Jeffrey R. Wagner and   
     Gouthaman S. Balaraman and   
       Michiel J. M. Niesen and   
           Adrien B. Larsen and   
            Abhinandan Jain and   
              Nagarajan Vaidehi   Advanced techniques for constrained
                                  internal coordinate molecular dynamics   904--914
              Xiaohua Zhang and   
             Sergio E. Wong and   
           Felice C. Lightstone   Message passing interface and
                                  multithreading hybrid for parallel
                                  molecular docking of large databases on
                                  petascale high performance computing
                                  machines . . . . . . . . . . . . . . . . 915--927
          Robert J. Buenker and   
     Heinz-Peter Liebermann and   
                   Yu Zhang and   
                    Yong Wu and   
               Lingling Yan and   
                Chunhua Liu and   
                   Yizhi Qu and   
                   Jianguo Wang   Adjustment of Born--Oppenheimer
                                  electronic wave functions to simplify
                                  close coupling calculations  . . . . . . 928--937
            Anthony Scemama and   
            Michel Caffarel and   
            Emmanuel Oseret and   
                  William Jalby   Quantum Monte Carlo for large chemical
                                  systems: Implementing efficient
                                  strategies for petascale platforms and
                                  beyond . . . . . . . . . . . . . . . . . 938--951
               Heng-Qing Wu and   
             Rong-Lin Zhong and   
                  Yu-He Kan and   
               Shi-Ling Sun and   
                  Min Zhang and   
              Hong-Liang Xu and   
                   Zhong-Min Su   After the electronic field: Structure,
                                  bonding, and the first
                                  hyperpolarizability of HArF  . . . . . . 952--957
                  Rahul Kar and   
              Jong-Won Song and   
                 Kimihiko Hirao   Long-range corrected functionals satisfy
                                  Koopmans' theorem: Calculation of
                                  correlation and relaxation energies  . . 958--964
             Nadine Homeyer and   
                  Holger Gohlke   Software News and Updates: FEW: a
                                  workflow tool for free energy
                                  calculations of ligand binding . . . . . 965--973
                Dong-Jun Yu and   
                     Jun Hu and   
                  Yan Huang and   
              Hong-Bin Shen and   
                    Yong Qi and   
              Zhen-Min Tang and   
                   Jing-Yu Yang   Software News and Updates:
                                  TargetATPsite: a template-free method
                                  for ATP-binding sites prediction with
                                  residue evolution image sparse
                                  representation and classifier ensemble   974--985

Journal of Computational Chemistry
Volume 34, Number 12, May 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 12 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 12 . . . . . . . . . . . . . . . . iii--iv
            Karina Kornobis and   
               Neeraj Kumar and   
             Piotr Lodowski and   
             Maria Jaworska and   
              Piotr Piecuch and   
              Jesse J. Lutz and   
              Bryan M. Wong and   
             Pawel M. Kozlowski   Electronic structure of the $ S_1 $
                                  state in methylcobalamin: Insight from
                                  CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT
                                  calculations . . . . . . . . . . . . . . 987--1004
               Yanliang Ren and   
                     Bo Chi and   
               Osama Melhem and   
                     Ke Wei and   
              Lingling Feng and   
                Yongjian Li and   
                  Xinya Han and   
                    Ding Li and   
                 Ying Zhang and   
                   Jian Wan and   
                     Xin Xu and   
                   Minghui Yang   Understanding the electronic energy
                                  transfer pathways in the trimeric and
                                  hexameric aggregation state of
                                  cyanobacteria phycocyanin within the
                                  framework of förster theory . . . . . . . 1005--1012
         Terutaka Yoshizawa and   
              Shigeyoshi Sakaki   NMR shielding constants of CuX, AgX, and
                                  AuX (X = F, Cl, Br, and I) investigated
                                  by density functional theory based on
                                  the Douglas--Kroll--Hess Hamiltonian . . 1013--1023
            Anita de Ruiter and   
             Stefan Boresch and   
              Chris Oostenbrink   Comparison of thermodynamic integration
                                  and Bennett's acceptance ratio for
                                  calculating relative protein-ligand
                                  binding free energies  . . . . . . . . . 1024--1034
         M. Rohrmüller and   
           S. Herres-Pawlis and   
                   M. Witte and   
                  W. G. Schmidt   Bis-$ \mu $-oxo and $ \mu $-$ \eta^2 $:$
                                  \eta^2 $-peroxo dicopper complexes
                                  studied within (time-dependent)
                                  density-functional and many-body
                                  perturbation theory  . . . . . . . . . . 1035--1045
              Zhanghui Chen and   
             Xiangwei Jiang and   
                  Jingbo Li and   
                 Shushen Li and   
                   Linwang Wang   PDECO: Parallel differential evolution
                                  for clusters optimization  . . . . . . . 1046--1059
            Debashree Ghosh and   
            Dmytro Kosenkov and   
          Vitalii Vanovschi and   
               Joanna Flick and   
               Ilya Kaliman and   
                 Yihan Shao and   
       Andrew T. B. Gilbert and   
             Anna I. Krylov and   
         Lyudmila V. Slipchenko   Effective fragment potential method in
                                  Q-CHEM: a guide for users and developers 1060--1070
                  Kunal Roy and   
         Pratim Chakraborty and   
              Indrani Mitra and   
          Probir Kumar Ojha and   
               Supratik Kar and   
              Rudra Narayan Das   Software News and Updates: Some case
                                  studies on application of ``$ r_m^2 $''
                                  metrics for judging quality of
                                  quantitative structure--activity
                                  relationship predictions: Emphasis on
                                  scaling of response data . . . . . . . . 1071--1082

Journal of Computational Chemistry
Volume 34, Number 13, May 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 13 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 13 . . . . . . . . . . . . . . . . iii--iv
              Jeremy P. Coe and   
           Daniel J. Taylor and   
             Martin J. Paterson   Monte Carlo configuration interaction
                                  applied to multipole moments, ionisation
                                  energies and electron affinities . . . . 1083--1093
      Liudmyla K. Sviatenko and   
                Leonid Gorb and   
            Frances C. Hill and   
              Jerzy Leszczynski   Theoretical study of ionization and
                                  one-electron oxidation potentials of
                                  N-heterocyclic compounds . . . . . . . . 1094--1100
                   Rui Yang and   
            Alistair P. Rendell   First principles study of gallium
                                  cleaning for hydrogen-contaminated $
                                  \alpha $-Al$_2$O$_3$ (0001) surfaces . . 1101--1111
             Michel Masella and   
              Daniel Borgis and   
              Philippe Cuniasse   A multiscale coarse-grained polarizable
                                  solvent model for handling long tail
                                  bulk electrostatics  . . . . . . . . . . 1112--1124
            Krystel El Hage and   
       Jean-Philip Piquemal and   
              Zeina Hobaika and   
          Richard G. Maroun and   
                    Nohad Gresh   Could an anisotropic molecular
                                  mechanics/dynamics potential account for
                                  sigma hole effects in the complexes of
                                  halogenated compounds? . . . . . . . . . 1125--1135
                 Xue X. Yao and   
                Chang G. Ji and   
                 Dai Q. Xie and   
               John Z. H. Zhang   Molecular dynamics study of DNA binding
                                  by INT-DBD under a polarized force field 1136--1142
                    E. Iype and   
             M. Hütter and   
            A. P. J. Jansen and   
                S. V. Nedea and   
                 C. C. M. Rindt   Parameterization of a reactive force
                                  field using a Monte Carlo algorithm  . . 1143--1154
             Torsten Kerber and   
    Rachel Nathaniel Kerber and   
            Xavier Rozanska and   
            Philippe Sautet and   
           Paul Fleurat-Lessard   Software news and updates: QMX: a
                                  versatile environment for hybrid
                                  calculations applied to the grafting of
                                  Al$_2$Cl$_3$Me$_3$ on a silica surface   1155--1163
        Nicholas F. Chilton and   
        Russell P. Anderson and   
          Lincoln D. Turner and   
         Alessandro Soncini and   
                Keith S. Murray   Software News and Updates: PHI: a
                                  powerful new program for the analysis of
                                  anisotropic monomeric and
                                  exchange-coupled polynuclear $d$- and
                                  $f$-block complexes  . . . . . . . . . . 1164--1175

Journal of Computational Chemistry
Volume 34, Number 14, May 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 14 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 14 . . . . . . . . . . . . . . . . iii--iv
         Claudia R. Herbers and   
                  Chunli Li and   
        Nico F. A. van der Vegt   Reviews: Grand challenges in
                                  quantum-classical modeling of
                                  molecule--surface interactions . . . . . 1177--1188
           Jenna A. Bilbrey and   
           Arianna H. Kazez and   
              Jason Locklin and   
                Wesley D. Allen   Exact ligand cone angles . . . . . . . . 1189--1197
         Sandra C. C. Nunes and   
                   P. Pinto and   
               A. A. C. C. Pais   Nonrandom adsorption of polyelectrolyte
                                  chains on finite regularly charged
                                  surfaces . . . . . . . . . . . . . . . . 1198--1209
           Daniel Strobusch and   
               Mathias Nest and   
             Christoph Scheurer   The adaptive hierarchical expansion of
                                  the kinetic energy operator  . . . . . . 1210--1217
             Yutaka Imamura and   
              Rie Kobayashi and   
                   Hiromi Nakai   Linearity condition for orbital energies
                                  in density functional theory (III):
                                  Benchmark of total energies  . . . . . . 1218--1225
            Trent E. Balius and   
           William J. Allen and   
          Sudipto Mukherjee and   
                Robert C. Rizzo   Grid-based molecular footprint
                                  comparison method for docking and de
                                  novo design: Application to HIVgp41  . . 1226--1240
                   Xinbi Li and   
        Sergei Y. Ponomarev and   
                    Qina Sa and   
       Daniel L. Sigalovsky and   
             George A. Kaminski   Polarizable simulations with second
                                  order interaction model (POSSIM) force
                                  field: Developing parameters for protein
                                  side-chain analogues . . . . . . . . . . 1241--1250
                   Le Chang and   
           Takeshi Ishikawa and   
               Kazuo Kuwata and   
                   Shoji Takada   Protein-specific force field derived
                                  from the fragment molecular orbital
                                  method can improve protein--ligand
                                  binding interactions . . . . . . . . . . 1251--1257
            Marcel Schumann and   
                 Roger S. Armen   Systematic and efficient side chain
                                  optimization for molecular docking using
                                  a cheapest-path procedure  . . . . . . . 1258--1269

Journal of Computational Chemistry
Volume 34, Number 15, June 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 15 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 15 . . . . . . . . . . . . . . . . iii--iv
                     Yao Wu and   
               Xiaodong Dai and   
                  Niu Huang and   
                    Lifeng Zhao   A partition function-based weighting
                                  scheme in force field parameter
                                  development using ab initio calculation
                                  results in global configurational space  1271--1282
           Maria Ana Castro and   
         Adrian E. Roitberg and   
             Fabio D. Cukiernik   Simulation of mesogenic diruthenium
                                  tetracarboxylates: Development of a
                                  force field for coordination polymers of
                                  the MMX type . . . . . . . . . . . . . . 1283--1290
          Kalipada Adhikari and   
        Sudip Chattopadhyay and   
             Barin Kumar De and   
             Amitava Sharma and   
         Ranendu Kumar Nath and   
                   Dhiman Sinha   Search of truncation of $ (N - 1) $
                                  electron basis containing full connected
                                  triple excitations in computing main and
                                  satellite ionization potentials via
                                  Fock-space coupled cluster approach  . . 1291--1310
    Ida-Marie Hòyvik and   
           Branislav Jansik and   
          Kasper Kristensen and   
          Poul Jòrgensen   Local Hartree--Fock orbitals using a
                                  three-level optimization strategy for
                                  the energy . . . . . . . . . . . . . . . 1311--1320
             David Casanova and   
               Pere Alemany and   
      Andrés Falceto and   
              Abel Carreras and   
               Santiago Alvarez   Pseudosymmetry analysis of molecular
                                  orbitals . . . . . . . . . . . . . . . . 1321--1331
        Sven Jakobtorweihen and   
              Thomas Ingram and   
                 Irina Smirnova   Combination of COSMOmic and molecular
                                  dynamics simulations for the calculation
                                  of membrane-water partition coefficients 1332--1340
          Karunakaran Remya and   
        Cherumuttathu H. Suresh   Which density functional is close to
                                  CCSD accuracy to describe geometry and
                                  interaction energy of small non-covalent
                                  dimers? A benchmark study using \tt
                                  gaussian09 . . . . . . . . . . . . . . . 1341--1353
          Silvia A. Martins and   
                Sergio F. Sousa   Comparative assessment of computational
                                  methods for the determination of
                                  solvation free energies in alcohol-based
                                  molecules  . . . . . . . . . . . . . . . 1354--1362

Journal of Computational Chemistry
Volume 34, Number 16, June 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 16 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 16 . . . . . . . . . . . . . . . . iii--iv
          Olle Falklöf and   
                     Bo Durbeej   Modeling of phytochrome absorption
                                  spectra  . . . . . . . . . . . . . . . . 1363--1374
          Tetsuya Morishita and   
             Satoru G. Itoh and   
            Hisashi Okumura and   
                Masuhiro Mikami   On-the-fly reconstruction of free-energy
                                  profiles using logarithmic mean-force
                                  dynamics . . . . . . . . . . . . . . . . 1375--1384
              Paul M. Zimmerman   Automated discovery of chemically
                                  reasonable elementary reaction steps . . 1385--1392
                Axel Schild and   
                   Beate Paulus   Multireference calculations for ring
                                  inversion and double bond shifting in
                                  cyclooctatetraene  . . . . . . . . . . . 1393--1397
        Jose Antonio Garate and   
              Chris Oostenbrink   Free-energy differences between states
                                  with different conformational ensembles  1398--1408
             Milan Randi\'c and   
            Marjana Novi\vc and   
              Dejan Plav\vsi\'c   Common vertex matrix: a novel
                                  characterization of molecular graphs by
                                  counting . . . . . . . . . . . . . . . . 1409--1419
             Mark P. Waller and   
         Thomas Dresselhaus and   
                      Jack Yang   Software News and Updates: JACOB: an
                                  enterprise framework for computational
                                  chemistry  . . . . . . . . . . . . . . . 1420--1428
         Eric D. Glendening and   
            Clark R. Landis and   
                 Frank Weinhold   Software News and Updates: NBO 6.0:
                                  Natural bond orbital analysis program    1429--1437

Journal of Computational Chemistry
Volume 34, Number 17, June 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 17 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 17 . . . . . . . . . . . . . . . . iii--iv
                    Ivana Antol   Photodeactivation paths in norbornadiene 1439--1445
       Aggelos Avramopoulos and   
              Heribert Reis and   
              Josep M. Luis and   
        Manthos G. Papadopoulos   On the vibrational linear and nonlinear
                                  optical properties of compounds
                                  involving noble gas atoms: HXeOXeH,
                                  HXeOXeF, and FXeOXeF . . . . . . . . . . 1446--1455
    Ida-Marie Hòyvik and   
           Branislav Jansik and   
          Poul Jòrgensen   Pipek--Mezey localization of occupied
                                  and virtual orbitals . . . . . . . . . . 1456--1462
                      Yi He and   
               Lidia Prieto and   
               Themis Lazaridis   Modeling peptide binding to anionic
                                  membrane pores . . . . . . . . . . . . . 1463--1475
         Marco De La Pierre and   
     Cédric Carteret and   
            Roberto Orlando and   
                 Roberto Dovesi   Use of ab initio methods for the
                                  interpretation of the experimental IR
                                  reflectance spectra of crystalline
                                  compounds  . . . . . . . . . . . . . . . 1476--1485
             Patrick Merlot and   
     Thomas Kjærgaard and   
            Trygve Helgaker and   
               Roland Lindh and   
        Francesco Aquilante and   
                Simen Reine and   
          Thomas Bondo Pedersen   Attractive electron--electron
                                  interactions within robust local fitting
                                  approximations . . . . . . . . . . . . . 1486--1496
       Ahmed A. K. Mohammed and   
          Peter A. Limacher and   
            Beno\^\it Champagne   Finding optimal finite field strengths
                                  allowing for a maximum of precision in
                                  the calculation of polarizabilities and
                                  hyperpolarizabilities  . . . . . . . . . 1497--1507
        Peter Schwerdtfeger and   
                 Lukas Wirz and   
                    James Avery   Software News and Updates: Program
                                  Fullerene: a software package for
                                  constructing and analyzing structures of
                                  regular fullerenes . . . . . . . . . . . 1508--1526

Journal of Computational Chemistry
Volume 34, Number 18, July 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 18 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 18 . . . . . . . . . . . . . . . . iii--iv
           Marat R. Talipov and   
        Dmitry G. Khomyakov and   
                  Ming Xian and   
           Qadir K. Timerghazin   Computational design of S-nitrosothiol
                                  ``click'' reactions  . . . . . . . . . . 1527--1530
   Petr \vSt\vepánek and   
                    Petr Bou\vr   Computation of magnetic circular
                                  dichroism by sum-over-states summations  1531--1539
   Alexandra T. P. Carvalho and   
         Ana F. S. Teixeira and   
                 Maria J. Ramos   Parameters for molecular dynamics
                                  simulations of iron-sulfur proteins  . . 1540--1548
   Azaria Solomon Eisenberg and   
              Laura J. Juszczak   Relating Trp-Glu dipeptide fluorescence
                                  to molecular conformation: the role of
                                  the discrete chi 1 and chi 2 angles  . . 1549--1560
             Paolo Nicolini and   
             Diego Frezzato and   
           Cristina Gellini and   
             Marco Bizzarri and   
                Riccardo Chelli   Toward quantitative estimates of binding
                                  affinities for protein--ligand systems
                                  involving large inhibitor compounds: a
                                  steered molecular dynamics simulation
                                  route  . . . . . . . . . . . . . . . . . 1561--1576
               Sonam Bhatia and   
         Yogesh J. Malkhede and   
             Prasad V. Bharatam   Existence of dynamic tautomerism and
                                  divalent N(I) character in
                                  N-(pyridin-2-yl)thiazol-2-amine  . . . . 1577--1588
             Han Myoung Lee and   
                   Kwang S. Kim   Dynamics and structural changes of small
                                  water clusters on ionization . . . . . . 1589--1597
                Peter Comba and   
                Bodo Martin and   
                    Avik Sanyal   An efficient fluctuating charge model
                                  for transition metal complexes . . . . . 1598--1608
           Yannick G. Spill and   
          Guillaume Bouvier and   
                 Michael Nilges   Erratum: A convective replica-exchange
                                  method for sampling new energy basins    1609--1609

Journal of Computational Chemistry
Volume 34, Number 19, July 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 19 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 19 . . . . . . . . . . . . . . . . iii--iv
                 Yu-Ai Duan and   
                   Yun Geng and   
                 Hai-Bin Li and   
               Jun-Ling Jin and   
                    Yong Wu and   
                   Zhong-Min Su   Theoretical characterization and design
                                  of small molecule donor material
                                  containing naphthodithiophene central
                                  unit for efficient organic solar cells   1611--1619
                Xueqin Pang and   
                   Keli Han and   
                      Qiang Cui   A simple but effective modeling strategy
                                  for structural properties of non-heme
                                  Fe(II) sites in proteins: Test of force
                                  field models and application to proteins
                                  in the AlkB family . . . . . . . . . . . 1620--1635
                     Li Rao and   
            Igor Ying Zhang and   
                Wenping Guo and   
                    Li Feng and   
               Eric Meggers and   
                         Xin Xu   Nonfitting protein--ligand interaction
                                  scoring function based on
                                  first-principles theoretical chemistry
                                  methods: Development and application on
                                  kinase inhibitors  . . . . . . . . . . . 1636--1646
        Justin E. Elenewski and   
                John C. Hackett   Cytochrome P450 compound I in the plane
                                  wave pseudopotential framework: GGA
                                  electronic and geometric structure of
                                  thiolate-ligated iron(IV)--oxo porphyrin 1647--1660
             Brajesh K. Rai and   
              Gregory A. Bakken   Fast and accurate generation of ab
                                  initio quality atomic charges using
                                  nonparametric statistical regression . . 1661--1671
               Rebecca Sure and   
                  Stefan Grimme   Corrected small basis set Hartree--Fock
                                  method for large systems . . . . . . . . 1672--1685
                Yongqing Li and   
             Jiuchuang Yuan and   
                 Maodu Chen and   
                 Fengcai Ma and   
                    Mengtao Sun   Accurate double many-body expansion
                                  potential energy surface by
                                  extrapolation to the complete basis set
                                  limit and dynamics calculations for
                                  ground state of NH$_2$ . . . . . . . . . 1686--1696
             Wouter Boomsma and   
               Jes Frellsen and   
                 Tim Harder and   
             Sandro Bottaro and   
    Kristoffer E. Johansson and   
               Pengfei Tian and   
    Kasper Stòvgaard and   
        Christian Andreetta and   
               Simon Olsson and   
            Jan B. Valentin and   
         Lubomir D. Antonov and   
      Anders S. Christensen and   
                Mikael Borg and   
              Jan H. Jensen and   
    Kresten Lindorff-Larsen and   
    Jesper Ferkinghoff-Borg and   
               Thomas Hamelryck   Software News and Updates: PHAISTOS: a
                                  framework for Markov chain Monte Carlo
                                  simulation and inference of protein
                                  structure  . . . . . . . . . . . . . . . 1697--1705

Journal of Computational Chemistry
Volume 34, Number 20, July 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 20 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 20 . . . . . . . . . . . . . . . . iii--iv
     Ranieri V. de Carvalho and   
        Daniel Lopez-Ferrer and   
  Katia S. Guimarães and   
                Roberto D. Lins   IMSPeptider: a computational peptide
                                  collision cross-section area calculator
                                  based on a novel molecular dynamics
                                  simulation protocol  . . . . . . . . . . 1707--1718
Christiane Regina Soares Brasil and   
Alexandre Claudio Botazzo Delbem and   
Fernando Luís Barroso da Silva   Multiobjective evolutionary algorithm
                                  with many tables for purely ab initio
                                  protein structure prediction . . . . . . 1719--1734
                 Ruifeng Lu and   
                Yunhui Wang and   
                   Kaiming Deng   Quantum wave packet and quasiclassical
                                  trajectory studies of the reaction
                                  H($^2$S) + CH(X$^2 \Pi $ ); $ v = 0 $, j
                                  = 1 $ \rightarrow $ C($^1$ D) + H$_2$
                                  (X$^1 \Sigma $ g+): Coriolis coupling
                                  effects and stereodynamics . . . . . . . 1735--1742
        Victoria A. Roberts and   
         Elaine E. Thompson and   
           Michael E. Pique and   
            Martin S. Perez and   
                 L. F. Ten Eyck   DOT2: Macromolecular docking with
                                  improved biophysical models  . . . . . . 1743--1758
              Neil Qiang Su and   
            Igor Ying Zhang and   
                         Xin Xu   Analytic derivatives for the XYG3 type
                                  of doubly hybrid density functionals:
                                  Theory, implementation, and assessment   1759--1774
          Ireneusz W. Bulik and   
           Robert Zale\'sny and   
        Wojciech Bartkowiak and   
              Josep M. Luis and   
            Bernard Kirtman and   
        Gustavo E. Scuseria and   
       Aggelos Avramopoulos and   
              Heribert Reis and   
        Manthos G. Papadopoulos   Performance of density functional theory
                                  in computing nonresonant vibrational
                                  (hyper)polarizabilities  . . . . . . . . 1775--1784
              Mark A. Olson and   
                 Michael S. Lee   Application of replica exchange umbrella
                                  sampling to protein structure refinement
                                  of nontemplate models  . . . . . . . . . 1785--1793
                   Sierra Rayne   Letters to the Editor: Comment on ``QSAR
                                  model reproducibility and applicability:
                                  a case study of rate constants of
                                  hydroxyl radical reaction models applied
                                  to polybrominated diphenyl ethers and
                                  (benzo-)triazoles''  . . . . . . . . . . 1794--1795
            Paola Gramatica and   
            Simona Kovarich and   
              Partha Pratim Roy   Letters to the Editor: Reply to the
                                  comment of S. Rayne on ``QSAR model
                                  reproducibility and applicability: a
                                  case study of rate constants of hydroxyl
                                  radical reaction models applied to
                                  polybrominated diphenyl ethers and
                                  (benzo-)triazoles''  . . . . . . . . . . 1796--1796

Journal of Computational Chemistry
Volume 34, Number 21, August 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 21 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 21 . . . . . . . . . . . . . . . . iii--iv
               Wiktor Beker and   
           Karol M. Langner and   
 Edyta Dyguda-Kazimierowicz and   
            Miko\laj Feliks and   
            W. Andrzej Sokalski   Low cost prediction of relative
                                  stabilities of hydrogen bonded complexes
                                  from atomic multipole moments for overly
                                  short intermolecular distances . . . . . 1797--1799
        Rafael López and   
   Guillermo Ramírez and   
                Ignacio Ema and   
    Jaime Fernández Rico   Improved partition--expansion of
                                  two-center distributions involving
                                  Slater functions . . . . . . . . . . . . 1800--1809
          Christoph Grebner and   
             Lukas P. Pason and   
                   Bernd Engels   PathOpt --- A global transition state
                                  search approach: Outline of algorithm    1810--1818
            Mirko Franchini and   
Pierre Herman Theodoor Philipsen and   
                 Lucas Visscher   The Becke Fuzzy Cells Integration Scheme
                                  in the Amsterdam Density Functional
                                  Program Suite  . . . . . . . . . . . . . 1819--1827
           Atsushi Ishikawa and   
              Hiroshi Nakatsuji   XPS of oxygen atoms on Ag(111) and
                                  Ag(110) surfaces: Accurate study with
                                  SAC/SAC-CI combined with dipped
                                  adcluster model  . . . . . . . . . . . . 1828--1834
                  Arnim Hellweg   Heuristic control of kinetic energy in
                                  dynamic reaction coordinate calculations 1835--1841
         Vladimir V. Rybkin and   
           Ulf Ekström and   
                Trygve Helgaker   Internal-to-Cartesian back
                                  transformation of molecular geometry
                                  steps using high-order geometric
                                  derivatives  . . . . . . . . . . . . . . 1842--1849
         Shaun M. Kandathil and   
        Timothy L. Fletcher and   
                Yongna Yuan and   
             Joshua Knowles and   
            Paul L. A. Popelier   Accuracy and tractability of a kriging
                                  model of intramolecular polarizable
                                  multipolar electrostatics and its
                                  application to histidine . . . . . . . . 1850--1861
        Birgit Hischenhuber and   
              Hans Havlicek and   
             Jelena Todoric and   
 Sonja Höllrigl-Binder and   
         Wolfgang Schreiner and   
                 Bernhard Knapp   Software News and Updates: Differential
                                  geometric analysis of alterations in MH$
                                  \alpha $-helices . . . . . . . . . . . . 1862--1879

Journal of Computational Chemistry
Volume 34, Number 22, August 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 22 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 22 . . . . . . . . . . . . . . . . iii--iv
          Benjamin L. Moore and   
         Lawrence A. Kelley and   
               James Barber and   
            James W. Murray and   
             James T. MacDonald   High-quality protein backbone
                                  reconstruction from alpha carbons using
                                  Gaussian mixture models  . . . . . . . . 1881--1889
         Stanislav Standara and   
       Petr Kulhánek and   
                Radek Marek and   
                  Michal Straka   $^{129}$Xe NMR chemical shift in
                                  Xe@C$_{60}$ calculated at experimental
                                  conditions: Essential role of the
                                  relativity, dynamics, and explicit
                                  solvent  . . . . . . . . . . . . . . . . 1890--1898
               Zhixiong Lin and   
       Wilfred F. van Gunsteren   Influence of variation of a side chain
                                  on the folding equilibrium of a $ \beta
                                  $-peptide: Limitations of one-step
                                  perturbation . . . . . . . . . . . . . . 1899--1906
               Chandan Sahu and   
                Kaushik Sen and   
           Srimanta Pakhira and   
             Bhaskar Mondal and   
                 Abhijit K. Das   Binding affinity of substituted
                                  ureido-benzenesulfonamide ligands to the
                                  carbonic anhydrase receptor: a
                                  theoretical study of enzyme inhibition   1907--1916
             Anton S. Nizovtsev   Activation of C--H bond in methane by Pd
                                  atom from the bonding evolution theory
                                  perspective  . . . . . . . . . . . . . . 1917--1924
           Priyanka Dhingra and   
          Bhyravabhotla Jayaram   A homology/ab initio hybrid algorithm
                                  for sampling near-native protein
                                  conformations  . . . . . . . . . . . . . 1925--1936
          Steven Vancoillie and   
     Mickaël G. Delcey and   
               Roland Lindh and   
           Victor Vysotskiy and   
    Per-Åke Malmqvist and   
                Valera Veryazov   Parallelization of a
                                  multiconfigurational perturbation theory 1937--1948
                   Chuan Li and   
           Marharyta Petukh and   
                     Lin Li and   
                    Emil Alexov   Continuous development of schemes for
                                  parallel computing of the electrostatics
                                  in biological systems: Implementation in
                                  DelPhi . . . . . . . . . . . . . . . . . 1949--1960
José J. Baldoví and   
     Salvador Cardona-Serra and   
      Juan M. Clemente-Juan and   
           Eugenio Coronado and   
Alejandro Gaita-Ariño and   
                   Andrew Palii   Software News and Updates: SIMPRE: a
                                  software package to calculate crystal
                                  field parameters, energy levels, and
                                  magnetic properties on mononuclear
                                  lanthanoid complexes based on charge
                                  distributions  . . . . . . . . . . . . . 1961--1967

Journal of Computational Chemistry
Volume 34, Number 23, September 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 23 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 23 . . . . . . . . . . . . . . . . iii--iv
              Yuichi Harano and   
                Roland Roth and   
                 Shuntaro Chiba   A morphometric approach for the accurate
                                  solvation thermodynamics of proteins and
                                  ligands  . . . . . . . . . . . . . . . . 1969--1974
        Daniel A. Götz and   
          Rolf Schäfer and   
            Peter Schwerdtfeger   The performance of density functional
                                  and wavefunction-based methods for $2$D
                                  and $3$D structures of Au$_{10}$ . . . . 1975--1981
            Takahiro Yamada and   
           Donald K. Phelps and   
            Adri C. T. van Duin   First principle and ReaxFF molecular
                                  dynamics investigations of formaldehyde
                                  dissociation on Fe(100) surface  . . . . 1982--1996
                     Yi Ren and   
               Xi-Guang Wei and   
                 Si-Jia Ren and   
              Kai-Chung Lau and   
              Ning-Bew Wong and   
                     Wai-Kee Li   The $ \alpha $-effect exhibited in
                                  gas-phase S$_N$2@N and S$_N$2@C
                                  reactions  . . . . . . . . . . . . . . . 1997--2005
Angelika Baranowska-\L\kaczkowska and   
     Krzysztof Z. \L\kaczkowski   The ORP basis set designed for optical
                                  rotation calculations  . . . . . . . . . 2006--2013
             Alexander V. Mitin   Polarization functions for the modified
                                  m6-31G basis sets for atoms Ga through
                                  Kr . . . . . . . . . . . . . . . . . . . 2014--2019
       Ringo Rey-Villaverde and   
            Hubert Cybulski and   
     Jesús R. Flores and   
         Berta Fernández   A high-accuracy theoretical study of the
                                  CH$_n$P systems $ n = 1 $--$3$ . . . . . 2020--2031
                   Likai Du and   
                    Jun Gao and   
                  Fuzhen Bi and   
                  Lili Wang and   
                    Chengbu Liu   A polarizable ellipsoidal force field
                                  for halogen bonds  . . . . . . . . . . . 2032--2040
      Ernesto Suárez and   
        Natalia Díaz and   
    Jefferson Méndez and   
            Dimas Suárez   Software News and Updates: CENCALC: a
                                  computational tool for conformational
                                  entropy calculations from molecular
                                  simulations  . . . . . . . . . . . . . . 2041--2054

Journal of Computational Chemistry
Volume 34, Number 24, September 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 24 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 24 . . . . . . . . . . . . . . . . iii--iv
                 Ge-Fei Hao and   
            Sheng-Gang Yang and   
              Guang-Fu Yang and   
                 Chang-Guo Zhan   Computational gibberellin-binding
                                  channel discovery unraveling the
                                  unexpected perception mechanism of
                                  hormone signal by gibberellin receptor   2055--2064
                     Bin Tu and   
                Minxin Chen and   
                    Yan Xie and   
                Linbo Zhang and   
              Bob Eisenberg and   
                     Benzhuo Lu   A parallel finite element simulator for
                                  ion transport through three-dimensional
                                  ion channel systems  . . . . . . . . . . 2065--2078
     Sérgio F. Sousa and   
         Gaspar R. P. Pinto and   
António J. M. Ribeiro and   
  João T. S. Coimbra and   
         Pedro A. Fernandes and   
        Maria João Ramos   Comparative analysis of the performance
                                  of commonly available density
                                  functionals in the determination of
                                  geometrical parameters for copper
                                  complexes  . . . . . . . . . . . . . . . 2079--2090
             Riadh Dardouri and   
          Héla Habli and   
               Brahim Oujia and   
    Florent Xavier Gadéa   Ab Initio Diabatic energies and dipole
                                  moments of the electronic states of RbLi
                                  molecule . . . . . . . . . . . . . . . . 2091--2099
                   Xin Feng and   
                  Kelin Xia and   
                  Zhan Chen and   
                Yiying Tong and   
                    Guo-Wei Wei   Multiscale geometric modeling of
                                  macromolecules II: Lagrangian
                                  representation . . . . . . . . . . . . . 2100--2120
            Paola Gramatica and   
             Nicola Chirico and   
                 Ester Papa and   
            Stefano Cassani and   
                Simona Kovarich   Software News and Updates: QSARINS: a
                                  new software for the development,
                                  analysis, and validation of QSAR MLR
                                  models . . . . . . . . . . . . . . . . . 2121--2132
          Kalipada Adhikari and   
        Sudip Chattopadhyay and   
             Barin Kumar De and   
             Amitava Sharma and   
         Ranendu Kumar Nath and   
                   Dhiman Sinha   Erratum: Search of truncation of $ (N -
                                  1) $ electron basis containing full
                                  connected triple excitations in
                                  computing main and satellite ionization
                                  potentials via Fock space coupled
                                  cluster approach . . . . . . . . . . . . 2133--2133
         Eric D. Glendening and   
            Clark R. Landis and   
                 Frank Weinhold   Erratum: NBO 6.0: Natural bond orbital
                                  analysis program . . . . . . . . . . . . 2134--2134

Journal of Computational Chemistry
Volume 34, Number 25, September 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 25 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 25 . . . . . . . . . . . . . . . . iii--iv
                 Jing Huang and   
     Alexander D. MacKerell Jr.   CHARMM36 all-atom additive protein force
                                  field: Validation based on comparison to
                                  NMR data . . . . . . . . . . . . . . . . 2135--2145
              Betsy M. Rice and   
              Edward F. C. Byrd   Evaluation of electrostatic descriptors
                                  for predicting crystalline density . . . 2146--2151
           Shigeki Yamamoto and   
                    Petr Bou\vr   Transition polarizability model of
                                  induced resonance Raman optical activity 2152--2158
           Henry A. Boateng and   
                  Robert Krasny   Comparison of treecodes for computing
                                  electrostatic potentials in charged
                                  particle systems with disjoint targets
                                  and sources  . . . . . . . . . . . . . . 2159--2167
                  J. Grant Hill   Auxiliary basis sets for density-fitting
                                  second-order Mòller--Plesset perturbation
                                  theory: Weighted core-valence
                                  correlation consistent basis sets for
                                  the $ 4 d $ elements Y--Pd . . . . . . . 2168--2177
          Henrik R. Larsson and   
        Adri C. T. van Duin and   
                   Bernd Hartke   Global optimization of parameters in the
                                  reactive force field ReaxFF for SiOH . . 2178--2189
José Fernando R. Bachega and   
Luís Fernando S. M. Timmers and   
             Lucas Assirati and   
        Leonardo R. Bachega and   
            Martin J. Field and   
                    Troy Wymore   Software News and Updates: GTKDynamo: A
                                  PyMOL plug-in for QC/MM hybrid potential
                                  simulations  . . . . . . . . . . . . . . 2190--2196
              You-Liang Zhu and   
                   Hong Liu and   
                Zhan-Wei Li and   
                Hu-Jun Qian and   
            Giuseppe Milano and   
                  Zhong-Yuan Lu   Software News and Updates: GALAMOST:
                                  GPU-accelerated large-scale molecular
                                  simulation toolkit . . . . . . . . . . . 2197--2211
         Sally R. Ellingson and   
            Jeremy C. Smith and   
                  Jerome Baudry   Software News and Updates: VinaMPI:
                                  Facilitating multiple receptor
                                  high-throughput virtual docking on
                                  high-performance computers . . . . . . . 2212--2221

Journal of Computational Chemistry
Volume 34, Number 26, October 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 26 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 26 . . . . . . . . . . . . . . . . iii--iv
                   Tao Yang and   
                 Xiang Zhao and   
                 Shigeru Nagase   1,3-Dipolar cycloadditions of
                                  Stone--Wales defective single-walled
                                  carbon nanotubes: a theoretical study    2223--2232
               Hyungjun Kim and   
              Joungwon Park and   
                   Yoon Sup Lee   A protocol to evaluate one electron
                                  redox potential for iron complexes . . . 2233--2241
            Laetitia Bomble and   
       Stephan N. Steinmann and   
        Nancy Perez-Peralta and   
             Gabriel Merino and   
           Clemence Corminboeuf   Bonding analysis of planar
                                  hypercoordinate atoms via the
                                  generalized BLW-LOL  . . . . . . . . . . 2242--2248
     Athanasios Anthopoulos and   
              Ian Grimstead and   
                Andrea Brancale   GPU-accelerated molecular mechanics
                                  computations . . . . . . . . . . . . . . 2249--2260
            Anna Stachowicz and   
               Jacek Korchowiec   Bond detectors for molecular dynamics
                                  simulations, Part I: Hydrogen bonds  . . 2261--2269
      Subha Kalyaanamoorthy and   
            Yi-Ping Phoebe Chen   Ligand release mechanisms and channels
                                  in histone deacetylases  . . . . . . . . 2270--2283
            Ilya A. Kaliman and   
         Lyudmila V. Slipchenko   Software News and Updates: LIBEFP: a new
                                  parallel implementation of the effective
                                  fragment potential method as a portable
                                  software library . . . . . . . . . . . . 2284--2292
         Evgeny Epifanovsky and   
             Michael Wormit and   
               Tomasz Ku\'s and   
                Arie Landau and   
                Dmitry Zuev and   
           Kirill Khistyaev and   
           Prashant Manohar and   
               Ilya Kaliman and   
              Andreas Dreuw and   
                 Anna I. Krylov   Software News and Updates: New
                                  implementation of high-level correlated
                                  methods using a general block tensor
                                  library for high-performance electronic
                                  structure calculations . . . . . . . . . 2293--2309
       Panagiotis I. Koukos and   
             Nicholas M. Glykos   Software News and Updates: Grcarma: a
                                  fully automated task-oriented interface
                                  for the analysis of molecular dynamics
                                  trajectories . . . . . . . . . . . . . . 2310--2312

