Table of contents for issues of Journal of Computational Chemistry

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Volume 19, Number 1, January 15, 1998
Volume 21, Number 1, January 15, 2000
Volume 21, Number 2, January 30, 2000
Volume 21, Number 3, February, 2000
Volume 21, Number 4, March, 2000
Volume 21, Number 5, April 15, 2000
Volume 21, Number 6, April 30, 2000
Volume 21, Number 7, May, 2000
Volume 21, Number 8, June, 2000
Volume 21, Number 9, July 15, 2000
Volume 21, Number 10, July 30, 2000
Volume 21, Number 11, August, 2000
Volume 21, Number 12, September, 2000
Volume 21, Number 13, October, 2000
Volume 21, Number 14, November 15, 2000
Volume 21, Number 15, November 30, 2000
Volume 21, Number 16, December, 2000
Volume 22, Number 6, April 30, 2001
Volume 22, Number 1, January 15, 2001
Volume 22, Number 2, January 30, 2001
Volume 22, Number 3, February, 2001
Volume 22, Number 4, March, 2001
Volume 22, Number 5, April 15, 2001
Volume 22, Number 6, April 30, 2001
Volume 22, Number 7, May, 2001
Volume 22, Number 8, June, 2001
Volume 22, Number 9, July 15, 2001
Volume 22, Number 10, July 30, 2001
Volume 22, Number 11, August, 2001
Volume 22, Number 12, September, 2001
Volume 22, Number 13, October, 2001
Volume 22, Number 14, November 15, 2001
Volume 22, Number 15, November 30, 2001
Volume 22, Number 16, December, 2001
Volume 23, Number 1, January 15, 2002
Volume 23, Number 2, January 30, 2002
Volume 23, Number 3, February, 2002
Volume 23, Number 4, March, 2002
Volume 23, Number 5, April 15, 2002
Volume 23, Number 6, April 30, 2002
Volume 23, Number 7, May, 2002
Volume 23, Number 8, June, 2002
Volume 23, Number 9, July 15, 2002
Volume 23, Number 10, July 30, 2002
Volume 23, Number 11, August, 2002
Volume 23, Number 12, September, 2002
Volume 23, Number 13, October, 2002
Volume 23, Number 14, November 15, 2002
Volume 23, Number 15, November 30, 2002
Volume 23, Number 16, December, 2002
Volume 24, Number 1, January 15, 2003
Volume 24, Number 2, January 30, 2003
Volume 24, Number 3, February, 2003
Volume 24, Number 4, March, 2003
Volume 24, Number 5, April 15, 2003
Volume 24, Number 6, April 30, 2003
Volume 24, Number 7, May, 2003
Volume 24, Number 8, June, 2003
Volume 24, Number 9, July 15, 2003
Volume 24, Number 10, July 30, 2003
Volume 24, Number 11, August, 2003
Volume 24, Number 12, September, 2003
Volume 24, Number 13, October, 2003
Volume 24, Number 14, November 15, 2003
Volume 24, Number 15, November 30, 2003
Volume 24, Number 16, December, 2003
Volume 25, Number 1, January 15, 2004
Volume 25, Number 2, January 30, 2004
Volume 25, Number 3, February, 2004
Volume 25, Number 4, March, 2004
Volume 25, Number 5, April 15, 2004
Volume 25, Number 6, April 30, 2004
Volume 25, Number 7, May, 2004
Volume 25, Number 8, June, 2004
Volume 25, Number 9, July 15, 2004
Volume 25, Number 10, July 30, 2004
Volume 25, Number 11, August, 2004
Volume 25, Number 12, September, 2004
Volume 25, Number 13, October, 2004
Volume 25, Number 14, November 15, 2004
Volume 25, Number 15, November 30, 2004
Volume 25, Number 16, December, 2004
Volume 26, Number 1, January 15, 2005
Volume 26, Number 2, January 30, 2005
Volume 26, Number 3, February, 2005
Volume 26, Number 4, March, 2005
Volume 26, Number 5, April 15, 2005
Volume 26, Number 6, April 30, 2005
Volume 26, Number 7, May, 2005
Volume 26, Number 8, June, 2005
Volume 26, Number 9, July 15, 2005
Volume 26, Number 10, July 30, 2005
Volume 26, Number 11, August, 2005
Volume 26, Number 12, September, 2005
Volume 26, Number 13, October, 2005
Volume 26, Number 14, November 15, 2005
Volume 26, Number 15, November 30, 2005
Volume 26, Number 16, December, 2005
Volume 27, Number 1, January 15, 2006
Volume 27, Number 2, January 30, 2006
Volume 27, Number 3, February, 2006
Volume 27, Number 4, March, 2006
Volume 27, Number 5, April 15, 2006
Volume 27, Number 6, April 30, 2006
Volume 27, Number 7, May, 2006
Volume 27, Number 8, June, 2006
Volume 27, Number 9, July 15, 2006
Volume 27, Number 10, July 30, 2006
Volume 27, Number 11, August, 2006
Volume 27, Number 12, September, 2006
Volume 27, Number 13, October, 2006
Volume 27, Number 14, November 15, 2006
Volume 27, Number 15, November 30, 2006
Volume 27, Number 16, December, 2006
Volume 28, Number 1, January 15, 2007
Volume 28, Number 2, January 30, 2007
Volume 28, Number 3, February, 2007
Volume 28, Number 4, March, 2007
Volume 28, Number 5, April 15, 2007
Volume 28, Number 6, April 30, 2007
Volume 28, Number 7, May, 2007
Volume 28, Number 8, June, 2007
Volume 28, Number 9, July 15, 2007
Volume 28, Number 10, July 30, 2007
Volume 28, Number 11, August, 2007
Volume 28, Number 12, September, 2007
Volume 28, Number 13, October, 2007
Volume 28, Number 14, November 15, 2007
Volume 28, Number 15, November 30, 2007
Volume 28, Number 16, December, 2007
Volume 29, Number 1, January 15, 2008
Volume 29, Number 2, January 30, 2008
Volume 29, Number 3, February, 2008
Volume 29, Number 4, March, 2008
Volume 29, Number 5, April 15, 2008
Volume 29, Number 6, April 30, 2008
Volume 29, Number 7, May, 2008
Volume 29, Number 8, June, 2008
Volume 29, Number 9, July 15, 2008
Volume 29, Number 10, July 30, 2008
Volume 29, Number 11, August, 2008
Volume 29, Number 12, September, 2008
Volume 29, Number 13, October, 2008
Volume 29, Number 14, November 15, 2008
Volume 29, Number 15, November 30, 2008
Volume 29, Number 16, December, 2008
Volume 30, Number 1, January 15, 2009
Volume 30, Number 2, January 30, 2009
Volume 30, Number 3, February, 2009
Volume 30, Number 4, March, 2009
Volume 30, Number 5, April 15, 2009
Volume 30, Number 6, April 30, 2009
Volume 30, Number 7, May, 2009
Volume 30, Number 8, June, 2009
Volume 30, Number 9, July 15, 2009
Volume 30, Number 10, July 30, 2009
Volume 30, Number 11, August, 2009
Volume 30, Number 12, September, 2009
Volume 30, Number 13, October, 2009
Volume 30, Number 14, November 15, 2009
Volume 30, Number 15, November 30, 2009
Volume 30, Number 16, December, 2009
Volume 32, Number 2, January 30, 2011
Volume 33, Number 3, January 30, 2012
Volume 33, Number 5, February 15, 2012
Volume 33, Number 8, March 30, 2012
Volume 33, Number 24, September 15, 2012
Volume 34, Number 27, October 15, 2013


Journal of Computational Chemistry
Volume 19, Number 1, January 15, 1998

        Timothy R. Forester and   
                  William Smith   SHAKE, rattle, and roll: Efficient
                                  constraint algorithms for linked rigid
                                  bodies . . . . . . . . . . . . . . . . . 102--111


Journal of Computational Chemistry
Volume 21, Number 1, January 15, 2000

            Finn Drablòs   Ab initio simulation of chemical shift
                                  effects from metal ion binding in
                                  Bacitracin A . . . . . . . . . . . . . . 1--7
                    Petr Bou\vr   Comparison of Hartree--Fock and
                                  Kohn--Sham determinants as wave
                                  functions  . . . . . . . . . . . . . . . 8--16
    Gerrit Schüürmann   Prediction of Henry's law constant of
                                  benzene derivatives using quantum
                                  chemical continuum-solvation models  . . 17--34
          E. del Río and   
            R. López and   
      M. I. Menéndez and   
                    T. L. Sordo   A theoretical study of the reaction of
                                  HCO$^+$ with C$_2$H$_2$  . . . . . . . . 35--42
            Jose M. Mercero and   
               Paul Barrett and   
               Cheuk W. Lam and   
           Joseph E. Fowler and   
            Jesus M. Ugalde and   
                Lee G. Pedersen   Quantum mechanical calculations on
                                  phosphate hydrolysis reactions . . . . . 43--51
               Roberto Izzo and   
              Martin Klessinger   Optimization of conical intersections
                                  using the semiempirical MNDOC--CI method
                                  with analytic gradients  . . . . . . . . 52--62
            Marie C. Vicens and   
        Gustavo E. López   Density functional studies of
                                  cation--water complexes  . . . . . . . . 63--68
                  Jon Baker and   
                    Peter Pulay   Efficient geometry optimization of
                                  molecular clusters . . . . . . . . . . . 69--76
             Kenny B. Lipkowitz   Book review: \booktitleEncyclopedia of
                                  Computational Chemistry, P. v. R.
                                  Schleyer, editor-in-chief, John Wiley &
                                  Sons, Chichester, UK, 1998, 3,500 pp.
                                  \$3,150. ISBN 0-471-96588-X} . . . . . . 77--78

Journal of Computational Chemistry
Volume 21, Number 2, January 30, 2000

                  Konrad Hinsen   The molecular modeling toolkit: a new
                                  approach to molecular simulations  . . . 79--85
            Nicolas Foloppe and   
    Alexander D. MacKerell, Jr.   All-atom empirical force field for
                                  nucleic acids: I. Parameter optimization
                                  based on small molecule and condensed
                                  phase macromolecular target data . . . . 86--104
 Alexander D. MacKerell Jr. and   
             Nilesh K. Banavali   All-atom empirical force field for
                                  nucleic acids: II. Application to
                                  molecular dynamics simulations of DNA
                                  and RNA in solution  . . . . . . . . . . 105--120
              See-Wing Chiu and   
              Michael Clark and   
        Shankar Subramaniam and   
                 Eric Jakobsson   Collective motion artifacts arising in
                                  long-duration molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 121--131
              Araz Jakalian and   
              Bruce L. Bush and   
              David B. Jack and   
           Christopher I. Bayly   Fast, efficient generation of
                                  high-quality atomic charges. AM1-BCC
                                  model: I. Method . . . . . . . . . . . . 132--146
              L. B. Morales and   
R. Garduño-Juárez and   
     J. M. Aguilar-Alvarado and   
           F. J. Riveros-Castro   A parallel tabu search for
                                  conformational energy optimization of
                                  oligopeptides  . . . . . . . . . . . . . 147--156
        Timothy R. Forester and   
                  William Smith   Erratum: SHAKE, rattle, and roll:
                                  Efficient constraint algorithms for
                                  linked rigid bodies  . . . . . . . . . . 157--157

Journal of Computational Chemistry
Volume 21, Number 3, February, 2000

                Hon M. Chun and   
          Carlos E. Padilla and   
            Donovan N. Chin and   
         Masakatsu Watanabe and   
           Valeri I. Karlov and   
            Howard E. Alper and   
               Keto Soosaar and   
               Kim B. Blair and   
             Oren M. Becker and   
            Leo S. D. Caves and   
               Robert Nagle and   
             David N. Haney and   
                Barry L. Farmer   MBO(N)D: a multibody method for
                                  long-time molecular dynamics simulations 159--184
                C. R. Sarma and   
           A. V. V. Nampoothiri   A labeling scheme for young tableaux
                                  spanning representations of permutation
                                  group S (N)  . . . . . . . . . . . . . . 185--190
      Vladimir A. Bushenkov and   
       J. P. Prates Ramalho and   
              Georgi V. Smirnov   Adsorption integral equation via complex
                                  approximation with constraints: the
                                  Langmuir kernel  . . . . . . . . . . . . 191--200
             Masaaki Kawata and   
                Masuhiro Mikami   Computationally efficient canonical
                                  molecular dynamics simulations by using
                                  a multiple time-step integrator
                                  algorithm combined with the particle
                                  mesh Ewald method and with the fast
                                  multipole method . . . . . . . . . . . . 201--217
       H. Donald B. Jenkins and   
        Luminita C. Jitariu and   
              Ingo Krossing and   
              Jack Passmore and   
                 Reijo Suontamo   Basis set and correlation effects in the
                                  calculation of accurate gas phase
                                  dimerization energies of two M to give M
                                  (M = S, Se)  . . . . . . . . . . . . . . 218--226
            Fakhr Abu-Awwad and   
                 Peter Politzer   Variation of parameters in Becke-3
                                  hybrid exchange-correlation functional   227--238
            Robert J. Bubel and   
           Warthen Douglass and   
                 David P. White   Molecular mechanics-based measures of
                                  steric effects: Customized code to
                                  compute Ligand repulsive energies  . . . 239--246

Journal of Computational Chemistry
Volume 21, Number 4, March, 2000

             Denton S. Ebel and   
            Mark S. Ghiorso and   
            Richard O. Sack and   
              Lawrence Grossman   Gibbs energy minimization in gas +
                                  liquid + solid systems . . . . . . . . . 247--256
         Marta Forés and   
               Miquel Duran and   
              Miquel Sol\`a and   
               Ludwik Adamowicz   Theoretical characterization of
                                  intramolecular proton transfer in the
                                  ground and the lowest-lying triplet
                                  excited states of 1-amino-3-propenal: a
                                  methodological comparison  . . . . . . . 257--269
                Bernd Mayer and   
              Giancarlo Marconi   Circular dichroic constrained structure
                                  optimization of homoalanine peptides . . 270--281
Jean-Didier Maréchal and   
                Guada Barea and   
              Feliu Maseras and   
Agustí Lledós and   
            Liliane Mouawad and   
           David Pérahia   Theoretical modeling of the heme group
                                  with a hybrid QM/MM method . . . . . . . 282--294
              Laurent David and   
                    Ray Luo and   
              Michael K. Gilson   Comparison of generalized Born and
                                  Poisson models: Energetics and dynamics
                                  of HIV protease  . . . . . . . . . . . . 295--309
               Eugene T. Knight   A radial probability density function
                                  for analysis of canonical molecular
                                  orbitals . . . . . . . . . . . . . . . . 310--321
          Redouan El-Bergmi and   
               J. A. Dobado and   
             Dolores Portal and   
      José Molina Molina   Stabilization in neutral bicyclic
                                  sulfoxide compounds  . . . . . . . . . . 322--327

Journal of Computational Chemistry
Volume 21, Number 5, April 15, 2000

                Guyan Liang and   
       Jennifer B. Sorensen and   
             David Whitmire and   
               J. Phillip Bowen   Molecular mechanics (MM3)
                                  parameterization for oxocarbenium ions   329--339
            Derek M. Dolney and   
         Gregory D. Hawkins and   
                Paul Winget and   
          Daniel A. Liotard and   
      Christopher J. Cramer and   
              Donald G. Truhlar   Universal solvation model based on
                                  conductor-like screening model . . . . . 340--366
        Emmanuelle Rousseau and   
                 Didier Mathieu   Atom equivalents for converting DFT
                                  energies calculated on molecular
                                  mechanics structures to formation
                                  enthalpies . . . . . . . . . . . . . . . 367--379
              Young Joo Lee and   
             Jae Yeol Maeng and   
               Eok-Kyun Lee and   
                Bongsoo Kim and   
                  Sehun Kim and   
                  Kyu-Kwang Han   Melting behaviors of icosahedral metal
                                  clusters studied by Monte Carlo
                                  simulations  . . . . . . . . . . . . . . 380--387
                 K. Tappura and   
        M. Lahtela-Kakkonen and   
                     O. Teleman   A new soft-core potential function for
                                  molecular dynamics applied to the
                                  prediction of protein loop conformations 388--397
          Giovanni Talarico and   
      Peter H. M. Budzelaar and   
                   Anton W. Gal   Ethylene coordination, insertion, and
                                  chain transfer at a cationic aluminum
                                  center: a comparative study with Ab
                                  Initio correlated level and density
                                  functional methods . . . . . . . . . . . 398--410
             Steven Feldgus and   
            Clark R. Landis and   
         Eric D. Glendening and   
                 Frank Weinhold   Natural resonance theory. I. General
                                  formalism  . . . . . . . . . . . . . . . 411--413

Journal of Computational Chemistry
Volume 21, Number 6, April 30, 2000

            L. V. Moskaleva and   
                      M. C. Lin   Unimolecular isomerization/decomposition
                                  of cyclopentadienyl and related
                                  bimolecular reverse process: ab initio
                                  MO/statistical theory study  . . . . . . 415--425
           Allan D. Headley and   
             Stephen D. Starnes   Theoretical analysis of fluoroglycine
                                  conformers . . . . . . . . . . . . . . . 426--431
        Pawe\l K\kedzierski and   
        W. Andrzej Sokalski and   
                  Morris Krauss   Nonempirical analysis of nature of
                                  catalytic effects in ribonuclease A
                                  active site  . . . . . . . . . . . . . . 432--445
            M. F. O'Donohue and   
                E. Minasian and   
                S. J. Leach and   
              A. W. Burgess and   
                H. R. Treutlein   PEPCAT --- a new tool for conformational
                                  analysis of peptides . . . . . . . . . . 446--461
           Luis Carballeira and   
     Ignacio Pérez-Juste   An ab initio interpretation in gas phase
                                  and aqueous solution of the generalized
                                  anomeric effect in
                                  R\bondO\bondCR$_2$\bondNR$_2$ (R = H,
                                  CH$_3$)  . . . . . . . . . . . . . . . . 462--477
          Stuart R. Gooding and   
              Peter J. Winn and   
          Richard I. Maurer and   
    György G. Ferenczy and   
             John R. Miller and   
            Jayne E. Harris and   
       D. Vaughan Griffiths and   
        Christopher A. Reynolds   Fully polarizable QM/MM calculations: an
                                  application to the nonbonded
                                  iodine--oxygen interaction in
                                  dimethyl-2-iodobenzoylphosphonate  . . . 478--482
         Dominique Dehareng and   
                   Georges Dive   Hartree--Fock instabilities and
                                  electronic properties  . . . . . . . . . 483--504
                John F. Stanton   Book review: \booktitleReviews in
                                  Computational Chemistry, Volume 13.
                                  Edited by Kenny B. Lipkowitz and Donald
                                  B. Boyd, Wiley-VCH, 1999, 426 pp.
                                  \$139.00. ISBN 0-471-33135-X}  . . . . . 505--507

Journal of Computational Chemistry
Volume 21, Number 7, May, 2000

              Franck Fuster and   
                Alain Sevin and   
                  Bernard Silvi   Determination of substitutional sites in
                                  heterocycles from the topological
                                  analysis of the electron localization
                                  function (ELF) . . . . . . . . . . . . . 509--514
                  S. Alcaro and   
              F. Gasparrini and   
                  O. Incani and   
                 S. Mecucci and   
                  D. Misiti and   
                 M. Pierini and   
                     C. Villani   A ``quasi-flexible'' automatic docking
                                  processing for studying stereoselective
                                  recognition mechanisms. Part I. Protocol
                                  validation . . . . . . . . . . . . . . . 515--530
              Reece K. Hart and   
             Rohit V. Pappu and   
                  Jay W. Ponder   Exploring the similarities between
                                  potential smoothing and simulated
                                  annealing  . . . . . . . . . . . . . . . 531--552
            Robert E. Tuzun and   
             Donald W. Noid and   
               Bobby G. Sumpter   Computation of internal coordinates,
                                  derivatives, and gradient expressions:
                                  torsion and improper torsion . . . . . . 553--561
        Ramón Bosque and   
                  Feliu Maseras   Performance of the semiempirical PM3
                                  (tm) method in the geometry optimization
                                  of transition metal complexes  . . . . . 562--571
     M. I. Bernal-Uruchurtu and   
     M. T. C. Martins-Costa and   
                  C. Millot and   
        M. F. Ruiz-López   Improving description of hydrogen bonds
                                  at the semiempirical level: water--water
                                  interactions as test case  . . . . . . . 572--581
            Philippe Derreumaux   Predicting helical hairpins from
                                  sequences by Monte Carlo simulations . . 582--589

Journal of Computational Chemistry
Volume 21, Number 8, June, 2000

                      Anonymous   In memoriam: Michael C. Zerner . . . . . 591--591
        Terry J. Frankcombe and   
                  Sean C. Smith   Solving the unimolecular master equation
                                  with a weighted subspace projection
                                  method . . . . . . . . . . . . . . . . . 592--606
              Jordi Vill\`a and   
         Jörg Bentzien and   
\`Angels González-Lafont and   
       José M. Lluch and   
               Juan Bertran and   
                  Arieh Warshel   Effective way of modeling chemical
                                  catalysis: Empirical valence bond
                                  picture of role of solvent and catalyst
                                  in alkylation reactions  . . . . . . . . 607--625
          Imre Jákli and   
      András Perczel and   
      Ödön Farkas and   
Attila G. Császár and   
                Carlos Sosa and   
              Imre G. Csizmadia   Peptide models XXIII. Conformational
                                  model for polar side-chain containing
                                  amino acid residues: a comprehensive
                                  analysis of RHF, DFT, and MP2 properties
                                  of HCO-L-SER-NH$_2$  . . . . . . . . . . 626--655
               M. Skowronek and   
                I. Roterman and   
               L. Konieczny and   
                   B. Stopa and   
                J. Rybarska and   
                   B. Piekarska   Why do Congo Red, Evans Blue, and Trypan
                                  Blue differ in their complexation
                                  properties?  . . . . . . . . . . . . . . 656--667
           Willian R. Rocha and   
           Wagner B. De Almeida   Carbonyl insertion reaction into the Pt
                                  C bond in heterobimetallic
                                  Pt(SnCl$_3$)(PH$_3$)$_2$(CO)(CH$_3$)
                                  compound: Theoretical study  . . . . . . 668--674
               Roger Arnaud and   
           Valentina Vetere and   
                Vincenzo Barone   Quantum mechanical study of
                                  regioselectivity of radical additions to
                                  substituted olefins  . . . . . . . . . . 675--691
          Delanie Lamprecht and   
              Gert J. Lamprecht   A molecular mechanics force field for
                                  rhodium(I) carbonyl phosphine complexes
                                  and its application on the oxidative
                                  addition reactions of these complexes    692--703

Journal of Computational Chemistry
Volume 21, Number 9, July 15, 2000

       M. L. Sánchez and   
        M. E. Martín and   
              M. A. Aguilar and   
       F. J. Olivares del Valle   Solvent effects by means of averaged
                                  solvent electrostatic potentials:
                                  Coupled method . . . . . . . . . . . . . 705--715
 Isidoro García-Cruz and   
              Miguel Castro and   
             Annik Vivier-Bunge   DFT and MP2 molecular orbital
                                  determination of OH--toluene--O$_2$
                                  isomeric structures in the atmospheric
                                  oxidation of toluene . . . . . . . . . . 716--730
          Steven M. LaValle and   
               Paul W. Finn and   
           Lydia E. Kavraki and   
            Jean-Claude Latombe   A randomized kinematics-based approach
                                  to pharmacophore-constrained
                                  conformational search and database
                                  screening  . . . . . . . . . . . . . . . 731--747
                Satoshi Ono and   
          Nobuyuki Nakajima and   
               Junichi Higo and   
                Haruki Nakamura   Peptide free-energy profile is strongly
                                  dependent on the force field: Comparison
                                  of C96 and AMBER95 . . . . . . . . . . . 748--762
     Laurie A. Christianson and   
          Melissa J. Lucero and   
          Daniel H. Appella and   
            Daniel A. Klein and   
              Samuel H. Gellman   Improved treatment of cyclic
                                  $\beta$-amino acids and successful
                                  prediction of $\beta$-peptide secondary
                                  structure using a modified force field:
                                  AMBER*C  . . . . . . . . . . . . . . . . 763--773
              Wolfgang Damm and   
       Wilfred F. van Gunsteren   Reversible peptide folding: Dependence
                                  on molecular force field used  . . . . . 774--787
      Stephen P. Greatbanks and   
             Jill E. Gready and   
             Ajay C. Limaye and   
            Alistair P. Rendell   Comparison of enzyme polarization of
                                  ligands and charge-transfer effects for
                                  dihydrofolate reductase using
                                  point-charge embedded ab initio quantum
                                  mechanical and linear-scaling
                                  semiempirical quantum mechanical methods 788--811

Journal of Computational Chemistry
Volume 21, Number 10, July 30, 2000

                  Buyong Ma and   
              Jenn-Huei Lii and   
             Norman L. Allinger   Molecular polarizabilities and induced
                                  dipole moments in molecular mechanics    813--825
               M. K. Shukla and   
               S. K. Mishra and   
                 Anil Kumar and   
                   P. C. Mishra   An ab initio study of excited states of
                                  guanine in the gas phase and aqueous
                                  media: Electronic transitions and
                                  mechanism of spectral oscillations . . . 826--846
                  Johan Wouters   Use of theoretical descriptors to
                                  characterize cation--$\pi$ binding sites
                                  in (macro)molecules  . . . . . . . . . . 847--855
                    Jian Wu and   
                Yuansheng Jiang   The valence bond calculations for
                                  conjugated hydrocarbons having 24--28
                                  $\pi$-electrons  . . . . . . . . . . . . 856--869
         M. D. Di Benedetto and   
               P. Lucibello and   
A. L. Sangiovanni-Vincentelli and   
                   K. Yamaguchi   A new procedure for exact ring closure   870--881
      András Perczel and   
Attila G. Császár   Toward direct determination of
                                  conformations of protein building units
                                  from multidimensional NMR experiments I.
                                  A theoretical case study of
                                  For-Gly-NH$_2$ and For-L-Ala-NH$_2$  . . 882--900
           Xavier Grabuleda and   
               Carlos Jaime and   
               Peter A. Kollman   Molecular dynamics simulation studies of
                                  liquid acetonitrile: New six-site model  901--908

Journal of Computational Chemistry
Volume 21, Number 11, August, 2000

                 F. Tielens and   
             W. Langenaeker and   
             A. R. Ocakoglu and   
                   P. Geerlings   Quantum chemical calculation of Henry
                                  constants of diatomic molecules in
                                  faujasite-type zeolites  . . . . . . . . 909--922
          Zlatko Vasilkoski and   
                David L. Weaver   A generator of protein folding kinetics
                                  states for the diffusion--collision
                                  model  . . . . . . . . . . . . . . . . . 923--932
        Anthony S. Mitchell and   
               Mark A. Spackman   Molecular surfaces from the promolecule:
                                  a comparison with Hartree--Fock ab
                                  initio electron density surfaces . . . . 933--942
            Thomas A. Baker and   
             Gregory I. Gellene   A hybrid ab initio /free electron
                                  computational model for conjugated dye
                                  molecules: Simple cyanines and oxonols   943--953
               Kenji Sayano and   
             Hidetoshi Kono and   
         M. Michael Gromiha and   
                  Akinori Sarai   Multicanonical Monte Carlo calculation
                                  of the free-energy map of the
                                  base--amino acid interaction . . . . . . 954--962
Françoise Rogalewicz and   
          Gilles Ohanessian and   
                    Nohad Gresh   Interaction of neutral and zwitterionic
                                  glycine with Zn$^{2+}$ in gas phase: ab
                                  initio and SIBFA molecular mechanics
                                  calculations . . . . . . . . . . . . . . 963--973
                   Karl Jug and   
            Gerald Geudtner and   
                Thorsten Homann   MSINDO parameterization for third-row
                                  main group elements  . . . . . . . . . . 974--987
             Jinn-Moon Yang and   
                  Cheng-Yan Kao   Flexible ligand docking using a robust
                                  evolutionary algorithm . . . . . . . . . 988--998
               N. A. Pierce and   
               J. A. Spriet and   
                  J. Desmet and   
                     S. L. Mayo   Conformational splitting: a more
                                  powerful criterion for dead-end
                                  elimination  . . . . . . . . . . . . . . 999--1009

Journal of Computational Chemistry
Volume 21, Number 12, September, 2000

          Gilles Tiraboschi and   
                Nohad Gresh and   
    Claude Giessner-Prettre and   
            Lee G. Pedersen and   
             David W. Deerfield   Parallel ab initio and molecular
                                  mechanics investigation of
                                  polycoordinated Zn(II) complexes with
                                  model hard and soft ligands: Variations
                                  of binding energy and of its components
                                  with number and charges of ligands . . . 1011--1039
   Friedrich Biegler-König   Calculation of atomic integration data   1040--1048
                Junmei Wang and   
              Piotr Cieplak and   
               Peter A. Kollman   How well does a restrained electrostatic
                                  potential (RESP) model perform in
                                  calculating conformational energies of
                                  organic and biological molecules?  . . . 1049--1074
                Takashi Amisaki   Precise and efficient Ewald summation
                                  for periodic fast multipole method . . . 1075--1087
            Martin J. Field and   
                  Marc Albe and   
         Céline Bret and   
   Flavien Proust-De Martin and   
                   Aline Thomas   The dynamo library for molecular
                                  simulations using hybrid quantum
                                  mechanical and molecular mechanical
                                  potentials . . . . . . . . . . . . . . . 1088--1100
                   Y. Z. Xu and   
                  Q. Ouyang and   
                   J. G. Wu and   
                J. A. Yorke and   
                   G. X. Xu and   
                   D. F. Xu and   
              R. D. Soloway and   
                      J. Q. Ren   Using fractal to solve the multiple
                                  minima problem in molecular mechanics
                                  calculation  . . . . . . . . . . . . . . 1101--1108
                Yuan-Jie Ye and   
                 Ling-Ling Shen   DFT approach to calculate electronic
                                  transfer through a segment of DNA double
                                  helix  . . . . . . . . . . . . . . . . . 1109--1117

Journal of Computational Chemistry
Volume 21, Number 13, October, 2000

         Hermes F. de Souza and   
        Paulo H. Guadagnini and   
    Rogério Custodio and   
                John D. Goddard   The correlation of proton affinities
                                  with atomic charges and
                                  electronegativities for the group 14 to
                                  17 hydrides  . . . . . . . . . . . . . . 1119--1131
                Aaron R. Dinner   Local deformations of polymers with
                                  nonplanar rigid main-chain internal
                                  coordinates  . . . . . . . . . . . . . . 1132--1144
            Ryan T. Koehler and   
                 Hugo O. Villar   Design of screening libraries biased for
                                  pharmaceutical discovery . . . . . . . . 1145--1152
                Carlo Adamo and   
                Vincenzo Barone   Structures and properties of lanthanide
                                  and actinide complexes by a new density
                                  functional approach: Lanthanum,
                                  gadolinium, lutetium, and thorium
                                  halides as case studies  . . . . . . . . 1153--1166
      F. J. Meléndez and   
           B. Gallego-Luxan and   
              Jean Demaison and   
                Yves G. Smeyers   Ab initio determination of the infrared
                                  phosphine torsion spectrum in
                                  vinylphosphine with ZPE correction . . . 1167--1175
            M. Pernpointner and   
                L. Visscher and   
              W. A. de Jong and   
                       R. Broer   Parallelization of four-component
                                  calculations. I. Integral generation,
                                  SCF, and four-index transformation in
                                  the Dirac--Fock package MOLFDIR  . . . . 1176--1186
      Kholmirzo Kholmurodov and   
              William Smith and   
              Kenji Yasuoka and   
                 Tom Darden and   
            Toshikazu Ebisuzaki   A smooth-particle mesh Ewald method for
                                  DL\_POLY molecular dynamics simulation
                                  package on the Fujitsu VPP700  . . . . . 1187--1191
         Cristobal Alhambra and   
                      Jiali Gao   Hydrogen-bonding interactions in the
                                  active site of a low molecular weight
                                  protein-tyrosine phosphatase . . . . . . 1192--1203
               F. A. Momany and   
                  J. L. Willett   Computational studies on carbohydrates:
                                  I. Density functional ab initio geometry
                                  optimization on maltose conformations    1204--1219

Journal of Computational Chemistry
Volume 21, Number 14, November 15, 2000

             Petter Persson and   
              Johnny Bustad and   
              Michael C. Zerner   INDO calculations of small copper
                                  clusters and CO adsorbed on copper(100)
                                  surfaces . . . . . . . . . . . . . . . . 1221--1228
         Norman L. Allinger and   
             Kathleen A. Durkin   Van der Waals effects between hydrogen
                                  and first-row atoms in molecular
                                  mechanics (MM3/MM4)  . . . . . . . . . . 1229--1242
                 Nino Russo and   
           Marirosa Toscano and   
             André Grand   Theoretical determination of electron
                                  affinity and ionization potential of DNA
                                  and RNA bases  . . . . . . . . . . . . . 1243--1250
              Fatih Ya\csar and   
         Tarik Çelik and   
              Bernd A. Berg and   
               Hagai Meirovitch   Multicanonical procedure for continuum
                                  peptide models . . . . . . . . . . . . . 1251--1261
                M. C. Wells and   
                 R. R. Lucchese   Computing the superexchange electronic
                                  factor of electron transfer theory using
                                  a grid-based numerical method  . . . . . 1262--1273
               J. Elezgaray and   
               Y. H. Sanejouand   Modal dynamics of proteins in water  . . 1274--1282
               Sreedhara V. Rao   Mechanism of some 1:2 hydrogen transfer
                                  reactions through bond variation indices 1283--1291
          Yoshinao Nakagawa and   
               Nobuo Tajima and   
                 Kimihiko Hirao   A theoretical study of catalytic
                                  hydration reactions of ethylene  . . . . 1292--1304
            Asit K. Chandra and   
          Tadafumi Uchimaru and   
                  Masaaki Sugie   Kinetics of the hydrogen abstraction
                                  reactions of 1,1- and 1,2-difluoroethane
                                  with hydroxyl radical: an ab initio
                                  study  . . . . . . . . . . . . . . . . . 1305--1318

Journal of Computational Chemistry
Volume 21, Number 15, November 30, 2000

                   M. Holst and   
                   N. Baker and   
                        F. Wang   Adaptive multilevel finite element
                                  solution of the Poisson--Boltzmann
                                  equation I. Algorithms and examples  . . 1319--1342
                   N. Baker and   
                   M. Holst and   
                        F. Wang   Adaptive multilevel finite element
                                  solution of the Poisson--Boltzmann
                                  equation II. Refinement at
                                  solvent-accessible surfaces in
                                  biomolecular systems . . . . . . . . . . 1343--1352
                     Nenad Raos   Iterative method for finding the
                                  low-energy conformations based on the
                                  concept of molecular volumes . . . . . . 1353--1360
             Xavier Fradera and   
               Miquel Duran and   
                  Jordi Mestres   Atomic transferability within the
                                  exchange-correlation density . . . . . . 1361--1374
         Josep Maria Bofill and   
Ibério de Pinho Ribeiro Moreira and   
        Josep Maria Anglada and   
                 Francesc Illas   Accurate and efficient determination of
                                  higher roots in diagonalization of large
                                  matrices based in function restricted
                                  optimization algorithms  . . . . . . . . 1375--1386
                 Yuxiang Bu and   
                    Chengbu Liu   The orientation and distance-dependence
                                  analysis of the electron transfer
                                  reactivity: an electron correlation
                                  level investigation of
                                  Mn$^{2+}$(H$_2$O)$_2$/Mn$^{3+}$(H$_2$O)$_2$ system 1387--1404
               Rois Benassi and   
                Fernando Taddei   Complete basis set model chemistry
                                  applied to molecules of increasing
                                  molecular complexity: Thermochemical
                                  properties of organic sulfur derivatives 1405--1418

Journal of Computational Chemistry
Volume 21, Number 16, December, 2000

                Thom Vreven and   
                 Keiji Morokuma   On the application of the IMOMO
                                  (integrated molecular orbital +
                                  molecular orbital) method  . . . . . . . 1419--1432
            Richard J. Hall and   
            Sally A. Hindle and   
             Neil A. Burton and   
                 Ian H. Hillier   Aspects of hybrid QM/MM calculations:
                                  the treatment of the QM/MM interface
                                  region and geometry optimization with an
                                  application to chorismate mutase . . . . 1433--1441
               R. B. Murphy and   
              D. M. Philipp and   
                 R. A. Friesner   A mixed quantum mechanics/molecular
                                  mechanics (QM/MM) method for large-scale
                                  modeling of chemistry in protein
                                  environments . . . . . . . . . . . . . . 1442--1457
                  Yirong Mo and   
                      Jiali Gao   Ab initio QM/MM simulations with a
                                  molecular orbital-valence bond (MOVB)
                                  method: application to an S$_N$2
                                  reaction in water  . . . . . . . . . . . 1458--1469
              Joachim Sauer and   
                   Marek Sierka   Combining quantum mechanics and
                                  interatomic potential functions in ab
                                  initio studies of extended systems . . . 1470--1493
        Arjan van der Vaart and   
           Valentin Gogonea and   
            Steven L. Dixon and   
            Kenneth M. Merz Jr.   Linear scaling molecular orbital
                                  calculations of biological systems using
                                  the semiempirical divide and conquer
                                  method . . . . . . . . . . . . . . . . . 1494--1504
           Peter M. W. Gill and   
       Andrew T. B. Gilbert and   
                 Terry R. Adams   Rapid evaluation of two-center
                                  two-electron integrals . . . . . . . . . 1505--1510
     S. J. A. van Gisbergen and   
          C. Fonseca Guerra and   
                 E. J. Baerends   Towards excitation energies and
                                  (hyper)polarizability calculations of
                                  large molecules. Application of
                                  parallelization and linear scaling
                                  techniques to time-dependent density
                                  functional response theory . . . . . . . 1511--1523
          Philippe Y. Ayala and   
            Gustavo E. Scuseria   Electron correlation in large molecular
                                  systems using the atomic orbital
                                  formalism. The case of intermolecular
                                  interactions in crystalline urea as an
                                  example  . . . . . . . . . . . . . . . . 1524--1531
                  Jing Kong and   
       Christopher A. White and   
             Anna I. Krylov and   
             David Sherrill and   
            Ross D. Adamson and   
          Thomas R. Furlani and   
             Michael S. Lee and   
               Aaron M. Lee and   
         Steven R. Gwaltney and   
             Terry R. Adams and   
       Christian Ochsenfeld and   
       Andrew T. B. Gilbert and   
           Gary S. Kedziora and   
         Vitaly A. Rassolov and   
           David R. Maurice and   
                Nikhil Nair and   
                 Yihan Shao and   
         Nicholas A. Besley and   
             Paul E. Maslen and   
        Jeremy P. Dombroski and   
             Holger Daschel and   
               Weimin Zhang and   
     Prakashan P. Korambath and   
                  Jon Baker and   
          Edward F. C. Byrd and   
           Troy Van Voorhis and   
                Manabu Oumi and   
                  So Hirata and   
              Chao-Ping Hsu and   
             Naoto Ishikawa and   
                Jan Florian and   
              Arieh Warshel and   
           Benny G. Johnson and   
           Peter M. W. Gill and   
         Martin Head-Gordon and   
                  John A. Pople   Q-Chem 2.0: a high-performance ab initio
                                  electronic structure program package . . 1532--1548
                   Karl Jug and   
                Daniel Wichmann   MSINDO study of large silsesquioxanes    1549--1553
                Gongyi Hong and   
              Marek Strajbl and   
       Tomasz A. Wesolowski and   
                  Arieh Warshel   Constraining the electron densities in
                                  DFT method as an effective way for ab
                                  initio studies of metal-catalyzed
                                  reactions  . . . . . . . . . . . . . . . 1554--1561
             Jana Khandogin and   
                 Anguang Hu and   
                 Darrin M. York   Electronic structure properties of
                                  solvated biomolecules: a quantum
                                  approach for macromolecular
                                  characterization . . . . . . . . . . . . 1562--1571
            Bernard Kirtman and   
           Benoit Champagne and   
                  Josep M. Luis   Efficient treatment of the effect of
                                  vibrations on electrical, magnetic, and
                                  spectroscopic properties . . . . . . . . 1572--1588
                Gernot Frenking   Foreword . . . . . . . . . . . . . . . . v--v


Journal of Computational Chemistry
Volume 22, Number 6, April 30, 2001

                  Xiang-Yuan Li   Electron transfer between tryptophan and
                                  tyrosine: Theoretical calculation of
                                  electron transfer matrix element for
                                  intramolecular hole transfer . . . . . . 565--579

Journal of Computational Chemistry
Volume 22, Number 1, January 15, 2001

                      Anonymous   New Section of the Journal of
                                  Computational Chemistry  . . . . . . . . 1--1
             Donald E. Williams   Improved intermolecular force field for
                                  crystalline oxohydrocarbons including
                                  O\bondH\dottedbondO hydrogen bonding . . 1--20
István Kolossváry and   
     György M. Keserü   Hessian-free low-mode conformational
                                  search for large-scale protein loop
                                  optimization: application to $c$-jun
                                  $N$-terminal kinase JNK3 . . . . . . . . 21--30
                 Masao Masamura   Ab initio molecular orbital study of
                                  OH$^-$(H$_2$O)$_n$ in the gas phase  . . 31--37
         Michael G. Razumov and   
       Vladimir L. Melnikov and   
                Igor V. Pletnev   Molecular mechanics calculations of
                                  $\beta$-diketonate, aqua, and
                                  aqua-$\beta$-diketonate complexes of
                                  lanthanide ions using Gillespie--Kepert
                                  model  . . . . . . . . . . . . . . . . . 38--50
           Mikko Linnolahti and   
                Pipsa Hirva and   
             Tapani A. Pakkanen   Geometry prediction of bridged
                                  zirconocene dichlorides by quantum
                                  chemical methods . . . . . . . . . . . . 51--64
           Alfred D. French and   
        Anne-Marie Kelterer and   
           Glenn P. Johnson and   
            Michael K. Dowd and   
          Christopher J. Cramer   HF/6-31G* energy surfaces for
                                  disaccharide analogs . . . . . . . . . . 65--78
               Marcel Swart and   
       Piet Th. van Duijnen and   
               Jaap G. Snijders   A charge analysis derived from an atomic
                                  multipole expansion  . . . . . . . . . . 79--88
              Thomas Bredow and   
            Gerald Geudtner and   
                       Karl Jug   Development of the cyclic cluster
                                  approach for ionic systems . . . . . . . 89--101
                    K. Endo and   
                 S. Koizumi and   
                  T. Otsuka and   
                  M. Suhara and   
                T. Morohasi and   
              E. Z. Kurmaev and   
                    D. P. Chong   Analysis of XPS and XES of diamond and
                                  graphite by DFT calculations using model
                                  molecules  . . . . . . . . . . . . . . . 102--108
              Michael Meyer and   
             Thomas Steinke and   
               Maria Brandl and   
        Jürgen Sühnel   Density functional study of guanine and
                                  uracil quartets and of guanine
                                  quartet/metal ion complexes  . . . . . . 109--124
                 Masao Masamura   Ab initio molecular orbital study on the
                                  structures and energetics of
                                  CH$_3$OH(H$_2$O)$_n$ and
                                  CH$_3$SH(H$_2$O)$_n$ in the gas phase    125--131
                 Matthias Prall   VMD: a graphical tool for the modern
                                  chemists . . . . . . . . . . . . . . . . 132--134

Journal of Computational Chemistry
Volume 22, Number 2, January 30, 2001

           Luis Carballeira and   
     Ignacio Pérez-Juste   Role of the anomeric effect in
                                  methanediamines in the gas phase and
                                  aqueous solutions  . . . . . . . . . . . 135--150
         Thomas Krüger and   
               Alexander F. Sax   Distorted silicon hydrides--- a
                                  comparative study with various density
                                  functionals  . . . . . . . . . . . . . . 151--161
       Salvador León and   
       Carlos Alemán and   
     Francesc Escalé and   
                    Manuel Laso   MCDP: an advanced tool to simulate
                                  comb-like polymers . . . . . . . . . . . 162--171
          Daniel Beuve-Mery and   
               Mehdi Rahman and   
           Philippe Ducarme and   
                Robert Brasseur   Practical aspects of computational
                                  chemistry calculations through PC
                                  networks: the RAMSES--Beowulf
                                  implementation . . . . . . . . . . . . . 172--177
               Sergey Vyazovkin   Modification of the integral
                                  isoconversional method to account for
                                  variation in the activation energy . . . 178--183
             Zhong-Hui Duan and   
                  Robert Krasny   An adaptive treecode for computing
                                  nonbonded potential energy in classical
                                  molecular systems  . . . . . . . . . . . 184--195
          Béla Paizs and   
             Pedro Salvador and   
Attila G. Császár and   
               Miquel Duran and   
            Sándor Suhai   Intermolecular bond lengths:
                                  extrapolation to the basis set limit on
                                  uncorrected and BSSE-corrected potential
                                  energy hypersurfaces . . . . . . . . . . 196--207
                Don Steiger and   
                  Rainer Glaser   Lattice sum calculations for $1/r^p$
                                  interactions via multipole expansions
                                  and Euler summation  . . . . . . . . . . 208--215
                 Elfi Kraka and   
                  Dieter Cremer   The para-didehydropyridine,
                                  para-didehydropyridinium, and related
                                  biradicals --- a contribution to the
                                  chemistry of enediyne antitumor drugs    216--229
 Didier Bégué and   
                 Claude Pouchan   Density functional finite cluster method
                                  for polarizability of large Be$_N$
                                  three-dimensional systems  . . . . . . . 230--240
Sándor Kristyán and   
         Gábor I. Csonka   Fitting atomic correlation parameters
                                  for RECEP (rapid estimation of
                                  correlation energy from partial charges)
                                  method to estimate molecular correlation
                                  energies within chemical accuracy  . . . 241--254
      Xavier Gironés and   
               David Robert and   
       Ramon Carbó-Dorca   TGSA: a molecular superposition program
                                  based on topo-geometrical considerations 255--263

Journal of Computational Chemistry
Volume 22, Number 3, February, 2001

               Hiroyuki Ito and   
              Hiroshi Nakatsuji   Roles of proteins in the electron
                                  transfer in the photosynthetic reaction
                                  center of \em Rhodopseudomonas viridis:
                                  bacteriopheophytin to ubiquinone . . . . 265--272
               R. de Gelder and   
                 R. Wehrens and   
                  J. A. Hageman   A generalized expression for the
                                  similarity of spectra: application to
                                  powder diffraction pattern
                                  classification . . . . . . . . . . . . . 273--289
    Siegfried Höfinger and   
                Thomas Simonson   Dielectric relaxation in proteins: a
                                  continuum electrostatics model
                                  incorporating dielectric heterogeneity
                                  of the protein and time-dependent
                                  charges  . . . . . . . . . . . . . . . . 290--305
        Padeleimon Karafiloglou   A method to calculate the weights of nbo
                                  electronic structures from Moffitt's
                                  theorem  . . . . . . . . . . . . . . . . 306--315
            Satoshi Okumoto and   
                Shinichi Yamabe   A computational study of base-catalyzed
                                  reactions between isocyanates and
                                  epoxides affording 2-oxazolidones and
                                  isocyanurates  . . . . . . . . . . . . . 316--326
                 Yong Zhang and   
                  Xiao-Zeng You   Charge redistribution effect on the
                                  properties of charge transfer complexes
                                  H$_n$R$\cdot$XY and H$_n$R$\cdot$X$_2$
                                  (X, Y = F, Cl, Br, I; R = O, S, N, P)    327--338
       Marcos R. Betancourt and   
               Jeffrey Skolnick   Finding the needle in a haystack:
                                  educing native folds from ambiguous ab
                                  initio protein structure predictions . . 339--353
          Andrzej J. Gor\kaczko   Multiisotopic modeling of fragmentation
                                  ion patterns in mass spectra of
                                  organometallic and coordination
                                  compounds  . . . . . . . . . . . . . . . 354--365
         Nathaniel R. Luman and   
            Michael P. King and   
           Joseph D. Augspurger   Predicting $^{15}$N amide chemical
                                  shifts in proteins. I. An additive model
                                  for the backbone contribution  . . . . . 366--372

Journal of Computational Chemistry
Volume 22, Number 4, March, 2001

       Dmitrii N. Rassokhin and   
          Victor S. Lobanov and   
         Dimitris K. Agrafiotis   Nonlinear mapping of massive data sets
                                  by fuzzy clustering and neural networks  373--386
        Josep Maria Anglada and   
        Emili Besalú and   
         Josep Maria Bofill and   
                  Ramon Crehuet   On the quadratic reaction path evaluated
                                  in a reduced potential energy surface
                                  model and the problem to locate
                                  transition states  . . . . . . . . . . . 387--406
              Ingolf Sommer and   
             Richard Brimacombe   Methods for refining interactively
                                  established models of ribosomal RNA
                                  towards a physico-chemically plausible
                                  structure  . . . . . . . . . . . . . . . 407--417
                    Ingo Muegge   Effect of ligand volume correction on
                                  PMF scoring  . . . . . . . . . . . . . . 418--425
                    Petr Bou\vr   Computations of the Raman optical
                                  activity via the sum-over-states
                                  expansions . . . . . . . . . . . . . . . 426--435
                   Pei Tang and   
             Igor Zubryzcki and   
                         Yan Xu   Ab initio calculation of structures and
                                  properties of halogenated general
                                  anesthetics: halothane and sevoflurane   436--444
            Kevin J. Naidoo and   
                Michelle Kuttel   Water structure about the dimer and
                                  hexamer repeat units of amylose from
                                  molecular dynamics computer simulations  445--456
                Alexey K. Mazur   Molecular dynamics of minimal B-DNA  . . 457--467
            Leonel F. Murga and   
              Mary Jo Ondrechen   Numerical Aspects of the Calculation of
                                  Second Hyperpolarizabilities Using the
                                  Finite Field Method Coupled with a
                                  Simple Lanczos Algorithm . . . . . . . . 468--474
                   M. Holst and   
                   N. Baker and   
                        F. Wang   Erratum: Adaptive multilevel finite
                                  element solution of the
                                  Poisson--Boltzmann equation I.
                                  Algorithms and examples  . . . . . . . . 475--475

Journal of Computational Chemistry
Volume 22, Number 5, April 15, 2001

          Francisco Torrens and   
José Sánchez-Marín and   
              Ignacio Nebot-Gil   New dimension indices for the
                                  characterization of the
                                  solvent-accessible surface . . . . . . . 477--487
     Dimitris K. Agrafiotis and   
       Dmitrii N. Rassokhin and   
              Victor S. Lobanov   Multidimensional scaling and
                                  visualization of large molecular
                                  similarity tables  . . . . . . . . . . . 488--500
      Vincent Kräutler and   
   Wilfred F. van Gunsteren and   
   Philippe H. Hünenberger   A fast SHAKE algorithm to solve distance
                                  constraint equations for small molecules
                                  in molecular dynamics simulations  . . . 501--508
         Kerstin Möhle and   
     Hans-Jörg Hofmann and   
                   Walter Thiel   Description of peptide and protein
                                  secondary structures employing
                                  semiempirical methods  . . . . . . . . . 509--520
              Yuhki Ohtsuka and   
            Kazufumi Ohkawa and   
              Hiroshi Nakatsuji   Electron transfer in the $c$-type
                                  cytochrome subunit of the photosynthetic
                                  reaction center of \em Rhodopseudomonas
                                  viridis: ab initio theoretical study . . 521--527
              Shuhei Fukawa and   
              Masahiko Hada and   
             Ryoichi Fukuda and   
              Shinji Tanaka and   
              Hiroshi Nakatsuji   Relativistic effects and the halogen
                                  dependencies in the $^{13}$C chemical
                                  shifts of CH$_{4 - n}$I$_n$, CH$_{4 -
                                  n}$Br$_n$, CCl$_{4 - n}$I$_n$, and
                                  CBr$_{4 - n}$I$_n$ ($n = 0$--$4$)  . . . 528--536
                 Wolfgang Quapp   Comment ``On the quadratic reaction path
                                  evaluated in a reduced potential energy
                                  surface model and the problem to locate
                                  transition states'' [by J. M. Anglada,
                                  E. Besalú, J. M. Bofill, and R. Crehuet,
                                  J Comput Chem 2001, \bf 22, 4, 387--406] 537--540
             Josep Maria Bofill   Reply on the comment ``On the quadratic
                                  reaction path evaluated in a reduced
                                  potential energy surface model and the
                                  problem to locate transition states''
                                  [by J. M. Anglada, E. Besalú, J. M.
                                  Bofill, and R. Crehuet, J Comput Chem
                                  2001, \bf 22, 4, 387--406] . . . . . . . 541--544
                      Anonymous   AIM2000  . . . . . . . . . . . . . . . . 545--559
                      Anonymous   CI benchmark calculations on PC  . . . . 560--563

Journal of Computational Chemistry
Volume 22, Number 6, April 30, 2001

               Jean-Loup Faulon   Stochastic generator of chemical
                                  structure. 4. Building polymeric systems
                                  with specified properties  . . . . . . . 580--590
             Linda Yu Zhang and   
          Emilio Gallicchio and   
        Richard A. Friesner and   
                 Ronald M. Levy   Solvent models for protein--ligand
                                  binding: Comparison of implicit solvent
                                  Poisson and surface generalized Born
                                  models with explicit solvent simulations 591--607
            J. Andrew Grant and   
            Barry T. Pickup and   
               Anthony Nicholls   A smooth permittivity function for
                                  Poisson--Boltzmann solvation methods . . 608--640
               Oleg Borodin and   
             Grant D. Smith and   
               Richard L. Jaffe   Ab initio quantum chemistry and
                                  molecular dynamics simulations studies
                                  of LiPF$_6$ /poly(ethylene oxide)
                                  interactions . . . . . . . . . . . . . . 641--654
           Fredrik Blomgren and   
               Sven Larsson and   
              Stephen F. Nelsen   Electron transfer in bis(hydrazines), a
                                  critical test for application of the
                                  Marcus model . . . . . . . . . . . . . . 655--664
             Fokke Dijkstra and   
             Joop H. van Lenthe   Software news and updates  . . . . . . . 665--672