Journal of Computational Chemistry
Volume 34, Number 27, October 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 27 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 27 . . . . . . . . . . . . . . . . iii--iv
           Steven K. Burger and   
      G. Andrés Cisneros   Efficient optimization of van der Waals
                                  parameters from bulk properties  . . . . 2313--2319
         Volker L. Deringer and   
               Marck Lumeij and   
            Ralf P. Stoffel and   
            Richard Dronskowski   Ab initio study of the high-temperature
                                  phase transition in crystalline GeO$_2$  2320--2326
           Sebastian Kozuch and   
               Jan M. L. Martin   Spin-component-scaled double hybrids: an
                                  extensive search for the best fifth-rung
                                  functionals blending DFT and
                                  perturbation theory  . . . . . . . . . . 2327--2344
                Tomoya Inui and   
           Yasuteru Shigeta and   
              Katsuki Okuno and   
               Takeshi Baba and   
               Ryohei Kishi and   
               Masayoshi Nakano   Finite-field method with unbiased
                                  polarizable continuum model for
                                  evaluation of the second
                                  hyperpolarizability of an open-shell
                                  singlet molecule in solvents . . . . . . 2345--2352
                  Rahul Kar and   
              Jong-Won Song and   
               Takeshi Sato and   
                 Kimihiko Hirao   Long-range corrected density functionals
                                  combined with local response dispersion:
                                  a promising method for weak interactions 2353--2359
          Camilo Velez-Vega and   
              Michael K. Gilson   Overcoming dissipation in the
                                  calculation of standard binding free
                                  energies by ligand extraction  . . . . . 2360--2371
      Tiago Quevedo Teodoro and   
   Roberto Luiz Andrade Haiduke   Accurate relativistic adapted Gaussian
                                  basis sets for francium through
                                  ununoctium without variational prolapse
                                  and to be used with both uniform sphere
                                  and Gaussian nucleus models  . . . . . . 2372--2379
                 Yingdi Jin and   
            Erin R. Johnson and   
               Xiangqian Hu and   
                Weitao Yang and   
                         Hao Hu   Contributions of Pauli repulsions to the
                                  energetics and physical properties
                                  computed in QM/MM methods  . . . . . . . 2380--2388
             Rong-Zhen Liao and   
                   Walter Thiel   Convergence in the QM-only and QM/MM
                                  modeling of enzymatic reactions: a case
                                  study for acetylene hydratase  . . . . . 2389--2397
              Neil Qiang Su and   
            Igor Ying Zhang and   
                         Xin Xu   Erratum: Analytic derivatives for the
                                  XYG3 type of doubly hybrid density
                                  functionals: Theory, implementation, and
                                  assessment . . . . . . . . . . . . . . . 2398--2399
                 M. E. Chen and   
                        W. Yang   Erratum: On-the-path random walk
                                  sampling for efficient optimization of
                                  minimum free energy path . . . . . . . . 2400--2400
                   M. Swart and   
                  M. Sol\`a and   
              F. M. Bickelhaupt   Corrigendum: Inter- and intramolecular
                                  dispersion interactions  . . . . . . . . 2401--2402

Journal of Computational Chemistry
Volume 34, Number 28, October 30, 2013

                      Anonymous   Cover Image, Volume 34, Issue 28 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 28 . . . . . . . . . . . . . . . . iii--iv
              Masashi Daido and   
            Yukio Kawashima and   
             Masanori Tachikawa   Nuclear quantum effect and temperature
                                  dependency on the hydrogen-bonded
                                  structure of base pairs  . . . . . . . . 2403--2411
               Jaewoon Jung and   
              Takaharu Mori and   
                    Yuji Sugita   Efficient lookup table using a linear
                                  function of inverse distance squared . . 2412--2420
           Patrick Bultinck and   
            Sofie Van Damme and   
          Andrés Cedillo   Bond Fukui indices: Comparison of frozen
                                  molecular orbital and finite differences
                                  through Mulliken populations . . . . . . 2421--2429
               Annia Galano and   
Juan Raúl Alvarez-Idaboy   A computational methodology for accurate
                                  predictions of rate constants in
                                  solution: Application to the assessment
                                  of primary antioxidant activity  . . . . 2430--2445
             Karl Wilkinson and   
          Chris-Kriton Skylaris   Porting ONETEP to graphical processing
                                  unit-based coprocessors. 1. FFT box
                                  operations . . . . . . . . . . . . . . . 2446--2459
Erix Wiliam Hernández-Rodríguez and   
   Ana Lilian Montero-Alejo and   
        Rafael López and   
Elsa Sánchez-García and   
Luis Alberto Montero-Cabrera and   
José Manuel García de la Vega   Electron density deformations provide
                                  new insights into the spectral shift of
                                  rhodopsins . . . . . . . . . . . . . . . 2460--2471
            Thomas Simonson and   
            Thomas Gaillard and   
               David Mignon and   
    Marcel Schmidt am Busch and   
                 Anne Lopes and   
              Najette Amara and   
         Savvas Polydorides and   
              Audrey Sedano and   
               Karen Druart and   
             Georgios Archontis   Computational protein design: the
                                  Proteus software and selected
                                  applications . . . . . . . . . . . . . . 2472--2484
              Thorsten Will and   
          Michael C. Hutter and   
               Johann Jauch and   
                 Volkhard Helms   Software News and Updates: Batch
                                  tautomer generation with MolTPC  . . . . 2485--2492

Journal of Computational Chemistry
Volume 34, Number 29, November 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 29 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 29 . . . . . . . . . . . . . . . . iii--iv
             Satoru G. Itoh and   
                Hisashi Okumura   Hamiltonian replica-permutation method
                                  and its applications to an alanine
                                  dipeptide and amyloid-$ \beta $ (29--42)
                                  peptides . . . . . . . . . . . . . . . . 2493--2497
             Masahiro Ehara and   
             Ryoichi Fukuda and   
                Carlo Adamo and   
                 Ilaria Ciofini   Chemically intuitive indices for
                                  charge-transfer excitation based on
                                  SAC-CI and TD-DFT calculations . . . . . 2498--2501
Carlos Campañá and   
               Ronald E. Miller   Transiting the molecular potential
                                  energy surface along low energy
                                  pathways: The TRREAT algorithm . . . . . 2502--2513
             Milan Randi\'c and   
            Marjana Novi\vc and   
            Marjan Vra\vcko and   
              Dejan Plav\vsi\'c   On the centrality of vertices of
                                  molecular graphs . . . . . . . . . . . . 2514--2523
                   Liang Xu and   
              Xiaojuan Wang and   
            Shengsheng Shan and   
                   Xicheng Wang   Characterization of the polymorphic
                                  states of copper(II)-bound A$ \beta $
                                  (1-16) peptides by computational
                                  simulations  . . . . . . . . . . . . . . 2524--2536
           Otilia Mó and   
        Al Mokhtar Lamsabhi and   
 Manuel Yáñez and   
   Gavin S. Heverly-Coulson and   
                Russell J. Boyd   Dramatic substituent effects on the
                                  mechanisms of nucleophilic attack on
                                  Se---S bridges . . . . . . . . . . . . . 2537--2547
          José Rogan and   
            Alejandro Varas and   
    Juan Alejandro Valdivia and   
                    Miguel Kiwi   A strategy to find minimal energy
                                  nanocluster structures . . . . . . . . . 2548--2556
              Stefan Maintz and   
         Volker L. Deringer and   
Andrei L. Tchougréeff and   
            Richard Dronskowski   Analytic projection from plane-wave and
                                  PAW wavefunctions and application to
                                  chemical-bonding analysis in solids  . . 2557--2567
              Masato Tanaka and   
             Michio Katouda and   
                 Shigeru Nagase   Optimization of RI-MP2 Auxiliary Basis
                                  Functions for 6-31G** and 6-311G** Basis
                                  Sets for First-, Second-, and Third-Row
                                  Elements . . . . . . . . . . . . . . . . 2568--2575

Journal of Computational Chemistry
Volume 34, Number 30, November 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 30 . . . . i--ii
                      Anonymous   Cover Image, Volume 34, Issue 30 . . . . iii--iv
        Ol'ha O. Brovarets' and   
              Dmytro M. Hovorun   Atomistic understanding of the C$ \cdot
                                  $T mismatched DNA base pair
                                  tautomerization via the DPT: QM and
                                  QTAIM computational approaches . . . . . 2577--2590
        Matthew A. Addicoat and   
               Syou Fukuoka and   
            Alister J. Page and   
                   Stephan Irle   Stochastic structure determination for
                                  conformationally flexible heterogeneous
                                  molecular clusters: Application to ionic
                                  liquids  . . . . . . . . . . . . . . . . 2591--2600
            Hironori Kokubo and   
           Toshimasa Tanaka and   
                   Yuko Okamoto   Two-dimensional replica-exchange method
                                  for predicting protein--ligand binding
                                  structures . . . . . . . . . . . . . . . 2601--2614
                   Yu. D. Fomin   Molecular dynamics simulation of benzene
                                  in graphite and amorphous carbon slit
                                  pores  . . . . . . . . . . . . . . . . . 2615--2624
                 David Robinson   Splitting multiple bonds: a comparison
                                  of methodologies on the accuracy of bond
                                  dissociation energies  . . . . . . . . . 2625--2634
           Mahesh R. Borkar and   
Raghuvir R. S. Pissurlenkar and   
              Evans C. Coutinho   HomoSAR: Bridging comparative protein
                                  modeling with quantitative structural
                                  activity relationship to design new
                                  peptides . . . . . . . . . . . . . . . . 2635--2646
             Woong-Hee Shin and   
               Jae-Kwan Kim and   
               Deok-Soo Kim and   
                     Chaok Seok   GalaxyDock2: Protein--ligand docking
                                  using beta-complex and global
                                  optimization . . . . . . . . . . . . . . 2647--2656
        Victor P. Vysotskiy and   
         Jonas Boström and   
                Valera Veryazov   Software News and Updates: A new module
                                  for constrained multi-fragment geometry
                                  optimization in internal coordinates
                                  implemented in the MOLCAS package  . . . 2657--2665

Journal of Computational Chemistry
Volume 34, Number 31, December 5, 2013

                      Anonymous   Cover Image, Volume 34, Issue 31 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 31 . . . . . . . . . . . . . . . . iii--iv
              Pekka Pyykkö   The RTAM electronic bibliography,
                                  version 17.0, on relativistic theory of
                                  atoms and molecules  . . . . . . . . . . 2667--2667
          Leonardo Pacifici and   
           Marco Verdicchio and   
        Noelia Faginas Lago and   
            Andrea Lombardi and   
          Alessandro Costantini   A high-level ab initio study of the
                                  N$_2$ + N$_2$ reaction channel . . . . . 2668--2676
                  Juan Zeng and   
                Xiangyu Jia and   
           John Z. H. Zhang and   
                         Ye Mei   The F130L mutation in streptavidin
                                  reduces its binding affinity to biotin
                                  through electronic polarization effect   2677--2686
          Marina \'Cendi\'c and   
         Zoran D. Matovi\'c and   
                Robert J. Deeth   Molecular modeling for
                                  Cu(II)-aminopolycarboxylate complexes:
                                  Structures, conformational energies, and
                                  ligand binding affinities  . . . . . . . 2687--2696
              Yung Ting Lee and   
                  Jyh Shing Lin   Ab Initio molecular dynamics study of
                                  ethylene adsorption onto Si(001)
                                  surface: Short-time Fourier transform
                                  analysis of structural coordinate
                                  autocorrelation function . . . . . . . . 2697--2706
           Stella Nickerson and   
            Denzil S. Frost and   
            Harrison Phelan and   
                  Lenore L. Dai   Comparison of the capillary wave method
                                  and pressure tensor route for
                                  calculation of interfacial tension in
                                  molecular dynamics simulations . . . . . 2707--2715
             Tobias Neumann and   
              Denis Danilov and   
         Christian Lennartz and   
                Wolfgang Wenzel   Modeling disordered morphologies in
                                  organic semiconductors . . . . . . . . . 2716--2725
               Gevorg Grigoryan   Absolute free energies of biomolecules
                                  from unperturbed ensembles . . . . . . . 2726--2741
         Savvas Polydorides and   
                Thomas Simonson   Monte Carlo simulations of proteins at
                                  constant pH with generalized Born
                                  solvent, flexible sidechains, and an
                                  effective dielectric boundary  . . . . . 2742--2756

Journal of Computational Chemistry
Volume 34, Number 32, December 15, 2013

                      Anonymous   Cover Image, Volume 34, Issue 32 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 34,
                                  Issue 32 . . . . . . . . . . . . . . . . iii--iv
       Christopher G. Mayne and   
                   Jan Saam and   
             Klaus Schulten and   
           Emad Tajkhorshid and   
               James C. Gumbart   Rapid parameterization of small
                                  molecules using the force field toolkit  2757--2770
               David Schmidling   A new set of bending T$_d$ symmetry
                                  coordinates for MX$_4$ molecules . . . . 2771--2773
               Vincent Hall and   
               Anthony Nash and   
                 Evor Hines and   
                  Alison Rodger   Elucidating protein secondary structure
                                  with circular dichroism and a neural
                                  network  . . . . . . . . . . . . . . . . 2774--2786
             Yutaka Imamura and   
                 Jun Suzuki and   
                   Hiromi Nakai   Kinetic energy decomposition scheme
                                  based on information theory  . . . . . . 2787--2795
               Zhixiong Lin and   
       Wilfred F. van Gunsteren   Refinement of the application of the
                                  GROMOS 54A7 force field to $ \beta
                                  $-peptides . . . . . . . . . . . . . . . 2796--2805
                Jen-Ping Su and   
              Yung-Ting Lee and   
                 Shao-Yu Lu and   
                  Jyh Shing Lin   Chemical mechanism of surface-enhanced
                                  Raman scattering spectrum of pyridine
                                  adsorbed on Ag cluster: Ab initio
                                  molecular dynamics approach  . . . . . . 2806--2815
     Nandun M. Thellamurege and   
                   Dejun Si and   
               Fengchao Cui and   
                 Hongbo Zhu and   
                    Rui Lai and   
                         Hui Li   Software News and Updates: QuanPol: a
                                  full spectrum and seamless QM/MM program 2816--2833
            B. Hischenhuber and   
                H. Havlicek and   
                 J. Todoric and   
    S. Höllrigl-Binder and   
               W. Schreiner and   
                       B. Knapp   Corrigendum: Differential geometric
                                  analysis of alterations in MH$ \alpha
                                  $-helices  . . . . . . . . . . . . . . . 2834--2834


Journal of Computational Chemistry
Volume 35, Number 1, January 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 1  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 1  . . . . iii--iv
               Anton Jesser and   
     Martin Rohrmüller and   
          Wolf Gero Schmidt and   
            Sonja Herres-Pawlis   Geometrical and optical benchmarking of
                                  copper guanidine--quinoline complexes:
                                  Insights from TD-DFT and many-body
                                  perturbation theory  . . . . . . . . . . 1--17
       Franziska D. Hofmann and   
           Michael Devereux and   
             Andreas Pfaltz and   
                  Markus Meuwly   Toward force fields for atomistic
                                  simulations of iridium-containing
                                  complexes  . . . . . . . . . . . . . . . 18--29
         Francesco Fracchia and   
            Claudia Filippi and   
               Claudio Amovilli   Multi-level quantum Monte Carlo wave
                                  functions for complex reactions: the
                                  decomposition of $ \alpha
                                  $-hydroxy-dimethylnitrosamine  . . . . . 30--38
               Jinzen Ikebe and   
              Shun Sakuraba and   
                 Hidetoshi Kono   Adaptive lambda square dynamics
                                  simulation: an efficient conformational
                                  sampling method for biomolecules . . . . 39--50
       Soumya Ganguly Neogi and   
               Pinaki Chaudhury   Structural, spectroscopic aspects, and
                                  electronic properties of (TiO$_2$ )$_n$
                                  clusters: a study based on the use of
                                  natural algorithms in association with
                                  quantum chemical methods . . . . . . . . 51--61
                   Pei-Kun Yang   Incorporating the excluded solvent
                                  volume and surface charges for computing
                                  solvation free energy  . . . . . . . . . 62--69
                  Zhijun Xu and   
                  Yang Yang and   
                 Ziqiu Wang and   
             Donald Mkhonto and   
                Cheng Shang and   
                Zhi-Pan Liu and   
                  Qiang Cui and   
                     Nita Sahai   Small molecule-mediated control of
                                  hydroxyapatite growth: Free energy
                                  calculations benchmarked to density
                                  functional theory  . . . . . . . . . . . 70--81
  Sébastien Canneaux and   
Frédéric Bohr and   
                     Eric Henon   Software News and Updates: KiSThelP: a
                                  program to predict thermodynamic
                                  properties and rate constants from
                                  quantum chemistry results  . . . . . . . 82--93

Journal of Computational Chemistry
Volume 35, Number 2, January 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 2  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 2  . . . . iii--iv
       Andreas W. Götz and   
           Matthew A. Clark and   
                 Ross C. Walker   An extensible interface for QM/MM
                                  molecular dynamics simulations with
                                  AMBER  . . . . . . . . . . . . . . . . . 95--108
               Panwang Zhou and   
               Jianyong Liu and   
                   Keli Han and   
                    Guozhong He   The photoisomerization of 11-cis-retinal
                                  protonated Schiff base in gas phase:
                                  Insight from spin-flip density
                                  functional theory  . . . . . . . . . . . 109--120
                 Feiwu Chen and   
                     Zhihui Fan   A new size extensive multireference
                                  perturbation theory  . . . . . . . . . . 121--129
            Fabien Cailliez and   
          Arnaud Bourasseau and   
                  Pascal Pernot   Calibration of forcefields for molecular
                                  simulation: Sequential design of
                                  computer experiments for building
                                  cost-efficient kriging metamodels  . . . 130--149
            Katja Ostermeir and   
               Martin Zacharias   Hamiltonian replica-exchange simulations
                                  with adaptive biasing of peptide
                                  backbone and side chain dihedral angles  150--158
                Shuai Jiang and   
                Yi-Rong Liu and   
                 Teng Huang and   
                    Hui Wen and   
               Kang-Ming Xu and   
             Wei-Xiong Zhao and   
              Wei-Jun Zhang and   
                      Wei Huang   Study of Cl$^-$ (H$_2$O)$_n$ ($n$ =
                                  1--4) using basin-hopping method coupled
                                  with density functional theory . . . . . 159--165
              Satoshi Maeda and   
          Tetsuya Taketsugu and   
                 Keiji Morokuma   Exploring transition state structures
                                  for intramolecular pathways by the
                                  artificial force induced reaction method 166--173
                Wenliang Li and   
                 Jingping Zhang   Multiscale simulation of pollution gases
                                  adsorption in porous organic cage CC3    174--180

Journal of Computational Chemistry
Volume 35, Number 3, January 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 3  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 3  . . . . iii--iv
                 Ivan Welsh and   
                  Matthias Lein   Accurate density functional theory
                                  description of binding constants and NMR
                                  chemical shifts of weakly interacting
                                  complexes of C$_{60}$ with
                                  corannulene-based molecular bowls  . . . 181--191
  Elisabeth Ortega-Carrasco and   
       Agusti Lledós and   
    Jean-Didier Maréchal   Assessing protein--ligand docking for
                                  the binding of organometallic compounds
                                  to proteins  . . . . . . . . . . . . . . 192--198
Angelika Baranowska-\L\kaczkowska and   
         Berta Fernández   Basis sets for the evaluation of van der
                                  Waals complex interaction energies:
                                  Ne--N$_2$ intermolecular potential and
                                  microwave spectrum . . . . . . . . . . . 199--203
           Edoardo Fertitta and   
            Elena Voloshina and   
                   Beate Paulus   Adsorption of multivalent alkylthiols on
                                  Au(111) surface: Insights from DFT . . . 204--213
       Vishwesh Venkatraman and   
     Per-Olof Åstrand and   
Bjòrn Kåre Alsberg   Quantitative structure--property
                                  relationship modeling of Grätzel solar
                                  cell dyes  . . . . . . . . . . . . . . . 214--226
              Maria M. Reif and   
              Chris Oostenbrink   Net charge changes in the calculation of
                                  relative ligand-binding free energies
                                  via classical atomistic molecular
                                  dynamics simulation  . . . . . . . . . . 227--243
              Mahdi Shirazi and   
               Simon D. Elliott   Atomistic kinetic Monte Carlo study of
                                  atomic layer deposition derived from
                                  density functional theory  . . . . . . . 244--259
            Magnus Lundborg and   
           Rossen Apostolov and   
     Daniel Spångberg and   
  Anders Gärdenäs and   
        David van der Spoel and   
                   Erik Lindahl   Software News and Updates: An efficient
                                  and extensible format, library, and API
                                  for binary trajectory data from
                                  molecular simulations  . . . . . . . . . 260--269

Journal of Computational Chemistry
Volume 35, Number 4, February 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 4  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 4  . . . . iii--iv
               Taro Udagawa and   
             Masanori Tachikawa   Why is N\dottedbondBe distance of
                                  NH$_3$H$^+$\dottedbondDBeH shorter than
                                  that of NH$_3$D$^+$\dottedbondHBeH?
                                  Paradoxical geometrical isotope effects
                                  for partially isotope-substituted
                                  dihydrogen-bonded isotopomers  . . . . . 271--274
               Marco Heinen and   
          Elshad Allahyarov and   
             Hartmut Löwen   Highly asymmetric electrolytes in the
                                  primitive model: Hypernetted chain
                                  solution in arbitrary spatial dimensions 275--289
      Otávio Beruski and   
               Luciano N. Vidal   Algorithms for computer detection of
                                  symmetry elements in molecular systems   290--299
                 Pai-Chi Li and   
          Naoyuki Miyashita and   
                  Wonpil Im and   
             Satoshi Ishido and   
                    Yuji Sugita   Multidimensional umbrella sampling and
                                  replica-exchange molecular dynamics
                                  simulations for structure prediction of
                                  transmembrane helix dimers . . . . . . . 300--308
              Jorge A. Vila and   
        Yelena A. Arnautova and   
          Osvaldo A. Martin and   
             Harold A. Scheraga   Are accurate computations of the
                                  $^{13}$C' shielding feasible at the DFT
                                  level of theory? . . . . . . . . . . . . 309--312
         Vitaly N. Glushkov and   
                 Xavier Assfeld   Multireference space without first
                                  solving the configuration interaction
                                  problem  . . . . . . . . . . . . . . . . 313--323
        Dimas Suárez and   
        Natalia Díaz and   
      Ramón López   A combined semiempirical and DFT
                                  computational protocol for studying
                                  bioorganometallic complexes: Application
                                  to molybdocene--cysteine complexes . . . 324--334
                Shide Liang and   
                  Chi Zhang and   
                     Yaoqi Zhou   LEAP: Highly accurate prediction of
                                  protein loop conformations by
                                  integrating coarse-grained sampling and
                                  optimized energy scores with all-atom
                                  refinement of backbone and side chains   335--341

Journal of Computational Chemistry
Volume 35, Number 5, February 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 5  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 5  . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 5  . . . . v--vi
                Yongna Yuan and   
        Matthew J. L. Mills and   
            Paul L. A. Popelier   Multipolar electrostatics for proteins:
                                  Atom--atom electrostatic energies in
                                  crambin  . . . . . . . . . . . . . . . . 343--359
         Dina T. Mirijanian and   
          Ranjan V. Mannige and   
       Ronald N. Zuckermann and   
               Stephen Whitelam   Development and use of an atomistic
                                  CHARMM-based forcefield for peptoid
                                  simulation . . . . . . . . . . . . . . . 360--370
    Israel Fernández and   
        F. Matthias Bickelhaupt   Origin of the ``endo rule'' in
                                  Diels--Alder reactions . . . . . . . . . 371--376
               David J. Huggins   Comparing distance metrics for rotation
                                  using the $k$-nearest neighbors
                                  algorithm for entropy estimation . . . . 377--385
           Alessandra Forni and   
         Stefano Pieraccini and   
            Stefano Rendine and   
                Maurizio Sironi   Halogen bonds with benzene: an
                                  assessment of DFT functionals  . . . . . 386--394
          Andrei V. Bandura and   
            Robert A. Evarestov   TiS$_2$ and ZrS$_2$ single- and
                                  double-wall nanotubes: First-principles
                                  study  . . . . . . . . . . . . . . . . . 395--405
       Antti-Pekka Hynninen and   
             Michael F. Crowley   Software News and Updates: New faster
                                  CHARMM molecular dynamics engine . . . . 406--413

Journal of Computational Chemistry
Volume 35, Number 6, March 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 6  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 6  . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 6  . . . . v--vi
                 Shu-Shi Li and   
             Cui-Ying Huang and   
              Jiao-Jiao Hao and   
               Chang-Sheng Wang   A polarizable dipole--dipole interaction
                                  model for evaluation of the interaction
                                  energies for NH\dottedbondOC and
                                  CH\dottedbondOC hydrogen-bonded
                                  complexes  . . . . . . . . . . . . . . . 415--426
Pablo García-Risueño and   
   Joseba Alberdi-Rodriguez and   
      Micael J. T. Oliveira and   
             Xavier Andrade and   
             Michael Pippig and   
            Javier Muguerza and   
       Agustin Arruabarrena and   
                    Angel Rubio   A survey of the parallel performance and
                                  accuracy of Poisson solvers for
                                  electronic structure calculations  . . . 427--444
                   Jie Chen and   
                  Yulong Xu and   
                    Dunyou Wang   A multilayered representation, quantum
                                  mechanical and molecular mechanics study
                                  of the CH$_3$F $+$ OH$^-$ reaction in
                                  water  . . . . . . . . . . . . . . . . . 445--450
        Ol'ha O. Brovarets' and   
       Roman O. Zhurakivsky and   
              Dmytro M. Hovorun   Is the DPT tautomerization of the long
                                  A$\cdot$G Watson--Crick DNA base mispair
                                  a source of the adenine and guanine
                                  mutagenic tautomers? A QM and QTAIM
                                  response to the biologically important
                                  question . . . . . . . . . . . . . . . . 451--466
               Tonghao Shen and   
              Neil Qiang Su and   
                    Anan Wu and   
                         Xin Xu   Perturbative treatment of anharmonic
                                  vibrational effects on bond distances:
                                  an extended Langevin dynamics method . . 467--478
         Eric Van Dornshuld and   
           Gregory S. Tschumper   Characterization of the potential energy
                                  surfaces of two small but challenging
                                  noncovalent dimers: (P$_2$)$_2$ and
                                  (PCCP)$_2$ . . . . . . . . . . . . . . . 479--487
      Leslie Sánchez and   
     Gonzalo A. Jaña and   
             Eduardo J. Delgado   A QM/MM study on the reaction pathway
                                  leading to $2$-Aceto-$2$-hydroxybutyrate
                                  in the catalytic cycle of AHAS . . . . . 488--494
          Abdullah Ozkanlar and   
                Aurora E. Clark   Software News and Updates: ChemNetworks:
                                  a complex network analysis tool for
                                  chemical systems . . . . . . . . . . . . 495--505

Journal of Computational Chemistry
Volume 35, Number 7, March 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 7  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 7  . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 7  . . . . iv--v
      Luís P. Viegas and   
  António J. C. Varandas   Coupled-cluster reaction barriers of
                                  HO$_2$ + H$_2$O + O$_3$: an application
                                  of the coupled-cluster/Kohn--Sham
                                  density functional theory model
                                  chemistry  . . . . . . . . . . . . . . . 507--517
        Mateusz Maciejewski and   
             Paul N. Barlow and   
                   Nico Tjandra   Decoding the components of dynamics in
                                  three-domain proteins  . . . . . . . . . 518--525
           Anita K. Nivedha and   
          Spandana Makeneni and   
      Bethany Lachele Foley and   
         Matthew B. Tessier and   
                Robert J. Woods   Importance of ligand conformational
                                  energies in carbohydrate docking:
                                  Sorting the wheat from the chaff . . . . 526--539
           Travis V. Harris and   
             Robert K. Szilagyi   Iron--sulfur bond covalency from
                                  electronic structure calculations for
                                  classical iron--sulfur clusters  . . . . 540--552
           Katharina Krause and   
                  Thomas Bredow   Conductor-like screening model for
                                  relaxed excited states: Implementation
                                  in the semiempirical method MSINDO . . . 553--564
              Alexey I. Baranov   Electron localizability indicators from
                                  spinor wavefunctions . . . . . . . . . . 565--585
     Talapunur Vikramaditya and   
             Kanakamma Sumithra   Effect of substitutionally boron-doped
                                  single-walled semiconducting zigzag
                                  carbon nanotubes on ammonia adsorption   586--594

Journal of Computational Chemistry
Volume 35, Number 8, March 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 8  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 8  . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 8  . . . . v--vi
         Uppula Purushotham and   
             G. Narahari Sastry   A comprehensive conformational analysis
                                  of tryptophan, its ionic and dimeric
                                  forms  . . . . . . . . . . . . . . . . . 595--610
                 Elda Rossi and   
        Stefano Evangelisti and   
           Antonio Lagan\`a and   
             Antonio Monari and   
             Sergio Rampino and   
           Marco Verdicchio and   
           Kim K. Baldridge and   
      Gian Luigi Bendazzoli and   
             Stefano Borini and   
           Renzo Cimiraglia and   
           Celestino Angeli and   
               Peter Kallay and   
         Hans P. Lüthi and   
               Kenneth Ruud and   
  José Sanchez-Marin and   
            Anthony Scemama and   
            Peter G. Szalay and   
                   Attila Tajti   Code interoperability and standard data
                                  formats in quantum chemistry and quantum
                                  dynamics: The Q5/D5Cost data model . . . 611--621
            Magnus Ringholm and   
                Dan Jonsson and   
                   Kenneth Ruud   A general, recursive, and open-ended
                                  response code  . . . . . . . . . . . . . 622--633
               Tony Anacker and   
              Joachim Friedrich   New accurate benchmark energies for
                                  large water clusters: DFT is better than
                                  expected . . . . . . . . . . . . . . . . 634--643
               Kevin J. Maurice   SSThread: Template-free protein
                                  structure prediction by threading pairs
                                  of contacting secondary structures
                                  followed by assembly of overlapping
                                  pairs  . . . . . . . . . . . . . . . . . 644--656
            Maarten G. Wolf and   
                Gerrit Groenhof   Software News and Updates: Explicit
                                  proton transfer in classical molecular
                                  dynamics simulations . . . . . . . . . . 657--671
       Kliment Olechnovi\vc and   
           \vCeslovas Venclovas   Software News and Updates: Voronota: a
                                  fast and reliable tool for computing the
                                  vertices of the Voronoi diagram of
                                  atomic balls . . . . . . . . . . . . . . 672--681

Journal of Computational Chemistry
Volume 35, Number 9, April 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 9  . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 9  . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 9  . . . . v--vi
            Sateesh Bandaru and   
           Niall J. English and   
              J. M. D. MacElroy   Implicit and explicit solvent models for
                                  modeling a bifunctional arene ruthenium
                                  hydrogen-storage catalyst: a classical
                                  and ab initio molecular simulation study 683--691
          Hugh S. C. Martin and   
               Shantenu Jha and   
               Peter V. Coveney   Comparative analysis of nucleotide
                                  translocation through protein nanopores
                                  using steered molecular dynamics and an
                                  adaptive biasing force . . . . . . . . . 692--702
                    Kun Liu and   
                  Yu-Xue Li and   
                Jia-Ling Su and   
                       Bin Wang   The reliability of DFT methods to
                                  predict electronic structures and
                                  minimum energy crossing point for
                                  [Fe$^{IV}$O](OH)$_2$ models: a
                                  comparison study with MCQDPT method  . . 703--710
          Pablo M. De Biase and   
            Suren Markosyan and   
                  Sergei Noskov   Microsecond simulations of DNA and ion
                                  transport in nanopores with novel
                                  ion--ion and ion--nucleotides effective
                                  potentials . . . . . . . . . . . . . . . 711--721
         Alexander Kurnosov and   
           Mario Cacciatore and   
           Antonio Lagan\`a and   
            Fernando Pirani and   
    Massimiliano Bartolomei and   
                 Ernesto Garcia   The effect of the intermolecular
                                  potential formulation on the
                                  state-selected energy exchange rate
                                  coefficients in N$_2$--N$_2$ collisions  722--736
                Xiangyu Jia and   
                  Juan Zeng and   
           John Z. H. Zhang and   
                         Ye Mei   Accessing the applicability of polarized
                                  protein-specific charge in linear
                                  interaction energy analysis  . . . . . . 737--747
                   Chaim Dryzun   Continuous symmetry measures for complex
                                  symmetry group . . . . . . . . . . . . . 748--755
             Bruce M. Allen and   
           Paul K. Predecki and   
                  Maciej Kumosa   Software News and Updates: Integrating
                                  open-source software applications to
                                  build molecular dynamics systems . . . . 756--764

Journal of Computational Chemistry
Volume 35, Number 10, April 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 10 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 10 . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 10 . . . . v--vi
        Anna K. Hildebrandt and   
           Matthias Dietzen and   
            Thomas Lengauer and   
          Hans-Peter Lenhof and   
              Ernst Althaus and   
            Andreas Hildebrandt   Efficient computation of root mean
                                  square deviations under rigid
                                  transformations  . . . . . . . . . . . . 765--771
 José Diogo L. Dutra and   
            Thiago D. Bispo and   
              Ricardo O. Freire   LUMPAC lanthanide luminescence software:
                                  Efficient and user friendly  . . . . . . 772--775
        Tsvetan K. Zahariev and   
        Radomir I. Slavchov and   
             Alia V. Tadjer and   
               Anela N. Ivanova   Fully atomistic molecular-mechanical
                                  model of liquid alkane oils:
                                  Computational validation . . . . . . . . 776--788
       Oliwia M. Szklarczyk and   
        Stephan J. Bachmann and   
       Wilfred F. van Gunsteren   A polarizable empirical force field for
                                  molecular dynamics simulation of liquid
                                  hydrocarbons . . . . . . . . . . . . . . 789--801
      Gian Luigi Bendazzoli and   
          Muammar El Khatib and   
        Stefano Evangelisti and   
              Thierry Leininger   The total Position Spread in
                                  mixed-valence compounds: a study on the
                                  H4+ model system . . . . . . . . . . . . 802--808
            Cheng-chau Chiu and   
        Georgi N. Vayssilov and   
           Alexander Genest and   
             Armando Borgna and   
              Notker Rösch   Predicting adsorption enthalpies on
                                  silicalite and HZSM-5: a benchmark study
                                  on DFT strategies addressing dispersion
                                  interactions . . . . . . . . . . . . . . 809--819
Eric Iván Sánchez-Flores and   
Rodrigo Chávez-Calvillo and   
              Todd A. Keith and   
             Gabriel Cuevas and   
   Tomás Rocha-Rinza and   
Fernando Cortés-Guzmán   Properties of atoms in electronically
                                  excited molecules within the formalism
                                  of TDDFT . . . . . . . . . . . . . . . . 820--828

Journal of Computational Chemistry
Volume 35, Number 11, April 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 11 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 11 . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 11 . . . . v--vi
      Panaghiotis Karamanis and   
       Nicolás Otero and   
             Claude Pouchan and   
    Juan José Torres and   
            William Tiznado and   
       Aggelos Avramopoulos and   
        Manthos G. Papadopoulos   Significant nonlinear-optical switching
                                  capacity in atomic clusters built from
                                  silicon and lithium: a combined ab
                                  initio and density functional study  . . 829--838
      Michael F. Peintinger and   
                  Thomas Bredow   The cyclic cluster model at
                                  Hartree--Fock level  . . . . . . . . . . 839--846
          Toshiaki Kawamura and   
                 Minori Abe and   
             Masaichi Saito and   
                  Masahiko Hada   Quantum-chemical analyses of
                                  aromaticity, UV spectra, and NMR
                                  chemical shifts in
                                  plumbacyclopentadienylidenes stabilized
                                  by Lewis bases . . . . . . . . . . . . . 847--853
               Arne Lüchow   Maxima of |$ \Psi $ |2: a connection
                                  between quantum mechanics and Lewis
                                  structures . . . . . . . . . . . . . . . 854--864
           Kazuaki Z. Takahashi   Design of a reaction field using a
                                  linear-combination-based isotropic
                                  periodic sum method  . . . . . . . . . . 865--875
            Anita Plazinska and   
         Wojciech Plazinski and   
              Krzysztof Jozwiak   Fast, metadynamics-based method for
                                  prediction of the
                                  stereochemistry-dependent relative free
                                  energies of ligand--receptor
                                  interactions . . . . . . . . . . . . . . 876--882
              Ana E. Torres and   
           Guadalupe Castro and   
        Ricardo Pablo-Pedro and   
            Fernando Colmenares   A two-step reaction scheme leading to
                                  singlet carbene species that can be
                                  detected under matrix conditions for the
                                  reaction of Zr($^3$ F) with either
                                  CH$_3$F or CH$_3$CN  . . . . . . . . . . 883--890

Journal of Computational Chemistry
Volume 35, Number 12, May 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 12 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 12 . . . . iii--iv
                      Anonymous   Cover Image, Volume 35, Issue 12 . . . . v--vi
            Sateesh Bandaru and   
           Niall J. English and   
         Andrew D. Phillips and   
              J. M. D. MacElroy   Towards the design of novel boron- and
                                  nitrogen-substituted ammonia-borane and
                                  bifunctional arene ruthenium catalysts
                                  for hydrogen storage . . . . . . . . . . 891--903
              Yi-Quan Zhang and   
              Cheng-Lin Luo and   
                    Qiang Zhang   Exchange coupling and magnetic
                                  anisotropy in a family of bipyrimidyl
                                  radical-bridged dilanthanide complexes:
                                  Density functional theory and ab initio
                                  calculations . . . . . . . . . . . . . . 904--909
          Karunakaran Remya and   
        Cherumuttathu H. Suresh   Cooperativity and cluster growth
                                  patterns in acetonitrile: a DFT study    910--922
                     Xinying Li   Metalophilic interaction in gold halide:
                                  Quantum chemical study of AuX (X =
                                  F--At) . . . . . . . . . . . . . . . . . 923--931
             Sam Z. Grinter and   
                    Xiaoqin Zou   A Bayesian statistical approach of
                                  improving knowledge-based scoring
                                  functions for protein--ligand
                                  interactions . . . . . . . . . . . . . . 932--943
                 David Casanova   How much tetraradical character is
                                  present in the Si$_6$ Ge$_9$ cluster?    944--949
                 Petr Popov and   
                Sergei Grudinin   Software News and Updates: Rapid
                                  determination of RMSDs corresponding to
                                  macromolecular rigid body motions  . . . 950--956
           Jong Cheol Jeong and   
                 Sunhwan Jo and   
               Emilia L. Wu and   
                   Yifei Qi and   
       Viviana Monje-Galvan and   
               Min Sun Yeom and   
             Lev Gorenstein and   
                  Feng Chen and   
          Jeffery B. Klauda and   
                      Wonpil Im   Software News and Updates: ST-analyzer:
                                  a Web-based user interface for
                                  simulation trajectory analysis . . . . . 957--963

Journal of Computational Chemistry
Volume 35, Number 13, May 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 13 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 13 . . . . iii--iv
              Dong-Xia Zhao and   
                 Zhong-Zhi Yang   Investigation of the distinction between
                                  van der Waals interaction and chemical
                                  bonding based on the PAEM-MO diagram . . 965--977
         David Ferro-Costas and   
 Ignacio Pérez-Juste and   
            Ricardo A. Mosquera   Electronegativity estimator built on
                                  QTAIM-based domains of the bond electron
                                  density  . . . . . . . . . . . . . . . . 978--985
         Doreen Mollenhauer and   
                  Nicola Gaston   A balanced procedure for the treatment
                                  of cluster--ligand interactions on gold
                                  phosphine systems in catalysis . . . . . 986--997
                    Zhi Sun and   
      Henry F. Schaefer III and   
                Yaoming Xie and   
               Yongdong Liu and   
                   Rugang Zhong   The reactions of Cr(CO)$_6$, Fe(CO)$_5$,
                                  and Ni(CO)$_4$ with O$_2$ yield viable
                                  oxo-metal carbonyls  . . . . . . . . . . 998--1009
           Gennady N. Chuev and   
                Ivan Vyalov and   
                 Nikolaj Georgi   Extraction of site--site bridge
                                  functions and effective pair potentials
                                  from simulations of polar molecular
                                  liquids  . . . . . . . . . . . . . . . . 1010--1023
       Georgios C. Boulougouris   Free energy calculations, enhanced by a
                                  Gaussian ansatz, for the ``chemical
                                  work'' distribution  . . . . . . . . . . 1024--1035
            Paola Gramatica and   
            Stefano Cassani and   
                 Nicola Chirico   Software News and Updates: QSARINS-chem:
                                  Insubria datasets and new QSAR/QSPR
                                  models for environmental pollutants in
                                  QSARINS  . . . . . . . . . . . . . . . . 1036--1044

Journal of Computational Chemistry
Volume 35, Number 14, May 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 14 . . . . i--ii
                      Anonymous   Cover Image: Inside Cover, Volume 35,
                                  Issue 14 . . . . . . . . . . . . . . . . iii--iv
               Marc Raupach and   
            Stefanie Dehnen and   
                    Ralf Tonner   Quantitative investigation of bonding
                                  characteristics in ternary Zintl anions:
                                  Charge and energy analysis of [Sn$_2$
                                  E$^{15}_2$ (ZnPh)]$^-$ (E$^{15}$ = Sb,
                                  Bi) and [Sn$_2$ Sb$_5$
                                  (ZnPh)$_2$]$^{3-}$ . . . . . . . . . . . 1045--1057
                Haining Liu and   
                C. Heath Turner   Oxygen adsorption characteristics on
                                  hybrid carbon and boron-nitride
                                  nanotubes  . . . . . . . . . . . . . . . 1058--1063
               Jaewoon Jung and   
              Takaharu Mori and   
                    Yuji Sugita   Midpoint cell method for hybrid (MPI +
                                  OpenMP) parallelization of molecular
                                  dynamics simulations . . . . . . . . . . 1064--1072
             Emine Soyda\cs and   
                 U\ugur Bozkaya   Assessment of the orbital-optimized
                                  coupled-electron pair theory for
                                  thermochemistry and kinetics: Improving
                                  on CCSD and CEPA(1)  . . . . . . . . . . 1073--1081
                     Po-Jen Hsu   A new perspective of shape recognition
                                  to discover the phase transition of
                                  finite-size clusters . . . . . . . . . . 1082--1092
              Takao Tsuneda and   
                 Raman K. Singh   Reactivity index based on orbital
                                  energies . . . . . . . . . . . . . . . . 1093--1100
                    Biao Fu and   
      Aleksandr B. Sahakyan and   
            Carlo Camilloni and   
     Gian Gaetano Tartaglia and   
              Emanuele Paci and   
            Amedeo Caflisch and   
        Michele Vendruscolo and   
                 Andrea Cavalli   Software News and Updates: ALMOST: an
                                  all atom molecular simulation toolkit
                                  for protein structure determination  . . 1101--1105

Journal of Computational Chemistry
Volume 35, Number 15, June 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 15 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 15 . . . . iii--iv
                    Hui Zhu and   
                  Zheng-Wang Qu   Toward product control in ring-opening
                                  oligomerization of 9H-9-borafluorenes    1107--1110
                    Fei Xia and   
                  Dudu Tong and   
                Lifeng Yang and   
                Dayong Wang and   
           Steven C. H. Hoi and   
              Patrice Koehl and   
                     Lanyuan Lu   Identifying essential pairwise
                                  interactions in elastic network model
                                  using the alpha shape theory . . . . . . 1111--1121
                    Xin Yan and   
                   Jiabo Li and   
                   Qiong Gu and   
                         Jun Xu   gWEGA: GPU-accelerated WEGA for
                                  molecular superposition and shape
                                  comparison . . . . . . . . . . . . . . . 1122--1130
         Ad\`ele D. Laurent and   
         Vitaly N. Glushkov and   
               Thibaut Very and   
                 Xavier Assfeld   Toward the understanding of the
                                  environmental effects on core
                                  ionizations  . . . . . . . . . . . . . . 1131--1139
            Shinichi Yamabe and   
              Guixiang Zeng and   
                   Wei Guan and   
              Shigeyoshi Sakaki   S$_N$1--S$_N$2 and S$_N$2--S$_N$3
                                  mechanistic changes revealed by
                                  transition states of the hydrolyses of
                                  benzyl chlorides and benzenesulfonyl
                                  chlorides  . . . . . . . . . . . . . . . 1140--1148
                 Martin Carlsen   Using operators to expand the block
                                  matrices forming the Hessian of a
                                  molecular potential  . . . . . . . . . . 1149--1158
               Solen Ekesan and   
                 Seyit Kale and   
                Judith Herzfeld   Transferable pseudoclassical electrons
                                  for aufbau of atomic ions  . . . . . . . 1159--1164

Journal of Computational Chemistry
Volume 35, Number 16, June 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 16 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 16 . . . . iii--iv
         Chérif F. Matta   Modeling biophysical and biological
                                  properties from the characteristics of
                                  the molecular electron density, electron
                                  localization and delocalization
                                  matrices, and the electrostatic
                                  potential  . . . . . . . . . . . . . . . 1165--1198
       Nicodemo Di Pasquale and   
          Richard J. Gowers and   
                  Paola Carbone   A multiple time step scheme for
                                  multiresolved models of macromolecules   1199--1207
          Alexander Mirzoev and   
        Alexander P. Lyubartsev   Systematic implicit solvent coarse
                                  graining of
                                  dimyristoylphosphatidylcholine lipids    1208--1218
            Alexey Savelyev and   
     Alexander D. MacKerell Jr.   All-atom polarizable force field for DNA
                                  based on the classical Drude oscillator
                                  model  . . . . . . . . . . . . . . . . . 1219--1239
               Takeshi Baba and   
              Ryuhei Harada and   
           Masayoshi Nakano and   
               Yasuteru Shigeta   On the induced-fit mechanism of
                                  substrate-enzyme binding structures of
                                  nylon-oligomer hydrolase . . . . . . . . 1240--1247
           Phillip V. Smith and   
            Marian W. Radny and   
                    G. Ali Shah   Surface electronic structure
                                  calculations using the MBJLDA potential:
                                  Application to Si(111)2 $ \times $ 1 . . 1248--1254
                 Bingjie Hu and   
                 Markus A. Lill   Software News and Updates: WATsite:
                                  Hydration site prediction program with
                                  PyMOL interface  . . . . . . . . . . . . 1255--1260

Journal of Computational Chemistry
Volume 35, Number 17, June 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 17 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 17 . . . . iii--iv
             Marcos Mandado and   
 Nicolás Ramos-Berdullas   Analyzing the electric response of
                                  molecular conductors using ``electron
                                  deformation'' orbitals and
                                  occupied-virtual electron transfer . . . 1261--1269
           Olga E. Glukhova and   
        Anna S. Kolesnikova and   
     Michael M. Slepchenkov and   
           Vladislav V. Shunaev   Moving of fullerene between potential
                                  wells in the external icosahedral shell  1270--1277
                Olivia Wise and   
                 Orkid Coskuner   New force field parameters for
                                  metalloproteins I: Divalent copper ion
                                  centers including three histidine
                                  residues and an oxygen-ligated amino
                                  acid residue . . . . . . . . . . . . . . 1278--1289
Alba Campo-Cacharrón and   
  Enrique M. Cabaleiro-Lago and   
Jorge A. Carrazana-García and   
Jesús Rodríguez-Otero   Interaction of aromatic units of amino
                                  acids with guanidinium cation: the
                                  interplay of $ \pi \cdots \pi $, XH$
                                  \cdots \pi $ and M$^+ \cdots \pi$
                                  contacts . . . . . . . . . . . . . . . . 1290--1301
               Kin-Yiu Wong and   
                  Yuqing Xu and   
                 Darrin M. York   Ab initio path-integral calculations of
                                  kinetic and equilibrium isotope effects
                                  on base-catalyzed RNA
                                  transphosphorylation models  . . . . . . 1302--1316
        Mikhail Panshenskov and   
          Ilia A. Solov'yov and   
            Andrey V. Solov'yov   Software News and Updates: Efficient
                                  $3$D kinetic Monte Carlo method for
                                  modeling of molecular structure and
                                  dynamics . . . . . . . . . . . . . . . . 1317--1329
          César Mogo and   
     João Brandão   Software News and Updates: The READY
                                  program: Building a global potential
                                  energy surface and reactive dynamic
                                  simulations for the hydrogen combustion  1330--1337

Journal of Computational Chemistry
Volume 35, Number 18, July 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 18 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 18 . . . . iii--iv
      Ariadna Blanca Romero and   
          Piotr M. Kowalski and   
             George Beridze and   
            Hartmut Schlenz and   
                   Dirk Bosbach   Performance of DFT+ U method for
                                  prediction of structural and
                                  thermodynamic parameters of
                                  monazite-type ceramics . . . . . . . . . 1339--1346
            Yutaka Maruyama and   
              Norio Yoshida and   
              Hiroto Tadano and   
          Daisuke Takahashi and   
             Mitsuhisa Sato and   
                   Fumio Hirata   Massively parallel implementation of
                                  $3$D-RISM calculation with volumetric
                                  $3$D-FFT . . . . . . . . . . . . . . . . 1347--1355
   Emilio San-Fabián and   
       Federico Moscardó   Cyclobutadiene automerization and
                                  rotation of ethylene: Energetics of the
                                  barriers by using spin-polarized wave
                                  functions  . . . . . . . . . . . . . . . 1356--1363
              Song-Ho Chong and   
                     Sihyun Ham   Site-directed analysis on protein
                                  hydrophobicity . . . . . . . . . . . . . 1364--1370
            Thomas Gaillard and   
                Thomas Simonson   Pairwise decomposition of an MMGBSA
                                  energy function for computational
                                  protein design . . . . . . . . . . . . . 1371--1387
             Gregory K. Pierens   $^1$H and $^{13}$C NMR scaling factors
                                  for the calculation of chemical shifts
                                  in commonly used solvents using density
                                  functional theory  . . . . . . . . . . . 1388--1394
César R. García-Jacas and   
       Yovani Marrero-Ponce and   
Liesner Acevedo-Martínez and   
         Stephen J. Barigye and   
José R. Valdés-Martiní and   
       Ernesto Contreras-Torres   Software News and Updates:
                                  QuBiLS--MIDAS: a parallel free-software
                                  for molecular descriptors computation
                                  based on multilinear algebraic maps  . . 1395--1409

Journal of Computational Chemistry
Volume 35, Number 19, July 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 19 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 19 . . . . iii--iv
              Daniel Roston and   
                Amnon Kohen and   
                 Dvir Doron and   
                   Dan T. Major   Simulations of remote mutants of
                                  dihydrofolate reductase reveal the
                                  nature of a network of residues coupled
                                  to hydride transfer  . . . . . . . . . . 1411--1417
            Roberta P. Dias and   
                     Lin Li and   
          Thereza A. Soares and   
                    Emil Alexov   Modeling the electrostatic potential of
                                  asymmetric lipopolysaccharide membranes:
                                  The MEMPOT algorithm implemented in
                                  DelPhi . . . . . . . . . . . . . . . . . 1418--1429
            Hsin-Lin Chiang and   
             Chun-Jung Chen and   
            Hisashi Okumura and   
                    Chin-Kun Hu   Transformation between $ \alpha $-helix
                                  and $ \beta $-sheet structures of one
                                  and two polyglutamine peptides in
                                  explicit water molecules by
                                  replica-exchange molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1430--1437
           Steven K. Burger and   
              Paul W. Ayers and   
               Jeremy Schofield   Efficient parameterization of torsional
                                  terms for force fields . . . . . . . . . 1438--1445
            Zden\vek Futera and   
              Jaroslav V. Burda   Reaction mechanism of Ru(II) piano-stool
                                  complexes: Umbrella sampling QM/MM MD
                                  study  . . . . . . . . . . . . . . . . . 1446--1456
           Frans T. I. Marx and   
        Johan H. L. Jordaan and   
           Gerhard Lachmann and   
          Hermanus C. M. Vosloo   A Molecular modeling study of the
                                  changes of some steric properties of the
                                  precatalysts during the olefin
                                  metathesis reaction  . . . . . . . . . . 1457--1463
           Frans T. I. Marx and   
        Johan H. L. Jordaan and   
           Gerhard Lachmann and   
          Hermanus C. M. Vosloo   A comparison of low and high activity
                                  precatalysts: Do the calculated energy
                                  barriers during the self-metathesis
                                  reaction of 1-Octene correlate with the
                                  precatalyst metathesis activity? . . . . 1464--1471

Journal of Computational Chemistry
Volume 35, Number 20, July 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 20 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 20 . . . . iii--iv
              Masaki Okoshi and   
                   Hiromi Nakai   Acceleration of self-consistent field
                                  convergence in ab initio molecular
                                  dynamics simulation with
                                  multiconfigurational wave function . . . 1473--1480
           Lewis C. Smeeton and   
             Mark T. Oakley and   
                Roy L. Johnston   Visualizing energy landscapes with
                                  metric disconnectivity graphs  . . . . . 1481--1490
                     Hao Hu and   
                       Lin Shen   In silico concurrent multisite pH
                                  titration in proteins  . . . . . . . . . 1491--1498
             Frank Weinhold and   
Paul von Ragué Schleyer and   
         William Chadwick McKee   Bay-type H$ \cdots $H ``bonding'' in
                                  cis-$2$-butene and related species:
                                  QTAIM versus NBO description . . . . . . 1499--1508
            Tobias Risthaus and   
             Marc Steinmetz and   
                  Stefan Grimme   Implementation of nuclear gradients of
                                  range-separated hybrid density
                                  functionals and benchmarking on
                                  rotational constants for organic
                                  molecules  . . . . . . . . . . . . . . . 1509--1516
               Masao Hayami and   
                Junji Seino and   
                   Hiromi Nakai   Extension of accompanying coordinate
                                  expansion and recurrence relation method
                                  for general-contraction basis sets . . . 1517--1527
                  Hung Dien and   
         Charlotte M. Deane and   
                 Bernhard Knapp   Software News and Updates: Gro2mat: a
                                  package to efficiently read \tt gromacs
                                  output in MATLAB . . . . . . . . . . . . 1528--1531

Journal of Computational Chemistry
Volume 35, Number 21, August 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 21 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 21 . . . . iii--iv
Alba Campo-Cacharrón and   
  Enrique M. Cabaleiro-Lago and   
Jesús Rodríguez-Otero   Interaction between ions and substituted
                                  buckybowls: a comprehensive
                                  computational study  . . . . . . . . . . 1533--1544
       Ahmed A. K. Mohammed and   
           Steven K. Burger and   
                  Paul W. Ayers   Drug release by pH-responsive molecular
                                  tweezers: Atomistic details from
                                  molecular modeling . . . . . . . . . . . 1545--1551
      Ji\vrí Kessler and   
                    Petr Bou\vr   Molecular dynamics with helical periodic
                                  boundary conditions  . . . . . . . . . . 1552--1559
                Po-Chun Liu and   
                    Wei-Ping Hu   The MC-DFT approach including the
                                  SCS-MP2 energies to the new
                                  minnesota-type functionals . . . . . . . 1560--1567
              Gurpreet Kaur and   
                          Vikas   On the mechanism of intramolecular
                                  nitrogen-atom hopping in the carbon
                                  chain of C$_6$N radical: a plausible
                                  3c--4e crossover $ \pi $--long-bond  . . 1568--1576
              Mike Devereux and   
                Nohad Gresh and   
       Jean-Philip Piquemal and   
                  Markus Meuwly   A supervised fitting approach to force
                                  field parametrization with application
                                  to the SIBFA polarizable force field . . 1577--1591
              Shun Sakuraba and   
            Nobuyuki Matubayasi   Software News and Updates: Ermod: Fast
                                  and versatile computation software for
                                  solvation free energy with approximate
                                  theory of solutions  . . . . . . . . . . 1592--1608

Journal of Computational Chemistry
Volume 35, Number 22, August 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 22 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 22 . . . . iii--iv
            Pooria Farahani and   
 Daniel Roca-Sanjuán and   
            Francesco Aquilante   Review: A two-scale approach to electron
                                  correlation in multiconfigurational
                                  perturbation theory  . . . . . . . . . . 1609--1617
      Johannes M. Dieterich and   
                   Bernd Hartke   A graph-based short-cut to low-energy
                                  structures . . . . . . . . . . . . . . . 1618--1620
               Sergio A. Hassan   Implicit treatment of solvent dispersion
                                  forces in protein simulations  . . . . . 1621--1629
             My-Phuong Pham and   
                Buu Q. Pham and   
               Lam K. Huynh and   
                 Ha Q. Pham and   
           Maurice J. Marks and   
                Thanh N. Truong   Density functional theory study on
                                  mechanisms of epoxy-phenol curing
                                  reaction . . . . . . . . . . . . . . . . 1630--1640
          Maxim R. Ryzhikov and   
        Vladimir A. Slepkov and   
        Svetlana G. Kozlova and   
           Svyatoslav P. Gabuda   Evolution of chemical bonding and
                                  electron density rearrangements during
                                  D$_{3h}$ D$_{3d}$ reaction in
                                  monolayered TiS$_2$: A QTAIM and ELF
                                  study  . . . . . . . . . . . . . . . . . 1641--1645
                Yunju Zhang and   
                 Jingyu Sun and   
              Wanqiao Zhang and   
                Yizhen Tang and   
                  Rongshun Wang   Theoretical study on the gas phase
                                  reaction of propargyl alcohol with
                                  hydroxyl radical . . . . . . . . . . . . 1646--1656
                   Pei Zhao and   
                   Tao Yang and   
                 Yi-Jun Guo and   
           Jing-Shuang Dang and   
                 Xiang Zhao and   
                 Shigeru Nagase   Dimetallic sulfide endohedral
                                  metallofullerene Sc$_2$S@C$_{76}$:
                                  Density functional theory
                                  characterization . . . . . . . . . . . . 1657--1663
                     Xinying Li   Erratum: Metalophilic interaction in
                                  gold halide: Quantum chemical study of
                                  AuX (X = F--At)  . . . . . . . . . . . . 1664--1664

Journal of Computational Chemistry
Volume 35, Number 23, September 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 23 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 23 . . . . iii--iv
             Mariano Spivak and   
           Celestino Angeli and   
          Carmen J. Calzado and   
                  Coen de Graaf   Improving the calculation of magnetic
                                  coupling constants in MRPT methods . . . 1665--1671
            Kirill Zinovjev and   
Iñaki Tuñón   Exploring chemical reactivity of complex
                                  systems with path-based coordinates:
                                  Role of the distance metric  . . . . . . 1672--1681
              Weihong Zhang and   
                   Jianhan Chen   Replica exchange with guided annealing
                                  for accelerated sampling of disordered
                                  protein conformations  . . . . . . . . . 1682--1689
             Zhong-Zhi Yang and   
            Jian-Jiang Wang and   
                  Dong-Xia Zhao   Valence state parameters of all
                                  transition metal atoms in
                                  metalloproteins --- development of
                                  ABEEM$ \sigma \pi $ fluctuating charge
                                  force field  . . . . . . . . . . . . . . 1690--1706
            Soran Jahangiri and   
                  Lemin Cai and   
            Gilles H. Peslherbe   Performance of density-functional
                                  tight-binding models in describing
                                  hydrogen-bonded anionic-water clusters   1707--1715
         Sebastian Höfener   Coupled-cluster frozen-density embedding
                                  using resolution of the identity methods 1716--1724
        Marcela Hrdá and   
      Tomá\vs Kulich and   
      Michal Repiský and   
                 Jozef Noga and   
            Olga L. Malkina and   
             Vladimir G. Malkin   Software News and Updates:
                                  Implementation of the
                                  diagonalization-free algorithm in the
                                  self-consistent field procedure within
                                  the four-component relativistic scheme   1725--1737

Journal of Computational Chemistry
Volume 35, Number 24, September 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 24 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 24 . . . . iii--iv
         Miros\law Jab\lo\'nski   Red and blue shifted hydridic bonds  . . 1739--1747
          Laura J. Kingsley and   
                 Markus A. Lill   Including ligand-induced protein
                                  flexibility into protein tunnel
                                  prediction . . . . . . . . . . . . . . . 1748--1756
                Sean M. Law and   
             Aaron T. Frank and   
          Charles L. Brooks III   PCASSO: a fast and efficient
                                  C$\alpha$-based method for accurately
                                  assigning protein secondary structure
                                  elements . . . . . . . . . . . . . . . . 1757--1761
          Athanassios C. Tsipis   DFT assessment of the spectroscopic
                                  constants and absorption spectra of
                                  neutral and charged diatomic species of
                                  group 11 and 14 elements . . . . . . . . 1762--1777
           Soroosh Pezeshki and   
                        Hai Lin   Molecular dynamics simulations of ion
                                  solvation by flexible-boundary QM/MM:
                                  On-the-fly partial charge transfer
                                  between QM and MM subsystems . . . . . . 1778--1788
               Marco Lorenz and   
       Bartolomeo Civalleri and   
            Lorenzo Maschio and   
                Mauro Sgroi and   
                Daniele Pullini   Benchmarking dispersion and geometrical
                                  counterpoise corrections for
                                  cost-effective large-scale DFT
                                  calculations of water adsorption on
                                  graphene . . . . . . . . . . . . . . . . 1789--1800
          Christoph Grebner and   
            Johannes Becker and   
               Daniel Weber and   
           Daniel Bellinger and   
           Maxim Tafipolski and   
    Charlotte Brückner and   
                   Bernd Engels   Software News and Updates: CAST: a new
                                  program package for the accurate
                                  characterization of large and flexible
                                  molecular systems  . . . . . . . . . . . 1801--1807

Journal of Computational Chemistry
Volume 35, Number 25, September 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 25 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 25 . . . . iii--iv
         Morten N. Pedersen and   
     Erik D. Hedegård and   
                 Jacob Kongsted   Basis set error estimation for DFT
                                  calculations of electronic g-tensors for
                                  transition metal complexes . . . . . . . 1809--1814
            Stefano Pelloni and   
Inmaculada García Cuesta   CCSD--CTOCD static dipole shielding
                                  polarizability for quantification of the
                                  chiral NMR effects in oxaziridine
                                  derivatives  . . . . . . . . . . . . . . 1815--1823
            David Ryan Koes and   
              Carlos J. Camacho   Shape-based virtual screening with
                                  volumetric aligned molecular shapes  . . 1824--1834
             Tatsuki Negami and   
            Kentaro Shimizu and   
                   Tohru Terada   Coarse-grained molecular dynamics
                                  simulations of protein--ligand binding   1835--1845
            Carlos T. Nieto and   
          David Díez and   
             Narciso M. Garrido   To be or not to be butterfly: New
                                  mechanistic insights in the Aza--Michael
                                  asymmetric addition of lithium
                                  (R)-N-benzyl-N-($ \alpha
                                  $-methylbenzyl)amide . . . . . . . . . . 1846--1853
             Pablo G. Garay and   
          Osvaldo A. Martin and   
         Harold A. Scheraga and   
                  Jorge A. Vila   Factors affecting the computation of the
                                  $^{13}$C shielding in disaccharides  . . 1854--1864
             Mirco Zerbetto and   
           Andrea Piserchia and   
                 Diego Frezzato   Looking for some free energy? Call
                                  JEFREE (\ldots)  . . . . . . . . . . . . 1865--1881

Journal of Computational Chemistry
Volume 35, Number 26, October 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 26 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 26 . . . . iii--iv
          Kiamars Eskandari and   
          Christian Van Alsenoy   Hydrogen--hydrogen interaction in planar
                                  biphenyl: a theoretical study based on
                                  the interacting quantum atoms and
                                  Hirshfeld atomic energy partitioning
                                  methods  . . . . . . . . . . . . . . . . 1883--1889
       Thong Nguyen-Minh Le and   
                    Bin Liu and   
                   Lam K. Huynh   SurfKin: an ab initio kinetic code for
                                  modeling surface reactions . . . . . . . 1890--1899
                 Jan Wenzel and   
             Michael Wormit and   
                  Andreas Dreuw   Calculating core-level excitations and
                                  X-ray absorption spectra of medium-sized
                                  closed-shell molecules with the
                                  algebraic--diagrammatic construction
                                  scheme for the polarization propagator   1900--1915
     Mohammad Reza Rezapour and   
   Arunkumar Chitteth Rajan and   
                   Kwang S. Kim   Molecular sensing using armchair
                                  graphene nanoribbon  . . . . . . . . . . 1916--1920
          Ivana Matanovi\'c and   
           Plamen Atanassov and   
               Boris Kiefer and   
         Fernando H. Garzon and   
                 Neil J. Henson   Applicability of density functional
                                  theory in reproducing accurate
                                  vibrational spectra of surface bound
                                  species  . . . . . . . . . . . . . . . . 1921--1929
José J. Baldoví and   
      Juan M. Clemente-Juan and   
           Eugenio Coronado and   
Alejandro Gaita-Ariño and   
                   Andrew Palii   Letters to the Editor: An updated
                                  version of the computational package
                                  SIMPRE that uses the standard
                                  conventions for Stevens crystal field
                                  parameters . . . . . . . . . . . . . . . 1930--1934
        Miros\law Karbowiak and   
              Czes\law Rudowicz   Letters to the Editor: Software package
                                  SIMPRE --- Revisited . . . . . . . . . . 1935--1941

Journal of Computational Chemistry
Volume 35, Number 27, October 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 27 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 27 . . . . iii--iv
         Alexander Hoffmann and   
            Richard Grunzke and   
            Sonja Herres-Pawlis   Insights into the influence of
                                  dispersion correction in the theoretical
                                  treatment of guanidine--quinoline
                                  copper(I) complexes  . . . . . . . . . . 1943--1950
        Chanin Nantasenamat and   
                 Saw Simeon and   
           Wiwat Owasirikul and   
            Napat Songtawee and   
               Maris Lapins and   
  Virapong Prachayasittikul and   
             Jarl E. S. Wikberg   Illuminating the origins of spectral
                                  properties of green fluorescent proteins
                                  via proteochemometric and molecular
                                  modeling . . . . . . . . . . . . . . . . 1951--1966
              Xiao-Jing Liu and   
                   Ian Hamilton   Adsorption of small molecules on helical
                                  gold nanorods: a relativistic density
                                  functional study . . . . . . . . . . . . 1967--1976
            Manoj K. Shukla and   
                   Frances Hill   Plane-wave density functional theory
                                  investigation of adsorption of
                                  2,4,6-trinitrotoluene on Al-hydroxylated
                                  (0001) surface of ($ 4 \times 4$) $
                                  \alpha $-alumina . . . . . . . . . . . . 1977--1985
                   Wei Chen and   
                   Jana K. Shen   Effects of system net charge and
                                  electrostatic truncation on all-atom
                                  constant pH molecular dynamics . . . . . 1986--1996
               Emilia L. Wu and   
                   Xi Cheng and   
                 Sunhwan Jo and   
                   Huan Rui and   
              Kevin C. Song and   
Eder M. Dávila-Contreras and   
                   Yifei Qi and   
                  Jumin Lee and   
       Viviana Monje-Galvan and   
         Richard M. Venable and   
          Jeffery B. Klauda and   
                      Wonpil Im   Software News and Updates: CHARMM--GUI
                                  Membrane Builder toward realistic
                                  biological membrane simulations  . . . . 1997--2004
      Alessandro Di Domizio and   
        Alessandro Vitriolo and   
             Giulio Vistoli and   
            Alessandro Pedretti   Software News and Updates: SPILLO--PBSS:
                                  Detecting hidden binding sites within
                                  protein $3$D-structures through a
                                  flexible structure-based approach  . . . 2005--2017

Journal of Computational Chemistry
Volume 35, Number 28, October 30, 2014

                      Anonymous   Cover Image, Volume 35, Issue 28 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 28 . . . . iii--iv
               Annia Galano and   
Juan Raúl Alvarez-Idaboy   Kinetics of radical-molecule reactions
                                  in aqueous solution: a benchmark study
                                  of the performance of density functional
                                  methods  . . . . . . . . . . . . . . . . 2019--2026
              Julia Setzler and   
              Carolin Seith and   
               Martin Brieg and   
                Wolfgang Wenzel   SLIM: an improved generalized Born
                                  implicit membrane model  . . . . . . . . 2027--2039
                James Lyons and   
          Abdollah Dehzangi and   
             Rhys Heffernan and   
                Alok Sharma and   
             Kuldip Paliwal and   
               Abdul Sattar and   
                 Yaoqi Zhou and   
                   Yuedong Yang   Predicting backbone C$ \alpha $ angles
                                  and dihedrals from protein sequences by
                                  stacked sparse auto-encoder deep neural
                                  network  . . . . . . . . . . . . . . . . 2040--2046
            Minhajul Arfeen and   
            Dhilon S. Patel and   
               Sheenu Abbat and   
               Nikhil Taxak and   
             Prasad V. Bharatam   Importance of cytochromes in cyclization
                                  reactions: Quantum chemical study on a
                                  model reaction of proguanil to
                                  cycloguanil  . . . . . . . . . . . . . . 2047--2055
      Taweetham Limpanuparb and   
             Josh Milthorpe and   
            Alistair P. Rendell   Resolutions of the Coulomb operator:
                                  VIII. Parallel implementation using the
                                  modern programming language X10  . . . . 2056--2069
        Martin P. Andersson and   
              Susan L. S. Stipp   Predicting hydration energies for
                                  multivalent ions . . . . . . . . . . . . 2070--2075
                Saleh Riahi and   
          Christopher N. Rowley   Software News and Updates: The
                                  CHARMM--TURBOMOLE interface for
                                  efficient and accurate QM/MM molecular
                                  dynamics, free energies, and excited
                                  state properties . . . . . . . . . . . . 2076--2086

Journal of Computational Chemistry
Volume 35, Number 29, November 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 29 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 29 . . . . iii--iv
         Laercio Pol-Fachin and   
                 Hugo Verli and   
                Roberto D. Lins   Extension and validation of the GROMOS
                                  53A6$_{glyc}$ parameter set for
                                  glycoproteins  . . . . . . . . . . . . . 2087--2095
                Nohad Gresh and   
            Krystel El Hage and   
              David Perahia and   
       Jean-Philip Piquemal and   
       Catherine Berthomieu and   
     Dorothée Berthomieu   Polarizable molecular mechanics studies
                                  of Cu(I)/Zn(II) superoxide dismutase:
                                  Bimetallic binding site and structured
                                  waters . . . . . . . . . . . . . . . . . 2096--2106
           Marta E. Alberto and   
             Gloria Mazzone and   
       Angelo D. Quartarolo and   
  Flavio Fortes Ramos Sousa and   
             Emilia Sicilia and   
                     Nino Russo   Electronic spectra and intersystem
                                  spin-orbit coupling in 1,2- and
                                  1,3-squaraines . . . . . . . . . . . . . 2107--2113
               Xavier Lucas and   
            Stefan Günther   Using chiral molecules as an approach to
                                  address low-druggability recognition
                                  sites  . . . . . . . . . . . . . . . . . 2114--2121
                Oliver Sala and   
      Hans Peter Lüthi and   
                  Antonio Togni   The solvent effect on two competing
                                  reaction mechanisms involving
                                  hypervalent iodine reagents ($
                                  \lambda^3$-iodanes): Facing the limit of
                                  the stationary quantum chemical approach 2122--2131
            Junya Yamagishi and   
            Noriaki Okimoto and   
           Gentaro Morimoto and   
                   Makoto Taiji   A new set of atomic radii for accurate
                                  estimation of solvation free energy by
                                  Poisson--Boltzmann solvent model . . . . 2132--2139
    Israel Fernández and   
           Lando P. Wolters and   
        F. Matthias Bickelhaupt   Controlling the oxidative addition of
                                  aryl halides to Au(I)  . . . . . . . . . 2140--2145
         Alexander Hoffmann and   
     Martin Rohrmüller and   
               Anton Jesser and   
     Ines dos Santos Vieira and   
          Wolf Gero Schmidt and   
            Sonja Herres-Pawlis   Geometrical and optical benchmarking of
                                  copper(II) guanidine--quinoline
                                  complexes: Insights from TD--DFT and
                                  many-body perturbation theory (part II)  2146--2161

Journal of Computational Chemistry
Volume 35, Number 30, November 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 30 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 30 . . . . iii--iv
             Ryoichi Fukuda and   
                 Masahiro Ehara   Efficiency of perturbation-selection and
                                  its orbital dependence in the SAC--CI
                                  calculations for valence excitations of
                                  medium-size molecules  . . . . . . . . . 2163--2176
               Huiying Zhao and   
               Yuedong Yang and   
          Mark von Itzstein and   
                     Yaoqi Zhou   Carbohydrate-binding protein
                                  identification by coupling structural
                                  similarity searching with binding
                                  affinity prediction  . . . . . . . . . . 2177--2183
          Olle Falklöf and   
                     Bo Durbeej   Distinguishing between keto--enol and
                                  acid--base forms of firefly oxyluciferin
                                  through calculation of excited-state
                                  equilibrium constants  . . . . . . . . . 2184--2194
            Shinichi Yamabe and   
              Guixiang Zeng and   
                   Wei Guan and   
              Shigeyoshi Sakaki   A DFT study on proton transfers in
                                  hydrolysis reactions of phosphate
                                  dianion and sulfate monoanion  . . . . . 2195--2204
               Yonaton Heit and   
            Gregory J. O. Beran   Exploiting space-group symmetry in
                                  fragment-based molecular crystal
                                  calculations . . . . . . . . . . . . . . 2205--2214
           Vincent A. Voelz and   
                 Guangfeng Zhou   Bayesian inference of conformational
                                  state populations from computational
                                  models and sparse experimental
                                  observables  . . . . . . . . . . . . . . 2215--2224
                  Dan Berco and   
                    Chin-Kun Hu   A spherical harmonic transform spectral
                                  analysis of a localized surface plasmon
                                  on a gold nano shell . . . . . . . . . . 2225--2230

Journal of Computational Chemistry
Volume 35, Number 31, December 5, 2014

                      Anonymous   Cover Image, Volume 35, Issue 31 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 31 . . . . iii--iv
                    Bing Fu and   
                    Li Chen and   
                Feifei Wang and   
                  Yiqun Xie and   
                       Xiang Ye   Melting of icosahedral nickel clusters
                                  under hydrostatic pressure . . . . . . . 2231--2238
        Jörg von Appen and   
        Richard Dronskowski and   
          Aurab Chakrabarty and   
             Tilmann Hickel and   
           Robert Spatschek and   
           Jörg Neugebauer   Impact of Mn on the solution enthalpy of
                                  hydrogen in austenitic Fe--Mn alloys: a
                                  first-principles study . . . . . . . . . 2239--2244
           Adrien B. Larsen and   
          Jeffrey R. Wagner and   
              Saugat Kandel and   
     Romelia Salomon-Ferrer and   
          Nagarajan Vaidehi and   
                Abhinandan Jain   GneimoSim: a modular internal
                                  coordinates molecular dynamics
                                  simulation package . . . . . . . . . . . 2245--2255
              Fabian Zeller and   
               Martin Zacharias   Efficient calculation of relative
                                  binding free energies by umbrella
                                  sampling perturbation  . . . . . . . . . 2256--2262
           Damien J. Carter and   
                 Andrew L. Rohl   van der Waals corrected density
                                  functional calculations of the
                                  adsorption of benzene on the Cu (111)
                                  surface  . . . . . . . . . . . . . . . . 2263--2271
Raymundo Hernández-Esparza and   
Sol-Milena Mejía-Chica and   
     Andy D. Zapata-Escobar and   
Alfredo Guevara-García and   
Apolinar Martínez-Melchor and   
Julio-M. Hernández-Pérez and   
           Rubicelia Vargas and   
                    Jorge Garza   Grid-based algorithm to search critical
                                  points, in the electron density,
                                  accelerated by graphics processing units 2272--2278