Journal of Computational Chemistry
Volume 22, Number 7, May, 2001

               Irene Nobeli and   
        John B. O. Mitchell and   
             Alexander Alex and   
              Janet M. Thornton   Evaluation of a knowledge-based
                                  potential of mean force for scoring
                                  docked protein--ligand complexes . . . . 673--688
             L. E. Dardenne and   
              A. S. Werneck and   
           M. Oliveira Neto and   
                    P. M. Bisch   Reassociation of fragments using
                                  multicentered multipolar expansions:
                                  peptide junction treatments to
                                  investigate electrostatic properties of
                                  proteins . . . . . . . . . . . . . . . . 689--701
               L. F. Pacios and   
             P. C. Gómez   Intramolecular interactions and
                                  intramolecular hydrogen bonding in
                                  conformers of gaseous glycine  . . . . . 702--716
                   Bilha Sandak   Multiscale fast summation of long-range
                                  charge and dipolar interactions  . . . . 717--731
 Péter Hudáky and   
          Imre Jákli and   
Attila G. Császár and   
          András Perczel   Peptide models XXXI. Conformational
                                  properties of hydrophobic residues
                                  shaping the core of proteins. An ab
                                  initio study of $N$-formyl- L-valinamide
                                  and $N$-formyl- L-phenylalaninamide  . . 732--751
            A. M. Tokmachev and   
       A. L. Tchougréeff   Semiempirical implementation of strictly
                                  localized geminals for analysis of
                                  molecular electronic structure . . . . . 752--764
             Pedro Salvador and   
          Béla Paizs and   
               Miquel Duran and   
            Sándor Suhai   On the effect of the BSSE on
                                  intermolecular potential energy
                                  surfaces. Comparison of a priori and a
                                  posteriori BSSE correction schemes . . . 765--786
          Zorka Smedarchina and   
Antonio Fernández-Ramos and   
                Willem Siebrand   DOIT: a program to calculate thermal
                                  rate constants and mode-specific
                                  tunneling splittings directly from
                                  quantum-chemical calculations  . . . . . 787--801
                   Pei Tang and   
             Igor Zubrzycki and   
                         Yan Xu   Erratum: Ab initio calculation of
                                  structures and properties of halogenated
                                  general anesthetics: halothane and
                                  sevoflurane  . . . . . . . . . . . . . . 802--802
        Josep Maria Anglada and   
        Emili Besalú and   
         Josep Maria Bofill and   
                  Ramon Crehuet   Erratum: On the quadratic reaction path
                                  evaluated in a reduced potential energy
                                  surface model and the problem to locate
                                  transition states  . . . . . . . . . . . 803--803

Journal of Computational Chemistry
Volume 22, Number 8, June, 2001

         Bouke P. van Eijck and   
        Wijnand T. M. Mooij and   
                      Jan Kroon   Ab initio crystal structure predictions
                                  for flexible hydrogen-bonded molecules.
                                  Part II. Accurate energy minimization    805--815
             Bouke P. van Eijck   Ab initio crystal structure predictions
                                  for flexible hydrogen-bonded molecules.
                                  Part III. Effect of lattice vibrations   816--826
              Chang Kon Kim and   
                 Jongok Won and   
               Hoon Sik Kim and   
              Yong Soo Kang and   
              Hong Guang Li and   
                 Chan Kyung Kim   Density functional theory studies on the
                                  dissociation energies of metallic salts:
                                  relationship between lattice and
                                  dissociation energies  . . . . . . . . . 827--834
           Mayumi Kamishima and   
             Masaaki Kojima and   
                 Yuzo Yoshikawa   Calculation of stacking geometries by a
                                  modified MM2 method  . . . . . . . . . . 835--845
         Hannes H. Loeffler and   
     Christoph A. Sotriffer and   
           Rudolf H. Winger and   
             Klaus R. Liedl and   
                  Bernd M. Rode   Calculation of sequence-dependent free
                                  energies of hydration of dipeptides
                                  formed by alanine and glycine  . . . . . 846--860
              Thomas Bredow and   
            Gerald Geudtner and   
                       Karl Jug   MSINDO parameterization for third-row
                                  transition metals  . . . . . . . . . . . 861--887
             Chong Hak Chae and   
              Dong Gweon Oh and   
                  Whanchul Shin   Flexible molecular superposition:
                                  development of a combined similarity
                                  index and application of the constrained
                                  optimization technique . . . . . . . . . 888--900

Journal of Computational Chemistry
Volume 22, Number 9, July 15, 2001

        Rafa\l Wysoki\'nski and   
               Danuta Michalska   The performance of different density
                                  functional methods in the calculation of
                                  molecular structures and vibrational
                                  spectra of platinum(II) antitumor drugs:
                                  cisplatin and carboplatin  . . . . . . . 901--912
                Luke Fisher and   
                   Thomas Holme   MM3 parameterization for the B N dative
                                  bond . . . . . . . . . . . . . . . . . . 913--922
     Sundaram Arulmozhiraja and   
              Tadatake Sato and   
                     Akira Yabe   Benzdiynes revisited: ab initio and
                                  density functional theory  . . . . . . . 923--930
                G. te Velde and   
          F. M. Bickelhaupt and   
             E. J. Baerends and   
          C. Fonseca Guerra and   
     S. J. A. van Gisbergen and   
             J. G. Snijders and   
                     T. Ziegler   Chemistry with ADF . . . . . . . . . . . 931--967
                 A. Toniolo and   
                     M. Persico   Efficient calculation of Franck--Condon
                                  factors and vibronic couplings in
                                  polyatomics  . . . . . . . . . . . . . . 968--975
         Vitaly A. Rassolov and   
             Mark A. Ratner and   
              John A. Pople and   
            Paul C. Redfern and   
               Larry A. Curtiss   6-31G* basis set for third-row atoms . . 976--984
J. J. Borrás-Almenar and   
        J. M. Clemente-Juan and   
                E. Coronado and   
               B. S. Tsukerblat   Software News and Updates: \tt MAGPACK:
                                  a package to calculate the energy
                                  levels, bulk magnetic properties, and
                                  inelastic neutron scattering spectra of
                                  high nuclearity spin clusters  . . . . . 985--991

Journal of Computational Chemistry
Volume 22, Number 10, July 30, 2001

          Paul D. Kirchhoff and   
                  Rob Brown and   
                 Scott Kahn and   
             Marvin Waldman and   
            C. M. Venkatachalam   Application of structure-based focusing
                                  to the estrogen receptor . . . . . . . . 993--1003
              Kyu-Kwang Han and   
                 Ki Hae Kim and   
             Byung Jin Mhin and   
                   Hyeon S. Son   Application of the multiensemble
                                  sampling to the hydration free energy    1004--1009
            Tran Trung Tran and   
          Herbert Treutlein and   
              Antony W. Burgess   Conformational analysis of thiopeptides:
                                  derivation of $sp^2$ sulfur parameters
                                  for the CFF91 force field  . . . . . . . 1010--1025
            Tran Trung Tran and   
          Herbert Treutlein and   
              Antony W. Burgess   Conformational analysis of thiopeptides:
                                  $(\varphi, \psi)$ maps of
                                  thio-substituted dipeptides  . . . . . . 1026--1037
          Gilles Tiraboschi and   
Marie-Claude Fournié-Zaluski and   
      Bernard-Pierre Roques and   
                    Nohad Gresh   Intramolecular chelation of Zn$^{2+}$ by
                                  $\alpha$- and
                                  $\beta$-mercaptocarboxamides. A parallel
                                  ab initio and polarizable molecular
                                  mechanics investigation. Assessment of
                                  the role of multipole transferability    1038--1047
              Piotr Cieplak and   
             James Caldwell and   
                  Peter Kollman   Molecular mechanical models for organic
                                  and biological systems going beyond the
                                  atom centered two body additive
                                  approximation: aqueous solution free
                                  energies of methanol and $N$-methyl
                                  acetamide, nucleic acid base, and amide
                                  hydrogen bonding and chloroform/water
                                  partition coefficients of the nucleic
                                  acid bases . . . . . . . . . . . . . . . 1048--1057
      Vladimir A. Bushenkov and   
       J. P. Prates Ramalho and   
              Georgi V. Smirnov   Adsorption integral equation via complex
                                  approximation with constraints: kernel
                                  of general form  . . . . . . . . . . . . 1058--1066
              Xiang-Yuan Li and   
                    Ji-Feng Liu   A theoretical study of solvent effect
                                  and reaction mechanism of electron
                                  transfer reaction between indole side
                                  chain and phenol side chain of peptide
                                  involving tryptophan and tyrosine  . . . 1067--1081
         Pawel K\kedzierski and   
            W. Andrzej Sokalski   Analysis of the transferability of
                                  atomic multipoles for amino acids in
                                  modeling macromolecular charge
                                  distribution from fragments  . . . . . . 1082--1097
           Narutoshi Kamiya and   
                   Junichi Higo   Repeated-annealing sampling combined
                                  with multicanonical algorithm for
                                  conformational sampling of bio-molecules 1098--1106
               Shoji Morita and   
                    Shogo Sakai   IMiCMO: a new integrated ab initio
                                  multicenter molecular orbitals method
                                  for molecular dynamics calculations in
                                  solvent cluster systems  . . . . . . . . 1107--1112
    Christopher J. Van Zele and   
         Mark A. Cunningham and   
              Marvin W. Makinen   Validation of nitroxyl spin-label
                                  force-field parameters through molecular
                                  dynamics simulations . . . . . . . . . . 1113--1123

Journal of Computational Chemistry
Volume 22, Number 11, August, 2001

                   M. Basma and   
                 S. Sundara and   
           D. Çalgan and   
                 T. Vernali and   
                    R. J. Woods   Solvated ensemble averaging in the
                                  calculation of partial atomic charges    1125--1137
               Annia Galano and   
J. Raúl Alvarez-Idaboy and   
            Luis A. Montero and   
             Annik Vivier-Bunge   OH hydrogen abstraction reactions from
                                  alanine and glycine: a quantum
                                  mechanical approach  . . . . . . . . . . 1138--1153
             Donald E. Williams   Improved intermolecular force field for
                                  molecules containing H, C, N, and O
                                  atoms, with application to nucleoside
                                  and peptide crystals . . . . . . . . . . 1154--1166
           Edward C. Sherer and   
          Christopher J. Cramer   Quantum chemical characterization of the
                                  cytosine: 2-Aminopurine base pair  . . . 1167--1179
           Carles Curutchet and   
             Modesto Orozco and   
                F. Javier Luque   Solvation in octanol: parametrization of
                                  the continuum MST model  . . . . . . . . 1180--1193
      Christopher J. Cramer and   
        Anne-Marie Kelterer and   
               Alfred D. French   When anomeric effects collide  . . . . . 1194--1204
           Lukas D. Schuler and   
               Xavier Daura and   
       Wilfred F. van Gunsteren   An improved GROMOS96 force field for
                                  aliphatic hydrocarbons in the condensed
                                  phase  . . . . . . . . . . . . . . . . . 1205--1218

Journal of Computational Chemistry
Volume 22, Number 12, September, 2001

                Junmei Wang and   
               Peter A. Kollman   Automatic parameterization of force
                                  field by systematic search and genetic
                                  algorithms . . . . . . . . . . . . . . . 1219--1228
             Tommi Hassinen and   
      Mikael Peräkylä   New energy terms for reduced protein
                                  models implemented in an off-lattice
                                  force field  . . . . . . . . . . . . . . 1229--1242
              Hiroaki Umeda and   
               Shiro Koseki and   
            Umpei Nagashima and   
             Michael W. Schmidt   Parallelization of multireference
                                  perturbation calculations with GAMESS    1243--1251
               H. Takahashi and   
                    T. Hori and   
               H. Hashimoto and   
                       T. Nitta   A hybrid QM/MM method employing real
                                  space grids for QM water in the TIP4P
                                  water solvents . . . . . . . . . . . . . 1252--1261
   Christian Silvio Pomelli and   
              Jacopo Tomasi and   
                  Roberto Cammi   A Symmetry adapted tessellation of the
                                  GEPOL surface: applications to molecular
                                  properties in solution . . . . . . . . . 1262--1272
          Gerhard Bringmann and   
  Jörg Mühlbacher and   
           Charlotte Repges and   
         Jörg Fleischhauer   MD-based CD calculations for the
                                  assignment of the absolute axial
                                  configuration of the
                                  naphthylisoquinoline alkaloid
                                  dioncophylline A . . . . . . . . . . . . 1273--1278
           Jerzy Cioslowski and   
             Agnieszka Szarecka   First-principles conformational analysis
                                  of the C$_{36}$H$_{36}$ spheriphane, a
                                  prototype hydrocarbon host cage  . . . . 1279--1286
              Shura Hayryan and   
                Chin-Kun Hu and   
                Shun-Yun Hu and   
                  Rung-Ji Shang   Multicanonical parallel simulations of
                                  proteins with continuous potentials  . . 1287--1296

Journal of Computational Chemistry
Volume 22, Number 13, October, 2001

Glênisson de Oliveira and   
           Jan M. L. Martin and   
        Indira K. C. Silwal and   
                Joel F. Liebman   Definitive heat of formation of
                                  methylenimine, CH$_2$NH, and of
                                  methylenimmonium ion, CH$_2$NH$_2^+$, by
                                  means of W2 theory . . . . . . . . . . . 1297--1305
                Wim Klopper and   
        Claire C. M. Samson and   
        György Tarczay and   
Attila G. Császár   Equilibrium inversion barrier of NH$_3$
                                  from extrapolated coupled-cluster pair
                                  energies . . . . . . . . . . . . . . . . 1306--1314
            Noboru Watanabe and   
               Yohei Kamata and   
              Kota Yamauchi and   
                  Yasuo Udagawa   Calculation of X-ray scattering
                                  intensities by means of the coupled
                                  cluster singles and doubles model  . . . 1315--1320
                    F. Wang and   
          H. Mackenzie-Ross and   
              D. A. Winkler and   
             I. E. McCarthy and   
                L. Campbell and   
                  M. J. Brunger   A high-resolution electron momentum
                                  spectroscopy and density functional
                                  theory study into the complete valence
                                  electronic structure of allene . . . . . 1321--1333
                Li Jie Wang and   
                      Se Li and   
                    Qian Shu Li   Theoretical studies on a possible
                                  synthesis reaction pathway on N$_8$
                                  (C$_S$) clusters . . . . . . . . . . . . 1334--1339
        Melissa L. P. Price and   
           Dennis Ostrovsky and   
           William L. Jorgensen   Gas-phase and liquid-state properties of
                                  esters, nitriles, and nitro compounds
                                  with the OPLS-AA force field . . . . . . 1340--1352
            Kaoru Kobayashi and   
                  Yuko Sano and   
                 Shigeru Nagase   Theoretical study of endohedral
                                  metallofullerenes: Sc$_{3 -
                                  n}$La$_n$N@C$_{80}$ ($n = 0$--$3$) . . . 1353--1358
                N. Balucani and   
                  O. Asvany and   
                  Y. T. Lee and   
               R. I. Kaiser and   
                 N. Galland and   
                M. T. Rayez and   
                    Y. Hannachi   Gas-phase detection of the HBCC
                                  (X$^1\Sigma$) molecule: a combined
                                  crossed beam and computational study of
                                  the B($^2$P) +
                                  C$_2$H$_2$($^1\Sigma_g^+$) reaction  . . 1359--1365
     Stanislav Ya. Umanskii and   
    Konstantin P. Novoselov and   
         Airat Kh. Minushev and   
         Magdalena Siodmiak and   
            Gernot Frenking and   
              Anatoli A. Korkin   Thermodynamics and kinetics of initial
                                  gas phase reactions in chemical vapor
                                  deposition of titanium nitride.
                                  Theoretical study of TiCl$_4$
                                  ammonolysis  . . . . . . . . . . . . . . 1366--1376
              Amnon Stanger and   
                Elena Tkachenko   Strain induced bond localization in
                                  strained aromatic compounds with
                                  extended $\pi$ systems . . . . . . . . . 1377--1386
          Petar M. Mitrasinovic   Quantitative characterization of the P C
                                  bonds in ylides of phosphorus  . . . . . 1387--1395
         Charles H. Langley and   
              Jenn-Huei Lii and   
             Norman L. Allinger   Molecular mechanics (MM4) calculations
                                  on carbonyl compounds part I: aldehydes  1396--1425
         Charles H. Langley and   
              Jenn-Huei Lii and   
             Norman L. Allinger   Molecular mechanics calculations on
                                  carbonyl compounds. II. Open-chain
                                  ketones  . . . . . . . . . . . . . . . . 1426--1450
         Charles H. Langley and   
              Jenn-Huei Lii and   
             Norman L. Allinger   Molecular mechanics calculations on
                                  carbonyl compounds. III. Cycloketones    1451--1475
         Charles H. Langley and   
              Jenn-Huei Lii and   
             Norman L. Allinger   Molecular mechanics calculations on
                                  carbonyl compounds. IV. Heats of
                                  formation  . . . . . . . . . . . . . . . 1476--1483
              Cheol Ho Choi and   
           Klaus Ruedenberg and   
                 Mark S. Gordon   New parallel optimal-parameter fast
                                  multipole method (OPFMM) . . . . . . . . 1484--1501
              Masahiko Hada and   
                   Jian Wan and   
             Ryoichi Fukuda and   
              Hiroshi Nakatsuji   Quasirelativistic study of $^{125}$Te
                                  nuclear magnetic shielding constants and
                                  chemical shifts  . . . . . . . . . . . . 1502--1508
            Asit K. Chandra and   
              Tadafumi Uchimaru   Reaction of OH radical with mono-, di-,
                                  and trichloroacetaldehyde: an ab initio
                                  study  . . . . . . . . . . . . . . . . . 1509--1521
              Trung Ngoc Le and   
         Alexander M. Mebel and   
                 Ralf I. Kaiser   Ab initio study of C$_4$H$_3$ potential
                                  energy surface and reaction of
                                  ground-state carbon atom with propargyl
                                  radical  . . . . . . . . . . . . . . . . 1522--1535
            Masae Takahashi and   
                Mitsuo Kira and   
          Kenkichi Sakamoto and   
         Thomas Müller and   
                Yitzhak Apeloig   Theoretical prediction of vertical
                                  transition energies of diaminosilylenes
                                  and aminosubstituted disilenes . . . . . 1536--1541
     Eluvathingal D. Jemmis and   
              M. Ramalingam and   
      Elambalassery G. Jayasree   Cationic closo carboranes --- promising
                                  weakly coordinating ions . . . . . . . . 1542--1551
                  Brian J. Duke   Choice of Spin--Orbit Correction Terms
                                  in Gaussian Model Chemistries  . . . . . 1552--1556
     Corinne Lacaze-Dufaure and   
              Tzonka Mineva and   
                     Nino Russo   On the interaction of Mo and Mo$_2$ with
                                  NH$_3$, C$_2$H$_4$, and C$_3$H$_6$ . . . 1557--1564
            David A. Hrovat and   
   Richard Vaughan Williams and   
              Alan C. Goren and   
         Weston Thatcher Borden   B3LYP calculations on bishomoaromaticity
                                  in substituted semibullvalenes*  . . . . 1565--1573
       Matthew L. Leininger and   
          C. David Sherrill and   
            Wesley D. Allen and   
          Henry F. Schaefer III   Systematic Study of Selected
                                  Diagonalization Methods for
                                  Configuration Interaction Matrices . . . 1574--1589
          Kathryn N. Rankin and   
                Russell J. Boyd   A density functional theory study of the
                                  dimers of HX (X = F, Cl, and Br) . . . . 1590--1597
                R. B. Sunoj and   
       P. Lakshminarasimhan and   
              V. Ramamurthy and   
               J. Chandrasekhar   Configuration interaction and density
                                  functional study of the influence of
                                  lithium cation complexation on vertical
                                  and adiabatic excitation energies of
                                  enones . . . . . . . . . . . . . . . . . 1598--1604
             Matthias Prall and   
         Alexander Wittkopp and   
            Andrey A. Fokin and   
             Peter R. Schreiner   Substituent effects on the Bergman
                                  cyclization of (Z)-1,5-hexadiyne-3-enes:
                                  a systematic computational study . . . . 1605--1614
            Gernot Frenking and   
             Norman L. Allinger   Editors' preface . . . . . . . . . . . . vii--viii
           Paul von R. Schleyer   An appreciation  . . . . . . . . . . . . ix--xi

Journal of Computational Chemistry
Volume 22, Number 14, November 15, 2001

     Verónica Barone and   
            Juan E. Peralta and   
      Rubén H. Contreras   NMR $^3$J(C$_1$,H$_3$) couplings in
                                  1-X-bicyclo[1.1.1]pentanes. FPT--DFT and
                                  NBO studies of hyperconjugative
                                  interactions and heavy atom substituent
                                  effects  . . . . . . . . . . . . . . . . 1615--1621
            Lewis Whitehead and   
              Colin M. Edge and   
              Jonathan W. Essex   Molecular dynamics simulation of the
                                  hydrocarbon region of a biomembrane
                                  using a reduced representation model . . 1622--1633
              P. E. M. Siegbahn   Modeling aspects of mechanisms for
                                  reactions catalyzed by metalloenzymes    1634--1645
    Jayaraman Chandrasekhar and   
            Martin Saunders and   
           William L. Jorgensen   Efficient exploration of conformational
                                  space using the stochastic search
                                  method: application to $\beta$-peptide
                                  oligomers  . . . . . . . . . . . . . . . 1646--1654
   J. Fernández Rico and   
            R. López and   
          G. Ramírez and   
                         I. Ema   Correspondence between GTO and STO
                                  molecular basis sets . . . . . . . . . . 1655--1665
               Jordi Poater and   
               Miquel Duran and   
                  Miquel Sol\`a   Parametrization of the Becke3-LYP hybrid
                                  functional for a series of small
                                  molecules using quantum molecular
                                  similarity techniques  . . . . . . . . . 1666--1678
    György G. Ferenczy and   
János G. Ángyán   Intra- and intermolecular interactions
                                  in crystals of polar molecules. A study
                                  by the mixed quantum
                                  mechanical/molecular mechanical
                                  SCMP-NDDO method . . . . . . . . . . . . 1679--1690
           V. D. de Viterbo and   
                 J. C. Belchior   Artificial neural networks applied for
                                  studying metallic complexes  . . . . . . 1691--1701
                  D. B. Chesnut   Localization function study of
                                  excitation processes in a set of small
                                  isoelectronic molecules  . . . . . . . . 1702--1711
     Dimitris K. Agrafiotis and   
              Victor S. Lobanov   Multidimensional scaling of
                                  combinatorial libraries without explicit
                                  enumeration  . . . . . . . . . . . . . . 1712--1722

Journal of Computational Chemistry
Volume 22, Number 15, November 30, 2001

                 Miroslav Pinak   Molecular dynamics simulation of thymine
                                  glycol-lesioned DNA reveals specific
                                  hydration at the lesion  . . . . . . . . 1723--1731
                A. Jongejan and   
             J. A. Jongejan and   
                    W. R. Hagen   Direct hydride transfer in the reaction
                                  mechanism of quinoprotein alcohol
                                  dehydrogenases: a quantum mechanical
                                  investigation  . . . . . . . . . . . . . 1732--1749
             Yuan-Ping Pang and   
            Emanuele Perola and   
                     Kun Xu and   
        Franklyn G. Prendergast   EUDOC: a computer program for
                                  identification of drug interaction sites
                                  in macromolecules and drug leads from
                                  chemical databases . . . . . . . . . . . 1750--1771
         Tatyana Kuznetsova and   
            Bjòrn Kvamme   Viabilty of atomistic potentials for
                                  thermodynamic properties of carbon
                                  dioxide at low temperatures  . . . . . . 1772--1781
               Carl S. Ewig and   
                Rajiv Berry and   
                  Uri Dinur and   
Jörg-Rüdiger Hill and   
            Ming-Jing Hwang and   
                 Haiying Li and   
                Chris Liang and   
                  Jon Maple and   
              Zhengwei Peng and   
       Thomas P. Stockfisch and   
          Thomas S. Thacher and   
                   Lisa Yan and   
               Xiangshan Ni and   
               Arnold T. Hagler   Derivation of class II force fields.
                                  VIII. Derivation of a general quantum
                                  mechanical force field for organic
                                  compounds  . . . . . . . . . . . . . . . 1782--1800
               Wolfgang Kliesch   EQUIPATH --- an equilibrial path tracing
                                  routine for the use with the program
                                  package GAUSSIAN94 . . . . . . . . . . . 1801--1816
Odonírio Abrahão-Júnior and   
  Paulo G. B. D. Nascimento and   
     Sérgio E. Galembeck   Conformational analysis of the HIV-1
                                  virus reverse transcriptase
                                  nonnucleoside inhibitors: TIBO and
                                  nevirapine . . . . . . . . . . . . . . . 1817--1829
                F. Fogolari and   
                G. Esposito and   
                 P. Viglino and   
                    H. Molinari   Molecular mechanics and dynamics of
                                  biomolecules using a solvent continuum
                                  model  . . . . . . . . . . . . . . . . . 1830--1842
             Xiaoliang Qian and   
              Daniel Strahs and   
                  Tamar Schlick   A new program for optimizing periodic
                                  boundary models of solvated biomolecules
                                  (PBCAID) . . . . . . . . . . . . . . . . 1843--1850
         Eduardo J. Delgado and   
               Joel B. Alderete   Prediction of infinite dilution activity
                                  coefficients of chlorinated organic
                                  compounds in aqueous solution from
                                  quantum-chemical descriptors . . . . . . 1851--1856
           Michael Schaefer and   
          Christian Bartels and   
            Fabrice Leclerc and   
                 Martin Karplus   Effective atom volumes for implicit
                                  solvent models: comparison between
                                  Voronoi volumes and minimum fluctuation
                                  volumes  . . . . . . . . . . . . . . . . 1857--1879

Journal of Computational Chemistry
Volume 22, Number 16, December, 2001

               Sor-Koon Goh and   
             Dennis S. Marynick   Ability of fullerenes to act as $\eta^6$
                                  ligands in transition metal complexes. A
                                  comparative PM3(tm)--density functional
                                  theory study . . . . . . . . . . . . . . 1881--1886
                  Bing Wang and   
           Ulrich Fleischer and   
            James F. Hinton and   
                    Peter Pulay   Accurate prediction of proton chemical
                                  shifts. I. Substituted aromatic
                                  hydrocarbons . . . . . . . . . . . . . . 1887--1895
           Daniel K. W. Mok and   
           Edmond P. F. Lee and   
               Foo-Tim Chau and   
                   John M. Dyke   Ab initio calculations on the and states
                                  of AlNC and simulation of the AlNC--
                                  emission spectra . . . . . . . . . . . . 1896--1906
                 Yu-guo Tao and   
               Yi-hong Ding and   
               Jian-jun Liu and   
                Ze-sheng Li and   
                Xu-ri Huang and   
                 Chia-Chung Sun   Theoretical study on reaction mechanism
                                  of the CF radical with nitrogen dioxide  1907--1919
             Olivier Quinet and   
        Beno\^\it Champagne and   
                Bernard Kirtman   Analytical TDHF second derivatives of
                                  dynamic electronic polarizability with
                                  respect to nuclear coordinates.
                                  Application to the dynamic ZPVA
                                  correction . . . . . . . . . . . . . . . 1920--1932
                B. Mannfors and   
               N. G. Mirkin and   
                   K. Palmo and   
                       S. Krimm   A polarizable electrostatic model of the
                                  $N$-methylacetamide dimer  . . . . . . . 1933--1943
                   J. Hauck and   
                        K. Mika   Ground-state structures of polymers  . . 1944--1955
              Nicolas Budin and   
             Nicolas Majeux and   
 Catherine Tenette-Souaille and   
                Amedeo Caflisch   Structure-based ligand design by a
                                  build-up approach and genetic algorithm
                                  search in conformational space . . . . . 1956--1970
           Michael Thormann and   
                    Miquel Pons   Massive docking of flexible ligands
                                  using environmental niches in
                                  parallelized genetic algorithms  . . . . 1971--1982
               Junichi Higo and   
          Yasunobu Sugimoto and   
        Katsuzo Wakabayashi and   
                Haruki Nakamura   Collective motions of myosin head
                                  derived from backbone molecular dynamics
                                  and combination with X-ray solution
                                  scattering data  . . . . . . . . . . . . 1983--1994
          Susumu Yanagisawa and   
              Takao Tsuneda and   
                 Kimihiko Hirao   Investigation of the use of density
                                  functionals in second- and third-row
                                  transition metal dimer calculations  . . 1995--2009
                  Young-Kyu Han   Density functional studies of AnF$_6$
                                  (An = U, Np, and Pu) and UF$_{6 -
                                  n}$Cl$_n$ ($n = 1$--$6$) using hybrid
                                  functionals: geometries and vibrational
                                  frequencies  . . . . . . . . . . . . . . 2010--2017
             Marta Filizola and   
           Silvina M. Tasso and   
              Gilda H. Loew and   
                 Hugo O. Villar   Global physicochemical properties as
                                  activity discriminants for the mGluR1
                                  subtype of metabotropic glutamate
                                  receptors  . . . . . . . . . . . . . . . 2018--2027
              Chao-Ping Liu and   
              J. J. Soares Neto   Revisiting the generator coordinate
                                  approximation for calculating the
                                  ro-vibrational energies of H . . . . . . 2028--2039
                Robert J. Woods   Book review: \booktitleComputational
                                  Chemistry. A Practical Guide for
                                  Applying Techniques to Real World
                                  Problems, By David Young . . . . . . . . 2040--2040


Journal of Computational Chemistry
Volume 23, Number 1, January 15, 2002

                 B. Jayaram and   
               K. McConnell and   
                S. B. Dixit and   
                     A. Das and   
                D. L. Beveridge   Free-energy component analysis of 40
                                  protein--DNA complexes: a consensus view
                                  on the thermodynamics of binding at the
                                  molecular level  . . . . . . . . . . . . 1--14
             Shuanghong Huo and   
              Irina Massova and   
               Peter A. Kollman   Computational alanine scanning of the
                                  1:1 human growth hormone--receptor
                                  complex  . . . . . . . . . . . . . . . . 15--27
         Harold A. Scheraga and   
          Jaroslaw Pillardy and   
                  Adam Liwo and   
               Jooyoung Lee and   
          Cezary Czaplewski and   
           Daniel R. Ripoll and   
       William J. Wedemeyer and   
            Yelena A. Arnautova   Evolution of physics-based methodology
                                  for exploring the conformational energy
                                  landscape of proteins  . . . . . . . . . 28--34
              Lalith Perera and   
           Thomas A. Darden and   
                Lee G. Pedersen   Predicted solution structure of zymogen
                                  human coagulation FVII . . . . . . . . . 35--47
                Martin J. Field   Simulating enzyme reactions: Challenges
                                  and perspectives . . . . . . . . . . . . 48--58
            Maricel Torrent and   
      Djamaladdin G. Musaev and   
               Harold Basch and   
                 Keiji Morokuma   Computational studies of reaction
                                  mechanisms of methane monooxygenase and
                                  ribonucleotide reductase . . . . . . . . 59--76
              Keith D. Ball and   
                Burak Erman and   
                    Ken A. Dill   The elastic net algorithm and protein
                                  structure prediction . . . . . . . . . . 77--83
           Dean J. Tantillo and   
                     K. N. Houk   Transition state docking: a probe for
                                  noncovalent catalysis in biological
                                  systems. Application to
                                  antibody-catalyzed ester hydrolysis  . . 84--95
          Ramkumar Rajamani and   
                      Jiali Gao   Combined QM/MM study of the opsin shift
                                  in bacteriorhodopsin . . . . . . . . . . 96--105
          Marek Orzechowski and   
              Piotr Cieplak and   
                   Lucjan Piela   Theoretical calculation of the
                                  coiled-coil stability in water in the
                                  context of its possible use as a
                                  molecular rack . . . . . . . . . . . . . 106--110
            Jaroslaw Meller and   
             Michael Wagner and   
                      Ron Elber   Maximum feasibility guideline in the
                                  design and analysis of protein folding
                                  potentials . . . . . . . . . . . . . . . 111--118
              Pemra Doruker and   
         Robert L. Jernigan and   
                     Ivet Bahar   Dynamics of large proteins through
                                  hierarchical levels of coarse-grained
                                  structures . . . . . . . . . . . . . . . 119--127
             Walter Rocchia and   
         Sundaram Sridharan and   
           Anthony Nicholls and   
                Emil Alexov and   
       Alessandro Chiabrera and   
                    Barry Honig   Rapid grid-based construction of the
                                  molecular surface and the use of induced
                                  surface charge to calculate reaction
                                  field energies: Applications to the
                                  molecular systems and geometric objects  128--137
               Corey Hardin and   
        Michael P. Eastwood and   
           Michael Prentiss and   
         Z. Luthey-Schulten and   
               Peter G. Wolynes   Folding funnels: the key to robust
                                  protein structure prediction . . . . . . 138--146
            Brian N. Dominy and   
          Charles L. Brooks and   
                            Iii   Identifying native-like protein
                                  structures using physics-based
                                  potentials . . . . . . . . . . . . . . . 147--160
               D. K. Klimov and   
                  D. Thirumalai   Is there a unique melting temperature
                                  for two-state proteins?  . . . . . . . . 161--165
               Hagai Meirovitch   Polymer collapse, protein folding, and
                                  the percolation threshold  . . . . . . . 166--171
                Ailan Cheng and   
            David J. Diller and   
            Steven L. Dixon and   
            William J. Egan and   
               George Lauri and   
            Kenneth M. Merz Jr.   Computation of the physio-chemical
                                  properties and data mining of large
                                  molecular collections  . . . . . . . . . 172--183
                  Sam Kalat and   
                 Geoff Mann and   
                    Jan Hermans   Qmd-plot: a graphical utility for rapid
                                  preliminary analysis of time series of
                                  fluctuating data, developed in the
                                  context of molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 184--188
        Marek Wojciechowski and   
               Jeffrey Skolnick   Docking of small ligands to
                                  low-resolution and theoretically
                                  predicted receptor structures  . . . . . 189--197

Journal of Computational Chemistry
Volume 23, Number 2, January 30, 2002

                I. Jen Chen and   
                   Daxu Yin and   
     Alexander D. MacKerell Jr.   Combined ab initio /empirical approach
                                  for optimization of Lennard-Jones
                                  parameters for polar-neutral compounds   199--213
              Olgun Guvench and   
           Jörg Weiser and   
              Peter Shenkin and   
István Kolossváry and   
                 W. Clark Still   Application of the frozen atom
                                  approximation to the GB/SA continuum
                                  model for solvation free energy  . . . . 214--221
   Aline Thaís Bruni and   
          Vitor B. P. Leite and   
   Márcia M. C. Ferreira   Conformational analysis: a new approach
                                  by means of chemometrics . . . . . . . . 222--236
                  Shuhua Li and   
                    Jing Ma and   
                Yuansheng Jiang   Linear scaling local correlation
                                  approach for solving the coupled cluster
                                  equations of large systems . . . . . . . 237--244
              J. L. Klepeis and   
                  C. A. Floudas   Ab initio prediction of helical segments
                                  in polypeptides  . . . . . . . . . . . . 245--266
                Yu-Dong Cai and   
               Xiao-Jun Liu and   
                Xue-Biao Xu and   
                  Kuo-Chen Chou   Support vector machines for predicting
                                  HIV protease cleavage sites in protein   267--274
              Andreas Klamt and   
               Frank Eckert and   
              Martin Hornig and   
            Michael E. Beck and   
           Thorsten Bürger   Prediction of aqueous solubility of
                                  drugs and pesticides with COSMO-RS . . . 275--281
           Thomas Strassner and   
              Markus Busold and   
           Wolfgang A. Herrmann   MM3 parametrization of four- and
                                  five-coordinated rhenium complexes by a
                                  genetic algorithm --- which factors
                                  influence the optimization performance?  282--290
        Patrizia Calaminici and   
                   Karl Jug and   
     Andreas M. Köster and   
 Cécile Arbez-Gindre and   
       Constantinos G. Screttas   Mechanism for large first
                                  hyperpolarizabilities of phosphonic acid
                                  stilbene derivatives . . . . . . . . . . 291--297
              Raiker Witter and   
               Wolfram Prie and   
               Ulrich Sternberg   Chemical shift driven geometry
                                  optimization . . . . . . . . . . . . . . 298--305
          Reinhart Ahlrichs and   
                Kakha Tsereteli   Efficient linear algebra routines for
                                  symmetric matrices stored in packed form 306--309
            Tsutomu Ikegami and   
                  Suehiro Iwata   Spectral density calculation by using
                                  the Chebyshev expansion  . . . . . . . . 310--318

Journal of Computational Chemistry
Volume 23, Number 3, February, 2002

                  S. Dennis and   
                       S. Vajda   Semiglobal simplex optimization and its
                                  application to determining the preferred
                                  solvation sites of proteins  . . . . . . 319--334
      Primo\vz Pristov\vsek and   
       Heinz Rüterjans and   
                   Roman Jerala   Semiautomatic sequence-specific
                                  assignment of proteins based on the
                                  tertiary structure --- the program \tt
                                  st2nmr . . . . . . . . . . . . . . . . . 335--340
             Caterina Benzi and   
            Roberto Improta and   
          Giovanni Scalmani and   
                Vincenzo Barone   Quantum mechanical study of the
                                  conformational behavior of proline and
                                  4R-hydroxyproline dipeptide analogues in
                                  vacuum and in aqueous solution . . . . . 341--350
           Emma Sigfridsson and   
                   Ulf Ryde and   
                  Bruce L. Bush   Restrained point-charge models for
                                  disaccharides  . . . . . . . . . . . . . 351--364
        Jacco Van de Streek and   
                Paul Verwer and   
               Piet Bennema and   
                    Elias Vlieg   On the irrelevance of electrostatics for
                                  the crystal structures and polymorphism
                                  of long even $n$-alkanes . . . . . . . . 365--370
         Thomas Krüger and   
               Alexander F. Sax   Oligovalent link atoms in embedding
                                  calculations . . . . . . . . . . . . . . 371--377
                Kazuhiro Ishida   Accompanying coordinate expansion
                                  formulas derived with the solid harmonic
                                  gradient . . . . . . . . . . . . . . . . 378--393
               Takao Otsuka and   
              Seiji Koizumi and   
              Kazunaka Endo and   
            Hiroyuki Kawabe and   
                Delano P. Chong   Theoretical Auger electron spectra of
                                  polymers by density functional theory
                                  calculations using model dimers  . . . . 394--401
                 Shuzo Yoshioki   Dynamics of a protein and water
                                  molecules surrounding the protein:
                                  Hydrogen-bonding between vibrating water
                                  molecules and a fluctuating protein  . . 402--413
              Zheng-wang Qu and   
                    Hui Zhu and   
                Ze-sheng Li and   
                  Qi-yuan Zhang   Theoretical study on the mechanism of
                                  the gas-phase reaction of diborane(3)
                                  anion with carbon disulfide  . . . . . . 414--419
          Alexander A. Auer and   
            Trygve Helgaker and   
                    Wim Klopper   Basis-set completeness profiles in two
                                  dimensions . . . . . . . . . . . . . . . 420--425

Journal of Computational Chemistry
Volume 23, Number 4, March, 2002

               Wensheng Cai and   
                  Xueguang Shao   A fast annealing evolutionary algorithm
                                  for global optimization  . . . . . . . . 427--435
            Kangcheng Zheng and   
                Juping Wang and   
                  Yong Shen and   
                Wenlie Peng and   
                    Fengcun Yun   Studies on $4,7$-di-substitution effects
                                  of one ligand in [Ru(Phen)$_3$]$^2$ with
                                  DFT method . . . . . . . . . . . . . . . 436--443
           H. Valdés and   
                    J. A. Sordo   Ab initio and DFT studies on van der
                                  Waals trimers: The OCS $\cdot$
                                  (CO$_2$)$_2$ complexes . . . . . . . . . 444--455
             Bouke P. Van Eijck   Crystal structure predictions using five
                                  space groups with two independent
                                  molecules. The case of small organic
                                  acids  . . . . . . . . . . . . . . . . . 456--462
             Shugo Nakamura and   
              Daisuke Kyono and   
         Mitsunori Ikeguchi and   
                Kentaro Shimizu   New method for parallel computation of
                                  Hessian matrix of conformational energy
                                  function in internal coordinates . . . . 463--469
                Satoshi Ono and   
            Masataka Kuroda and   
               Junichi Higo and   
          Nobuyuki Nakajima and   
                Haruki Nakamura   Calibration of force-field dependency in
                                  free energy landscapes of peptide
                                  conformations by quantum chemical
                                  calculations . . . . . . . . . . . . . . 470--476
                Gwon Hee Ko and   
                William H. Fink   Rapidly converging lattice sums for
                                  nonelectrostatic interactions  . . . . . 477--483
            Khuloud Jaqaman and   
              Peter J. Ortoleva   New space warping method for the
                                  simulation of large-scale macromolecular
                                  conformational changes . . . . . . . . . 484--491
                  Bing Wang and   
            James F. Hinton and   
                    Peter Pulay   Accurate prediction of proton chemical
                                  shifts. II. Peptide analogues  . . . . . 492--497
         Matthew P. Repasky and   
    Jayaraman Chandrasekhar and   
           William L. Jorgensen   Improved semiempirical heats of
                                  formation through the use of bond and
                                  group equivalents  . . . . . . . . . . . 498--510
               Hideaki Nakamura   Monte Carlo sampling algorithm for
                                  searching a scale-transformed energy
                                  space of polypeptides  . . . . . . . . . 511--516

Journal of Computational Chemistry
Volume 23, Number 5, April 15, 2002

          Emilio Gallicchio and   
             Linda Yu Zhang and   
                 Ronald M. Levy   The SGB/NP hydration free energy model
                                  based on the surface generalized Born
                                  solvent reaction field and novel
                                  nonpolar hydration free energy
                                  estimators . . . . . . . . . . . . . . . 517--529
               S. K. Mishra and   
                   P. C. Mishra   An ab initio theoretical study of
                                  electronic structure and properties of
                                  2'-deoxyguanosine in gas phase and
                                  aqueous media  . . . . . . . . . . . . . 530--540
            Philippe Marsal and   
                   Michel Roche   Variational treatment of the vibrational
                                  Hamiltonian for NH$_3$ and H$_2$NO . . . 541--547
           Alessandra Villa and   
                   Alan E. Mark   Calculation of the free energy of
                                  solvation for neutral analogs of amino
                                  acid side chains . . . . . . . . . . . . 548--553
            J. Muñoz and   
                  X. Barril and   
        B. Hernández and   
             Modesto Orozco and   
                F. Javier Luque   Hydrophobic similarity between
                                  molecules: a MST-based hydrophobic
                                  similarity index . . . . . . . . . . . . 554--563
                Wenjian Liu and   
                  Robert Franke   Comprehensive relativistic ab initio and
                                  density functional theory studies on
                                  PtH, PtF, PtCl, and Pt(NH$_3$)$_2$Cl$_2$ 564--575
              Michal Dallos and   
               Hans Lischka and   
   Elizete Ventura Do Monte and   
             Michael Hirsch and   
                 Wolfgang Quapp   Determination of energy minima and
                                  saddle points using multireference
                                  configuration interaction methods in
                                  combination with reduced gradient
                                  following: the S$_0$ surface of H$_2$CO
                                  and the T$_1$ and T$_2$ surfaces of
                                  acetylene  . . . . . . . . . . . . . . . 576--583
              Chang Kon Kim and   
                 Hongok Won and   
               Hoon Sik Kim and   
              Yong Soo Kang and   
              Hong Guang Li and   
                 Chan Kyung Kim   Erratum: Density functional theory
                                  studies on the dissociation energies of
                                  metallic salts: Relationship between
                                  lattice and dissociation energies  . . . 584--584

Journal of Computational Chemistry
Volume 23, Number 6, April 30, 2002

                 Roger A. Klein   Ab initio conformational studies on
                                  diols and binary diol-water systems
                                  using DFT methods. Intramolecular
                                  hydrogen bonding and 1:1 complex
                                  formation with water . . . . . . . . . . 585--599
           Oleg V. Tsodikov and   
       M. Thomas Record Jr. and   
                Yuri V. Sergeev   Novel computer program for fast exact
                                  calculation of accessible and molecular
                                  surface areas and average surface
                                  curvature  . . . . . . . . . . . . . . . 600--609
       Nicolas Ferré and   
             Xavier Assfeld and   
              Jean-Louis Rivail   Specific force field parameters
                                  determination for the hybrid ab initio
                                  QM/MM LSCF method  . . . . . . . . . . . 610--624
               Jian-Jun Liu and   
               Yi-Hong Ding and   
                 Yu-Guo Tao and   
               Ji-Kang Feng and   
                 Chia-Chung Sun   Theoretical study on the mechanism of
                                  the $^1$CHCl + NO reaction . . . . . . . 625--649
              Emma Langella and   
                 Nadia Rega and   
            Roberto Improta and   
          Orlando Crescenzi and   
                Vincenzo Barone   Conformational analysis of the tyrosine
                                  dipeptide analogue in the gas phase and
                                  in aqueous solution by a density
                                  functional/continuum solvent model . . . 650--661
         Jean-Luc Fattebert and   
           François Gygi   Density functional theory for efficient
                                  ab initio molecular dynamics simulations
                                  in solution  . . . . . . . . . . . . . . 662--666
              John E. Carpenter   Computation of pressure components due
                                  to Class II force fields . . . . . . . . 667--672
            Robert D. Skeel and   
              Ismail Tezcan and   
                 David J. Hardy   Multiple grid methods for classical
                                  molecular dynamics . . . . . . . . . . . 673--684

Journal of Computational Chemistry
Volume 23, Number 7, May, 2002

       Salvador León and   
                David Zanuy and   
           Carlos Alemán   Influence of the presence of small gas
                                  molecules in the structure of comblike
                                  polyacrylates: a Monte Carlo study . . . 685--696
                Peter Comba and   
                 Rainer Remenyi   A new molecular mechanics force field
                                  for the oxidized form of blue copper
                                  proteins . . . . . . . . . . . . . . . . 697--705
Paulo F. B. Gonçalves and   
                 Hubert Stassen   New approach to free energy of solvation
                                  applying continuum models to molecular
                                  dynamics simulation  . . . . . . . . . . 706--714
   Rajmund Ka\'zmierkiewicz and   
                  Adam Liwo and   
             Harold A. Scheraga   Energy-based reconstruction of a protein
                                  backbone from its $\alpha$-carbon trace
                                  by a Monte-Carlo method  . . . . . . . . 715--723
Jérôme Golebiowski and   
    Véronique Lamare and   
    Manuel F. Ruiz-López   Rb$^+$ /Cs$^+$ selectivity of benzo and
                                  tribenzo derivatives of the 21C7 crown
                                  ether. A density functional study  . . . 724--731
        Obis Castaño and   
       Raúl Palmeiro and   
         Luis Manuel Frutos and   
  José Luisandrés   Role of bifurcation in the bond shifting
                                  of cyclooctatetraene . . . . . . . . . . 732--736
         Vladislav Vasilyev and   
             Enrico O. Purisima   A fast pairwise evaluation of molecular
                                  surface area . . . . . . . . . . . . . . 737--745
           Patrick Bultinck and   
           Stijn Augustynen and   
            Hans W. Hilbers and   
                Ed E. Moret and   
              Jan P. Tollenaere   Generate: a program for $3$-D structure
                                  generation and conformational analysis
                                  of peptides and peptidomimetics  . . . . 746--754
          John E. Carpenter and   
          Alan Christoffels and   
              Yael Weinbach and   
                Winston A. Hide   Assessment of the parallelization
                                  approach of \tt d2\_cluster for
                                  high-performance sequence clustering . . 755--757

Journal of Computational Chemistry
Volume 23, Number 8, June, 2002

                 Lucas Visscher   The Dirac equation in quantum chemistry:
                                  Strategies to overcome the current
                                  computational problems . . . . . . . . . 759--766
              Hermann Stoll and   
              Bernhard Metz and   
                   Michael Dolg   Relativistic energy-consistent
                                  pseudopotentials --- recent developments 767--778
      Christoph Van Wüllen   Spin densities in two-component
                                  relativistic density functional
                                  calculations: Noncollinear versus
                                  collinear approach . . . . . . . . . . . 779--785
               Kenneth G. Dyall   A systematic sequence of relativistic
                                  approximations . . . . . . . . . . . . . 786--793
               Martin Kaupp and   
            Roman Reviakine and   
            Olga L. Malkina and   
          Alexei Arbuznikov and   
      Bernd Schimmelpfennig and   
             Vladimir G. Malkin   Calculation of electronic $g$-tensors
                                  for transition metal complexes using
                                  hybrid density functionals and atomic
                                  meanfield spin-orbit operators . . . . . 794--803
              J. Autschbach and   
              S. Siekierski and   
                    M. Seth and   
           P. Schwerdtfeger and   
               W. H. E. Schwarz   Dependence of relativistic effects on
                                  electronic configuration in the neutral
                                  atoms of $d$- and $f$-block elements . . 804--813
                 Trond Saue and   
                Trygve Helgaker   Four-component relativistic Kohn--Sham
                                  theory . . . . . . . . . . . . . . . . . 814--823
        Martin Kleinschmidt and   
          Jörg Tatchen and   
             Christel M. Marian   Spin-orbit coupling of DFT/MRCI
                                  wavefunctions: Method, test
                                  calculations, and application to
                                  thiophene  . . . . . . . . . . . . . . . 824--833
Maite García-Hernández and   
         Christa Lauterbach and   
           Sven Krüger and   
             Alexei Matveev and   
              Notker Rösch   Comparative study of relativistic
                                  density functional methods applied to
                                  actinide species AcO$_2^{2+}$ and
                                  AcF$_6$ for Ac = U, Np . . . . . . . . . 834--846
          Takahito Nakajima and   
              Takeshi Yanai and   
                 Kimihiko Hirao   Relativistic electronic structure theory 847--860

Journal of Computational Chemistry
Volume 23, Number 9, July 15, 2002

        Richard H. Henchman and   
             J. Andrew McCammon   Extracting hydration sites around
                                  proteins from explicit water simulations 861--869
Andre Elvas Pereira Da Silva and   
        Geraldo Magela E. Silva   Quantum bits with polyacetylene  . . . . 870--873
              Xiang-Yuan Li and   
                    Chun-Xiu Hu   Theoretical investigation of electron
                                  transfer transition in
                                  tetracyanoethylene-contained organic
                                  complexes  . . . . . . . . . . . . . . . 874--886
             Michael Hirsch and   
                 Wolfgang Quapp   Improved RGF method to find saddle
                                  points . . . . . . . . . . . . . . . . . 887--894
        Johannes Neugebauer and   
              Markus Reiher and   
               Carsten Kind and   
                  Bernd A. Hess   Quantum chemical calculation of
                                  vibrational spectra of large molecules
                                  --- Raman and IR spectra for
                                  Buckminsterfullerene . . . . . . . . . . 895--910
            Effendi Widjaja and   
                   Marc Garland   Pure component spectral reconstruction
                                  from mixture data using SVD, global
                                  entropy minimization, and simulated
                                  annealing. Numerical investigations of
                                  admissible objective functions using a
                                  synthetic 7-species data set . . . . . . 911--919
                   Fan Wang and   
                       Lemin Li   Analytical energy gradient evaluation in
                                  relativistic and nonrelativistic density
                                  functional calculations  . . . . . . . . 920--927
              Yoshiaki Amatatsu   Ab initio study on the electronic
                                  structures of styrene in the
                                  Franck--Condon region  . . . . . . . . . 928--937
        Katherine R. Greene and   
                  Kyle A. Beran   Isomers of C$_{20}$: an energy profile   938--942

Journal of Computational Chemistry
Volume 23, Number 10, July 30, 2002

              R. J. Buenker and   
              J. L. Whitten and   
           E. I. Izgorodina and   
           H.-P. Liebermann and   
                     D. B. Kokh   Use of exchange maximization to generate
                                  starting vectors for self-consistent
                                  field calculations on metal
                                  cluster/adsorbate systems  . . . . . . . 943--949
              Yoshiaki Amatatsu   Ab initio study on the photochemical
                                  behavior of styrene  . . . . . . . . . . 950--956
            Henryk A. Witek and   
             Yoong-Kee Choe and   
            James P. Finley and   
                 Kimihiko Hirao   Intruder state avoidance multireference
                                  Mòller--Plesset perturbation theory . . . 957--965
           Mustafa R. Helal and   
            Yaser A. Yousef and   
                 Akef T. Afaneh   Ab initio calculations of the
                                  stabilization energies of the
                                  conformational and the structural
                                  isomers of C$_3$H$_7$X where X = F, Cl,
                                  and Br . . . . . . . . . . . . . . . . . 966--976
                 Kalju Kahn and   
               Thomas C. Bruice   Parameterization of OPLS--AA force field
                                  for the conformational analysis of
                                  macrocyclic polyketides  . . . . . . . . 977--996
                   Hajime Torii   Intensity-carrying modes important for
                                  vibrational polarizabilities and
                                  hyperpolarizabilities of molecules:
                                  Derivation from the algebraic properties
                                  of formulas and applications . . . . . . 997--1006
André Severo Pereira Gomes and   
        Rogério Custodio   Exact Gaussian expansions of Slater-type
                                  atomic orbitals  . . . . . . . . . . . . 1007--1012
              A.-L. Derepas and   
               J.-M. Soudan and   
                 V. Brenner and   
               J.-P. Dognon and   
              Ph. Millié   Can we understand the different
                                  coordinations and structures of
                                  closed-shell metal cation-water
                                  clusters?  . . . . . . . . . . . . . . . 1013--1030