Journal of Computational Chemistry
Volume 35, Number 32, December 15, 2014

                      Anonymous   Cover Image, Volume 35, Issue 32 . . . . i--ii
                      Anonymous   Cover Image, Volume 35, Issue 32 . . . . iii--iv
            Charleen G. Don and   
                Sereina Riniker   Review: Scents and sense: In silico
                                  perspectives on olfactory receptors  . . 2279--2287
      Rafael Grande-Aztatzi and   
Paulina R. Martínez-Alanis and   
  José Luis Cabellos and   
              Edison Osorio and   
        Ana Martínez and   
                 Gabriel Merino   Structural evolution of small gold
                                  clusters doped by one and two boron
                                  atoms  . . . . . . . . . . . . . . . . . 2288--2296
         Aleksandra Karolak and   
            Arjan van der Vaart   Enhanced sampling simulations of DNA
                                  step parameters  . . . . . . . . . . . . 2297--2304
                Tod D. Romo and   
          Nicholas Leioatts and   
                Alan Grossfield   Lightweight object oriented structure
                                  analysis: Tools for building tools to
                                  analyze molecular dynamics simulations   2305--2318
              Maria M. Reif and   
              Chris Oostenbrink   Molecular dynamics simulation of
                                  configurational ensembles compatible
                                  with experimental FRET efficiency data
                                  through a restraint on instantaneous
                                  FRET efficiencies  . . . . . . . . . . . 2319--2332
               Natalja Vogt and   
              Jean Demaison and   
           Jürgen Vogt and   
           Heinz Dieter Rudolph   Why it is sometimes difficult to
                                  determine the accurate position of a
                                  hydrogen atom by the semiexperimental
                                  method: Structure of molecules
                                  containing the OH or the CH$_3$ group    2333--2342


Journal of Computational Chemistry
Volume 36, Number 1, January 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 1  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 1  . . . . iii--iv
          Lorenzo Rovigatti and   
                Petr \vSulc and   
    István Z. Reguly and   
                  Flavio Romano   A comparison between parallelization
                                  approaches in molecular dynamics
                                  simulations on GPUs  . . . . . . . . . . 1--8
               Chiara Ricca and   
    Armelle Ringuedé and   
              Michel Cassir and   
                Carlo Adamo and   
                 Frederic Labat   A comprehensive DFT investigation of
                                  bulk and low-index surfaces of ZrO$_2$
                                  polymorphs . . . . . . . . . . . . . . . 9--21
                    Qi Song and   
               Zhenyi Jiang and   
              Zhiyong Zhang and   
                 Yuqing Hou and   
                 Xiaodong Zhang   From orientation disordered to ordered
                                  --- an ab initio simulation on ammonia
                                  borane phase transition within van der
                                  Waals corrections  . . . . . . . . . . . 22--32
               Hyungjun Kim and   
              Joungwon Park and   
                   Yoon Sup Lee   Prediction of the reduction potential of
                                  tris(2,2$^\prime
                                  $-bipyridinyl)iron(III/II) derivatives   33--41
        Andrey A. Kirilchuk and   
     Aleksandr A. Yurchenko and   
       Aleksandr N. Kostyuk and   
          Alexander B. Rozhenko   1,2-migration in $N$-phosphano
                                  functionalized $N$-heterocyclic carbenes 42--48
               Chengfei Yan and   
                    Xiaoqin Zou   Predicting peptide binding sites on
                                  protein surfaces by clustering chemical
                                  interactions . . . . . . . . . . . . . . 49--61
          Iwona E. Weidlich and   
               Yuri Pevzner and   
         Benjamin T. Miller and   
           Igor V. Filippov and   
            H. Lee Woodcock and   
              Bernard R. Brooks   Software News and Updates: Development
                                  and implementation of (Q)SAR modeling
                                  within the CHARMMing web-user interface  62--67

Journal of Computational Chemistry
Volume 36, Number 2, January 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 2  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 2  . . . . iii--iv
                      Anonymous   Cover Image, Volume 36, Issue 2  . . . . v--vi
            Gegham Galstyan and   
             Ernst-Walter Knapp   Computing pK$_A$ values of hexa-aqua
                                  transition metal complexes . . . . . . . 69--78
              Robin M. Betz and   
                 Ross C. Walker   Paramfit: Automated optimization of
                                  force field parameters for molecular
                                  dynamics simulations . . . . . . . . . . 79--87
               Rebecca Sure and   
                Ralf Tonner and   
            Peter Schwerdtfeger   A systematic study of rare gas atoms
                                  encapsulated in small fullerenes using
                                  dispersion corrected density functional
                                  theory . . . . . . . . . . . . . . . . . 88--96
              Ryuhei Harada and   
          Tomotake Nakamura and   
                  Yu Takano and   
               Yasuteru Shigeta   Protein folding pathways extracted by
                                  OFLOOD: Outlier FLOODing method  . . . . 97--102
                    Peter Clote   Expected degree for RNA secondary
                                  structure networks . . . . . . . . . . . 103--117
           Shabbir Muhammad and   
                Ahmad Irfan and   
                 Mohd Shkir and   
          Aijaz R. Chaudhry and   
                 Abul Kalam and   
              Salem AlFaify and   
      Abdullah G. Al-Sehemi and   
            A. E. Al-Salami and   
                I. S. Yahia and   
              Hong-Liang Xu and   
                   Zhong-Min Su   How does hybrid bridging core
                                  modification enhance the nonlinear
                                  optical properties in donor-$ \pi
                                  $-acceptor configuration? A case study
                                  of dinitrophenol derivatives . . . . . . 118--128
            Ilya A. Kaliman and   
         Lyudmila V. Slipchenko   Software News and Updates: Hybrid
                                  MPI/OpenMP parallelization of the
                                  effective fragment potential method in
                                  the \tt libefp software library  . . . . 129--135
                      Anonymous   Erratum: Corrigendum: A spherical
                                  harmonic transform spectral analysis of
                                  a localized surface plasmon on a gold
                                  nano shell . . . . . . . . . . . . . . . 136--136

Journal of Computational Chemistry
Volume 36, Number 3, January 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 3  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 3  . . . . iii--iv
               Yanliang Ren and   
               Osama Melhem and   
                Yongjian Li and   
                     Bo Chi and   
                  Xinya Han and   
                    Hao Zhu and   
              Lingling Feng and   
                   Jian Wan and   
                         Xin Xu   Clarifying and illustrating the
                                  electronic energy transfer pathways in
                                  trimeric and hexameric aggregation state
                                  of cyanobacteria allophycocyanin within
                                  the framework of Förster theory . . . . . 137--145
          Timothy J. Fuhrer and   
               Angel M. Lambert   Isolated pentagon rule violating
                                  endohedral metallofullerenes explained
                                  using the Hückel rule: a statistical
                                  mechanical study of the C$_{84}$
                                  Isomeric Set . . . . . . . . . . . . . . 146--150
                 Jing Huang and   
                   Likai Du and   
                  Deping Hu and   
                  Zhenggang Lan   Theoretical analysis of excited states
                                  and energy transfer mechanism in
                                  conjugated dendrimers  . . . . . . . . . 151--163
          Takeshi Yoshikawa and   
                   Hiromi Nakai   Linear-scaling self-consistent field
                                  calculations based on divide-and-conquer
                                  method using resolution-of-identity
                                  approximation on graphical processing
                                  units  . . . . . . . . . . . . . . . . . 164--170
         Mariusz P. Mitoraj and   
          Goran V. Janji\'c and   
       Vesna B. Medakovi\'c and   
   Du\vsan \vZ. Veljkovi\'c and   
             Artur Michalak and   
       Sne\vzana D. Zari\'c and   
          Milo\vs K. Mil\vci\'c   Nature of the water/aromatic parallel
                                  alignment interactions . . . . . . . . . 171--180
         Nick M. Vandewiele and   
        Ruben Van de Vijver and   
          Kevin M. Van Geem and   
Marie-Françoise Reyniers and   
                   Guy B. Marin   Symmetry calculation for molecules and
                                  transition states  . . . . . . . . . . . 181--192
            Andrii Shyichuk and   
            Marcin Runowski and   
                 Stefan Lis and   
           Jakub Kaczkowski and   
              Andrzej Jezierski   Semiempirical and DFT computations of
                                  the influence of Tb(III) dopant on unit
                                  cell dimensions of cerium(III) fluoride  193--199

Journal of Computational Chemistry
Volume 36, Number 4, February 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 4  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 4  . . . . iii--iv
               Jonny Proppe and   
                Carmen Herrmann   Communication through molecular bridges:
                                  Different bridge orbital trends result
                                  in common property trends  . . . . . . . 201--209
            Krystel El Hage and   
       Jean-Philip Piquemal and   
              Zeina Hobaika and   
          Richard G. Maroun and   
                    Nohad Gresh   Could the ``Janus-like'' properties of
                                  the halobenzene CX bond (X = Cl, Br) be
                                  leveraged to enhance molecular
                                  recognition? . . . . . . . . . . . . . . 210--221
Emilio Martínez-Núñez   An automated method to find transition
                                  states using chemical dynamics
                                  simulations  . . . . . . . . . . . . . . 222--234
           Marcia O. Fenley and   
           Robert C. Harris and   
              Travis Mackoy and   
        Alexander H. Boschitsch   Features of CPB: A Poisson--Boltzmann
                                  solver that uses an adaptive cartesian
                                  grid . . . . . . . . . . . . . . . . . . 235--243
         Elaine Limé and   
                 Per-Ola Norrby   Improving the Q2MM method for transition
                                  state force field modeling . . . . . . . 244--250
         Robert J. Pantazes and   
       Matthew J. Grisewood and   
                    Tong Li and   
       Nathanael P. Gifford and   
              Costas D. Maranas   Software News and Updates: The Iterative
                                  Protein Redesign and Optimization (IPRO)
                                  suite of programs  . . . . . . . . . . . 251--263
          Pablo M. De Biase and   
            Suren Markosyan and   
                  Sergei Noskov   Software News and Updates: BROMOC suite:
                                  Monte Carlo/Brownian dynamics suite for
                                  studies of ion permeation and DNA
                                  transport in biological and artificial
                                  pores with effective potentials  . . . . 264--271
         Alexander Hoffmann and   
     Martin Rohrmüller and   
               Anton Jesser and   
     Ines dos Santos Vieira and   
          Wolf Gero Schmidt and   
            Sonja Herres-Pawlis   Errata: Corrigendum: Geometrical and
                                  optical benchmarking of copper(II)
                                  guanidine--quinoline complexes: Insights
                                  from TD-DFT and many-body perturbation
                                  theory (Part II) . . . . . . . . . . . . 272--272

Journal of Computational Chemistry
Volume 36, Number 5, February 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 5  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 5  . . . . iii--iv
                      Anonymous   Cover Image, Volume 36, Issue 5  . . . . v--vi
                Dmitry Zuev and   
         Eugene Vecharynski and   
                  Chao Yang and   
               Natalie Orms and   
                 Anna I. Krylov   New algorithms for iterative matrix-free
                                  eigensolvers in quantum chemistry  . . . 273--284
                Todor Dudev and   
              Mike Devereux and   
              Markus Meuwly and   
                 Carmay Lim and   
       Jean-Philip Piquemal and   
                    Nohad Gresh   Quantum-chemistry based calibration of
                                  the alkali metal cation series
                                  (Li$^+$Cs$^+$) for large-scale
                                  polarizable molecular mechanics/dynamics
                                  simulations  . . . . . . . . . . . . . . 285--302
           Yasuhiro Ikabata and   
           Yusuke Tsukamoto and   
             Yutaka Imamura and   
                   Hiromi Nakai   Local response dispersion method in
                                  periodic systems: Implementation and
                                  assessment . . . . . . . . . . . . . . . 303--311
              Igor Schapiro and   
 Daniel Roca-Sanjuán and   
               Roland Lindh and   
               Massimo Olivucci   A surface hopping algorithm for
                                  nonadiabatic minimum energy path
                                  calculations . . . . . . . . . . . . . . 312--320
             Daniele Licari and   
            Alberto Baiardi and   
       Ma\lgorzata Biczysko and   
               Franco Egidi and   
           Camille Latouche and   
                Vincenzo Barone   Software News and Updates:
                                  Implementation of a graphical user
                                  interface for the virtual multifrequency
                                  spectrometer: The VMS-Draw tool  . . . . 321--334
                   Susi Lehtola   Software News and Updates: Automatic
                                  algorithms for completeness-optimization
                                  of Gaussian basis sets . . . . . . . . . 335--347
            Vytautas Gapsys and   
       Servaas Michielssens and   
            Daniel Seeliger and   
               Bert L. de Groot   Software News and Updates: \tt pmx:
                                  Automated protein structure and topology
                                  generation for alchemical perturbations  348--354

Journal of Computational Chemistry
Volume 36, Number 6, March 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 6  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 6  . . . . iii--iv
                    Jing Xu and   
                   Yi-hong Ding   Pentaatomic planar tetracoordinate
                                  silicon with 14 valence electrons: a
                                  large-scale global search of
                                  SiX$_n$Y$_m^q$ ($ n + m = 4$; $ q = 0,
                                  \pm 1, - 2$; X, Y = main group elements
                                  from H to Br)  . . . . . . . . . . . . . 355--360
Víctor Duarte Alaniz and   
   Tomás Rocha-Rinza and   
                 Gabriel Cuevas   Assessment of hydrophobic interactions
                                  and their contributions through the
                                  analysis of the methane dimer  . . . . . 361--375
                 Siyan Chen and   
                  Shasha Yi and   
                 Wenmei Gao and   
              Chuncheng Zuo and   
                    Zhonghan Hu   Force field development for organic
                                  molecules: Modifying dihedral and $ 1 -
                                  n $ pair interaction parameters  . . . . 376--384
             \.Iskender Muz and   
                Osman Canko and   
               Murat Ati\cs and   
Erdem Kamil Yìldìrìm   Search for the global minimum structures
                                  of AlB$_3$H$_2$$_n$ ($ n = 0$--$6$)
                                  clusters . . . . . . . . . . . . . . . . 385--391
                Tibor Dubaj and   
    Zuzana Cibulková and   
                  Peter \vSimon   An incremental isoconversional method
                                  for kinetic analysis based on the
                                  orthogonal distance regression . . . . . 392--398
          Maira D'Alessando and   
              Andrea Amadei and   
               Mauro Stener and   
             Massimiliano Aschi   Essential dynamics for the study of
                                  microstructures in liquids . . . . . . . 399--407
                  Kelin Xia and   
                   Xin Feng and   
                Yiying Tong and   
                    Guo Wei Wei   Persistent homology for the quantitative
                                  prediction of fullerene stability  . . . 408--422

Journal of Computational Chemistry
Volume 36, Number 7, March 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 7  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 7  . . . . iii--iv
                      Anonymous   Obituary: Paul Schleyer 1930--2014 . . . 423--423
Gustavo Pierdominici-Sottile and   
                  Juliana Palma   New insights into the meaning and
                                  usefulness of principal component
                                  analysis of concatenated trajectories    424--432
           Hamed Akbarzadeh and   
          Amir Nasser Shamkhali   H$_2$ adsorption on Ag-nanocluster
                                  single-walled carbon nanotube
                                  composites: a molecular dynamics study
                                  on the effects of nanocluster size,
                                  diameter, and chirality of nanotube  . . 433--440
                   Fang Liu and   
                   Likai Du and   
                    Jun Gao and   
                  Lili Wang and   
                    Bo Song and   
                    Chengbu Liu   Application of polarizable ellipsoidal
                                  force field model to pnicogen bonds  . . 441--448
                 Wen-Xin Ji and   
                     Wei Xu and   
        W. H. Eugen Schwarz and   
                 Shu-Guang Wang   Ionic bonding of lanthanides, as
                                  influenced by $d$- and $f$-atomic
                                  orbitals, by core-shells and by
                                  relativity . . . . . . . . . . . . . . . 449--458
              Yusuke Ootani and   
          Yoshinobu Akinaga and   
              Takahito Nakajima   Theoretical investigation of
                                  enantioselectivity of cage-like
                                  supramolecular assembly: the insights
                                  into the shape complementarity and
                                  host--guest interaction  . . . . . . . . 459--466
                Sta\vs Bevc and   
         Christoph Junghans and   
               Matej Praprotnik   Software News and Updates: STOCK:
                                  Structure mapper and online
                                  coarse-graining kit for molecular
                                  simulations  . . . . . . . . . . . . . . 467--477
                Hiram Ponce and   
                Pedro Ponce and   
                  Arturo Molina   Software News and Updates: The
                                  development of an artificial organic
                                  networks toolkit for LabVIEW . . . . . . 478--492

Journal of Computational Chemistry
Volume 36, Number 8, March 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 8  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 8  . . . . iii--iv
            Abraham Yosipof and   
             Hanoch Senderowitz   $k$-Nearest neighbors optimization-based
                                  outlier removal  . . . . . . . . . . . . 493--506
              Pin-Kuang Lai and   
                 Shiang-Tai Lin   Internal coordinate density of state
                                  from molecular dynamics simulation . . . 507--517
                   Kun Yuan and   
           Jing-Shuang Dang and   
                 Yi-Jun Guo and   
                     Xiang Zhao   Theoretical prediction of the
                                  host--guest interactions between novel
                                  photoresponsive nanorings and C$_{60}$:
                                  a strategy for facile encapsulation and
                                  release of fullerene . . . . . . . . . . 518--528
             Bhaskar Sharma and   
    Hemant Kumar Srivastava and   
        Gaddamanugu Gayatri and   
     Garikapati Narahari Sastry   Energy decomposition analysis of
                                  cation--$ \pi $, metal ion--lone pair,
                                  hydrogen bonded, charge-assisted
                                  hydrogen bonded, and $ \pi $--$ \pi $
                                  interactions . . . . . . . . . . . . . . 529--538
            Siladitya Padhi and   
   Siddabattula Ramakrishna and   
             U. Deva Priyakumar   Prediction of the structures of helical
                                  membrane proteins based on a minimum
                                  unfavorable contacts approach  . . . . . 539--552
            Martin T. Stiebritz   MetREx: a protein design approach for
                                  the exploration of sequence-reactivity
                                  relationships in metalloenzymes  . . . . 553--563
          Elixabete Rezabal and   
                  Gilles Frison   Estimating $ \pi $ binding energy of
                                  $N$-heterocyclic carbenes: the role of
                                  polarization . . . . . . . . . . . . . . 564--572
          Andrew J. Schultz and   
                 David A. Kofke   Software News and Updates: Etomica: an
                                  object-oriented framework for molecular
                                  simulation . . . . . . . . . . . . . . . 573--583

Journal of Computational Chemistry
Volume 36, Number 9, April 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 9  . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 9  . . . . iii--iv
          Federico Fogolari and   
         Alessandra Corazza and   
               Gennaro Esposito   Accuracy assessment of the linear
                                  Poisson--Boltzmann equation and
                                  reparametrization of the OBC generalized
                                  Born model for nucleic acids and nucleic
                                  acid--protein complexes  . . . . . . . . 585--596
               Caleb Carlin and   
                 Mark S. Gordon   Ab initio calculation of anion proton
                                  affinity and ionization potential for
                                  energetic ionic liquids  . . . . . . . . 597--600
              Paul M. Zimmerman   Single-ended transition state finding
                                  with the growing string method . . . . . 601--611
            Topi Karilainen and   
             Oana Cramariuc and   
              Mikael Kuisma and   
              Kirsi Tappura and   
                Terttu I. Hukka   van der Waals interactions are critical
                                  in Car--Parrinello molecular dynamics
                                  simulations of porphyrin--fullerene
                                  dyads  . . . . . . . . . . . . . . . . . 612--621
                Amir Karton and   
                   Lars Goerigk   Accurate reaction barrier heights of
                                  pericyclic reactions: Surprisingly large
                                  deviations for the CBS-QB3 composite
                                  method and their consequences in DFT
                                  benchmark studies  . . . . . . . . . . . 622--632
                Letif Mones and   
               Andrew Jones and   
       Andreas W. Götz and   
              Teodoro Laino and   
             Ross C. Walker and   
             Ben Leimkuhler and   
 Gábor Csányi and   
                 Noam Bernstein   The adaptive buffered force QM/MM method
                                  in the CP2K and AMBER software packages  633--648
           Vincent Tognetti and   
          Christophe Morell and   
                Laurent Joubert   Quantifying electro/nucleophilicity by
                                  partitioning the dual descriptor . . . . 649--659
                Simone Morpurgo   A DFT study on Cu(I) coordination in
                                  Cu-ZSM-5: Effects of the functional
                                  choice and tuning of the ONIOM approach  660--669
                 Avijit Sen and   
                Sangita Sen and   
     Pradipta Kumar Samanta and   
             Debashis Mukherjee   Unitary group adapted state specific
                                  multireference perturbation theory:
                                  Formulation and pilot applications . . . 670--688
       Alexander A. Kantardjiev   Software News and Updates:
                                  irGPU.proton.Net: Irregular strong
                                  charge interaction networks of
                                  protonatable groups in protein molecules
                                  --- a GPU solver using the fast
                                  multipole method and statistical
                                  thermodynamics . . . . . . . . . . . . . 689--693

Journal of Computational Chemistry
Volume 36, Number 10, April 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 10 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 10 . . . . iii--iv
                      Anonymous   Cover Image, Volume 36, Issue 10 . . . . v--vi
              Jin-Dou Huang and   
               Wen-Liang Li and   
                Shu-Hao Wen and   
                       Bin Dong   Electronic structure and microscopic
                                  charge-transport properties of a
                                  new-type diketopyrrolopyrrole-based
                                  material . . . . . . . . . . . . . . . . 695--706
          Paolo Della Porta and   
            Riccardo Zanasi and   
               Guglielmo Monaco   Hydrogen--hydrogen bonding: the current
                                  density perspective  . . . . . . . . . . 707--716
                  Xiao Wang and   
                  Juan Yang and   
                 Ruoming Li and   
                 Hong Jiang and   
                         Yan Li   Deformation of single-walled carbon
                                  nanotubes by interaction with graphene:
                                  a first-principles study . . . . . . . . 717--722
   Petr \vSt\vepánek and   
                    Petr Bou\vr   Origin-independent sum over states
                                  simulations of magnetic and electronic
                                  circular dichroism spectra via the
                                  localized orbital/local origin method    723--730
                Haiyan Yuan and   
               Yiying Zheng and   
                      Bo Li and   
                Wenliang Li and   
                 Jingping Zhang   The multieffects of DMF and DBU on the $
                                  [5 + 1] $ benzannulation of nitroethane
                                  and $ \alpha $-alkenoyl
                                  ketene-(S,S)-acetals: Hydrogen bonding
                                  and electrostatic interactions . . . . . 731--738
            Hanne S. Antila and   
                  Emppu Salonen   On combining Thole's induced point
                                  dipole model with fixed charge
                                  distributions in molecular mechanics
                                  force fields . . . . . . . . . . . . . . 739--750
             Andrzej Eilmes and   
                 Piotr Kubisiak   Stability of ion triplets in ionic
                                  liquid/lithium salt solutions: Insights
                                  from implicit and explicit solvent
                                  models and molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 751--762
              Ryuhei Harada and   
                  Yu Takano and   
               Yasuteru Shigeta   Enhanced conformational sampling method
                                  for proteins based on the TaBoo SeArch
                                  algorithm: Application to the folding of
                                  a mini-protein, chignolin  . . . . . . . 763--772
          Adelene Y. L. Sim and   
                  Chandra Verma   How does a hydrocarbon staple affect
                                  peptide hydrophobicity?  . . . . . . . . 773--784

Journal of Computational Chemistry
Volume 36, Number 11, April 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 11 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 11 . . . . iii--iv
                      Anonymous   Cover Image, Volume 36, Issue 11 . . . . v--vi
                Oliver Sala and   
      Hans Peter Lüthi and   
              Antonio Togni and   
          Marcella Iannuzzi and   
               Jürg Hutter   Dividing a complex reaction involving a
                                  hypervalent iodine reagent into three
                                  limiting mechanisms by ab initio
                                  molecular dynamics . . . . . . . . . . . 785--794
         Nishamol Kuriakose and   
                    Kumar Vanka   Can substituted allenes be highly
                                  efficient leaving groups in catalytic
                                  processes? A computational investigation 795--804
            Nguyen Minh Tam and   
             Tran Dieu Hang and   
              Hung Tan Pham and   
           Huyen Thi Nguyen and   
          My Phuong Pham-Ho and   
             Pablo A. Denis and   
                Minh Tho Nguyen   Bonding and singlet--triplet gap of
                                  silicon trimer: Effects of protonation
                                  and attachment of alkali metal cations   805--815
             Keisuke Nemoto and   
                 Minori Abe and   
                Junji Seino and   
                  Masahiko Hada   An ab initio study of nuclear volume
                                  effects for isotope fractionations using
                                  two-component relativistic methods . . . 816--820
         Wiktor Zierkiewicz and   
        Dariusz C. Bie\'nko and   
           Danuta Michalska and   
Thér\`ese Zeegers-Huyskens   Theoretical investigation of the halogen
                                  bonded complexes between carbonyl bases
                                  and molecular chlorine . . . . . . . . . 821--832
     Marcos Menéndez and   
Roberto Álvarez Boto and   
           Evelio Francisco and   
Ángel Martín Pendás   One-electron images in real space:
                                  Natural adaptive orbitals  . . . . . . . 833--843
              Wen-Yang Zhao and   
                     Jie Yu and   
                 Si-Jia Ren and   
               Xi-Guang Wei and   
              Fang-Zhou Qiu and   
                Peng-Hui Li and   
                      He Li and   
               Yi-Peng Zhou and   
             Chang-Zhen Yin and   
                 An-Pu Chen and   
                     Hao Li and   
                  Lei Zhang and   
                    Jun Zhu and   
                     Yi Ren and   
                  Kai-Chung Lau   Probing the reactivity of microhydrated
                                  $ \alpha $-nucleophile in the anionic
                                  gas-phase S$_N$ 2 reaction . . . . . . . 844--852
            Nils Middendorf and   
           Katharina Krause and   
         Sebastian Höfener   Solvatochromic shifts of Br$_2$ and
                                  I$_2$ in water cages of type $ 5^{12}$,
                                  $ 5^{12}$ $ 6^2$, $ 5^{12}$ $ 6^3$, and
                                  $ 5^{12}$ $ 6^4$ . . . . . . . . . . . . 853--860
               Alex Domingo and   
           Celestino Angeli and   
              Coen de Graaf and   
                 Vincent Robert   Electronic reorganization triggered by
                                  electron transfer: the intervalence
                                  charge transfer of a Fe$^{3+}$
                                  /Fe$^{2+}$ bimetallic complex  . . . . . 861--869

Journal of Computational Chemistry
Volume 36, Number 12, May 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 12 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 12 . . . . iii--iv
                   Bun Chan and   
              Jong-Won Song and   
            Yukio Kawashima and   
                 Kimihiko Hirao   Toward the complete range separation of
                                  non-hybrid exchange--correlation
                                  functional . . . . . . . . . . . . . . . 871--877
       Polina V. Banushkina and   
               Sergei V. Krivov   Fep1d: a script for the analysis of
                                  reaction coordinates . . . . . . . . . . 878--882
                     Jan Dillen   The topology of the Ehrenfest force
                                  density revisited. A different
                                  perspective based on Slater-type
                                  orbitals . . . . . . . . . . . . . . . . 883--890
                   Xu Zhang and   
                Xiaodi Yang and   
                   Hua Geng and   
               Guangjun Nan and   
                Xingwen Sun and   
                 Jinyang Xi and   
                         Xin Xu   Theoretical comparative studies on
                                  transport properties of pentacene,
                                  pentathienoacene, and
                                  6,13-dichloropentacene . . . . . . . . . 891--900
              Yury D. Fomin and   
             Elena N. Tsiok and   
             Valentin N. Ryzhov   The behavior of benzene confined in a
                                  single wall carbon nanotube  . . . . . . 901--906
        Sudip Chattopadhyay and   
         Rajat K. Chaudhuri and   
          Uttam Sinha Mahapatra   State-specific multireference
                                  perturbation theory with improved
                                  virtual orbitals: Taming the ground
                                  state of F$_2$, Be$_2$, and N$_2$  . . . 907--925
          Russell Thackston and   
            Ryan C. Fortenberry   The performance of low-cost commercial
                                  cloud computing as an alternative in
                                  computational chemistry  . . . . . . . . 926--933
            Matthew Welborn and   
                Jiahao Chen and   
              Lee-Ping Wang and   
               Troy Van Voorhis   Why many semiempirical molecular orbital
                                  theories fail for liquid water and how
                                  to fix them  . . . . . . . . . . . . . . 934--939
              Adam K. Sieradzan   Software News and Updates: Introduction
                                  of periodic boundary conditions into
                                  UNRES force field  . . . . . . . . . . . 940--946

Journal of Computational Chemistry
Volume 36, Number 13, May 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 13 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 13 . . . . iii--iv
           Anna Stachiewicz and   
                 Andrzej Molski   A coarse-grained MARTINI-like force
                                  field for DNA unzipping in nanopores . . 947--956
        Robert A. Evarestov and   
                Andrej I. Panin   Symmetry classification of electron and
                                  phonon states in TiO$_2$ -based
                                  nanowires and nanotubes  . . . . . . . . 957--969
           Maria T. Panteva and   
         George M. Giambasu and   
                 Darrin M. York   Comparison of structural, thermodynamic,
                                  kinetic and mass transport properties of
                                  Mg$^{2+}$ ion models commonly used in
                                  biomolecular simulations . . . . . . . . 970--982
            Antonio Cardone and   
            Aaron Bornstein and   
             Harish C. Pant and   
                 Mary Brady and   
                 Ram Sriram and   
               Sergio A. Hassan   Detection and characterization of
                                  nonspecific, sparsely populated binding
                                  modes in the early stages of
                                  complexation . . . . . . . . . . . . . . 983--995
              Elmar Krieger and   
                    Gert Vriend   New ways to boost molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 996--1007
                    Yi Wang and   
            William Yi Wang and   
             Long-Qing Chen and   
                     Zi-Kui Liu   Bonding charge density from atomic
                                  perturbations  . . . . . . . . . . . . . 1008--1014
          Louis Vanduyfhuys and   
        Steven Vandenbrande and   
           Toon Verstraelen and   
              Rochus Schmid and   
           Michel Waroquier and   
       Veronique Van Speybroeck   Software News and Updates: QuickFF: a
                                  program for a quick and easy derivation
                                  of force fields for metal-organic
                                  frameworks from ab initio input  . . . . 1015--1027

Journal of Computational Chemistry
Volume 36, Number 14, May 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 14 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 14 . . . . iii--iv
      Liudmyla K. Sviatenko and   
            Olexandr Isayev and   
                Leonid Gorb and   
            Frances C. Hill and   
         Danuta Leszczynska and   
              Jerzy Leszczynski   Are the reduction and oxidation
                                  properties of nitrocompounds dissolved
                                  in water different from those produced
                                  when adsorbed on a silica surface? A DFT
                                  M05-2X computational study . . . . . . . 1029--1035
                 Hongzhi Li and   
                Ziyan Zhong and   
                     Lin Li and   
                    Rui Gao and   
                Jingxia Cui and   
                   Ting Gao and   
                 Li Hong Hu and   
                 Yinghua Lu and   
               Zhong-Min Su and   
                         Hui Li   A cascaded QSAR model for efficient
                                  prediction of overall power conversion
                                  efficiency of all-organic dye-sensitized
                                  solar cells  . . . . . . . . . . . . . . 1036--1046
              Shenggao Zhou and   
              Li-Tien Cheng and   
                    Hui Sun and   
                Jianwei Che and   
          Joachim Dzubiella and   
                      Bo Li and   
             J. Andrew McCammon   LS--VISM: a software package for
                                  analysis of biomolecular solvation . . . 1047--1059
             Tirtharaj Dash and   
                Prabhat K. Sahu   Gradient gravitational search: an
                                  efficient metaheuristic algorithm for
                                  global optimization  . . . . . . . . . . 1060--1068
             Milan Randi\'c and   
                 Tomaz Pisanski   Protein alignment: Exact versus
                                  approximate. An illustration . . . . . . 1069--1074
              Masaki Okoshi and   
               Teruo Atsumi and   
                   Hiromi Nakai   Revisiting the extrapolation of
                                  correlation energies to complete basis
                                  set limit  . . . . . . . . . . . . . . . 1075--1082
       Kenno Vanommeslaeghe and   
               Mingjun Yang and   
     Alexander D. MacKerell Jr.   Robustness in the fitting of molecular
                                  mechanics parameters . . . . . . . . . . 1083--1101

Journal of Computational Chemistry
Volume 36, Number 15, June 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 15 . . . . i--ii
                 Hujun Shen and   
                     Yan Li and   
                  Peijun Xu and   
                Xiaofang Li and   
                Huiying Chu and   
              Dinglin Zhang and   
                      Guohui Li   An anisotropic coarse-grained model
                                  based on Gay--Berne and electric
                                  multipole potentials and its application
                                  to simulate a DMPC bilayer in an
                                  implicit solvent model . . . . . . . . . 1103--1113
          Claudia Loerbroks and   
         Andreas Heimermann and   
                   Walter Thiel   Solvents effects on the mechanism of
                                  cellulose hydrolysis: A QM/MM study  . . 1114--1123
           Robert Zale\'sny and   
              Guangjun Tian and   
       Christof Hättig and   
        Wojciech Bartkowiak and   
               Hans Ågren   Toward assessment of density functionals
                                  for vibronic coupling in two-photon
                                  absorption: a case study of
                                  $4$-nitroaniline . . . . . . . . . . . . 1124--1131
           William J. Allen and   
            Trent E. Balius and   
          Sudipto Mukherjee and   
           Scott R. Brozell and   
       Demetri T. Moustakas and   
            P. Therese Lang and   
              David A. Case and   
             Irwin D. Kuntz and   
                Robert C. Rizzo   DOCK 6: Impact of new features and
                                  current docking performance  . . . . . . 1132--1156
           Adam B. Birkholz and   
           H. Bernhard Schlegel   Using bonding to guide transition state
                                  optimization . . . . . . . . . . . . . . 1157--1166
           Benoit de Courcy and   
              Etienne Derat and   
           Jean-Philip Piquemal   Bridging organometallics and quantum
                                  chemical topology: Understanding
                                  electronic relocalisation during
                                  palladium-catalyzed reductive
                                  elimination  . . . . . . . . . . . . . . 1167--1175
         Sadanandam Namsani and   
            Nisanth N. Nair and   
                Jayant K. Singh   Interaction potential models for bulk
                                  Zns, Zns nanoparticle, and Zns
                                  nanoparticle-PMMA from first principles  1176--1186

Journal of Computational Chemistry
Volume 36, Number 16, June 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 16 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 16 . . . . iii--iv
               David Z. Gao and   
    Filippo Federici Canova and   
         Matthew B. Watkins and   
           Alexander L. Shluger   Efficient parametrization of complex
                                  molecule--surface force fields . . . . . 1187--1195
               Shu-Ching Ou and   
                     Di Cui and   
           Matthew Wezowicz and   
             Michela Taufer and   
                  Sandeep Patel   Free energetics of carbon nanotube
                                  association in aqueous inorganic NaI
                                  salt solutions: Temperature effects
                                  using all-atom molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1196--1212
Frédéric Cazals and   
                Tom Dreyfus and   
            Dorian Mazauric and   
      Christine-Andrea Roth and   
              Charles H. Robert   Conformational ensembles and sampled
                                  energy landscapes: Analysis and
                                  comparison . . . . . . . . . . . . . . . 1213--1231
                    Xun Zhu and   
                    Yuriko Aoki   Development of minimized mixing
                                  molecular orbital method for designing
                                  organic ferromagnets . . . . . . . . . . 1232--1239
               Hiroo Nozaki and   
                 Yuji Ikeda and   
          Kazuhide Ichikawa and   
              Akitomo Tachibana   Electronic stress tensor analysis of
                                  molecules in gas phase of CVD process
                                  for GeSbTe alloy . . . . . . . . . . . . 1240--1251
               Ayman Farhat and   
              Saleh N. Abdul-Al   Ab initio calculations of the ground and
                                  excited states of the ZrN molecule
                                  including spin-orbit effects . . . . . . 1252--1258
         Re\vs\vci\vc Jurij and   
                      Linse Per   Software News and Updates: MOLSIM: a
                                  modular molecular simulation software    1259--1274

Journal of Computational Chemistry
Volume 36, Number 17, June 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 17 . . . . i--ii
            Justin A. Drake and   
          B. Montgomery Pettitt   Force field-dependent solution
                                  properties of glycine oligomers  . . . . 1275--1285
                    Jacek Koput   Ab initio ground-state potential energy
                                  function and vibration-rotation energy
                                  levels of imidogen, NH . . . . . . . . . 1286--1294
                Haiyan Yuan and   
                 Jingping Zhang   [DBU-H]$^+$ and H$_2$O as effective
                                  catalyst form for
                                  2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-ones: a DFT study  1295--1303
                Thomas Long and   
           Owen M. McDougal and   
                   Tim Andersen   GAMPMS: Genetic algorithm managed
                                  peptide mutant screening . . . . . . . . 1304--1310
       Oliwia M. Szklarczyk and   
            Eirini Arvaniti and   
       Wilfred F. van Gunsteren   Polarizable coarse-grained models for
                                  molecular dynamics simulation of liquid
                                  cyclohexane  . . . . . . . . . . . . . . 1311--1321
             Sandro Marmitt and   
   Paulo F. B. Gonçalves   A DFT study on the insertion of CO$_2$
                                  into styrene oxide catalyzed by
                                  $1$-butyl-$3$-methyl-Imidazolium bromide
                                  ionic liquid . . . . . . . . . . . . . . 1322--1333
      Athanassios C. Tsipis and   
         Alexandros V. Stalikas   Electronic, bonding, and optical
                                  properties of $1$ d [CuCN]$_n$ ($ n =
                                  1$--$ 10$) chains, $ 24 $ d [Cu CN]$_n$
                                  ($ n = 2$ -- $ 10$) nanorings, and $3$ d
                                  [Cu$_n$ (CN)$_n$]$_m$  ($ n = 4$, $ m =
                                  2, 3$; $ n = 10$, $ m = 2$) tubes
                                  studied by DFT /TD--DFT methods  . . . . 1334--1347