Journal of Computational Chemistry
Volume 23, Number 11, August, 2002

               Jian-Jun Liu and   
               Yi-Hong Ding and   
                 Yu-Guo Tao and   
               Ji-Kang Feng and   
                 Chia-Chung Sun   Theoretical study on the mechanism of
                                  the $^3$CH$_2$ + NO$_2$ reaction . . . . 1031--1044
            Daniel J. Price and   
          Charles L. Brooks III   Modern protein force fields behave
                                  comparably in molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1045--1057
                   Ulf Ryde and   
                 Lars Olsen and   
               Kristina Nilsson   Quantum chemical geometry optimizations
                                  in proteins using crystallographic raw
                                  data . . . . . . . . . . . . . . . . . . 1058--1070
                     T. Ida and   
                  M. Mizuno and   
                        K. Endo   Electronic state of small and large
                                  cavities for methane hydrate . . . . . . 1071--1075
           Maciej Bobrowski and   
                  Adam Liwo and   
        Stanis\law O\ldziej and   
            Danuta Jeziorek and   
               Tadeusz Ossowski   Ab initio study of the mechanism of
                                  singlet-dioxygen addition to
                                  hydroxyaromatic compounds: Negative
                                  evidence for the involvement of peroxa
                                  and endoperoxide intermediates . . . . . 1076--1089
           Buddhadeb Mallik and   
              Artem Masunov and   
               Themis Lazaridis   Distance and exposure dependent
                                  effective dielectric function  . . . . . 1090--1099
            T. W. Whitfield and   
                 John E. Straub   Gravitational smoothing as a global
                                  optimization strategy  . . . . . . . . . 1100--1103
                  A. S. Shalabi   F$_A$(I):Au$^+$ and F$_A$(II):Cu$^+$
                                  laser activity and photographic
                                  sensitization at the low coordinated
                                  surfaces of AgBr ab initio calculations  1104--1120
                Ron Shepard and   
             Isaiah Shavitt and   
                   Hans Lischka   Reducing I/O costs for the eigenvalue
                                  procedure in large-scale configuration
                                  interaction calculations . . . . . . . . 1121--1125

Journal of Computational Chemistry
Volume 23, Number 12, September, 2002

              Fatih Ya\csar and   
               Handan Arkin and   
         Tarik Çelik and   
              Bernd A. Berg and   
               Hagai Meirovitch   Efficiency of the multicanonical
                                  simulation method as applied to peptides
                                  of increasing size: the heptapeptide
                                  deltorphin . . . . . . . . . . . . . . . 1127--1134
     L. Y. A. Dávila and   
                   M. J. Caldas   Applicability of MNDO techniques AM1 and
                                  PM3 to ring-structured polymers  . . . . 1135--1142
          Sonja M. Schwarzl and   
          Thomas B. Tschopp and   
            Jeremy C. Smith and   
                 Stefan Fischer   Can the calculation of ligand binding
                                  free energies be improved with continuum
                                  solvent electrostatics and an ideal-gas
                                  entropy correction?  . . . . . . . . . . 1143--1149
                  Jon Baker and   
                    Peter Pulay   An efficient parallel algorithm for the
                                  calculation of canonical MP2 energies    1150--1156
   José Pitarch-Ruiz and   
José Sánchez-Marín and   
                  Daniel Maynau   Reducing CAS-SDCI space. Using selected
                                  spaces in configuration interaction
                                  calculations in an efficient way . . . . 1157--1165
            Haruyuki Nakano and   
             Ryuma Uchiyama and   
                 Kimihiko Hirao   Quasi-degenerate perturbation theory
                                  with general multiconfiguration
                                  self-consistent field reference
                                  functions  . . . . . . . . . . . . . . . 1166--1175
            Thomas E. Exner and   
              Matthias Keil and   
          Jürgen Brickmann   Pattern recognition strategies for
                                  molecular surfaces. I. Pattern
                                  generation using fuzzy set theory  . . . 1176--1187
            Thomas E. Exner and   
              Matthias Keil and   
          Jürgen Brickmann   Pattern recognition strategies for
                                  molecular surfaces. II. Surface
                                  complementarity  . . . . . . . . . . . . 1188--1197
                F. De Proft and   
             C. Van Alsenoy and   
                 A. Peeters and   
             W. Langenaeker and   
                   P. Geerlings   Atomic charges, dipole moments, and
                                  Fukui functions using the Hirshfeld
                                  partitioning of the electron density . . 1198--1209

Journal of Computational Chemistry
Volume 23, Number 13, October, 2002

                 Pekka Mark and   
                Lennart Nilsson   Structure and dynamics of liquid water
                                  with different long-range interaction
                                  truncation and temperature control
                                  methods in molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1211--1219
                   He Jiang and   
            Dominic Appadoo and   
             Evan Robertson and   
                 Don McNaughton   A comparison of predicted and
                                  experimental vibrational spectra in some
                                  small fluorocarbons  . . . . . . . . . . 1220--1225
                 Kenzi Hori and   
              Nobumitsu Dou and   
            Katsuhiko Okano and   
                  Ai Ohgami and   
                Hiroshi Tsukube   Stable conformations of 12-crown-O$_3$N
                                  and its Li$^+$ complex in aqueous
                                  solution . . . . . . . . . . . . . . . . 1226--1235
            Michelle Kuttel and   
                J. W. Brady and   
                Kevin J. Naidoo   Carbohydrate solution simulations:
                                  Producing a force field with
                                  experimentally consistent primary
                                  alcohol rotational frequencies and
                                  populations  . . . . . . . . . . . . . . 1236--1243
                    Ray Luo and   
              Laurent David and   
              Michael K. Gilson   Accelerated Poisson--Boltzmann
                                  calculations for static and dynamic
                                  systems  . . . . . . . . . . . . . . . . 1244--1253
             Vladislav Vasilyev   Determination of the effective
                                  dielectric constant from the accurate
                                  solution of the Poisson equation . . . . 1254--1265
      Athanassios C. Tsipis and   
         Constantinos A. Tsipis   Mechanistic aspects of the dehydration
                                  and dehydrohalogenation of
                                  halo-hydroxyformaldoxime conformers. A
                                  quantum chemical model study . . . . . . 1266--1280
                Jens Antony and   
                Nohad Gresh and   
                 Lars Olsen and   
            Lars Hemmingsen and   
   Christopher J. Schofield and   
                   Rogert Bauer   Binding of D- and L-captopril inhibitors
                                  to metallo-$\beta$-lactamase studied by
                                  polarizable molecular mechanics and
                                  quantum mechanics  . . . . . . . . . . . 1281--1296

Journal of Computational Chemistry
Volume 23, Number 14, November 15, 2002

            Alexey Onufriev and   
              David A. Case and   
                Donald Bashford   Effective Born radii in the generalized
                                  Born approximation: the importance of
                                  being perfect  . . . . . . . . . . . . . 1297--1304
                  Pere Constans   Linear scaling approaches to quantum
                                  macromolecular similarity: Evaluating
                                  the similarity function  . . . . . . . . 1305--1313
         Stephen J. Titmuss and   
           Peter L. Cummins and   
        Alistair P. Rendell and   
         Andrey A. Bliznyuk and   
                 Jill E. Gready   Comparison of linear-scaling
                                  semiempirical methods and combined
                                  quantum mechanical/molecular mechanical
                                  methods for enzymic reactions. II. An
                                  energy decomposition analysis  . . . . . 1314--1322
               Junichi Higo and   
             Masayoshi Nakasako   Hydration structure of human lysozyme
                                  investigated by molecular dynamics
                                  simulation and cryogenic X-ray crystal
                                  structure analyses: On the correlation
                                  between crystal water sites, solvent
                                  density, and solvent dipole  . . . . . . 1323--1336
           Hajime Takashima and   
                  So Yamada and   
              Shigeru Obara and   
          Kunihiro Kitamura and   
           Shinjiro Inabata and   
           Nobuaki Miyakawa and   
           Kazutoshi Tanabe and   
                Umpei Nagashima   A novel parallel algorithm for
                                  large-scale Fock matrix construction
                                  with small locally distributed memory
                                  architectures: RT parallel algorithm . . 1337--1346
             Xavier Fradera and   
                  Miquel Sol\`a   Electron localization and delocalization
                                  in open-shell molecules  . . . . . . . . 1347--1356
               Qingzhang Lu and   
                 Guoli Shen and   
                       Ruqin Yu   Genetic training of network using chaos
                                  concept: Application to QSAR studies of
                                  vibration modes of tetrahedral halides   1357--1365
                    Yang Wu and   
               Yi-Hong Ding and   
               Jing-Fa Xiao and   
                Ze-Sheng Li and   
                Xu-Ri Huang and   
                 Chia-Chung Sun   Direct ab initio dynamics study on the
                                  rate constants and kinetic isotope
                                  effect for the reactions of H atoms with
                                  GeD$_n$ (CH$_3$)$_{4 - n}$ ($n =
                                  1$--$4$) . . . . . . . . . . . . . . . . 1366--1374
    Konstantin P. Novoselov and   
       Denis B. Shirabaikin and   
     Stanislav Ya. Umanskii and   
    Alexander S. Vladimirov and   
         Airat Kh. Minushev and   
              Anatoli A. Korkin   CHIMERA: a software tool for reaction
                                  rate calculations and kinetics and
                                  thermodynamics analysis  . . . . . . . . 1375--1389

Journal of Computational Chemistry
Volume 23, Number 15, November 30, 2002

            Meng-Sheng Liao and   
                 Steve Scheiner   Comparative study of metal-porphyrins,
                                  -porphyrazines, and -phthalocyanines . . 1391--1403
                     Li Xie and   
                     Haiyan Liu   The treatment of solvation by a
                                  generalized Born model and a
                                  self-consistent charge-density
                                  functional theory-based tight-binding
                                  method . . . . . . . . . . . . . . . . . 1404--1415
                    D. Kony and   
                    W. Damm and   
                   S. Stoll and   
            W. F. Van Gunsteren   An improved OPLS--AA force field for
                                  carbohydrates  . . . . . . . . . . . . . 1416--1429
            Denis Jacquemin and   
        Beno\^\it Champagne and   
    Jean-Marie André and   
               Erik Deumens and   
                Yngve öhrn   Integral algorithm and density matrix
                                  integration scheme for ab initio band
                                  structure calculations on polymeric
                                  systems  . . . . . . . . . . . . . . . . 1430--1444
         Masahiro Kinoshita and   
                  Yoshiki Sugai   Methodology of predicting approximate
                                  shapes and size distribution of
                                  micelles: Illustration for simple models 1445--1455
               Jing-Fa Xiao and   
                Ze-Sheng Li and   
               Jing-Yao Liu and   
                   Li Sheng and   
                 Chia-Chung Sun   DFT and ab initio direct dynamics
                                  studies on the hydrogen abstraction
                                  reactions of chlorine atoms with CH$_{4
                                  - n}$F$_n$ ($n = 1$--$3$)  . . . . . . . 1456--1465
                 Akihiro Morita   Water polarizability in condensed phase:
                                  ab initio evaluation by cluster approach 1466--1471
               Shingo Urata and   
              Seiji Tsuzuki and   
            Masuhiro Mikami and   
               Akira Takada and   
          Tadafumi Uchimaru and   
                   Akira Sekiya   Analysis of the intermolecular
                                  interaction between CH$_3$OCH$_3$,
                                  CF$_3$OCH$_3$, CF$_3$OCF$_3$, and
                                  CH$_4$: High level ab initio
                                  calculations . . . . . . . . . . . . . . 1472--1479
             Grant D. Smith and   
               Oleg Borodin and   
                  Dmitry Bedrov   A revised quantum chemistry-based
                                  potential for poly(ethylene oxide) and
                                  its oligomers in aqueous solution  . . . 1480--1488
Friedrich Biegler-König and   
            Jens Schönbohm   Update of the AIM2000-Program for atoms
                                  in molecules . . . . . . . . . . . . . . 1489--1494
             Olivier Quinet and   
        Beno\^\it Champagne and   
                Bernard Kirtman   Analytical TDHF second derivatives of
                                  dynamic electronic polarizability with
                                  respect to nuclear coordinates.
                                  Application to the dynamic ZPVA
                                  correction . . . . . . . . . . . . . . . 1495--1496

Journal of Computational Chemistry
Volume 23, Number 16, December, 2002

                 Pengyu Ren and   
                  Jay W. Ponder   Consistent treatment of inter- and
                                  intramolecular polarization in molecular
                                  mechanics calculations . . . . . . . . . 1497--1506
                 Jan Sefcik and   
             Ersan Demiralp and   
                Tahir Cagin and   
         William A. Goddard III   Dynamic Charge Equilibration-Morse
                                  stretch force field: Application to
                                  energetics of pure silica zeolites . . . 1507--1514
         George A. Kaminski and   
             Harry A. Stern and   
                B. J. Berne and   
        Richard A. Friesner and   
             Yixiang X. Cao and   
           Robert B. Murphy and   
                Ruhong Zhou and   
              Thomas A. Halgren   Development of a polarizable force field
                                  for proteins via ab initio quantum
                                  chemistry: First generation model and
                                  gas phase tests  . . . . . . . . . . . . 1515--1531
             Alain Chaumont and   
                  Georges Wipff   Macrotricyclic quaternary tetraammonium
                                  receptors: Halide anion recognition and
                                  interfacial activity at an aqueous
                                  interface. A molecular dynamics
                                  investigation  . . . . . . . . . . . . . 1532--1543
            E. Keith Davies and   
                 Meir Glick and   
           Karl N. Harrison and   
             W. Graham Richards   Pattern recognition and massively
                                  distributed computing  . . . . . . . . . 1544--1550
                Jin-Qiu Lin and   
                Shi-Wei Luo and   
                    Yun-Dong Wu   Theoretical study of sheets formed by
                                  $\beta$-peptides . . . . . . . . . . . . 1551--1558
              Irina Massova and   
               Peter A. Kollman   p K$_a$, MM, and QM studies of
                                  mechanisms of $\beta$-lactamases and
                                  penicillin-binding proteins: Acylation
                                  step . . . . . . . . . . . . . . . . . . 1559--1576
            Philippe Barthe and   
       Christian Roumestand and   
Hél\`ene Déméné and   
                 Laurent Chiche   Helix motion in protein C12A-p8$^{MTCP}
                                  1$: Comparison of molecular dynamics
                                  simulations and multifield NMR
                                  relaxation data  . . . . . . . . . . . . 1577--1586
        Dimas Suárez and   
        Natalia Díaz and   
            Kenneth M. Merz Jr.   Molecular dynamics simulations of the
                                  dinuclear zinc-$\beta$-lactamase from
                                  Bacteroides fragilis complexed with
                                  imipenem . . . . . . . . . . . . . . . . 1587--1600
         Matthew P. Repasky and   
    Jayaraman Chandrasekhar and   
           William L. Jorgensen   PDDG/PM3 and PDDG/MNDO: Improved
                                  semiempirical methods  . . . . . . . . . 1601--1622
              Araz Jakalian and   
              David B. Jack and   
           Christopher I. Bayly   Fast, efficient generation of
                                  high-quality atomic charges. AM1-BCC
                                  model: II. Parameterization and
                                  validation . . . . . . . . . . . . . . . 1623--1641
                Qian-Shu Li and   
            Rui-Hua Lü and   
                Yaoming Xie and   
          Henry F. Schaefer III   Molecules for materials: Germanium
                                  hydride neutrals and anions. Molecular
                                  structures, electron affinities, and
                                  thermochemistry of GeH$_n$ /GeH ($n =
                                  0$--$4$) and Ge$_2$H$_n$ /Ge$_2$H ($n =
                                  0$--$6$) . . . . . . . . . . . . . . . . 1642--1655
           Visvaldas Kairys and   
              Michael K. Gilson   Enhanced docking with the mining minima
                                  optimizer: Acceleration and side-chain
                                  flexibility  . . . . . . . . . . . . . . 1656--1670
            Gernot Frenking and   
           William L. Jorgensen   Foreword . . . . . . . . . . . . . . . . vi--vii


Journal of Computational Chemistry
Volume 24, Number 1, January 15, 2003

          Stephen C. Harvey and   
               Chunlin Wang and   
         Stephane Teletchea and   
                 Richard Lavery   Motifs in nucleic acids: Molecular
                                  mechanics restraints for base pairing
                                  and base stacking  . . . . . . . . . . . 1--9
             Andrew Smellie and   
             Robert Stanton and   
                Randy Henne and   
                     Steve Teig   Conformational analysis by intersection:
                                  CONAN  . . . . . . . . . . . . . . . . . 10--20
                  Asim Okur and   
         Bentley Strockbine and   
              Viktor Hornak and   
              Carlos Simmerling   Using PC clusters to evaluate the
                                  transferability of molecular mechanics
                                  force fields for proteins  . . . . . . . 21--31
               C. Curutchet and   
                 A. Salichs and   
                  X. Barril and   
             Modesto Orozco and   
                F. Javier Luque   Transferability of fragmental
                                  contributions to the octanol/water
                                  partition coefficient: an NDDO-based MST
                                  study  . . . . . . . . . . . . . . . . . 32--45
           Giuliano Alagona and   
              Caterina Ghio and   
               Peter A. Kollman   The intramolecular mechanism for the
                                  second proton transfer in
                                  triosephosphate isomerase (TIM): a QM/FE
                                  approach . . . . . . . . . . . . . . . . 46--56
           Edward C. Sherer and   
             Darrin M. York and   
          Christopher J. Cramer   Fast approximate methods for calculating
                                  nucleic acid base pair interaction
                                  energies . . . . . . . . . . . . . . . . 57--67
                Scott Brown and   
             Teresa Head-Gordon   Cool walking: a new Markov chain Monte
                                  Carlo sampling method  . . . . . . . . . 68--76
               Danny Barash and   
               Linjing Yang and   
             Xiaoliang Qian and   
                  Tamar Schlick   Inherent speedup limitations in multiple
                                  time step/particle mesh Ewald algorithms 77--88
                 Chaok Seok and   
                J. B. Rosen and   
            John D. Chodera and   
                    Ken A. Dill   MOPED: Method for optimizing physical
                                  energy parameters using decoys . . . . . 89--97
             Gregori Ujaque and   
           Dean J. Tantillo and   
                 Yunfeng Hu and   
                 K. N. Houk and   
                Kinya Hotta and   
                 Donald Hilvert   Catalysis on the coastline: Theozyme,
                                  molecular dynamics, and free energy
                                  perturbation analysis of antibody 21D8
                                  catalysis of the decarboxylation of
                                  5-nitro-3-carboxybenzisoxazole . . . . . 98--110
            K. N. Kirschner and   
                A. H. Lewin and   
                    J. P. Bowen   Molecular mechanics force-field
                                  development for amino acid zwitterions   111--128

Journal of Computational Chemistry
Volume 24, Number 2, January 30, 2003

          Matteo Ceccarelli and   
             Piero Procacci and   
                 Massimo Marchi   An ab initio force field for the
                                  cofactors of bacterial photosynthesis    129--142
            Francesca Massi and   
                 John E. Straub   Structural and dynamical analysis of the
                                  hydration of the Alzheimer's
                                  $\beta$-amyloid peptide  . . . . . . . . 143--153
         Alexander V. Mitin and   
                  Jon Baker and   
         Krzysztof Wolinski and   
                    Peter Pulay   Parallel stored-integral and semidirect
                                  Hartree--Fock and DFT methods with data
                                  compression  . . . . . . . . . . . . . . 154--160
Jose Manuel Hermida-Ramón and   
             Steve Brdarski and   
      Gunnar Karlström and   
                       Ulf Berg   Inter- and intramolecular potential for
                                  the $N$-formylglycinamide-water system.
                                  A comparison between theoretical
                                  modeling and empirical force fields  . . 161--176
       Mireia Garcia-Viloca and   
  Cristóbal Alhambra and   
          Donald G. Truhlar and   
                      Jiali Gao   Hydride transfer catalyzed by xylose
                                  isomerase: Mechanism and quantum effects 177--190
              J. L. Klepeis and   
                  C. A. Floudas   Prediction of $\beta$-sheet topology and
                                  disulfide bridges in polypeptides  . . . 191--208
                Takumi Hori and   
          Hideaki Takahashi and   
                Tomoshige Nitta   Hybrid QM/MM molecular dynamics
                                  simulations for an ionic S$_N$2 reaction
                                  in the supercritical water: OH$^-$ +
                                  CH$_3$Cl $\rightarrow$ CH$_3$OH + Cl$^-$ 209--221
         Robert J. Petrella and   
           Ioan Andricioaei and   
          Bernard R. Brooks and   
                 Martin Karplus   An improved method for nonbonded list
                                  generation: Rapid determination of
                                  near-neighbor pairs  . . . . . . . . . . 222--231
         D. Benjamin Gordon and   
            Geoffrey K. Hom and   
            Stephen L. Mayo and   
                Niles A. Pierce   Exact rotamer optimization for protein
                                  design . . . . . . . . . . . . . . . . . 232--243
            Satoshi Okumoto and   
                Shinichi Yamabe   Computational study of epoxy-amine
                                  reactions  . . . . . . . . . . . . . . . 244--253
          Vsevolod Katritch and   
               Maxim Totrov and   
                  Ruben Abagyan   ICFF: a new method to incorporate
                                  implicit flexibility into an internal
                                  coordinate force field . . . . . . . . . 254--265

Journal of Computational Chemistry
Volume 24, Number 3, February, 2003

         George A. Kaminski and   
        Richard A. Friesner and   
                    Ruhong Zhou   A computationally inexpensive
                                  modification of the point dipole
                                  electrostatic polarization model for
                                  molecular simulations  . . . . . . . . . 267--276
                 Genyuan Li and   
            Herschel Rabitz and   
             Sheng-Wei Wang and   
          Panos G. Georgopoulos   Correlation method for variance
                                  reduction of Monte Carlo integration in
                                  RS-HDMR  . . . . . . . . . . . . . . . . 277--283
           Carles Curutchet and   
      Christopher J. Cramer and   
          Donald G. Truhlar and   
Manuel F. Ruiz-López and   
             Daniel Rinaldi and   
             Modesto Orozco and   
                F. Javier Luque   Electrostatic component of solvation:
                                  Comparison of SCRF continuum models  . . 284--297
        Christopher S. Page and   
               Massimo Olivucci   Ground and excited state CASPT 2
                                  geometry optimizations of small organic
                                  molecules  . . . . . . . . . . . . . . . 298--309
            Kazuyoshi Ikeda and   
       Oxana V. Galzitskaya and   
            Haruki Nakamura and   
                   Junichi Higo   $\beta$-Hairpins, $\alpha$-helices, and
                                  the intermediates among the secondary
                                  structures in the energy landscape of a
                                  peptide from a distal $\beta$-hairpin of
                                  SH3 domain . . . . . . . . . . . . . . . 310--318
            Takashi Yoshida and   
        Kazuhisa Sakakibara and   
            Masatoshi Asami and   
            Kuo-Hsiang Chen and   
              Jenn-Huei Lii and   
             Norman L. Allinger   Molecular mechanics (MM3) calculations
                                  on lithium amide compounds . . . . . . . 319--327
          Alicia C. Lorenzo and   
          Pedro G. Pascutti and   
                 Paulo M. Bisch   Nonspecific interaction forces at
                                  water--membrane interface by forced
                                  molecular dynamics simulations . . . . . 328--339
              Zheng-Wang Qu and   
                    Hui Zhu and   
            Xing-Kang Zhang and   
                  Qi-Yuan Zhang   Density functional investigation on
                                  electron-transfer catalysis of
                                  cycloreversion of cyclobutane: Radical
                                  anion mechanism  . . . . . . . . . . . . 340--344
                 Jinshan Li and   
                  Feng Zhao and   
                    Fuqian Jing   An ab initio study of intermolecular
                                  interactions of nitromethane dimer and
                                  nitromethane trimer  . . . . . . . . . . 345--352
              A. J. Bordner and   
                    G. A. Huber   Boundary element solution of the linear
                                  Poisson--Boltzmann equation and a
                                  multipole method for the rapid
                                  calculation of forces on macromolecules
                                  in solution  . . . . . . . . . . . . . . 353--367
              Jaroslav Koca and   
             Chang-Guo Zhan and   
      Robert C. Rittenhouse and   
               Rick L. Ornstein   Coordination number of zinc ions in the
                                  phosphotriesterase active site by
                                  molecular dynamics and quantum mechanics 368--378
                Yi-Gui Wang and   
            Nick Henry Werstiuk   A practical and efficient method to
                                  calculate AIM localization and
                                  delocalization indices at post-HF levels
                                  of theory  . . . . . . . . . . . . . . . 379--385
   Christofer S. Tautermann and   
         Andreas F. Voegele and   
            Thomas Loerting and   
                 Peter Kaps and   
                 Klaus R. Liedl   Extended method for adiabatic mode
                                  reordering . . . . . . . . . . . . . . . 386--395
            Asit K. Chandra and   
          Tadafumi Uchimaru and   
              Masaaki Sugie and   
                   Akira Sekiya   Ab initio study on the structures of
                                  fluorinated formates and hydrogen
                                  abstraction reaction with OH radical . . 396--407

Journal of Computational Chemistry
Volume 24, Number 4, March, 2003

              Christophe Chipot   Rational determination of charge
                                  distributions for free energy
                                  calculations . . . . . . . . . . . . . . 409--415
               Ibon Alkorta and   
               Jose Elguero and   
           Enrique Espinosa and   
                Ignasi Mata and   
                   Elies Molins   Comparison of electron density
                                  properties in frozen and relaxed
                                  electronic distributions . . . . . . . . 416--421
                Carlo Gatti and   
            Fausto Cargnoni and   
                   Luca Bertini   Chemical information from the source
                                  function . . . . . . . . . . . . . . . . 422--436
    Nathaniel O. J. Malcolm and   
            Paul L. A. Popelier   An improved algorithm to locate critical
                                  points in a $3$D scalar field as
                                  implemented in the program MORPHY  . . . 437--442
                George Maroulis   Ab initio determination of the electric
                                  multipole moments and static
                                  (hyper)polarizability of HCCX, X = F,
                                  Cl, Br, and I  . . . . . . . . . . . . . 443--452
         Chérif F. Matta   Application of the quantum theory of
                                  atoms in molecules to selected
                                  physico-chemical and biophysical
                                  problems: Focus on correlation with
                                  experiment . . . . . . . . . . . . . . . 453--463
                F. De Proft and   
             R. Vivas-Reyes and   
                 A. Peeters and   
             C. Van Alsenoy and   
                   P. Geerlings   Hirshfeld partitioning of the electron
                                  density: Atomic dipoles and their
                                  relation with functional group
                                  properties . . . . . . . . . . . . . . . 463--470
         Daniel J. Grimwood and   
               Ian Bytheway and   
               Dylan Jayatilaka   Wave functions derived from experiment.
                                  V. Investigation of electron densities,
                                  electrostatic potentials, and electron
                                  localization functions for
                                  noncentrosymmetric crystals  . . . . . . 470--483
                    K. Babu and   
              Shridhar R. Gadre   Ab initio quality one-electron
                                  properties of large molecules:
                                  Development and testing of molecular
                                  tailoring approach . . . . . . . . . . . 484--495
                E. Chamorro and   
              P. Fuentealba and   
                       A. Savin   Electron probability distribution in AIM
                                  and ELF basins . . . . . . . . . . . . . 496--504
             Peter Politzer and   
             Jane S. Murray and   
                       Pat Lane   Electrostatic potentials and covalent
                                  radii  . . . . . . . . . . . . . . . . . 505--511
            C. E. Whitehead and   
             C. M. Breneman and   
                 N. Sukumar and   
                     M. D. Ryan   Transferable atom equivalent
                                  multicentered multipole expansion method 512--529
              Shridhar R. Gadre   Foreword . . . . . . . . . . . . . . . . vii--vii

Journal of Computational Chemistry
Volume 24, Number 5, April 15, 2003

             Marcin Król   Comparison of various implicit solvent
                                  models in molecular dynamics simulations
                                  of immunoglobulin G light chain dimer    531--546
             Paola Facchini and   
             Felice Grandinetti   Concerning the reaction between singlet
                                  nitrenium ions and water: a
                                  computational investigation on
                                  competitive reaction paths . . . . . . . 547--564
             Marcus Elstner and   
                  Qiang Cui and   
                Petra Munih and   
          Efthimios Kaxiras and   
          Thomas Frauenheim and   
                 Martin Karplus   Modeling zinc in biomolecules with the
                                  self consistent charge-density
                                  functional tight binding (SCC-DFTB)
                                  method: Applications to structural and
                                  energetic analysis . . . . . . . . . . . 565--581
            Takashi Amisaki and   
            Shinjiro Toyoda and   
             Hiroh Miyagawa and   
              Kunihiro Kitamura   Development of hardware accelerator for
                                  molecular dynamics simulations: a
                                  computation board that calculates
                                  nonbonded interactions in cooperation
                                  with fast multipole method . . . . . . . 582--592
                 Jia-Yan Wu and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                Xu-Ri Huang and   
                 Chia-Chung Sun   Dual-level direct dynamics studies for
                                  the reactions of dimethyl ether with
                                  hydrogen atom and methyl radical . . . . 593--600
            Gabriela L. Borosky   Theoretical study concerning the
                                  reactivity of imine derivatives of
                                  polycyclic aromatic hydrocarbons . . . . 601--608
   José Pitarch-Ruiz and   
José Sánchez-Marín and   
                  Daniel Maynau   Vertical spectrum of the C$_2$H system.
                                  An open shell (SC)$^2$--CAS--SDCI study  609--617
          Chandra Saravanan and   
                 Yihan Shao and   
                   Roi Baer and   
             Philip N. Ross and   
             Martin Head-Gordon   Sparse matrix multiplications for linear
                                  scaling electronic structure
                                  calculations in an atom-centered basis
                                  set using multiatom blocks . . . . . . . 618--622
            Meng-Sheng Liao and   
                     Yun Lu and   
                 Steve Scheiner   Performance assessment of
                                  density-functional methods for study of
                                  charge-transfer complexes  . . . . . . . 623--631
           Andrea C. Vaiana and   
             Andreas Schulz and   
        Jürgen Wolfrum and   
               Markus Sauer and   
                Jeremy C. Smith   Molecular mechanics force field
                                  parameterization of the fluorescent
                                  probe rhodamine 6G using automated
                                  frequency matching . . . . . . . . . . . 632--639
            C. F. Cloud III and   
                    M. Schwartz   Systematic errors in DFT calculations of
                                  haloalkane heats of formation  . . . . . 640--646
                 Genyuan Li and   
            Maxim Artamonov and   
            Herschel Rabitz and   
             Sheng-wei Wang and   
      Panos G. Georgopoulos and   
                 Metin Demiralp   High-dimensional model representations
                                  generated from low order terms ---
                                  lp-RS-HDMR . . . . . . . . . . . . . . . 647--656
              T. Róg and   
                  K. Murzyn and   
                  K. Hinsen and   
                  G. R. Kneller   n Moldyn: a program package for a
                                  neutron scattering oriented analysis of
                                  molecular dynamics simulations . . . . . 657--667

Journal of Computational Chemistry
Volume 24, Number 6, April 30, 2003

             Maurizio Cossi and   
                 Nadia Rega and   
          Giovanni Scalmani and   
                Vincenzo Barone   Energies, structures, and electronic
                                  properties of molecules in solution with
                                  the C-PCM solvation model  . . . . . . . 669--681
                David Bosch and   
          Mercedes Campillo and   
                 Leonardo Pardo   Binding of proteins to the minor groove
                                  of DNA: What are the structural and
                                  energetic determinants for kinking a
                                  basepair step? . . . . . . . . . . . . . 682--691
               A. S. Zyubin and   
                    A. M. Mebel   Performance of time-dependent density
                                  functional and Green functions methods
                                  for calculations of excitation energies
                                  in radicals and for Rydberg electronic
                                  states . . . . . . . . . . . . . . . . . 692--700
              Laura Masgrau and   
\`Angels González-Lafont and   
           José M. Lluch   Dependence of the rate constants on the
                                  treatment of internal rotation modes:
                                  the reaction OH + CH$_3$SH $\rightarrow$
                                  CH$_3$S + H$_2$O as an example . . . . . 701--706
               Luis Lorenzo and   
            Ricardo A. Mosquera   A box-counting-based algorithm for
                                  computing Shannon entropy in molecular
                                  dynamics simulations . . . . . . . . . . 707--713
             Axel Koslowski and   
            Michael E. Beck and   
                   Walter Thiel   Implementation of a general
                                  multireference configuration interaction
                                  procedure with analytic gradients in a
                                  semiempirical context using the
                                  graphical unitary group approach . . . . 714--726
                Yu-Dong Cai and   
               Xiao-Jun Liu and   
                  Kuo-Chen Chou   Prediction of protein secondary
                                  structure content by artificial neural
                                  network  . . . . . . . . . . . . . . . . 727--731
           Peter M. W. Gill and   
                 Siu-Hung Chien   Radial quadrature for multiexponential
                                  integrands . . . . . . . . . . . . . . . 732--740
         Tanja Schulz-Gasch and   
                   Martin Stahl   Mechanistic insights into oxidosqualene
                                  cyclizations through homology modeling   741--753
        Markus Pernpointner and   
                 Lucas Visscher   Parallelization of four-component
                                  calculations. II. Symmetry-driven
                                  parallelization of the 4-Spinor CCSD
                                  algorithm  . . . . . . . . . . . . . . . 754--759
                Thom Vreven and   
             Keiji Morokuma and   
      Ödön Farkas and   
       H. Bernhard Schlegel and   
              Michael J. Frisch   Geometry optimization with QM/MM, ONIOM,
                                  and other combined methods. I.
                                  Microiterations and constraints  . . . . 760--769
                David Zanuy and   
       Carlos Alemán and   
                Manuel Laso and   
Sebastián Muñoz-Guerra   Thermally induced phase transition in
                                  helical comblike poly($\beta$-peptide)s:
                                  an atomistic simulation  . . . . . . . . 770--778
          Matteo Pappalardo and   
             Danilo Milardi and   
         Domenico M. Grasso and   
                Carmelo La Rosa   Free energy perturbation and molecular
                                  dynamics calculations of copper binding
                                  to azurin  . . . . . . . . . . . . . . . 779--785
                Mark Pinsky and   
           Dina Yogev-Einot and   
                    David Avnir   Statistical analysis of the estimation
                                  of distance measures . . . . . . . . . . 786--796

Journal of Computational Chemistry
Volume 24, Number 7, May, 2003

            Philippe Arnaud and   
        Krystyna Zakrzewska and   
                Bernard Meunier   Theoretical study of the interaction
                                  between a high-valent manganese
                                  porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP
                                  and double-stranded DNA  . . . . . . . . 797--805
         Majda Rahal-Sekkal and   
               Nezha Sekkal and   
               Dirk C. Kleb and   
                 Paul Bleckmann   Structures and energies of D-galactose
                                  and galabiose conformers as calculated
                                  by ab initio and semiempirical methods   806--818
José Mario Martínez and   
        Leandro Martínez   Packing optimization for automated
                                  generation of complex system's initial
                                  configurations for molecular dynamics
                                  and docking  . . . . . . . . . . . . . . 819--825
              Kenshu Kamiya and   
              Yoko Sugawara and   
                Hideaki Umeyama   Algorithm for normal mode analysis with
                                  general internal coordinates . . . . . . 826--841
               Yu-Ren Jiang and   
                Jing-Ya Liu and   
                 Yue-Hua Hu and   
                Toyohisa Fujita   Novel topological index for research on
                                  structure-property relationships of
                                  complex organic compounds  . . . . . . . 842--849
           Valentina Vetere and   
            Pascale Maldivi and   
                    Carlo Adamo   Comparative studies of
                                  quasi-relativistic density functional
                                  methods for the description of
                                  lanthanide and actinide complexes  . . . 850--858
                     I. Ema and   
J. M. García de la Vega and   
          G. Ramírez and   
            R. López and   
   J. Fernández Rico and   
                H. Meissner and   
                      J. Paldus   Polarized basis sets of Slater-type
                                  orbitals: H to Ne atoms  . . . . . . . . 859--868
    Carlos Renato Zacharias and   
  Maurício Ruv Lemes and   
Arnaldo Dal Pino Júnior and   
             David Santo Orcero   Predicting structural models for silicon
                                  clusters . . . . . . . . . . . . . . . . 869--875
                 Mark Bathe and   
            Gregory C. Rutledge   Inverse Monte Carlo procedure for
                                  conformation determination of
                                  macromolecules . . . . . . . . . . . . . 876--890
           Joseph V. Turner and   
            David J. Cutler and   
                 Ian Spence and   
           Desmond J. Maddalena   Selective descriptor pruning for
                                  QSAR/QSPR studies using artificial
                                  neural networks  . . . . . . . . . . . . 891--897
                 Miroslav Pinak   8-oxoguanine lesioned B-DNA molecule
                                  complexed with repair enzyme hOGG1: a
                                  molecular dynamics study . . . . . . . . 898--907

Journal of Computational Chemistry
Volume 24, Number 8, June, 2003

           Fillmore Freeman and   
                    Elika Derek   A computational study of conformational
                                  interconversions in
                                  1,4-dithiacyclohexane (1,4-dithiane) . . 909--919
             Wataru Shinoda and   
                Masuhiro Mikami   Rigid-body dynamics in the
                                  isothermal-isobaric ensemble: a test on
                                  the accuracy and computational
                                  efficiency . . . . . . . . . . . . . . . 920--930
                    Yong Wu and   
                Daiqian Xie and   
                       Ying Xue   Ab initio studies for the
                                  photodissociation mechanism of
                                  hydroxyacetone . . . . . . . . . . . . . 931--938
            Shinichi Yamabe and   
                Noriko Tsuchida   A computational study of interactions
                                  between acetic acid and water molecules  939--947
             Zhongfang Chen and   
                Haijun Jiao and   
           Gotthard Seifert and   
          Anselm H. C. Horn and   
                  Dengke Yu and   
                  Tim Clark and   
               Walter Thiel and   
 Paul von Ragué Schleyer   The structure and stability of Si$_{60}$
                                  and Ge$_{60}$ cages: a computational
                                  study  . . . . . . . . . . . . . . . . . 948--953
          Kathryn N. Rankin and   
               Traian Sulea and   
             Enrico O. Purisima   On the transferability of
                                  hydration-parametrized continuum
                                  electrostatics models to solvated
                                  binding calculations . . . . . . . . . . 954--962
                   Ying Xue and   
               Chun Ho Kang and   
             Chan Kyung Kim and   
                    Ikchoon Lee   Theoretical studies on the gas-phase
                                  pyrolysis of 2-phenoxycarboxylic acids:
                                  an ONIOM approach  . . . . . . . . . . . 963--972
  Marcelo Zaldini Hernandes and   
João Bosco P. Da Silva and   
               Ricardo L. Longo   Chemometric study of liquid water
                                  simulations. I. The parameters of the
                                  TIP4P model potential  . . . . . . . . . 973--981
                Eliseo Ruiz and   
Antonio Rodríguez-Fortea and   
                  Joan Cano and   
           Santiago Alvarez and   
                   Pere Alemany   About the calculation of exchange
                                  coupling constants in polynuclear
                                  transition metal complexes . . . . . . . 982--989
         Dominic R. Alfonso and   
              Kenneth D. Jordan   A flexible nudged elastic band program
                                  for optimization of minimum energy
                                  pathways using ab initio electronic
                                  structure methods  . . . . . . . . . . . 990--996
János G. Ángyán and   
          Christophe Chipot and   
      François Dehez and   
       Christof Hättig and   
               Georg Jansen and   
                  Claude Millot   OPEP: a tool for the optimal
                                  partitioning of electric properties  . . 997--1008

Journal of Computational Chemistry
Volume 24, Number 9, July 15, 2003

     Christopher C. Lovallo and   
            Mariusz Klobukowski   Development of new pseudopotential
                                  methods: Improved model core potentials
                                  for the first-row transition metals  . . 1009--1015
         Kristin L. Meagher and   
             Luke T. Redman and   
             Heather A. Carlson   Development of polyphosphate parameters
                                  for use with the AMBER force field . . . 1016--1025
      András Perczel and   
      Ödön Farkas and   
          Imre Jákli and   
              Igor A. Topol and   
              Imre G. Csizmadia   Peptide models. XXXIII. Extrapolation of
                                  low-level Hartree--Fock data of peptide
                                  conformation to large basis set SCF,
                                  MP2, DFT, and CCSD(T) results. The
                                  Ramachandran surface of alanine
                                  dipeptide computed at various levels of
                                  theory . . . . . . . . . . . . . . . . . 1026--1042
              J. A. Hageman and   
                 R. Wehrens and   
               R. De Gelder and   
               L. M. C. Buydens   Powder pattern indexing using the
                                  weighted crosscorrelation and genetic
                                  algorithms . . . . . . . . . . . . . . . 1043--1051
         David C. Chatfield and   
            Alberto Augsten and   
            Cassian D'Cunha and   
                 Sergio E. Wong   Methyl dynamics in crystalline amino
                                  acids: MD and NMR  . . . . . . . . . . . 1052--1058
               Shenghua Shi and   
                   Lisa Yan and   
                  Yang Yang and   
       Jodi Fisher-Shaulsky and   
                    Tom Thacher   An extensible and systematic force
                                  field, ESFF, for molecular modeling of
                                  organic, inorganic, and organometallic
                                  systems  . . . . . . . . . . . . . . . . 1059--1076
           Toshimasa Ishida and   
               George C. Schatz   A local interpolation scheme using no
                                  derivatives in potential sampling:
                                  Application to O($^1$D) + H$_2$ system   1077--1086
         Alice Glättli and   
               Xavier Daura and   
       Wilfred F. Van Gunsteren   A novel approach for designing simple
                                  point charge models for liquid water
                                  with three interaction sites . . . . . . 1087--1096
              Lionello Pogliani   Complete graph conjecture for inner-core
                                  electrons: Homogeneous index case  . . . 1097--1109
                  S. Sirois and   
              E. I. Proynov and   
              J.-F. Truchon and   
              C. M. Tsoukas and   
                  D. R. Salahub   A density functional study of the
                                  hydrogen-bond network within the HIV-1
                                  protease catalytic site cleft  . . . . . 1110--1119
                 Roger A. Klein   Hydrogen bonding in diols and binary
                                  diol--water systems investigated using
                                  DFT methods. II. Calculated infrared
                                  OH-stretch frequencies, force constants,
                                  and NMR chemical shifts correlate with
                                  hydrogen bond geometry and electron
                                  density topology. A reevaluation of
                                  geometrical criteria for hydrogen
                                  bonding  . . . . . . . . . . . . . . . . 1120--1131
               N. A. Anikin and   
             V. L. Bugaenko and   
                M. V. Frash and   
                    L. Gorb and   
                 J. Leszczynski   Localized basis orbitals: Minimization
                                  of 2-electron integrals array and
                                  orthonormality of basis set  . . . . . . 1132--1141
              E. Van Lenthe and   
                 E. J. Baerends   Optimized Slater-type basis sets for the
                                  elements 1--118  . . . . . . . . . . . . 1142--1156

Journal of Computational Chemistry
Volume 24, Number 10, July 30, 2003

      András Perczel and   
 Anna K. Füzéry and   
Attila G. Császár   Toward direct determination of
                                  conformations of protein building units
                                  from multidimensional NMR experiments.
                                  V. NMR chemical shielding analysis of
                                  N-formyl-serinamide, a model for polar
                                  side-chain containing peptides . . . . . 1157--1171
            Vladimir Hnizdo and   
            Adam Fedorowicz and   
           Harshinder Singh and   
                 Eugene Demchuk   Statistical thermodynamics of internal
                                  rotation in a hindering potential of
                                  mean force obtained from computer
                                  simulations  . . . . . . . . . . . . . . 1172--1183
                  Jon Baker and   
                    Peter Pulay   Assessment of the OLYP and O3LYP density
                                  functionals for first-row transition
                                  metals . . . . . . . . . . . . . . . . . 1184--1191
              Michio Iwaoka and   
                   Shuji Tomoda   The SAAP force field. A simple approach
                                  to a new all-atom protein force field by
                                  using single amino acid potential (SAAP)
                                  functions in various solvents  . . . . . 1192--1200
            Sean A. C. McDowell   A computational study of the LiH dimer   1201--1207
         David Curcó and   
                David Zanuy and   
           Carlos Alemán   EVEBAT: a fast strategy for the
                                  examination of the empty space in
                                  polymer matrices . . . . . . . . . . . . 1208--1214
         Dimitris K. Agrafiotis   Stochastic proximity embedding . . . . . 1215--1221
                     B. Das and   
              H. Meirovitch and   
                    I. M. Navon   Performance of hybrid methods for
                                  large-scale unconstrained optimization
                                  as applied to models of proteins . . . . 1222--1231
             Hannes H. Loeffler   Many-body effects on structure and
                                  dynamics of aqueous ionic solutions  . . 1232--1239
          Markus J. Loferer and   
         Hannes H. Loeffler and   
                 Klaus R. Liedl   A QM--MM interface between CHARMM and
                                  TURBOMOLE: Implementation and
                                  application to systems in bulk phase and
                                  biologically active systems  . . . . . . 1240--1249
              Joseph Ivanic and   
               Klaus Ruedenberg   A MCSCF method for ground and excited
                                  states based on full optimizations of
                                  successive Jacobi rotations  . . . . . . 1250--1262
           Carles Curutchet and   
  Josep María Bofill and   
Begoña Hernández and   
             Modesto Orozco and   
                F. Javier Luque   Energy decomposition in molecular
                                  complexes: Implications for the
                                  treatment of polarization in molecular
                                  simulations  . . . . . . . . . . . . . . 1263--1275
    Nathaniel O. J. Malcolm and   
            Paul L. A. Popelier   An algorithm to delineate and integrate
                                  topological basins in a
                                  three-dimensional quantum mechanical
                                  density function . . . . . . . . . . . . 1276--1282
         Charles H. Langley and   
              Jenn-Huei Lii and   
                Norman Allinger   Molecular mechanics (MM4) calculations
                                  on carbonyl compounds. I--IV.  . . . . . 1283--1286

Journal of Computational Chemistry
Volume 24, Number 11, August, 2003

                  Kyle A. Beran   Isomers of C$_{20}$: an energy profile
                                  II . . . . . . . . . . . . . . . . . . . 1287--1290
          Jason D. Thompson and   
      Christopher J. Cramer and   
              Donald G. Truhlar   Parameterization of charge model 3 for
                                  AM1, PM3, BLYP, and B3LYP  . . . . . . . 1291--1304
            Clovis Darrigan and   
        Michel Rérat and   
            Giuseppe Mallia and   
                 Roberto Dovesi   Implementation of the finite field
                                  perturbation method in the CRYSTAL
                                  program for calculating the dielectric
                                  constant of periodic systems . . . . . . 1305--1312
              Shandar Ahmad and   
             M. Michael Gromiha   Design and training of a neural network
                                  for predicting the solvent accessibility
                                  of proteins  . . . . . . . . . . . . . . 1313--1320
Julio Peiró-García and   
Víctor M. Ramírez-Ramírez and   
              Ignacio Nebot-Gil   A theoretical ab initio study on the
                                  H$_2$NO + O$_3$ reaction . . . . . . . . 1321--1328
            Osamu Takahashi and   
            Masanori Joyabu and   
              Masaki Mitani and   
                   Ko Saito and   
                  Suehiro Iwata   Theoretical studies on the molecular
                                  dependence of bond dissociation after
                                  core excitations II:
                                  CH$_3$CO(CH$_2$)$_n$CN, $n = 0$--$3$ . . 1329--1335
             D. M. Upadhyay and   
                   P. C. Mishra   An ab initio study of microsolvation of
                                  LiF in water: Structures and properties
                                  of LiF--W$_n$, $n = 1$--$9$ complexes    1336--1347
             Michael S. Lee and   
               Michael Feig and   
    Freddie R. Salsbury Jr. and   
          Charles L. Brooks III   New analytic approximation to the
                                  standard molecular volume definition and
                                  its application to generalized Born
                                  calculations . . . . . . . . . . . . . . 1348--1356
            Marco Garavelli and   
           Fabrizio Ruggeri and   
    François Ogliaro and   
        Michael J. Bearpark and   
          Fernando Bernardi and   
           Massimo Olivucci and   
                Michael A. Robb   A simple approach for improving the
                                  hybrid MMVB force field: Application to
                                  the photoisomerization of $s$-cis
                                  butadiene  . . . . . . . . . . . . . . . 1357--1363
                Sean Cahill and   
             Michael Cahill and   
                   Kevin Cahill   On the kinematics of protein folding . . 1364--1370

Journal of Computational Chemistry
Volume 24, Number 12, September, 2003

           Lillian T. Chong and   
     Pradipta Bandyopadhyay and   
          Thomas S. Scanlan and   
             Irwin D. Kuntz and   
               Peter A. Kollman   Direct hydroxide attack is a plausible
                                  mechanism for amidase antibody 43C9  . . 1371--1377
             Mutsumi Hirama and   
           Toshimasa Ishida and   
                Jun-Ichi Aihara   Possible molecular hydrogen formation
                                  mediated by the radical cations of
                                  anthracene and pyrene  . . . . . . . . . 1378--1382
             Peter Carlsson and   
                Lennart Nilsson   Improved precision and efficiency of
                                  free energy calculations for small
                                  systems using $\lambda$-scaled atomic
                                  masses and separating conformational and
                                  transformational sampling  . . . . . . . 1383--1389
            Henryk A. Witek and   
            Haruyuki Nakano and   
                 Kimihiko Hirao   Multireference perturbation theory with
                                  optimized partitioning. II. Applications
                                  to molecular systems . . . . . . . . . . 1390--1400
          Masahiro Yamanaka and   
              Akiko Inagaki and   
                Eiichi Nakamura   Theoretical studies on structures and
                                  reactivities of organocuprate(I) and
                                  organocopper(III) species  . . . . . . . 1401--1409
             A. V. Nemukhin and   
           B. L. Grigorenko and   
                I. A. Topol and   
                     S. K. Burt   Flexible effective fragment QM/MM
                                  method: Validation through the
                                  challenging tests  . . . . . . . . . . . 1410--1420
             Abhijit K. Das and   
            Jun-Ya Hasegawa and   
             Tomoo Miyahara and   
             Masahiro Ehara and   
              Hiroshi Nakatsuji   Electronic excitations of the green
                                  fluorescent protein chromophore in its
                                  protonation states: SAC/SAC--CI study    1421--1431
             Bojan Zagrovic and   
                    Vijay Pande   Solvent viscosity dependence of the
                                  folding rate of a small protein:
                                  Distributed computing study  . . . . . . 1432--1436
                 Mark N. Kobrak   Systematic and statistical error in
                                  histogram-based free energy calculations 1437--1446
         Norman L. Allinger and   
            Kuo-Hsiang Chen and   
              Jenn-Huei Lii and   
             Kathleen A. Durkin   Alcohols, ethers, carbohydrates, and
                                  related compounds. I. The MM4 force
                                  field for simple compounds . . . . . . . 1447--1472
              Jenn-Huei Lii and   
            Kuo-Hsiang Chen and   
         Kathleen A. Durkin and   
             Norman L. Allinger   Alcohols, ethers, carbohydrates, and
                                  related compounds. II. The anomeric
                                  effect . . . . . . . . . . . . . . . . . 1473--1489
              Jenn-Huei Lii and   
            Kuo-Hsiang Chen and   
          T. Bruce Grindley and   
             Norman L. Allinger   Alcohols, ethers, carbohydrates, and
                                  related compounds. III. The
                                  1,2-dimethoxyethane system . . . . . . . 1490--1503
              Jenn-Huei Lii and   
            Kuo-Hsiang Chen and   
             Norman L. Allinger   Alcohols, ethers, carbohydrates, and
                                  related compounds. IV. carbohydrates . . 1504--1513
           H. Bernhard Schlegel   Exploring potential energy surfaces for
                                  chemical reactions: an overview of some
                                  practical methods  . . . . . . . . . . . 1514--1527

Journal of Computational Chemistry
Volume 24, Number 13, October, 2003

                  Stefan Grimme   Improved third-order Mòller--Plesset
                                  perturbation theory  . . . . . . . . . . 1529--1537
          Tadafumi Uchimaru and   
            Asit K. Chandra and   
              Seiji Tsuzuki and   
              Masaaki Sugie and   
                   Akira Sekiya   Ab initio investigation on the reaction
                                  path and rate for the gas-phase reaction
                                  of HO + H$_2$O $\leftrightarrow$ H$_2$O
                                  + OH . . . . . . . . . . . . . . . . . . 1538--1548
                Guosheng Wu and   
        Daniel H. Robertson and   
      Charles L. Brooks III and   
                   Michal Vieth   Detailed analysis of grid-based
                                  molecular docking: a case study of
                                  CDOCKER --- a CHARMm-based MD docking
                                  algorithm  . . . . . . . . . . . . . . . 1549--1562
           Brian W. Hopkins and   
           Gregory S. Tschumper   A multicentered approach to integrated
                                  QM/QM calculations. Applications to
                                  multiply hydrogen bonded systems . . . . 1563--1568
           Niall J. English and   
              J. M. D. Macelroy   Structural and dynamical properties of
                                  methane clathrate hydrates . . . . . . . 1569--1581
            Delano P. Chong and   
         Myrta Grüning and   
             Evert Jan Baerends   STO and GTO field-induced polarization
                                  functions for H to Kr  . . . . . . . . . 1582--1591
              Takao Tsuneda and   
             Muneaki Kamiya and   
                 Kimihiko Hirao   Regional self-interaction correction of
                                  density functional theory  . . . . . . . 1592--1598
           Rajeev Prabhakar and   
             Per E. M. Siegbahn   A comparison of the mechanism for the
                                  reductive half-reaction between pea
                                  seedling and other copper amine oxidases
                                  (CAOs) . . . . . . . . . . . . . . . . . 1599--1609
           Antonio Morreale and   
   Josep Lluis Gelpí and   
            F. Javier Luque and   
                 Modesto Orozco   Continuum and discrete calculation of
                                  fractional contributions to solvation
                                  free energy  . . . . . . . . . . . . . . 1610--1623
                 Dirk Reith and   
          Mathias Pütz and   
     Florian Müller-Plathe   Deriving effective mesoscale potentials
                                  from atomistic simulations . . . . . . . 1624--1636
          Richard D. Taylor and   
         Philip J. Jewsbury and   
              Jonathan W. Essex   FDS: Flexible ligand and receptor
                                  docking with a continuum solvent model
                                  and soft-core energy function  . . . . . 1637--1656
Julio Peiró-García and   
              Ignacio Nebot-Gil   Ab initio study of the mechanism of the
                                  atmospheric reaction: NO$_2$ + O$_3$
                                  $\rightarrow$ NO$_3$ + O$_2$ . . . . . . 1657--1663
            Robert M. Dirks and   
                Niles A. Pierce   A partition function algorithm for
                                  nucleic acid secondary structure
                                  including pseudoknots  . . . . . . . . . 1664--1677
             Mikhail Kozhin and   
                 Ilya Yanov and   
              Jerzy Leszczynski   Network visualization system for
                                  computational chemistry  . . . . . . . . 1678--1687
         Hannes H. Loeffler and   
                  Bernd M. Rode   Erratum: Many-body effects on structure
                                  and dynamics of aqueous ionic solutions  1688--1688