Journal of Computational Chemistry
Volume 36, Number 18, July 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 18 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 18 . . . . iii--iv
                     Wei Li and   
                 Yanli Zeng and   
                 Xiaoyan Li and   
                  Zheng Sun and   
                  Lingpeng Meng   The competition of Y $ \cdot $ O and X $
                                  \cdot $ N halogen bonds to enhance the
                                  group V $ \sigma $-hole interaction in
                                  the NCY $ \cdot $ o PH$_3$ $ \cdot $ NCX
                                  and O PH$_3$ $ \cdot $ NCX $ \cdot $ NCY
                                  (X, Y F, Cl, and Br) complexes . . . . . 1349--1358
              Tomonari Sumi and   
            Ayori Mitsutake and   
                Yutaka Maruyama   A solvation-free-energy functional: a
                                  reference-modified density functional
                                  formulation  . . . . . . . . . . . . . . 1359--1369
                 Ming Huang and   
           Timothy J. Giese and   
                 Darrin M. York   Nucleic acid reactivity: Challenges for
                                  next-generation semiempirical quantum
                                  models . . . . . . . . . . . . . . . . . 1370--1389
      Alexander K. H. Weiss and   
           Christian Ochsenfeld   A rigorous and optimized strategy for
                                  the evaluation of the Boys function
                                  kernel in molecular electronic structure
                                  theory . . . . . . . . . . . . . . . . . 1390--1398
          Kyle D. Fernandes and   
          C. Alicia Renison and   
                Kevin J. Naidoo   Quantum supercharger library:
                                  Hyper-parallelism of the Hartree--Fock
                                  method . . . . . . . . . . . . . . . . . 1399--1409
          C. Alicia Renison and   
          Kyle D. Fernandes and   
                Kevin J. Naidoo   Quantum supercharger library:
                                  Hyper-parallel integral derivatives
                                  algorithms for ab initio QM\slash MM
                                  dynamics . . . . . . . . . . . . . . . . 1410--1419
        Carsten Müller and   
         Daniel Spångberg   Calculation of the stability of
                                  nonperiodic solids using classical force
                                  fields and the method of increments:
                                  N$_2$O as an example . . . . . . . . . . 1420--1427

Journal of Computational Chemistry
Volume 36, Number 19, July 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 19 . . . . i--ii
             Maike Bergeler and   
            Carmen Herrmann and   
                  Markus Reiher   Mode-tracking based stationary-point
                                  optimization . . . . . . . . . . . . . . 1429--1438
       Raffaella Demichelis and   
                Marco Bruno and   
       Francesco R. Massaro and   
             Mauro Prencipe and   
         Marco De La Pierre and   
               Fabrizio Nestola   First-principle modelling of forsterite
                                  surface properties: Accuracy of methods
                                  and basis sets . . . . . . . . . . . . . 1439--1445
         Raimondas Galvelis and   
                    Yuji Sugita   Replica state exchange metadynamics for
                                  improving the convergence of free energy
                                  estimates  . . . . . . . . . . . . . . . 1446--1455
  Alonso Ramirez-Manzanares and   
        Joaquin Peña and   
             Jon M. Azpiroz and   
                 Gabriel Merino   A hierarchical algorithm for molecular
                                  similarity (H-FORMS) . . . . . . . . . . 1456--1466
           Kim Julia Hintze and   
           Arne Lützen and   
                  Thomas Bredow   Structure and stability of
                                  supramolecular crown ether complexes . . 1467--1472
           Justin A. Lemkul and   
             Beno\^\it Roux and   
        David van der Spoel and   
     Alexander D. MacKerell Jr.   Software News and Updates:
                                  Implementation of extended Lagrangian
                                  dynamics in GROMACS for polarizable
                                  simulations using the classical Drude
                                  oscillator model . . . . . . . . . . . . 1473--1479
           Semen O. Yesylevskyy   Software News and Updates: Pteros 2.0:
                                  Evolution of the fast parallel molecular
                                  analysis library for C++ and Python  . . 1480--1488

Journal of Computational Chemistry
Volume 36, Number 20, July 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 20 . . . . i--ii
               Junichi Higo and   
           Bhaskar Dasgupta and   
            Tadaaki Mashimo and   
              Kota Kasahara and   
        Yoshifumi Fukunishi and   
                Haruki Nakamura   Virtual-system-coupled adaptive umbrella
                                  sampling to compute free-energy
                                  landscape for flexible molecular docking 1489--1501
                  Kelin Xia and   
                    Guo-Wei Wei   Multidimensional persistence in
                                  biomolecular data  . . . . . . . . . . . 1502--1520
        Luká\vs Grajciar   Low-memory iterative density fitting . . 1521--1535
              Yinglong Miao and   
              Ferran Feixas and   
               Changsun Eun and   
             J. Andrew McCammon   Accelerated molecular dynamics
                                  simulations of protein folding . . . . . 1536--1549
               Mark Dittner and   
         Julian Müller and   
        Hasan Metin Aktulga and   
                   Bernd Hartke   Efficient global optimization of
                                  reactive force-field parameters  . . . . 1550--1561
            Sudhir K. Sahoo and   
                Nisanth N. Nair   A potential with low point charges for
                                  pure siliceous zeolites  . . . . . . . . 1562--1567
                   Bing Xia and   
              Artem Mamonov and   
               Seppe Leysen and   
             Karen N. Allen and   
         Sergei V. Strelkov and   
    Ioannis Ch. Paschalidis and   
               Sandor Vajda and   
                   Dima Kozakov   Software News and Updates: Accounting
                                  for observed small angle X-ray
                                  scattering profile in the
                                  protein--protein docking server cluspro  1568--1572

Journal of Computational Chemistry
Volume 36, Number 21, August 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 21 . . . . i--ii
Joseelyne G. Hernández-Lima and   
    Jose E. Barquera-Lozada and   
             Gabriel Cuevas and   
Fernando Cortés-Guzmán   The role of induced current density in
                                  steroelectronic effects: Perlin effect   1573--1578
         Sandra C. C. Nunes and   
           Marie Skepö and   
          Alberto A. C. C. Pais   Confined polyelectrolytes: the
                                  complexity of a simple system  . . . . . 1579--1586
         Benjamin D. Jensen and   
         Kristopher E. Wise and   
             Gregory M. Odegard   The effect of time step, thermostat, and
                                  strain rate on ReaxFF simulations of
                                  mechanical failure in diamond, graphene,
                                  and carbon nanotube  . . . . . . . . . . 1587--1596
               Jakub Gunera and   
                     Peter Kolb   Fragment-based similarity searching with
                                  infinite color space . . . . . . . . . . 1597--1608
              Felix Plasser and   
         Benjamin Thomitzni and   
   Stefanie A. Bäppler and   
                 Jan Wenzel and   
               Dirk R. Rehn and   
             Michael Wormit and   
                  Andreas Dreuw   Statistical analysis of electronic
                                  excitation processes: Spatial location,
                                  compactness, charge transfer, and
                                  electron-hole correlation  . . . . . . . 1609--1620
       Tatiana Vasilevskaya and   
          Maria G. Khrenova and   
      Alexander V. Nemukhin and   
                   Walter Thiel   Mechanism of proteolysis in matrix
                                  metalloproteinase-2 revealed by QM/MM
                                  modeling . . . . . . . . . . . . . . . . 1621--1630
           Michael Martinez and   
              Neil J. Bruce and   
           Julia Romanowska and   
              Daria B. Kokh and   
              Musa Ozboyaci and   
                Xiaofeng Yu and   
Mehmet Ali Öztürk and   
             Stefan Richter and   
                Rebecca C. Wade   Software News and Updates: SDA 7: a
                                  modular and parallel implementation of
                                  the simulation of diffusional
                                  association software . . . . . . . . . . 1631--1645

Journal of Computational Chemistry
Volume 36, Number 22, August 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 22 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 22 . . . . iii--iv
               Taro Udagawa and   
             Masanori Tachikawa   H/D isotope effect on charge-inverted
                                  hydrogen-bonded systems: Systematic
                                  classification of three different types
                                  in H$_3$ XH$^\ldots $ YH$_3$ (X = C, Si,
                                  or Ge, and Y = B, Al, or Ga) with
                                  multicomponent calculation . . . . . . . 1647--1654
              Yuichi Tanaka and   
              Norio Yoshida and   
                Haruyuki Nakano   Three-dimensional reference interaction
                                  site model self-consistent field
                                  analysis of solvent and substituent
                                  effects on the absorption spectra of
                                  Brooker's merocyanine  . . . . . . . . . 1655--1663
                     Qiming Sun   Libcint: an efficient general integral
                                  library for Gaussian basis functions . . 1664--1671
     Martin Rohrmüller and   
         Alexander Hoffmann and   
      Christian Thierfelder and   
        Sonja Herres-Pawlis and   
              Wolf Gero Schmidt   The Cu$_2$ O$_2$ torture track for a
                                  real-life system: [Cu$_2$
                                  (btmgp)$_2$O$_2$]$^{2+}$ oxo and peroxo
                                  species in density functional
                                  calculations . . . . . . . . . . . . . . 1672--1685
             Noah S. Bieler and   
   Philippe H. Hünenberger   Orthogonal sampling in free-energy
                                  calculations of residue mutations in a
                                  tripeptide: TI versus $\lambda$-LEUS . . 1686--1697
            Michael Stenrup and   
               Roland Lindh and   
    Ignacio Fdez. Galván   Constrained numerical gradients and
                                  composite gradients: Practical tools for
                                  geometry optimization and potential
                                  energy surface navigation  . . . . . . . 1698--1708
          Takakazu Ishikura and   
                 Yuki Iwata and   
             Tatsuro Hatano and   
                Takahisa Yamato   Energy exchange network of inter-residue
                                  interactions within a thermally
                                  fluctuating protein molecule: a
                                  computational study  . . . . . . . . . . 1709--1718

Journal of Computational Chemistry
Volume 36, Number 23, September 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 23 . . . . i--ii
                 X. W. Zhou and   
                 D. K. Ward and   
                   M. E. Foster   An analytical bond-order potential for
                                  carbon . . . . . . . . . . . . . . . . . 1719--1735
            Ignacio Viciano and   
            Raquel Castillo and   
            Sergio Martí   QM/MM modeling of the hydroxylation of
                                  the androstenedione substrate catalyzed
                                  by cytochrome P450 aromatase (CYP19A1)   1736--1747
         Stephen J. Barigye and   
             Matheus P. Freitas   Is molecular alignment an indispensable
                                  requirement in the MIA-QSAR method?  . . 1748--1755
           Yury Yu. Rusakov and   
              Leonid B. Krivdin   Four-component relativistic DFT
                                  calculations of $^{77}$Se NMR chemical
                                  shifts: a gateway to a reliable
                                  computational scheme for the
                                  medium-sized organoselenium molecules    1756--1762
               Weizhou Wang and   
                    Tao Sun and   
                   Yu Zhang and   
                     Yi-Bo Wang   Benchmark calculations of the adsorption
                                  of aromatic molecules on graphene  . . . 1763--1771
                Junchao Xia and   
           William F. Flynn and   
          Emilio Gallicchio and   
               Bin W. Zhang and   
                    Peng He and   
               Zhiqiang Tan and   
                 Ronald M. Levy   Large-scale asynchronous and distributed
                                  multidimensional replica exchange
                                  molecular simulations and efficiency
                                  analysis . . . . . . . . . . . . . . . . 1772--1785

Journal of Computational Chemistry
Volume 36, Number 24, September 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 24 . . . . i--ii
          Sergey Kazachenko and   
            Mark Giovinazzo and   
              Kyle Wm. Hall and   
                Natalie M. Cann   Algorithms for GPU-based molecular
                                  dynamics simulations of complex fluids:
                                  Applications to water, mixtures, and
                                  liquid crystals  . . . . . . . . . . . . 1787--1804
            Manuel Hochheim and   
                  Thomas Bredow   Adsorption-induced changes of
                                  intramolecular optical transitions:
                                  PTCDA/NaCl and PTCDA/KCl . . . . . . . . 1805--1811
                Norah Heinz and   
               Michael Dolg and   
             Albrecht Berkessel   A theoretical study of imine
                                  hydrocyanation catalyzed by
                                  halogen-bonding  . . . . . . . . . . . . 1812--1817
          Murugesan Thenraj and   
            Ashoka G. Samuelson   Contrasting electronic requirements for
                                  C H binding and C H activation in $ d^6
                                  $ half-sandwich complexes of rhenium and
                                  tungsten . . . . . . . . . . . . . . . . 1818--1830
       Nicolás Otero and   
      Christian Van Alsenoy and   
             Claude Pouchan and   
          Panaghiotis Karamanis   Hirshfeld-based intrinsic polarizability
                                  density representations as a tool to
                                  analyze molecular polarizability . . . . 1831--1843
          Timothy J. Hughes and   
        Salvatore Cardamone and   
            Paul L. A. Popelier   Realistic sampling of amino acid
                                  geometries for a multipolar polarizable
                                  force field  . . . . . . . . . . . . . . 1844--1857
                 Jing Huang and   
                   Likai Du and   
                  Deping Hu and   
                  Zhenggang Lan   Erratum: Theoretical analysis of excited
                                  states and energy transfer mechanism in
                                  conjugated dendrimers  . . . . . . . . . 1858--1858

Journal of Computational Chemistry
Volume 36, Number 25, September 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 25 . . . . i--ii
                Pin-Chih Su and   
           Cheng-Chieh Tsai and   
            Shahila Mehboob and   
            Kirk E. Hevener and   
             Michael E. Johnson   Comparison of radii sets, entropy, QM
                                  methods, and sampling on MM--PBSA,
                                  MM--GBSA, and QM/MM--GBSA ligand binding
                                  energies of \em F. tularensis enoyl-ACP
                                  reductase (FabI) . . . . . . . . . . . . 1859--1873
      Marie Zgarbová and   
         Andreana M. Rosnik and   
            F. Javier Luque and   
           Carles Curutchet and   
                 Petr Jure\vcka   Transferability and additivity of
                                  dihedral parameters in polarizable and
                                  nonpolarizable empirical force fields    1874--1884
                   Rui Duan and   
               Raudah Lazim and   
                    Dawei Zhang   Understanding the basis of I50V-induced
                                  affinity decrease in HIV-1 protease via
                                  molecular dynamics simulations using
                                  polarized force field  . . . . . . . . . 1885--1892
      M. Luz Sánchez and   
    José C. Corchado and   
     M. Elena Martín and   
Ignacio Fdez. Galván and   
        Rute Barata-Morgado and   
              Manuel A. Aguilar   A new QM/MM method oriented to the study
                                  of ionic liquids . . . . . . . . . . . . 1893--1901
            Liangxiao Zhang and   
                   Peiwu Li and   
                    Jin Mao and   
                     Fei Ma and   
               Xiaoxia Ding and   
                       Qi Zhang   An enhanced Monte Carlo outlier
                                  detection method . . . . . . . . . . . . 1902--1906
        Italo Curvelo Anjos and   
               Gerd Bruno Rocha   A topological assessment of the
                                  electronic structure of mesoionic
                                  compounds  . . . . . . . . . . . . . . . 1907--1918
                Haisheng Li and   
              Weiguang Chen and   
                 Xiaoyu Han and   
                   Liben Li and   
                  Qiang Sun and   
              Zhengxiao Guo and   
                         Yu Jia   Van der Waals Effects on semiconductor
                                  clusters . . . . . . . . . . . . . . . . 1919--1927

Journal of Computational Chemistry
Volume 36, Number 26, October 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 26 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 26 . . . . iii--iv
        Manuel Hitzenberger and   
                Thomas S. Hofer   Probing the range of applicability of
                                  structure- and energy-adjusted QM/MM
                                  link bonds . . . . . . . . . . . . . . . 1929--1939
             Silvia Casassa and   
            Alessandro Erba and   
               Jacopo Baima and   
                Roberto Orlando   Electron density analysis of large
                                  (molecular and periodic) systems: a
                                  parallel implementation  . . . . . . . . 1940--1946
            Joshua J. Eller and   
                   Karen Downey   Computational assessment of electron
                                  density in metallo-organic nickel pincer
                                  complexes for formation of P C bonds . . 1947--1953
              Anirban Ghosh and   
         Rajat K. Chaudhuri and   
        Sudip Chattopadhyay and   
          Uttam Sinha Mahapatra   Relativistic state-specific
                                  multireference perturbation theory
                                  incorporating improved virtual orbitals:
                                  Application to the ground state
                                  single-bond dissociation . . . . . . . . 1954--1972
           Arina Afanasyeva and   
            Sergey Izmailov and   
           Michel Grigoriev and   
               Michael Petukhov   Software News and Updates: AquaBridge: a
                                  novel method for systematic search of
                                  structural water molecules within the
                                  protein active sites . . . . . . . . . . 1973--1977
     Tomá\vs Kuba\vr and   
                  Kai Welke and   
                Gerrit Groenhof   Software News and Updates: New QM/MM
                                  implementation of the DFTB3 method in
                                  the \tt gromacs package  . . . . . . . . 1978--1989
            Carsten Kutzner and   
 Szilárd Páll and   
             Martin Fechner and   
          Ansgar Esztermann and   
           Bert L. de Groot and   
         Helmut Grubmüller   Software News and Updates: Best bang for
                                  your buck: GPU nodes for GROMACS
                                  biomolecular simulations . . . . . . . . 1990--2008
              Tomonari Sumi and   
            Ayori Mitsutake and   
                Yutaka Maruyama   Erratum: ``A solvation-free-energy
                                  functional: a reference-modified density
                                  functional formulation'' [J. Comput.
                                  Chem. 2015, \bf 36, 1359--1369]  . . . . 2009--2011

Journal of Computational Chemistry
Volume 36, Number 27, October 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 27 . . . . i--ii
                   Yun Ding and   
                    Ye Fang and   
           Wei P. Feinstein and   
      Jagannathan Ramanujam and   
         David M. Koppelman and   
               Juana Moreno and   
           Michal Brylinski and   
                   Mark Jarrell   GeauxDock: a novel approach for
                                  mixed-resolution ligand docking using a
                                  descriptor-based force field . . . . . . 2013--2026
 Railton Barbosa de Andrade and   
Ezequiel Fragoso Vieira Leitão and   
Miguel Angelo Fonseca de Souza and   
            Elizete Ventura and   
        Silmar Andrade do Monte   Effect of methylation on relative
                                  energies of tautomers and on the
                                  intramolecular proton transfer barriers
                                  of protonated nitrosamine: a MR--CISD
                                  study  . . . . . . . . . . . . . . . . . 2027--2036
        Sergei F. Vyboishchikov   Modeling exact exchange potential in
                                  spherically confined atoms . . . . . . . 2037--2043
          Guillaume Chevrot and   
        Eudes Eterno Fileti and   
               Vitaly V. Chaban   Enhanced stability of the model
                                  mini-protein in amino acid ionic liquids
                                  and their aqueous solutions  . . . . . . 2044--2051
               Anna Pavlova and   
                James C Gumbart   Parametrization of macrolide antibiotics
                                  using the force field toolkit  . . . . . 2052--2063
           Jonah Z. Vilseck and   
               Jakub Kostal and   
        Julian Tirado-Rives and   
           William L. Jorgensen   Application of a BOSS-Gaussian interface
                                  for QM/MM simulations of Henry and
                                  methyl transfer reactions  . . . . . . . 2064--2074
               Arnaud Fihey and   
          Christian Hettich and   
Jérémy Touzeau and   
     François Maurel and   
     Aurélie Perrier and   
       Christof Köhler and   
        Bálint Aradi and   
              Thomas Frauenheim   SCC--DFTB parameters for simulating
                                  hybrid gold-thiolates compounds  . . . . 2075--2087

Journal of Computational Chemistry
Volume 36, Number 28, October 30, 2015

                      Anonymous   Cover Image, Volume 36, Issue 28 . . . . i--ii
                Holger Vach and   
            Lena V. Ivanova and   
       Qadir K. Timerghazin and   
              Fatme Jardali and   
                 Ha-Linh Thi Le   A deeper insight into strain for the
                                  sila-bi[6]prismane (Si$_{18}$H$_{12}$)
                                  cluster with its endohedrally trapped
                                  silicon atom, Si$_{19}$H$_{12}$  . . . . 2089--2094
       Grygoriy A. Dolgonos and   
                 Koshka Mekalka   Strain in nonclassical silicon hydrides:
                                  an insight into the ``ultrastability''
                                  of sila-bi[6]prismane (Si$_{18}$
                                  H$_{12}$) cluster with the endohedrally
                                  trapped silicon atom, Si$_{19}$ H$_{12}$ 2095--2102
            Yuuichi Orimoto and   
                    Kai Liu and   
                    Yuriko Aoki   Elongation method for electronic
                                  structure calculations of random DNA
                                  sequences  . . . . . . . . . . . . . . . 2103--2113
            Samuel Genheden and   
                   Ulf Ryde and   
       Pär Söderhjelm   Binding affinities by alchemical
                                  perturbation using QM\slash MM with a
                                  large QM system and polarizable MM model 2114--2124
Régis Tadeu Santiago and   
   Roberto Luiz Andrade Haiduke   New density functional parameterizations
                                  to accurate calculations of electric
                                  field gradient variations among
                                  compounds  . . . . . . . . . . . . . . . 2125--2130
          Maxim R. Ryzhikov and   
        Vladimir A. Slepkov and   
        Svetlana G. Kozlova and   
       Svyatoslav P. Gabuda and   
            Vladimir E. Fedorov   Solid-state reaction as a mechanism of
                                  1T $ \leftrightarrow $ 2H transformation
                                  in MoS$_2$ monolayers  . . . . . . . . . 2131--2134
        Al Mokhtar Lamsabhi and   
Soledad Gutiérrez-Oliva and   
           Otilia Mó and   
Alejandro Toro-Labbé and   
     Manuel Yáñez   Effects of the ionization in the
                                  tautomerism of uracil: a reaction
                                  electronic flux perspective  . . . . . . 2135--2145

Journal of Computational Chemistry
Volume 36, Number 29, November 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 29 . . . . i--ii
              Ilkay Sakalli and   
             Ernst-Walter Knapp   pK$_A$ in proteins solving the
                                  Poisson--Boltzmann equation with finite
                                  elements . . . . . . . . . . . . . . . . 2147--2157
             Kestutis Aidas and   
            Kiril Lanevskij and   
             Rytis Kubilius and   
            Liutauras Juska and   
      Daumantas Petkevicius and   
                Pranas Japertas   Aqueous acidities of primary
                                  benzenesulfonamides: Quantum chemical
                                  predictions based on density functional
                                  theory and SMD . . . . . . . . . . . . . 2158--2167
                  Sudip Pan and   
             Ashutosh Gupta and   
               Ranajit Saha and   
             Gabriel Merino and   
            Pratim K. Chattaraj   A coupled-cluster study on the noble gas
                                  binding ability of metal cyanides versus
                                  metal halides (metal = Cu, Ag, Au) . . . 2168--2176
        Krishnakanta Mondal and   
              Arup Banerjee and   
      Alessandro Fortunelli and   
                Tapan K. Ghanty   Does enhanced oxygen activation always
                                  facilitate CO oxidation on gold
                                  clusters?  . . . . . . . . . . . . . . . 2177--2187
         Pouya Partovi-Azar and   
           Thomas D. Kühne   Efficient ``On-the-Fly'' calculation of
                                  Raman Spectra from Ab-Initio molecular
                                  dynamics: Application to
                                  hydrophobic/hydrophilic solutes in bulk
                                  water  . . . . . . . . . . . . . . . . . 2188--2192
          Olga A. Gapurenko and   
         Andrey G. Starikov and   
          Ruslan M. Minyaev and   
             Vladimir I. Minkin   Germanium, carbon-germanium, and
                                  silicon-germanium triangulenes . . . . . 2193--2199
               Marat Sibaev and   
          Deborah L. Crittenden   Software News and Updates: The PyPES
                                  library of high quality semi-global
                                  potential energy surfaces  . . . . . . . 2200--2207
                 Jing Huang and   
                   Likai Du and   
                  Deping Hu and   
                  Zhenggang Lan   Erratum: Theoretical analysis of excited
                                  states and energy transfer mechanism in
                                  conjugated dendrimers  . . . . . . . . . 2208--2208

Journal of Computational Chemistry
Volume 36, Number 30, November 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 30 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 30 . . . . iii--iv
               Takao Otsuka and   
            Noriaki Okimoto and   
                   Makoto Taiji   Assessment and acceleration of binding
                                  energy calculations for protein-ligand
                                  complexes by the fragment molecular
                                  orbital method . . . . . . . . . . . . . 2209--2218
                    Jacek Koput   Ab Initio spectroscopic characterization
                                  of borane, BH, in its X $^1 \Sigma^+$
                                  electronic state . . . . . . . . . . . . 2219--2227
               Wenjing Gong and   
                   Ruibo Wu and   
                  Yingkai Zhang   Thiol versus hydroxamate as zinc binding
                                  group in HDAC inhibition: An Ab initio
                                  QM/MM molecular dynamics study . . . . . 2228--2235
             Tobias Neumann and   
              Denis Danilov and   
                Wolfgang Wenzel   Multiparticle moves in acceptance rate
                                  optimized Monte Carlo  . . . . . . . . . 2236--2245
                  Roberto Cammi   A new extension of the polarizable
                                  continuum model: Toward a quantum
                                  chemical description of chemical
                                  reactions at extreme high pressure . . . 2246--2259
        Lucas Modesto-Costa and   
                  Elmar Uhl and   
               Itamar Borges Jr   Water solvent effects using continuum
                                  and discrete models: the nitromethane
                                  molecule, CH$_3$ NO$_2$  . . . . . . . . 2260--2269
                      Anonymous   Erratum to Csonka, G. I., Nguyen, N. A.,
                                  & Kolossváry, I. (1997). Simple tests for
                                  density functional methods. Journal of
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                                  1534--1545. (DOI: \urlc7rfjv)  . . . . . 2270--2270

Journal of Computational Chemistry
Volume 36, Number 31, December 5, 2015

                      Anonymous   Cover Image, Volume 36, Issue 31 . . . . i--ii
                      Anonymous   Cover Image, Volume 36, Issue 31 . . . . iii--iv
                      Anonymous   Cover Image, Volume 36, Issue 31 . . . . v--vi
              Ivan Carnimeo and   
            Chiara Cappelli and   
                Vincenzo Barone   Analytical gradients for MP2, double
                                  hybrid functionals, and TD-DFT with
                                  polarizable embedding described by
                                  fluctuating charges  . . . . . . . . . . 2271--2290
              M. Bartolomei and   
                  F. Pirani and   
               J. M. C. Marques   Low-energy structures of benzene
                                  clusters with a novel accurate potential
                                  surface  . . . . . . . . . . . . . . . . 2291--2301
                   Dan Fraenkel   Ion strength limit of computed excess
                                  functions based on the linearized
                                  Poisson--Boltzmann equation  . . . . . . 2302--2316
              Guo-Liang Fan and   
             Xiao-Yan Zhang and   
               Yan-Ling Liu and   
                    Yi Nang and   
                       Hui Wang   DSPMP: Discriminating secretory proteins
                                  of malaria parasite by hybridizing
                                  different descriptors of Chou's pseudo
                                  amino acid patterns  . . . . . . . . . . 2317--2327
        Pradeep R. Varadwaj and   
            Arpita Varadwaj and   
                    Bih-Yaw Jin   Hexahalogenated and their mixed benzene
                                  derivatives as prototypes for the
                                  understanding of halogen$ \cdots $
                                  halogen intramolecular interactions: New
                                  insights from combined DFT, QTAIM-, and
                                  RDG-based NCI analyses . . . . . . . . . 2328--2343
             Yoshiharu Mori and   
                Hisashi Okumura   Simulated tempering based on global
                                  balance or detailed balance conditions:
                                  Suwa--Todo, heat bath, and Metropolis
                                  algorithms . . . . . . . . . . . . . . . 2344--2349
                Anmol Kumar and   
            Sachin D. Yeole and   
          Shridhar R. Gadre and   
        Rafael López and   
              Jaime F. Rico and   
   Guillermo Ramírez and   
                Ignacio Ema and   
                 David Zorrilla   Software News and Updates: DAMQT 2.1.0:
                                  a new version of the DAMQT package
                                  enabled with the topographical analysis
                                  of electron density and electrostatic
                                  potential in molecules . . . . . . . . . 2350--2359

Journal of Computational Chemistry
Volume 36, Number 32, December 15, 2015

                      Anonymous   Cover Image, Volume 36, Issue 32 . . . . i--ii
        Salvatore Cardamone and   
            Paul L. A. Popelier   Prediction of conformationally dependent
                                  atomic multipole moments in
                                  carbohydrates  . . . . . . . . . . . . . 2361--2373
                Yuanyuan Li and   
                    Li Wang and   
                 Xugeng Guo and   
                  Jinglai Zhang   A CASSCF/CASPT2 insight into
                                  excited-state intramolecular proton
                                  transfer of four imidazole derivatives   2374--2380
           Marharyta Petukh and   
                  Min Zhang and   
                    Emil Alexov   Statistical investigation of surface
                                  bound ions and further development of
                                  BION server to include pH and salt
                                  dependence . . . . . . . . . . . . . . . 2381--2393
       Matti Hellström and   
     Daniel Spångberg and   
              Kersti Hermansson   Treatment of delocalized electron
                                  transfer in periodic and embedded
                                  cluster DFT calculations: the case of Cu
                                  on ZnO (10$ \bar 1 $0) . . . . . . . . . 2394--2405
              Takuma Nozawa and   
       Kazuaki Z. Takahashi and   
               Tetsu Narumi and   
                  Kenji Yasuoka   Comparison of the accuracy of periodic
                                  reaction field methods in molecular
                                  dynamics simulations of a model liquid
                                  crystal system . . . . . . . . . . . . . 2406--2411
          Sirous Yourdkhani and   
             Tatiana Korona and   
             Nasser L. Hadipour   Interplay between tetrel and triel bonds
                                  in RC$_6$H$_4$CN$ \cdot $MF$_3$ CN$
                                  \cdot $BX$_3$ complexes: a combined
                                  symmetry-adapted perturbation theory,
                                  Mòller--Plesset, and quantum theory of
                                  atoms-in-molecules study . . . . . . . . 2412--2428
Eric Iván Sánchez-Flores and   
Rodrigo Chávez-Calvillo and   
              Todd A. Keith and   
             Gabriel Cuevas and   
   Tomás Rocha-Rinza and   
Fernando Cortés-Guzmán   Erratum: Properties of atoms in
                                  electronically excited molecules within
                                  the formalism of TDDFT [J. Comput Chem.
                                  2014, \bf 35, 820--828]  . . . . . . . . 2429--2429


Journal of Computational Chemistry
Volume 37, Number 1, January 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 1  . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 1  . . . . ii--ii
                      Anonymous   Cover Image, Volume 37, Issue 1  . . . . iii--iii
                      Anonymous   Issue Information --- Coming Soon,
                                  Volume 37, Issue 1 . . . . . . . . . . . 1--1
                      Anonymous   Issue Information --- Copyright, Volume
                                  37, Issue 1  . . . . . . . . . . . . . . 2--2
                      Anonymous   Issue Information -- Editorial Board,
                                  Volume 37, Issue 1 . . . . . . . . . . . 3--3
                      Anonymous   Issue Information --- Table of Contents
                                  Volume 37, Issue 1 . . . . . . . . . . . 4--8
                      Anonymous   Editorial: Paul Von Ragué Schleyer
                                  (1930--2014) . . . . . . . . . . . . . . 9--9
              Lukas N. Wirz and   
                Ralf Tonner and   
            Andreas Hermann and   
               Rebecca Sure and   
            Peter Schwerdtfeger   From small fullerenes to the graphene
                                  limit: a harmonic force-field method for
                                  fullerenes and a comparison to density
                                  functional calculations for
                                  Goldberg--Coxeter fullerenes up to
                                  C$_{980}$  . . . . . . . . . . . . . . . 10--17
          Andreas J. Achazi and   
    Larissa K. S. von Krbek and   
      Christoph A. Schalley and   
                   Beate Paulus   Theoretical and experimental
                                  investigation of crown/ammonium
                                  complexes in solution  . . . . . . . . . 18--24
       Rodrigo A. Cormanich and   
            Roberto Rittner and   
              David O'Hagan and   
              Michael Bühl   Inter- and intramolecular CF$ \cdots
                                  $C\doublebond O interactions on
                                  aliphatic and cyclohexane carbonyl
                                  derivatives  . . . . . . . . . . . . . . 25--33
              Changwei Wang and   
               Liangyu Guan and   
             David Danovich and   
                Sason Shaik and   
                      Yirong Mo   The origins of the directionality of
                                  noncovalent intermolecular interactions  34--45
                Yunfei Zhou and   
              Xiaoguang Bao and   
         Weston Thatcher Borden   Nucleus-independent chemical shift
                                  analysis of the electronic states of the
                                  (CO)$_4$, (CS)$_4$, and (CSe)$_4$
                                  molecules  . . . . . . . . . . . . . . . 46--48
                Amir Karton and   
         Peter R. Schreiner and   
               Jan M. L. Martin   Heats of formation of platonic
                                  hydrocarbon cages by means of high-level
                                  thermochemical procedures  . . . . . . . 49--58
                Megha Anand and   
    Israel Fernández and   
      Henry F. Schaefer III and   
                 Judy I-Chia Wu   Hydrogen bond--aromaticity cooperativity
                                  in self-assembling $4$-pyridone chains   59--63
            Alexandru Lupan and   
                  R. Bruce King   Molybdatricarbaboranes as examples of
                                  isocloso metallaborane deltahedra with
                                  three carbon vertices  . . . . . . . . . 64--69
             George A. Olah and   
        G. K. Surya Prakash and   
                    Golam Rasul   Ab initio /GIAO-CCSD(T)$^{13}$ C NMR
                                  study of the rearrangement and dynamic
                                  aspects of rapidly equilibrating
                                  tertiary carbocations, C$_6$H$_{13}^+$
                                  and C$_7$H$_{15}^+$  . . . . . . . . . . 70--77
       Ramon Carbó-Dorca   Aromaticity, quantum multimolecular
                                  polyhedra, and quantum QSPR fundamental
                                  equation . . . . . . . . . . . . . . . . 78--82
         Riccardo Petraglia and   
          Adrien Nicola\"\i and   
         Matthew D. Wodrich and   
           Michele Ceriotti and   
           Clemence Corminboeuf   Beyond static structures: Putting forth
                                  REMD as a tool to solve problems in
                                  computational organic chemistry  . . . . 83--92
               Martin Kaupp and   
          Simon Gückel and   
                Manuel Renz and   
             Sascha Klawohn and   
           Kolja Theilacker and   
           Matthias Parthey and   
              Christoph Lambert   Electron transfer pathways in
                                  mixed-valence paracyclophane-bridged
                                  bis-triarylamine radical cations . . . . 93--102
                  Xiaohu Yu and   
            Artem R. Oganov and   
              Ivan A. Popov and   
          Alexander I. Boldyrev   d-AO spherical aromaticity in
                                  Ce$_6$O$_8$  . . . . . . . . . . . . . . 103--109
                 Klara Edel and   
           Reinhold F. Fink and   
            Holger F. Bettinger   Isomerization and fragmentation pathways
                                  of 1,2-azaborine . . . . . . . . . . . . 110--116
       Brian J. Levandowski and   
                 Lufeng Zou and   
                     K. N. Houk   Schleyer hyperconjugative aromaticity
                                  and Diels--Alder reactivity of
                                  $5$-substituted cyclopentadienes . . . . 117--123
              Jenn-Huei Lii and   
         Norman L. Allinger and   
               Ching-Han Hu and   
          Henry F. Schaefer III   Catenanes: a molecular mechanics
                                  analysis of the (C$_{13}$H$_{26}$)$_2$
                                  Structure 13-13 D2 . . . . . . . . . . . 124--129
                 Elfi Kraka and   
              Dani Setiawan and   
                  Dieter Cremer   Re-evaluation of the bond length--bond
                                  strength rule: the stronger bond is not
                                  always the shorter bond  . . . . . . . . 130--142
     Chérif F. Matta and   
    Seyed Abdolreza Sadjadi and   
             Dale A. Braden and   
                Gernot Frenking   The barrier to the methyl rotation in
                                  Cis-$2$-butene and its isomerization
                                  energy to Trans-$2$-butene, revisited    143--154

Journal of Computational Chemistry
Volume 37, Number 2, January 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 2  . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 2  . . . . ii--ii
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                                  Volume 37, Issue 2 . . . . . . . . . . . 155--155
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                                  37, Issue 2  . . . . . . . . . . . . . . 156--156
                      Anonymous   Issue Information --- Editorial Board,
                                  Volume 37, Issue 2 . . . . . . . . . . . 157--157
                      Anonymous   Issue Information --- Table of Contents,
                                  Volume 37, Issue 2 . . . . . . . . . . . 158--161
     Jose L. Mendoza-Cortes and   
                      Qi An and   
     William A. Goddard III and   
                 Caichao Ye and   
                   Sergey Zybin   Prediction of the crystal packing of
                                  di-tetrazine-tetroxide (DTTO) energetic
                                  material . . . . . . . . . . . . . . . . 163--167
                Haijun Jiao and   
              Kathrin Junge and   
        Elisabetta Alberico and   
                Matthias Beller   A comparative computationally study
                                  about the defined m(II) pincer
                                  hydrogenation catalysts (m = FE, Ru, Os) 168--176
                Guoliang Li and   
                   Hui Wang and   
                Qian-Shu Li and   
                Yaoming Xie and   
          Henry F. Schaefer III   The Reaction between Bromine and the
                                  Water Dimer and the Highly Exothermic
                                  Reverse Reaction . . . . . . . . . . . . 177--182
                   Bun Chan and   
               Lars Goerigk and   
                      Leo Radom   On the inclusion of post-MP2
                                  contributions to double-Hybrid density
                                  functionals  . . . . . . . . . . . . . . 183--193
            Habib U. Rehman and   
              Nida A. McKee and   
               Michael L. McKee   Saturn Systems . . . . . . . . . . . . . 194--209
       Andrey V. Shernyukov and   
        Alexander M. Genaev and   
         George E. Salnikov and   
             Henry S. Rzepa and   
           Vyacheslav G. Shubin   Noncatalytic bromination of benzene: a
                                  combined computational and experimental
                                  study  . . . . . . . . . . . . . . . . . 210--225
                  Sudip Pan and   
               Diego Moreno and   
               Sreyan Ghosh and   
        Pratim K. Chattaraj and   
                 Gabriel Merino   Structure and stability of noble gas
                                  bound EX$_3^+$ compounds (E = C, Ge, Sn,
                                  Pb; X = H, F, Cl, Br)  . . . . . . . . . 226--236
               C. R. Landis and   
                    F. Weinhold   $ 18$-electron rule and the 3c/4e
                                  hyperbonding saturation limit  . . . . . 237--241
             Masahiro Ehara and   
             Ryoichi Fukuda and   
              Thomas Sommerfeld   Projected CAP/SAC-CI method with smooth
                                  Voronoi potential for calculating
                                  resonance states . . . . . . . . . . . . 242--249
               Hongyan Wang and   
                   Hui Wang and   
              R. Bruce King and   
          Henry F. Schaefer III   Bis(azulene) ``submarine'' metal dimer
                                  sandwich compounds (C$_{10}$H$_8$)$_2$
                                  M$_2$ (M = Ti, V, Cr, Mn, Fe, Co, Ni):
                                  Parallel and opposed orientations  . . . 250--260
              Xue-Feng Zhao and   
                  Haixia Li and   
               Cai-Xia Yuan and   
                 Yan-Qin Li and   
                  Yan-Bo Wu and   
                 Zhi-Xiang Wang   Linear, planar, and tubular molecular
                                  structures constructed by double planar
                                  tetracoordinate carbon D$_{2h}$ C$_2$
                                  (BeH)$_4$ species via hydrogen-bridged
                                  BeH$_2$Be bonds  . . . . . . . . . . . . 261--269
               Jyothish Joy and   
                  Anex Jose and   
         Eluvathingal D. Jemmis   Continuum in the X--Z---Y weak bonds: Z
                                  = main group elements  . . . . . . . . . 270--279
               Berit Heggen and   
             Mahendra Patil and   
                   Walter Thiel   Cyclization of an $ \alpha $, $ \beta
                                  $-Unsaturated hydrazone catalyzed by a
                                  BINOL-phosphoric acid: Pericyclic or
                                  not? . . . . . . . . . . . . . . . . . . 280--285
         Arkajyoti Sengupta and   
   Raghunath O. Ramabhadran and   
          Krishnan Raghavachari   Breaking a bottleneck: Accurate
                                  extrapolation to ``gold standard''
                                  CCSD(T) energies for large open shell
                                  organic radicals at reduced
                                  computational cost . . . . . . . . . . . 286--295
              Xue-Feng Zhao and   
               Cai-Xia Yuan and   
                 Xiang Wang and   
                 Jia-Jia Li and   
                  Yan-Bo Wu and   
                   Xiaotai Wang   Computational design of organometallic
                                  oligomers featuring 1,3-metal-carbon
                                  bonding and planar tetracoordinate
                                  carbon atoms . . . . . . . . . . . . . . 296--303
           Joshua R. Mulder and   
Célia Fonseca Guerra and   
          J. Chris Slootweg and   
            Koop Lammertsma and   
        F. Matthias Bickelhaupt   Substituent effects on the optical
                                  properties of naphthalenediimides: a
                                  frontier orbital analysis across the
                                  periodic table . . . . . . . . . . . . . 304--313

Journal of Computational Chemistry
Volume 37, Number 3, January 30, 2016

                      Anonymous   Cover Image, Volume 37, Issue 3  . . . . i--i
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                                  Volume 37, Issue 3 . . . . . . . . . . . 315--315
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                                  37, Issue 3  . . . . . . . . . . . . . . 316--316
                      Anonymous   Issue Information --- Editorial Board,
                                  Volume 37, Issue 3 . . . . . . . . . . . 317--317
                      Anonymous   Issue Information --- Table of Contents,
                                  Volume 37, Issue 3 . . . . . . . . . . . 318--319
                 Yingdi Jin and   
              Neil Qiang Su and   
                     Xin Xu and   
                         Hao Hu   Self-consistent field for fragmented
                                  quantum mechanical model of large
                                  molecular systems  . . . . . . . . . . . 321--326
                     Arifin and   
          Maneeporn Puripat and   
           Daisuke Yokogawa and   
          Vudhichai Parasuk and   
                   Stephan Irle   Glucose transformation to
                                  $5$-hydroxymethylfurfural in acidic
                                  ionic liquid: a quantum mechanical study 327--335
                     Li Rao and   
                     Bo Chi and   
               Yanliang Ren and   
                Yongjian Li and   
                     Xin Xu and   
                       Jian Wan   DOX: a new computational protocol for
                                  accurate prediction of the
                                  protein--ligand binding structures . . . 336--344
               Dilan Yildiz and   
                 U\ugur Bozkaya   Assessment of the extended Koopmans'
                                  theorem for the chemical reactivity:
                                  Accurate computations of chemical
                                  potentials, chemical hardnesses, and
                                  electrophilicity indices . . . . . . . . 345--353
         Wojciech Plazinski and   
              Alice Lonardi and   
   Philippe H. Hünenberger   Revision of the GROMOS 56A6$_{CARBO}$
                                  force field: Improving the description
                                  of ring-conformational equilibria in
                                  hexopyranose-based carbohydrates chains  354--365
          M. Althaf Hussain and   
                Dolly Vijay and   
             G. Narahari Sastry   Buckybowls as adsorbents for CO$_2$,
                                  CH$_4$, and C$_2$H$_2$: Binding and
                                  structural insights from computational
                                  study  . . . . . . . . . . . . . . . . . 366--377
            Sheng-Chun Yang and   
              Yong-Lei Wang and   
             Gui-Sheng Jiao and   
                Hu-Jun Qian and   
                  Zhong-Yuan Lu   Software News and Updates: Accelerating
                                  electrostatic interaction calculations
                                  with graphical processing units based on
                                  new developments of Ewald method using
                                  non-uniform Fast Fourier Transform . . . 378--387

Journal of Computational Chemistry
Volume 37, Number 4, February 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 4  . . . . i--i
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                                  Volume 37, Issue 4 . . . . . . . . . . . 389--389
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                                  37, Issue 4  . . . . . . . . . . . . . . 390--390
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                                  Volume 37, Issue 4 . . . . . . . . . . . 391--391
                      Anonymous   Issue Information --- Table of Contents,
                                  Volume 37, Issue 4 . . . . . . . . . . . 392--393
          Marzena Jankowska and   
              Teobald Kupka and   
         Leszek Stobi\'nski and   
               Rasmus Faber and   
    Evanildo G. Lacerda Jr. and   
            Stephan P. A. Sauer   Spin-orbit ZORA and four-component
                                  Dirac--Coulomb estimation of
                                  relativistic corrections to isotropic
                                  nuclear shieldings and chemical shifts
                                  of noble gas dimers  . . . . . . . . . . 395--403
               Karen Druart and   
              Zoltan Palmai and   
               Eyaz Omarjee and   
                Thomas Simonson   Protein:Ligand binding free energies: a
                                  stringent test for computational protein
                                  design . . . . . . . . . . . . . . . . . 404--415
   Sirish Kaushik Lakkaraju and   
           Justin A. Lemkul and   
                 Jing Huang and   
     Alexander D. MacKerell Jr.   DIRECT--ID: an automated method to
                                  identify and quantify conformational
                                  variations --- application to $
                                  \beta_2$-adrenergic GPCR . . . . . . . . 416--425
            Ngaam J. Cheung and   
              Xue-Ming Ding and   
                  Hong-Bin Shen   Protein folds recognized by an
                                  intelligent predictor based-on
                                  evolutionary and structural information  426--436
              Vincent Zoete and   
         Thierry Schuepbach and   
         Christophe Bovigny and   
             Prasad Chaskar and   
              Antoine Daina and   
         Ute F. Röhrig and   
              Olivier Michielin   Attracting cavities for docking.
                                  Replacing the rough energy landscape of
                                  the protein by a smooth attracting
                                  landscape  . . . . . . . . . . . . . . . 437--447
        Murat Keçeli and   
                 Hong Zhang and   
                Peter Zapol and   
             David A. Dixon and   
               Albert F. Wagner   Shift-and-invert parallel spectral
                                  transformation eigensolver: Massively
                                  parallel performance for
                                  density-functional based tight-binding   448--459

Journal of Computational Chemistry
Volume 37, Number 5, February 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 5  . . . . i--i
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                                  Volume 37, Issue 5 . . . . . . . . . . . 461--461
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                                  37, Issue 5  . . . . . . . . . . . . . . 462--462
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                                  Volume 37, Issue 5 . . . . . . . . . . . 463--463
                      Anonymous   Issue Information --- Table of Contents,
                                  Volume 37, Issue 5 . . . . . . . . . . . 464--465
           Anna Stachiewicz and   
                 Andrzej Molski   Diffusive dynamics of DNA unzipping in a
                                  nanopore . . . . . . . . . . . . . . . . 467--476
           Rahul V. Pinjari and   
     Mickaël G. Delcey and   
                Meiyuan Guo and   
            Michael Odelius and   
                Marcus Lundberg   Cost and sensitivity of restricted
                                  active-space calculations of metal
                                  L-edge X-ray absorption spectra  . . . . 477--486
               Yu Harabuchi and   
                 Yuriko Ono and   
              Satoshi Maeda and   
          Tetsuya Taketsugu and   
         Kristopher Keipert and   
                 Mark S. Gordon   Nontotally symmetric trifurcation of an
                                  S$_N$2 reaction pathway  . . . . . . . . 487--493
           Christophe Narth and   
          Louis Lagard\`ere and   
      Étienne Polack and   
                Nohad Gresh and   
               Qiantao Wang and   
              David R. Bell and   
          Joshua A. Rackers and   
              Jay W. Ponder and   
              Pengyu Y. Ren and   
           Jean-Philip Piquemal   Scalable improvement of SPME multipolar
                                  electrostatics in anisotropic
                                  polarizable molecular mechanics using a
                                  general short-range penetration
                                  correction up to quadrupoles . . . . . . 494--506
        Francesco Aquilante and   
          Jochen Autschbach and   
         Rebecca K. Carlson and   
         Liviu F. Chibotaru and   
     Mickaël G. Delcey and   
               Luca De Vico and   
Ignacio Fdez. Galván and   
       Nicolas Ferré and   
         Luis Manuel Frutos and   
            Laura Gagliardi and   
            Marco Garavelli and   
            Angelo Giussani and   
              Chad E. Hoyer and   
          Giovanni Li Manni and   
               Hans Lischka and   
                 Dongxia Ma and   
    Per Åke Malmqvist and   
         Thomas Müller and   
                Artur Nenov and   
           Massimo Olivucci and   
      Thomas Bondo Pedersen and   
               Daoling Peng and   
              Felix Plasser and   
              Ben Pritchard and   
              Markus Reiher and   
               Ivan Rivalta and   
              Igor Schapiro and   
Javier Segarra-Martí and   
            Michael Stenrup and   
          Donald G. Truhlar and   
                Liviu Ungur and   
          Alessio Valentini and   
          Steven Vancoillie and   
            Valera Veryazov and   
        Victor P. Vysotskiy and   
            Oliver Weingart and   
              Felipe Zapata and   
                   Roland Lindh   Software News and Updates: Molcas 8: New
                                  capabilities for multiconfigurational
                                  quantum chemical calculations across the
                                  periodic table . . . . . . . . . . . . . 506--541

Journal of Computational Chemistry
Volume 37, Number 6, March 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 6  . . . . i--i
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                                  Volume 37, Issue 6 . . . . . . . . . . . 543--543
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                                  37, Issue 6  . . . . . . . . . . . . . . 544--544
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                                  Volume 37, Issue 6 . . . . . . . . . . . 545--545
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 6 . . . . . . . . . . . 546--548
                       Wei Yang   Editorial: Advanced Sampling for
                                  Molecular Simulation is Coming of Age    549--549
                Kuo Hao Lee and   
                   Jianhan Chen   Multiscale enhanced sampling of
                                  intrinsically disordered protein
                                  conformations  . . . . . . . . . . . . . 550--557
              Gregory R. Bowman   Accurately modeling nanosecond protein
                                  dynamics requires at least microseconds
                                  of simulation  . . . . . . . . . . . . . 558--566
                    Chao Lv and   
         Erick W. Aitchison and   
               Dongsheng Wu and   
             Lianqing Zheng and   
              Xiaolin Cheng and   
                       Wei Yang   Comparative exploration of hydrogen
                                  sulfide and water transmembrane free
                                  energy surfaces via orthogonal space
                                  tempering free energy sampling . . . . . 567--574
          Davide Branduardi and   
         Fabrizio Marinelli and   
José D. Faraldo-Gómez   Atomic-resolution dissection of the
                                  energetics and mechanism of
                                  isomerization of hydrated ATP-Mg$^{2+}$
                                  through the SOMA string method . . . . . 575--586
               Alex Dickson and   
          Logan S. Ahlstrom and   
          Charles L. Brooks III   Coupled folding and binding with 2D
                                  Window-Exchange Umbrella Sampling  . . . 587--594
                 Xiongwu Wu and   
          Bernard R. Brooks and   
            Eric Vanden-Eijnden   Self-guided Langevin dynamics via
                                  generalized Langevin equation  . . . . . 595--601
        Juan M. Bello-Rivas and   
                      Ron Elber   Simulations of thermodynamics and
                                  kinetics on rough energy landscapes with
                                  milestoning  . . . . . . . . . . . . . . 602--613
               Xiangda Peng and   
               Yuebin Zhang and   
                Huiying Chu and   
                      Guohui Li   Free energy simulations with the AMOEBA
                                  polarizable force field and metadynamics
                                  on GPU platform  . . . . . . . . . . . . 614--622
         Raimondas Galvelis and   
                    Yuji Sugita   The Following Articles were Published in
                                  Past Issues of the \booktitleJournal of
                                  Computational Chemistry: Replica State
                                  Exchange Metadynamics for Improving the
                                  Convergence of Free Energy Estimates . . 
              Yinglong Miao and   
              Ferran Feixas and   
               Changsun Eun and   
             J. Andrew McCammon   The Following Articles were Published in
                                  Past Issues of the \booktitleJournal of
                                  Computational Chemistry: Accelerated
                                  Molecular Dynamics Simulations of
                                  Protein Folding  . . . . . . . . . . . . 
                Junchao Xia and   
           William F. Flynn and   
          Emilio Gallicchio and   
               Bin W. Zhang and   
                    Peng He and   
               Zhiqiang Tan and   
                 Ronald M. Levy   The Following Articles were Published in
                                  Past Issues of the \booktitleJournal of
                                  Computational Chemistry: Large-Scale
                                  Asynchronous and Distributed
                                  Multidimensional Replica Exchange
                                  Molecular Simulations and Efficiency
                                  Analysis . . . . . . . . . . . . . . . . 

Journal of Computational Chemistry
Volume 37, Number 7, March 15, 2016

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                                  37, Issue 7  . . . . . . . . . . . . . . 624--624
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                                  Volume 37, Issue 7 . . . . . . . . . . . 625--625
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                                  Volume 37, Issue 7 . . . . . . . . . . . 626--627
      Alexander Cumberworth and   
            Jennifer M. Bui and   
              Jörg Gsponer   Free energies of solvation in the
                                  context of protein folding: Implications
                                  for implicit and explicit solvent models 629--640
          Andrei V. Bandura and   
           Vitaly V. Porsev and   
            Robert A. Evarestov   Application of zone-folding approach to
                                  the first-principles estimation of
                                  thermodynamic properties of carbon and
                                  ZrS$_2$-based nanotubes  . . . . . . . . 641--652
                   Zhao Jin and   
               Chunwei Yang and   
                Fenglei Cao and   
                    Feng Li and   
               Zhifeng Jing and   
                  Long Chen and   
                   Zhe Shen and   
                  Liang Xin and   
                 Sijia Tong and   
                       Huai Sun   Hierarchical atom type definitions and
                                  extensible all-atom force fields . . . . 653--664
              Arne Scherrer and   
              Daniel Sebastiani   Moment expansion of the linear
                                  density-density response function  . . . 665--674
Gessenildo Pereira Rodrigues and   
            Elizete Ventura and   
    Silmar Andrade do Monte and   
                 Mario Barbatti   UV-photoexcitation and ultrafast
                                  dynamics of HCFC-132b (CF$_2$ ClCH$_2$
                                  Cl)  . . . . . . . . . . . . . . . . . . 675--683
                 Haitao Sun and   
                Shian Zhang and   
                Cheng Zhong and   
                   Zhenrong Sun   Theoretical study of excited states of
                                  DNA base dimers and tetramers using
                                  optimally tuned range-separated density
                                  functional theory  . . . . . . . . . . . 684--693

Journal of Computational Chemistry
Volume 37, Number 8, March 30, 2016

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                                  Volume 37, Issue 8 . . . . . . . . . . . 695--695
                      Anonymous   Issue Information --- Copyright: Volume
                                  37, Issue 8  . . . . . . . . . . . . . . 696--696
                      Anonymous   Issue Information --- Editorial Board:
                                  Volume 37, Issue 8 . . . . . . . . . . . 697--697
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 8 . . . . . . . . . . . 698--699
      Miguel A. F. de Souza and   
            Elizete Ventura and   
         Silmar A. do Monte and   
     José M. Riveros and   
               Ricardo L. Longo   Revisiting the concept of the
                                  (a)synchronicity of Diels--Alder
                                  reactions based on the dynamics of
                                  quasiclassical trajectories  . . . . . . 701--711
              Hiraku Oshima and   
             Masahiro Kinoshita   A highly efficient hybrid method for
                                  calculating the hydration free energy of
                                  a protein  . . . . . . . . . . . . . . . 712--723
              Ryuhei Harada and   
          Tomotake Nakamura and   
               Yasuteru Shigeta   Sparsity-weighted outlier FLOODing
                                  (OFLOOD) method: Efficient rare event
                                  sampling method using sparsity of
                                  distribution . . . . . . . . . . . . . . 724--738
      Christine-Andrea Roth and   
                Tom Dreyfus and   
          Charles H. Robert and   
  Frédéric Cazals   Hybridizing rapidly exploring random
                                  trees and basin hopping yields an
                                  improved exploration of energy
                                  landscapes . . . . . . . . . . . . . . . 739--752
          Jessica K. Gagnon and   
                Sean M. Law and   
          Charles L. Brooks III   Flexible CDOCKER: Development and
                                  application of a pseudo-explicit
                                  structure-based docking method within
                                  CHARMM . . . . . . . . . . . . . . . . . 753--762
          Simon W. L. Hogan and   
               Tanja van Mourik   Competition between hydrogen and halogen
                                  bonding in halogenated
                                  1-methyluracil:water systems . . . . . . 763--770
              Julien Racine and   
    Denis Hagebaum-Reignier and   
           Yannick Carissan and   
         Stéphane Humbel   Recasting wave functions into valence
                                  bond structures: a simple projection
                                  method to describe excited states  . . . 771--779

Journal of Computational Chemistry
Volume 37, Number 9, April 5, 2016

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                                  Volume 37, Issue 9 . . . . . . . . . . . 781--781
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                                  37, Issue 9  . . . . . . . . . . . . . . 782--782
                      Anonymous   Issue Information --- Editorial Board:
                                  Volume 37, Issue 9 . . . . . . . . . . . 783--783
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 9 . . . . . . . . . . . 784--785
  Cláudio M. Lousada and   
             Pavel A. Korzhavyi   Surface chemistry of oxygen on aluminum
                                  --- Performance of the density
                                  functionals: PBE, PBE0, M06, and M06-L   787--794
                     Min Li and   
           John Z. H. Zhang and   
                        Fei Xia   A new algorithm for construction of
                                  coarse-grained sites of large
                                  biomolecules . . . . . . . . . . . . . . 795--804
           Alain C. Vaucher and   
             Moritz P. Haag and   
                  Markus Reiher   Real-time feedback from iterative
                                  electronic structure calculations  . . . 805--812
                    Xi Chen and   
                Fu-Quan Bai and   
                Yongan Tang and   
                Hong-Xing Zhang   How the substituents in corannulene and
                                  sumanene derivatives alter their
                                  molecular assemblings and charge
                                  transport properties? --- A theoretical
                                  study with a dimer model . . . . . . . . 813--824
                   Bolong Huang   $ 4 f $ fine-structure levels as the
                                  dominant error in the electronic
                                  structures of binary lanthanide oxides   825--835
                Pin-Chih Su and   
             Michael E. Johnson   Evaluating thermodynamic integration
                                  performance of the new Amber molecular
                                  dynamics package and assess potential
                                  halogen bonds of enoyl-ACP reductase
                                  (FabI) benzimidazole inhibitors  . . . . 836--847
        Maciej Dziubi\'nski and   
                  Bogdan Lesyng   Toward the identification of molecular
                                  cogs . . . . . . . . . . . . . . . . . . 848--860
              Davide Presti and   
Frédéric Labat and   
             Alfonso Pedone and   
          Michael J. Frisch and   
         Hrant P. Hratchian and   
             Ilaria Ciofini and   
    Maria Cristina Menziani and   
                    Carlo Adamo   Modeling emission features of
                                  salicylidene aniline molecular crystals:
                                  A QM/QM' approach  . . . . . . . . . . . 861--870

Journal of Computational Chemistry
Volume 37, Number 10, April 15, 2016

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                                  Volume 37, Issue 10  . . . . . . . . . . 871--871
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                                  37, Issue 10 . . . . . . . . . . . . . . 872--872
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                                  Volume 37, Issue 10  . . . . . . . . . . 873--873
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 10  . . . . . . . . . . 874--875
                  Hongbo Du and   
                 Xianghong Qian   The hydration properties of
                                  carboxybetaine zwitterion brushes  . . . 877--885
                        Y. Ohta   Possible mechanism of BN fullerene
                                  formation from a boron cluster:
                                  Density-functional tight-binding
                                  molecular dynamics simulations . . . . . 886--895
                     You Xu and   
       Kenno Vanommeslaeghe and   
         Alexey Aleksandrov and   
 Alexander D. MacKerell Jr. and   
                Lennart Nilsson   Additive CHARMM force field for
                                  naturally occurring modified
                                  ribonucleotides  . . . . . . . . . . . . 896--912
                Roman Osman and   
               Mihaly Mezei and   
                Stanislav Engel   The role of protein ``Stability
                                  patches'' in molecular recognition: a
                                  case study of the human growth
                                  hormone-receptor complex . . . . . . . . 913--919
               Leebyn Chong and   
               Fikret Aydin and   
                 Meenakshi Dutt   Implicit solvent coarse-grained model of
                                  polyamidoamine dendrimers: Role of
                                  generation and pH  . . . . . . . . . . . 920--926
             Evan J. Arthur and   
          Charles L. Brooks III   Parallelization and improvements of the
                                  generalized born model with a simple
                                  switching function for modern graphics
                                  processors . . . . . . . . . . . . . . . 927--939
    Rodrigo Galindo-Murillo and   
Luis Enrique Aguilar-Suárez and   
  Joaquín Barroso-Flores   A mixed DFT-MD methodology for the \em
                                  in silico development of drug releasing
                                  macrocycles. Calix and
                                  thia-calix[N]arenes as carriers for
                                  Bosutinib and Sorafenib  . . . . . . . . 940--946
                 Sergi Vela and   
              Maria Fumanal and   
   Jordi Ribas-Ariño and   
                 Vincent Robert   On the zeroth-order Hamiltonian for
                                  CASPT2 calculations of spin crossover
                                  compounds  . . . . . . . . . . . . . . . 947--953

Journal of Computational Chemistry
Volume 37, Number 11, April 30, 2016

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                                  Volume 37, Issue 11  . . . . . . . . . . 955--955
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                                  37, Issue 11 . . . . . . . . . . . . . . 956--956
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                                  Volume 37, Issue 11  . . . . . . . . . . 957--957
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 11  . . . . . . . . . . 958--959
           Artem B. Mamonov and   
         Mohammad Moghadasi and   
             Hanieh Mirzaei and   
         Shahrooz Zarbafian and   
            Laurie E. Grove and   
            Tanggis Bohnuud and   
              Pirooz Vakili and   
    Ioannis Ch. Paschalidis and   
               Sandor Vajda and   
                   Dima Kozakov   Focused grid-based resampling for
                                  protein docking and mapping  . . . . . . 961--970
              Il Seung Youn and   
               Woo Jong Cho and   
                   Kwang S. Kim   Effects of an electric field on
                                  interaction of aromatic systems  . . . . 971--975
               Yuedong Yang and   
                     Yaoqi Zhou   Effective protein conformational
                                  sampling based on predicted torsion
                                  angles . . . . . . . . . . . . . . . . . 976--980
           Ingrid G. Prandi and   
                Lucas Viani and   
         Oliviero Andreussi and   
             Benedetta Mennucci   Combining classical molecular dynamics
                                  and quantum mechanical methods for the
                                  description of electronic excitations:
                                  the case of carotenoids  . . . . . . . . 981--991
             Bhaskar Sharma and   
             Y. Indra Neela and   
             G. Narahari Sastry   Structures and energetics of
                                  complexation of metal ions with ammonia,
                                  water, and benzene: a computational
                                  study  . . . . . . . . . . . . . . . . . 992--1004
                   M. Witte and   
               U. Gerstmann and   
                   A. Neuba and   
                  G. Henkel and   
                  W. G. Schmidt   Density functional theory of the
                                  Cu$_A$-like Cu$_2$S$_2$ diamond core in
                                  Cu$_2$II(NGuaS)$_2$Cl$_2$  . . . . . . . 1005--1018
              Eric G. Kratz and   
            Alice R. Walker and   
          Louis Lagard\`ere and   
          Filippo Lipparini and   
       Jean-Philip Piquemal and   
      G. Andrés Cisneros   Software News and Updates: LICHEM: A
                                  QM/MM program for simulations with
                                  multipolar and polarizable force fields  1019--1029
              Stefan Maintz and   
         Volker L. Deringer and   
Andrei L. Tchougréeff and   
            Richard Dronskowski   Software News and Updates: LOBSTER: a
                                  tool to extract chemical bonding from
                                  plane-wave based DFT . . . . . . . . . . 1030--1035

Journal of Computational Chemistry
Volume 37, Number 12, May 5, 2016

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                                  Volume 37, Issue 12  . . . . . . . . . . 1037--1037
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                                  37, Issue 12 . . . . . . . . . . . . . . 1038--1038
                      Anonymous   Issue Information --- Editorial Board:
                                  Volume 37, Issue 12  . . . . . . . . . . 1039--1039
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 12  . . . . . . . . . . 1040--1042
                   Jiaye Su and   
                      Keda Yang   Temperature dependence of the transport
                                  of single-file water molecules through a
                                  hydrophobic channel  . . . . . . . . . . 1043--1047
       Seydou Traoré and   
            Kyle E. Roberts and   
             David Allouche and   
            Bruce R. Donald and   
      Isabelle André and   
              Thomas Schiex and   
                   Sophie Barbe   Fast search algorithms for computational
                                  protein design . . . . . . . . . . . . . 1048--1058
                Jiri Brabec and   
                  Chao Yang and   
         Evgeny Epifanovsky and   
             Anna I. Krylov and   
                      Esmond Ng   Reduced-cost sparsity-exploiting
                                  algorithm for solving coupled-cluster
                                  equations  . . . . . . . . . . . . . . . 1059--1067
          Daniela E. Ortega and   
        Quynh Nhu N. Nguyen and   
           Dean J. Tantillo and   
    Alejandro Toro-Labbé   The catalytic effect of the NH$_3$ base
                                  on the chemical events in the
                                  caryolene-forming carbocation cascade    1068--1081
           Emanuele Rossini and   
             Ernst-Walter Knapp   Proton solvation in protic and aprotic
                                  solvents . . . . . . . . . . . . . . . . 1082--1091
            Johannes Heuser and   
         Sebastian Höfener   Wave-function frozen-density embedding:
                                  Approximate analytical nuclear
                                  ground-state gradients . . . . . . . . . 1092--1101
                    Bachir Aoun   Fullrmc, a rigid body reverse Monte
                                  Carlo modeling package enabled with
                                  machine learning and artificial
                                  intelligence . . . . . . . . . . . . . . 1102--1111
        Ronald D. Hills Jr. and   
            Nicholas McGlinchey   Model parameters for simulation of
                                  physiological lipids . . . . . . . . . . 1112--1118
          Md Tamjidul Hoque and   
               Yuedong Yang and   
              Avdesh Mishra and   
                     Yaoqi Zhou   Software News and Updates: sDFIRE:
                                  Sequence-specific statistical energy
                                  function for protein structure
                                  prediction by decoy selections . . . . . 1119--1124
                  Yu Takano and   
              Kazuto Nakata and   
         Yasushige Yonezawa and   
                Haruki Nakamura   Software News and Updates: Development
                                  of massive multilevel molecular dynamics
                                  simulation program, PLATYpus (PLATform
                                  for dYnamic protein unified simulation),
                                  for the elucidation of protein functions 1125--1132

Journal of Computational Chemistry
Volume 37, Number 13, May 15, 2016

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                                  Volume 37, Issue 13  . . . . . . . . . . 1133--1133
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                                  37, Issue 13 . . . . . . . . . . . . . . 1134--1134
                      Anonymous   Issue Information --- Editorial Board:
                                  Volume 37, Issue 13  . . . . . . . . . . 1135--1135
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 13  . . . . . . . . . . 1136--1138
             Yasushige Yonezawa   A method for predicting protein
                                  conformational pathways by using
                                  molecular dynamics simulations guided by
                                  difference distance matrices . . . . . . 1139--1146
              Tiziana Ginex and   
Jordi Muñoz-Muriedas and   
              Enric Herrero and   
               Enric Gibert and   
             Pietro Cozzini and   
                    F. J. Luque   Development and validation of
                                  hydrophobic molecular fields derived
                                  from the quantum mechanical IEF/PCM-MST
                                  solvation models in $3$D-QSAR  . . . . . 1147--1162
                  Xin Zhang and   
                  Yuan Zhao and   
                Honggao Yan and   
                 Zexing Cao and   
                      Yirong Mo   Combined QM(DFT)\slash MM molecular
                                  dynamics simulations of the deamination
                                  of cytosine by yeast cytosine deaminase
                                  (yCD)  . . . . . . . . . . . . . . . . . 1163--1174
                 Yuwei Zhou and   
                Jianming Wu and   
                         Xin Xu   Improving B3LYP heats of formation with
                                  three-dimensional molecular descriptors  1175--1190
          Svetlana Artemova and   
     Léonard Jaillet and   
                 Stephane Redon   Automatic molecular structure perception
                                  for the universal force field  . . . . . 1191--1205
      Liudmyla K. Sviatenko and   
                Leonid Gorb and   
            Frances C. Hill and   
         Danuta Leszczynska and   
              Jerzy Leszczynski   Structure and electrochemical properties
                                  for complexes of nitrocompounds with
                                  inorganic ions: a theoretical approach   1206--1213
                    Xiao Ru and   
                    Ce Song and   
                     Zijing Lin   A genetic algorithm encoded with the
                                  structural information of amino acids
                                  and dipeptides for efficient
                                  conformational searches of oligopeptides 1214--1222
        Ghazaleh Taherzadeh and   
               Yuedong Yang and   
                  Tuo Zhang and   
        Alan Wee-Chung Liew and   
                     Yaoqi Zhou   Sequence-based prediction of
                                  protein--peptide binding sites using
                                  support vector machine . . . . . . . . . 1223--1229
           Jan \vRezá\vc   Software News and Updates: Cuby: an
                                  integrative framework for computational
                                  chemistry  . . . . . . . . . . . . . . . 1230--1237
     Salvador Cardona-Serra and   
       Luis Escalera-Moreno and   
José J. Baldoví and   
Alejandro Gaita-Ariño and   
      Juan M. Clemente-Juan and   
               Eugenio Coronado   Software News and Updates: SIMPRE1.2:
                                  Considering the hyperfine and
                                  quadrupolar couplings and the nuclear
                                  spin bath decoherence  . . . . . . . . . 1238--1244

Journal of Computational Chemistry
Volume 37, Number 14, May 30, 2016

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                                  Volume 37, Issue 14  . . . . . . . . . . 1245--1245
                      Anonymous   Issue Information --- Copyright: Volume
                                  37, Issue 14 . . . . . . . . . . . . . . 1246--1246
                      Anonymous   Issue Information --- Editorial Board:
                                  Volume 37, Issue 14  . . . . . . . . . . 1247--1247
                      Anonymous   Issue Information --- Table of Contents:
                                  Volume 37, Issue 14  . . . . . . . . . . 1248--1250
               Hanzhong Liu and   
                 Minghai Li and   
                    Jue Fan and   
                 Shuanghong Huo   Inherent structure versus geometric
                                  metric for state space discretization    1251--1258
          Anna V. Pomogaeva and   
             Keiji Morokuma and   
            Alexey Y. Timoshkin   Trimeric cluster of lithium amidoborane
                                  --- the smallest unit for the modeling
                                  of hydrogen release mechanism  . . . . . 1259--1264
    Israel Fernández and   
      Fernando P. Cossío   Interplay between aromaticity and strain
                                  in double group transfer reactions to
                                  1,2-benzyne  . . . . . . . . . . . . . . 1265--1273
         David G. Tomlinson and   
            Andrey Asadchev and   
                 Mark S. Gordon   A new approach for second-order
                                  perturbation theory  . . . . . . . . . . 1274--1282
           Kristopher Opron and   
                  Kelin Xia and   
                Zach Burton and   
                    Guo-Wei Wei   Flexibility--rigidity index for
                                  protein--nucleic acid flexibility and
                                  fluctuation analysis . . . . . . . . . . 1283--1295
            Hoora Shaghaghi and   
     Hossein Pasha Ebrahimi and   
               Fariba Fathi and   
     Niloufar Bahrami Panah and   
        Mehdi Jalali-Heravi and   
               Mohsen Tafazzoli   A simple graphical approach to predict
                                  local residue conformation using NMR
                                  chemical shifts and density functional
                                  theory . . . . . . . . . . . . . . . . . 1296--1305
                   Bun Chan and   
              Jong-Won Song and   
            Yukio Kawashima and   
                 Kimihiko Hirao   Performance of the OP correlation
                                  functional in relation to its
                                  formulation: Influence of the exchange
                                  component and the effect of
                                  incorporating same-spin correlations . . 1306--1312
                 Shulai Lei and   
               Beate Paulus and   
                 Shujuan Li and   
               Burkhard Schmidt   Curvature-dependent adsorption of water
                                  inside and outside armchair carbon
                                  nanotubes  . . . . . . . . . . . . . . . 1313--1320
                    Lei Gao and   
                 Yanli Zeng and   
              Xueying Zhang and   
                  Lingpeng Meng   Comparative studies on group III $
                                  \sigma $-hole and $ \pi $-hole
                                  interactions . . . . . . . . . . . . . . 1321--1327

Journal of Computational Chemistry
Volume 37, Number 15, June 5, 2016

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                      Anonymous   Cover Image, Volume 37, Issue 15 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 1329--1333
    Charlotte Brückner and   
                   Bernd Engels   A theoretical description of charge
                                  reorganization energies in molecular
                                  organic P-type semiconductors  . . . . . 1335--1344
   Dumitru-Claudiu Sergentu and   
      Grégoire David and   
            Gilles Montavon and   
        Rémi Maurice and   
                Nicolas Galland   Scrutinizing ``Invisible'' astatine: a
                                  challenge for modern density functionals 1345--1354
             Majid El-Hamdi and   
              Miquel Sol\`a and   
               Jordi Poater and   
            Alexey Y. Timoshkin   Complexes of adamantane-based group 13
                                  Lewis acids and superacids: Bonding
                                  analysis and thermodynamics of hydrogen
                                  splitting  . . . . . . . . . . . . . . . 1355--1362
               Wei-Wei Wang and   
           Jing-Shuang Dang and   
                 Xiang Zhao and   
                 Shigeru Nagase   Regioselective multistep reconstructions
                                  of half-saturated zigzag carbon
                                  nanotubes  . . . . . . . . . . . . . . . 1363--1366
          Irina L. Rusakova and   
           Yury Yu. Rusakov and   
              Leonid B. Krivdin   First example of the correlated
                                  calculation of the one-bond
                                  tellurium--carbon spin--spin coupling
                                  constants: Relativistic effects,
                                  vibrational corrections, and solvent
                                  effects  . . . . . . . . . . . . . . . . 1367--1372
           Ignacy Cukrowski and   
            Paidamwoyo Mangondo   Interacting quantum fragments-rooted
                                  preorganized-interacting fragments
                                  attributed relative molecular stability
                                  of the Be$^{II}$ complexes of
                                  nitrilotriacetic acid and
                                  nitrilotri-$3$-propionic acid  . . . . . 1373--1387
         Muhammad A. Hagras and   
        Alexei A. Stuchebrukhov   Electron tunneling in proteins program   1388--1395
 Juan Pablo Martínez and   
              Miquel Sol\`a and   
           Alexander A. Voityuk   Theoretical estimation of the rate of
                                  photoinduced charge transfer reactions
                                  in triphenylamine C$_{60}$
                                  donor--acceptor conjugate  . . . . . . . 1396--1405