Journal of Computational Chemistry
Volume 24, Number 14, November 15, 2003

                  Wonpil Im and   
             Michael S. Lee and   
          Charles L. Brooks III   Generalized Born model with a simple
                                  smoothing function . . . . . . . . . . . 1691--1702
          M. B. Darkhovskii and   
              I. V. Pletnev and   
       A. L. Tchougréeff   Low- and high-spin iron (II) complexes
                                  studied by effective crystal field
                                  method combined with molecular mechanics 1703--1719
                Yi-Gui Wang and   
               Cherif Matta and   
            Nick Henry Werstiuk   Comparison of localization and
                                  delocalization indices obtained with
                                  Hartree--Fock and conventional
                                  correlated methods: Effect of Coulomb
                                  correlation  . . . . . . . . . . . . . . 1720--1729
          Chris Oostenbrink and   
       Wilfred F. Van Gunsteren   Single-step perturbations to calculate
                                  free energy differences from unphysical
                                  reference states: Limits on size,
                                  flexibility, and character . . . . . . . 1730--1739
                    Frank Neese   An improvement of the resolution of the
                                  identity approximation for the formation
                                  of the Coulomb matrix  . . . . . . . . . 1740--1747
            Alain Laederach and   
                Peter J. Reilly   Specific empirical free energy function
                                  for automated docking of carbohydrates
                                  to proteins  . . . . . . . . . . . . . . 1748--1757
Paulo F. B. Gonçalves and   
                 Hubert Stassen   Free energy of solvation from molecular
                                  dynamics simulations for low dielectric
                                  solvents . . . . . . . . . . . . . . . . 1758--1765
            Scott Habershon and   
       Kenneth D. M. Harris and   
                Roy L. Johnston   Development of a multipopulation
                                  parallel genetic algorithm for structure
                                  solution from powder diffraction data    1766--1774
          Ramkumar Rajamani and   
            Kevin J. Naidoo and   
                      Jiali Gao   Implementation of an adaptive umbrella
                                  sampling method for the calculation of
                                  multidimensional potential of mean force
                                  of chemical reactions in solution  . . . 1775--1781
     Aimée Tomlinson and   
                    David Yaron   Direct INDO/SCI method for excited state
                                  calculations . . . . . . . . . . . . . . 1782--1788
         Bülent Balata and   
              Viktorya Aviyente   Solvent effects on glycine. I. A
                                  supermolecule modeling of
                                  tautomerization via intramolecular
                                  proton transfer  . . . . . . . . . . . . 1789--1802
        Brian D. Wladkowski and   
             Paul Ostazeski and   
            Sarah Chenoweth and   
       Steven J. Broadwater and   
                  Morris Krauss   Hydrolysis of cyclic phosphates by
                                  ribonuclease A: a computational study
                                  using a simplified ab initio quantum
                                  model  . . . . . . . . . . . . . . . . . 1803--1811
                  Feng Yang and   
             Zhen-Dong Wang and   
             Yun-Ping Huang and   
                  Hai-Liang Zhu   Novel topological index F based on
                                  incidence matrix . . . . . . . . . . . . 1812--1820
             Michael S. Lee and   
               Michael Feig and   
    Freddie R. Salsbury Jr. and   
          Charles L. Brooks III   Erratum: New analytic approximation to
                                  the standard molecular volume definition
                                  and its application to generalized Born
                                  calculations . . . . . . . . . . . . . . 1821--1821

Journal of Computational Chemistry
Volume 24, Number 15, November 30, 2003

           Hiroshi Tatewaki and   
             Yoshihiro Watanabe   Gaussian-type function set without
                                  prolapse for the Dirac--Fock--Roothaan
                                  equation . . . . . . . . . . . . . . . . 1823--1828
               Robert Ponec and   
              Gleb Yuzhakov and   
       Ramon Carbó-Dorca   Chemical structures from the analysis of
                                  domain-averaged Fermi holes: Multiple
                                  metal metal bonding in transition metal
                                  compounds  . . . . . . . . . . . . . . . 1829--1838
                    Hua Zhu and   
                Daiqian Xie and   
                     Guosen Yan   Theoretical studies for structures and
                                  energetics of Rg$_n$N$_2$O (Rg = He, Ne,
                                  Ar) clusters . . . . . . . . . . . . . . 1839--1845
                D. W. Zhang and   
                 X. H. Chen and   
                 J. Z. H. Zhang   Molecular caps for full quantum
                                  mechanical computation of peptide--water
                                  interaction energy . . . . . . . . . . . 1846--1852
 Adélia J. A. Aquino and   
              Daniel Tunega and   
           Georg Haberhauer and   
         Martin H. Gerzabek and   
                   Hans Lischka   Adsorption of organic substances on
                                  broken clay surfaces: a quantum chemical
                                  study  . . . . . . . . . . . . . . . . . 1853--1863
        Natalia Díaz and   
        Dimas Suárez and   
          Tomás L. Sordo   Conformational properties of
                                  penicillins: Quantum chemical
                                  calculations and molecular dynamics
                                  simulations of benzylpenicillin  . . . . 1864--1873
                Kazuhiro Ishida   Molecular integrals over the
                                  gauge-including atomic orbitals. II. The
                                  Breit--Pauli interaction . . . . . . . . 1874--1890
     Filip Ryjá\vcek and   
     Tomá\vs Kuba\vr and   
                    Pavel Hobza   New parameterization of the Cornell et
                                  al. empirical force field covering amino
                                  group nonplanarity in nucleic acid bases 1891--1902
              R. Bochicchio and   
                    L. Lain and   
                       A. Torre   Determination of atomic valence indices
                                  from population analyses at correlated
                                  level  . . . . . . . . . . . . . . . . . 1902--1909
             Karine Bastard and   
    Aurélien Thureau and   
             Richard Lavery and   
         Chantal Prévost   Docking macromolecules with flexible
                                  segments . . . . . . . . . . . . . . . . 1910--1920
              Illia Horenko and   
                  Martin Weiser   Adaptive integration of molecular
                                  dynamics . . . . . . . . . . . . . . . . 1921--1929
        Justin L. MacCallum and   
              D. Peter Tieleman   Calculation of the water--cyclohexane
                                  transfer free energies of neutral amino
                                  acid side-chain analogs using the OPLS
                                  all-atom force field . . . . . . . . . . 1930--1935
         Urs Haberthür and   
             Nicolas Majeux and   
             Philipp Werner and   
                Amedeo Caflisch   Efficient evaluation of the effective
                                  dielectric function of a macromolecule
                                  in aqueous solution  . . . . . . . . . . 1936--1949
                 R. Gautier and   
              P. Tufféry   Critical assessment of side-chain
                                  conformational space sampling procedures
                                  designed for quantifying the effect of
                                  side-chain environment . . . . . . . . . 1950--1961

Journal of Computational Chemistry
Volume 24, Number 16, December, 2003

       Jean-Philip Piquemal and   
       Ben Williams-Hubbard and   
                Natalie Fey and   
            Robert J. Deeth and   
                Nohad Gresh and   
        Claude Giessner-Prettre   Inclusion of the ligand field
                                  contribution in a polarizable molecular
                                  mechanics: SIBFA-LF  . . . . . . . . . . 1963--1970
            Pablo A. Molina and   
                     Hui Li and   
                  Jan H. Jensen   Intraprotein electrostatics derived from
                                  first principles: Divide-and-conquer
                                  approaches for QM/MM calculations  . . . 1971--1979
            Thomas E. Exner and   
                  Paul G. Mezey   Ab initio quality properties for
                                  macromolecules using the ADMA approach   1980--1986
              Chia-En Chang and   
              Michael K. Gilson   Tork: Conformational analysis method for
                                  molecules and complexes  . . . . . . . . 1987--1998
                  Yong Duan and   
                    Chun Wu and   
        Shibasish Chowdhury and   
              Mathew C. Lee and   
              Guoming Xiong and   
                  Wei Zhang and   
                  Rong Yang and   
              Piotr Cieplak and   
                    Ray Luo and   
                Taisung Lee and   
             James Caldwell and   
                Junmei Wang and   
                  Peter Kollman   A point-charge force field for molecular
                                  mechanics simulations of proteins based
                                  on condensed-phase quantum mechanical
                                  calculations . . . . . . . . . . . . . . 1999--2012
                   Karl Jug and   
                Gerald Geudtner   Bond energies for molecules, clusters,
                                  and deposit systems  . . . . . . . . . . 2013--2022
                   L. Claes and   
      J.-P. François and   
                  M. S. Deleuze   Theoretical study of the internal
                                  elimination reactions of xanthate
                                  precursors . . . . . . . . . . . . . . . 2023--2031
          Jorng-Tzong Horng and   
             Hsien-Da Huang and   
            Shih-Hsien Wang and   
              Ming-You Chen and   
              Shir-Ly Huang and   
                Jenn-Kang Hwang   Computing motif correlations in proteins 2032--2043
         Pedro Braña and   
           José A. Sordo   Theoretical approach to the mechanism of
                                  reactions between halogen atoms and
                                  unsaturated hydrocarbons: the Cl +
                                  propene reaction . . . . . . . . . . . . 2044--2062
                 Qing Zhang and   
            Daniel A. Beard and   
                  Tamar Schlick   Constructing irregular surfaces to
                                  enclose macromolecular complexes for
                                  mesoscale modeling using the discrete
                                  surface charge optimization (DISCO)
                                  algorithm  . . . . . . . . . . . . . . . 2063--2074
              E. Valderrama and   
                 R. J. Wheatley   An environmental pseudopotential
                                  approach to molecular interactions:
                                  Implementation in MOLPRO . . . . . . . . 2075--2082
           Satoshi Yokojima and   
               Guanhua Chen and   
                  Ruixue Xu and   
                     Yijing Yan   A dynamic mean field theory for
                                  dissipative interacting many-electron
                                  systems: Markovian formalism and its
                                  implementation . . . . . . . . . . . . . 2083--2092
            Alberto Del Rio and   
           Abdou Boucekkine and   
                   Jean Meinnel   Reassessment of methyl rotation barriers
                                  and conformations by correlated quantum
                                  chemistry methods  . . . . . . . . . . . 2093--2100


Journal of Computational Chemistry
Volume 25, Number 1, January 15, 2004

              Sandeep Patel and   
          Charles L. Brooks III   CHARMM fluctuating charge force field
                                  for proteins: I parameterization and
                                  application to bulk organic liquid
                                  simulations  . . . . . . . . . . . . . . 1--16
              Stewart A. Adcock   Peptide backbone reconstruction using
                                  dead-end elimination and a
                                  knowledge-based forcefield . . . . . . . 16--27
                  Nandou Lu and   
             David A. Kofke and   
                Thomas B. Woolf   Improving the efficiency and reliability
                                  of free energy perturbation calculations
                                  using overlap sampling methods . . . . . 28--40
                  Luc Claes and   
Jean-Pierre François and   
             Michael S. Deleuze   Theoretical study of the internal
                                  conversion of sulfoxide precursors of
                                  poly-isothianaphthene and related
                                  polymers . . . . . . . . . . . . . . . . 40--50
            Haruhiko Fukaya and   
                      Taizo Ono   DFT--GIAO calculations of $^{19}$F NMR
                                  chemical shifts for perfluoro compounds  51--60
         Michael J. McQuaid and   
                   Huai Sun and   
                    David Rigby   Development and validation of COMPASS
                                  force field parameters for molecules
                                  with aliphatic azide chains  . . . . . . 61--71
                   Li Sheng and   
                Ze-Sheng Li and   
               Jing-Yao Liu and   
               Jing-Fa Xiao and   
                 Chia-Chung Sun   Ab initio direct dynamics studies on the
                                  reaction of H atom with CH$_3$CH$_2$Cl   72--82
                M. Piacenza and   
                      S. Grimme   Systematic quantum chemical study of
                                  DNA-base tautomers . . . . . . . . . . . 83--99
    Ricard Casadesús and   
              Miquel Moreno and   
\`angels González-Lafont and   
       José M. Lluch and   
             Matthew P. Repasky   Testing electronic structure methods for
                                  describing intermolecular H\dottedbondH
                                  interactions in supramolecular chemistry 99--105
               Takao Motoki and   
                  Akinobu Shiga   New reaction simulator ``LUMMOX'' and
                                  its application for prediction of
                                  catalytic activities . . . . . . . . . . 106--111
                  M. Preuss and   
              W. G. Schmidt and   
                   K. Seino and   
        J. Furthmüller and   
                   F. Bechstedt   Ground- and excited-state properties of
                                  DNA base molecules from plane-wave
                                  calculations using ultrasoft
                                  pseudopotentials . . . . . . . . . . . . 112--122
              Juha Linnanto and   
           Jouko Korppi-Tommola   Semiempirical PM5 molecular orbital
                                  study on chlorophylls and
                                  bacteriochlorophylls: Comparison of
                                  semiempirical, ab initio, and density
                                  functional results . . . . . . . . . . . 123--138
        Ivan Tubert-Brohman and   
Cristiano Ruch Werneck Guimarães and   
         Matthew P. Repasky and   
           William L. Jorgensen   Extension of the PDDG/PM3 and PDDG/MNDO
                                  semiempirical molecular orbital methods
                                  to the halogens  . . . . . . . . . . . . 138--150
         Bülent Balata and   
              Viktorya Aviyente   Erratum: Solvent effects on glycine. I.
                                  A supermolecule modeling of
                                  tautomerization via intramolecular
                                  proton transfer  . . . . . . . . . . . . 151--151
      North American Editorship   Announcement . . . . . . . . . . . . . . i--i

Journal of Computational Chemistry
Volume 25, Number 2, January 30, 2004

      Xavier Gironés and   
       Ramon Carbó-Dorca   TGSA-Flex: Extending the capabilities of
                                  the Topo-Geometrical superposition
                                  algorithm to handle flexible molecules   153--159
                Nohad Gresh and   
                    Gen-Bin Shi   Conformation-dependent intermolecular
                                  interaction energies of the triphosphate
                                  anion with divalent metal cations.
                                  Application to the ATP-binding site of a
                                  binuclear bacterial enzyme. A parallel
                                  quantum chemical and polarizable
                                  molecular mechanics investigation  . . . 160--168
                 Ho-Jin Lee and   
              Jong Hyun Kim and   
              Hee Jung Jung and   
              Kun-Young Kim and   
               Eun-Jung Kim and   
            Young-Sang Choi and   
                  Chang-Ju Yoon   Computational study of conformational
                                  preferences of thioamide-containing
                                  azaglycine peptides  . . . . . . . . . . 169--178
                  A. Nakata and   
                    T. Baba and   
               H. Takahashi and   
                       H. Nakai   Theoretical study on the excited states
                                  of psoralen compounds bonded to a
                                  thymine residue  . . . . . . . . . . . . 179--188
Célia Fonseca Guerra and   
       Jan-Willem Handgraaf and   
         Evert Jan Baerends and   
        F. Matthias Bickelhaupt   Voronoi deformation density (VDD)
                                  charges: Assessment of the Mulliken,
                                  Bader, Hirshfeld, Weinhold, and VDD
                                  methods for charge analysis  . . . . . . 189--210
            Thomas S. Hofer and   
               Hung T. Tran and   
       Christian F. Schwenk and   
                  Bernd M. Rode   Characterization of dynamics and
                                  reactivities of solvated ions by ab
                                  initio simulations . . . . . . . . . . . 211--217
                  Yue Zhang and   
              Shaowen Zhang and   
                    Qian Shu Li   A dual-level ab initio and hybrid
                                  density functional theory dynamics study
                                  on the unimolecular decomposition
                                  reaction C$_2$H$_5$O $\rightarrow$
                                  CH$_2$O + CH$_3$ . . . . . . . . . . . . 218--226
             Susana Pereira and   
Pedro Alexandrino Fernandes and   
        Maria João Ramos   Theoretical study of ribonucleotide
                                  reductase mechanism-based inhibition by
                                  2'-azido-2'-deoxyribonucleoside
                                  5'-diphosphates  . . . . . . . . . . . . 227--237
              Holger Gohlke and   
                  David A. Case   Converging free energy estimates:
                                  MM-PB(GB)SA studies on the
                                  protein--protein complex Ras--Raf  . . . 238--250
                Qian-Shu Li and   
                 Chao Yang Wang   Direct dynamic study on the hydrogen
                                  abstraction reaction CH$_3$CN + OH
                                  $\rightarrow$ CH$_2$CN + H$_2$O  . . . . 251--257
              Zheng-Wang Qu and   
                    Hui Zhu and   
                Ze-Sheng Li and   
            Xing-Kang Zhang and   
                  Qi-Yuan Zhang   Density functional investigation of
                                  reaction of borohydride cation BH with
                                  propylene  . . . . . . . . . . . . . . . 258--264
               Michael Feig and   
            Alexey Onufriev and   
             Michael S. Lee and   
                  Wonpil Im and   
              David A. Case and   
          Charles L. Brooks III   Performance comparison of generalized
                                  Born and Poisson methods in the
                                  calculation of electrostatic solvation
                                  energies for protein structures  . . . . 265--284
          Tamás Beke and   
          Imre G. Csizmadia and   
          András Perczel   On the flexibility of $\beta$-peptides   285--307
       Jean-Philip Piquemal and   
       Ben Williams-Hubbard and   
                Natalie Fey and   
            Robert J. Deeth and   
                Nohad Gresh and   
        Claude Giessner-Prettre   Erratum: Inclusion of the ligand field
                                  contribution in a polarizable molecular
                                  mechanics: SIBFA-LF  . . . . . . . . . . 308--308
                Yi-Gui Wang and   
            Cherif F. Matta and   
            Nick Henry Werstiuk   Erratum: Comparison of localization and
                                  delocalization indices obtained with
                                  Hartree--Fock and conventional
                                  correlated methods: Effect of Coulomb
                                  correlation  . . . . . . . . . . . . . . 309--309

Journal of Computational Chemistry
Volume 25, Number 3, February, 2004

                  A. Nakata and   
                    T. Baba and   
               H. Takahashi and   
                       H. Nakai   Erratum: Theoretical study on the
                                  excited states of psoralen compounds
                                  bonded to a thymine residue  . . . . . . 309--309
     Vladimir Pelmenschikov and   
              Kyung-Bin Cho and   
             Per E. M. Siegbahn   Class I ribonucleotide reductase
                                  revisited: the effect of removing a
                                  proton on Glu441 . . . . . . . . . . . . 311--321
         Jennifer I. Chavez and   
          Maira M. Carrillo and   
                  Kyle A. Beran   Isomers of C$_{20}$: an energy profile
                                  III  . . . . . . . . . . . . . . . . . . 322--327
             Robert J. Harrison   Krylov subspace accelerated inexact
                                  Newton method for linear and nonlinear
                                  equations  . . . . . . . . . . . . . . . 328--334
           Ji\vrí Kolafa   Time-reversible always stable
                                  predictor--corrector method for
                                  molecular dynamics of polarizable
                                  molecules  . . . . . . . . . . . . . . . 335--342
                Vinzenz Bachler   A simple computational scheme for
                                  obtaining localized bonding schemes and
                                  their weights from a CASSCF wave
                                  function . . . . . . . . . . . . . . . . 343--367
             A. N. Artemyev and   
        E. V. Ludeña and   
             V. V. Karasiev and   
         A. J. Hernández   A finite B-spline basis set for accurate
                                  diatomic molecule calculations . . . . . 368--374
              Luca Frediani and   
              Roberto Cammi and   
       Christian S. Pomelli and   
              Jacopo Tomasi and   
                   Kenneth Ruud   New developments in the symmetry-adapted
                                  algorithm of the Polarizable Continuum
                                  Model  . . . . . . . . . . . . . . . . . 375--385
               Ivan Infante and   
                 Lucas Visscher   QM/MM study of aqueous solvation of the
                                  uranyl fluoride [UO$_2$F] complex  . . . 386--392
             Serena Donnini and   
         André H. Juffer   Calculation of affinities of peptides
                                  for proteins . . . . . . . . . . . . . . 393--411
             Marco Cecchini and   
                 Peter Kolb and   
             Nicolas Majeux and   
                Amedeo Caflisch   Automated docking of highly flexible
                                  ligands by genetic algorithms: a
                                  critical assessment  . . . . . . . . . . 412--422
                   Li Sheng and   
                Ze-Sheng Li and   
               Jing-Yao Liu and   
               Jing-Fa Xiao and   
                 Chia-Chung Sun   Theoretical study on the rate constants
                                  for the C$_2$H$_5$ + HBr $\rightarrow$
                                  C$_2$H$_6$ + Br reaction . . . . . . . . 423--428
        Rachel Crespo-Otero and   
            Luis A. Montero and   
           Giselle Rosquete and   
J. Alexander Padrón-García and   
Raúl H. González-Jonte   Theoretical model of internal rotation
                                  in monosubstituted derivatives of
                                  furfural . . . . . . . . . . . . . . . . 429--438
             Xavier Fradera and   
                  Miquel Sol\`a   Second-order atomic Fukui indices from
                                  the electron-pair density in the
                                  framework of the atoms in molecules
                                  theory . . . . . . . . . . . . . . . . . 439--446
               Shingo Urata and   
              Seiji Tsuzuki and   
               Akira Takada and   
            Masuhiro Mikami and   
          Tadafumi Uchimaru and   
                   Akira Sekiya   Analysis of the intermolecular
                                  interactions between CH$_3$OCH$_3$,
                                  CF$_3$OCH$_3$, CF$_3$OCF$_3$, and
                                  CH$_2$F$_2$, CHF$_3$ . . . . . . . . . . 447--459

Journal of Computational Chemistry
Volume 25, Number 4, March, 2004

                     Yi Ren and   
                    San-Yan Chu   Modified Gaussian-2 level investigation
                                  of the identity ion-pair S$_N$2
                                  reactions of lithium halide and methyl
                                  halide with inversion and retention
                                  mechanisms . . . . . . . . . . . . . . . 461--471
              Lingchun Song and   
                     Wei Wu and   
               Qianer Zhang and   
                    Sason Shaik   A practical valence bond method: a
                                  configuration interaction method
                                  approach with perturbation theoretic
                                  facility . . . . . . . . . . . . . . . . 472--478
          Emilio Gallicchio and   
                 Ronald M. Levy   AGBNP: an analytic implicit solvent
                                  model suitable for molecular dynamics
                                  simulations and high-resolution modeling 479--499
              Xiang-Yuan Li and   
                    Ke-Xiang Fu   Continuous medium theory for
                                  nonequilibrium solvation: I. How to
                                  correctly evaluate solvation free energy
                                  of nonequilibrium  . . . . . . . . . . . 500--509
      Evangelos A. Coutsias and   
                 Chaok Seok and   
        Matthew P. Jacobson and   
                    Ken A. Dill   A kinematic view of loop closure . . . . 510--528
             Mitsunori Ikeguchi   Partial rigid-body dynamics in NPT, NPAT
                                  and NP$\gamma$T ensembles for proteins
                                  and membranes  . . . . . . . . . . . . . 529--541
         Michael J. Liddell and   
             Davor Margetic and   
        Anthony S. Mitchell and   
             Ronald N. Warrener   An AM1 semiempirical study of
                                  host--guest complexation in
                                  hemicarcerand complexes  . . . . . . . . 542--557
                    Li Wang and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   Direct ab initio dynamics studies on the
                                  hydrogen-abstraction reactions of OH
                                  radicals with HOX (X = F, Cl, and Br)    558--564
              S. Banu Ozkan and   
               Hagai Meirovitch   Conformational search of peptides and
                                  proteins: Monte Carlo minimization with
                                  an adaptive bias method applied to the
                                  heptapeptide deltorphin  . . . . . . . . 565--572
          Francisco Corzana and   
        Mohammed S. Motawia and   
Catherine Hervé Du Penhoat and   
                Serge Perez and   
         Sarah M. Tschampel and   
            Robert J. Woods and   
       Sòren B. Engelsen   A hydration study of (1$\rightarrow$4)
                                  and (1$\rightarrow$6) linked
                                  $\alpha$-glucans by comparative 10 ns
                                  molecular dynamics simulations and
                                  500-MHz NMR  . . . . . . . . . . . . . . 573--586
        Johannes Neugebauer and   
                  Markus Reiher   Vibrational center--ligand couplings in
                                  transition metal complexes . . . . . . . 587--597
            Shinichi Yamabe and   
                Noriko Tsuchida   A computational study of the role of
                                  hydrogen bonds in S$_N$1 and E1
                                  reactions  . . . . . . . . . . . . . . . 598--608
                   Maxim Totrov   Accurate and efficient generalized Born
                                  model based on solvent accessibility:
                                  Derivation and application for Log P
                                  octanol/water prediction and flexible
                                  peptide docking  . . . . . . . . . . . . 609--619

Journal of Computational Chemistry
Volume 25, Number 5, April 15, 2004

                Martin Saunders   Stochastic search for isomers on a
                                  quantum mechanical surface . . . . . . . 621--626
          Richard I. Maurer and   
        Christopher A. Reynolds   A multilayered approach to approximating
                                  solute polarization  . . . . . . . . . . 627--631
                 Zheng Yuan and   
            John S. Mattick and   
              Rohan D. Teasdale   SVM\TM: Support vector machines to
                                  predict transmembrane segments . . . . . 632--636
                    John Cullen   Performance of the Harris functional for
                                  extended basis sets at the Hartree--Fock
                                  and density functional levels  . . . . . 637--648
       Siân T. Howard and   
             Colin D. Abernethy   Intramolecular C H\ldotsC$_{carbene}$
                                  hydrogen bonds and competing
                                  interactions in monoprotonated tripodal
                                  carbenes . . . . . . . . . . . . . . . . 649--659
        Ali Khalaf Al-Matar and   
             David A. Rockstraw   A generating equation for mixing rules
                                  and two new mixing rules for interatomic
                                  potential energy parameters  . . . . . . 660--668
                   Fan Wang and   
                       Lemin Li   Numerical examination of performance of
                                  some exchange-correlation functionals
                                  for molecules containing heavy elements  669--677
              Michael Patra and   
                Mikko Karttunen   Systematic comparison of force fields
                                  for microscopic simulations of NaCl in
                                  aqueous solutions: Diffusion, free
                                  energy of hydration, and structural
                                  properties . . . . . . . . . . . . . . . 678--689
          Bülent Balta and   
              Viktorya Aviyente   Solvent effects on glycine II.
                                  Water-assisted tautomerization . . . . . 690--703
                P. Zarzycki and   
                 R. Charmas and   
                   P. Szabelski   Study of proton adsorption at
                                  heterogeneous oxide/electrolyte
                                  interface. Prediction of the surface
                                  potential using Monte Carlo simulations
                                  and 1-pK approach  . . . . . . . . . . . 704--711
                  Eran Eyal and   
         Rafael Najmanovich and   
        Brendan J. Mcconkey and   
             Marvin Edelman and   
               Vladimir Sobolev   Importance of solvent accessibility and
                                  contact surfaces in modeling side-chain
                                  conformations in proteins  . . . . . . . 712--724
                Paul Winget and   
                  Timothy Clark   Enthalpies of formation from B3LYP
                                  calculations . . . . . . . . . . . . . . 725--733
              D. B. Chesnut and   
                     L. D. Quin   Nature of bonding in the sulfuryl group  734--738
                Kazuhiro Ishida   Accurate and fast algorithm of the
                                  molecular incomplete gamma function with
                                  a complex argument . . . . . . . . . . . 739--748
                 Harry A. Stern   Simple algorithm for
                                  isothermal--isobaric molecular dynamics  749--761
         M. Michael Gromiha and   
              Shandar Ahmad and   
                    Makiko Suwa   Neural network-based prediction of
                                  transmembrane $\beta$-strand segments in
                                  outer membrane proteins  . . . . . . . . 762--767
               M. K. Shukla and   
              Jerzy Leszczynski   TDDFT investigation on nucleic acid
                                  bases: Comparison with experiments and
                                  standard approach  . . . . . . . . . . . 768--778

Journal of Computational Chemistry
Volume 25, Number 6, April 30, 2004

              Matthias Keil and   
            Thomas E. Exner and   
          Jürgen Brickmann   Pattern recognition strategies for
                                  molecular surfaces: III. Binding site
                                  prediction with a neural network . . . . 779--789
         David Curcó and   
           Carlos Alemán   Performance of SuSi: a method for
                                  generating atomistic models of amorphous
                                  polymers based on a random search of
                                  energy minima  . . . . . . . . . . . . . 790--798
                  Rochus Schmid   Car--Parrinello simulations with a real
                                  space method . . . . . . . . . . . . . . 799--812
                   Jun Zeng and   
                    Daiqian Xie   Hydrogen bonding and solvent effects on
                                  the lowest $^1$(n, $\pi^*$) excitations
                                  of triazines in water  . . . . . . . . . 813--822
                Nohad Gresh and   
           Sherif A. Kafafi and   
Jean-François Truchon and   
              Dennis R. Salahub   Intramolecular interaction energies in
                                  model alanine and glycine tetrapeptides.
                                  Evaluation of anisotropy, polarization,
                                  and correlation effects. A parallel ab
                                  initio HF/MP2, DFT, and polarizable
                                  molecular mechanics study  . . . . . . . 823--834
              Xiang-Yuan Li and   
                Ke-Xiang Fu and   
                   Quan Zhu and   
                   Min-Hua Shan   Continuous medium theory for
                                  nonequilibrium solvation: II.
                                  Interaction energy between solute charge
                                  and reaction field and single-sphere
                                  model for spectral shift . . . . . . . . 835--842
                 Jinn-Moon Yang   Development and evaluation of a generic
                                  evolutionary method for protein--ligand
                                  docking  . . . . . . . . . . . . . . . . 843--857
         Ricardo L. Mancera and   
          Per Källblad and   
             Nikolay P. Todorov   Ligand--protein docking using a quantum
                                  stochastic tunneling optimization method 858--864
                 Yang Zhang and   
               Jeffrey Skolnick   SPICKER: a clustering approach to
                                  identify near-native protein folds . . . 865--871
          Dmitri G. Fedorov and   
              Ryan M. Olson and   
              Kazuo Kitaura and   
             Mark S. Gordon and   
                   Shiro Koseki   A new hierarchical parallelization
                                  scheme: Generalized distributed data
                                  interface (GDDI), and an application to
                                  the fragment molecular orbital method
                                  (FMO)  . . . . . . . . . . . . . . . . . 872--880
                  Feng Yang and   
             Zhen-Dong Wang and   
                 Yun-Ping Huang   Modification of the Wiener index 4 . . . 881--887
                 F. Pascale and   
      C. M. Zicovich-Wilson and   
       F. López Gejo and   
               B. Civalleri and   
                 R. Orlando and   
                      R. Dovesi   The calculation of the vibrational
                                  frequencies of crystalline compounds and
                                  its implementation in the CRYSTAL code   888--897

Journal of Computational Chemistry
Volume 25, Number 7, May, 2004

               Harold Basch and   
                 Mark A. Ratner   Reduced basis set for the gold atom in
                                  cluster complexes  . . . . . . . . . . . 899--906
                    Yi Zhao and   
                  Wenguo Xu and   
                 Qianshu Li and   
                Yaoming Xie and   
          Henry F. Schaefer III   The arsenic clusters As$_n$ ($n =
                                  1$--$5$) and their anions: Structures,
                                  thermochemistry, and electron affinities 907--920
            Anatoliy Volkov and   
                 Philip Coppens   Calculation of electrostatic interaction
                                  energies in molecular dimers from atomic
                                  multipole moments obtained by different
                                  methods of electron density partitioning 921--934
    Alexander H. Boschitsch and   
               Marcia O. Fenley   Hybrid boundary element and finite
                                  difference method for solving the
                                  nonlinear Poisson--Boltzmann equation    935--955
           J. Cortés and   
           T. Siméon and   
    M. Remaud-Siméon and   
                        V. Tran   Geometric algorithms for the
                                  conformational analysis of long protein
                                  loops  . . . . . . . . . . . . . . . . . 956--967
               Xiaoping Han and   
                  Yue Zhang and   
                      Huibin Xu   First-principles pair potentials across
                                  the metal--ceramic interface . . . . . . 968--973
         Massimiliano Aschi and   
           Costantino Zazza and   
            Riccardo Spezia and   
              Cecilia Bossa and   
            Alfredo Di Nola and   
              Maurizio Paci and   
                  Andrea Amadei   Conformational fluctuations and
                                  electronic properties in myoglobin . . . 974--984
                 Arnaud Blondel   Ensemble variance in free energy
                                  calculations by thermodynamic
                                  integration: Theory, optimal
                                  ``Alchemical'' path, and practical
                                  solutions  . . . . . . . . . . . . . . . 985--993
              Mihai V. Putz and   
                 Nino Russo and   
                 Emilia Sicilia   On the applicability of the HSAB
                                  principle through the use of improved
                                  computational schemes for chemical
                                  hardness evaluation  . . . . . . . . . . 994--1003

Journal of Computational Chemistry
Volume 25, Number 8, June, 2004

              Olgun Guvench and   
          Charles L. Brooks III   Efficient approximate all-atom solvent
                                  accessible surface area method
                                  parameterized for folded and denatured
                                  protein conformations  . . . . . . . . . 1005--1014
         Nathalie Basdevant and   
              Daniel Borgis and   
                   Tap Ha-Duong   A semi-implicit solvent model for the
                                  simulation of peptides and proteins  . . 1015--1029
            Delano P. Chong and   
            Erik Van Lenthe and   
         Stan Van Gisbergen and   
             Evert Jan Baerends   Even-tempered Slater-type orbitals
                                  revisited: From hydrogen to krypton  . . 1030--1036
                Henk Bekker and   
        Jur P. Van Den Berg and   
            Tsjerk A. Wassenaar   A method to obtain a near-minimal-volume
                                  molecular simulation of a macromolecule,
                                  using periodic boundary conditions and
                                  rotational constraints . . . . . . . . . 1037--1046
                 Anil Kumar and   
   Michaela Knapp-Mohammady and   
               P. C. Mishra and   
            Sándor Suhai   A theoretical study of structures and
                                  electron affinities of radical anions of
                                  guanine-cytosine, adenine-thymine, and
                                  hypoxanthine-cytosine base pairs . . . . 1047--1059
          Arturo Robertazzi and   
                James A. Platts   Hydrogen bonding, solvation, and
                                  hydrolysis of cisplatin: a theoretical
                                  study  . . . . . . . . . . . . . . . . . 1060--1067
      Abdallah Sayyed-Ahmad and   
               Kagan Tuncay and   
              Peter J. Ortoleva   Efficient solution technique for solving
                                  the Poisson--Boltzmann equation  . . . . 1068--1074
            Les\law K. Bieniasz   Improving the accuracy of the spatial
                                  discretization in finite-difference
                                  electrochemical kinetic simulations, by
                                  means of the extended Numerov method . . 1075--1083
      András Perczel and   
 Péter Hudáky and   
 Anna K. Füzéry and   
              Imre G. Csizmadia   Stability issues of covalently and
                                  noncovalently bonded peptide subunits    1084--1100
          Zlatko Vasilkoski and   
                David L. Weaver   Diffusion--collision model algorithms
                                  for protein folding kinetics . . . . . . 1101--1107

Journal of Computational Chemistry
Volume 25, Number 9, July 15, 2004

          J. Ulises Reveles and   
         Andreas M. Köster   Geometry optimization in density
                                  functional methods . . . . . . . . . . . 1109--1116
                   A. Becue and   
                 N. Meurice and   
                 L. Leherte and   
              D. P. Vercauteren   Evaluation of the protein
                                  solvent-accessible surface using reduced
                                  representations in terms of critical
                                  points of the electron density . . . . . 1117--1126
          Kenneth B. Wiberg and   
                    Yi-Gui Wang   Conformational energies for
                                  2-substituted butanes  . . . . . . . . . 1127--1132
                   Ming Lei and   
         Maria I. Zavodszky and   
             Leslie A. Kuhn and   
                   M. F. Thorpe   Sampling protein conformations and
                                  pathways . . . . . . . . . . . . . . . . 1133--1148
                 Genyuan Li and   
      Jacqueline Schoendorf and   
                 Tak-San Ho and   
                Herschel Rabitz   Multicut-HDMR with an application to an
                                  ionospheric model  . . . . . . . . . . . 1149--1156
                Junmei Wang and   
             Romain M. Wolf and   
          James W. Caldwell and   
           Peter A. Kollman and   
                  David A. Case   Development and testing of a general
                                  AMBER force field  . . . . . . . . . . . 1157--1174
              Hiroaki Umeda and   
               Shiro Koseki and   
                Umpei Nagashima   Improvement of parallelization
                                  performance of GAMESS: Global sum and
                                  (semi-)direct integral calculation in
                                  multireference perturbation calculation  1175--1183
               Jia-Xu Zhang and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   Theoretical study on the mechanism of
                                  the $^1$CHCl + NO$_2$ reactions  . . . . 1184--1190
                  Sergio Aragon   A precise boundary element method for
                                  macromolecular transport properties  . . 1191--1205
     Christopher C. Lovallo and   
            Mariusz Klobukowski   Improved model core potentials for the
                                  second- and third-row transition metals  1206--1213
                      Anonymous   Publisher's note: Sir John A. Pople,
                                  1925--2004 . . . . . . . . . . . . . . . fmv--viii

Journal of Computational Chemistry
Volume 25, Number 10, July 30, 2004

          Delia Soto-Castro and   
            Patricia Guadarrama   Macrocyclic vs. dendrimeric effect. A
                                  DFT study  . . . . . . . . . . . . . . . 1215--1226
     I. Fdez. Galván and   
        M. E. Martín and   
                  M. A. Aguilar   A new method to locate saddle points for
                                  reactions in solution by using the
                                  free-energy gradient method and the mean
                                  field approximation  . . . . . . . . . . 1227--1233
            D. Muñoz and   
                C. De Graaf and   
                       F. Illas   Putting error bars on the Ab Initio
                                  theoretical estimates of the magnetic
                                  coupling constants: the parent compounds
                                  of superconducting cuprates as a case
                                  study  . . . . . . . . . . . . . . . . . 1234--1241
         Martin Almlöf and   
  BjÒrn O. Brandsdal and   
             Johan Åqvist   Binding affinity prediction with
                                  different force fields: Examination of
                                  the linear interaction energy method . . 1242--1254
            Nisanth N. Nair and   
              Thomas Bredow and   
                       Karl Jug   Molecular dynamics implementation in
                                  MSINDO: Study of silicon clusters  . . . 1255--1263
                   K. Fiaty and   
              C. Charcosset and   
                  B. Perrin and   
               R. Couturier and   
              B. Ma\"\isterrena   ATP-dependent active transport
                                  simulations based on a
                                  phosphatase--channel--kinase membrane
                                  structure  . . . . . . . . . . . . . . . 1264--1276
                 Wolfgang Quapp   Reaction pathways and projection
                                  operators: Application to string methods 1277--1285
             Susana Pereira and   
Pedro Alexandrino Fernandes and   
        Maria João Ramos   Mechanism for ribonucleotide reductase
                                  inactivation by the anticancer drug
                                  gemcitabine  . . . . . . . . . . . . . . 1286--1294
            Robert M. Dirks and   
                Niles A. Pierce   An algorithm for computing nucleic acid
                                  base-pairing probabilities including
                                  pseudoknots  . . . . . . . . . . . . . . 1295--1304
              Gordon M. Crippen   Cluster distance geometry of polypeptide
                                  chains . . . . . . . . . . . . . . . . . 1305--1312

Journal of Computational Chemistry
Volume 25, Number 11, August, 2004

           Yuri A. Kosinsky and   
          Pavel E. Volynsky and   
            Philippe Lagant and   
            Gerard Vergoten and   
           Ei-Ichiro Suzuki and   
      Alexander S. Arseniev and   
               Roman G. Efremov   Development of the force field
                                  parameters for phosphoimidazole and
                                  phosphohistidine . . . . . . . . . . . . 1313--1321
    Marina Udier-Blagovi\'c and   
 Patricia Morales De Tirado and   
     Shoshannah A. Pearlman and   
           William L. Jorgensen   Accuracy of free energies of hydration
                                  using CM1 and CM3 atomic charges . . . . 1322--1332
            Roberto Improta and   
                Vincenzo Barone   Assessing the reliability of density
                                  functional methods in the conformational
                                  study of polypeptides: the treatment of
                                  intraresidue nonbonding interactions . . 1333--1341
              Kenneth B. Wiberg   Basis set effects on calculated
                                  geometries: 6-311++G** vs. aug-cc-pVDZ   1342--1346
   J. Fernández Rico and   
            R. López and   
                     I. Ema and   
              G. Ramírez   Electrostatic potentials and fields from
                                  density expansions of deformed atoms in
                                  molecules  . . . . . . . . . . . . . . . 1347--1354
   J. Fernández Rico and   
            R. López and   
          G. Ramírez and   
                     I. Ema and   
            E. V. Ludeña   Analytical method for the representation
                                  of atoms-in-molecules densities  . . . . 1355--1363
                    Bo Liao and   
                 Tian-Ming Wang   New $2$D graphical representation of DNA
                                  sequences  . . . . . . . . . . . . . . . 1364--1368
           Gennady N. Chuev and   
               Maxim V. Fedorov   Wavelet algorithm for solving integral
                                  equations of molecular liquids. A test
                                  for the reference interaction site model 1369--1377
          Aisha El-Sherbiny and   
             Raymond A. Poirier   An evaluation of the radial part of
                                  numerical integration commonly used in
                                  DFT  . . . . . . . . . . . . . . . . . . 1378--1384
                Dawoon Jung and   
                  Jie Floyd and   
                 Tamara M. Gund   A comparative molecular field analysis
                                  (CoMFA) study using semiempirical,
                                  density functional, ab initio methods
                                  and pharmacophore derivation using
                                  DISCOtech on sigma 1 ligands . . . . . . 1385--1399
 Alexander D. Mackerell Jr. and   
               Michael Feig and   
          Charles L. Brooks III   Extending the treatment of backbone
                                  energetics in protein force fields:
                                  Limitations of gas-phase quantum
                                  mechanics in reproducing protein
                                  conformational distributions in
                                  molecular dynamics simulations . . . . . 1400--1415
              Peter A. Sims and   
              Chung F. Wong and   
             J. Andrew McCammon   Charge optimization of the interface
                                  between protein kinases and their
                                  ligands  . . . . . . . . . . . . . . . . 1416--1429

Journal of Computational Chemistry
Volume 25, Number 12, September, 2004

                  Yun Xiang and   
                Da W. Zhang and   
               John Z. H. Zhang   Fully quantum mechanical energy
                                  optimization for protein--ligand
                                  structure  . . . . . . . . . . . . . . . 1431--1437
Jörg-Rüdiger Hill and   
                   Johann Plank   Retardation of setting of plaster of
                                  Paris by organic acids: Understanding
                                  the mechanism through molecular modeling 1438--1448
                     Hui Li and   
                  Jan H. Jensen   Improving the efficiency and convergence
                                  of geometry optimization with the
                                  polarizable continuum model: New energy
                                  gradients and molecular surface
                                  tessellation . . . . . . . . . . . . . . 1449--1462
                  Stefan Grimme   Accurate description of van der Waals
                                  complexes by density functional theory
                                  including empirical corrections  . . . . 1463--1473
               Tim N. Heinz and   
   Philippe H. Hünenberger   A fast pairlist-construction algorithm
                                  for molecular simulations under periodic
                                  boundary conditions  . . . . . . . . . . 1474--1486
                Daiqian Xie and   
                       Jun Zeng   Hydrogen bonding and solvatochromatic
                                  shift of the lowest$^1$ (n, $\pi^*$)
                                  excitation of s-tetrazine in its
                                  hydrated clusters and dilute solutions   1487--1495
       Bahram Hemmateenejad and   
      Mohammad A. Safarpour and   
                 Ramin Miri and   
                 Fariba Taghavi   Application of ab initio theory to QSAR
                                  study of 1,4-dihydropyridine-based
                                  calcium channel blockers using GA-MLR
                                  and PC-GA-ANN procedures . . . . . . . . 1495--1503
              Sandeep Patel and   
 Alexander D. Mackerell Jr. and   
          Charles L. Brooks III   CHARMM fluctuating charge force field
                                  for proteins: II. Protein/solvent
                                  properties from molecular dynamics
                                  simulations using a nonadditive
                                  electrostatic model  . . . . . . . . . . 1504--1514
            Les\law K. Bieniasz   A fourth-order accurate, Numerov-type,
                                  three-point finite-difference
                                  discretization of electrochemical
                                  reaction-diffusion equations on
                                  nonuniform (exponentially expanding)
                                  spatial grids in one-dimensional space
                                  geometry . . . . . . . . . . . . . . . . 1515--1521
        Ilona Hudáky and   
 Péter Hudáky and   
          András Perczel   Solvation model induced structural
                                  changes in peptides. A quantum chemical
                                  study on Ramachandran surfaces and
                                  conformers of alanine diamide using the
                                  polarizable continuum model  . . . . . . 1522--1531
       Christian Silvio Pomelli   A tessellationless integration grid for
                                  the polarizable continuum model reaction
                                  field  . . . . . . . . . . . . . . . . . 1532--1541
        Xavier López and   
  Jorge A. Fernández and   
               Susanna Romo and   
  Jean François Paul and   
            Leonid Kazansky and   
                Josep M. Poblet   Are the solvent effects critical in the
                                  modeling of polyoxoanions? . . . . . . . 1542--1549

Journal of Computational Chemistry
Volume 25, Number 13, October, 2004

                   Karl Jug and   
                  Thomas Bredow   Models for the treatment of crystalline
                                  solids and surfaces  . . . . . . . . . . 1551--1567
                 H. Merlitz and   
                  T. Herges and   
                      W. Wenzel   Fluctuation analysis and accuracy of a
                                  large-scale in silico screen . . . . . . 1568--1575
 Chinapong Kritayakornupong and   
     Kristof Plankensteiner and   
                  Bernd M. Rode   Structure and dynamics of the Cr(III)
                                  ion in aqueous solution: ab initio QM/MM
                                  molecular dynamics simulation  . . . . . 1576--1583
     Alexander D. Mackerell Jr.   Empirical force fields for biological
                                  macromolecules: Overview and issues  . . 1584--1604
          Eric F. Pettersen and   
          Thomas D. Goddard and   
            Conrad C. Huang and   
           Gregory S. Couch and   
       Daniel M. Greenblatt and   
             Elaine C. Meng and   
               Thomas E. Ferrin   UCSF Chimera --- a visualization system
                                  for exploratory research and analysis    1605--1612
           Felix Autenrieth and   
           Emad Tajkhorshid and   
              Jerome Baudry and   
          Zaida Luthey-Schulten   Classical force field parameters for the
                                  heme prosthetic group of cytochrome c    1613--1622
              Jason Wagoner and   
                Nathan A. Baker   Solvation forces on biomolecular
                                  structures: a comparison of explicit
                                  solvent and Poisson--Boltzmann models    1623--1629
        Richard E. Gillilan and   
                 Ryan H. Lilien   Optimization and dynamics of
                                  protein--protein complexes using
                                  B-splines  . . . . . . . . . . . . . . . 1630--1646
 Maria Del Carmen Michelini and   
                 Nino Russo and   
Mohammad Esma\"\il Alikhani and   
                  Bernard Silvi   Energetic and topological analysis of
                                  the reaction of Mo and Mo$_2$ with
                                  NH$_3$, C$_2$H$_2$, and C$_2$H$_4$
                                  molecules  . . . . . . . . . . . . . . . 1647--1655
          Chris Oostenbrink and   
           Alessandra Villa and   
               Alan E. Mark and   
       Wilfred F. Van Gunsteren   A biomolecular force field based on the
                                  free enthalpy of hydration and
                                  solvation: the GROMOS force-field
                                  parameter sets 53A5 and 53A6 . . . . . . 1656--1676

Journal of Computational Chemistry
Volume 25, Number 14, November 15, 2004

         Edward N. Brothers and   
               Dimas Suarez and   
      David W. Deerfield II and   
            Kenneth M. Merz Jr.   PM3-compatible zinc parameters optimized
                                  for metalloenzyme active sites . . . . . 1677--1692
              Xueguang Shao and   
              Longjiu Cheng and   
                   Wensheng Cai   A dynamic lattice searching method for
                                  fast optimization of Lennard-Jones
                                  clusters . . . . . . . . . . . . . . . . 1693--1698
             Zhi-Xiang Wang and   
                      Yong Duan   Solvation effects on alanine dipeptide:
                                  a MP2/cc-pVTZ//MP2/6-31G** study of
                                  $(\Phi, \Psi)$ energy maps and
                                  conformers in the gas phase, ether, and
                                  water  . . . . . . . . . . . . . . . . . 1699--1716
            Joseph P. Kenny and   
           Steven J. Benson and   
               Yuri Alexeev and   
               Jason Sarich and   
          Curtis L. Janssen and   
       Lois Curfman Mcinnes and   
        Manojkumar Krishnan and   
            Jarek Nieplocha and   
           Elizabeth Jurrus and   
             Carl Fahlstrom and   
              Theresa L. Windus   Component-based integration of chemistry
                                  and optimization software  . . . . . . . 1717--1725
                    Qi Shen and   
             Jian-Hui Jiang and   
               Chen-Xu Jiao and   
                 Wei-Qi Lin and   
                Guo-Li Shen and   
                      Ru-Qin Yu   Hybridized particle swarm algorithm for
                                  adaptive structure training of
                                  multilayer feed-forward neural network:
                                  QSAR studies of bioactivity of organic
                                  compounds  . . . . . . . . . . . . . . . 1726--1735
Cristina P. Gonçalves and   
        José R. Mohallem   A new algorithm to handle finite nuclear
                                  mass effects in electronic calculations:
                                  the ISOTOPE program  . . . . . . . . . . 1736--1739
                Oh-Seuk Lee and   
                Kiyull Yang and   
             Keum Duck Kang and   
                 In Sun Koo and   
             Chan-Kyung Kim and   
                    Ikchoon Lee   Ab initio and DFT studies on hydrolyses
                                  of phosphorus halides  . . . . . . . . . 1740--1748
          F. Marty Ytreberg and   
            Daniel M. Zuckerman   Efficient use of nonequilibrium
                                  measurement to estimate free energy
                                  differences for molecular systems  . . . 1749--1759
              Julien Michel and   
          Richard D. Taylor and   
              Jonathan W. Essex   The parameterization and validation of
                                  generalized Born models using the
                                  pairwise descreening approximation . . . 1760--1770
                 Masao Masamura   The effect of basis set superposition
                                  error on the convergence of
                                  intermolecular interaction energies for
                                  deprotonated complexes . . . . . . . . . 1771--1778
           Pawe\l Szabelski and   
                  Julian Talbot   Kinetics and equilibrium of
                                  multicomponent adsorption on chiraly
                                  templated surfaces . . . . . . . . . . . 1779--1786
            Ernesto Estrada and   
         Eduardo J. Delgado and   
           Joel B. Alderete and   
         Gonzalo A. Jaña   Quantum-connectivity descriptors in
                                  modeling solubility of environmentally
                                  important organic compounds  . . . . . . 1787--1796
             Premal S. Shah and   
            Geoffrey K. Hom and   
                Stephen L. Mayo   Preprocessing of rotamers for protein
                                  design calculations  . . . . . . . . . . 1797--1800
              Jason Wagoner and   
                Nathan A. Baker   Erratum: Jason Wagoner and Nathan A.
                                  Baker, ``Solvation forces on
                                  biomolecular structures: A comparison of
                                  explicit solvent and Poisson--Boltzmann
                                  models,'' Journal of Computational
                                  Chemistry (2004) \bf 25(13) 1623--1629   1801--1801
                      Anonymous   Publisher's Note: ``Software News and
                                  Updates'' section of the Journal of
                                  Computational Chemistry  . . . . . . . . i--i