Journal of Computational Chemistry
Volume 37, Number 16, June 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 16 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1407--1412
            Shalini Awasthi and   
               Venkat Kapil and   
                Nisanth N. Nair   Sampling free energy surfaces as slices
                                  by combining umbrella sampling and
                                  metadynamics . . . . . . . . . . . . . . 1413--1424
                Yixiang Cao and   
              Thomas Hughes and   
                Dave Giesen and   
            Mathew D. Halls and   
         Alexander Goldberg and   
      Tati Reddy Vadicherla and   
             Madhavi Sastry and   
              Bhargav Patel and   
              Woody Sherman and   
          Andrew L. Weisman and   
            Richard A. Friesner   Highly efficient implementation of
                                  pseudospectral time-dependent
                                  density-functional theory for the
                                  calculation of excitation energies of
                                  large molecules  . . . . . . . . . . . . 1425--1441
           Vitaly V. Porsev and   
          Andrei V. Bandura and   
            Robert A. Evarestov   Temperature dependence of strain energy
                                  and thermodynamic properties of
                                  V$_2$O$_5$ -based single-walled
                                  nanotubes: Zone-folding approach . . . . 1442--1450
              Takao Tsuneda and   
             Raman K. Singh and   
                   Ayako Nakata   Relationship between orbital energy gaps
                                  and excitation energies for long-chain
                                  systems  . . . . . . . . . . . . . . . . 1451--1462
            Andrea Lombardi and   
            Fernando Pirani and   
           Antonio Lagan\`a and   
        Massimiliano Bartolomei   Energy transfer dynamics and kinetics of
                                  elementary processes (promoted) by
                                  gas-phase CO$_2$--N$_2$ collisions:
                                  Selectivity control by the anisotropy of
                                  the interaction  . . . . . . . . . . . . 1463--1475
              Zhenlian Chen and   
                         Jun Li   A new method applicable to study solid
                                  compounds with multiple polyhedral
                                  structures . . . . . . . . . . . . . . . 1476--1483
          Bitupon Borthakur and   
              Bernard Silvi and   
           Rian D. Dewhurst and   
              Ashwini K. Phukan   Theoretical strategies toward
                                  stabilization of singlet remote
                                  N-heterocyclic carbenes  . . . . . . . . 1484--1490
              John Kendrick and   
              Andrew D. Burnett   Software News and Updates: PDielec: the
                                  calculation of infrared and terahertz
                                  absorption for powdered crystals . . . . 1491--1504
             Shilpa R. Nath and   
           Sudheer S. Kurup and   
              Kaustubh A. Joshi   Software News and Updates: PyGlobal: a
                                  toolkit for automated compilation of
                                  DFT-based descriptors  . . . . . . . . . 1505--1510
             Gunter Hermann and   
               Vincent Pohl and   
   Jean Christophe Tremblay and   
               Beate Paulus and   
        Hans-Christian Hege and   
                    Axel Schild   Software News and Updates: ORBKIT: a
                                  modular Python toolbox for
                                  cross-platform postprocessing of quantum
                                  chemical wavefunction data . . . . . . . 1511--1520
          César Mogo and   
     João Brandão   Software News and Updates:
                                  $N$-dimensional switch function for
                                  energy conservation in multiprocess
                                  reaction dynamics  . . . . . . . . . . . 1521--1524

Journal of Computational Chemistry
Volume 37, Number 17, June 30, 2016

                      Anonymous   Cover Image, Volume 37, Issue 17 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1525--1530
              N. L. Moreira and   
             B. G. A. Brito and   
      J. N. Teixeira Rabelo and   
            Ladir Cândido   Quantum Monte Carlo study of the
                                  energetics of small hydrogenated and
                                  fluoride lithium clusters  . . . . . . . 1531--1536
          Andrey Alekseenko and   
              Olga Kononova and   
          Yaroslav Kholodov and   
            Kenneth A. Marx and   
                Valeri Barsegov   SOP-GPU: influence of solvent-induced
                                  hydrodynamic interactions on dynamic
                                  structural transitions in protein
                                  assemblies . . . . . . . . . . . . . . . 1537--1551
             Natalia Zarycz and   
        Patricio F. Provasi and   
          Gabriel I. Pagola and   
           Marta B. Ferraro and   
            Stefano Pelloni and   
               Paolo Lazzeretti   Computational study of basis set and
                                  electron correlation effects on anapole
                                  magnetizabilities of chiral molecules    1552--1558
                 Xianjin Xu and   
                  Zhiwei Ma and   
                Hongmin Sun and   
                    Xiaoqin Zou   SM-TF: a structural database of small
                                  molecule-transcription factor complexes  1559--1564
              Changjun Chen and   
                  Yanzhao Huang   Walking freely in the energy and
                                  temperature space by the modified
                                  replica exchange molecular dynamics
                                  method . . . . . . . . . . . . . . . . . 1565--1575
               Indrajit Deb and   
                  Rupak Pal and   
           Joanna Sarzynska and   
                 Ansuman Lahiri   Reparameterizations of the $ \chi $
                                  torsion and Lennard-Jones $ \sigma $
                                  parameters improve the conformational
                                  characteristics of modified uridines . . 1576--1588
           Martin A. Olsson and   
   Pär Söderhjelm and   
                       Ulf Ryde   Converging ligand-binding free energies
                                  obtained with free-energy perturbations
                                  at the quantum mechanical level  . . . . 1589--1600
           Daniel Bellinger and   
             Volker Settels and   
                 Wenlan Liu and   
           Reinhold F. Fink and   
                   Bernd Engels   Influence of a polarizable surrounding
                                  on the electronically excited states of
                                  aggregated perylene materials  . . . . . 1601--1610
             Simona Tu\vsar and   
                 Antonija Lesar   Hydrogen bonding in the hydroxysulfinyl
                                  radical-formic acid-water system: a
                                  theoretical study  . . . . . . . . . . . 1611--1625
               Alexey V. Akimov   Software News and Updates: Libra: an
                                  open-source ``methodology discovery''
                                  library for quantum and classical
                                  dynamics simulations . . . . . . . . . . 1626--1649

Journal of Computational Chemistry
Volume 37, Number 18, July 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 18 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1651--1656
            Sudhir K. Sahoo and   
                Nisanth N. Nair   CPMD/GULP QM/MM interface for modeling
                                  periodic solids: Implementation and its
                                  application in the study of Y-zeolite
                                  supported Rh$_n$ clusters  . . . . . . . 1657--1667
                 Donghai Yu and   
                 Ruobing Du and   
                  Ji-Chang Xiao   pK a prediction for acidic
                                  phosphorus-containing compounds using
                                  multiple linear regression with
                                  computational descriptors  . . . . . . . 1668--1671
         Francesco Zaccaria and   
           Lando P. Wolters and   
Célia Fonseca Guerra and   
                    Laura Orian   Insights on selenium and tellurium
                                  diaryldichalcogenides: a benchmark DFT
                                  study  . . . . . . . . . . . . . . . . . 1672--1680
           Travis V. Harris and   
             Robert K. Szilagyi   Protein environmental effects on
                                  iron-sulfur clusters: a set of rules for
                                  constructing computational models for
                                  inner and outer coordination spheres . . 1681--1696
             Leighton Jones and   
           Benjamin J. Whitaker   Modeling a halogen dance reaction
                                  mechanism: a density functional theory
                                  study  . . . . . . . . . . . . . . . . . 1697--1703
             Sean T. Holmes and   
                Fahri Alkan and   
         Robbie J. Iuliucci and   
            Karl T. Mueller and   
                 Cecil Dybowski   Analysis of the bond-valence method for
                                  calculating $^{29}$Si and $^{31}$P
                                  magnetic shielding in covalent network
                                  solids . . . . . . . . . . . . . . . . . 1704--1710
              Maria M. Reif and   
               Martin Zacharias   Rapid approximate calculation of water
                                  binding free energies in the whole
                                  hydration domain of (bio)macromolecules  1711--1724
               Zhiguang Jia and   
                   Jianhan Chen   Necessity of high-resolution for
                                  coarse-grained modeling of flexible
                                  proteins . . . . . . . . . . . . . . . . 1725--1733
               Yuedong Yang and   
                  Jian Zhan and   
                     Yaoqi Zhou   Software News and Updates: SPOT-Ligand:
                                  Fast and effective structure-based
                                  virtual screening by binding homology
                                  search according to ligand and receptor
                                  similarity . . . . . . . . . . . . . . . 1734--1739
      Israel Cabeza de Vaca and   
              Sandra Acebes and   
                 Victor Guallar   Software News and Updates: Ecoupling
                                  server: a tool to compute and analyze
                                  electronic couplings . . . . . . . . . . 1740--1745

Journal of Computational Chemistry
Volume 37, Number 19, July 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 19 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1747--1747
Fernando José Holguín-Gallego and   
Rodrigo Chávez-Calvillo and   
Marco García-Revilla and   
           Evelio Francisco and   
Ángel Martín Pendás and   
       Tomás Rocha-Rinza   Electron correlation in the interacting
                                  quantum atoms partition via
                                  coupled-cluster Lagrangian densities . . 1753--1765
Tereza Zábojníková and   
                Radim Cajzl and   
                Jakob Kljun and   
             Zden\vek Chval and   
                Iztok Turel and   
              Jaroslav V. Burda   Interactions of the ``piano-stool''
                                  [ruthenium(II)($
                                  \eta^6$-arene)(quinolone)Cl]$^+$
                                  complexes with water; DFT computational
                                  study  . . . . . . . . . . . . . . . . . 1766--1780
               David Mignon and   
                Thomas Simonson   Comparing three stochastic search
                                  algorithms for computational protein
                                  design: Monte Carlo, replica exchange
                                  Monte Carlo, and a multistart,
                                  steepest-descent heuristic . . . . . . . 1781--1793
         Stefan Vogt-Geisse and   
    Alejandro Toro-Labbé   Chemical potential and reaction
                                  electronic flux in symmetry controlled
                                  reactions  . . . . . . . . . . . . . . . 1794--1800
       Tatiana Vasilevskaya and   
          Maria G. Khrenova and   
      Alexander V. Nemukhin and   
                   Walter Thiel   Methodological aspects of QM/MM
                                  calculations: a case study on matrix
                                  metalloproteinase-2  . . . . . . . . . . 1801--1809
   Margareta R. A. Blomberg and   
             Per E. M. Siegbahn   Improved free energy profile for
                                  reduction of NO in cytochrome c
                                  dependent nitric oxide reductase (cNOR)  1810--1818
                 Piero Procacci   Reformulating the entropic contribution
                                  in molecular docking scoring functions   1819--1827
        Andreas Köster and   
               Thomas Spura and   
        Gábor Rutkai and   
                Jan Kessler and   
           Hendrik Wiebeler and   
              Jadran Vrabec and   
           Thomas D. Kühne   Assessing the accuracy of improved
                                  force-matched water models derived from
                                  ab initio molecular dynamics simulations 1828--1838
                Junpyo Kwon and   
             Myeongsang Lee and   
                     Sungsoo Na   Sodium chloride's effect on
                                  self-assembly of diphenylalanine bilayer 1839--1846
                Dmytro Kosenkov   Software News and Updates: PyFREC:
                                  Software for Förster electronic coupling
                                  evaluation in molecular fragments  . . . 1847--1854

Journal of Computational Chemistry
Volume 37, Number 20, July 30, 2016

                      Anonymous   Cover Image, Volume 37, Issue 20 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1855--1855
          Laura J. Kingsley and   
Juan Esquivel-Rodríguez and   
                  Ying Yang and   
             Daisuke Kihara and   
                 Markus A. Lill   Ranking protein--protein docking results
                                  using steered molecular dynamics and
                                  potential of mean force calculations . . 1861--1865
            Anthony Scemama and   
         Thomas Applencourt and   
             Emmanuel Giner and   
                Michel Caffarel   Quantum Monte Carlo with very large
                                  multideterminant wavefunctions . . . . . 1866--1875
          Emilia Makarewicz and   
                Jan Lundell and   
        Agnieszka J. Gordon and   
                Slawomir Berski   On the nature of interactions in the
                                  F$_2$OXe$^{\ldots }$NCCH$_3$ complex: Is
                                  there the Xe(IV)\bond N bond?  . . . . . 1876--1886
     Morten S. Nòrby and   
Jógvan Magnus Haugaard Olsen and   
             Jacob Kongsted and   
Hans Jòrgen Aagard Jensen   Multipole moments for embedding
                                  potentials: Exploring different atomic
                                  allocation algorithms  . . . . . . . . . 1887--1896
                 Jan Huwald and   
            Stephan Richter and   
             Bashar Ibrahim and   
                 Peter Dittrich   Compressing molecular dynamics
                                  trajectories: Breaking the
                                  one-bit-per-sample barrier . . . . . . . 1897--1906
                 Li-Hua Gan and   
                    Dan Lei and   
              Patrick W. Fowler   Structural interconnections and the role
                                  of heptagonal rings in endohedral
                                  trimetallic nitride template fullerenes  1907--1913
              Nils Herrmann and   
                Norah Heinz and   
               Michael Dolg and   
                    Xiaoyan Cao   Quantum chemical study of the
                                  autoxidation of ascorbate  . . . . . . . 1914--1923
               Hiroo Nozaki and   
               Yosuke Fujii and   
          Kazuhide Ichikawa and   
              Taku Watanabe and   
              Yuichi Aihara and   
              Akitomo Tachibana   Theoretical study of lithium ionic
                                  conductors by electronic stress tensor
                                  density and electronic kinetic energy
                                  density  . . . . . . . . . . . . . . . . 1924--1934
                Amani Tahat and   
             Jordi Martí   Multistate empirical valence bond study
                                  of temperature and confinement effects
                                  on proton transfer in water inside
                                  hydrophobic nanochannels . . . . . . . . 1935--1946

Journal of Computational Chemistry
Volume 37, Number 21, August 05, 2016

                      Anonymous   Cover Image, Volume 37, Issue 21 . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 21 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 1947--1952
              Ana M. Torres and   
             Steve Scheiner and   
                Ajit K. Roy and   
Andrés M. Garay-Tapia and   
            John Bustamante and   
                      Tapas Kar   Segmentation and additive approach: a
                                  reliable technique to study noncovalent
                                  interactions of large molecules at the
                                  surface of single-wall carbon nanotubes  1953--1961
Gabriel Aires Urquiza-Carvalho and   
     Wallace Duarte Fragoso and   
               Gerd Bruno Rocha   Assessment of semiempirical enthalpy of
                                  formation in solution as an effective
                                  energy function to discriminate
                                  native-like structures in protein decoy
                                  sets . . . . . . . . . . . . . . . . . . 1962--1972
         Tigran M. Abramyan and   
            James A. Snyder and   
         Aby A. Thyparambil and   
           Steven J. Stuart and   
               Robert A. Latour   Cluster analysis of molecular simulation
                                  trajectories for systems where both
                                  conformation and orientation of the
                                  sampled states are important . . . . . . 1973--1982
          Hiroaki Nishizawa and   
        Yoshifumi Nishimura and   
           Masato Kobayashi and   
               Stephan Irle and   
                   Hiromi Nakai   Three pillars for achieving quantum
                                  mechanical molecular dynamics
                                  simulations of huge systems:
                                  Divide-and-conquer, density-functional
                                  tight-binding, and massively parallel
                                  computation  . . . . . . . . . . . . . . 1983--1992
            Benjamin G. Janesko   Topological analysis of the electron
                                  delocalization range . . . . . . . . . . 1993--2005
                A. Lamiable and   
                P. Thevenet and   
              P. Tufféry   A critical assessment of hidden Markov
                                  model sub-optimal sampling strategies
                                  applied to the generation of peptide
                                  $3$D models  . . . . . . . . . . . . . . 2006--2016
              Tetsuro Nagai and   
     George A. Pantelopulos and   
           Takuya Takahashi and   
                 John E. Straub   On the use of mass scaling for stable
                                  and efficient simulated tempering with
                                  molecular dynamics . . . . . . . . . . . 2017--2028
              Steven Ramsey and   
             Crystal Nguyen and   
     Romelia Salomon-Ferrer and   
             Ross C. Walker and   
          Michael K. Gilson and   
                   Tom Kurtzman   Software News and Updates: Solvation
                                  thermodynamic mapping of molecular
                                  surfaces in AmberTools: GIST . . . . . . 2029--2037
            Maarten G. Wolf and   
            Martin Hoefling and   
Camilo Aponte-Santamaría and   
     Helmut Grubmüller and   
                Gerrit Groenhof   Erratum: Corrigendum: \tt g\_membed:
                                  Efficient insertion of a membrane
                                  protein into an equilibrated lipid
                                  bilayer with minimal perturbation  . . . 2038--2038

Journal of Computational Chemistry
Volume 37, Number 22, August 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 22 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2039--2043
            Kyrylo Klimenko and   
             Victor Kuz'min and   
        Liudmila Ognichenko and   
                Leonid Gorb and   
               Manoj Shukla and   
              Natalia Vinas and   
             Edward Perkins and   
           Pavel Polishchuk and   
          Anatoly Artemenko and   
              Jerzy Leszczynski   Novel enhanced applications of QSPR
                                  models: Temperature dependence of
                                  aqueous solubility . . . . . . . . . . . 2045--2051
       Heiner Schröder and   
                 Tobias Schwabe   Efficient determination of accurate
                                  atomic polarizabilities for polarizeable
                                  embedding calculations . . . . . . . . . 2052--2059
                 Steven W. Rick   A polarizable, charge transfer model of
                                  water using the Drude oscillator . . . . 2060--2066
               Dennis M. Elking   Torque and atomic forces for Cartesian
                                  tensor atomic multipoles with an
                                  application to crystal unit cell
                                  optimization . . . . . . . . . . . . . . 2067--2080
             Szymon \'Smiga and   
           Fabio Della Sala and   
              Adam Buksztel and   
         Ireneusz Grabowski and   
                Eduardo Fabiano   Accurate Kohn--Sham ionization
                                  potentials from scaled-opposite-spin
                                  second-order optimized effective
                                  potential methods  . . . . . . . . . . . 2081--2090
          Iwona E. Weidlich and   
               Igor V. Filippov   Software News and Updates: Using the
                                  Gini coefficient to measure the chemical
                                  diversity of small-molecule libraries    2091--2097
         Michelle M. Kuttel and   
         Jonas Ståhle and   
             Göran Widmalm   Software News and Updates: CarbBuilder:
                                  Software for building molecular models
                                  of complex oligo- and polysaccharide
                                  structures . . . . . . . . . . . . . . . 2098--2105
     Efthymios I. Ioannidis and   
           Terry Z. H. Gani and   
               Heather J. Kulik   Software News and Updates: molSimplify:
                                  a toolkit for automating discovery in
                                  inorganic chemistry  . . . . . . . . . . 2106--2117

Journal of Computational Chemistry
Volume 37, Number 23, September 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 23 . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 23 . . . . ii--ii
                      Anonymous   Cover Image, Volume 37, Issue 23 . . . . iii--iii
                      Anonymous   Issue Information  . . . . . . . . . . . 2119--2123
           Oleksandr Loboda and   
         Francesca Ingrosso and   
Manuel F. Ruiz-López and   
              Heribert Reis and   
                  Claude Millot   Dipole and quadrupole polarizabilities
                                  of the water molecule as a function of
                                  geometry . . . . . . . . . . . . . . . . 2125--2132
       Christian Tantardini and   
            Davide Ceresoli and   
                 Enrico Benassi   Source function and plane waves: Toward
                                  complete Bader analysis  . . . . . . . . 2133--2139
           Yusuke Kanematsu and   
         Masanori Tachikawa and   
                      Yu Takano   Inverse Ubbelohde effect in the short
                                  hydrogen bond of photosystem II:
                                  Relation between H/D isotope effect and
                                  symmetry in potential energy profile . . 2140--2145
                 Vera Stehr and   
           Reinhold F. Fink and   
             Carsten Deibel and   
                   Bernd Engels   Charge carrier mobilities in organic
                                  semiconductor crystals based on the
                                  spectral overlap . . . . . . . . . . . . 2146--2156
                Xiping Gong and   
               Zhenhua Chen and   
                         Wei Wu   The application of Cholesky
                                  decomposition in valence bond
                                  calculation  . . . . . . . . . . . . . . 2157--2162
           Emanuele Rossini and   
             Ernst-Walter Knapp   Erratum: Proton solvation in protic and
                                  aprotic solvents [J. Comput. Chem. 2015,
                                  37, 1082--1091]  . . . . . . . . . . . . 2163--2164

Journal of Computational Chemistry
Volume 37, Number 24, September 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 24 . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 24 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 2165--2169
             Evan J. Arthur and   
          Charles L. Brooks III   Efficient implementation of constant pH
                                  molecular dynamics on modern graphics
                                  processors . . . . . . . . . . . . . . . 2171--2180
             Matthias Witte and   
    Benjamin Grimm-Lebsanft and   
                  Arne Goos and   
             Stephan Binder and   
     Michael Rübhausen and   
             Martin Bernard and   
                 Adam Neuba and   
             Serge Gorelsky and   
              Uwe Gerstmann and   
              Gerald Henkel and   
          Wolf Gero Schmidt and   
            Sonja Herres-Pawlis   Optical response of the Cu$_2$S$_2$
                                  diamond core in Cu2II(NGuaS)$_2$Cl$_2$   2181--2192
              Sunghwan Choi and   
             Oh-Kyoung Kwon and   
                Jaewook Kim and   
                   Woo Youn Kim   Performance of heterogeneous computing
                                  with graphics processing unit and many
                                  integrated core for Hartree potential
                                  calculations on a numerical grid . . . . 2193--2201
                Manas Ghara and   
                  Sudip Pan and   
                Anand Kumar and   
             Gabriel Merino and   
            Pratim K. Chattaraj   Structure, stability, and nature of
                                  bonding in carbon monoxide bound EX3+
                                  complexes (E = group 14 element; X = H,
                                  F, Cl, Br, I)  . . . . . . . . . . . . . 2202--2211
                Li-Hong Liu and   
                     Dan Wu and   
                Shu-Hua Xia and   
                   Ganglong Cui   Theoretical study on photooxidation
                                  mechanism of ruthenium complex
                                  [Ru(II)-(bpy)$_2$ (TMBiimH$_2$)]$^{2+}$
                                  with molecular oxygen  . . . . . . . . . 2212--2219
           Andreas Erlebach and   
                   Timm Ott and   
            Christoph Otzen and   
         Stephanie Schubert and   
         Justyna Czaplewska and   
         Ulrich S. Schubert and   
                   Marek Sierka   Thermodynamic compatibility of actives
                                  encapsulated into PEG-PLA nanoparticles:
                                  In silico predictions and experimental
                                  verification . . . . . . . . . . . . . . 2220--2227
               Pingying Liu and   
               Qiufeng Chen and   
                        Jing Ma   Design of [2]rotaxane through image
                                  threshold segmentation of electrostatic
                                  potential image  . . . . . . . . . . . . 2228--2241

Journal of Computational Chemistry
Volume 37, Number 25, September 30, 2016

                      Anonymous   Cover Image, Volume 37, Issue 25 . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 25 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 2243--2247
   Praphasiri Dolbundalchok and   
       Daniel Peláez and   
               Emad F. Aziz and   
                   Annika Bande   Geometrical control of the interatomic
                                  coulombic decay process in quantum dots
                                  for infrared photodetectors  . . . . . . 2249--2259
            Lynn Groß and   
                Carmen Herrmann   Local electric dipole moments: a
                                  generalized approach . . . . . . . . . . 2260--2265
                 Jingbai Li and   
     Giovana da Silva Ramos and   
             Andrey Yu Rogachev   Stability of functionalized corannulene
                                  cations [R-C$_{20}$H$_{10}$]$^+$: an
                                  influence of the nature of R-Group . . . 2266--2278
 Jorge I. Martínez-Araya   A generalized operational formula based
                                  on total electronic densities to obtain
                                  $3$D pictures of the dual descriptor to
                                  reveal nucleophilic and electrophilic
                                  sites accurately on closed-shell
                                  molecules  . . . . . . . . . . . . . . . 2279--2303
                Junji Seino and   
                   Hiromi Nakai   Informatics-Based Energy Fitting Scheme
                                  for Correlation Energy at Complete Basis
                                  Set Limit  . . . . . . . . . . . . . . . 2304--2315
                 Xiaojun Li and   
                 Zhijun Yan and   
                       Shuna Li   The nature of structure and bonding
                                  between transition metal and mixed
                                  Si\bond Ge tetramers: a $ 20$-electron
                                  superatom system . . . . . . . . . . . . 2316--2323
            Lynn Groß and   
                Carmen Herrmann   Software News and Updates: GenLocDip: A
                                  Generalized Program to Calculate and
                                  Visualize Local Electric Dipole Moments  2324--2334

Journal of Computational Chemistry
Volume 37, Number 26, October 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 26 . . . . i--i
                      Anonymous   Cover Image, Volume 37, Issue 26 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 2335--2339
            Kaori Ueno-Noto and   
                   Keiko Takano   Water molecules inside protein structure
                                  affect binding of monosaccharides with
                                  HIV-1 antibody 2G12  . . . . . . . . . . 2341--2348
               Ruixing Wang and   
         Mikhail Ozhgibesov and   
                   Hajime Hirao   Partial Hessian fitting for determining
                                  force constant parameters in molecular
                                  mechanics  . . . . . . . . . . . . . . . 2349--2359
                D. Paschoal and   
          C. Fonseca Guerra and   
       M. A. L. de Oliveira and   
              T. C. Ramalho and   
               H. F. Dos Santos   Predicting Pt-195 NMR chemical shift
                                  using new relativistic all-electron
                                  basis set  . . . . . . . . . . . . . . . 2360--2373
            A. Daniel Boese and   
                  Joachim Sauer   Accurate adsorption energies for small
                                  molecules on oxide surfaces: CH$_4$
                                  /MgO(001) and C$_2$H$_6$ /MgO(001) . . . 2374--2385
                 Jiahui Liu and   
               Yiying Zheng and   
                   Ying Liu and   
                Haiyan Yuan and   
                 Jingping Zhang   Mechanistic insight on (E)-methyl
                                  3-(2-aminophenyl)acrylate cyclization
                                  reaction by multicatalysis of solvent
                                  and substrate  . . . . . . . . . . . . . 2386--2394
                    Jacek Koput   Ab initio potential energy surface and
                                  vibration-rotation energy levels of
                                  silicon dicarbide, SiC$_2$ . . . . . . . 2395--2402

Journal of Computational Chemistry
Volume 37, Number 27, October 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 27 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2403--2407
             Stuart J Davie and   
       Nicodemo Di Pasquale and   
            Paul L. A. Popelier   Incorporation of local structure into
                                  kriging models for the prediction of
                                  atomistic properties in the water
                                  decamer  . . . . . . . . . . . . . . . . 2409--2422
              Xingqing Xiao and   
           Michelle E. Hung and   
          Joshua N. Leonard and   
                  Carol K. Hall   Adding energy minimization strategy to
                                  peptide-design algorithm enables better
                                  search for RNA-binding peptides:
                                  Redesigned $ \lambda N $ peptide binds
                                  boxB RNA . . . . . . . . . . . . . . . . 2423--2435
              Changhao Wang and   
            Peter H. Nguyen and   
                 Kevin Pham and   
             Danielle Huynh and   
        Thanh-Binh Nancy Le and   
                Hongli Wang and   
                 Pengyu Ren and   
                        Ray Luo   Calculating protein--ligand binding
                                  affinities with MMPBSA: Method and error
                                  analysis . . . . . . . . . . . . . . . . 2436--2446
              Yu-ya Ohnishi and   
               Seiichiro Ten-no   Explicitly correlated
                                  frequency-independent second-order
                                  Green's function for accurate ionization
                                  energies . . . . . . . . . . . . . . . . 2447--2453
              Maria Fumanal and   
                 Chantal Daniel   Description of excited states in
                                  [Re(Imidazole)(CO)$_3$ (Phen)]$^+$
                                  including solvent and spin-orbit
                                  coupling effects: Density functional
                                  theory versus multiconfigurational
                                  wavefunction approach  . . . . . . . . . 2454--2466
             Wolfgang Quapp and   
             Josep Maria Bofill   Reaction rates in a theory of
                                  mechanochemical pathways . . . . . . . . 2467--2478

Journal of Computational Chemistry
Volume 37, Number 28, October 30, 2016

                      Anonymous   Cover Image, Volume 37, Issue 28 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2479--2483
      Václav Bazgier and   
                Karel Berka and   
             Michal Otyepka and   
           Pavel Baná\vs   Exponential repulsion improves
                                  structural predictability of molecular
                                  docking  . . . . . . . . . . . . . . . . 2485--2494
          Arghya Chakavorty and   
                     Lin Li and   
                    Emil Alexov   Electrostatic component of binding
                                  energy: Interpreting predictions from
                                  Poisson--Boltzmann equation and modeling
                                  protocols  . . . . . . . . . . . . . . . 2495--2507
                  D. Jiajun and   
                 J. R. Maza and   
                      Y. Xu and   
                      T. Xu and   
                   R. Momen and   
                 S. R. Kirk and   
                     S. Jenkins   A stress tensor and QTAIM perspective on
                                  the substituent effects of biphenyl
                                  subjected to torsion . . . . . . . . . . 2508--2517
            Roman \Lazarski and   
 Asbjörn Manfred Burow and   
    Luká\vs Grajciar and   
                   Marek Sierka   Density functional theory for molecular
                                  and periodic systems using density
                                  fitting and continuous fast multipole
                                  method: Analytical gradients . . . . . . 2518--2526
          Gennady L. Gutsev and   
            Kalayu G. Belay and   
         Lavrenty G. Gutsev and   
           Bala R. Ramachandran   Structure and properties of iron oxide
                                  clusters: From Fe$_6$ to Fe$_6$O$_{20}$
                                  and from Fe$_7$ to Fe$_7$O$_{24}$  . . . 2527--2536
      Benjamin P. Pritchard and   
                    Edmond Chow   Horizontal vectorization of electron
                                  repulsion integrals  . . . . . . . . . . 2537--2546

Journal of Computational Chemistry
Volume 37, Number 29, November 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 29 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2547--2551
           Steven C. Howell and   
               Xiangyun Qiu and   
               Joseph E. Curtis   Monte Carlo simulation algorithm for
                                  B-DNA  . . . . . . . . . . . . . . . . . 2553--2563
            Pierre O. Hubin and   
            Denis Jacquemin and   
           Laurence Leherte and   
          Daniel P. Vercauteren   Parameterization of the ReaxFF reactive
                                  force field for a proline-catalyzed
                                  aldol reaction . . . . . . . . . . . . . 2564--2572
           Velin Z. Spassov and   
                       Lisa Yan   A pH-dependent computational approach to
                                  the effect of mutations on protein
                                  stability  . . . . . . . . . . . . . . . 2573--2587
               Ming Xing Hu and   
                  Tianlv Xu and   
                 Roya Momen and   
                   Guo Huan and   
             Steven R. Kirk and   
           Samantha Jenkins and   
                Michael Filatov   A QTAIM and stress tensor investigation
                                  of the torsion path of a light-driven
                                  fluorene molecular rotary motor  . . . . 2588--2596
         Michael M. H. Graf and   
             Manuela Maurer and   
              Chris Oostenbrink   Free-energy calculations of residue
                                  mutations in a tripeptide using various
                                  methods to overcome inefficient sampling 2597--2605
       Nicodemo Di Pasquale and   
               Michael Bane and   
            Stuart J. Davie and   
            Paul L. A. Popelier   Software News and Updates: FEREBUS:
                                  Highly parallelized engine for kriging
                                  training . . . . . . . . . . . . . . . . 2606--2616

Journal of Computational Chemistry
Volume 37, Number 30, November 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 30 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2617--2621
             Michio Katouda and   
               Akira Naruse and   
            Yukihiko Hirano and   
              Takahito Nakajima   Massively parallel algorithm and
                                  implementation of RI-MP2 energy
                                  calculation for peta-scale many-core
                                  supercomputers . . . . . . . . . . . . . 2623--2633
                   Hong Liu and   
              You-Liang Zhu and   
              Zhong-Yuan Lu and   
     Florian Müller-Plathe   A kinetic chain growth algorithm in
                                  coarse-grained simulations . . . . . . . 2634--2646
         Carlos Silva Lopez and   
          Olalla Nieto Faza and   
             Frank De Proft and   
            Antonios Kolocouris   Assessing the attractive/repulsive force
                                  balance in axial cyclohexane C--H$_{ax}$
                                  \dottedbondY$_{ax}$ contacts: a combined
                                  computational analysis in
                                  monosubstituted cyclohexanes . . . . . . 2647--2658
           Matteo Signorile and   
           Alessandro Damin and   
           Francesca Bonino and   
       Valentina Crocell\`a and   
             Carlo Lamberti and   
                 Silvia Bordiga   The role of dispersive forces
                                  determining the energetics of adsorption
                                  in Ti zeolites . . . . . . . . . . . . . 2659--2666
           Patrick V. Holec and   
             Benjamin J. Hackel   Software News and Updates: PyMOL360:
                                  Multi-user gamepad control of molecular
                                  visualization software . . . . . . . . . 2667--2669

Journal of Computational Chemistry
Volume 37, Number 31, December 5, 2016

                      Anonymous   Cover Image, Volume 37, Issue 31 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2671--2671
        Sergei F. Vyboishchikov   Correlation energy, correlated electron
                                  density, and exchange-correlation
                                  potential in some spherically confined
                                  atoms  . . . . . . . . . . . . . . . . . 2677--2686
                Shinji Iida and   
            Tadaaki Mashimo and   
           Takashi Kurosawa and   
              Hironobu Hojo and   
                Hiroya Muta and   
                  Yuji Goto and   
        Yoshifumi Fukunishi and   
            Haruki Nakamura and   
                   Junichi Higo   Variation of free-energy landscape of
                                  the p53 C-terminal domain induced by
                                  acetylation: Enhanced conformational
                                  sampling . . . . . . . . . . . . . . . . 2687--2700
          Hiroaki Nishizawa and   
                Hisashi Okumura   Rapid QM/MM approach for biomolecular
                                  systems under periodic boundary
                                  conditions: Combination of the
                                  density-functional tight-binding theory
                                  and particle mesh Ewald method . . . . . 2701--2711
                  Tianlv Xu and   
              James Farrell and   
                  Yuning Xu and   
                 Roya Momen and   
             Steven R. Kirk and   
           Samantha Jenkins and   
                 David J. Wales   QTAIM and stress tensor interpretation
                                  of the (H$_2$O)$_5$ potential energy
                                  surface  . . . . . . . . . . . . . . . . 2712--2721
                   Huan Guo and   
  Alejandro Morales-Bayuelo and   
                  Tianlv Xu and   
                 Roya Momen and   
              Lingling Wang and   
                  Ping Yang and   
             Steven R. Kirk and   
               Samantha Jenkins   Distinguishing and quantifying the
                                  torquoselectivity in competitive
                                  ring-opening reactions using the stress
                                  tensor and QTAIM . . . . . . . . . . . . 2722--2733
               Son Tung Ngo and   
            Huynh Minh Hung and   
                Minh Tho Nguyen   Fast and accurate determination of the
                                  relative binding affinities of small
                                  compounds to HIV-1 protease using
                                  non-equilibrium work . . . . . . . . . . 2734--2742

Journal of Computational Chemistry
Volume 37, Number 32, December 15, 2016

                      Anonymous   Cover Image, Volume 37, Issue 32 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 2743--2747
        Noor Asidah Mohamed and   
        Richard T. Bradshaw and   
              Jonathan W. Essex   Evaluation of solvation free energies
                                  for small molecules with the AMOEBA
                                  polarizable force field  . . . . . . . . 2749--2758
           Shintaro Maekawa and   
          Krzysztof Moorthi and   
               Yasuteru Shigeta   Refractive indices of organo-metallic
                                  and -metalloid compounds: a long-range
                                  corrected DFT study  . . . . . . . . . . 2759--2769
                Nohad Gresh and   
              David Perahia and   
           Benoit de Courcy and   
              Johanna Foret and   
         Céline Roux and   
              Lea El-Khoury and   
       Jean-Philip Piquemal and   
                 Laurent Salmon   Complexes of a Zn-metalloenzyme binding
                                  site with hydroxamate-containing
                                  ligands. A case for detailed
                                  benchmarkings of polarizable molecular
                                  mechanics/dynamics potentials when the
                                  experimental binding structure is
                                  unknown  . . . . . . . . . . . . . . . . 2770--2782
           Ignacy Cukrowski and   
                Filip Sagan and   
         Mariusz Pawe\l Mitoraj   On the Stability of Cis- and
                                  Trans-2-Butene Isomers. An Insight Based
                                  on the FAMSEC, IQA, and ETS-NOCV Schemes 2783--2798
          Sadegh Salehzadeh and   
                Farahnaz Maleki   New equation for calculating total
                                  interaction energy in one noncyclic ABC
                                  triad and new insights into
                                  cooperativity of noncovalent bonds . . . 2799--2807
                 Youhan Lee and   
             Roberta Poloni and   
                      Jihan Kim   Probing gas adsorption in MOFs using an
                                  efficient ab initio Widom insertion
                                  Monte Carlo method . . . . . . . . . . . 2808--2815
                   Dan Fraenkel   Erratum: Corrigendum: Ion strength limit
                                  of computed excess functions based on
                                  the linearized Poisson--Boltzmann
                                  equation . . . . . . . . . . . . . . . . 2816--2816


Journal of Computational Chemistry
Volume 38, Number 1, January 05, 2017

                      Anonymous   Cover Image, Volume 38, Issue 1  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1--5
               Hiromi Nakai and   
          Takeshi Yoshikawa and   
                  Yutaro Nonaka   Efficient pole-search algorithm for
                                  dynamic polarizability: Toward
                                  alternative excited-state calculation
                                  for large systems  . . . . . . . . . . . 7--14
                Axel Wuttke and   
                Ricardo A. Mata   Visualizing dispersion interactions
                                  through the use of local orbital spaces  15--23
              Duc D. Nguyen and   
                    Guo-Wei Wei   The impact of surface area, volume,
                                  curvature, and Lennard-Jones potential
                                  to solvation modeling  . . . . . . . . . 24--36
                    Jacek Koput   Ab initio potential energy surface and
                                  vibration-rotation energy levels of
                                  beryllium monohydroxide  . . . . . . . . 37--43
 Alvaro Muñoz-Castro and   
                  R. Bruce King   Evaluation of bonding, electron
                                  affinity, and optical properties of
                                  M@C$_{28}$ (M = Zr, Hf, Th, and U): Role
                                  of $d$- and $f$-orbitals in endohedral
                                  fullerenes from relativistic DFT
                                  calculations . . . . . . . . . . . . . . 44--50
             Sebastian Dohm and   
              Eckhard Spohr and   
                   Martin Korth   Software News and Updates: Developing
                                  adaptive QM/MM computer simulations for
                                  electrochemistry . . . . . . . . . . . . 51--58