Journal of Computational Chemistry
Volume 25, Number 15, November 30, 2004

               Shunzhou Wan and   
              Peter Coveney and   
               Darren R. Flower   Large-scale molecular dynamics
                                  simulations of HLA-A*0201 complexed with
                                  a tumor-specific antigenic peptide: Can
                                  the $\alpha$3 and $\beta_2 m$ domains be
                                  neglected? . . . . . . . . . . . . . . . 1803--1813
                M. Belmares and   
                  M. Blanco and   
          W. A. Goddard III and   
                 R. B. Ross and   
                G. Caldwell and   
                 S.-H. Chou and   
                    J. Pham and   
              P. M. Olofson and   
                Cristina Thomas   Hildebrand and Hansen solubility
                                  parameters from Molecular Dynamics with
                                  applications to electronic nose polymer
                                  sensors  . . . . . . . . . . . . . . . . 1814--1826
                   Jian Wan and   
                   Li Zhang and   
                   Guangfu Yang   Quantitative structure--activity
                                  relationships for phenyl triazolinones
                                  of protoporphyrinogen oxidase
                                  inhibitors: a density functional theory
                                  study  . . . . . . . . . . . . . . . . . 1827--1832
               Weizhong Yan and   
                   Ying Xue and   
                    Hua Zhu and   
                   Jun Zeng and   
                    Daiqian Xie   A theoretical study of solvent effects
                                  on tautomerism and electronic absorption
                                  spectra of 3-hydroxy-2-mercaptopyridine
                                  and 2,3-dihydroxypyridine  . . . . . . . 1833--1839
            Robert J. Deeth and   
                    Natalie Fey   The performance of nonhybrid density
                                  functionals for calculating the
                                  structures and spin states of Fe(II) and
                                  Fe(III) complexes  . . . . . . . . . . . 1840--1848
      Evangelos A. Coutsias and   
                 Chaok Seok and   
                    Ken A. Dill   Using quaternions to calculate RMSD  . . 1849--1857
            Henryk A. Witek and   
                 Keiji Morokuma   Systematic study of vibrational
                                  frequencies calculated with the
                                  self-consistent charge density
                                  functional tight-binding method  . . . . 1858--1864
                 Bernd Kuhn and   
           Peter A. Kollman and   
                   Martin Stahl   Prediction of pK$_a$ shifts in proteins
                                  using a combination of molecular
                                  mechanical and continuum solvent
                                  calculations . . . . . . . . . . . . . . 1865--1872
      C. M. Zicovich-Wilson and   
                 F. Pascale and   
                  C. Roetti and   
             V. R. Saunders and   
                 R. Orlando and   
                      R. Dovesi   Calculation of the vibration frequencies
                                  of $\alpha$-quartz: the effect of
                                  Hamiltonian and basis set  . . . . . . . 1873--1881
          Yoshiumi Kawamura and   
                   Hiromi Nakai   A hybrid approach combining energy
                                  density analysis with the interaction
                                  energy decomposition method  . . . . . . 1882--1887
               Jia-Xu Zhang and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   Theoretical study on reaction mechanism
                                  of the fluoromethylene radical with
                                  nitrogen dioxide . . . . . . . . . . . . 1888--1894
             Eric Martineau and   
      Pierre-Jean L'Heureux and   
                   John R. Gunn   Biased fragment distribution in MC
                                  simulation of protein folding  . . . . . 1895--1903
      Roberto L. A. Haiduke and   
       Luiz G. M. De Macedo and   
          Rugles C. Barbosa and   
 Albérico B. F. Da Silva   A polynomial version of the generator
                                  coordinate Dirac--Fock method  . . . . . 1904--1909
              Yasuhito Ohta and   
                      Koji Ohta   Interconversion behavior of the C H bond
                                  in the CH radical cation: ab initio
                                  molecular dynamics study . . . . . . . . 1910--1919
             Philippe Soler and   
              Franck Fuster and   
               Hilaire Chevreau   Fast topological analysis of $2$D and
                                  $3$D grids of data: Application to the
                                  atoms in molecule (AIM) and the electron
                                  localization function (ELF)  . . . . . . 1920--1925
        Heather M. Netzloff and   
                 Mark S. Gordon   Fast fragments: the development of a
                                  parallel effective fragment potential
                                  method . . . . . . . . . . . . . . . . . 1926--1936

Journal of Computational Chemistry
Volume 25, Number 16, December, 2004

         Francesc J. Corcho and   
                Josep Canto and   
                  Juan J. Perez   Comparative analysis of the
                                  conformational profile of substance P
                                  using simulated annealing and molecular
                                  dynamics . . . . . . . . . . . . . . . . 1937--1952
            Joseph M. Hayes and   
             James C. Greer and   
          David A. Morton-Blake   A force-field description of short-range
                                  repulsions for high density alkane
                                  molecular dynamics simulations . . . . . 1953--1966
             Michael S. Lee and   
    Freddie R. Salsbury Jr. and   
                  Mark A. Olson   An efficient hybrid explicit/implicit
                                  solvent method for biomolecular
                                  simulations  . . . . . . . . . . . . . . 1967--1978
                 Otto Exner and   
            Stanislav Böhm   Enthalpies of formation of
                                  monoderivatives of hydrocarbons:
                                  Interaction of polar groups with an
                                  alkyl group  . . . . . . . . . . . . . . 1979--1986
   J. Fernández Rico and   
            R. López and   
                     I. Ema and   
              G. Ramírez   Efficiency of the algorithms for the
                                  calculation of Slater molecular
                                  integrals in polyatomic molecules  . . . 1987--1994
                Rie Tatsumi and   
        Yoshifumi Fukunishi and   
                Haruki Nakamura   A hybrid method of molecular dynamics
                                  and harmonic dynamics for docking of
                                  flexible ligand to flexible receptor . . 1995--2005
         Ramkumar V. Vadali and   
                    Yan Shi and   
               Sameer Kumar and   
          Laxmikant V. Kale and   
          Mark E. Tuckerman and   
               Glenn J. Martyna   Scalable fine-grained parallelization of
                                  plane-wave--based ab initio molecular
                                  dynamics for large supercomputers  . . . 2006--2022
                 Xingfa Gao and   
                   Hui Yuan and   
              Zhenling Chen and   
                   Yuliang Zhao   Theoretical studies of structures and
                                  stabilities of a new odd-numbered
                                  fullerene dimer: C$_{141}$ . . . . . . . 2023--2030
 Nuno M. F. S. A. Cerqueira and   
Pedro Alexandrino Fernandes and   
           Leif A. Eriksson and   
        Maria João Ramos   Ribonucleotide activation by enzyme
                                  ribonucleotide reductase: Understanding
                                  the role of the enzyme . . . . . . . . . 2031--2037
                John Mongan and   
              David A. Case and   
             J. Andrew McCammon   Constant pH molecular dynamics in
                                  generalized Born implicit solvent  . . . 2038--2048
            Ninad V. Prabhu and   
                Peijuan Zhu and   
                   Kim A. Sharp   Implementation and testing of stable,
                                  fast implicit solvation in molecular
                                  dynamics using the smooth-permittivity
                                  finite difference Poisson--Boltzmann
                                  method . . . . . . . . . . . . . . . . . 2049--2064
    Joris van Droogenbroeck and   
                 Ben Swerts and   
        Lothar Schäfer and   
          Christian van Alsenoy   Solids modeled by ab initio crystal
                                  field methods, part 22: the Fock matrix
                                  transformed supermolecule model and the
                                  structure determination of D-erythronic
                                  acid-3,4-carbonate . . . . . . . . . . . 2065--2072
             Chan Kyung Kim and   
               Kyung A. Lee and   
             Kwan Hoon Hyun and   
             Heung Jin Park and   
             In Young Kwack and   
              Chang Kon Kim and   
              Hai Whang Lee and   
                     Bon-Su Lee   Prediction of physicochemical properties
                                  of organic molecules using van der Waals
                                  surface electrostatic potentials . . . . 2073--2079


Journal of Computational Chemistry
Volume 26, Number 1, January 15, 2005

             Kaori Fukuzawa and   
              Kazuo Kitaura and   
            Masami Uebayasi and   
              Kotoko Nakata and   
        Tsuguchika Kaminuma and   
                 Tatsuya Nakano   Ab initio quantum mechanical study of
                                  the binding energies of human estrogen
                                  receptor $\alpha$ with its ligands: an
                                  application of fragment molecular
                                  orbital method . . . . . . . . . . . . . 1--10
          Maria Kontoyianni and   
             Glenn S. Sokol and   
             Laura M. Mcclellan   Evaluation of library ranking efficacy
                                  in virtual screening . . . . . . . . . . 11--22
                Steve Dixon and   
        Kenneth M. Merz Jr. and   
              Giorgio Lauri and   
                 James C. Ianni   QMQSAR: Utilization of a semiempirical
                                  probe potential in a field-based QSAR
                                  method . . . . . . . . . . . . . . . . . 23--34
             Zhong-Zhi Yang and   
               Li-Dong Gong and   
              Dong-Xia Zhao and   
                  Ming-Bo Zhang   Method and algorithm of obtaining the
                                  molecular intrinsic characteristic
                                  contours (MICCs) of organic molecules    35--47
                 Art E. Cho and   
             John A. Wendel and   
          Nagarajan Vaidehi and   
    Peter M. Kekenes-Huskey and   
           Wely B. Floriano and   
            Prabal K. Maiti and   
         William A. Goddard III   The MPSim--Dock hierarchical docking
                                  algorithm: Application to the eight
                                  trypsin inhibitor cocrystals . . . . . . 48--71
              Malek O. Khan and   
             Gareth Kennedy and   
               Derek Y. C. Chan   A scalable parallel Monte Carlo method
                                  for free energy simulations of molecular
                                  systems  . . . . . . . . . . . . . . . . 72--77
              Kyoungrim Lee and   
          Cezary Czaplewski and   
             Seung-Yeon Kim and   
                   Jooyoung Lee   An efficient molecular docking using
                                  conformational space annealing . . . . . 78--87
                   Bing Suo and   
               Gaohong Zhai and   
                 Yubin Wang and   
                 Zhenyi Wen and   
               Xiangqian Hu and   
                       Lemin Li   Parallelization of MRCI based on
                                  hole-particle symmetry . . . . . . . . . 88--96
                  F. Martin and   
                       H. Zipse   Charge distribution in the water
                                  molecule --- a comparison of methods . . 97--105
                  Wenli Zou and   
                    Wenjian Liu   Extensive theoretical studies on the
                                  low-lying electronic states of indium
                                  monochloride cation, InCl$^+$  . . . . . 106--113
                Junmei Wang and   
             Romain M. Wolf and   
          James W. Caldwell and   
           Peter A. Kollman and   
                  David A. Case   Erratum: Junmei Wang, Romain M. Wolf,
                                  James W. Caldwell, Peter A. Kollman, and
                                  David A. Case, ``Development and testing
                                  of a general AMBER force field'' Journal
                                  of Computational Chemistry (2004) \bf
                                  25(9) 1157--1174 . . . . . . . . . . . . 114--114

Journal of Computational Chemistry
Volume 26, Number 2, January 30, 2005

             Serena Donnini and   
               Alan E. Mark and   
     André H. Juffer and   
               Alessandra Villa   Incorporating the effect of ionic
                                  strength in free energy calculations
                                  using explicit ions  . . . . . . . . . . 115--122
            Robert J. Deeth and   
                Natalie Fey and   
      Benjamin Williams-Hubbard   DommiMOE: an implementation of ligand
                                  field molecular mechanics in the
                                  molecular operating environment  . . . . 123--130
            David De Sancho and   
               Lidia Prieto and   
               Ana M. Rubio and   
                    Antonio Rey   Evolutionary method for the assembly of
                                  rigid protein fragments  . . . . . . . . 131--141
 Daniela Bertolini Depizzol and   
Marcia Helena Moreira Paiva and   
 Thiago Oliveira Dos Santos and   
          Anderson Coser Gaudio   MoCalc: a new graphical user interface
                                  for molecular calculations . . . . . . . 142--144
             Zuzana Benkova and   
          Andrzej J. Sadlej and   
              Roma E. Oakes and   
              Steven E. J. Bell   Reduced-size polarized basis sets for
                                  calculations of molecular electric
                                  properties. I. The basis set generation  145--153
              Roma E. Oakes and   
          Steven E. J. Bell and   
             Zuzana Benkova and   
              Andrzej J. Sadlej   Reduced-size polarized basis sets for
                                  calculations of molecular electric
                                  properties. II. Simulation of the Raman
                                  spectra  . . . . . . . . . . . . . . . . 154--159
             Mitsuhito Wada and   
                 Minoru Sakurai   A quantum chemical method for rapid
                                  optimization of protein structures . . . 160--168
                     H. Sun and   
                  P. W.-C. Kung   Urea: an ab initio and force field study
                                  of the gas and solid phases  . . . . . . 169--174
                  S. Chiodo and   
                   N. Russo and   
                     E. Sicilia   Newly developed basis sets for density
                                  functional calculations  . . . . . . . . 175--184
                    Li Wang and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   Theoretical study and rate constant
                                  calculation for the reactions of SH (SD)
                                  with Cl$_2$, Br$_2$, and BrCl  . . . . . 184--193
             W. Dean Harman and   
                   Carl Trindle   Charge donation to and dearomatization
                                  of benzene attending complexation: DFT
                                  estimates of binding energies of
                                  TpMXO(L) with benzene, for Tp =
                                  hydridotris(pyrazolyl) borate, MXO =
                                  MoNO, ReCO, and WNO, and L = ammonia,
                                  $N$-methylimidazole, pyridine,
                                  phosphine, methyl isocyanide, and carbon
                                  monoxide . . . . . . . . . . . . . . . . 194--200

Journal of Computational Chemistry
Volume 26, Number 3, February, 2005

                   K. Fiaty and   
              C. Charcosset and   
                  B. Perrin and   
               R. Couturier and   
              B. Ma\"\isterrena   Simulations of the active transport of a
                                  neutral solute based on a
                                  kinase-channel-phosphatase topology  . . 201--213
          Robert J. Gdanitz and   
              Gary D. Black and   
          Carina S. Lansing and   
            Bruce J. Palmer and   
            Karen L. Schuchardt   Registering the Amica electronic
                                  structure code in the Extensible
                                  Computational Chemistry Environment  . . 214--225
                   Yuhui Qu and   
                   Xiufang Bian   Electronic structure and stability of
                                  Al$_n$P$_n$ ($n = 2$--$4$) clusters  . . 226--234
            Joanna Makowska and   
           Mariusz Makowski and   
                  Adam Liwo and   
             Lech Chmurzy\'nski   Theoretical calculations of
                                  homoconjugation equilibrium constants in
                                  systems modeling acid--base interactions
                                  in side chains of biomolecules using the
                                  potential of mean force  . . . . . . . . 235--242
       Charles F. F. Karney and   
           Jason E. Ferrara and   
                Stephan Brunner   Method for computing protein binding
                                  affinity . . . . . . . . . . . . . . . . 243--251
         Matthew A. Meineke and   
     Charles F. Vardeman II and   
                   Teng Lin and   
     Christopher J. Fennell and   
             J. Daniel Gezelter   OOPSE: an object-oriented parallel
                                  simulation engine for molecular dynamics 252--271
               Minoru Saito and   
               Isao Okazaki and   
               Masayuki Oda and   
                     Ikuo Fujii   A free energy calculation study of the
                                  effect of H$\rightarrow$F substitution
                                  on binding affinity in ligand--antibody
                                  interactions . . . . . . . . . . . . . . 272--282
                F. Wennmohs and   
                   M. Schindler   Development of a multipoint model for
                                  sulfur in proteins: a new
                                  parametrization scheme to reproduce
                                  high-level ab initio interaction
                                  energies . . . . . . . . . . . . . . . . 283--293
               Josef \vSeda and   
          Jaroslav V. Burda and   
              Jerzy Leszczynski   Study of electronic spectra of free-base
                                  porphin and Mg-porphin: Comprehensive
                                  comparison of variety of ab initio, DFT,
                                  and semiempirical methods  . . . . . . . 294--303
Panagiotis G. Karamertzanis and   
     Constantinos C. Pantelides   Ab initio crystal structure prediction
                                  --- I. Rigid molecules . . . . . . . . . 304--324

Journal of Computational Chemistry
Volume 26, Number 4, March, 2005

              Yasuyo Hatano and   
        Shigeyoshi Yamamoto and   
               Hiroshi Tatewaki   Characterization of molecular orbitals
                                  by counting nodal regions  . . . . . . . 325--333
              Shura Hayryan and   
                Chin-Kun Hu and   
Jaroslav Sk\vrivánek and   
              Edik Hayryane and   
          Imrich Pokorný   A new analytical method for computing
                                  solvent-accessible surface area of
                                  macromolecules and its gradients . . . . 334--343
A. Martín Pendás and   
               E. Francisco and   
                   M. A. Blanco   Two-electron integrations in the Quantum
                                  Theory of Atoms in Molecules with
                                  correlated wave functions  . . . . . . . 344--351
              Michael Meyer and   
          Alexandre Hocquet and   
        Jürgen Sühnel   Interaction of sodium and potassium ions
                                  with sandwiched cytosine-, guanine-,
                                  thymine-, and uracil-base tetrads  . . . 352--364
           Pablo Campomanes and   
  M. Isabel Menéndez and   
  Ramón López and   
          Tomás L. Sordo   Stereodynamics of bond rotation in
                                  tertiary 1-naphthoic acid amides: a
                                  computational study  . . . . . . . . . . 365--373
           Eckart Bindewald and   
               Jeffrey Skolnick   A scoring function for docking ligands
                                  to low-resolution protein structures . . 374--383
       Philippe Carbonniere and   
                Tecla Lucca and   
             Claude Pouchan and   
                 Nadia Rega and   
                Vincenzo Barone   Vibrational computations beyond the
                                  harmonic approximation: Performances of
                                  the B3LYP density functional for
                                  semirigid molecules  . . . . . . . . . . 384--388
                Mehdi Mobli and   
             Raymond J. Abraham   Quantum vs. classical models of the
                                  nitro group for proton chemical shift
                                  calculations and conformational analysis 389--398
                   Quan Zhu and   
                Ke-Xiang Fu and   
              Xiang-Yuan Li and   
                  Zhen Gong and   
                     Jian-Yi Ma   Continuous medium theory for
                                  nonequilibrium solvation: III. Solvation
                                  shift by monopole approximation and
                                  multipole expansion in spherical cavity  399--409

Journal of Computational Chemistry
Volume 26, Number 5, April 15, 2005

   Veronika Kasalová and   
          Henry F. Schaefer III   Structures and electron affinities of
                                  the di-arsenic fluorides As$_2$F$_n$
                                  /As$_2$F ($n = 1$--$8$)  . . . . . . . . 411--435
               Mari Tamaoki and   
            Yusuke Yamauchi and   
                   Hiromi Nakai   Short-time Fourier transform analysis of
                                  ab initio molecular dynamics simulation:
                                  Collision reaction between CN and
                                  C$_4$H$_6$ . . . . . . . . . . . . . . . 436--442
           Rajeev Prabhakar and   
             Keiji Morokuma and   
          Djamaladdin G. Musaev   A comparative study of various
                                  computational approaches in calculating
                                  the structure of pyridoxal 5'-phosphate
                                  (PLP)-dependent $\beta$-lyase protein.
                                  The importance of protein environment    443--446
               Robert Ponec and   
              Gleb Yuzhakov and   
             Markku R. Sundberg   Chemical structures from the analysis of
                                  domain-averaged Fermi holes. Nature of
                                  the Mn Mn bond in
                                  bis(pentacarbonylmanganese)  . . . . . . 447--454
                A. Gallegos and   
      R. Carbó-Dorca and   
                  F. Lodier and   
                E. Canc\`es and   
                       A. Savin   Maximal probability domains in linear
                                  molecules  . . . . . . . . . . . . . . . 455--460
                   Qishi Du and   
                P. G. Mezey and   
                  Kuo-Chen Chou   Heuristic molecular lipophilicity
                                  potential (HMLP): a $2$D-QSAR study to
                                  LADH of molecular family pyrazole and
                                  derivatives  . . . . . . . . . . . . . . 461--470
               Carlos A. Stortz   Comparative performance of MM3(92) and
                                  two TINKER\TM MM3 versions for the
                                  modeling of carbohydrates  . . . . . . . 471--483
                   Bing Liu and   
                     Jiaju Zhou   SARS-CoV protease inhibitors design
                                  using virtual screening method from
                                  natural products libraries . . . . . . . 484--490
            A. M. Tokmachev and   
       A. L. Tchougréeff   Transferability of parameters of
                                  strictly local geminals' wave function
                                  and possibility of sequential derivation
                                  of molecular mechanics . . . . . . . . . 491--505
             Pierre Tuffery and   
Frédéric Guyon and   
            Philippe Derreumaux   Improved greedy algorithm for protein
                                  structure reconstruction . . . . . . . . 506--513
              Lingchun Song and   
                  Yirong Mo and   
               Qianer Zhang and   
                         Wei Wu   XMVB: a program for ab initio
                                  nonorthogonal valence bond computations  514--521
                      Anonymous   Announcements  . . . . . . . . . . . . . v--v

Journal of Computational Chemistry
Volume 26, Number 6, April 30, 2005

Raúl A. Bustos Marún and   
        Eduardo A. Coronado and   
                Juan C. Ferrero   Fitting complex potential energy
                                  surfaces to simple model potentials:
                                  Application of the simplex-annealing
                                  method . . . . . . . . . . . . . . . . . 523--531
                Vinzenz Bachler   The behavior of transition metal nitrido
                                  bonds towards protonation rationalized
                                  by means of localized bonding schemes
                                  and their weights  . . . . . . . . . . . 532--551
                    Ping Li and   
                     Yuxiang Bu   Double proton transfer and one-electron
                                  oxidation behavior in double H-bonded
                                  glycinamide--glycine complex in the gas
                                  phase  . . . . . . . . . . . . . . . . . 552--560
           Peter L. Cummins and   
                 Jill E. Gready   Computational methods for the study of
                                  enzymic reaction mechanisms III: a
                                  perturbation plus QM/MM approach for
                                  calculating relative free energies of
                                  protonation  . . . . . . . . . . . . . . 561--568
Núria González-García and   
\`Angels González-Lafont and   
           José M. Lluch   Electronic structure study of the
                                  initiation routes of the dimethyl
                                  sulfide oxidation by OH  . . . . . . . . 569--583
                Qingyu Kong and   
                    Li Zhao and   
               Wenning Wang and   
                  Chen Wang and   
                     Can Xu and   
              Wingham Zhang and   
                    Lei Liu and   
               Kangnian Fan and   
                   Yufen Li and   
                     Jun Zhuang   Magic number silicon dioxide-based
                                  clusters: Laser ablation-mass
                                  spectrometric and density functional
                                  theory studies . . . . . . . . . . . . . 584--598
                Peter Pulay and   
                Svein Saebo and   
           Massimo Malagoli and   
                      Jon Baker   Accuracy and efficiency of atomic basis
                                  set methods versus plane wave
                                  calculations with ultrasoft
                                  pseudopotentials for DNA base molecules  599--605
           T. K. Manojkumar and   
                Chunzhi Cui and   
                   Kwang S. Kim   Theoretical insights into the mechanism
                                  of acetylcholinesterase-catalyzed
                                  acylation of acetylcholine . . . . . . . 606--611
          Pedro L. Muiño   The OH$^\bullet$ + CH$_3$SH reaction:
                                  Support for an addition-elimination
                                  mechanism from ab initio calculations    612--618
                Manfred Rudolph   Attaining exponential convergence for
                                  the flux error with second- and
                                  fourth-order accurate finite-difference
                                  equations. I. Presentation of the basic
                                  concept and application to a pure
                                  diffusion system . . . . . . . . . . . . 619--632
                Manfred Rudolph   Attaining exponential convergence for
                                  the flux error with second- and
                                  fourth-order accurate finite-difference
                                  equations. II. Application to systems
                                  comprising first-order chemical
                                  reactions  . . . . . . . . . . . . . . . 633--641
               Hong-Qing He and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   Theoretical study for the reaction of
                                  CH$_3$OCl with Cl atom . . . . . . . . . 642--650

Journal of Computational Chemistry
Volume 26, Number 7, May, 2005

                 Eva Darian and   
            Vladimir Hnizdo and   
            Adam Fedorowicz and   
           Harshinder Singh and   
                 Eugene Demchuk   Estimation of the absolute
                                  internal-rotation entropy of molecules
                                  with two torsional degrees of freedom
                                  from stochastic simulations  . . . . . . 651--660
            Marcus Lundberg and   
             Per E. M. Siegbahn   Agreement between experiment and hybrid
                                  DFT calculations for O H bond
                                  dissociation enthalpies in manganese
                                  complexes  . . . . . . . . . . . . . . . 661--667
              Peter A. Sims and   
              Chung F. Wong and   
                 Danka Vuga and   
         J. Andrew McCammon and   
          Bartholomew M. Sefton   Relative contributions of desolvation,
                                  inter- and intramolecular interactions
                                  to binding affinity in protein kinase
                                  systems  . . . . . . . . . . . . . . . . 668--681
              Eric J. Sorin and   
                 Vijay S. Pande   Empirical force-field assessment: the
                                  interplay between backbone torsions and
                                  noncovalent term scaling . . . . . . . . 682--690
                Min-Yi Shen and   
                  Karl F. Freed   A simple method for faster nonbonded
                                  force evaluations  . . . . . . . . . . . 691--698
             L. Renee Olano and   
                 Steven W. Rick   Fluctuating charge normal modes: an
                                  algorithm for implementing molecular
                                  dynamics simulations with polarizable
                                  potentials . . . . . . . . . . . . . . . 699--707
   Alán Aspuru-Guzik and   
Romelia Salomón-Ferrer and   
               Brian Austin and   
          William A. Lester Jr.   A sparse algorithm for the evaluation of
                                  the local energy in quantum Monte Carlo  708--715
                Anti Liivat and   
                Alvo Aabloo and   
                 John O. Thomas   Development of a force field for
                                  Li$_2$SiF$_6$  . . . . . . . . . . . . . 716--724
          Thereza A. Soares and   
Philippe H. Hünenberger and   
         Mika A. Kastenholz and   
      Vincent Kräutler and   
                Thomas Lenz and   
            Roberto D. Lins and   
          Chris Oostenbrink and   
       Wilfred F. van Gunsteren   An improved nucleic acid parameter set
                                  for the GROMOS force field . . . . . . . 725--737
           Fredrik Blomgren and   
                   Sven Larsson   Exploring the potential energy surface
                                  of retinal, a comparison of the
                                  performance of different methods . . . . 738--742
                Neil Gohaud and   
               Didier Begue and   
            Clovis Darrigan and   
                 Claude Pouchan   New parallel software (\tt P\_Anhar) for
                                  anharmonic vibrational calculations:
                                  Application to (CH$_3$Li)$_2$  . . . . . 743--754

Journal of Computational Chemistry
Volume 26, Number 8, June, 2005

         Robert J. Petrella and   
                 Martin Karplus   Electrostatic energies and forces
                                  computed without explicit interparticle
                                  interactions: a linear time complexity
                                  formulation  . . . . . . . . . . . . . . 755--787
          Hirofumi Fujimoto and   
             Miroslav Pinak and   
           Toshiyuki Nemoto and   
              Peter O'Neill and   
                 Etsuo Kume and   
              Kimiaki Saito and   
                Hideaki Maekawa   Molecular dynamics simulation of
                                  clustered DNA damage sites containing
                                  8-oxoguanine and abasic site . . . . . . 788--798
                 Si-Dian Li and   
            Chang-Qing Miao and   
              Jin-Chang Guo and   
                 Guang-Ming Ren   Carbon boronyls: Species with higher
                                  viable possibility than boron carbonyls
                                  at the density functional theory . . . . 799--802
                 Frank J. Owens   Stability of (C$_{60}$)$_2$ and epoxide
                                  dimers, (C$_{60}$)$_2$O$_N$, and their
                                  anions . . . . . . . . . . . . . . . . . 803--806
               Jia-Xu Zhang and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   Theoretical study on the reaction
                                  mechanism of the methyl radical with
                                  nitrogen oxides  . . . . . . . . . . . . 807--817
                Akifumi Oda and   
          Noriyuki Yamaotsu and   
                 Shuichi Hirono   New AMBER force field parameters of heme
                                  iron for cytochrome P450s determined by
                                  quantum chemical calculations of
                                  simplified models  . . . . . . . . . . . 818--826
          Alessandro Genoni and   
            Arianna Fornili and   
                Maurizio Sironi   Optimal virtual orbitals to relax wave
                                  functions built up with transferred
                                  extremely localized molecular orbitals   827--835
             Theodore S. Dibble   Computations on the $\tilde{A}$--X$^-$;
                                  transition of isoprene-OH-O$_2$ peroxy
                                  radicals . . . . . . . . . . . . . . . . 836--845
   J. Fernández Rico and   
            R. López and   
                     I. Ema and   
              G. Ramírez   Translation of STO charge distributions  846--855
   Alán Aspuru-Guzik and   
Romelia Salomón-Ferrer and   
               Brian Austin and   
Raul Perusquía-Flores and   
            Mary A. Griffin and   
           Ricardo A. Oliva and   
              David Skinner and   
              Dominik Domin and   
          William A. Lester Jr.   Zori 1.0: a parallel quantum Monte Carlo
                                  electronic structure package . . . . . . 856--862
              Jason Wagoner and   
                Nathan A. Baker   Erratum to ``Solvation forces on
                                  biomolecular structures: A comparison of
                                  explicit solvent and Poisson--Boltzmann
                                  models,'' by Jason Wagoner and Nathan A.
                                  Baker  . . . . . . . . . . . . . . . . . 863--863

Journal of Computational Chemistry
Volume 26, Number 9, July 15, 2005

Ia. I. Dobrogorskaia-Méreau and   
                 A. V. Nemukhin   Quantum chemical modeling of the
                                  reduction of cis-diammineplatinum(IV)
                                  tetrachloride [Pt(NH$_3$)$_2$Cl$_4$] by
                                  methyl thiolate anion  . . . . . . . . . 865--870
             Gui-Chang Wang and   
                     Jun Li and   
                Xiu-Fang Xu and   
                Rui-Fang Li and   
                 Junji Nakamura   The relationship between adsorption
                                  energies of methyl on metals and the
                                  metallic electronic properties: a
                                  first-principles DFT study . . . . . . . 871--878
          Andreas Schreiber and   
            Michael Humbert and   
             Alexander Benz and   
                Ursula Dietrich   $3$D-Epitope-Explorer (3DEX):
                                  Localization of conformational epitopes
                                  within three-dimensional structures of
                                  proteins . . . . . . . . . . . . . . . . 879--887
         Per E. M. Siegbahn and   
         Alexander F. Shestakov   Quantum chemical modeling of CO
                                  oxidation by the active site of
                                  molybdenum CO dehydrogenase  . . . . . . 888--898
                   Wayne Pullan   An unbiased population-based search for
                                  the geometry optimization of
                                  Lennard-Jones clusters: $2 \leq {N} \leq
                                  372$ . . . . . . . . . . . . . . . . . . 899--906
          Jaroslav V. Burda and   
           Michal Zeizinger and   
              Jerzy Leszczynski   Hydration process as an activation of
                                  trans- and cisplatin complexes in
                                  anticancer treatment. DFT and ab initio
                                  computational study of thermodynamic and
                                  kinetic parameters . . . . . . . . . . . 907--914
                 Art E. Cho and   
             Victor Guallar and   
             Bruce J. Berne and   
               Richard Friesner   Importance of accurate charges in
                                  molecular docking: Quantum
                                  mechanical/molecular mechanical (QM/MM)
                                  approach . . . . . . . . . . . . . . . . 915--931
      Roberto L. A. Haiduke and   
       Luiz G. M. de Macedo and   
 Albérico B. F. da Silva   An accurate relativistic universal
                                  Gaussian basis set for hydrogen through
                                  Nobelium without variational prolapse
                                  and to be used with both uniform sphere
                                  and Gaussian nucleus models  . . . . . . 932--940
              Illia Horenko and   
          Sönke Lorenz and   
      Christof Schütte and   
               Wilhelm Huisinga   Adaptive approach for nonlinear
                                  sensitivity analysis of reaction
                                  kinetics . . . . . . . . . . . . . . . . 941--948
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Structure-breaking effects of solvated
                                  Rb(I) in dilute aqueous solution --- an
                                  ab initio QM/MM MD approach  . . . . . . 949--956
            Sanjay Banerjee and   
              John A. Board Jr.   Efficient charge assignment and back
                                  interpolation in multigrid methods for
                                  molecular dynamics . . . . . . . . . . . 957--967

Journal of Computational Chemistry
Volume 26, Number 10, July 30, 2005

                    Li Yang and   
               Ji-Kang Feng and   
                     Ai-Min Ren   Theoretical studies on the electronic
                                  and optical properties of two new
                                  alternating fluorene/carbazole
                                  copolymers . . . . . . . . . . . . . . . 969--979
             Chang-Guo Zhan and   
              Shi-Xian Deng and   
             Jaime G. Skiba and   
              Beth A. Hayes and   
         Sarah M. Tschampel and   
          George C. Shields and   
               Donald W. Landry   First-principle studies of
                                  intermolecular and intramolecular
                                  catalysis of protonated cocaine  . . . . 980--986
                 Toru Inaba and   
              Saisei Tahara and   
          Nobutaka Nisikawa and   
          Hiroshi Kashiwagi and   
                 Fumitoshi Sato   All-electron density functional
                                  calculation on insulin with
                                  quasi-canonical localized orbitals . . . 987--993
                   Ying Xue and   
             Chan Kyung Kim and   
                   Yong Guo and   
               Dai Qian Xie and   
                    Guo Sen Yan   DFT study and Monte Carlo simulation on
                                  proton transfers of 2-amino-2-oxazoline,
                                  2-amino-2-thiazoline, and
                                  2-amino-2-imidazoline in the gas phase
                                  and in water . . . . . . . . . . . . . . 994--1005
        G. Theodoor De Jong and   
             Daan P. Geerke and   
            Axel Diefenbach and   
              Miquel Sol\`a and   
        F. Matthias Bickelhaupt   Oxidative addition of the ethane C C
                                  bond to Pd. An ab initio benchmark and
                                  DFT validation study . . . . . . . . . . 1006--1020
         Michael S. Crocker and   
           Scott S. Hampton and   
            Thierry Matthey and   
      Jesús A. Izaguirre   \sc MDSimAid: Automatic parameter
                                  optimization in fast electrostatic
                                  algorithms . . . . . . . . . . . . . . . 1021--1031
             Hsien-Da Huang and   
               Tzong-Yi Lee and   
             Shih-Wei Tzeng and   
                Li-Cheng Wu and   
          Jorng-Tzong Horng and   
              Ann-Ping Tsou and   
                Kuan-Tsae Huang   Incorporating hidden Markov models for
                                  identifying protein kinase-specific
                                  phosphorylation sites  . . . . . . . . . 1032--1041
             Stefano Borini and   
              Daniel Maynau and   
            Stefano Evangelisti   A combined freeze-and-cut strategy for
                                  the description of large molecular
                                  systems using a localized orbitals
                                  approach . . . . . . . . . . . . . . . . 1042--1051
       Jean-Philip Piquemal and   
            Antonio Marquez and   
            Olivier Parisel and   
        Claude Giessner-Prettre   A CSOV study of the difference between
                                  HF and DFT intermolecular interaction
                                  energy values: the importance of the
                                  charge transfer contribution . . . . . . 1052--1062
              Jerod Parsons and   
          J. Bradley Holmes and   
           J. Maurice Rojas and   
                 Jerry Tsai and   
          Charlie E. M. Strauss   Practical conversion from torsion space
                                  to Cartesian space for in silico protein
                                  synthesis  . . . . . . . . . . . . . . . 1063--1068
            Lesley D. Lloyd and   
            Roy L. Johnston and   
                     Said Salhi   Strategies for increasing the efficiency
                                  of a genetic algorithm for the
                                  structural optimization of nanoalloy
                                  clusters . . . . . . . . . . . . . . . . 1069--1078
             Piotr Zarzycki and   
           Pawe\l Szabelski and   
                 Robert Charmas   Role of the surface heterogeneity in
                                  adsorption of hydrogen ions on metal
                                  oxides: Theory and simulations . . . . . 1079--1088

Journal of Computational Chemistry
Volume 26, Number 11, August, 2005

             A. M. Ruvinsky and   
                A. V. Kozintsev   New and fast statistical-thermodynamic
                                  method for computation of protein-ligand
                                  binding entropy substantially improves
                                  docking accuracy . . . . . . . . . . . . 1089--1095
             Caterina Benzi and   
             Maurizio Cossi and   
            Roberto Improta and   
                Vincenzo Barone   Building cavities in a fluid of
                                  spherical or rod-like particles: a
                                  contribution to the solvation free
                                  energy in isotropic and anisotropic
                                  polarizable continuum model  . . . . . . 1096--1105
       Michael S. Schuurman and   
            Wesley D. Allen and   
          Henry F. Schaefer III   The ab initio limit quartic force field
                                  of BH$_3$  . . . . . . . . . . . . . . . 1106--1112
                Nohad Gresh and   
       Jean-Philip Piquemal and   
                  Morris Krauss   Representation of Zn(II) complexes in
                                  polarizable molecular mechanics. Further
                                  refinements of the electrostatic and
                                  short-range contributions. Comparisons
                                  with parallel ab initio computations . . 1113--1130
                Jens Antony and   
       Jean-Philip Piquemal and   
                    Nohad Gresh   Complexes of thiomandelate and captopril
                                  mercaptocarboxylate inhibitors to
                                  metallo-$\beta$-lactamase by polarizable
                                  molecular mechanics. Validation on model
                                  binding sites by quantum chemistry . . . 1131--1147
        Siegfried Höfinger   Solving the Poisson--Boltzmann equation
                                  with the specialized computer chip
                                  MD-GRAPE-2 . . . . . . . . . . . . . . . 1148--1154
      András Perczel and   
Zoltán Gáspári and   
              Imre G. Csizmadia   Structure and stability of
                                  $\beta$-pleated sheets . . . . . . . . . 1155--1168
          Florian Koskowski and   
                   Bernd Hartke   Towards protein folding with
                                  evolutionary techniques  . . . . . . . . 1169--1179
             Maxence Launay and   
            Richard Dronskowski   A theoretical study on the structures
                                  and energetics of hypothetical
                                  TiM(NCN)$_3$ compounds of the $3 d$
                                  transition metals  . . . . . . . . . . . 1180--1188
                 Hongzhi Li and   
                     Yaoqi Zhou   SCUD: Fast structure clustering of
                                  decoys using reference state to remove
                                  overall rotation . . . . . . . . . . . . 1189--1192
                Manfred Rudolph   Attaining exponential convergence for
                                  the flux error with second- and
                                  fourth-order accurate finite-difference
                                  equations. Part 3. Application to
                                  electrochemical systems comprising
                                  second-order chemical reactions  . . . . 1193--1204

Journal of Computational Chemistry
Volume 26, Number 12, September, 2005

               Robert Ponec and   
                 Joaquin Chaves   Electron pairing and chemical bonds.
                                  Electron fluctuation and pair
                                  localization in ELF domains  . . . . . . 1205--1213
                 Zexing Cao and   
                   Qianer Zhang   Computational analyses of
                                  singlet--singlet and singlet--triplet
                                  transitions in mononuclear gold-capped
                                  carbon-rich conjugated complexes . . . . 1214--1221
               Po-Ssu Huang and   
               John J. Love and   
                Stephen L. Mayo   Adaptation of a fast Fourier
                                  transform-based docking algorithm for
                                  protein design . . . . . . . . . . . . . 1222--1232
            Thanh Ha Nguyen and   
             David E. Hibbs and   
           Siân T. Howard   Conformations, energies, and
                                  intramolecular hydrogen bonds in
                                  dicarboxylic acids: Implications for the
                                  design of synthetic dicarboxylic acid
                                  receptors  . . . . . . . . . . . . . . . 1233--1241
       Andreas W. Götz and   
          Christian Kollmar and   
                  Bernd A. Hess   Optimization of auxiliary basis sets for
                                  the LEDO expansion and a projection
                                  technique for LEDO--DFT  . . . . . . . . 1242--1253
J. M. Junquera-Hernández and   
            J. Pitarch-Ruiz and   
J. Sánchez-Marín and   
             S. Evangelisti and   
                      D. Maynau   Multistate active spaces from local
                                  CAS-SCF molecular orbitals: the
                                  photodissociation of HFCO as an example  1254--1262
                 Xue-Hai Ju and   
                   Xin Wang and   
                    Feng-Li Bei   Substituent effects on heats of
                                  formation, group interactions, and
                                  detonation properties of
                                  polyazidocubanes . . . . . . . . . . . . 1263--1269
            Marek Freindorf and   
                 Yihan Shao and   
          Thomas R. Furlani and   
                      Jing Kong   Lennard-Jones parameters for the
                                  combined QM/MM method using the
                                  B3LYP/6-31G*/AMBER potential . . . . . . 1270--1278
               Zhigang Wang and   
                 Keyan Lian and   
                 Shoufu Pan and   
                   Xianhong Fan   A path from I$_h$ to C$_1$ symmetry for
                                  C$_{20}$ cage molecule . . . . . . . . . 1279--1283
 Maria Del Carmen Michelini and   
                 Nino Russo and   
Mohammad Esma\"\il Alikhani and   
                  Bernard Silvi   Energetic and topological analyses of
                                  the oxidation reaction between Mo$_n$
                                  ($n = 1, 2$) and N$_2$O  . . . . . . . . 1284--1293
          Christian Bartels and   
               Armin Widmer and   
                 Claus Ehrhardt   Absolute free energies of binding of
                                  peptide analogs to the HIV-1 protease
                                  from molecular dynamics simulations  . . 1294--1305

Journal of Computational Chemistry
Volume 26, Number 13, October, 2005

 Péter Hudáky and   
          András Perczel   Toward direct determination of
                                  conformations of protein building units
                                  from multidimensional NMR experiments
                                  VI. Chemical shift analysis of his to
                                  gain $3$D structure and protonation
                                  state information  . . . . . . . . . . . 1307--1317
                  David E. Shaw   A fast, scalable method for the parallel
                                  evaluation of distance-limited pairwise
                                  particle interactions  . . . . . . . . . 1318--1328
    Pathumwadee Intharathep and   
              Anan Tongraar and   
               Kritsana Sagarik   Structure and dynamics of hydrated NH:
                                  an ab initio QM/MM molecular dynamics
                                  simulation . . . . . . . . . . . . . . . 1329--1338
                 Yu-Hua Yao and   
                Xu-Ying Nan and   
                 Tian-Ming Wang   A class of $2$D graphical
                                  representations of RNA secondary
                                  structures and the analysis of
                                  similarity based on them . . . . . . . . 1339--1346
                  R. Villar and   
                  M. J. Gil and   
        J. I. García and   
      V. Martínez-Merino   Are AM1 ligand-protein binding
                                  enthalpies good enough for use in the
                                  rational design of new drugs?  . . . . . 1347--1358
          Sonja M. Schwarzl and   
               Danzhi Huang and   
            Jeremy C. Smith and   
                 Stefan Fischer   Nonuniform charge scaling (NUCS): a
                                  practical approximation of solvent
                                  electrostatic screening in proteins  . . 1359--1371
             Hitoshi Kusama and   
                Hideki Sugihara   Theoretical study of quinolines--I$_2$
                                  intermolecular interaction and
                                  implications on dye-sensitized solar
                                  cell performance . . . . . . . . . . . . 1372--1382
                Zoe Cournia and   
            Jeremy C. Smith and   
            G. Matthias Ullmann   A molecular mechanics force field for
                                  biologically important sterols . . . . . 1383--1399
            Roberto D. Lins and   
   Philippe H. Hünenberger   A new GROMOS force field for
                                  hexopyranose-based carbohydrates . . . . 1400--1412
                Youdong Lin and   
              Mark A. Stadtherr   Deterministic global optimization of
                                  molecular structures using interval
                                  analysis . . . . . . . . . . . . . . . . 1413--1420
                  Hui Zhang and   
                 Jia-Yan Wu and   
                Ze-Sheng Li and   
               Jing-Yao Liu and   
                   Li Sheng and   
                 Chia-Chung Sun   Dual-level direct dynamics studies on
                                  the reaction Cl + CHBr$_2$Cl . . . . . . 1421--1426

Journal of Computational Chemistry
Volume 26, Number 14, November 15, 2005

                Victor Polo and   
             Juan Andrés   A joint study based on the electron
                                  localization function and catastrophe
                                  theory of the chameleonic and centauric
                                  models for the Cope rearrangement of
                                  1,5-hexadiene and its cyano derivatives  1427--1437
              Gernot Katzer and   
               Alexander F. Sax   Identification and thermodynamic
                                  treatment of several types of
                                  large-amplitude motions  . . . . . . . . 1438--1451
             Alba T. Macias and   
     Alexander D. MacKerell Jr.   CH/$\pi$ interactions involving aromatic
                                  amino acids: Refinement of the CHARMM
                                  tryptophan force field . . . . . . . . . 1452--1463
        Nicholas P. Labello and   
        Antonio M. Ferreira and   
                 Henry A. Kurtz   An augmented effective core potential
                                  basis set for the calculation of
                                  molecular polarizabilities . . . . . . . 1464--1471
              Marian Nanias and   
          Maurizio Chinchio and   
        Stanis\law O\ldziej and   
          Cezary Czaplewski and   
             Harold A. Scheraga   Protein structure prediction with the
                                  UNRES force-field using Replica-Exchange
                                  Monte Carlo-with-Minimization;
                                  Comparison with MCM, CSA, and CFMC . . . 1472--1486
                Daiqian Xie and   
                       Jun Zeng   Electronic excitations of green
                                  fluorescent proteins: Protonation states
                                  of chromophore model compound in
                                  solutions  . . . . . . . . . . . . . . . 1487--1496
   A. Patrícia Bento and   
              Miquel Sol\`a and   
        F. Matthias Bickelhaupt   Ab initio and DFT benchmark study for
                                  nucleophilic substitution at carbon
                                  (S$_N$2@C) and silicon (S$_N$2@Si) . . . 1497--1504
              Max C. Holthausen   Benchmarking approximate density
                                  functional theory. I. $s/d$ excitation
                                  energies in $3 d$ transition metal
                                  cations  . . . . . . . . . . . . . . . . 1505--1518
                    Bo Liao and   
                    Kequan Ding   Graphical approach to analyzing DNA
                                  sequences  . . . . . . . . . . . . . . . 1519--1523
          Ricardo O. Freire and   
              Gerd B. Rocha and   
               Alfredo M. Simas   Modeling lanthanide complexes:
                                  Sparkle/AM1 parameters for ytterbium
                                  (III)  . . . . . . . . . . . . . . . . . 1524--1528
            Daniel J. Price and   
          Charles L. Brooks III   Detailed considerations for a balanced
                                  and broadly applicable force field: a
                                  study of substituted benzenes modeled
                                  with OPLS-AA . . . . . . . . . . . . . . 1529--1541

Journal of Computational Chemistry
Volume 26, Number 15, November 30, 2005

                 Hui-Yin Wu and   
             Ajay Chaudhari and   
                  Shyi-Long Lee   Theoretical studies on nonlinear optical
                                  properties of formaldehyde oligomers by
                                  ab initio and density functional theory
                                  methods  . . . . . . . . . . . . . . . . 1543--1564
               Jianhan Chen and   
                  Wonpil Im and   
          Charles L. Brooks III   Application of torsion angle molecular
                                  dynamics for efficient sampling of
                                  protein conformations  . . . . . . . . . 1565--1578
              M. Tafipolsky and   
                      R. Schmid   Calculation of rotational partition
                                  functions by an efficient Monte Carlo
                                  importance sampling technique  . . . . . 1579--1591
         Chompoonut Rungnim and   
        Vithaya Ruangpornvisuti   A density functional study of propylene
                                  glycol conversion to propanal and
                                  propanone of various acid-catalyzed
                                  reaction models: a water-addition effect 1592--1599
             Yoong-Kee Choe and   
                 Shigeru Nagase   Effect of the axial cysteine ligand on
                                  the electronic structure and reactivity
                                  of high-valent iron(IV) oxo-porphyrins
                                  (Compound I): a theoretical study  . . . 1600--1611
              Sanghyun Park and   
          Randall J. Radmer and   
              Teri E. Klein and   
                 Vijay S. Pande   A new set of molecular mechanics
                                  parameters for hydroxyproline and its
                                  use in molecular dynamics simulations of
                                  collagen-like peptides . . . . . . . . . 1612--1616
               Shantenu Jha and   
           Peter V. Coveney and   
            Charles A. Laughton   Force field validation for nucleic acid
                                  simulations: Comparing energies and
                                  dynamics of a DNA dodecamer  . . . . . . 1617--1627
       Emanuel H. Rubensson and   
                  Pawe\l Sa\lek   Systematic sparse matrix error control
                                  for linear scaling electronic structure
                                  calculations . . . . . . . . . . . . . . 1628--1637
             Mark T. Oakley and   
      Jonathan M. Garibaldi and   
              Jonathan D. Hirst   Lattice models of peptide aggregation:
                                  Evaluation of conformational search
                                  algorithms . . . . . . . . . . . . . . . 1638--1646
        Michael A. Johnston and   
Ignacio Fdez. Galván and   
           Jordi Vill\`a-Freixa   Framework-based design of a new
                                  all-purpose molecular simulation
                                  application: the Adun simulator  . . . . 1647--1659
                  G. R. Kneller   Comment on ``Using quaternions to
                                  calculate RMSD'' [J. Comp. Chem. \bf 25,
                                  1849 (2004)] . . . . . . . . . . . . . . 1660--1662
      Evangelos A. Coutsias and   
                 Chaok Seok and   
                    Ken A. Dill   Rotational superposition and least
                                  squares: the SVD and quaternions
                                  approaches yield identical results.
                                  Reply to the preceding comment by G.
                                  Kneller  . . . . . . . . . . . . . . . . 1663--1665

Journal of Computational Chemistry
Volume 26, Number 16, December, 2005

          Charles L. Brooks III   Editorial  . . . . . . . . . . . . . . . 1667--1667
              David A. Case and   
     Thomas E. Cheatham III and   
                 Tom Darden and   
              Holger Gohlke and   
                    Ray Luo and   
        Kenneth M. Merz Jr. and   
            Alexey Onufriev and   
          Carlos Simmerling and   
                  Bing Wang and   
                Robert J. Woods   The AMBER biomolecular simulation
                                  programs . . . . . . . . . . . . . . . . 1668--1688
       William L. Jorgensen and   
            Julian Tirado-Rives   Molecular modeling of organic and
                                  biomolecular systems using BOSS and
                                  MCPRO  . . . . . . . . . . . . . . . . . 1689--1700
        David Van Der Spoel and   
               Erik Lindahl and   
                  Berk Hess and   
            Gerrit Groenhof and   
               Alan E. Mark and   
         Herman J. C. Berendsen   GROMACS: Fast, flexible, and free  . . . 1701--1718
            Markus Christen and   
Philippe H. Hünenberger and   
              Dirk Bakowies and   
             Riccardo Baron and   
          Roland Bürgi and   
             Daan P. Geerke and   
               Tim N. Heinz and   
         Mika A. Kastenholz and   
      Vincent Kräutler and   
          Chris Oostenbrink and   
            Christine Peter and   
           Daniel Trzesniak and   
       Wilfred F. van Gunsteren   The GROMOS software for biomolecular
                                  simulation: GROMOS05 . . . . . . . . . . 1719--1751
               Jay L. Banks and   
              Hege S. Beard and   
                Yixiang Cao and   
                 Art E. Cho and   
              Wolfgang Damm and   
                 Ramy Farid and   
           Anthony K. Felts and   
          Thomas A. Halgren and   
            Daniel T. Mainz and   
               Jon R. Maple and   
              Robert Murphy and   
            Dean M. Philipp and   
         Matthew P. Repasky and   
             Linda Y. Zhang and   
             Bruce J. Berne and   
        Richard A. Friesner and   
          Emilio Gallicchio and   
                 Ronald M. Levy   Integrated Modeling Program, Applied
                                  Chemical Theory (IMPACT) . . . . . . . . 1752--1780
          James C. Phillips and   
             Rosemary Braun and   
                   Wei Wang and   
              James Gumbart and   
           Emad Tajkhorshid and   
            Elizabeth Villa and   
          Christophe Chipot and   
            Robert D. Skeel and   
      Laxmikant Kalé and   
                 Klaus Schulten   Scalable molecular dynamics with NAMD    1781--1802
                      Anonymous   Erratum: David E. Shaw. ``A fast,
                                  scalable method for the parallel
                                  evaluation of distance-limited pairwise
                                  particle interactions'', Journal of
                                  Computational Chemistry (2005) \bf 26
                                  (13) 1318--1328  . . . . . . . . . . . . 1803--1803


Journal of Computational Chemistry
Volume 27, Number 1, January 15, 2006

             Zhong-Zhi Yang and   
                    Qiang Zhang   Study of peptide conformation in terms
                                  of the ABEEM/MM method . . . . . . . . . 1--10
               Frank Eckert and   
                  Andreas Klamt   Accurate prediction of basicity in
                                  aqueous solution with COSMO-RS . . . . . 11--19
          Tamás Beke and   
               Csaba Somlai and   
          András Perczel   Toward a rational design of
                                  $\beta$-peptide structures . . . . . . . 20--38
                    Jing Ma and   
                  Shuhua Li and   
                         Wei Li   A multireference configuration
                                  interaction method based on the
                                  separated electron pair wave functions   39--47
         Yoshihiro Watanabe and   
           Hiroshi Tatewaki and   
            Toshikatsu Koga and   
                 Osamu Matsuoka   Relativistic Gaussian basis sets for
                                  molecular calculations: Fully optimized
                                  single-family exponent basis sets for H
                                  Hg . . . . . . . . . . . . . . . . . . . 48--52
            Kaori Ueno-Noto and   
         Miki Hara-Yokoyama and   
                   Keiko Takano   Recognition of tandem sialic acid
                                  residues by CD38: a theoretical study    53--60
      Roberto L. A. Haiduke and   
 Albérico B. F. da Silva   Accurate relativistic adapted Gaussian
                                  basis sets for hydrogen through xenon
                                  without variational prolapse and to be
                                  used with both uniform sphere and
                                  Gaussian nucleus models  . . . . . . . . 61--71
                  Zhiyun Yu and   
        Matthew P. Jacobson and   
            Richard A. Friesner   What role do surfaces play in GB models?
                                  A new-generation of surface-generalized
                                  Born model based on a novel Gaussian
                                  surface for biomolecules . . . . . . . . 72--89
           Yasemin Kurtulus and   
     Michael Gilleßen and   
            Richard Dronskowski   Electronic structure, chemical bonding,
                                  and finite-temperature magnetic
                                  properties of full Heusler alloys  . . . 90--102
         Brent A. Gregersen and   
                 Darrin M. York   A charge-scaling implementation of the
                                  variational electrostatic projection
                                  method . . . . . . . . . . . . . . . . . 103--115
  Carlos Silva López and   
          Olalla Nieto Faza and   
Susana López Estévez and   
               Angel R. de Lera   Computation of vertical excitation
                                  energies of retinal and analogs: Scope
                                  and limitations  . . . . . . . . . . . . 116--123

Journal of Computational Chemistry
Volume 27, Number 2, January 30, 2006

                 Hairong Ma and   
                Martin Gruebele   Low barrier kinetics: Dependence on
                                  observables and free energy surface  . . 125--134
      Christoph van Wüllen   Numerical instabilities in the
                                  computation of pseudopotential matrix
                                  elements . . . . . . . . . . . . . . . . 135--141
      Christophe Gourlaouen and   
       Jean-Philip Piquemal and   
                 Trond Saue and   
                Olivier Parisel   Revisiting the geometry of $nd^{10} (n +
                                  1)s^0$ [M(H$_2$O)]$^{p+}$ complexes
                                  using four-component relativistic DFT
                                  calculations and scalar relativistic
                                  correlated CSOV energy decompositions
                                  (M$^{p+}$ = Cu$^+$, Zn$^{2+}$, Ag$^+$,
                                  Cd$^{2+}$, Au$^+$, Hg$^{2+}$)  . . . . . 142--156
                 Anne Milet and   
               Yves Gimbert and   
               Andrew E. Greene   Reaction of nitrones with silyl ketene
                                  acetals: a DFT study . . . . . . . . . . 157--162
          Chantal T. Falzon and   
            Delano P. Chong and   
                      Feng Wang   Prediction of spectroscopic constants
                                  for diatomic molecules in the ground and
                                  excited states using time-dependent
                                  density functional theory  . . . . . . . 163--173
               Ivan Rivalta and   
                 Nino Russo and   
                 Emilia Sicilia   Methane activation by chromium oxide
                                  cations in the gas phase: a theoretical
                                  study  . . . . . . . . . . . . . . . . . 174--187
         Fernando D. Suvire and   
          Luis N. Santagata and   
   José A. Bombasaro and   
               Ricardo D. Enriz   Dynamics of flexible cycloalkanes. Ab
                                  initio and DFT study of the
                                  conformational energy hypersurface of
                                  cyclononane  . . . . . . . . . . . . . . 188--202
                     Jie Hu and   
                      Ao Ma and   
                Aaron R. Dinner   Monte Carlo simulations of biomolecules:
                                  the MC module in CHARMM  . . . . . . . . 203--216
       Marcelo Alves-Santos and   
Liliana Y. A. Dávila and   
         Helena M. Petrilli and   
           Rodrigo B. Capaz and   
       Marília J. Caldas   Application of standard DFT theory for
                                  nonbonded interactions in soft matter:
                                  Prototype study of poly-para-phenylene   217--227
               Chultack Lim and   
               Hee Soon Lee and   
             Young-Woo Kwak and   
                  Cheol Ho Choi   A theoretical study of thermal
                                  [1,3]-sigmatropic rearrangements of
                                  3-trimethylsilyl-1-pyrazoline: Concerted
                                  vs. stepwise mechanisms  . . . . . . . . 228--237
    José Luis Alonso and   
                Pablo Echenique   A physically meaningful method for the
                                  comparison of potential energy functions 238--252
            J. A. L. Rabone and   
                 N. H. De Leeuw   Interatomic potential models for natural
                                  apatite crystals: Incorporating
                                  strontium and the lanthanides  . . . . . 253--266

Journal of Computational Chemistry
Volume 27, Number 3, February, 2006

                     Zhijian Wu   Electronic structures of $3 d$-metal
                                  mononitrides . . . . . . . . . . . . . . 267--276
     Kaushalya S. Ekanayake and   
             Pierre R. Lebreton   Activation barriers for DNA alkylation
                                  by carcinogenic methane diazonium ions   277--286
                Andrzej Bil and   
              Zdzis\law Latajka   The hydroperoxy radical as a hydrogen
                                  bond acceptor. HOO HCl complexes --- ab
                                  initio study . . . . . . . . . . . . . . 287--295
            A. M. Tokmachev and   
                 R. Dronskowski   Electron group functions for the
                                  analysis of the electronic structures of
                                  molecules  . . . . . . . . . . . . . . . 296--308
              Heinz Sklenar and   
        Daniel Wüstner and   
                      Remo Rohs   Using internal and collective variables
                                  in Monte Carlo simulations of nucleic
                                  acid structures: Chain breakage/closure
                                  algorithm and associated Jacobians . . . 309--315
        Tsjerk A. Wassenaar and   
                   Alan E. Mark   The effect of box shape on the dynamic
                                  properties of proteins simulated under
                                  periodic boundary conditions . . . . . . 316--325
       Eirik Fossgård and   
                   Kenneth Ruud   Superlinear scaling in master-slave
                                  quantum chemical calculations using
                                  in-core storage of two-electron
                                  integrals  . . . . . . . . . . . . . . . 326--333
         Prasad V. Bharatam and   
                    Pansy Iqbal   Theoretical studies on electron
                                  delocalization in diaminoguanidine . . . 334--343
Inmaculada García Cuesta and   
Alfredo M. J. Sánchez De Merás and   
               Paolo Lazzeretti   Structure, magnetizability, and nuclear
                                  magnetic shielding tensors of
                                  bis-heteropentalenes. IV.
                                  Dihydrophospholophosphole isomers  . . . 344--351
          Timothy J. Dudley and   
              Ryan M. Olson and   
         Michael W. Schmidt and   
                 Mark S. Gordon   Parallel coupled perturbed CASSCF
                                  equations and analytic CASSCF second
                                  derivatives  . . . . . . . . . . . . . . 352--362
                  Jian Wang and   
               Yi-Hong Ding and   
               Gong-Bing Wu and   
                 Chia-Chung Sun   Gaseous reaction mechanism of C$_2$F
                                  radical with water . . . . . . . . . . . 363--367
                Ke-Xiang Fu and   
                   Quan Zhu and   
              Xiang-Yuan Li and   
                  Zhen Gong and   
                 Jian-Yi Ma and   
                   Rong-Xing He   Continuous medium theory for
                                  nonequilibrium solvation: IV. Solvent
                                  reorganization energy of electron
                                  transfer based on conductor-like
                                  screening model  . . . . . . . . . . . . 368--374
            Geoffrey K. Hom and   
                Stephen L. Mayo   A search algorithm for fixed-composition
                                  protein design . . . . . . . . . . . . . 375--378
            Hisashi Okumura and   
                   Yuko Okamoto   Multibaric--multithermal ensemble
                                  molecular dynamics simulations . . . . . 379--395
R. Svobodová Va\vreková and   
                      J. Ko\vca   Optimized and parallelized
                                  implementation of the electronegativity
                                  equalization method and the atom-bond
                                  electronegativity equalization method    396--405

Journal of Computational Chemistry
Volume 27, Number 4, March, 2006

            Kazuya Ishimura and   
                Peter Pulay and   
                 Shigeru Nagase   A new parallel algorithm of MP2 energy
                                  calculations . . . . . . . . . . . . . . 407--413
                Arnaldo Rapallo   An algorithm for the uniform sampling of
                                  iso-energy surfaces and for the
                                  calculation of microcanonical averages   414--425
         Hiroyuki Nakashima and   
            Jun-Ya Hasegawa and   
              Hiroshi Nakatsuji   On the reversible O$_2$ binding of the
                                  Fe--porphyrin complex  . . . . . . . . . 426--433
             Pekka Manninen and   
                     Juha Vaara   Systematic Gaussian basis-set limit
                                  using completeness-optimized primitive
                                  sets. A case for magnetic properties . . 434--445
              Franci Merzel and   
         Milan Hodo\vs\vcek and   
      Du\vsanka Jane\vzi\vc and   
                   Alain Sanson   New force field for calcium binding
                                  sites in annexin--membrane complexes . . 446--452
              Norio Yoshida and   
                   Fumio Hirata   A new method to determine electrostatic
                                  potential around a macromolecule in
                                  solution from molecular wave functions   453--462
            Masahiro Sekiya and   
               Takeshi Noro and   
             Eisaku Miyoshi and   
                 You Osanai and   
                Toshikatsu Koga   Relativistic correlating basis sets for
                                  lanthanide atoms from Ce to Lu . . . . . 463--470
           Hideaki Nakamura and   
                   Masaru Aniya   Thermodynamic properties of
                                  Ag$_2$OB$_2$O$_3$ glasses by a modified
                                  scale-transformed energy space sampling
                                  Monte Carlo method . . . . . . . . . . . 471--477
                  Xuan Xiao and   
             Shi-Huang Shao and   
             Zheng-De Huang and   
                  Kuo-Chen Chou   Using pseudo amino acid composition to
                                  predict protein structural classes:
                                  Approached with complexity measure
                                  factor . . . . . . . . . . . . . . . . . 478--482
            Gerald Geudtner and   
           Florian Janetzko and   
     Andreas M. Köster and   
               Alberto Vela and   
            Patrizia Calaminici   Parallelization of the deMon2k code  . . 483--490
             Mark P. Waller and   
          Arturo Robertazzi and   
            James A. Platts and   
             David E. Hibbs and   
              Peter A. Williams   Hybrid density functional theory for
                                  $\pi$-stacking interactions: Application
                                  to benzenes, pyridines, and DNA bases    491--504
                 Qiang Wang and   
               Yi-Hong Ding and   
               Hong-Bin Xie and   
                 Chia-Chung Sun   Theoretical study on structures and
                                  stabilities of [H,Ge,C,N]  . . . . . . . 505--514
            Arianna Fornili and   
              Yohann Moreau and   
            Maurizio Sironi and   
                 Xavier Assfeld   On the suitability of strictly localized
                                  orbitals for hybrid QM/MM calculations   515--523
             Josep M. Oliva and   
     Luis Serrano-Andrés   A computational study of the lowest
                                  singlet and triplet states of neutral
                                  and dianionic 1,2-substituted
                                  icosahedral and octahedral
                                  $o$-carboranes . . . . . . . . . . . . . 524--535

Journal of Computational Chemistry
Volume 27, Number 5, April 15, 2006

              Min Hsien Liu and   
                     Cheng Chen   Modified calculations of hydrocarbon
                                  thermodynamic properties . . . . . . . . 537--544
               Hong-Bin Xie and   
               Yi-Hong Ding and   
                 Chia-Chung Sun   Ylidic radical--molecule reactions . . . 545--551
      Mikhail V. Basilevsky and   
           Igor V. Leontyev and   
        Sofia V. Luschekina and   
          Olga A. Kondakova and   
            Vladimir B. Sulimov   Computation of hydration free energies
                                  of organic solutes with an implicit
                                  water model  . . . . . . . . . . . . . . 552--570
        Stanislav Böhm and   
                     Otto Exner   Are calculated enthalpies of formation
                                  sometimes more reliable than
                                  experimental? A test on alkyl
                                  substituted benzoic acids  . . . . . . . 571--577
               Li-Ming Yang and   
               Yi-Hong Ding and   
                 Qiang Wang and   
                 Chia-Chung Sun   Monosilicon-substituted cyanoacetylene:
                                  a computational study  . . . . . . . . . 578--595
            Diego R. Alcoba and   
                  Luis Lain and   
               Alicia Torre and   
          Roberto C. Bochicchio   An orbital localization criterion based
                                  on the theory of ``fuzzy'' atoms . . . . 596--608
            Anna Fiorentino and   
            Deepangi Pandit and   
        Kathleen M. Gilbert and   
               Milind Misra and   
                  Rose Dios and   
               Carol A. Venanzi   Singular value decomposition of
                                  torsional angles of analogs of the
                                  dopamine reuptake inhibitor GBR 12909    609--620
             Giulio Gianese and   
             Stefano Pascarella   A consensus procedure improving solvent
                                  accessibility prediction . . . . . . . . 621--626
        P. Cassam-Chena\"\i and   
               J. Liévin   The VMFCI method: a flexible tool for
                                  solving the molecular vibration problem  627--640
               Hong-Bin Xie and   
               Yi-Hong Ding and   
                 Chia-Chung Sun   Radical reaction C$_3$H + NO: a
                                  mechanistic study  . . . . . . . . . . . 641--660
               Jia-Xu Zhang and   
                Ze-Sheng Li and   
               Jing-Yao Liu and   
                 Chia-Chung Sun   Theoretical mechanistic study on the
                                  radical-molecule reaction of CHCl$_2$
                                  /CCl$_3$ with NO$_2$ . . . . . . . . . . 661--671
    Håkan W. Hugosson and   
            Alessandro Laio and   
             Patrick Maurer and   
           Ursula Rothlisberger   A comparative theoretical study of
                                  dipeptide solvation in water . . . . . . 672--684

Journal of Computational Chemistry
Volume 27, Number 6, April 30, 2006

                  Qi-Shi Du and   
                 Da-Peng Li and   
               Wen-Zhang He and   
                  Kuo-Chen Chou   Heuristic molecular lipophilicity
                                  potential (HMLP): Lipophilicity and
                                  hydrophilicity of amino acid side chains 685--692
        Satyavani Vemparala and   
              Ivaylo Ivanov and   
       Vojislava Pophristic and   
             Katrin Spiegel and   
               Michael L. Klein   Ab initio calculations of intramolecular
                                  parameters for a class of arylamide
                                  polymers . . . . . . . . . . . . . . . . 693--700
                  Yasunobu Seno   Allostery of the two-state model of
                                  hemoglobin studied by ECEPP energy
                                  minimization . . . . . . . . . . . . . . 701--710
              Chunsheng Shi and   
              Masahiko Morinaga   Doping effects on proton incorporation
                                  and conduction in SrZrO$_3$  . . . . . . 711--718
Jana Chocholou\vsová and   
                   Michael Feig   Balancing an accurate representation of
                                  the molecular surface in generalized
                                  Born formalisms with integrator
                                  stability in molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 719--729
             Siu-Hung Chien and   
               Peter M. W. Gill   SG-0: a small standard grid for DFT
                                  quadrature on large systems  . . . . . . 730--739
            Tomasz Borowski and   
              Ewa Broclawik and   
   Christopher J. Schofield and   
             Per E. M. Siegbahn   Epimerization and desaturation by
                                  carbapenem synthase (CarC). A hybrid DFT
                                  study  . . . . . . . . . . . . . . . . . 740--748
               Guang-Tao Yu and   
                Xu-Ri Huang and   
               Yi-Hong Ding and   
             Chia-Chung Sun and   
                   Au-Chin Tang   Theoretical study on the [Si, C, N, O]
                                  potential energy surface . . . . . . . . 749--761
               Fabio E. Penotti   Orbital-orthogonality constraints and
                                  basis-set optimization . . . . . . . . . 762--772
             Ram Kinkar Roy and   
                    V. Usha and   
            Bhisma K. Patel and   
                 Kimihiko Hirao   Acetalization and thioacetalization of
                                  cabonyl compounds: a case study based on
                                  global and local electrophilicity
                                  descriptors  . . . . . . . . . . . . . . 773--780
             Zhi-Xiang Wang and   
                  Wei Zhang and   
                    Chun Wu and   
               Hongxing Lei and   
              Piotr Cieplak and   
                      Yong Duan   Strike a balance: Optimization of
                                  backbone torsion parameters of AMBER
                                  polarizable force field for simulations
                                  of proteins and peptides . . . . . . . . 781--790
      Primo\vz Pristov\vsek and   
               Lorella Franzoni   Stereospecific assignments of protein
                                  NMR resonances based on the tertiary
                                  structure and $2$D/$3$D NOE data . . . . 791--797
                Li-Cheng Wu and   
          Jorng-Tzong Horng and   
              Shir-Ly Huang and   
             Hsien-Da Huang and   
                 Baw-Jhiune Liu   Detection of discriminative sequence
                                  motifs in proteins obtained from
                                  prokaryotes grown at various
                                  temperatures . . . . . . . . . . . . . . 798--808

Journal of Computational Chemistry
Volume 27, Number 7, May, 2006

                   Peng Bao and   
                  Zhong-Heng Yu   Theoretical studies on the role of
                                  $\pi$-electron delocalization in
                                  determining the conformation of
                                  $N$-benzylideneaniline with three types
                                  of LMO basis sets  . . . . . . . . . . . 809--824
               Seongho Moon and   
                  David A. Case   A comparison of quantum chemical models
                                  for calculating NMR shielding parameters
                                  in peptides: Mixed basis set and ONIOM
                                  methods combined with a complete basis
                                  set extrapolation  . . . . . . . . . . . 825--836
 Jean-François Fuchs and   
               Hristo Nedev and   
                David Poger and   
             Michel Ferrand and   
     Valérie Brenner and   
         Jean-Pierre Dognon and   
                   Serge Crouzy   New model potentials for
                                  sulfur--copper(I) and
                                  sulfur--mercury(II) interactions in
                                  proteins: From ab initio to molecular
                                  dynamics . . . . . . . . . . . . . . . . 837--856
                    Yu Zhou and   
          Chris Oostenbrink and   
              Aldo Jongejan and   
   Wilfred F. Van Gunsteren and   
           Wilfred R. Hagen and   
          Simon W. De Leeuw and   
               Jaap A. Jongejan   Computational study of ground-state
                                  chiral induction in small peptides:
                                  Comparison of the relative stability of
                                  selected amino acid dimers and oligomers
                                  in homochiral and heterochiral
                                  combinations . . . . . . . . . . . . . . 857--867
              Lionello Pogliani   The hydrogen perturbation in molecular
                                  connectivity computations  . . . . . . . 868--882
                    Lin Jin and   
               Yi-Hong Ding and   
                  Jian Wang and   
                 Chia-Chung Sun   Reaction mechanism of the CCN radical
                                  with nitric oxide  . . . . . . . . . . . 883--893
               Jia-Xu Zhang and   
                Ze-Sheng Li and   
               Jing-Yao Liu and   
                 Chia-Chung Sun   Theoretical study on the mechanism of
                                  the CH$_2$F + NO$_2$ reaction  . . . . . 894--905
                Kazuki Ohno and   
                 Minoru Sakurai   Linear-scaling molecular orbital
                                  calculations for the pKa values of
                                  ionizable residues in proteins . . . . . 906--916

Journal of Computational Chemistry
Volume 27, Number 8, June, 2006

               Hiromi Nakai and   
                Yasuaki Kikuchi   Energy density analysis of cluster size
                                  dependence of surface--molecule
                                  interactions (II): Formate adsorption
                                  onto a Cu(111) surface . . . . . . . . . 917--925
           J. H. Van Lenthe and   
                  R. Zwaans and   
           H. J. J. Van Dam and   
                    M. F. Guest   Starting SCF calculations by
                                  superposition of atomic densities  . . . 926--932
                     Ju Xie and   
               Dacheng Feng and   
                   Shengyu Feng   Theoretical study on the isomeric
                                  structures and the stability of
                                  silylenoid (Tsi)Cl$_2$SiLi (Tsi =
                                  C(SiMe$_3$)$_3$) . . . . . . . . . . . . 933--940
                     Shiqi Zhou   Rapidly convergent procedure to solve
                                  the density profile equation in the
                                  classical density functional theory  . . 941--947
             Kaori Fukuzawa and   
               Yuto Komeiji and   
             Yuji Mochizuki and   
               Akifumi Kato and   
             Tatsuya Nakano and   
               Shigenori Tanaka   Intra- and intermolecular interactions
                                  between cyclic-AMP receptor protein and
                                  DNA: ab initio fragment molecular
                                  orbital study  . . . . . . . . . . . . . 948--960
               K. Darowicki and   
                    W. Felisiak   On the joint time-frequency
                                  characteristics of chemical oscillations 961--965
   Alexandra T. P. Carvalho and   
            P. A. Fernandes and   
                 Maria J. Ramos   Determination of the $\Delta$pKa between
                                  the active site cysteines of thioredoxin
                                  and DsbA . . . . . . . . . . . . . . . . 966--975
          Dmitri G. Fedorov and   
              Kazuo Kitaura and   
                     Hui Li and   
              Jan H. Jensen and   
                 Mark S. Gordon   The polarizable continuum model (PCM)
                                  interfaced with the fragment molecular
                                  orbital method (FMO) . . . . . . . . . . 976--985
                  Zhi-Ru Li and   
             Fang-Fang Wang and   
                      Di Wu and   
                    Ying Li and   
                   Wei Chen and   
              Xiao-Ying Sun and   
               Feng Long Gu and   
                    Yuriko Aoki   Royal crown-shaped electride
                                  Li$_3$--N$_3$--Be containing two
                                  superatoms: New knowledge on aromaticity 986--993
                      Anonymous   Erratum: Zhi-Xiang Wang, Wei Zhang, Chun
                                  Wu, Hongxing Lei, Piotr Cieplak, Yong
                                  Duan, ``Strike a balance: Optimization
                                  of backbone torsion parameters of AMBER
                                  polarizable force field for simulations
                                  of proteins and peptides'', Journal of
                                  Computational Chemistry (2006) \bf 27(6)
                                  781--790 . . . . . . . . . . . . . . . . 994--994

Journal of Computational Chemistry
Volume 27, Number 9, July 15, 2006

         Antonio Cervellino and   
            Cinzia Giannini and   
          Antonietta Guagliardi   On the efficient evaluation of Fourier
                                  patterns for nanoparticles and clusters  995--1008
      Roberto Flores-Moreno and   
  Rodrigo J. Alvarez-Mendez and   
               Alberto Vela and   
         Andreas M. Köster   Half-numerical evaluation of
                                  pseudopotential integrals  . . . . . . . 1009--1019
               Tzong-Yi Lee and   
          Jorng-Tzong Horng and   
             Hsueh-Fen Juan and   
             Hsien-Da Huang and   
                Li-Cheng Wu and   
             Meng-Fong Tsai and   
              Hsuan-Cheng Huang   An agent-based system to discover
                                  protein--protein interactions, identify
                                  protein complexes and proteins with
                                  multiple peptide mass fingerprints . . . 1020--1032
       Aggeliki Kosmopoulou and   
             Metaxia Vlassi and   
   Athanassios Stavrakoudis and   
    Constantinos Sakarellos and   
    Maria Sakarellos-Daitsiotis   T-cell epitopes of the La/SSB
                                  autoantigen: Prediction based on the
                                  homology modeling of HLA-DQ2/DQ7 with
                                  the insulin-B peptide/HLA-DQ8 complex    1033--1044
                    Hua Zhu and   
                   Yong Guo and   
                   Ying Xue and   
                    Daiqian Xie   Ab initio potential energy surface and
                                  predicted microwave spectra for
                                  Ar\bondOCS dimer and structures of
                                  Ar$_n$\bondOCS ($n = 2$--$14$) clusters  1045--1053

Journal of Computational Chemistry
Volume 27, Number 10, July 30, 2006

              Patrick Musch and   
                   Bernd Engels   DIESEL--MP2: a new program to perform
                                  large-scale multireference-MP2
                                  computations . . . . . . . . . . . . . . 1055--1062
          Andrew E. Whitten and   
         Joshua J. McKinnon and   
               Mark A. Spackman   Electric field-derived point charges to
                                  mimic the electrostatics in molecular
                                  crystals . . . . . . . . . . . . . . . . 1063--1070
          Benjamin D. Allen and   
                Stephen L. Mayo   Dramatic performance enhancements for
                                  the FASTER optimization algorithm  . . . 1071--1075
            Pablo Echenique and   
                   J. L. Alonso   Definition of Systematic, Approximately
                                  Separable, and Modular Internal
                                  Coordinates (SASMIC) for macromolecular
                                  simulation . . . . . . . . . . . . . . . 1076--1087
                   Karl Jug and   
      Viatcheslav A. Tikhomirov   Anion substitution in zinc chalcogenides 1088--1092
           T. S. Venkatesan and   
                 K. Deepika and   
                   S. Mahapatra   The Jahn--Teller and pseudo-Jahn--Teller
                                  effects in the anion photoelectron
                                  spectroscopy of B$_3$ cluster  . . . . . 1093--1100
              Gerd B. Rocha and   
          Ricardo O. Freire and   
           Alfredo M. Simas and   
            James J. P. Stewart   RM1: a reparameterization of AM1 for H,
                                  C, N, O, P, S, F, Cl, Br, and I  . . . . 1101--1111
                 Genyuan Li and   
                Herschel Rabitz   Ratio control variate method for
                                  efficiently determining high-dimensional
                                  model representations  . . . . . . . . . 1112--1118

Journal of Computational Chemistry
Volume 27, Number 11, August, 2006

                  Liwei Liu and   
                  Tianming Wang   $2$D representation of protein secondary
                                  structure sequences and its applications 1119--1124
       Bahram Hemmateenejad and   
                 Ramin Miri and   
      Mohammad A. Safarpour and   
             Ahmad R. Mehdipour   Accurate prediction of the blood--brain
                                  partitioning of a large set of solutes
                                  using ab initio calculations and genetic
                                  neural network modeling  . . . . . . . . 1125--1135
               Hyunbum Jang and   
                Thomas B. Woolf   Multiple pathways in conformational
                                  transitions of the alanine dipeptide: an
                                  application of dynamic importance
                                  sampling . . . . . . . . . . . . . . . . 1136--1141
         Flavia P. Agostini and   
   Diogo De O. Soares-Pinto and   
           Marcelo A. Moret and   
              Carla Osthoff and   
              Pedro G. Pascutti   Generalized simulated annealing applied
                                  to protein folding studies . . . . . . . 1142--1155
               Ivan Infante and   
            Bas van Stralen and   
                 Lucas Visscher   A QM/MM study on the aqueous solvation
                                  of the tetrahydroxouranylate [UO$_2$
                                  (OH)$_4$]$^{2-}$ complex ion . . . . . . 1156--1162
      Vincent Kräutler and   
   Philippe H. Hünenberger   A multiple time step algorithm
                                  compatible with a large number of
                                  distance classes and an arbitrary
                                  distance dependence of the time step
                                  size for the fast evaluation of
                                  nonbonded interactions in molecular
                                  simulations  . . . . . . . . . . . . . . 1163--1176
        Dusan P. Djurdjevic and   
                  Mark J. Biggs   Ab initio protein fold prediction using
                                  evolutionary algorithms: Influence of
                                  design and control parameters on
                                  performance  . . . . . . . . . . . . . . 1177--1195
                    Bo Liao and   
                 Xuyu Xiang and   
                        Wen Zhu   Coronavirus phylogeny based on $2$D
                                  graphical representation of DNA sequence 1196--1202
               Annia Galano and   
  J. Raúl Alvarez-Idaboy   A new approach to counterpoise
                                  correction to BSSE . . . . . . . . . . . 1203--1210
              E. S. Ferrari and   
               R. C. Burton and   
                R. J. Davey and   
                  A. Gavezzotti   Simulation of phase separation in
                                  alcohol/water mixtures using two-body
                                  force field and standard molecular
                                  dynamics . . . . . . . . . . . . . . . . 1211--1219

Journal of Computational Chemistry
Volume 27, Number 12, September, 2006

            Gernot Frenking and   
              Max C. Holthausen   Foreword . . . . . . . . . . . . . . . . 1221--1222
            Carmen Herrmann and   
                    Lian Yu and   
                  Markus Reiher   Spin states in polynuclear clusters: The
                                  [Fe$_2$O$_2$] core of the methane
                                  monooxygenase active site  . . . . . . . 1223--1239
          Guillermina Estiu and   
        Dimas Suárez and   
                Kenneth M. Merz   Quantum mechanical and molecular
                                  dynamics simulations of ureases and Zn
                                  $\beta$-lactamases . . . . . . . . . . . 1240--1262
            Mihail Atanasov and   
                Peter Comba and   
                Bodo Martin and   
           Vera Müller and   
          Gopalan Rajaraman and   
               Heidi Rohwer and   
             Steffen Wunderlich   DFT models for copper(II) bispidine
                                  complexes: Structures, stabilities,
                                  isomerism, spin distribution, and
                                  spectroscopy . . . . . . . . . . . . . . 1263--1277
                Felix Studt and   
                   Felix Tuczek   Theoretical, spectroscopic, and
                                  mechanistic studies on transition-metal
                                  dinitrogen complexes: Implications to
                                  reactivity and relevance to the
                                  nitrogenase problem  . . . . . . . . . . 1278--1291
                 Wen-Ge Han and   
                 Tiqing Liu and   
             Timothy Lovell and   
                Louis Noodleman   DFT calculations of $^{57}$Fe Mössbauer
                                  isomer shifts and quadrupole splittings
                                  for iron complexes in polar dielectric
                                  media: Applications to methane
                                  monooxygenase and ribonucleotide
                                  reductase  . . . . . . . . . . . . . . . 1292--1306
       Jonathan P. McNamara and   
        Mahesh Sundararajan and   
             Ian H. Hillier and   
                     Jun Ge and   
            Andrew Campbell and   
                Claudio Morgado   Can the semiempirical PM3 scheme
                                  describe iron-containing bioinorganic
                                  molecules? . . . . . . . . . . . . . . . 1307--1323
                Ahmet Altun and   
                Sason Shaik and   
                   Walter Thiel   Systematic QM/MM investigation of
                                  factors that affect the cytochrome
                                  P450-catalyzed hydrogen abstraction of
                                  camphor  . . . . . . . . . . . . . . . . 1324--1337
            Nicolai Lehnert and   
          V. K. K. Praneeth and   
                 Florian Paulat   Electronic structure of
                                  iron(II)--porphyrin nitroxyl complexes:
                                  Molecular mechanism of fungal nitric
                                  oxide reductase (P450nor)  . . . . . . . 1338--1351
           Jeremy N. Harvey and   
       Christine M. Bathelt and   
           Adrian J. Mulholland   QM/MM modeling of compound I active
                                  species in cytochrome P450, cytochrome C
                                  peroxidase, and ascorbate peroxidase . . 1352--1362
         Hiroyuki Nakashima and   
            Jun-ya Hasegawa and   
              Hiroshi Nakatsuji   On the O$_2$ binding of Fe--porphyrin,
                                  Fe--porphycene, and Fe--corrphycene
                                  complexes  . . . . . . . . . . . . . . . 1363--1372
   Margareta R. A. Blomberg and   
             Per E. M. Siegbahn   Quantum chemistry applied to the
                                  mechanisms of transition metal
                                  containing enzymes --- Cytochrome $c$
                                  oxidase, a particularly challenging case 1373--1384
         Robert K. Szilagyi and   
                Mark A. Winslow   On the accuracy of density functional
                                  theory for iron--sulfur clusters . . . . 1385--1397
Lubomír Rulí\vsek and   
           Kasper P. Jensen and   
        Kristoffer Lundgren and   
                       Ulf Ryde   The reaction mechanism of iron and
                                  manganese superoxide dismutases studied
                                  by theoretical calculations  . . . . . . 1398--1414
          Edward I. Solomon and   
          Serge I. Gorelsky and   
                   Abhishek Dey   Metal--thiolate bonds in bioinorganic
                                  chemistry  . . . . . . . . . . . . . . . 1415--1428
               Jadwiga Kuta and   
        Seguei Patchkovskii and   
          Marek Z. Zgierski and   
             Pawel M. Kozlowski   Performance of DFT in modeling
                                  electronic and structural properties of
                                  cobalamins . . . . . . . . . . . . . . . 1429--1437
           Rajeev Prabhakar and   
             Keiji Morokuma and   
          Djamaladdin G. Musaev   A DFT study of the mechanism of Ni
                                  superoxide dismutase (NiSOD): Role of
                                  the active site cysteine-6 residue in
                                  the oxidative half-reaction  . . . . . . 1438--1445
Jean-Didier Maréchal and   
              Feliu Maseras and   
Agustí Lledós and   
            Liliane Mouawad and   
                  David Perahia   A DFT study on the relative affinity for
                                  oxygen of the $\alpha$ and $\beta$
                                  subunits of hemoglobin . . . . . . . . . 1446--1453
               Jesse W. Tye and   
    Marcetta Y. Darensbourg and   
                Michael B. Hall   Correlation between computed gas-phase
                                  and experimentally determined
                                  solution-phase infrared spectra: Models
                                  of the iron--iron hydrogenase enzyme
                                  active site  . . . . . . . . . . . . . . 1454--1462
        Sebastian Sinnecker and   
                    Frank Neese   QM/MM calculations with DFT for taking
                                  into account protein effects on the EPR
                                  and optical spectra of metalloproteins.
                                  Plastocyanin as a case study . . . . . . 1463--1475

Journal of Computational Chemistry
Volume 27, Number 13, October, 2006

             Myungshim Kang and   
                  Paul E. Smith   A Kirkwood-Buff derived force field for
                                  amides . . . . . . . . . . . . . . . . . 1477--1485
               Marcel Swart and   
          Ernst Rösler and   
        F. Matthias Bickelhaupt   Proton affinities of maingroup-element
                                  hydrides and noble gases: Trends across
                                  the periodic table, structural effects,
                                  and DFT validation . . . . . . . . . . . 1486--1493
                   Haibo Yu and   
             Daan P. Geerke and   
                 Haiyan Liu and   
       Wilfred F. van Gunsteren   Molecular dynamics simulations of liquid
                                  methanol and methanol--water mixtures
                                  with polarizable models  . . . . . . . . 1494--1504
                P. Salvador and   
                D. Asturiol and   
                       I. Mayer   A general efficient implementation of
                                  the BSSE-free SCF and MP2 methods based
                                  on the chemical Hamiltonian approach . . 1505--1516
         Alexey Aleksandrov and   
                Thomas Simonson   The tetracycline: Mg$^{2+}$ complex: a
                                  molecular mechanics force field  . . . . 1517--1533
               Elena Herzog and   
             Tomaso Frigato and   
             Volkhard Helms and   
            C. Roy D. Lancaster   Energy barriers of proton transfer
                                  reactions between amino acid side chain
                                  analogs and water from ab initio
                                  calculations . . . . . . . . . . . . . . 1534--1547
         Anders Irbäck and   
               Sandipan Mohanty   PROFASI: a Monte Carlo simulation
                                  package for protein folding and
                                  aggregation  . . . . . . . . . . . . . . 1548--1555
                   Yi-Yu Ke and   
               Yun-Chu Chen and   
                    Thy-Hou Lin   Structure of the virus capsid protein
                                  VP1 of enterovirus 71 predicted by some
                                  homology modeling and molecular docking
                                  studies  . . . . . . . . . . . . . . . . 1556--1570
                    Zhen Xi and   
                 Zhihong Yu and   
                Congwei Niu and   
                Shurong Ban and   
                   Guangfu Yang   Development of a general
                                  quantum-chemical descriptor for steric
                                  effects: Density functional theory based
                                  QSAR study of herbicidal sulfonylurea
                                  analogues  . . . . . . . . . . . . . . . 1571--1576
            Meng-Sheng Liao and   
              John D. Watts and   
                  Ming-Ju Huang   Assessment of the performance of
                                  density-functional methods for
                                  calculations on iron porphyrins and
                                  related compounds  . . . . . . . . . . . 1577--1592
               Yuedong Yang and   
                     Haiyan Liu   Genetic algorithms for protein
                                  conformation sampling and optimization
                                  in a discrete backbone dihedral angle
                                  space  . . . . . . . . . . . . . . . . . 1593--1602
            Marcin Makowski and   
           Jacek Korchowiec and   
               Feng Long Gu and   
                    Yuriko Aoki   Efficiency and accuracy of the
                                  elongation method as applied to the
                                  electronic structures of large systems   1603--1619
                      Anonymous   Erratum: Matteo Ceccarelli, Piero
                                  Procacci, Massimo Marchi ``An ab initio
                                  force field for the cofactors of
                                  bacterial photosynthesis,'' Journal of
                                  Computational Chemistry (2003) \bf 24(2)
                                  129--142 . . . . . . . . . . . . . . . . 1620--1620
                      Anonymous   Erratum: Felix Studt, Felix Tuczek,
                                  ``Theoretical, spectroscopic, and
                                  mechanistic studies on transition-metal
                                  dinitrogen complexes: Implications to
                                  reactivity and relevance to the
                                  nitrogenase problem,'' Journal of
                                  Computational Chemistry (2006) \bf
                                  27(12) 1278--1291  . . . . . . . . . . . 1621--1621

Journal of Computational Chemistry
Volume 27, Number 14, November 15, 2006

             Azuma Matsuura and   
              Hiroyuki Sato and   
            Hirohiko Houjou and   
                Shino Saito and   
           Tomohiko Hayashi and   
                 Minoru Sakurai   Accurate evaluation of the absorption
                                  maxima of retinal proteins based on a
                                  hybrid QM/MM method  . . . . . . . . . . 1623--1630
          Peter C. Anderson and   
                 Sandro Mecozzi   Minimum sequence requirements for
                                  selective RNA-ligand binding: a
                                  molecular mechanics algorithm using
                                  molecular dynamics and free-energy
                                  techniques . . . . . . . . . . . . . . . 1631--1640
                 Luis F. Pacios   Computational study of the process of
                                  hydrogen bond breaking: the case of the
                                  formamide--formic acid complex . . . . . 1641--1649
             Luis F. Pacios and   
      Pedro C. Gómez and   
            Oscar Gálvez   Variation of atomic charges on proton
                                  transfer in strong hydrogen bonds: the
                                  case of anionic and neutral
                                  imidazole--acetate complexes . . . . . . 1650--1661
           Russell A. Brown and   
                  David A. Case   Second derivatives in generalized Born
                                  theory . . . . . . . . . . . . . . . . . 1662--1675
             N. N. Medvedev and   
             V. P. Voloshin and   
            V. A. Luchnikov and   
                M. L. Gavrilova   An algorithm for three-dimensional
                                  Voronoi S-network  . . . . . . . . . . . 1676--1692
            Oliver F. Lange and   
       Lars V. Schäfer and   
         Helmut Grubmüller   Flooding in GROMACS: Accelerated barrier
                                  crossings in molecular dynamics  . . . . 1693--1702
             S. Knippenberg and   
      J.-P. François and   
                  M. S. Deleuze   Green's function study of the
                                  one-electron and shake-up ionization
                                  spectra of unsaturated hydrocarbon cage
                                  compounds  . . . . . . . . . . . . . . . 1703--1722
    Pathumwadee Intharathep and   
              Anan Tongraar and   
               Kritsana Sagarik   Ab initio QM/MM dynamics of H$_3$O$^+$
                                  in water . . . . . . . . . . . . . . . . 1723--1732
            Pablo Echenique and   
          Iván Calvo and   
                   J. L. Alonso   Quantum mechanical calculation of the
                                  effects of stiff and rigid constraints
                                  in the conformational equilibrium of the
                                  alanine dipeptide  . . . . . . . . . . . 1733--1747
            Pablo Echenique and   
              Iván Calvo   Explicit factorization of external
                                  coordinates in constrained statistical
                                  mechanics models . . . . . . . . . . . . 1748--1755
                  Jian Wang and   
               Yi-Hong Ding and   
                 Chia-Chung Sun   Theoretical mechanistic study on the
                                  radical--molecule reactions of
                                  cyanomethylidyne with PH$_3$, H$_2$S,
                                  and HCl  . . . . . . . . . . . . . . . . 1756--1764
             Nicholas M. Glykos   Software news and updates carma: a
                                  molecular dynamics analysis program  . . 1765--1768

Journal of Computational Chemistry
Volume 27, Number 15, November 30, 2006

           Carles Curutchet and   
             Modesto Orozco and   
            F. Javier Luque and   
         Benedetta Mennucci and   
                  Jacopo Tomasi   Dispersion and repulsion contributions
                                  to the solvation free energy: Comparison
                                  of quantum mechanical and classical
                                  approaches in the polarizable continuum
                                  model  . . . . . . . . . . . . . . . . . 1769--1780
    Leticia González and   
                 Chantal Daniel   Photochemistry of CH$_3$Mn(CO)$_5$: a
                                  multiconfigurational ab initio study . . 1781--1786
                  Stefan Grimme   Semiempirical GGA-type density
                                  functional constructed with a long-range
                                  dispersion correction  . . . . . . . . . 1787--1799
               Laurence Leherte   Similarity measures based on
                                  Gaussian-type promolecular electron
                                  density models: Alignment of small rigid
                                  molecules  . . . . . . . . . . . . . . . 1800--1816
                 Jian Zhang and   
               Mingyu Zhang and   
              Yuanyuan Zhao and   
                Baoguo Chen and   
                 Chia-Chung Sun   Ab initio studies on isomers of
                                  macropolyhedral borane ions
                                  [B$_{20}$H$_{18}$]$^n$ ($n = 0$, $-2$,
                                  $-4$)  . . . . . . . . . . . . . . . . . 1817--1821
    Rogério Custodio and   
André Severo Pereira Gomes and   
Fabrício Ronil Sensato and   
Júlio Murilo dos Santos Trevas   Analysis of the segmented contraction of
                                  basis functions using density matrix
                                  theory . . . . . . . . . . . . . . . . . 1822--1829
                     Qi Dai and   
              Xiao-Qing Liu and   
                 Tian-Ming Wang   Numerical characterization of DNA
                                  sequences based on the $k$-step Markov
                                  chain transition probability . . . . . . 1830--1842
              Vincent Zoete and   
                  Markus Meuwly   Importance of individual side chains for
                                  the stability of a protein fold:
                                  Computational alanine scanning of the
                                  insulin monomer  . . . . . . . . . . . . 1843--1857
                 Si-Dian Li and   
            Chang-Qing Miao and   
              Jin-Chang Guo and   
                 Guang-Ming Ren   Transition metal--boron complexes
                                  B$_n$M: From bowls ($n = 8$--$14$) to
                                  tires ($n = 14$) . . . . . . . . . . . . 1858--1865
            Sheng-You Huang and   
                    Xiaoqin Zou   An iterative knowledge-based scoring
                                  function to predict protein--ligand
                                  interactions: I. Derivation of
                                  interaction potentials . . . . . . . . . 1866--1875
            Sheng-You Huang and   
                    Xiaoqin Zou   An iterative knowledge-based scoring
                                  function to predict protein--ligand
                                  interactions: II. Validation of the
                                  scoring function . . . . . . . . . . . . 1876--1882
        Padeleimon Karafiloglou   Control of delocalization and structural
                                  changes by means of an electric field    1883--1891
          Hugo R. R. Santos and   
             Gregori Ujaque and   
             Maria J. Ramos and   
     José A. N. F. Gomes   QM/QM study of the coverage effects on
                                  the adsorption of amino-cyclopentene at
                                  the Si(100) surface  . . . . . . . . . . 1892--1897

Journal of Computational Chemistry
Volume 27, Number 16, December, 2006

               Sathesh Bhat and   
               Traian Sulea and   
             Enrico O. Purisima   Coupled atomic charge selectivity for
                                  optimal ligand-charge distributions at
                                  protein binding sites  . . . . . . . . . 1899--1907
                     Yu Sun and   
               Robert A. Latour   Comparison of implicit solvent models
                                  for the simulation of protein--surface
                                  interactions . . . . . . . . . . . . . . 1908--1922
          Mark S. Formaneck and   
                      Qiang Cui   The use of a generalized Born model for
                                  the analysis of protein conformational
                                  transitions: a comparative study with
                                  explicit solvent simulations for
                                  chemotaxis Y protein (CheY)  . . . . . . 1923--1943
          Hannes H. Loffler and   
          Ahmed M. Mohammed and   
             Yasuhiro Inada and   
            Shigenobu Funahashi   Water exchange dynamics of
                                  manganese(II), cobalt(II), and
                                  nickel(II) ions in aqueous solution  . . 1944--1949
        Benjamin F. Gherman and   
          William B. Tolman and   
          Christopher J. Cramer   Characterization of the structure and
                                  reactivity of monocopper--oxygen
                                  complexes supported by
                                  $\beta$-diketiminate and anilido-imine
                                  ligands  . . . . . . . . . . . . . . . . 1950--1961
            Sergei Izrailev and   
              Fangqiang Zhu and   
         Dimitris K. Agrafiotis   A distance geometry heuristic for
                                  expanding the range of geometries
                                  sampled during conformational search . . 1962--1969
      Roberto L. A. Haiduke and   
 Albérico B. F. Da Silva   Accurate relativistic adapted Gaussian
                                  basis sets for cesium through radon
                                  without variational prolapse and to be
                                  used with both uniform sphere and
                                  Gaussian nucleus models  . . . . . . . . 1970--1979
    I. García Cuesta and   
A. Sánchez de Merás and   
                  P. Lazzeretti   Diatropicity of tetraazanaphthalenes . . 1980--1989
        Christopher S. Page and   
                  Paul A. Bates   Can MM-PBSA calculations predict the
                                  specificities of protein kinase
                                  inhibitors?  . . . . . . . . . . . . . . 1990--2007


Journal of Computational Chemistry
Volume 28, Number 1, January 15, 2007

            Gernot Frenking and   
                    Sason Shaik   Foreword . . . . . . . . . . . . . . . . 1--3
             R. F. W. Bader and   
J. Hernández-Trujillo and   
 F. Cortés-Guzmán   Essay: Chemical bonding: from Lewis to
                                  atoms in molecules . . . . . . . . . . . 4--14
            Gernot Frenking and   
                  Andreas Krapp   Essay: Unicorns in the world of chemical
                                  bonding models . . . . . . . . . . . . . 15--24
              Werner Kutzelnigg   Essay: What I like about Hückel theory    25--34
          Jean-Paul Malrieu and   
    Nathalie Guihéry and   
Carmen Jiménez Calzado and   
               Celestino Angeli   Essay: Bond electron pair: Its relevance
                                  and analysis from the quantum chemistry
                                  point of view  . . . . . . . . . . . . . 35--50
                    Sason Shaik   Essay: The Lewis legacy: the chemical
                                  bond --- a territory and heartland of
                                  chemistry  . . . . . . . . . . . . . . . 51--61
              Ana Simões   Essay: In between worlds: G. N. Lewis,
                                  the shared pair bond and its
                                  multifarious contexts  . . . . . . . . . 62--72
              Donald G. Truhlar   Essay: Valence bond theory for chemical
                                  dynamics . . . . . . . . . . . . . . . . 73--86
            R. J. Gillespie and   
                 E. A. Robinson   Essay: Gilbert N. Lewis and the chemical
                                  bond: the electron pair and the octet
                                  rule from 1916 to the present day  . . . 87--97
                    Mary Jo Nye   Essay: Working tools for theoretical
                                  chemistry: Polanyi, Eyring, and debates
                                  over the ``semiempirical method''  . . . 98--108
               Robert Ponec and   
                 Joaquin Chaves   Electron pairing and chemical bonds:
                                  Pair localization in ELF domains from
                                  the analysis of domain averaged Fermi
                                  holes  . . . . . . . . . . . . . . . . . 109--116
            Gernot Frenking and   
          Christoph Loschen and   
              Andreas Krapp and   
                 Stefan Fau and   
              Steven H. Strauss   Electronic structure of CO --- an
                                  exercise in modern chemical bonding
                                  theory . . . . . . . . . . . . . . . . . 117--126
             Marcos Mandado and   
María J. González-Moa and   
            Ricardo A. Mosquera   QTAIM $n$-center delocalization indices
                                  as descriptors of aromaticity in mono
                                  and poly heterocycles  . . . . . . . . . 127--136
        Philippe C. Hiberty and   
                    Sason Shaik   A survey of recent developments in ab
                                  initio valence bond theory . . . . . . . 137--151
           Patrick Bultinck and   
               Robert Ponec and   
       Ramon Carbó-Dorca   Aromaticity in linear polyacenes:
                                  Generalized population analysis and
                                  molecular quantum similarity approach    152--160
A. Martín Pendás and   
               M. A. Blanco and   
                   E. Francisco   Chemical fragments in real space:
                                  Definitions, properties, and energetic
                                  decompositions . . . . . . . . . . . . . 161--184
                 Peifeng Su and   
              Lingchun Song and   
                     Wei Wu and   
        Philippe C. Hiberty and   
                    Sason Shaik   A valence bond study of the dioxygen
                                  molecule . . . . . . . . . . . . . . . . 185--197
               C. R. Landis and   
                    F. Weinhold   Valence and extra-valence orbitals in
                                  main group and transition metal bonding  198--203
                       I. Mayer   Bond order and valence indices: a
                                  personal account . . . . . . . . . . . . 204--221
          Dmitri G. Fedorov and   
                  Kazuo Kitaura   Pair interaction energy decomposition
                                  analysis . . . . . . . . . . . . . . . . 222--237
          F. M. Bickelhaupt and   
                  M. Sol\`a and   
              C. Fonseca Guerra   Covalent versus ionic bonding in
                                  alkalimetal fluoride oligomers . . . . . 238--250
         Dmitry Yu. Zubarev and   
          Alexander I. Boldyrev   Comprehensive analysis of chemical
                                  bonding in boron clusters  . . . . . . . 251--268
             Lionel Goodman and   
               Ronald R. Sauers   Diffuse functions in natural bond
                                  orbital analysis . . . . . . . . . . . . 269--275
     Lyudmila V. Slipchenko and   
                 Mark S. Gordon   Electrostatic energy in the effective
                                  fragment potential method: Theory and
                                  application to benzene dimer . . . . . . 276--291
                   M. Rafat and   
              P. L. A. Popelier   Atom--atom partitioning of total
                                  (super)molecular energy: the hidden
                                  terms of classical force fields  . . . . 292--301
               Thomas Heine and   
               Rafael Islas and   
                 Gabriel Merino   $\sigma$ and $\pi$ contributions to the
                                  induced magnetic field: Indicators for
                                  the mobility of electrons in molecules   302--309
        Dandamudi Usha Rani and   
     Dasari L. V. K. Prasad and   
              John F. Nixon and   
         Eluvathingal D. Jemmis   Electronic structure and bonding studies
                                  on triple-decker sandwich complexes with
                                  a P$_6$ middle ring  . . . . . . . . . . 310--319
                   Martin Kaupp   The role of radial nodes of atomic
                                  orbitals for chemical bonding and the
                                  periodic table . . . . . . . . . . . . . 320--325
Iñigo García-Yoldi and   
              Fernando Mota and   
                  Juan J. Novoa   The origin of the
                                  two-electron/four-centers C\bondC bond
                                  in $\pi$-TCNE$_2^{2-}$ dimers:
                                  Electrostatic or dispersion? . . . . . . 326--334
                 B. Sateesh and   
          A. Srinivas Reddy and   
             G. Narahari Sastry   Towards design of the smallest planar
                                  tetracoordinate carbon and boron systems 335--343
       Chaitanya S. Wannere and   
                 Ankan Paul and   
              Rainer Herges and   
                 K. N. Houk and   
      Henry F. Schaefer III and   
 Paul von Ragué Schleyer   The existence of secondary orbital
                                  interactions . . . . . . . . . . . . . . 344--361
             Gabriel Merino and   
Miguel A. Méndez-Rojas and   
               Alberto Vela and   
                   Thomas Heine   Recent advances in planar
                                  tetracoordinate carbon chemistry . . . . 362--372
           Igor V. Alabugin and   
            Mariappan Manoharan   Rehybridization as a general mechanism
                                  for maximizing chemical and
                                  supramolecular bonding and a driving
                                  force for chemical reactions . . . . . . 373--390
           Klaus Ruedenberg and   
             Michael W. Schmidt   Why does electron sharing lead to
                                  covalent bonding? A variational analysis 391--410
                  T. Bitter and   
              K. Ruedenberg and   
               W. H. E. Schwarz   Toward a physical understanding of
                                  electron-sharing two-center bonds. I.
                                  General aspects  . . . . . . . . . . . . 411--422
        Dmitry V. Khoroshun and   
      Djamaladdin G. Musaev and   
                 Keiji Morokuma   Electronic reorganization: Origin of
                                  sigma trans promotion effect . . . . . . 423--441
            Anthony Scemama and   
            Michel Caffarel and   
                  Andreas Savin   Maximum probability domains from Quantum
                                  Monte Carlo calculations . . . . . . . . 442--454
        John Frederick Beck and   
                      Yirong Mo   How resonance assists hydrogen bonding
                                  interactions: an energy decomposition
                                  analysis . . . . . . . . . . . . . . . . 455--466

Journal of Computational Chemistry
Volume 28, Number 2, January 30, 2007

               Zi-Zhang Wei and   
                 Bu-Tong Li and   
            Hong-Xing Zhang and   
             Chia-Chung Sun and   
                      Ke-Li Han   A theoretical investigation of the
                                  excited states of OCLO radical, cation,
                                  and anion using the CASSCF/CASPT2 method 467--477
             Ross C. Walker and   
              Ian P. Mercer and   
               Ian R. Gould and   
                  David R. Klug   Comparison of basis set effects and the
                                  performance of ab initio and DFT methods
                                  for probing equilibrium fluctuations . . 478--490
              M. Rami Reddy and   
                U. C. Singh and   
                  Mark D. Erion   Ab initio quantum mechanics-based free
                                  energy perturbation method for
                                  calculating relative solvation free
                                  energies . . . . . . . . . . . . . . . . 491--494
              Evelyn Mayaan and   
                 Adam Moser and   
 Alexander D. MacKerell Jr. and   
                 Darrin M. York   CHARMM force field parameters for
                                  simulation of reactive intermediates in
                                  native and thio-substituted ribozymes    495--507
                    Chun Li and   
                Ai-hua Wang and   
                      Lili Xing   Similarity of RNA secondary structures   508--512
            Sheng-Yong Yang and   
              Ming-Li Xiang and   
               Li-Juan Chen and   
                Guo-Bin Xie and   
                   Bing Shi and   
                Yu-Quan Wei and   
                    Tom Ziegler   Free energy profiles for monomer capture
                                  in Grubbs- and SHOP-type olefin
                                  polymerization catalysts: a constraint
                                  ab initio molecular dynamics study . . . 513--518
                 Wei-Qi Lin and   
             Jian-Hui Jiang and   
              Yan-Ping Zhou and   
                Hai-Long Wu and   
                Guo-Li Shen and   
                      Ru-Qin Yu   Support vector machine based training of
                                  multilayer feedforward neural networks
                                  as optimized by particle swarm
                                  algorithm: Application in QSAR studies
                                  of bioactivity of organic compounds  . . 519--527
           S. A. De Marothy and   
          M. R. A. Blomberg and   
              P. E. M. Siegbahn   Elucidating the mechanism for the
                                  reduction of nitrite by copper nitrite
                                  reductase --- a contribution from
                                  quantum chemical studies . . . . . . . . 528--539
Jose M. Hermida-Ramón and   
            Ana M. Graña   Blue-shifting hydrogen bond in the
                                  benzene--benzene and
                                  benzene--naphthalene complexes . . . . . 540--546
                 Kalju Kahn and   
          Alex A. Granovsky and   
                     Jozef Noga   Convergence of third order correlation
                                  energy in atoms and molecules  . . . . . 547--554
             Petr Jure\vcka and   
Ji\vrí \vCerný and   
                Pavel Hobza and   
              Dennis R. Salahub   Density functional theory augmented with
                                  an empirical dispersion term.
                                  Interaction energies and geometries of
                                  80 noncovalent complexes compared with
                                  ab initio quantum mechanics calculations 555--569
                   Pedro Gonnet   A simple algorithm to accelerate the
                                  computation of non-bonded interactions
                                  in cell-based molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 570--573
    Miquel Torrent-Sucarrat and   
             Pedro Salvador and   
             Paul Geerlings and   
                  Miquel Sol\`a   On the quality of the hardness kernel
                                  and the Fukui function to evaluate the
                                  global hardness  . . . . . . . . . . . . 574--583
                   R. Conte and   
            G. P. Arrighini and   
                    C. Guidotti   Direct evaluation via forced oscillation
                                  method of the electronic state density
                                  of sizable clusters  . . . . . . . . . . 584--593
                 Hong Seok Kang   A theoretical study of
                                  fullerene--ferrocene hybrids . . . . . . 594--600
        Svetlana Stepanenko and   
                   Bernd Engels   Gradient tabu search . . . . . . . . . . 601--611
             Hung-Ming Chen and   
                  Bo-Fu Liu and   
             Hui-Ling Huang and   
            Shiow-Fen Hwang and   
                  Shinn-Ying Ho   SODOCK: Swarm optimization for highly
                                  flexible protein--ligand docking . . . . 612--623