Journal of Computational Chemistry
Volume 38, Number 2, January 15, 2017

                      Anonymous   Cover Image, Volume 38, Issue 2  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 59--63
                 Ity Sharma and   
             George A. Kaminski   Using polarizable POSSIM force field and
                                  fuzzy-border continuum solvent model to
                                  calculate pK$_a$ shifts of protein
                                  residues . . . . . . . . . . . . . . . . 65--80
       James S. M. Anderson and   
   Juan I. Rodríguez and   
              Paul W. Ayers and   
           Andreas W. Götz   Relativistic (SR-ZORA) quantum theory of
                                  atoms in molecules properties  . . . . . 81--86
                 Enrico Benassi   Benchmarking of density functionals for
                                  a soft but accurate prediction and
                                  assignment of $^1$H and $^{13}$C NMR
                                  chemical shifts in organic and
                                  biological molecules . . . . . . . . . . 87--92
     Charles C. Kirkpatrick and   
             John N. Truong and   
                Bruce A. Kowert   $d$-electron count, ion-pairing and
                                  diagonal twist angles in
                                  metallo-bis(dithiolene) complexes  . . . 93--100
              Yosuke Sumiya and   
          Tetsuya Taketsugu and   
                  Satoshi Maeda   Full rate constant matrix contraction
                                  method for obtaining branching ratio of
                                  unimolecular decomposition . . . . . . . 101--109
           Peter L. Walters and   
            Thomas C. Allen and   
                    Nancy Makri   Direct determination of discrete
                                  harmonic bath parameters from molecular
                                  dynamics simulations . . . . . . . . . . 110--115
         Christopher Ehlert and   
              Tillmann Klamroth   The quest for best suited references for
                                  configuration interaction singles
                                  calculations of core excited states  . . 116--126

Journal of Computational Chemistry
Volume 38, Number 3, January 30, 2017

                      Anonymous   Cover Image, Volume 38, Issue 3  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 127--131
          Bastien Belzunces and   
               Sophie Hoyau and   
              Magali Benoit and   
            Nathalie Tarrat and   
                Fabienne Bessac   Theoretical study of the atrazine
                                  pesticide interaction with pyrophyllite
                                  and Ca$^{2+}$-montmorillonite clay
                                  surfaces . . . . . . . . . . . . . . . . 133--143
                 Li-Hua Gan and   
                     Rui Wu and   
              Jian-Lei Tian and   
              Joseph Clarke and   
         Christopher Gibson and   
              Patrick W. Fowler   From C$_{58}$ to C$_{62}$ and back:
                                  Stability, structural similarity, and
                                  ring current . . . . . . . . . . . . . . 144--151
                   Song Liu and   
                  Lizhe Zhu and   
              Fu Kit Sheong and   
                   Wei Wang and   
                    Xuhui Huang   Adaptive partitioning by local
                                  density-peaks: an efficient
                                  density-based clustering algorithm for
                                  analyzing molecular dynamics
                                  trajectories . . . . . . . . . . . . . . 152--160
          John P. Cvitkovic and   
             George A. Kaminski   Developing multisite empirical force
                                  field models for Pt(II) and cisplatin    161--168
                 Cheng Wang and   
                  Yingkai Zhang   Improving scoring-docking-screening
                                  powers of protein--ligand scoring
                                  functions using random forest  . . . . . 169--177
   Valter H. Carvalho-Silva and   
         Vincenzo Aquilanti and   
   Heibbe C. B. de Oliveira and   
               Kleber C. Mundim   Deformed transition-state theory:
                                  Deviation from Arrhenius behavior and
                                  application to bimolecular hydrogen
                                  transfer reaction rates in the tunneling
                                  regime . . . . . . . . . . . . . . . . . 178--188

Journal of Computational Chemistry
Volume 38, Number 4, February 5, 2017

                      Anonymous   Cover Image, Volume 38, Issue 4  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 189--193
            Fahimeh Ghasemi and   
             Afshin Fassihi and   
Horacio Pérez-Sánchez and   
          Alireza Mehri Dehnavi   The role of different sampling methods
                                  in improving biological activity
                                  prediction using deep belief network . . 195--203
            Julien Pilmé   Electron localization function from
                                  density components . . . . . . . . . . . 204--210
              Yuta Kajiwara and   
             Satoshi Yasuda and   
             Yuuki Takamuku and   
             Takeshi Murata and   
             Masahiro Kinoshita   Identification of thermostabilizing
                                  mutations for a membrane protein whose
                                  three-dimensional structure is unknown   211--223
     Salvador Cardona-Serra and   
                Stefano Sanvito   Influence of the dipolar interactions on
                                  the relative stability in spin crossover
                                  systems  . . . . . . . . . . . . . . . . 224--227
               Dmytro Bykov and   
              Thomas Kjaergaard   The GPU-enabled
                                  divide-expand-consolidate RI-MP2 method
                                  (DEC-RI-MP2) . . . . . . . . . . . . . . 228--237
         Danny Schlüns and   
            Mirko Franchini and   
       Andreas W. Götz and   
        Johannes Neugebauer and   
         Christoph R. Jacob and   
                 Lucas Visscher   Software News and Updates: Analytical
                                  gradients for subsystem density
                                  functional theory within the
                                  Slater-function-based Amsterdam density
                                  functional program . . . . . . . . . . . 238--249

Journal of Computational Chemistry
Volume 38, Number 5, February 15, 2017

                      Anonymous   Cover Image, Volume 38, Issue 5  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 251--255
            Alessandro Erba and   
         Dominique Caglioti and   
Claudio Marcelo Zicovich-Wilson and   
                 Roberto Dovesi   Nuclear-relaxed elastic and
                                  piezoelectric constants of materials:
                                  Computational aspects of two
                                  quantum-mechanical approaches  . . . . . 257--264
           Peter P. Passler and   
                Thomas S. Hofer   Conserving the linear momentum in
                                  stochastic dynamics: Dissipative
                                  particle dynamics as a general strategy
                                  to achieve local thermostatization in
                                  molecular dynamics simulations . . . . . 265--275
           Jason W. Labonte and   
       Jared Adolf-Bryfogle and   
          William R. Schief and   
                Jeffrey J. Gray   Residue-centric modeling and design of
                                  saccharide and glycoconjugate structures 276--287
          Marek Szczepaniak and   
                      Jerzy Moc   Anomerization reaction of bare and
                                  microhydrated $d$-erythrose via
                                  explicitly correlated coupled cluster
                                  approach. Two water molecules are
                                  optimal  . . . . . . . . . . . . . . . . 288--303
              Xiaoling Zhan and   
                     Hu Shi and   
              Hongguang Liu and   
                   Jin Yong Lee   Applying strong external electric field
                                  to thiophene-based oligomers: a
                                  promising approach to upgrade
                                  semiconducting performance . . . . . . . 304--311

Journal of Computational Chemistry
Volume 38, Number 6, March 5, 2017

                      Anonymous   Cover Image, Volume 38, Issue 6  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 313--317
              Marco Pagliai and   
           Giordano Mancini and   
              Ivan Carnimeo and   
            Nicola De Mitri and   
                Vincenzo Barone   Electronic absorption spectra of
                                  pyridine and nicotine in aqueous
                                  solution with a combined molecular
                                  dynamics and polarizable QM/MM approach  319--335
        Timothy L. Fletcher and   
            Paul L. A. Popelier   Toward amino acid typing for proteins in
                                  FFLUX  . . . . . . . . . . . . . . . . . 336--345
               Miguel Jorge and   
            Nuno M. Garrido and   
 Carlos J. V. Simões and   
     Cândida G. Silva and   
                Rui M. M. Brito   Predicting hydrophobic solvation by
                                  molecular simulation: 1. Testing
                                  united-atom alkane models  . . . . . . . 346--358
                   Miguel Jorge   Predicting hydrophobic solvation by
                                  molecular simulation: 2. New united-atom
                                  model for alkanes, alkenes, and alkynes  359--369
                    Amir Karton   How reliable is DFT in predicting
                                  relative energies of polycyclic aromatic
                                  hydrocarbon isomers? Comparison of
                                  functionals from different rungs of
                                  Jacob's ladder . . . . . . . . . . . . . 370--382
           Katharina Krause and   
                    Wim Klopper   Software News and Updates:
                                  Implementation of the Bethe--Salpeter
                                  equation in the TURBOMOLE program  . . . 383--388
              Ingo Heimbach and   
              Florian Rhiem and   
               Fabian Beule and   
                David Knodt and   
               Josef Heinen and   
                Robert O. Jones   Software News and Updates: pyMolDyn:
                                  Identification, structure, and
                                  properties of cavities/vacancies in
                                  condensed matter and molecules . . . . . 389--394

Journal of Computational Chemistry
Volume 38, Number 7, March 15, 2017

                      Anonymous   Cover Image, Volume 38, Issue 7  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 395--399
          Elena I. Davydova and   
          Anna S. Lisovenko and   
            Alexey Y. Timoshkin   Complex beryllium amidoboranes:
                                  Structures, stability, and evaluation of
                                  their potential as hydrogen storage
                                  materials  . . . . . . . . . . . . . . . 401--405
           Yoshio Nishimoto and   
              Dmitri G. Fedorov   Three-body expansion of the fragment
                                  molecular orbital method combined with
                                  density-functional tight-binding . . . . 406--418
              Antoni Oliver and   
      Christopher A. Hunter and   
              Rafel Prohens and   
       Josep L. Rosselló   A surface site interaction point
                                  methodology for macromolecules and huge
                                  molecular databases  . . . . . . . . . . 419--426
  Martina Rube\vsová and   
Veronika Jurásková and   
         Petr Slaví\vcek   Efficient modeling of liquid phase
                                  photoemission spectra and reorganization
                                  energies: Difficult case of multiply
                                  charged anions . . . . . . . . . . . . . 427--437
                Haiyan Yuan and   
                 Jingping Zhang   Mechanistic insights on DBU catalyzed $
                                  \beta $-amination of NBS to chalcone
                                  driving by water: Multiple roles of
                                  water  . . . . . . . . . . . . . . . . . 438--445
                 Beibei Liu and   
                   Bao Wang and   
               Rundong Zhao and   
                Yiying Tong and   
                    Guo-Wei Wei   Software News and Updates: ESES:
                                  Software for Eulerian solvent excluded
                                  surface  . . . . . . . . . . . . . . . . 446--466
Braulio Valdebenito-Maturana and   
  Jose Antonio Reyes-Suarez and   
            Jaime Henriquez and   
            David S. Holmes and   
            Raquel Quatrini and   
                 Ehmke Pohl and   
        Mauricio Arenas-Salinas   Software News and Updates: Mutantelec:
                                  An In Silico mutation simulation
                                  platform for comparative electrostatic
                                  potential profiling of proteins  . . . . 467--474

Journal of Computational Chemistry
Volume 38, Number 8, March 30, 2017

                      Anonymous   Cover Image, Volume 38, Issue 8  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 475--479
          Ricardo Pino-Rios and   
       Osvaldo Yañez and   
            Diego Inostroza and   
                  Lina Ruiz and   
            Carlos Cardenas and   
        Patricio Fuentealba and   
                William Tiznado   Proposal of a simple and effective local
                                  reactivity descriptor through a
                                  topological analysis of an
                                  orbital-weighted Fukui function  . . . . 481--488
             Michio Katouda and   
              Takahito Nakajima   MPI/OpenMP hybrid parallel algorithm for
                                  resolution of identity second-order
                                  Mòller--Plesset perturbation calculation
                                  of analytical energy gradient for
                                  massively parallel multicore
                                  supercomputers . . . . . . . . . . . . . 489--507
           Koen M. Visscher and   
           C. Ruben Vosmeer and   
            Rosa A. Luirink and   
                 Daan P. Geerke   A systematic approach to calibrate a
                                  transferable polarizable force field
                                  parameter set for primary alcohols . . . 508--517
   No\`elia Pueyo Bellafont and   
      Francesc Viñes and   
         Wolfgang Hieringer and   
                 Francesc Illas   Predicting core level binding energies
                                  shifts: Suitability of the projector
                                  augmented wave approach as implemented
                                  in VASP  . . . . . . . . . . . . . . . . 518--522
      Francesc Viñes and   
                 Francesc Illas   Electronic structure of stoichiometric
                                  and reduced ZnO from periodic
                                  relativistic all electron hybrid density
                                  functional calculations using numeric
                                  atom-centered orbitals . . . . . . . . . 523--529
      Isabel Lage-Estebanez and   
           Lourdes del Olmo and   
        Rafael López and   
José Manuel García de la Vega   The role of errors related to DFT
                                  methods in calculations involving ion
                                  pairs of ionic liquids . . . . . . . . . 530--540
                   Yang Xie and   
               Jinyong Ying and   
                     Dexuan Xie   Software News and Updates: SMPBS: Web
                                  server for computing biomolecular
                                  electrostatics using finite element
                                  solvers of size modified
                                  Poisson--Boltzmann equation  . . . . . . 541--552
          Adam K. Sieradzan and   
              Rafa\l Jakubowski   Software News and Updates: Introduction
                                  of steered molecular dynamics into UNRES
                                  coarse-grained simulations package . . . 553--562

Journal of Computational Chemistry
Volume 38, Number 9, April 5, 2017

                      Anonymous   Cover Image, Volume 38, Issue 9  . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 563--567
                  Zhubin Hu and   
                   Bin Zhou and   
               Zhenrong Sun and   
                     Haitao Sun   Prediction of excited-state properties
                                  of oligoacene crystals using polarizable
                                  continuum model-tuned range-separated
                                  hybrid functional approach . . . . . . . 569--575
       Guido F. von Rudorff and   
           Tobias Watermann and   
             Xiang-Yang Guo and   
              Daniel Sebastiani   Conformational Space of a Polyphilic
                                  Molecule with a Fluorophilic Side Chain
                                  Integrated in a DPPC Bilayer . . . . . . 576--583
                     Lin Li and   
         Arghya Chakravorty and   
                    Emil Alexov   DelPhiForce, a tool for electrostatic
                                  force calculations: Applications to
                                  macromolecular binding . . . . . . . . . 584--593
                  Chao Wang and   
               Yizhong Yuan and   
                   Xiaohui Tian   Assessment of range-separated exchange
                                  functionals and nonempirical functional
                                  tuning for calculating the static second
                                  hyperpolarizabilities of streptocyanines 594--600
               Sarah Witzke and   
       Nanna Holmgaard List and   
Jógvan Magnus Haugaard Olsen and   
           Casper Steinmann and   
           Michael Petersen and   
    Maarten T. P. Beerepoot and   
                 Jacob Kongsted   An averaged polarizable potential for
                                  multiscale modeling in phospholipid
                                  membranes  . . . . . . . . . . . . . . . 601--611
               Jingyuan Gao and   
                Wenliang Li and   
                 Jingping Zhang   Theoretical simulation of CO$_2$ capture
                                  in organic cage impregnated with
                                  polyoxometalates . . . . . . . . . . . . 612--619
                 Marc Esser and   
              Stefan Maintz and   
            Richard Dronskowski   Automated first-principles mapping for
                                  phase-change materials . . . . . . . . . 620--628
               Volker Lesch and   
              Diddo Diddens and   
     Carlos E. S. Bernardes and   
             Benjamin Golub and   
              Alain Dequidt and   
       Veronika Zeindlhofer and   
              Marcello Sega and   
        Christian Schröder   Software News and Updates: ForConX: a
                                  forcefield conversion tool based on XML  629--638

Journal of Computational Chemistry
Volume 38, Number 10, April 15, 2017

                      Anonymous   Cover Image, Volume 38, Issue 10 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 639--644
                Mina Jafari and   
              Paul M. Zimmerman   Reliable and efficient reaction path and
                                  transition state finding for surface
                                  reactions with the growing string method 645--658
Marilia T. C. Martins-Costa and   
    Manuel F. Ruiz-López   Reaching multi-nanosecond timescales in
                                  combined QM/MM molecular dynamics
                                  simulations through parallel horsetail
                                  sampling . . . . . . . . . . . . . . . . 659--668
                Koichi Ohno and   
            Naoki Kishimoto and   
            Takeaki Iwamoto and   
                   Hiroko Satoh   Global exploration of isomers and
                                  isomerization channels on the quantum
                                  chemical potential energy surface of
                                  H$_3$CNO$_3$ . . . . . . . . . . . . . . 669--687
      Vijay Madhav Miriyala and   
           Jan \vRezá\vc   Description of non-covalent interactions
                                  in SCC-DFTB methods  . . . . . . . . . . 688--697
         Pouya Partovi-Azar and   
                Payam Kaghazchi   Time-dependent density functional theory
                                  study on direction-dependent electron
                                  and hole transfer processes in molecular
                                  systems  . . . . . . . . . . . . . . . . 698--703
           Yoshimichi Andoh and   
            Noriyuki Yoshii and   
             Atsushi Yamada and   
                 Susumu Okazaki   Evaluation of atomic pressure in the
                                  multiple time-step integration algorithm 704--713
      Christian Margreitter and   
              Maria M. Reif and   
              Chris Oostenbrink   Update on phosphate and charged
                                  post-translationally modified amino acid
                                  parameters in the GROMOS force field . . 714--720
                Xiaojuan Yu and   
                    Hua Hou and   
                   Baoshan Wang   Prediction on dielectric strength and
                                  boiling point of gaseous molecules for
                                  replacement of SF$_6$  . . . . . . . . . 721--729
                   Kun Yuan and   
             Rui-Sheng Zhao and   
              Jia-Jia Zheng and   
                 Hong Zheng and   
             Shigeru Nagase and   
             Sheng-Dun Zhao and   
                Yan-Zhi Liu and   
                     Xiang Zhao   Van der Waals heterogeneous layer-layer
                                  carbon nanostructures involving $ \pi
                                  \cdots $H-C-C-H$ \cdots \pi \cdots
                                  $H-C-C-H stacking based on graphene and
                                  graphane sheets  . . . . . . . . . . . . 730--739
              Baofeng Zhang and   
             Denise Kilburg and   
              Peter Eastman and   
             Vijay S. Pande and   
              Emilio Gallicchio   Efficient Gaussian density formulation
                                  of volume and surface areas of
                                  macromolecules on graphical processing
                                  units  . . . . . . . . . . . . . . . . . 740--752
         Carlos E. S. Bernardes   Software News and Updates: AGGREGATES:
                                  Finding structures in simulation results
                                  of solutions . . . . . . . . . . . . . . 753--765

Journal of Computational Chemistry
Volume 38, Number 11, April 30, 2017

                      Anonymous   Cover Image, Volume 38, Issue 11 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 767--771
          Sirous Yourdkhani and   
         Miros\law Jab\lo\'nski   Revealing the physical nature and the
                                  strength of charge-inverted hydrogen
                                  bonds by SAPT(DFT), MP2, SCS-MP2, MP2C,
                                  and CCSD(T) methods  . . . . . . . . . . 773--780
      Francesc Viñes and   
 Oriol Lamiel-García and   
             Kyoung Chul Ko and   
               Jin Yong Lee and   
                 Francesc Illas   Systematic study of the effect of HSE
                                  functional internal parameters on the
                                  electronic structure and band gap of a
                                  representative set of metal oxides . . . 781--789
              Ryuhei Harada and   
                  Yu Takano and   
               Yasuteru Shigeta   Common folding processes of
                                  mini-proteins: Partial formations of
                                  secondary structures initiate the
                                  immediate protein folding  . . . . . . . 790--797
               Xiaojun Zhou and   
                       Fan Wang   Barrier heights of hydrogen-transfer
                                  reactions with diffusion quantum Monte
                                  Carlo method . . . . . . . . . . . . . . 798--806
    Álvaro Vega-Vega and   
          Carmen Barrientos and   
                  Antonio Largo   Metallic monoboronyl compounds:
                                  Prediction of their structure and
                                  comparison with the cyanide analogues    807--815
           Evelio Francisco and   
Daniel Menéndez Crespo and   
            Aurora Costales and   
Ángel Martín Pendás   A multipolar approach to the interatomic
                                  covalent interaction energy  . . . . . . 816--829
            Ellie L. Fought and   
          Vaibhav Sundriyal and   
            Masha Sosonkina and   
              Theresa L. Windus   Saving time and energy with
                                  oversubscription and semi-direct
                                  Mòller--Plesset second order perturbation
                                  methods  . . . . . . . . . . . . . . . . 830--841
            Ilya A. Kaliman and   
                 Anna I. Krylov   Software News and Updates: New algorithm
                                  for tensor contractions on multi-core
                                  CPUs, GPUs, and accelerators enables
                                  CCSD and EOM-CCSD calculations with over
                                  1000 basis functions on a single compute
                                  node . . . . . . . . . . . . . . . . . . 842--853

Journal of Computational Chemistry
Volume 38, Number 12, May 5, 2017

                      Anonymous   Cover Image, Volume 38, Issue 12 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 855--859
            Lynn Groß and   
        Marc Philipp Bahlke and   
           Torben Steenbock and   
           Christian Klinke and   
                Carmen Herrmann   Modeling adsorbate-induced property
                                  changes of carbon nanotubes  . . . . . . 861--868
           Saswata Dasgupta and   
                John M. Herbert   Standard grids for high-precision
                                  integration of modern density
                                  functionals: SG-2 and SG-3 . . . . . . . 869--882
      Renato Pereira Orenha and   
Régis Tadeu Santiago and   
Roberto Luiz Andrade Haiduke and   
Sérgio Emanuel Galembeck   How computational methods and
                                  relativistic effects influence the study
                                  of chemical reactions involving Ru--NO
                                  complexes? . . . . . . . . . . . . . . . 883--891
                    Jacek Koput   Ab initio potential energy surface and
                                  vibration-rotation energy levels of
                                  sulfur dioxide . . . . . . . . . . . . . 892--900
          Yaowarat Surakhot and   
              Viktor Laszlo and   
        Chirawat Chitpakdee and   
            Vinich Promarak and   
        Taweesak Sudyoadsuk and   
              Nawee Kungwan and   
              Tim Kowalczyk and   
               Stephan Irle and   
         Siriporn Jungsuttiwong   Theoretical rationalization for reduced
                                  charge recombination in bulky
                                  carbazole-based sensitizers in solar
                                  cells  . . . . . . . . . . . . . . . . . 901--909
              Rei Matsuzaki and   
              Satoshi Yabushita   Optimization of complex Slater-type
                                  functions with analytic derivative
                                  methods for describing photoionization
                                  differential cross sections  . . . . . . 910--925
               Anton Raskovalov   Software News and Updates: A new
                                  extension of classical molecular
                                  dynamics: an electron transfer algorithm 926--932
          Simon W. L. Hogan and   
               Tanja van Mourik   Erratum: Corrigendum: Competition
                                  between Hydrogen and Halogen Bonding in
                                  Halogenated 1-Methyluracil:Water Systems 933--933

Journal of Computational Chemistry
Volume 38, Number 13, May 15, 2017

                      Anonymous   Cover Image, Volume 38, Issue 13 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 935--939
              Duc D. Nguyen and   
                   Bao Wang and   
                    Guo-Wei Wei   Accurate, robust, and reliable
                                  calculations of Poisson--Boltzmann
                                  binding energies . . . . . . . . . . . . 941--948
             Sean T. Holmes and   
                    Shi Bai and   
         Robbie J. Iuliucci and   
            Karl T. Mueller and   
                 Cecil Dybowski   Calculations of solid-state $^{43}$Ca
                                  NMR parameters: a comparison of periodic
                                  and cluster approaches and an evaluation
                                  of DFT functionals . . . . . . . . . . . 949--956
Jesús Jara-Cortés and   
José Manuel Guevara-Vela and   
Ángel Martín Pendás and   
Jesús Hernández-Trujillo   Chemical bonding in excited states:
                                  Energy transfer and charge
                                  redistribution from a real space
                                  perspective  . . . . . . . . . . . . . . 957--970
                 Hujun Shen and   
               Mingsen Deng and   
                   Yachao Zhang   Extension of CAVS coarse-grained model
                                  to phospholipid membranes: the
                                  importance of electrostatics . . . . . . 971--980
   Jurgens Hendrik de Lange and   
               Ignacy Cukrowski   Toward deformation densities for
                                  intramolecular interactions without
                                  radical reference states using the
                                  fragment, atom, localized, delocalized,
                                  and interatomic (FALDI) charge density
                                  decomposition scheme . . . . . . . . . . 981--997
        Stefania Di Tommaso and   
             Diane Bousquet and   
            Delphine Moulin and   
Frédéric Baltenneck and   
             Priscilla Riva and   
         Hervé David and   
                 Aziz Fadli and   
  Jérôme Gomar and   
             Ilaria Ciofini and   
                    Carlo Adamo   Theoretical approaches for predicting
                                  the color of rigid dyes in solution  . . 998--1004
        Timothy L. Fletcher and   
            Paul L. A. Popelier   FFLUX: Transferability of polarizable
                                  machine-learned electrostatics in
                                  peptide chains . . . . . . . . . . . . . 1005--1014
                      Anonymous   Erratum  . . . . . . . . . . . . . . . . 1015--1015

Journal of Computational Chemistry
Volume 38, Number 14, May 30, 2017

                      Anonymous   Cover Image, Volume 38, Issue 14 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1017--1021
          Florian Krausbeck and   
            Jan-Grimo Sobez and   
                  Markus Reiher   Stabilization of activated fragments by
                                  shell-wise construction of an embedding
                                  environment  . . . . . . . . . . . . . . 1023--1038
             Riccardo Volpi and   
                Mathieu Linares   Study of the cold charge transfer state
                                  separation at the TQ1/PC$_{71}$ BM
                                  interface  . . . . . . . . . . . . . . . 1039--1048
             Jih\`ene Jerbi and   
             Michael Springborg   Computational study of the reactivity of
                                  cytosine derivatives . . . . . . . . . . 1049--1056
              Changhao Wang and   
                    Li Xiao and   
                        Ray Luo   Numerical interpretation of molecular
                                  surface field in dielectric modeling of
                                  solvation  . . . . . . . . . . . . . . . 1057--1070
          Gaëtan Rubez and   
    Jean-Matthieu Etancelin and   
           Xavier Vigouroux and   
           Michael Krajecki and   
       Jean-Charles Boisson and   
              Eric Hénon   GPU accelerated implementation of NCI
                                  calculations using promolecular density  1071--1083
            Marika Savarese and   
             Umberto Raucci and   
             Ryoichi Fukuda and   
                Carlo Adamo and   
             Masahiro Ehara and   
                 Nadia Rega and   
                 Ilaria Ciofini   Comparing the performance of TD-DFT and
                                  SAC-CI methods in the description of
                                  excited states potential energy
                                  surfaces: an excited state proton
                                  transfer reaction as case study  . . . . 1084--1092
                 Uyen Q. Ly and   
             My-Phuong Pham and   
           Maurice J. Marks and   
                Thanh N. Truong   Density functional theory study of
                                  mechanism of epoxy-carboxylic acid
                                  curing reaction  . . . . . . . . . . . . 1093--1102

Journal of Computational Chemistry
Volume 38, Number 15, June 5, 2017

                      Anonymous   Cover Image, Volume 38, Issue 15 . . . . i--i
                      Anonymous   Cover Image, Volume 38, Issue 15 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 1103--1110
             Jonathan Hirst and   
                  Wonpil Im and   
                 Joan-Emma Shea   Introduction: Simulating Biomolecules:
                                  Festschrift to commemorate the 60th
                                  birthday of Charles L. Brooks III  . . . 1111--1113
                 Sunhwan Jo and   
                   Xi Cheng and   
                  Jumin Lee and   
              Seonghoon Kim and   
              Sang-Jun Park and   
            Dhilon S. Patel and   
           Andrew H. Beaven and   
                 Kyu Il Lee and   
                   Huan Rui and   
              Soohyung Park and   
                Hui Sun Lee and   
             Beno\^\it Roux and   
  Alexander D. MacKerell Jr and   
          Jeffrey B. Klauda and   
                   Yifei Qi and   
                      Wonpil Im   Review: CHARMM--GUI 10 years for
                                  biomolecular modeling and simulation . . 1114--1124
              Ester Sesmero and   
            Jodian A. Brown and   
                  Ian F. Thorpe   Molecular simulations to delineate
                                  functional conformational transitions in
                                  the HCV polymerase . . . . . . . . . . . 1125--1137
               Alex Dickson and   
      Christopher T. Bailey and   
               John Karanicolas   Optimal allosteric stabilization sites
                                  using contact stabilization analysis . . 1138--1146
                     You Xu and   
           Alessandra Villa and   
                Lennart Nilsson   The free energy of locking a ring:
                                  Changing a deoxyribonucleoside to a
                                  locked nucleic acid  . . . . . . . . . . 1147--1157
     Hossein Mohammadiarani and   
                Harish Vashisth   Insulin mimetic peptide S371 folds into
                                  a helical structure  . . . . . . . . . . 1158--1166
             Yoshiharu Mori and   
                   Yuko Okamoto   Conformational changes of ubiquitin
                                  under high pressure conditions: a
                                  pressure simulated tempering molecular
                                  dynamics study . . . . . . . . . . . . . 1167--1173
                   Qi Huang and   
         Jocelyn M. Rodgers and   
          Russell J. Hemley and   
                 Toshiko Ichiye   Extreme biophysics: Enzymes under
                                  pressure . . . . . . . . . . . . . . . . 1174--1182
                    Zhe Jia and   
          Christine Ackroyd and   
               Tingting Han and   
             Vibhor Agrawal and   
                Yinling Liu and   
        Kenneth Christensen and   
                   Brian Dominy   Effects from metal ion in tumor
                                  endothelial marker 8 and anthrax
                                  protective antigen: BioLayer
                                  Interferometry experiment and molecular
                                  dynamics simulation study  . . . . . . . 1183--1190
       Christopher G. Myers and   
          B. Montgomery Pettitt   Phage-like packing structures with mean
                                  field sequence dependence  . . . . . . . 1191--1197
           Robert C. Harris and   
                Nanjie Deng and   
             Ronald M. Levy and   
           Ryosuke Ishizuka and   
            Nobuyuki Matubayasi   Computing conformational free energy
                                  differences in explicit solvent: an
                                  efficient thermodynamic cycle using an
                                  auxiliary potential and a free energy
                                  functional constructed from the end
                                  points . . . . . . . . . . . . . . . . . 1198--1208
             Leon A. Sakkal and   
          Kyle Z. Rajkowski and   
                 Roger S. Armen   Prediction of consensus binding mode
                                  geometries for related chemical series
                                  of positive allosteric modulators of
                                  adenosine and muscarinic acetylcholine
                                  receptors  . . . . . . . . . . . . . . . 1209--1228
                    Cen Gao and   
             Jeremy Desaphy and   
                   Michal Vieth   Are induced fit protein conformational
                                  changes caused by ligand-binding
                                  predictable? A molecular dynamics
                                  investigation  . . . . . . . . . . . . . 1229--1237
            E. Prabhu Raman and   
   Sirish Kaushik Lakkaraju and   
        Rajiah Aldrin Denny and   
      Alexander D. MacKerell Jr   Estimation of relative free energies of
                                  binding using pre-computed ensembles
                                  based on the single-step free energy
                                  perturbation and the site-identification
                                  by ligand competitive saturation
                                  approaches . . . . . . . . . . . . . . . 1238--1251
        Sam Tonddast-Navaei and   
         Bharath Srinivasan and   
               Jeffrey Skolnick   On the importance of composite protein
                                  multiple ligand interactions in protein
                                  pockets  . . . . . . . . . . . . . . . . 1252--1259
       Christopher R. Ellis and   
           Cheng-Chieh Tsai and   
                Fang-Yu Lin and   
                      Jana Shen   Conformational dynamics of cathepsin D
                                  and binding to a small-molecule BACE1
                                  inhibitor  . . . . . . . . . . . . . . . 1260--1269
                  Shuai Wei and   
      Charles L. Brooks III and   
                 Aaron T. Frank   A rapid solvent accessible surface area
                                  estimator for coarse grained molecular
                                  simulations  . . . . . . . . . . . . . . 1270--1274
            Lisa E. Felberg and   
           David H. Brookes and   
                Eng-Hui Yap and   
           Elizabeth Jurrus and   
            Nathan A. Baker and   
             Teresa Head-Gordon   PB-AM: an open-source, fully analytical
                                  linear Poisson--Boltzmann solver . . . . 1275--1282

Journal of Computational Chemistry
Volume 38, Number 16, June 15, 2017

                      Anonymous   Cover Image, Volume 38, Issue 16 . . . . i--i
                      Anonymous   Cover Image, Volume 38, Issue 16 . . . . ii--ii
                      Anonymous   Issue Information  . . . . . . . . . . . 1283--1290
             Garrett B. Goh and   
            Nathan O. Hodas and   
                 Abhinav Vishnu   Review: Deep learning for computational
                                  chemistry  . . . . . . . . . . . . . . . 1291--1307
            Bercem Dutagaci and   
              Maryam Sayadi and   
                   Michael Feig   Heterogeneous dielectric generalized
                                  Born model with a van der Waals term
                                  provides improved association energetics
                                  of membrane-embedded transmembrane
                                  helices  . . . . . . . . . . . . . . . . 1308--1320
             Andrea Bazzoli and   
               John Karanicolas   ``Solvent hydrogen-bond occlusion'': a
                                  new model of polar desolvation for
                                  biomolecular energetics  . . . . . . . . 1321--1331
                Kuo Hao Lee and   
                   Jianhan Chen   Optimization of the GBMV2 implicit
                                  solvent force field for accurate
                                  simulation of protein conformational
                                  equilibria . . . . . . . . . . . . . . . 1332--1341
              Mark A. Olson and   
             Michael S. Lee and   
                    In-Chul Yeh   Membrane insertion of fusion peptides
                                  from Ebola and Marburg viruses studied
                                  by replica-exchange molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1342--1352
                   Bin Song and   
          Nathaniel Charest and   
Herbert Alexander Morriss-Andrews and   
           Valeria Molinero and   
                 Joan-Emma Shea   Systematic derivation of implicit
                                  solvent models for the study of polymer
                                  collapse . . . . . . . . . . . . . . . . 1353--1361
          Fouad S. Husseini and   
             David Robinson and   
               Neil T. Hunt and   
          Anthony W. Parker and   
              Jonathan D. Hirst   Computing infrared spectra of proteins
                                  using the exciton model  . . . . . . . . 1362--1375
            Fiona L. Kearns and   
          Phillip S. Hudson and   
          Henry L. Woodcock and   
                 Stefan Boresch   Computing converged free energy
                                  differences between levels of theory via
                                  nonequilibrium work methods: Challenges
                                  and opportunities  . . . . . . . . . . . 1376--1388
        Sudipta Kumar Sinha and   
                Mohit Mehta and   
                  Sandeep Patel   A charge equilibration formalism for
                                  treating charge transfer effects in MD
                                  simulations: Application to water
                                  clusters . . . . . . . . . . . . . . . . 1389--1409
               Jaewoon Jung and   
                    Yuji Sugita   Multiple program/multiple data molecular
                                  dynamics method with multiple time step
                                  integrator for large biological systems  1410--1418
            Travis Johnston and   
                 Boyu Zhang and   
                  Adam Liwo and   
            Silvia Crivelli and   
                 Michela Taufer   In situ data analytics and indexing of
                                  protein trajectories . . . . . . . . . . 1419--1430
          Catherine A. Hurd and   
         Nicholas A. Besley and   
                 David Robinson   A QM/MM study of the nature of the
                                  entatic state in plastocyanin  . . . . . 1431--1437
                   Cathy Ng and   
 Padmavathy Nandha Premnath and   
                  Olgun Guvench   Rigidity and flexibility in the
                                  tetrasaccharide linker of proteoglycans
                                  from atomic-resolution molecular
                                  simulation . . . . . . . . . . . . . . . 1438--1446
            Osamu Miyashita and   
          Chigusa Kobayashi and   
              Takaharu Mori and   
                Yuji Sugita and   
                  Florence Tama   Flexible fitting to cryo-EM density map
                                  using ensemble molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1447--1461
            Michael D. Ward and   
            Shivangi Nangia and   
                    Eric R. May   Evaluation of the hybrid resolution PACE
                                  model for the study of folding,
                                  insertion, and pore formation of
                                  membrane associated peptides . . . . . . 1462--1471
                Greg Starek and   
         J. Alfredo Freites and   
           Simon Bern\`eche and   
              Douglas J. Tobias   Gating energetics of a voltage-dependent
                                  K$^+$ channel pore domain  . . . . . . . 1472--1478
             Asanga Bandara and   
                Afra Panahi and   
     George A. Pantelopulos and   
                 John E. Straub   Exploring the structure and stability of
                                  cholesterol dimer formation in
                                  multicomponent lipid bilayers  . . . . . 1479--1488

Journal of Computational Chemistry
Volume 38, Number 17, June 30, 2017

                      Anonymous   Cover Image, Volume 38, Issue 17 . . . . i--i
                      Anonymous   Issue Information  . . . . . . . . . . . 1489--1494
         Christian J. Suess and   
          Jonathan D. Hirst and   
             Nicholas A. Besley   Quantum chemical calculations of
                                  tryptophan heme electron and excitation
                                  energy transfer rates in myoglobin . . . 1495--1502
               Hiroto Tachikawa   Effects of zero point vibration on the
                                  reaction dynamics of water dimer cations
                                  following ionization . . . . . . . . . . 1503--1508
Juan Carlos Sancho-García and   
Ángel José Pérez-Jiménez and   
            Marika Savarese and   
 Éric Brémond and   
                    Carlo Adamo   Determining the role of the underlying
                                  orbital-dependence of PBE0-DH and
                                  PBE-QIDH double-hybrid density
                                  functionals  . . . . . . . . . . . . . . 1509--1514
               Vincent Pohl and   
             Gunter Hermann and   
       Jean Christophe Tremblay   An open-source framework for analyzing
                                  $N$-electron dynamics. I.
                                  Multideterminantal wave functions  . . . 1515--1527
                 Chong Yang and   
                  Andreas Dreuw   Evaluation of the restricted virtual
                                  space approximation in the
                                  algebraic-diagrammatic construction
                                  scheme for the polarization propagator
                                  to speed-up excited-state calculations   1528--1537
         Sjoerd J. de Vries and   
               Martin Zacharias   Fast and accurate grid representations
                                  for atom-based docking with partne