Journal of Computational Chemistry
Volume 28, Number 3, February, 2007

               Chang K. Kim and   
                Dong J. Kim and   
                   Y. Hsieh and   
                 Hai W. Lee and   
                 Bon-Su Lee and   
                    Chan K. Kim   Effects of entropy on the gas-phase
                                  pyrolysis of ethyl N,
                                  $N$-dimethylcarbamate  . . . . . . . . . 625--631
           Beno\^\it Bories and   
              Daniel Maynau and   
             Marie-Laure Bonnet   Selected excitation for CAS-SDCI
                                  calculations . . . . . . . . . . . . . . 632--643
           Irina S. Moreira and   
         Pedro A. Fernandes and   
                 Maria J. Ramos   Computational alanine scanning
                                  mutagenesis --- an improved
                                  methodological approach  . . . . . . . . 644--654
            Vladimir Hnizdo and   
                 Eva Darian and   
            Adam Fedorowicz and   
             Eugene Demchuk and   
               Shengqiao Li and   
               Harshinder Singh   Nearest-neighbor nonparametric method
                                  for estimating the configurational
                                  entropy of complex molecules . . . . . . 655--668
                Jinhyuk Lee and   
                      Wonpil Im   Implementation and application of
                                  helix--helix distance and crossing angle
                                  restraint potentials . . . . . . . . . . 669--680
                 Tomasz Panczyk   Collisions of ideal gas molecules with a
                                  rough/fractal surface. A computational
                                  study  . . . . . . . . . . . . . . . . . 681--688
                  Zhitao Xu and   
               Harry H. Luo and   
              D. Peter Tieleman   Modifying the OPLS-AA force field to
                                  improve hydration free energies for
                                  several amino acid side chains using new
                                  atomic charges and an off-plane charge
                                  model for aromatic residues  . . . . . . 689--697
              Dimitri N. Laikov   Neglect of four- and approximation of
                                  one-, two-, and three-center
                                  two-electron integrals in a
                                  symmetrically orthogonalized basis . . . 698--702
                   Z. J. Wu and   
                 M. Y. Wang and   
                       Z. M. Su   Electronic structures and chemical
                                  bonding in diatomic ScX to ZnX (X = S,
                                  Se, Te)  . . . . . . . . . . . . . . . . 703--714
     Ruben G. Ghulghazaryan and   
              Shura Hayryan and   
                    Chin-Kun Hu   Efficient combination of Wang--Landau
                                  and transition matrix Monte Carlo
                                  methods for protein simulations  . . . . 715--726

Journal of Computational Chemistry
Volume 28, Number 4, March, 2007

             Yoong-Kee Choe and   
             Shigeru Nagase and   
            Kichisuke Nishimoto   Theoretical study of the electronic
                                  spectra of oxidized and reduced states
                                  of lumiflavin and its derivative . . . . 727--739
         Terutaka Yoshizawa and   
                  Masahiko Hada   Calculations of frequency-dependent
                                  molecular magnetizabilities with
                                  quasi-relativistic time-dependent
                                  generalized unrestricted Hartree--Fock
                                  method . . . . . . . . . . . . . . . . . 740--747
   J. Fernández Rico and   
            R. López and   
                     I. Ema and   
              G. Ramírez   Generation of basis sets with high
                                  degree of fulfillment of the
                                  Hellmann--Feynman theorem  . . . . . . . 748--758
              Bryan M. Wong and   
                  Sumathy Raman   Thermodynamic calculations for molecules
                                  with asymmetric internal rotors ---
                                  application to 1,3-butadiene . . . . . . 759--766
                Ernesto Estrada   Point scattering: a new geometric
                                  invariant with applications from
                                  (Nano)clusters to biomolecules . . . . . 767--777
      Vladimir I. Bolshakov and   
      Vladimir V. Rossikhin and   
         Eugene O. Voronkov and   
         Sergiy I. Okovytyy and   
              Jerzy Leszczynski   The performance of the new
                                  6-31G$^{\#\#}$ basis set: Molecular
                                  structures and vibrational frequencies
                                  of transition metal carbonyls  . . . . . 778--782
               Hsiu-Feng Lu and   
                Feng-Yin Li and   
                      S. H. Lin   Site specificity of $\alpha$-H
                                  abstraction reaction among secondary
                                  structure motif --- an ab initio study   783--794
                 Xingfa Gao and   
                   Yuliang Zhao   The way of stabilizing non-IPR
                                  fullerenes and structural elucidation of
                                  C$_{54}$Cl$_8$ . . . . . . . . . . . . . 795--801
                  Ying Wang and   
               Jing-Yao Liu and   
                Ze-Sheng Li and   
                    Li Wang and   
                 Chia-Chung Sun   Theoretical study and rate constant
                                  calculation for reaction of
                                  CF$_3$CH$_2$OH with OH . . . . . . . . . 802--810
               M. L. Ellzey Jr.   Finite group theory for large systems.
                                  3. Symmetry-generation of reduced matrix
                                  elements for icosahedral C$_{20}$ and
                                  C$_{60}$ molecules . . . . . . . . . . . 811--817
              Jeb Kegerreis and   
                    Nancy Makri   Optimized Monte Carlo sampling in
                                  forward--backward semiclassical dynamics 818--824
      Dorota Rutkowska-Zbik and   
          Ma\lgorzata Witko and   
                Grazyna Stochel   Theoretical density functional theory
                                  studies on interactions of small
                                  biologically active molecules with
                                  isolated heme group  . . . . . . . . . . 825--831
               Michel Rafat and   
            Paul L. A. Popelier   Long range behavior of high-rank
                                  topological multipole moments  . . . . . 832--838

Journal of Computational Chemistry
Volume 28, Number 5, April 15, 2007

     Robert A. Distasio Jr. and   
             Ryan P. Steele and   
             Young Min Rhee and   
                 Yihan Shao and   
             Martin Head-Gordon   An improved algorithm for analytical
                                  gradient evaluation in
                                  resolution-of-the-identity second-order
                                  Mòller--Plesset perturbation theory:
                                  Application to alanine tetrapeptide
                                  conformational analysis  . . . . . . . . 839--856
                Victor Polo and   
                Juan Andres and   
                  Bernard Silvi   New insights on the bridge
                                  carbon--carbon bond in propellanes: a
                                  theoretical study based on the analysis
                                  of the electron localization function    857--864
                  Jian Wang and   
               Yi-Hong Ding and   
             Shao-Wen Zhang and   
                 Chia-Chung Sun   Theoretical study on the methyl radical
                                  with chlorinated methyl radicals CH$_{3
                                  - n}$Cl$_n$ ($n = 1$, $2$, $3$) and
                                  CCl$_2$  . . . . . . . . . . . . . . . . 865--876
          Martin R. Siegert and   
           Matthias Heuchel and   
                 Dieter Hofmann   A generalized direct-particle-deletion
                                  scheme for the calculation of chemical
                                  potential and solubilities of small- and
                                  medium-sized molecules in amorphous
                                  polymers . . . . . . . . . . . . . . . . 877--889
             Frits Daeyaert and   
              Marc De Jonge and   
                Luc Koymans and   
                Maarten Vinkers   An ant algorithm for the conformational
                                  analysis of flexible molecules . . . . . 890--898
            Edward Sanville and   
            Steven D. Kenny and   
                Roger Smith and   
               Graeme Henkelman   Improved grid-based algorithm for Bader
                                  charge allocation  . . . . . . . . . . . 899--908
    Alexander H. Boschitsch and   
               Marcia O. Fenley   A new outer boundary formulation and
                                  energy corrections for the nonlinear
                                  Poisson--Boltzmann equation  . . . . . . 909--921
             Hassan Sabzyan and   
             Davood Farmanzadeh   Electric field effects on the
                                  performance of a candidate multipole
                                  molecular switch: a quantum
                                  computational study  . . . . . . . . . . 922--931
        Ravichandra Mutyala and   
                R. N. Reddy and   
               M. Sumakanth and   
                P. Reddanna and   
                  M. Rami Reddy   Calculation of relative binding
                                  affinities of fructose
                                  1,6-bisphosphatase mutants with
                                  adenosine monophosphate using free
                                  energy perturbation method . . . . . . . 932--937
                Celine Roux and   
                Nohad Gresh and   
           Lalith E. Perera and   
       Jean-Philip Piquemal and   
                 Laurent Salmon   Binding of 5-phospho-
                                  D-arabinonohydroxamate and 5-phospho-
                                  D-arabinonate inhibitors to zinc
                                  phosphomannose isomerase from Candida
                                  albicans studied by polarizable
                                  molecular mechanics and quantum
                                  mechanics  . . . . . . . . . . . . . . . 938--957
                V. R. Ferro and   
            R. López and   
                    S. Omar and   
 J. M. García De La Vega   On the molecular electron structure of
                                  three phosphinine-containing macrocycles 958--966
                  W. J. Fan and   
                R. Q. Zhang and   
                     Shubin Liu   Computation of large systems with an
                                  economic basis set: Structures and
                                  reactivity indices of nucleic acid base
                                  pairs from density functional theory . . 967--974
                Yue-meng Ji and   
              Xiao-lei Zhao and   
                Ze-sheng Li and   
                   Jing-yao Liu   Kinetic mechanism of the hydrogen
                                  abstraction reactions of the chlorine
                                  atoms with CH$_3$CF$_2$Cl and
                                  CH$_3$CFCl$_2$: a dual level direct
                                  dynamics study . . . . . . . . . . . . . 975--983
                 Toru Inaba and   
                 Fumitoshi Sato   Development of parallel density
                                  functional program using distributed
                                  matrix to calculate all-electron
                                  canonical wavefunction of large
                                  molecules  . . . . . . . . . . . . . . . 984--995

Journal of Computational Chemistry
Volume 28, Number 6, April 30, 2007

              Ismael Tejero and   
\`Angels González-Lafont and   
           José M. Lluch   A PM3/d specific reaction
                                  parameterization for iron atom in the
                                  hydrogen abstraction catalyzed by
                                  soybean lipoxygenase-1 . . . . . . . . . 997--1005
       Viwat Vchirawongkwin and   
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Tl(I)-the strongest structure-breaking
                                  metal ion in water? A quantum
                                  mechanical/molecular mechanical
                                  simulation study . . . . . . . . . . . . 1006--1016
       Arnau Cordomí and   
                Olle Edholm and   
                  Juan J. Perez   Effect of different treatments of
                                  long-range interactions and sampling
                                  conditions in molecular dynamic
                                  simulations of rhodopsin embedded in a
                                  dipalmitoyl phosphatidylcholine bilayer  1017--1030
             Anna Marabotti and   
           Giovanni Colonna and   
               Angelo Facchiano   New computational strategy to analyze
                                  the interactions of ER$\alpha$ and
                                  ER$\beta$ with different ERE sequences   1031--1041
Humberto González-díaz and   
     Liane Saíz-urra and   
            Reinaldo Molina and   
Yenny González-díaz and   
Angeles Sánchez-gonzález   Computational chemistry approach to
                                  protein kinase recognition using $3$D
                                  stochastic van der Waals spectral
                                  moments  . . . . . . . . . . . . . . . . 1042--1048
Humberto González-díaz and   
Guillermín Agüero-chapin and   
              Javier Varona and   
            Reinaldo Molina and   
            Giovanna Delogu and   
            Lourdes Santana and   
            Eugenio Uriarte and   
                   Gianni Podda   $2$D-RNA-coupling numbers: a new
                                  computational chemistry approach to link
                                  secondary structure topology with
                                  biological function  . . . . . . . . . . 1049--1056
       Viwat Vchirawongkwin and   
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Quantum mechanical/molecular mechanical
                                  simulations of the Tl(III) ion in water  1057--1067
             Anna Jagielska and   
             Harold A. Scheraga   Influence of temperature, friction, and
                                  random forces on folding of the B-domain
                                  of staphylococcal protein A: All-atom
                                  molecular dynamics in implicit solvent   1068--1082
         P. Söderhjelm and   
                J. W. Krogh and   
          G. Karlström and   
                    U. Ryde and   
                       R. Lindh   Accuracy of distributed multipoles and
                                  polarizabilities: Comparison between the
                                  LoProp and MpProp models . . . . . . . . 1083--1090
                Hitomi Yuki and   
           Yoshikazu Tanaka and   
              Masayuki Hata and   
          Hidenori Ishikawa and   
                Saburo Neya and   
                  Tyuji Hoshino   Implementation of $\pi$-$\pi$
                                  interactions in molecular dynamics
                                  simulation . . . . . . . . . . . . . . . 1091--1099
            Kyoung Hoon Kim and   
               Jaehoon Jung and   
               Bo Keun Park and   
              Young-Kyu Han and   
                   Joon T. Park   Cyclic voltammetry modeling, geometries,
                                  and electronic properties for
                                  metallofullerene complexes with
                                  $\mu_3$--$\eta^2$: $\eta^2$:
                                  $\eta^2$-C$_{60}$ bonding mode . . . . . 1100--1106
                Sang-Ho Lee and   
                  Kim Palmo and   
                   Samuel Krimm   A comparative study of molecular
                                  dynamics in Cartesian and in internal
                                  coordinates: Dynamical instability in
                                  the latter caused by nonlinearity of the
                                  equations of motion  . . . . . . . . . . 1107--1118
                  S. Alcaro and   
              F. Gasparrini and   
                  O. Incani and   
                L. Caglioti and   
                 M. Pierini and   
                     C. Villani   ``Quasi flexible'' automatic docking
                                  processing for studying stereoselective
                                  recognition mechanisms, part 2:
                                  Prediction of $\Delta\Delta$G of
                                  complexation and $^1$H-NMR NOE
                                  correlation  . . . . . . . . . . . . . . 1119--1128
               Minoru Saito and   
                   Isao Okazaki   A 45-ns molecular dynamics simulation of
                                  hemoglobin in water by vectorizing and
                                  parallelizing COSMOS90 on the earth
                                  simulator: Dynamics of tertiary and
                                  quaternary structures  . . . . . . . . . 1129--1136
               Takao Otsuka and   
                   Hiromi Nakai   Wavelet transform analysis of ab initio
                                  molecular dynamics simulation:
                                  Application to core-excitation dynamics
                                  of BF$_3$  . . . . . . . . . . . . . . . 1137--1144
                  Ruth Huey and   
          Garrett M. Morris and   
            Arthur J. Olson and   
              David S. Goodsell   A semiempirical free energy force field
                                  with charge-based desolvation  . . . . . 1145--1152

Journal of Computational Chemistry
Volume 28, Number 7, May, 2007

                  Hui Zhang and   
             Gui-Ling Zhang and   
                    Li Wang and   
                     Bo Liu and   
               Xiao-Yang Yu and   
                    Ze-Sheng Li   Theoretical study on the Br +
                                  CH$_3$SCH$_3$ reaction . . . . . . . . . 1153--1159
 Sérgio Filipe Sousa and   
Pedro Alexandrino Fernandes and   
        Maria João Ramos   Theoretical studies on farnesyl
                                  transferase: Evidence for thioether
                                  product coordination to the active-site
                                  zinc sphere  . . . . . . . . . . . . . . 1160--1168
           Maxim Tafipolsky and   
          Saeed Amirjalayer and   
                  Rochus Schmid   Ab initio parametrized MM3 force field
                                  for the metal-organic framework MOF-5    1169--1176
               Seth T. Call and   
         Dmitry Yu. Zubarev and   
          Alexander I. Boldyrev   Global minimum structure searches via
                                  particle swarm optimization  . . . . . . 1177--1186
            David De Sancho and   
                    Antonio Rey   Evaluation of coarse grained models for
                                  hydrogen bonds in proteins . . . . . . . 1187--1199
         Adelio R. Matamala and   
        Daniel E. Almonacid and   
    Maximiliano F. Figueroa and   
José Martínez-oyanedel and   
               Marta C. Bunster   A semiempirical approach to the
                                  intra-phycocyanin and inter-phycocyanin
                                  fluorescence resonance energy-transfer
                                  pathways in phycobilisomes . . . . . . . 1200--1207
        Nicholas Y. Palermo and   
      József Csontos and   
            Michael C. Owen and   
          Richard F. Murphy and   
            Sándor Lovas   Aromatic-backbone interactions in model
                                  $\alpha$-helical peptides  . . . . . . . 1208--1214
               Alan R. Ford and   
            Tomasz Janowski and   
                    Peter Pulay   Array files for computational chemistry:
                                  MP2 energies . . . . . . . . . . . . . . 1215--1220
                Yan-Li Zhao and   
                    Wei Kan and   
                  Hua Zhong and   
                 Hai-Tao Yu and   
                   Hong-Gang Fu   Combined DFT, QCISD(T), and G2 mechanism
                                  investigation for the reactions of
                                  carbon monophosphide CP with unsaturated
                                  hydrocarbons allene CH$_2$CCH$_2$ and
                                  methylacetylene CH$_3$CCH  . . . . . . . 1221--1233
              Fangqiang Zhu and   
         Dimitris K. Agrafiotis   Self-organizing superimposition
                                  algorithm for conformational sampling    1234--1239
        Evgueni B. Kadossov and   
           Karen J. Gaskell and   
            Marjorie A. Langell   Effect of surrounding point charges on
                                  the density functional calculations of
                                  Ni$_x$O$_x$ clusters ($x = 4$--$12$) . . 1240--1251
     Manuel Urbano Cuadrado and   
           Irene Luque Ruiz and   
Miguel Ángel Gómez-Nieto   QSAR models based on isomorphic and
                                  nonisomorphic data fusion for predicting
                                  the blood brain barrier permeability . . 1252--1260
              Dennis Elking and   
                 Tom Darden and   
                Robert J. Woods   Gaussian induced dipole polarization
                                  model  . . . . . . . . . . . . . . . . . 1261--1274
        Chanin Nantasenamat and   
Chartchalerm Isarankura-Na-Ayudhya and   
              Natta Tansila and   
           Thanakorn Naenna and   
      Virapong Prachayasittikul   Prediction of GFP spectral properties
                                  using artificial neural network  . . . . 1275--1289
             Anthony K. Grafton   Vibalizer: a free, Web-based tool for
                                  rapid, quantitative comparison and
                                  analysis of calculated vibrational modes 1290--1305

Journal of Computational Chemistry
Volume 28, Number 8, June, 2007

               David P. Tew and   
                Wim Klopper and   
                Trygve Helgaker   Electron correlation: the many-body
                                  problem at the heart of chemistry  . . . 1307--1320
                 N. R. Jena and   
                   P. C. Mishra   Formation of 8-nitroguanine and
                                  8-oxoguanine due to reactions of
                                  peroxynitrite with guanine . . . . . . . 1321--1335
          Andrew Leaver-Fay and   
        Glenn L. Butterfoss and   
              Jack Snoeyink and   
                  Brian Kuhlman   Maintaining solvent accessible surface
                                  area under rotamer substitution for
                                  protein design . . . . . . . . . . . . . 1336--1341
               Michael L. Mckee   Modeling the nitrogenase FeMo cofactor
                                  with high-spin Fe$_8$S$_9$X$^+$ (X = N,
                                  C) clusters. Is the first step for N$_2$
                                  reduction to NH$_3$ a concerted
                                  dihydrogen transfer? . . . . . . . . . . 1342--1356
              Chin-Hung Lai and   
                    Pi-Tai Chou   Can an OH radical form a strong hydrogen
                                  bond? A theoretical comparison with
                                  H$_2$O . . . . . . . . . . . . . . . . . 1357--1363
            Anatoly M. Ruvinsky   Role of binding entropy in the
                                  refinement of protein--ligand docking
                                  predictions: Analysis based on the use
                                  of 11 scoring functions  . . . . . . . . 1364--1372
   Veronika Kasalová and   
            Wesley D. Allen and   
      Henry F. Schaefer III and   
              Eszter Czinki and   
Attila G. Császár   Molecular structures of the two most
                                  stable conformers of free glycine  . . . 1373--1383
          Sönke Lorenz and   
           Elmar Diederichs and   
            Regina Telgmann and   
          Christof Schütte   Discrimination of dynamical system
                                  models for biological and chemical
                                  processes  . . . . . . . . . . . . . . . 1384--1399
                  Kilho Eom and   
            Seung-Chul Baek and   
               Jung-Hee Ahn and   
                     Sungsoo Na   Coarse-graining of protein structures
                                  for the normal mode studies  . . . . . . 1400--1410
  Carlos Silva López and   
          Olalla Nieto Faza and   
       José A. Souto and   
      Rosana Álvarez and   
        Ángel R. De Lera   Pseudopericyclic design drives
                                  antara-antara [1,5] methylene
                                  sigmatropic shifts from a stepwise to a
                                  concerted mechanism  . . . . . . . . . . 1411--1416
              Jin Qiang Hou and   
                 Hong Seok Kang   A DFT study on the dimerization of
                                  C$_{62}$, H$_2$C$_{62}$, and
                                  F$_2$C$_{62}$  . . . . . . . . . . . . . 1417--1426
                Xiaoli Yang and   
               Wensheng Cai and   
                  Xueguang Shao   A dynamic lattice searching method with
                                  constructed core for optimization of
                                  large Lennard-Jones clusters . . . . . . 1427--1433
                     Qi Dai and   
              Xiao-Qing Liu and   
             Tian-Ming Wang and   
                Damir Vukicevic   Linear regression model of DNA sequences
                                  and its application  . . . . . . . . . . 1434--1445
                Qian Shu Li and   
                          Yu Xu   A quantum chemistry study: a new kind of
                                  boron nitrides . . . . . . . . . . . . . 1446--1455
               Didier Begue and   
                 Claude Pouchan   Vibrational anharmonic calculations in
                                  solution: Performance of various DFT
                                  approaches . . . . . . . . . . . . . . . 1456--1462

Journal of Computational Chemistry
Volume 28, Number 9, July 15, 2007

                    Hao Lin and   
                  Qian-Zhong Li   Using pseudo amino acid composition to
                                  predict protein structural class:
                                  Approached by incorporating 400
                                  dipeptide components . . . . . . . . . . 1463--1466
                  Wei-Qi Li and   
              Wei-Quan Tian and   
               Ji-Kang Feng and   
               Zi-Zhong Liu and   
                 Ai-Min Ren and   
             Chia-Chung Sun and   
                    Yuriko Aoki   Electronic properties of tricoordinated
                                  phosphorus in hexagonal phosphininium
                                  compounds and molecular aromaticity  . . 1467--1475
          Dmitri G. Fedorov and   
            Kazuya Ishimura and   
            Toyokazu Ishida and   
              Kazuo Kitaura and   
                Peter Pulay and   
                 Shigeru Nagase   Accuracy of the three-body fragment
                                  molecular orbital method applied to
                                  Mòller--Plesset perturbation theory . . . 1476--1484
        H. Lee Woodcock III and   
         Milan Hodo\vs\vcek and   
       Andrew T. B. Gilbert and   
           Peter M. W. Gill and   
      Henry F. Schaefer III and   
              Bernard R. Brooks   Interfacing Q-Chem and CHARMM to perform
                                  QM/MM reaction path calculations . . . . 1485--1502
               Stephan Raub and   
             Christel M. Marian   Quantum chemical investigation of
                                  hydrogen-bond strengths and partition
                                  into donor and acceptor contributions    1503--1515
               Antonio Vila and   
            Ricardo A. Mosquera   Atoms in molecules interpretation of the
                                  anomeric effect in the O\bondC\bondO
                                  unit . . . . . . . . . . . . . . . . . . 1516--1530
             Mark P. Waller and   
              Michael Bühl   Vibrational corrections to geometries of
                                  transition metal complexes from density
                                  functional theory  . . . . . . . . . . . 1531--1537
               Setsuko Nakagawa   Polarizable model potential function for
                                  nucleic acid bases . . . . . . . . . . . 1538--1550
               Marcel Swart and   
              Miquel Sol\`a and   
        F. Matthias Bickelhaupt   Energy landscapes of nucleophilic
                                  substitution reactions: a comparison of
                                  density functional theory and coupled
                                  cluster methods  . . . . . . . . . . . . 1551--1560
            Shinichi Yamabe and   
            Noriko Tsuchida and   
                 Shoko Yamazaki   Theoretical study of the role of solvent
                                  H$_2$O in neopentyl and pinacol
                                  rearrangements . . . . . . . . . . . . . 1561--1571
           Matthew C. Zwier and   
            Justin M. Shorb and   
               Brent P. Krueger   Hybrid molecular dynamics-quantum
                                  mechanics simulations of solute spectral
                                  properties in the condensed phase:
                                  Evaluation of simulation parameters  . . 1572--1581
           Edmond P. F. Lee and   
               John M. Dyke and   
                Wan-Ki Chow and   
               Foo-Tim Chau and   
               Daniel K. W. Mok   DFT and ab initio calculations on two
                                  reactions between hydrogen atoms and the
                                  fire suppressants 2-H heptafluoropropane
                                  and CF$_3$Br . . . . . . . . . . . . . . 1582--1592
              Dominik Gront and   
          Sebastian Kmiecik and   
               Andrzej Kolinski   Backbone building from quadrilaterals: a
                                  fast and accurate algorithm for protein
                                  backbone reconstruction from alpha
                                  carbon coordinates . . . . . . . . . . . 1593--1597
            Olexandr Isayev and   
                Leonid Gorb and   
              Jerzy Leszczynski   Theoretical calculations: Can Gibbs free
                                  energy for intermolecular complexes be
                                  predicted efficiently and accurately?    1598--1609
         T. Daniel Crawford and   
          C. David Sherrill and   
           Edward F. Valeev and   
          Justin T. Fermann and   
             Rollin A. King and   
       Matthew L. Leininger and   
             Shawn T. Brown and   
          Curtis L. Janssen and   
            Edward T. Seidl and   
            Joseph P. Kenny and   
                Wesley D. Allen   PSI3: an open-source Ab Initio
                                  electronic structure package . . . . . . 1610--1616

Journal of Computational Chemistry
Volume 28, Number 10, July 30, 2007

           Petr Dan\ue\vcek and   
                    Petr Bou\vr   Comparison of the numerical stability of
                                  methods for anharmonic calculations of
                                  vibrational molecular energies . . . . . 1617--1624
             Marcos Mandado and   
María J. González-Moa and   
            Ricardo A. Mosquera   Chemical graph theory and $n$-center
                                  electron delocalization indices: a study
                                  on polycyclic aromatic hydrocarbons  . . 1625--1633
José D. Faraldo-Gómez and   
                 Beno\^\it Roux   Characterization of conformational
                                  equilibria through Hamiltonian and
                                  temperature replica-exchange
                                  simulations: Assessing entropic and
                                  environmental effects  . . . . . . . . . 1634--1647
             Anna Jagielska and   
               Jeffrey Skolnick   Origin of intrinsic $3_{10}$-helix
                                  versus strand stability in
                                  homopolypeptides and its implications
                                  for the accuracy of the AMBER force
                                  field  . . . . . . . . . . . . . . . . . 1648--1657
                Yongjian Li and   
                   Jian Wan and   
                         Xin Xu   Theoretical study of the vertical
                                  excited states of benzene, pyrimidine,
                                  and pyrazine by the symmetry adapted
                                  cluster--configuration interaction
                                  method . . . . . . . . . . . . . . . . . 1658--1667
               Dorota Latek and   
          Dariusz Ekonomiuk and   
               Andrzej Kolinski   Protein structure prediction: Combining
                                  de novo modeling with sparse
                                  experimental data  . . . . . . . . . . . 1668--1676
                    Ying Li and   
                      Di Wu and   
                  Zhi-Ru Li and   
                 Chia-Chung Sun   Structural and electronic properties of
                                  boron-doped lithium clusters: ab initio
                                  and DFT studies  . . . . . . . . . . . . 1677--1684
               Yuri Alexeev and   
         Michael W. Schmidt and   
          Theresa L. Windus and   
                 Mark S. Gordon   A parallel distributed data CPHF
                                  algorithm for analytic Hessians  . . . . 1685--1694
                A. V. Larin and   
              W. J. Mortier and   
              D. P. Vercauteren   Quick scheme for evaluation of atomic
                                  charges in arbitrary aluminophosphate
                                  sieves on the basis of electron
                                  densities calculated with DFT methods    1695--1703
            M. Qaiser Fatmi and   
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Quantum mechanical charge field
                                  molecular dynamics simulation of the
                                  TiO$^{2+}$ ion in aqueous solution . . . 1704--1710
         Pedro J. Ballester and   
             W. Graham Richards   Ultrafast shape recognition to search
                                  compound databases for similar molecular
                                  shapes . . . . . . . . . . . . . . . . . 1711--1723
                S. F. Braga and   
            D. S. Galvão   Molecular dynamics simulation of single
                                  wall carbon nanotubes polymerization
                                  under compression  . . . . . . . . . . . 1724--1734
         Rungtiwa Chidthong and   
            Supa Hannongbua and   
        Adelia J. A. Aquino and   
            Peter Wolschann and   
                   Hans Lischka   Excited state properties, fluorescence
                                  energies, and lifetime of a
                                  poly(fluorene-pyridine) copolymer, based
                                  on TD-DFT investigation  . . . . . . . . 1735--1742
         David Curcó and   
           Carlos Alemán   Computational tool to model the packing
                                  of polycyclic chains: Structural
                                  analysis of amorphous polythiophene  . . 1743--1749
               Yuto Komeiji and   
            Toyokazu Ishida and   
          Dmitri G. Fedorov and   
                  Kazuo Kitaura   Change in a protein's electronic
                                  structure induced by an explicit
                                  solvent: an ab initio fragment molecular
                                  orbital study of ubiquitin . . . . . . . 1750--1762
             Hossein Eslami and   
     Florian Müller-Plathe   Molecular dynamics simulation in the
                                  grand canonical ensemble . . . . . . . . 1763--1773

Journal of Computational Chemistry
Volume 28, Number 11, August, 2007

      Charles L. Brooks III and   
            Gernot Frenking and   
              Shigeyoshi Sakaki   Letter from the Editors  . . . . . . . . 1775--1775
                 Remmick So and   
                    Saman Alavi   Vertical excitation energies for ribose
                                  and deoxyribose nucleosides  . . . . . . 1776--1782
        Stanislav Böhm and   
                     Otto Exner   Inductive effects in radicals calculated
                                  from DFT energies; substituted
                                  bicyclo[2.2.2]octan-1-yloxy radicals . . 1783--1789
                  Jiande Gu and   
                  Jing Wang and   
              Jerzy Leszczynski   Iso-guanine quintet complexes
                                  coordinated by mono valent cations
                                  (Na$^+$, K$^+$, Rb$^+$, and Cs$^+$)  . . 1790--1795
               Michael L. Mckee   Modeling hydrogen evolution from the
                                  Fe$_4$S$_4$ and Fe$_8$S$_9$X (X = N, C)
                                  clusters. Can a FeS high-spin cluster
                                  serve as a surrogate for the FeMo
                                  cofactor?  . . . . . . . . . . . . . . . 1796--1808
                Yao-Yuan Chuang   Calculating rate constants with updated
                                  Hessians using variational transition
                                  state theory with multidimensional
                                  tunneling  . . . . . . . . . . . . . . . 1809--1816
                    R. Maul and   
                 F. Ortmann and   
                  M. Preuss and   
               K. Hannewald and   
                   F. Bechstedt   DFT studies using supercells and
                                  projector-augmented waves for structure,
                                  energetics, and dynamics of glycine,
                                  alanine, and cysteine  . . . . . . . . . 1817--1833
                 Wolfgang Quapp   Finding the transition state without
                                  initial guess: the growing string method
                                  for Newton trajectory to isomerization
                                  and enantiomerization reaction of
                                  alanine dipeptide and poly(15)alanine    1834--1847
                 Tian Zhang and   
              Haoping Zheng and   
                        Shu Yan   Equivalent potential of water molecules
                                  for electronic structure of glutamic
                                  acid . . . . . . . . . . . . . . . . . . 1848--1857
Thenmalarchelvi Rathinavelan and   
                      Wonpil Im   Explicit treatment of force contribution
                                  from alignment tensor using
                                  overdetermined linear equations and its
                                  application in NMR structure
                                  determination  . . . . . . . . . . . . . 1858--1864
             V. A. Levashov and   
          S. J. L. Billinge and   
                   M. F. Thorpe   Quantum correction to the pair
                                  distribution function  . . . . . . . . . 1865--1882
                     Yu Sun and   
            Brian N. Dominy and   
               Robert A. Latour   Comparison of solvation-effect methods
                                  for the simulation of peptide
                                  interactions with a hydrophobic surface  1883--1892
     Constantinos A. Tsipis and   
        Ioannis G. Depastas and   
          Christos E. Kefalidis   Growth format, electronic architecture,
                                  magnetic, and optical properties of
                                  aromatic cyclo-Cu$_3$Au$_3$ homotops . . 1893--1908
     Maykel Cruz-Monteagudo and   
Humberto González-Díaz and   
Guillermín Agüero-Chapín and   
            Lourdes Santana and   
            Fernanda Borges and   
Elena Rosa Domínguez and   
               Gianni Podda and   
                Eugenio Uriarte   Computational chemistry development of a
                                  unified free energy Markov model for the
                                  distribution of 1300 chemicals to 38
                                  different environmental or biological
                                  systems  . . . . . . . . . . . . . . . . 1909--1923
            Sofie Van Damme and   
               Patrick Bultinck   A new computer program for
                                  QSAR-analysis: ARTE-QSAR . . . . . . . . 1924--1928

Journal of Computational Chemistry
Volume 28, Number 12, September, 2007

         David Curcó and   
           Carlos Alemán   Coarse-graining: a procedure to generate
                                  equilibrated and relaxed models of
                                  amorphous polymers . . . . . . . . . . . 1929--1935
               Imre Berente and   
              Eszter Czinki and   
Gábor Náray-szabó   A combined electronegativity
                                  equalization and electrostatic potential
                                  fit method for the determination of
                                  atomic point charges . . . . . . . . . . 1936--1942
              Gaurav Porwal and   
               Swapnil Jain and   
             S. Dhilly Babu and   
               Deepak Singh and   
            Hemant Nanavati and   
                Santosh Noronha   Protein structure prediction aided by
                                  geometrical and probabilistic
                                  constraints  . . . . . . . . . . . . . . 1943--1952
               Yousung Jung and   
                 Yihan Shao and   
             Martin Head-Gordon   Fast evaluation of scaled opposite spin
                                  second-order Mòller--Plesset correlation
                                  energies using auxiliary basis
                                  expansions and exploiting sparsity . . . 1953--1964
               Ian R. Gould and   
     Hoda Abdel-Aal Bettley and   
               Richard A. Bryce   Correlated ab initio quantum chemical
                                  calculations of di- and trisaccharide
                                  conformations  . . . . . . . . . . . . . 1965--1973
             Georgy Rychkov and   
               Michael Petukhov   Joint neighbors approximation of
                                  macromolecular solvent accessible
                                  surface area . . . . . . . . . . . . . . 1974--1989
Humberto González-Díaz and   
Yunierkis Pérez-Castillo and   
               Gianni Podda and   
                Eugenio Uriarte   Computational chemistry comparison of
                                  stable/nonstable protein mutants
                                  classification models based on $3$D and
                                  topological indices  . . . . . . . . . . 1990--1995
             Andrew J. Moad and   
            Charles W. Moad and   
              John M. Perry and   
          Ronald D. Wampler and   
            G. Scott Goeken and   
            Nathan J. Begue and   
                  Tian Shen and   
              Randy Heiland and   
               Garth J. Simpson   NLOPredict: Visualization and data
                                  analysis software for nonlinear optics   1996--2002
               Tomoko Akama and   
           Masato Kobayashi and   
                   Hiromi Nakai   Implementation of divide-and-conquer
                                  method including Hartree--Fock exchange
                                  interaction  . . . . . . . . . . . . . . 2003--2012
                Vinzenz Bachler   Orthogonal natural atomic orbitals form
                                  an appropriate one-electron basis for
                                  expanding CASSCF wave functions into
                                  localized bonding schemes and their
                                  weights  . . . . . . . . . . . . . . . . 2013--2019
          Alexei M. Nikitin and   
        Alexander P. Lyubartsev   New six-site acetonitrile model for
                                  simulations of liquid acetonitrile and
                                  its aqueous mixtures . . . . . . . . . . 2020--2026
                    T. Zeng and   
                Z. Jamshidi and   
                    H. Mori and   
                 E. Miyoshi and   
                 M. Klobukowski   Electron affinities of heavier
                                  phosphoryl and thiophosphoryl halides
                                  APX$_3$ (A = O, S and X = Br, I) . . . . 2027--2033
            Kazuya Ishimura and   
                Peter Pulay and   
                 Shigeru Nagase   New parallel algorithm for MP2 energy
                                  gradient calculations  . . . . . . . . . 2034--2042
                  Qi-Shi Du and   
                Ri-Bo Huang and   
                 Yu-Tuo Wei and   
             Cheng-Hua Wang and   
                  Kuo-Chen Chou   Peptide reagent design based on physical
                                  and chemical properties of amino acid
                                  residues . . . . . . . . . . . . . . . . 2043--2050
Balázs Jójárt and   
       Tamás A. Martinek   Performance of the general AMBER force
                                  field in modeling aqueous POPC membrane
                                  bilayers . . . . . . . . . . . . . . . . 2051--2058
         Liliana Wroblewska and   
               Jeffrey Skolnick   Can a physics-based, all-atom potential
                                  find a protein's native structure among
                                  misfolded structures? I. Large scale
                                  AMBER benchmarking . . . . . . . . . . . 2059--2066
             Yutaka Imamura and   
               Takao Otsuka and   
                   Hiromi Nakai   Description of core excitations by
                                  time-dependent density functional theory
                                  with local density approximation,
                                  generalized gradient approximation,
                                  meta-generalized gradient approximation,
                                  and hybrid functionals . . . . . . . . . 2067--2074
            Carsten Kutzner and   
        David Van Der Spoel and   
             Martin Fechner and   
               Erik Lindahl and   
             Udo W. Schmitt and   
           Bert L. De Groot and   
         Helmut Grubmüller   Speeding up parallel GROMACS on
                                  high-latency networks  . . . . . . . . . 2075--2084

Journal of Computational Chemistry
Volume 28, Number 13, October, 2007

         Francesco Ferrante and   
            Gianfranco La Manna   Theoretical study of the interaction
                                  between sodium ion and a cyclopeptidic
                                  tubular structure  . . . . . . . . . . . 2085--2090
              Run-Feng Chen and   
                 Chao Zheng and   
                  Qu-Li Fan and   
                      Wei Huang   Structural, electronic, and optical
                                  properties of 9-heterofluorenes: a
                                  quantum chemical study . . . . . . . . . 2091--2101
     Javier González and   
      Xavier Giménez and   
             Josep Maria Bofill   Algorithm to evaluate rate constants for
                                  polyatomic chemical reactions. I. Theory
                                  and computational details  . . . . . . . 2102--2110
     Javier González and   
      Xavier Giménez and   
             Josep Maria Bofill   Algorithm to evaluate rate constants for
                                  polyatomic chemical reactions. II.
                                  Applications . . . . . . . . . . . . . . 2111--2121
               Chen Yanover and   
            Menachem Fromer and   
               Julia M. Shifman   Dead-end elimination for multistate
                                  protein design . . . . . . . . . . . . . 2122--2129
     Bård Buttingsrud and   
    Bjòrn K. Alsberg and   
         Per-Olof Åstrand   Validation of critical points in the
                                  electron density as descriptors by
                                  building quantitative
                                  structure--property relationships for
                                  the atomic polar tensor  . . . . . . . . 2130--2139
             Mine Ilk Capar and   
                     Emine Cebe   Odd--even effects in the homologous
                                  series of alkyl-cyanobiphenyl liquid
                                  crystals: a molecular dynamic study  . . 2140--2146
             Jingjing Zheng and   
                Ahmet Altun and   
                   Walter Thiel   Common system setup for the entire
                                  catalytic cycle of cytochrome
                                  P450$_{cam}$ in quantum
                                  mechanical/molecular mechanical studies  2147--2158
                  R. Zanasi and   
                 S. Pelloni and   
                  P. Lazzeretti   Chiral discrimination via nuclear
                                  magnetic shielding polarisabilities from
                                  NMR spectroscopy: Theoretical study of
                                  (R$_a$)-1,3-dimethylallene, (2
                                  R)-2-methyloxirane, and (2 R)-
                                  $N$-methyloxaziridine  . . . . . . . . . 2159--2163
              Yuanqiang Zhu and   
                   Yong Guo and   
               Lidong Zhang and   
                    Daiqian Xie   A computational investigation on the
                                  sequential rearrangement mechanism of
                                  2-allyl-2,4,5-hexatrienaldehyde
                                  involving [1,5]-hydrogen migration and
                                  8$\pi$-electrocyclization  . . . . . . . 2164--2169
             Josep M. Porta and   
           Lluís Ros and   
            Federico Thomas and   
            Francesc Corcho and   
         Josep Cantó and   
 Juan Jesús Pérez   Complete maps of molecular-loop
                                  conformational spaces  . . . . . . . . . 2170--2189
                   L. Cheng and   
                 M. Y. Wang and   
                   Z. J. Wu and   
                       Z. M. Su   Electronic structures and chemical
                                  bonding in 4d transition metal
                                  monohalides  . . . . . . . . . . . . . . 2190--2202
                  G. Milani and   
                      F. Milani   Genetic algorithm for the determination
                                  of binodal curves in ternary systems
                                  polymer--liquid(1)--liquid(2) and
                                  polymer(1)--polymer(2)--solvent  . . . . 2203--2215
             Santiago Vilar and   
       M. Carmen Villaverde and   
                  Fredy Sussman   Inhibitor docking screened by the
                                  modified SAFE\_p scoring function:
                                  Application to cyclic urea HIV-1 PR
                                  inhibitors . . . . . . . . . . . . . . . 2216--2225
          Peter H. M. Budzelaar   Geometry optimization using generalized,
                                  chemically meaningful constraints  . . . 2226--2236
             Kaori Fukuzawa and   
               Yuto Komeiji and   
             Yuji Mochizuki and   
               Akifumi Kato and   
             Tatsuya Nakano and   
               Shigenori Tanaka   Intra- and intermolecular interactions
                                  between cyclic-AMP receptor protein and
                                  DNA: ab initio fragment molecular
                                  orbital study  . . . . . . . . . . . . . 2237--2239

Journal of Computational Chemistry
Volume 28, Number 14, November 15, 2007

              Huynh-Hoa Bui and   
       Alexandra J. Schiewe and   
                 Ian S. Haworth   WATGEN: an algorithm for modeling water
                                  networks at protein--protein interfaces  2241--2251
             Mikhail Pykavy and   
      Christoph Van Wüllen   A systematic quantum chemical
                                  investigation of the C H bond activation
                                  in methane by gas phase vanadium oxide
                                  cation VO$^+$  . . . . . . . . . . . . . 2252--2259
              Guiling Zhang and   
                  Hui Zhang and   
                   Miao Sun and   
                Yanhong Liu and   
              Xiaohong Pang and   
                Xiaoyang Yu and   
                     Bo Liu and   
                     Zesheng Li   Substitution effect on the geometry and
                                  electronic structure of the ferrocene    2260--2274
                M. Piacenza and   
            I. Hyla-Kryspin and   
                      S. Grimme   A comparative quantum chemical study of
                                  the ruthenium catalyzed olefin
                                  metathesis . . . . . . . . . . . . . . . 2275--2285
                  Wenli Zou and   
                    Wenjian Liu   Theoretical study on the low-lying
                                  electronic states of NiH and NiAt  . . . 2286--2298
            Marko Schreiber and   
        Leticia González   Structure and bonding of Ag(I)--DNA base
                                  complexes and Ag(I)--adenine--cytosine
                                  mispairs: an ab initio study . . . . . . 2299--2308
           David R. Kent IV and   
          Richard P. Muller and   
           Amos G. Anderson and   
     William A. Goddard III and   
            Michael T. Feldmann   Efficient algorithm for ``on-the-fly''
                                  error analysis of local or distributed
                                  serially correlated data . . . . . . . . 2309--2316
                Julian Henn and   
               Dirk Leusser and   
                 Dietmar Stalke   Chemical interpretation of molecular
                                  electron density distributions . . . . . 2317--2324
             Edda Kloppmann and   
        G. Matthias Ullmann and   
                 Torsten Becker   An extended dead-end elimination
                                  algorithm to determine gap-free lists of
                                  low energy states  . . . . . . . . . . . 2325--2335
                Xinliang Yu and   
                    Bing Yi and   
                     Xueye Wang   Prediction of refractive index of vinyl
                                  polymers by using density functional
                                  theory . . . . . . . . . . . . . . . . . 2336--2341
               Xizhen Zhang and   
                 Jiawei Luo and   
                        Li Yang   New invariant of DNA sequence based on
                                  $3$DD-curves and its application on
                                  phylogeny  . . . . . . . . . . . . . . . 2342--2346
                Zengjian Hu and   
            William Southerland   Windock: Structure-based drug discovery
                                  on Windows-based PCs . . . . . . . . . . 2347--2351
     Kaushalya S. Ekanayake and   
             Pierre R. Lebreton   Model transition states for methane
                                  diazonium ion methylation of guanine
                                  runs in oligomeric DNA . . . . . . . . . 2352--2365
     Riccardo Nifosí and   
                Pietro Amat and   
              Valentina Tozzini   Variation of spectral, structural, and
                                  vibrational properties within the
                                  intrinsically fluorescent proteins
                                  family: a density functional study . . . 2366--2377
           Arnab B. Chowdry and   
       Kimberly A. Reynolds and   
           Melinda S. Hanes and   
              Mark Voorhies and   
               Navin Pokala and   
                Tracy M. Handel   An object-oriented library for
                                  computational protein design . . . . . . 2378--2388
           Klaus Ruedenberg and   
             Michael W. Schmidt   Erratum: Why does electron sharing lead
                                  to covalent bonding? A variational
                                  analysis . . . . . . . . . . . . . . . . 2389--2389

Journal of Computational Chemistry
Volume 28, Number 15, November 30, 2007

            Kuo-Hsiang Chen and   
              Jenn-Huei Lii and   
                     Yi Fan and   
             Norman L. Allinger   Molecular mechanics (MM4) study of
                                  amines . . . . . . . . . . . . . . . . . 2391--2412
                Congyi Zhou and   
              Changming Nie and   
                    Shan Li and   
                    Zhonghai Li   A novel semi-empirical topological
                                  descriptor Nt and the application to
                                  study on QSPR/QSAR . . . . . . . . . . . 2413--2423
            Hidenori Anjima and   
           Shinya Tsukamoto and   
             Hirotoshi Mori and   
                Masaki Mine and   
        Mariusz Klobukowski and   
                 Eisaku Miyoshi   Revised model core potentials of
                                  $s$-block elements . . . . . . . . . . . 2424--2430
                    Anan Wu and   
                 Ying Zhang and   
                     Xin Xu and   
                     Yijing Yan   Systematic studies on the computation of
                                  nuclear magnetic resonance shielding
                                  constants and chemical shifts: the
                                  density functional models  . . . . . . . 2431--2442
            Jun-Ya Hasegawa and   
          Kazuhiro Fujimoto and   
                 Ben Swerts and   
             Tomoo Miyahara and   
              Hiroshi Nakatsuji   Excited states of GFP chromophore and
                                  active site studied by the SAC--CI
                                  method: Effect of protein-environment
                                  and mutations  . . . . . . . . . . . . . 2443--2452
          Alexander Fischer and   
           Sonja Waldhausen and   
              Illia Horenko and   
              Eike Meerbach and   
          Christof Schütte   Identification of biomolecular
                                  conformations from incomplete torsion
                                  angle observations by hidden Markov
                                  models . . . . . . . . . . . . . . . . . 2453--2464
                  A. Slepoy and   
               M. D. Peters and   
                 A. P. Thompson   Searching for globally optimal
                                  functional forms for interatomic
                                  potentials using genetic programming
                                  with parallel tempering  . . . . . . . . 2465--2471
                    Wei Kan and   
                 Hai-Tao Yu and   
               Hong-Gang Fu and   
                      Yi-Qun Wu   Theoretical investigation on the
                                  protonation reactions and products of
                                  the stable [N,C,C,S] isomers . . . . . . 2472--2482
                    D. Duca and   
                  G. Barone and   
               S. Giuffrida and   
                      Zs. Varga   IDEA: Interface dynamics and energetics
                                  algorithm  . . . . . . . . . . . . . . . 2483--2499
               Yan-Ling Liu and   
               Ji-Kang Feng and   
                     Ai-Min Ren   Structural, electronic, and optical
                                  properties of phosphole-containing
                                  $\pi$-conjugated oligomers for
                                  light-emitting diodes  . . . . . . . . . 2500--2509
        Nicholas Y. Palermo and   
      József Csontos and   
            Michael C. Owen and   
               R. F. Murphy and   
            Sándor Lovas   Erratum: Aromatic-backbone interactions
                                  in model $\alpha$-helical peptides . . . 2510--2510

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

               Takeshi Noro and   
            Masahiro Sekiya and   
                 You Osanai and   
            Toshikatsu Koga and   
              Hisashi Matsuyama   Relativistic correlating basis sets for
                                  actinide atoms from $_{90}$Th to
                                  $_{103}$Lr . . . . . . . . . . . . . . . 2511--2516
                  Ying Wang and   
               Jing-Yao Liu and   
                    Ze-Sheng Li   Ab initio direct dynamics studies on the
                                  reactions of chlorine atom with CH$_{3 -
                                  n}$F$_n$CH$_2$OH ($n = 1$--$3$)  . . . . 2517--2530
       Emanuel H. Rubensson and   
              Elias Rudberg and   
                  Pawe\l Sa\lek   A hierarchic sparse matrix data
                                  structure for large-scale
                                  Hartree--Fock/Kohn--Sham calculations    2531--2537
                Parimal Kar and   
                 Yanjie Wei and   
      Ulrich H. E. Hansmann and   
        Siegfried Höfinger   Systematic study of the boundary
                                  composition in Poisson Boltzmann
                                  calculations . . . . . . . . . . . . . . 2538--2544
               Xiaoqing Liu and   
                Zhilong Xiu and   
                     Xiaohui Li   Numerical characterization of the
                                  conformation of cyclic peptides and its
                                  application  . . . . . . . . . . . . . . 2545--2551
              Abhinav Verma and   
         Srinivasa M. Gopal and   
                 Jung S. Oh and   
                 Kyu H. Lee and   
                Wolfgang Wenzel   All-atom de novo protein folding with a
                                  scalable evolutionary algorithm  . . . . 2552--2558
Ángel J. Pérez-Jiménez and   
José M. Pérez-Jordá and   
Ibério de P. R. Moreira and   
                 Francesc Illas   Merging multiconfigurational
                                  wavefunctions and correlation
                                  functionals to predict magnetic coupling
                                  constants  . . . . . . . . . . . . . . . 2559--2568
              Pawe\l Sa\lek and   
             Andreas Hesselmann   A self-contained and portable density
                                  functional theory library for use in Ab
                                  Initio quantum chemistry programs  . . . 2569--2575
                    K. Hamacher   Information theoretical measures to
                                  analyze trajectories in rational
                                  molecular design . . . . . . . . . . . . 2576--2580
                  Jon Baker and   
         Krzysztof Wolinski and   
                    Peter Pulay   Parallel DFT gradients using the Fourier
                                  Transform Coulomb method . . . . . . . . 2581--2588
                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
                   M. Rafat and   
              P. L. A. Popelier   Visualization and integration of quantum
                                  topological atoms by spatial
                                  discretization into finite elements  . . 2602--2617
              John E. Stone and   
          James C. Phillips and   
        Peter L. Freddolino and   
             David J. Hardy and   
        Leonardo G. Trabuco and   
                 Klaus Schulten   Accelerating molecular modeling
                                  applications with graphics processors    2618--2640


Journal of Computational Chemistry
Volume 29, Number 1, January 15, 2008

               Tanja Van Mourik   Comment on ``Aromatic-Backbone
                                  Interactions in Model $\alpha$-Helical
                                  Peptides'' [Palermo et al., J. Comput
                                  Chem 2007, 28, 1208] . . . . . . . . . . 1--3
      József Csontos and   
        Nicholas Y. Palermo and   
          Richard F. Murphy and   
            Sándor Lovas   Reply to ``Comment on Aromatic-Backbone
                                  Interactions in Model $\alpha$-Helical
                                  Peptides'' . . . . . . . . . . . . . . . 4--7
        Michael T. Feldmann and   
         Julian C. Cummings and   
           David R. Kent IV and   
          Richard P. Muller and   
         William A. Goddard III   Manager--worker-based model for the
                                  parallelization of quantum Monte Carlo
                                  on heterogeneous and homogeneous
                                  networks . . . . . . . . . . . . . . . . 8--16
                   Kun Song and   
              Viktor Hornak and   
       Carlos De Los Santos and   
         Arthur P. Grollman and   
              Carlos Simmerling   Molecular mechanics parameters for the
                                  FapydG DNA lesion  . . . . . . . . . . . 17--23
                 Lula Rosso and   
                   Ian R. Gould   Structure and dynamics of phospholipid
                                  bilayers using recently developed
                                  general all-atom force fields  . . . . . 24--37
             Katrin Spiegel and   
      Alessandra Magistrato and   
             Patrick Maurer and   
            Paolo Ruggerone and   
       Ursula Rothlisberger and   
              Paolo Carloni and   
                Jan Reedijk and   
               Michael L. Klein   Parameterization of azole-bridged
                                  dinuclear platinum anticancer drugs via
                                  a QM/MM force matching procedure . . . . 38--49
              R. J. Milgram and   
               Guanfeng Liu and   
                  J. C. Latombe   On the structure of the inverse
                                  kinematics map of a fragment of protein
                                  backbone . . . . . . . . . . . . . . . . 50--68
Francisco Rodríguez-Ropero and   
            Jordi Casanovas and   
           Carlos Alemán   Ab initio calculations on $\pi$-stacked
                                  thiophene dimer, trimer, and tetramer:
                                  Structure, interaction energy,
                                  cooperative effects, and intermolecular
                                  electronic parameters  . . . . . . . . . 69--78
        Evgenii V. Kovalyov and   
        Vladimir I. Elokhin and   
      Aleksandr V. Myshlyavtsev   Stochastic simulation of physicochemical
                                  processes performance over supported
                                  metal nanoparticles  . . . . . . . . . . 79--86
                 Y. C. Zhou and   
               Michael Feig and   
                      G. W. Wei   Highly accurate biomolecular
                                  electrostatics in continuum dielectric
                                  environments . . . . . . . . . . . . . . 87--97
                 N. R. Jena and   
             P. S. Kushwaha and   
                   P. C. Mishra   Reaction of hypochlorous acid with
                                  imidazole: Formation of 2-chloro- and
                                  2-oxoimidazoles  . . . . . . . . . . . . 98--107
           Ewgenij Proschak and   
              Matthias Rupp and   
           Swetlana Derksen and   
              Gisbert Schneider   Shapelets: Possibilities and limitations
                                  of shape-based virtual screening . . . . 108--114
     Chinapong Kritayakornupong   The Jahn--Teller effect of the Cr$^{2+}$
                                  ion in aqueous solution: ab initio QM/MM
                                  molecular dynamics simulations . . . . . 115--121
           Matej Praprotnik and   
           Stanko Ho\vcevar and   
         Milan Hodo\vs\vcek and   
                Matej Penca and   
          Du\vsanka Jane\vzi\vc   New all-atom force field for molecular
                                  dynamics simulation of an AlPO$_4$-34
                                  molecular sieve  . . . . . . . . . . . . 122--129
                A. V. Larin and   
            D. N. Trubnikov and   
              D. P. Vercauteren   Electric field convergence versus atomic
                                  basis sets in all-siliceous zeolites . . 130--138
Ignacio Fdez. Galván and   
                Martin J. Field   Improving the efficiency of the NEB
                                  reaction path finding algorithm  . . . . 139--143
             Josep M. Porta and   
           Lluís Ros and   
            Federico Thomas and   
            Francesc Corcho and   
         Josep Cantó and   
 Juan Jesús Pérez   Complete maps of molecular-loop
                                  conformational spaces  . . . . . . . . . 144--155

Journal of Computational Chemistry
Volume 29, Number 2, January 30, 2008

            Markus Christen and   
       Wilfred F. van Gunsteren   On searching in, sampling of, and
                                  dynamically moving through
                                  conformational space of biomolecular
                                  systems: a review  . . . . . . . . . . . 157--166
                Florian Weigend   Hartree--Fock exchange fitting basis
                                  sets for H to Rn . . . . . . . . . . . . 167--175
                 Weihua Zhu and   
                    Heming Xiao   Ab initio study of electronic structure
                                  and optical properties of heavy-metal
                                  azides: TlN$_3$, AgN$_3$, and CuN$_3$    176--184
          Nathan E. Schultz and   
                   Yan Zhao and   
              Donald G. Truhlar   Benchmarking approximate density
                                  functional theory for $s/d$ excitation
                                  energies in $3d$ transition metal
                                  cations  . . . . . . . . . . . . . . . . 185--189
                Mark Pinsky and   
             David Casanova and   
               Pere Alemany and   
           Santiago Alvarez and   
                David Avnir and   
               Chaim Dryzun and   
                 Ziv Kizner and   
              Alexander Sterkin   Symmetry operation measures  . . . . . . 190--197
                 Jian-Yi Ma and   
               Jing-Bo Wang and   
              Xiang-Yuan Li and   
                  Yao Huang and   
                   Quan Zhu and   
                    Ke-Xiang Fu   A study on orientation and absorption
                                  spectrum of interfacial molecules by
                                  using continuum model  . . . . . . . . . 198--210
                  Qi-Shi Du and   
                Ri-Bo Huang and   
                 Yu-Tuo Wei and   
                  Li-Qin Du and   
                  Kuo-Chen Chou   Multiple field three dimensional
                                  quantitative structure--activity
                                  relationship (MF-3D-QSAR)  . . . . . . . 211--219
              D. N. Tarasov and   
                    R. P. Tiger   Numerical computations of molecular
                                  reactions in associated systems caused
                                  by the formation of fractal structures   220--224
               Yasuji Inada and   
                    Hideo Orita   Efficiency of numerical basis sets for
                                  predicting the binding energies of
                                  hydrogen bonded complexes: Evidence of
                                  small basis set superposition error
                                  compared to Gaussian basis sets  . . . . 225--232
       Milan On\vcák and   
                   Martin Srnec   Electronic structure and physical
                                  properties of M$_i$ X$_i$ clusters (M =
                                  B, Al; X = N, P; i = 1, 2, 3): ab initio
                                  study  . . . . . . . . . . . . . . . . . 233--246
                  Jing Yang and   
                Qian Shu Li and   
                  Shaowen Zhang   Direct dynamics study on the reaction of
                                  acetaldehyde with ozone  . . . . . . . . 247--255
                    Kun Liu and   
                  Wensheng Bian   Extensive theoretical study on the
                                  low-lying electronic states of silicon
                                  monofluoride cation including spin-orbit
                                  coupling . . . . . . . . . . . . . . . . 256--265
       Bahram Hemmateenejad and   
                Afshan Mohajeri   Application of quantum topological
                                  molecular similarity descriptors in QSPR
                                  study of the O-methylation of
                                  substituted phenols  . . . . . . . . . . 266--274
                   Yun Ding and   
                     Ye Mei and   
           John Z. H. Zhang and   
                    Fu-Ming Tao   Efficient bond function basis set for
                                  $\pi$-$\pi$ interaction energies . . . . 275--279
           Miguel A. Zamora and   
         Fernando D. Suvire and   
               Ricardo D. Enriz   Ring inversion in 1,4,7 cyclononatriene
                                  and analogues: ab initio and DFT
                                  calculations and topological analysis    280--290
                     Y. Wei and   
                  T. Singer and   
                    H. Mayr and   
               G. N. Sastry and   
                       H. Zipse   Assessment of theoretical methods for
                                  the calculation of methyl cation
                                  affinities . . . . . . . . . . . . . . . 291--297
            Sean A. C. McDowell   A comparative study of some red- and
                                  blue-shifted linear H-bonded complexes
                                  of N$_2$ . . . . . . . . . . . . . . . . 298--305
                 Mohamed Zerara   pyVib, a computer program for the
                                  analysis of infrared and Raman optical
                                  activity . . . . . . . . . . . . . . . . 306--311
       Willem-Jan Van Zeist and   
Célia Fonseca Guerra and   
        F. Matthias Bickelhaupt   PyFrag --- streamlining your reaction
                                  path analysis  . . . . . . . . . . . . . 312--315

Journal of Computational Chemistry
Volume 29, Number 3, February, 2008

Yoanna María Alvarez-Ginarte and   
       Yovani Marrero-Ponce and   
José Alberto Ruiz-García and   
Luis Alberto Montero-Cabrera and   
Jose Manuel García De La Vega and   
         Pedro Noheda Marin and   
        Rachel Crespo-Otero and   
 Francisco Torrens Zaragoza and   
Ramón García-Domenech   Applying pattern recognition methods
                                  plus quantum and physico-chemical
                                  molecular descriptors to analyze the
                                  anabolic activity of structurally
                                  diverse steroids . . . . . . . . . . . . 317--333
                    Koji Yasuda   Two-electron integral evaluation on the
                                  graphics processor unit  . . . . . . . . 334--342
            Arvids Stashans and   
              Gaston Chamba and   
                    Henry Pinto   Electronic structure, chemical bonding,
                                  and geometry of pure and Sr-doped
                                  CaCO$_3$ . . . . . . . . . . . . . . . . 343--349
                   Ruibo Wu and   
                     Zexing Cao   QM/MM study of catalytic methyl transfer
                                  by the N$^5$-glutamine SAM-dependent
                                  methyltransferase and its inhibition by
                                  the nitrogen analogue of coenzyme  . . . 350--357
                 Stijn Fias and   
            Sofie Van Damme and   
               Patrick Bultinck   Multidimensionality of delocalization
                                  indices and nucleus independent chemical
                                  shifts in polycyclic aromatic
                                  hydrocarbons . . . . . . . . . . . . . . 358--366
          Norberto Castillo and   
     Katherine N. Robertson and   
                 S. C. Choi and   
            Russell J. Boyd and   
                    Osvald Knop   Bond length and the electron density at
                                  the bond critical point: X\bondX,
                                  Z\bondZ, and C\bondZ bonds (X = Li--F, Z
                                  = Na--Cl)  . . . . . . . . . . . . . . . 367--379
                P. W. Bates and   
                  G. W. Wei and   
                      Shan Zhao   Minimal molecular surfaces and their
                                  applications . . . . . . . . . . . . . . 380--391
             Daniel Norberg and   
      Nessima Salhi-Benachenhou   McLafferty rearrangement of the radical
                                  cations of butanal and 3-fluorobutanal:
                                  a theoretical investigation of the
                                  concerted and stepwise mechanisms  . . . 392--406
          Sebastian Schlund and   
         Robert Müller and   
     Carsten Graßmann and   
                   Bernd Engels   Conformational analysis of arginine in
                                  gas phase --- a strategy for scanning
                                  the potential energy surface effectively 407--415
              Gilles Frison and   
              Gilles Ohanessian   A comparative study of semiempirical, ab
                                  initio, and DFT methods in evaluating
                                  metal--ligand bond strength, proton
                                  affinity, and interactions between first
                                  and second shell ligands in
                                  Zn-biomimetic complexes  . . . . . . . . 416--433
                    Bin Gao and   
                  Jun Jiang and   
                    Kai Liu and   
                    Ziyu Wu and   
                     Wei Lu and   
                         Yi Luo   An efficient first-principle approach
                                  for electronic structures calculations
                                  of nanomaterials . . . . . . . . . . . . 434--444
            Richard J. Wheatley   Time-dependent coupled-cluster
                                  calculations of polarizabilities and
                                  dispersion energy coefficients . . . . . 445--450
                M. Piacenza and   
              F. Della Sala and   
                 E. Fabiano and   
                  T. Maiolo and   
                       G. Gigli   Torsional effects on excitation energies
                                  of thiophene derivatives induced by
                                  $\beta$-substituents: Comparison between
                                  time-dependent density functional theory
                                  and approximated coupled cluster
                                  approaches . . . . . . . . . . . . . . . 451--457
         Toshiaki Matsubara and   
              Michel Dupuis and   
                    Misako Aida   An insight into the environmental
                                  effects of the pocket of the active site
                                  of the enzyme. Ab initio ONIOM-molecular
                                  dynamics (MD) study on cytosine
                                  deaminase  . . . . . . . . . . . . . . . 458--465
                  Chao Deng and   
               Qiang-Gen Li and   
                     Yi Ren and   
              Ning-Bew Wong and   
                San-Yan Chu and   
                    Hua-Jie Zhu   A comprehensive theoretical study on the
                                  hydrolysis of carbonyl sulfide in the
                                  neutral water  . . . . . . . . . . . . . 466--480
              Bryan M. Wong and   
             Maria M. Fadri and   
                  Sumathy Raman   Thermodynamic calculations for molecules
                                  with asymmetric internal rotors. II.
                                  Application to the 1,2-dihaloethanes . . 481--487
                  V. Ganesh and   
          Ritwik Kavathekar and   
             Anuja Rahalkar and   
              Shridhar R. Gadre   WebProp: Web interface for ab initio
                                  calculation of molecular one-electron
                                  properties . . . . . . . . . . . . . . . 488--495

Journal of Computational Chemistry
Volume 29, Number 4, March, 2008

                    John Cullen   An approximate diatomics in molecules
                                  formulation of generalized valence bond
                                  theory . . . . . . . . . . . . . . . . . 497--504
               Xiao-Wei Fan and   
                     Xue-Hai Ju   Theoretical studies on four-membered
                                  ring compounds with NF$_2$, ONO$_2$,
                                  N$_3$, and NO$_2$ groups . . . . . . . . 505--513
                  Jiali Gao and   
               Kin-Yiu Wong and   
                   Dan T. Major   Combined QM/MM and path integral
                                  simulations of kinetic isotope effects
                                  in the proton transfer reaction between
                                  nitroethane and acetate ion in water . . 514--522
            J. Pitarch-Ruiz and   
J. Sánchez-Marín and   
                  A. M. Velasco   Full configuration interaction
                                  calculation of the low lying valence and
                                  Rydberg states of BeH  . . . . . . . . . 523--532
     Maykel Cruz-Monteagudo and   
M. Natália D. S. Cordeiro and   
                Fernanda Borges   Computational chemistry approach for the
                                  early detection of drug-induced
                                  idiosyncratic liver toxicity . . . . . . 533--549
                   Lei Yang and   
               Jing-Yao Liu and   
                    Li Wang and   
               Hong-Qing He and   
                  Ying Wang and   
                    Ze-Sheng Li   Theoretical study of the reactions
                                  CF$_3$CH$_2$OCHF$_2$ + OH/Cl and its
                                  product radicals and parent ether
                                  (CH$_3$CH$_2$OCH$_3$) with OH  . . . . . 550--561
            Joseph P. Kenny and   
          Curtis L. Janssen and   
           Edward F. Valeev and   
              Theresa L. Windus   Components for integral evaluation in
                                  quantum chemistry  . . . . . . . . . . . 562--577
               Flavio Forti and   
              Xavier Barril and   
            F. Javier Luque and   
                 Modesto Orozco   Extension of the MST continuum solvation
                                  model to the RM1 semiempirical
                                  Hamiltonian  . . . . . . . . . . . . . . 578--587
            M. L. Contreras and   
                 J. Alvarez and   
                D. Guajardo and   
                       R. Rozas   Understanding topological symmetry: a
                                  heuristic approach to its determination  588--600
                 Aibing Liu and   
               Steven J. Stuart   Empirical bond-order potential for
                                  hydrocarbons: Adaptive treatment of van
                                  der Waals interactions . . . . . . . . . 601--611
              Yasushi Honda and   
           Atsushi Kurihara and   
              Masahiko Hada and   
              Hiroshi Nakatsuji   Excitation and circular dichroism
                                  spectra of (-)-(3a S, 7a
                                  S)-2-chalcogena-trans-hydrindans (Ch =
                                  S, Se, Te): SAC and SAC--CI calculations 612--621
          Karl N. Kirschner and   
           Austin B. Yongye and   
         Sarah M. Tschampel and   
Jorge González-Outeiriño and   
        Charlisa R. Daniels and   
           B. Lachele Foley and   
                Robert J. Woods   GLYCAM06: a generalizable biomolecular
                                  force field. Carbohydrates . . . . . . . 622--655
Humberto González-Díaz and   
       Francisco J. Prado-Prado   Unified QSAR and network-based
                                  computational chemistry approach to
                                  antimicrobials, part 1: Multispecies
                                  activity models for antifungals  . . . . 656--667
                   Wei Yang and   
               Hugh Nymeyer and   
            Huan-Xiang Zhou and   
                 Bernd Berg and   
       Rafael Brüschweiler   Quantitative computer simulations of
                                  biomolecules: a snapshot . . . . . . . . 668--672

Journal of Computational Chemistry
Volume 29, Number 5, April 15, 2008

  Kitiyaporn Wittayanarakul and   
           Supot Hannongbua and   
                   Michael Feig   Accurate prediction of protonation state
                                  as a prerequisite for reliable
                                  MM-PB(GB)SA binding free energy
                                  calculations of HIV-1 protease
                                  inhibitors . . . . . . . . . . . . . . . 673--685
               Cai-Yun Geng and   
                  Ji-Lai Li and   
                Xu-Ri Huang and   
               Hui-Ling Liu and   
                    Zhuo Li and   
                 Chia-Chung Sun   Theoretical elucidation of the
                                  rhodium-catalyzed [4 + 2] annulation
                                  reactions  . . . . . . . . . . . . . . . 686--693
             Alex Robertson and   
             Edgar Luttmann and   
                 Vijay S. Pande   Effects of long-range electrostatic
                                  forces on simulated protein folding
                                  kinetics . . . . . . . . . . . . . . . . 694--700
         Urs Haberthür and   
                Amedeo Caflisch   FACTS: Fast analytical continuum
                                  treatment of solvation . . . . . . . . . 701--715
          R. C. Binning Jr. and   
               Daniel E. Bacelo   High-spin versus broken symmetry ---
                                  effect of DFT spin density
                                  representation on the geometries of
                                  three diiron (III) model compounds . . . 716--723
               Marcel Swart and   
        F. Matthias Bickelhaupt   QUILD: QUantum-regions interconnected by
                                  local descriptions . . . . . . . . . . . 724--734
             Yutaka Imamura and   
            Hiroyoshi Kiryu and   
                   Hiromi Nakai   Colle--Salvetti-type correction for
                                  electron--nucleus correlation in the
                                  nuclear orbital plus molecular orbital
                                  theory . . . . . . . . . . . . . . . . . 735--740
         Robert M. Whitnell and   
               Dow P. Hurst and   
         Patricia H. Reggio and   
                Frank Guarnieri   Conformational memories with variable
                                  bond angles  . . . . . . . . . . . . . . 741--752
        Mikael P. Johansson and   
          Ville R. I. Kaila and   
                Liisa Laakkonen   Charge parameterization of the metal
                                  centers in cytochrome $c$ oxidase  . . . 753--767
        Svetlana Stepanenko and   
                   Bernd Engels   New tabu search based global
                                  optimization methods outline of
                                  algorithms and study of efficiency . . . 768--780
                  Zhen Zhou and   
                 Jijun Zhao and   
Paul von Ragué Schleyer and   
                 Zhongfang Chen   Insertion of C$_{50}$ into single-walled
                                  carbon nanotubes: Selectivity in
                                  interwall spacing and C$_{50}$ isomers   781--787
          Emilio Gallicchio and   
             Ronald M. Levy and   
                Manish Parashar   Asynchronous replica exchange for
                                  molecular simulations  . . . . . . . . . 788--794
             Matteo Masetti and   
             Andrea Cavalli and   
            Maurizio Recanatini   Modeling the hERG potassium channel in a
                                  phospholipid bilayer: Molecular dynamics
                                  and drug docking studies . . . . . . . . 795--808
                Yue-meng Ji and   
              Xiao-lei Zhao and   
               Jing-yao Liu and   
                  Ying Wang and   
                    Ze-sheng Li   Theoretical dynamic studies on the
                                  reactions of CH$_3$C(O)CH$_{3 -
                                  n}$Cl$_n$ ($n = 0$--$3$) with the
                                  chlorine atom  . . . . . . . . . . . . . 809--819
              Mark A. Olson and   
               Michael Feig and   
          Charles L. Brooks III   Prediction of protein loop conformations
                                  using multiscale modeling methods with
                                  physical energy scoring functions  . . . 820--831
            Mahmoud Mirzaei and   
             Nasser L. Hadipour   A computational NQR study on the
                                  hydrogen-bonded lattice of
                                  cytosine-5-acetic acid . . . . . . . . . 832--838
            Noel M. O'Boyle and   
         Adam L. Tenderholt and   
               Karol M. Langner   \tt cclib: a library for
                                  package-independent computational
                                  chemistry algorithms . . . . . . . . . . 839--845

Journal of Computational Chemistry
Volume 29, Number 6, April 30, 2008

            Rainer Grohmann and   
              Torsten Schindler   Toward robust QSPR models: Synergistic
                                  utilization of robust regression and
                                  variable elimination . . . . . . . . . . 847--860
Haydée Valdés and   
    Vojt\uech Klusák and   
    Michal Pito\unák and   
                 Otto Exner and   
           Ivo Starý and   
                Pavel Hobza and   
Lubomír Rulí\vsek   Evaluation of the intramolecular basis
                                  set superposition error in the
                                  calculations of larger molecules:
                                  $[n]$helicenes and Phe-Gly-Phe
                                  tripeptide . . . . . . . . . . . . . . . 861--870
           Tatsuhiko Miyata and   
                   Fumio Hirata   Combination of molecular dynamics method
                                  and 3D-RISM theory for conformational
                                  sampling of large flexible molecules in
                                  solution . . . . . . . . . . . . . . . . 871--882
               Huancong Shi and   
          David C. Roettger and   
               Allan L. L. East   Photochemistry studied with ab initio
                                  orbital-correlation and
                                  state-correlation plots: Classic
                                  cyclobutene ring opening, and the
                                  reaction of N$_2$ with photoexcited
                                  O$_2$  . . . . . . . . . . . . . . . . . 883--891
            Fabienne Bessac and   
                  Feliu Maseras   DFT modeling of reactivity in an ionic
                                  liquid: How many ion pairs?  . . . . . . 892--899
                 Kalju Kahn and   
                     Iiris Kahn   Improved efficiency of focal point
                                  conformational analysis with truncated
                                  correlation consistent basis sets  . . . 900--911
              Sandro Chiodo and   
                     Nino Russo   Determination of spin-orbit coupling
                                  contributions in the framework of
                                  density functional theory  . . . . . . . 912--920
            Denis Jacquemin and   
     Eric A. Perpéte and   
             Ilaria Ciofini and   
                    Carlo Adamo   Revisiting the relationship between the
                                  bond length alternation and the first
                                  hyperpolarizability with range-separated
                                  hybrid functionals . . . . . . . . . . . 921--925
                      C. H. Mak   RNA conformational sampling. I.
                                  Single-nucleotide loop closure . . . . . 926--933
               Stefan Duret and   
          Ahmed Bouferguene and   
                 Hassan Safouhi   Strategies for an efficient
                                  implementation of the Gauss--Bessel
                                  quadrature for the evaluation of
                                  multicenter integral over STFs . . . . . 934--944
Lívia B. Pártay and   
         György Hantal and   
      Pál Jedlovszky and   
 Árpád Vincze and   
                  George Horvai   A new method for determining the
                                  interfacial molecules and characterizing
                                  the surface roughness in computer
                                  simulations. Application to the
                                  liquid--vapor interface of water . . . . 945--956
           Fabrizio Santoro and   
            Vincenzo Barone and   
                Roberto Improta   Can TD-DFT calculations accurately
                                  describe the excited states behavior of
                                  stacked nucleobases? The cytosine dimer
                                  as a test case . . . . . . . . . . . . . 957--964
       Deepak Bandyopadhyay and   
         Dimitris K. Agrafiotis   A self-organizing algorithm for
                                  molecular alignment and pharmacophore
                                  development  . . . . . . . . . . . . . . 965--982
            Alicia M. Davis and   
                Gary Joanis and   
                   Lorena Tribe   Molecular modeling of polymer--clay
                                  nanocomposite precursors: Lysine in
                                  montmorillonite interlayers  . . . . . . 983--987
                 Grzegorz Mazur   An improved SCPF scheme for polarization
                                  energy calculations  . . . . . . . . . . 988--993
       Núria Queralt and   
             David Taratiel and   
              Coen de Graaf and   
              Rosa Caballol and   
           Renzo Cimiraglia and   
               Celestino Angeli   On the applicability of multireference
                                  second-order perturbation theory to
                                  study weak magnetic coupling in
                                  molecular complexes  . . . . . . . . . . 994--1003
           Sabine Schweizer and   
         Jörg Kussmann and   
                Bernd Doser and   
           Christian Ochsenfeld   Linear-scaling Cholesky decomposition    1004--1010
         Christoph R. Jacob and   
        Johannes Neugebauer and   
                 Lucas Visscher   A flexible implementation of
                                  frozen-density embedding for use in
                                  multilevel simulations . . . . . . . . . 1011--1018

Journal of Computational Chemistry
Volume 29, Number 7, May, 2008

             Ross C. Walker and   
         Michael F. Crowley and   
                  David A. Case   The implementation of a fast and
                                  accurate QM/MM potential method in AMBER 1019--1031
                Sunil Patil and   
                R. C. Aiyer and   
                   K. C. Sharma   Globally convergent computation of
                                  chemical equilibrium composition . . . . 1032--1036
          Mette Alstrup Lie and   
          Birgit Schiòtt   A DFT study of solvation effects on the
                                  tautomeric equilibrium and catalytic
                                  ylide generation of thiamin models . . . 1037--1047
               Sven Lammers and   
               Stephan Lutz and   
                  Markus Meuwly   Reactive force fields for proton
                                  transfer dynamics  . . . . . . . . . . . 1048--1063
    Miquel Torrent-Sucarrat and   
             Pedro Salvador and   
              Miquel Sol\`a and   
                 Paul Geerlings   The hardness kernel as the basis for
                                  global and local reactivity indices  . . 1064--1072
               Woo Youn Kim and   
                   Kwang S. Kim   Carbon nanotube, graphene, nanowire, and
                                  molecule-based electron and spin
                                  transport phenomena using the
                                  nonequilibrium Green's function method
                                  at the level of first principles theory  1073--1083
        Asbjòrn Holt and   
          Gunnar Karlström   An intramolecular induction correction
                                  model of the molecular dipole moment . . 1084--1091
    Marcel Schmidt Am Busch and   
                 Anne Lopes and   
               David Mignon and   
                Thomas Simonson   Computational protein design: Software
                                  implementation, parameter optimization,
                                  and performance of a simple model  . . . 1092--1102
                Udo Schnupf and   
         Julious L. Willett and   
             Wayne B. Bosma and   
                Frank A. Momany   DFT conformational studies of
                                  $\alpha$-maltotriose . . . . . . . . . . 1103--1112
            Ninad V. Prabhu and   
           Manoranjan Panda and   
                Qingyi Yang and   
                   Kim A. Sharp   Explicit ion, implicit water solvation
                                  for molecular dynamics of nucleic acids
                                  and highly charged molecules . . . . . . 1113--1130
            Anthony D. Hill and   
                Peter J. Reilly   A Gibbs free energy correlation for
                                  automated docking of carbohydrates . . . 1131--1141
                 Yang Zhong and   
              G. Lee Warren and   
                  Sandeep Patel   Thermodynamic and structural properties
                                  of methanol--water solutions using
                                  nonadditive interaction models . . . . . 1142--1152
      Christina L. Vizcarra and   
              Naigong Zhang and   
        Shannon A. Marshall and   
            Ned S. Wingreen and   
                  Chen Zeng and   
                Stephen L. Mayo   An improved pairwise decomposable
                                  finite-difference Poisson--Boltzmann
                                  method for computational protein design  1153--1162
               Elad Project and   
            Esther Nachliel and   
                Menachem Gutman   Parameterization of Ca$^{+2}$--protein
                                  interactions for molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1163--1169
                  Hui Zhang and   
             Gui-Ling Zhang and   
               Jing-Yao Liu and   
                     Bo Liu and   
               Xiao-Yang Yu and   
                    Ze-Sheng Li   Theoretical study on the OH +
                                  CH$_3$NHC(O)OCH$_3$ reaction . . . . . . 1170--1176
           Oliver J. Clarke and   
               Martin J. Parker   Time-averaged predictions of folded and
                                  misfolded peptides using a reduced
                                  physicochemical model  . . . . . . . . . 1177--1185

Journal of Computational Chemistry
Volume 29, Number 8, June, 2008

              Seiken Tokura and   
               Takeshi Sato and   
              Takao Tsuneda and   
          Takahito Nakajima and   
                 Kimihiko Hirao   A dual-level state-specific
                                  time-dependent density-functional theory 1187--1197
             Viktor Bezugly and   
              Pawel Wielgus and   
            Frank R. Wagner and   
            Miroslav Kohout and   
                      Yuri Grin   Electron localizability indicators ELI
                                  and ELIA: the case of highly correlated
                                  wavefunctions for the argon atom . . . . 1198--1207
              Seung Kyu Min and   
              Eun Cheol Lee and   
             Han Myoung Lee and   
             Dong Young Kim and   
               Dongwook Kim and   
                   Kwang S. Kim   Complete basis set limit of ab initio
                                  binding energies and geometrical
                                  parameters for various typical types of
                                  complexes  . . . . . . . . . . . . . . . 1208--1221
                    Yong Wu and   
                     Lu Jin and   
                   Ying Xue and   
               Dai Qian Xie and   
             Chan Kyung Kim and   
                   Yong Guo and   
                    Guo Sen Yan   Theoretical study on the hydrolysis
                                  mechanism of N, N-dimethyl--N'-(2-oxo-1,
                                  2-dihydro-pyrimidinyl)formamidine:
                                  Water-assisted mechanism and
                                  cluster-continuum model  . . . . . . . . 1222--1232
Francisco Rodríguez-Ropero and   
                David Zanuy and   
           Carlos Alemán   Molecular dynamics of a
                                  calix[4]arene-containing polymer in
                                  dichloromethane solution: Ability of the
                                  solvent molecules to fill the cavity of
                                  the macrocycle . . . . . . . . . . . . . 1233--1241
       Alexander G. Donchev and   
          Nikolay G. Galkin and   
       Alexey A. Illarionov and   
          Oleg V. Khoruzhii and   
        Michael A. Olevanov and   
          Vladimir D. Ozrin and   
    Leonid B. Pereyaslavets and   
            Vladimir I. Tarasov   Assessment of performance of the general
                                  purpose polarizable force field QMPFF3
                                  in condensed phase . . . . . . . . . . . 1242--1249
                    Yong Wu and   
                   Ying Xue and   
                 Chan Kyung Kim   Computational studies on the dimers and
                                  the thermal dimerization of
                                  norbornadiene  . . . . . . . . . . . . . 1250--1258
                 Ying Xiong and   
                Hai-Ting Lu and   
                 Chang-Guo Zhan   Dynamic structures of
                                  phosphodiesterase-5 active site by
                                  combined molecular dynamics simulations
                                  and hybrid quantum mechanical/molecular
                                  mechanical calculations  . . . . . . . . 1259--1267
                  Chen Levi and   
           Jan M. L. Martin and   
                      Ilana Bar   Fundamental vibrational frequencies and
                                  dominant resonances in methylamine
                                  isotopologues by ab initio and density
                                  functional theory methods  . . . . . . . 1268--1276
           Maciej Haranczyk and   
              John Holliday and   
              Peter Willett and   
                Maciej Gutowski   Structure and singly occupied molecular
                                  orbital analysis of anionic tautomers of
                                  guanine  . . . . . . . . . . . . . . . . 1277--1291
                     Qi Dai and   
                 Tian-Ming Wang   Use of statistical measures for
                                  analyzing RNA secondary structures . . . 1292--1305
              Wai-Leung Yim and   
           Thorsten Klüner   Atoms-in-molecules analysis for
                                  planewave DFT calculations --- a
                                  numerical approach on a successively
                                  interpolated charge density grid . . . . 1306--1315
               Ryangguk Kim and   
               Jeffrey Skolnick   Assessment of programs for ligand
                                  binding affinity prediction  . . . . . . 1316--1331
        Olexander Yakovenko and   
    Alexander A. Oliferenko and   
       Volodymyr G. Bdzhola and   
       Vladimir A. Palyulin and   
             Nikolai S. Zefirov   Kirchhoff atomic charges fitted to
                                  multipole moments: Implementation for a
                                  virtual screening system . . . . . . . . 1332--1343
      József Csontos and   
        Nicholas Y. Palermo and   
          Richard F. Murphy and   
            Sándor Lovas   Calculation of weakly polar interaction
                                  energies in polypeptides using density
                                  functional and local Mòller--Plesset
                                  perturbation theory  . . . . . . . . . . 1344--1352

Journal of Computational Chemistry
Volume 29, Number 9, July 15, 2008

               Sophie Barbe and   
                   Marc Le Bret   Ab initio determination of the
                                  flexibility of 2'-aminoribonucleosides
                                  and 2'-aminoarabinonucleosides inserted
                                  in duplexes  . . . . . . . . . . . . . . 1353--1363
               Yi-yuan Chiu and   
            Jenn-kang Hwang and   
                 Jinn-moon Yang   Soft energy function and generic
                                  evolutionary method for discriminating
                                  native from nonnative protein
                                  conformations  . . . . . . . . . . . . . 1364--1373
    Vill\Ho K. Pálfi and   
          András Perczel   How stable is a collagen triple helix?
                                  An ab initio study on various collagen
                                  and $\beta$-sheet forming sequences  . . 1374--1386
               Robert Ponec and   
        György Lendvay and   
                 Joaquin Chaves   Structure and bonding in binuclear metal
                                  carbonyls from the analysis of domain
                                  averaged Fermi holes. I. Fe$_2$ (CO)$_9$
                                  and Co$_2$ (CO)$_8$  . . . . . . . . . . 1387--1398
                   Hajime Hirao   A reactive bond orbital investigation of
                                  the Diels--Alder reaction between
                                  1,3-butadiene and ethylene: Energy
                                  decomposition, state correlation
                                  diagram, and electron density analyses   1399--1407
            Pablo Echenique and   
        José Luis Alonso   Efficient model chemistries for
                                  peptides. I. General framework and a
                                  study of the heterolevel approximation
                                  in RHF and MP2 with Pople split-valence
                                  basis sets . . . . . . . . . . . . . . . 1408--1422
                 Xueye Wang and   
             Hengliang Wang and   
                  Yuanqiang Tan   DFT study of the cryptand and
                                  benzocryptand and their complexes with
                                  alkali metal cations: Li$^+$, Na$^+$,
                                  K$^+$  . . . . . . . . . . . . . . . . . 1423--1428
               Karine Voltz and   
             Joanna Trylska and   
          Valentina Tozzini and   
     Vandana Kurkal-Siebert and   
        Jörg Langowski and   
                   Jeremy Smith   Coarse-grained force field for the
                                  nucleosome from self-consistent
                                  multiscaling . . . . . . . . . . . . . . 1429--1439
        Julien Pilmé and   
           Jean-Philip Piquemal   Advancing beyond charge analysis using
                                  the electronic localization function:
                                  Chemically intuitive distribution of
                                  electrostatic moments  . . . . . . . . . 1440--1449
              Mauro Ferrero and   
        Michel Rérat and   
            Roberto Orlando and   
                 Roberto Dovesi   The calculation of static
                                  polarizabilities of $1$--$3$D periodic
                                  compounds. The implementation in the
                                  CRYSTAL code . . . . . . . . . . . . . . 1450--1459
           Piotr Rotkiewicz and   
               Jeffrey Skolnick   Fast procedure for reconstruction of
                                  full-atom protein models from reduced
                                  representations  . . . . . . . . . . . . 1460--1465
      József Csontos and   
Péter Kálmán and   
                 Gyula Tasi and   
Miklós Kálmán and   
          Richard F. Murphy and   
            Sándor Lovas   The effect of electron correlation on
                                  the conformational space of melatonin    1466--1471
           Laurence Leherte and   
          Daniel P. Vercauteren   Collective motions of rigid fragments in
                                  protein structures from smoothed
                                  electron density distributions . . . . . 1472--1489
            Asit K. Chandra and   
              Salma Parveen and   
                Subojit Das and   
Thér\`ese Zeegers-Huyskens   Blue shifts of the C H stretching
                                  vibrations in hydrogen-bonded and
                                  protonated trimethylamine. Effect of
                                  hyperconjugation on bond properties  . . 1490--1496
        Matthew A. Addicoat and   
            Mark A. Buntine and   
                Brian Yates and   
               Gregory F. Metha   Associative versus dissociative binding
                                  of CO to $4 d$ transition metal trimers:
                                  a density functional study . . . . . . . 1497--1506
            Riccardo Chelli and   
           Victor V. Volkov and   
                Roberto Righini   Retrieval of spectral and dynamic
                                  properties from two-dimensional infrared
                                  pump-probe experiments . . . . . . . . . 1507--1516
                     Qi Liu and   
                   V. Olman and   
                Huiqing Liu and   
                   Xiuzi Ye and   
                 Shilun Qiu and   
                        Ying Xu   RNACluster: an integrated tool for RNA
                                  secondary structure comparison and
                                  clustering . . . . . . . . . . . . . . . 1517--1526

Journal of Computational Chemistry
Volume 29, Number 10, July 30, 2008

            Ivelin Georgiev and   
             Ryan H. Lilien and   
                Bruce R. Donald   The minimized dead-end elimination
                                  criterion and its application to protein
                                  redesign in a hybrid scoring and search
                                  algorithm for computing partition
                                  functions over molecular ensembles . . . 1527--1542
              Ferran Feixas and   
              Eduard Matito and   
               Jordi Poater and   
                  Miquel Sol\`a   On the performance of some aromaticity
                                  indices: a critical assessment using a
                                  test set . . . . . . . . . . . . . . . . 1543--1554
             Yutaka Imamura and   
                   Hiromi Nakai   Energy density analysis for second-order
                                  Mòller--Plesset perturbation theory and
                                  coupled-cluster theory with singles and
                                  doubles: Application to C$_2$H$_4$CH$_4$
                                  complexes  . . . . . . . . . . . . . . . 1555--1563
                Juan Torras and   
       Gustavo de M. Seabra and   
               Erik Deumens and   
              S. B. Trickey and   
             Adrian E. Roitberg   A versatile AMBER--Gaussian QM/MM
                                  interface through PUPIL  . . . . . . . . 1564--1573
           Michal Brylinski and   
               Jeffrey Skolnick   Q-Dock: Low-resolution flexible ligand
                                  docking with pocket-specific threading
                                  restraints . . . . . . . . . . . . . . . 1574--1588
                L. A. Zotti and   
                G. Teobaldi and   
          K. Palotás and   
                      W. Ji and   
                  H.-J. Gao and   
                    W. A. Hofer   Adsorption of benzene, fluorobenzene and
                                  meta-di-fluorobenzene on Cu(110): a
                                  computational study  . . . . . . . . . . 1589--1595
                    Ke Chen and   
           Lukasz A. Kurgan and   
                    Jishou Ruan   Prediction of protein structural class
                                  using novel evolutionary
                                  collocation-based sequence
                                  representation . . . . . . . . . . . . . 1596--1604
            Vladimir Hnizdo and   
                    Jun Tan and   
        Benjamin J. Killian and   
              Michael K. Gilson   Efficient calculation of configurational
                                  entropy from molecular simulations by
                                  combining the mutual-information
                                  expansion and nearest-neighbor methods   1605--1614
               Pawe\l Szabelski   Spontaneous segregation on a hybrid
                                  chiral surface . . . . . . . . . . . . . 1615--1625
              Jong Chan Kim and   
            Kyoung Hoon Kim and   
               Jaehoon Jung and   
                  Young-Kyu Han   Reaction mechanisms of dissociative
                                  chemisorption of HI, I$_2$, and CH$_3$I
                                  on a magic cluster Al  . . . . . . . . . 1626--1631
                 Yu-hua Yao and   
                     Qi Dai and   
                Xu-Ying Nan and   
                 Ping-An He and   
               Zuo-Ming Nie and   
             Song-Ping Zhou and   
                 Yao-Zhou Zhang   Analysis of similarity/dissimilarity of
                                  DNA sequences based on a class of $2$D
                                  graphical representation . . . . . . . . 1632--1639
Thenmalarchelvi Rathinavelan and   
                      Wonpil Im   A novel strategy to determine protein
                                  structures using exclusively residual
                                  dipolar coupling . . . . . . . . . . . . 1640--1649
                  Qingxu Li and   
                Yuanping Yi and   
                  Zhigang Shuai   Local approach to coupled cluster
                                  evaluation of polarizabilities for long
                                  conjugated molecules . . . . . . . . . . 1650--1655
                    F. Iori and   
                       S. Corni   Including image charge effects in the
                                  molecular dynamics simulations of
                                  molecules on metal surfaces  . . . . . . 1656--1666
              Xiao-Jing Liu and   
              Chuan-Lu Yang and   
                Xiang Zhang and   
                  Ke-Li Han and   
                   Zi-Chao Tang   Theoretical study on the structure and
                                  formation mechanism of
                                  [C$_6$H$_5$M$_m$]$^-$ (M = Ag, Au; $m =
                                  1$--$3$) . . . . . . . . . . . . . . . . 1667--1674
          Liang-Tsung Huang and   
             M. Michael Gromiha   Analysis and prediction of protein
                                  folding rates using quadratic response
                                  surface models . . . . . . . . . . . . . 1675--1683
            David de Sancho and   
                    Antonio Rey   Energy minimizations with a combination
                                  of two knowledge-based potentials for
                                  protein folding  . . . . . . . . . . . . 1684--1692
                    Paul Labute   The generalized Born/volume integral
                                  implicit solvent model: Estimation of
                                  the free energy of hydration using
                                  London dispersion instead of atomic
                                  surface area . . . . . . . . . . . . . . 1693--1698

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

             Nitin S. Sapre and   
         Nilanjana Pancholi and   
              Swagata Gupta and   
                  Neelima Sapre   Computational modeling of
                                  tetrahydroimidazo-[4,5,1-jk][1,4]-benzodiazepinone derivatives: an atomistic drug design approach using Kier-Hall electrotopological state (E-state) indices 1699--1706
             Michel Masella and   
              Daniel Borgis and   
              Philippe Cuniasse   Combining a polarizable force-field and
                                  a coarse-grained polarizable solvent
                                  model: Application to long dynamics
                                  simulations of bovine pancreatic trypsin
                                  inhibitor  . . . . . . . . . . . . . . . 1707--1724
            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
           Alexander G. Donchev   Nonadditive effects in ternary H$_2$
                                  --cation--PAH systems  . . . . . . . . . 1733--1739
            Luca Monticelli and   
              Eric J. Sorin and   
          D. Peter Tieleman and   
             Vijay S. Pande and   
                Giorgio Colombo   Molecular simulation of multistate
                                  peptide dynamics: a comparison between
                                  microsecond timescale sampling and
                                  multiple shorter trajectories  . . . . . 1740--1752
               Max W. Chang and   
           Richard K. Belew and   
            Kate S. Carroll and   
            Arthur J. Olson and   
              David S. Goodsell   Empirical entropic contributions in
                                  computational docking: Evaluation in APS
                                  reductase complexes  . . . . . . . . . . 1753--1761
              Naigong Zhang and   
                      Chen Zeng   Reference energy extremal optimization:
                                  a stochastic search algorithm applied to
                                  computational protein design . . . . . . 1762--1771
              Xueguang Shao and   
                Xiaoli Yang and   
                   Wensheng Cai   A dynamic lattice searching method with
                                  interior operation for unbiased
                                  optimization of large Lennard-Jones
                                  clusters . . . . . . . . . . . . . . . . 1772--1779
                 Tian Zhang and   
              Haoping Zheng and   
                        Shu Yan   The equivalent potential of water for
                                  electronic structure of aspartic acid    1780--1787
     Siamkhanthang Neihsial and   
      Richard H. Duncan Lyngdoh   Novel H-bonded base dimers as repeat
                                  units for information-bearing
                                  self-associative duplexes: a
                                  B3LYP/6-31G* search  . . . . . . . . . . 1788--1797
                 Ying Zhang and   
                     Xin Xu and   
                     Yijing Yan   Systematic investigation on the
                                  geometric dependence of the calculated
                                  nuclear magnetic shielding constants . . 1798--1807
    K. Periya Vijayalakshmi and   
        Cherumuttathu H. Suresh   Theoretical studies on the
                                  carcinogenicity of polycyclic aromatic
                                  hydrocarbons . . . . . . . . . . . . . . 1808--1817
             Chan Kyung Kim and   
             Soo Gyeong Cho and   
              Chang Kon Kim and   
            Hyung-Yeon Park and   
                  Hui Zhang and   
                  Hai Whang Lee   Prediction of densities for solid
                                  energetic molecules with molecular
                                  surface electrostatic potentials . . . . 1818--1824
                 M. Y. Wang and   
                   L. Cheng and   
                       Z. J. Wu   Density functional study on the reaction
                                  mechanism of palladium-catalyzed
                                  addition of cyanoboranes to alkynes  . . 1825--1839
    Cherumuttathu H. Suresh and   
     Aswathy Mary Vargheese and   
    K. Periya Vijayalakshmi and   
               Neetha Mohan and   
                   Nobuaki Koga   Role of structural water molecule in HIV
                                  protease-inhibitor complexes: a QM/MM
                                  study  . . . . . . . . . . . . . . . . . 1840--1849
                    Ning He and   
               Hong-Bin Xie and   
                   Yi-Hong Ding   Structures and stability of lithium
                                  monosilicide clusters SiLi$_n$ ($n =
                                  4$--$16$): What is the maximum number,
                                  magic number, and core number for
                                  lithium coordination to silicon? . . . . 1850--1858
                 Sunhwan Jo and   
                Taehoon Kim and   
      Vidyashankara G. Iyer and   
                      Wonpil Im   CHARMM-GUI: a Web-based graphical user
                                  interface for CHARMM . . . . . . . . . . 1859--1865

Journal of Computational Chemistry
Volume 29, Number 12, September, 2008

                 Xiuzhen Hu and   
                   Qianzhong Li   Using support vector machine to predict
                                  $\beta$- and $\gamma$-turns in proteins  1867--1875
               Witold Dyrka and   
           Andy T. Augousti and   
           Ma\lgorzata Kotulska   Ion flux through membrane channels ---
                                  an enhanced algorithm for the
                                  Poisson--Nernst--Planck model  . . . . . 1876--1888
               Fahrettin Gogtas   Time-dependent quantum study of the
                                  kinetics of the H($^2$S) + FO($^2\Pi$)
                                  $\rightarrow$ OH($^2\Pi$) + F($^2$P)
                                  reaction . . . . . . . . . . . . . . . . 1889--1894
           Timothy J. Giese and   
                 Darrin M. York   Extension of adaptive tree code and fast
                                  multipole methods to high angular
                                  momentum particle charge densities . . . 1895--1904
        Asbjòrn Holt and   
        Gunnar Karlstròm   Induction correction model for rotation
                                  of two or three dihedral angles  . . . . 1905--1911
              Keiko Shinoda and   
             Wataru Shinoda and   
                Masuhiro Mikami   Efficient free energy calculation of
                                  water across lipid membranes . . . . . . 1912--1918
             Rong-Zhen Liao and   
              Wan-Jian Ding and   
                Jian-Guo Yu and   
               Wei-Hai Fang and   
                 Ruo-Zhuang Liu   Theoretical studies on pyridoxal
                                  5'-phosphate-dependent transamination of
                                  $\alpha$-amino acids . . . . . . . . . . 1919--1929
           Daisuke Katagiri and   
             Hideyoshi Fuji and   
                Saburo Neya and   
                  Tyuji Hoshino   Ab initio protein structure prediction
                                  with force field parameters derived from
                                  water-phase quantum chemical calculation 1930--1944
             Pankaj R. Daga and   
             Robert J. Doerksen   Stereoelectronic properties of
                                  spiroquinazolinones in differential PDE7
                                  inhibitory activity  . . . . . . . . . . 1945--1954
             Anna Marabotti and   
         Francesca Spyrakis and   
           Angelo Facchiano and   
             Pietro Cozzini and   
            Saverio Alberti and   
            Glen E. Kellogg and   
              Andrea Mozzarelli   Energy-based prediction of amino
                                  acid-nucleotide base recognition . . . . 1955--1969
          Magdalena Gruziel and   
           Pawel Grochowski and   
                 Joanna Trylska   The Poisson--Boltzmann model for tRNA:
                                  Assessment of the calculation set-up and
                                  ionic concentration cutoff . . . . . . . 1970--1981
         Inés Corral and   
        Leticia González   Theoretical investigation of
                                  anthracene-9,10-endoperoxide vertical
                                  singlet and triplet excitation spectra   1982--1991
                   Amit Mor and   
                    Guy Ziv and   
                    Yaakov Levy   Simulations of proteins with
                                  inhomogeneous degrees of freedom: the
                                  effect of thermostats  . . . . . . . . . 1992--1998
István Komáromi and   
            Michael C. Owen and   
          Richard F. Murphy and   
            Sándor Lovas   Development of glycyl radical parameters
                                  for the OPLS-AA/L force field  . . . . . 1999--2009
             Guang-Jiu Zhao and   
                      Ke-Li Han   Time-dependent density functional theory
                                  study on hydrogen-bonded intramolecular
                                  charge-transfer excited state of
                                  4-dimethylamino-benzonitrile in methanol 2010--2017
                  Xuan Xiao and   
              Wei-Zhong Lin and   
                  Kuo-Chen Chou   Using grey dynamic modeling and pseudo
                                  amino acid composition to predict
                                  protein structural classes . . . . . . . 2018--2024
                  Hujun Xie and   
                   Ruibo Wu and   
                    Fei Xia and   
                     Zexing Cao   Effects of electron attachment on
                                  C$_{5'}$O$_{5'}$ and C$_{1'}$N$_1$ bond
                                  cleavages of pyrimidine nucleotides: a
                                  theoretical study  . . . . . . . . . . . 2025--2032
        Asbjòrn Holt and   
          Gunnar Karlström   Inclusion of the quadrupole moment when
                                  describing polarization. The effect of
                                  the dipole-quadrupole polarizability . . 2033--2038

Journal of Computational Chemistry
Volume 29, Number 13, October, 2008

        Richard Dronskowski and   
                Gernot Frenking   Foreword . . . . . . . . . . . . . . . . 2039--2043
             Jürgen Hafner   Ab-initio simulations of materials using
                                  VASP: Density-functional theory and
                                  beyond . . . . . . . . . . . . . . . . . 2044--2078
            R. A. Evarestov and   
              A. V. Bandura and   
                M. V. Losev and   
              E. A. Kotomin and   
          Yu. F. Zhukovskii and   
                    D. Bocharov   A first-principles DFT study of UN bulk
                                  and (001) surface: Comparative LCAO and
                                  PW calculations  . . . . . . . . . . . . 2079--2087
             Torsten Kerber and   
               Marek Sierka and   
                  Joachim Sauer   Application of semiempirical long-range
                                  dispersion corrections to periodic
                                  systems in density functional theory . . 2088--2097
               M. J. Gillan and   
                  D. Alf\`e and   
            S. de Gironcoli and   
                    F. R. Manby   High-precision calculation of
                                  Hartree--Fock energy of crystals . . . . 2098--2106
            Elena Voloshina and   
                   Beate Paulus   Cohesive properties of CeN and LaN from
                                  first principles . . . . . . . . . . . . 2107--2112
              Cesare Pisani and   
            Lorenzo Maschio and   
             Silvia Casassa and   
                 Migen Halo and   
         Martin Schütz and   
                   Denis Usvyat   Periodic local MP2 method for the study
                                  of electronic correlation in crystals:
                                  Theory and preliminary applications  . . 2113--2124
             Sheng-Qing Xia and   
                   Svilen Bobev   Are Ba$_{11}$Cd$_6$Sb$_{12}$ and
                                  Sr$_{11}$Cd$_6$Sb$_{12}$ Zintl phases or
                                  not? A density-functional theory study   2125--2133
                Jianxiao Xu and   
                 Holger Kleinke   Unusual Sb--Sb bonding in high
                                  temperature thermoelectric materials . . 2134--2143
               Pere Alemany and   
             Miquel Llunell and   
                 Enric Canadell   Roles of cations, electronegativity
                                  difference, and anionic interlayer
                                  interactions in the metallic versus
                                  nonmetallic character of Zintl phases
                                  related to arsenic . . . . . . . . . . . 2144--2153
              Changhoon Lee and   
         Myung-Hwan Whangbo and   
        Jürgen Köhler   Analysis of electronic structures and
                                  chemical bonding of metal-rich
                                  compounds. I. Density functional study
                                  of Pt metal, LiPt$_2$, LiPt, and
                                  Li$_2$Pt . . . . . . . . . . . . . . . . 2154--2160
              A. I. Baranov and   
                      M. Kohout   Electron localizability for hexagonal
                                  element structures . . . . . . . . . . . 2161--2171
              Dong-Kyun Seo and   
                  Sang-Hwan Kim   Nature of Stoner condition for metallic
                                  ferromagnetism . . . . . . . . . . . . . 2172--2176
         German D. Samolyuk and   
               Gordon J. Miller   Relation between chemical bonding and
                                  exchange coupling approaches to the
                                  description of ordering in itinerant
                                  magnets  . . . . . . . . . . . . . . . . 2177--2186
                   Dadi Dai and   
              Hongjun Xiang and   
             Myung-Hwan Whangbo   Effects of spin-orbit coupling on
                                  magnetic properties of discrete and
                                  extended magnetic systems  . . . . . . . 2187--2209
             Daniel Fritsch and   
            Klaus Koepernik and   
             Manuel Richter and   
                 Helmut Eschrig   Transition metal dimers as potential
                                  molecular magnets: a challenge to
                                  computational chemistry  . . . . . . . . 2210--2219
Anderi L. Tchougréeff and   
            Richard Dronskowski   A computational study of the crystal and
                                  electronic structure of the room
                                  temperature organometallic ferromagnet
                                  V(TCNE)$_2$  . . . . . . . . . . . . . . 2220--2233
       C. Richard A. Catlow and   
           Samuel A. French and   
            Alexey A. Sokol and   
     Abdullah A. Al-Sunaidi and   
               Scott M. Woodley   Zinc oxide: a case study in contemporary
                                  computational solid state chemistry  . . 2234--2249
                   Karl Jug and   
      Viatcheslav A. Tikhomirov   Influence of intrinsic defects on the
                                  properties of zinc oxide . . . . . . . . 2250--2254
               Atsushi Togo and   
                    Peter Kroll   First-principles lattice dynamics
                                  calculations of the phase boundary
                                  between $\beta$-Si$_3$N$_4$ and
                                  $\gamma$-Si$_3$N$_4$ at elevated
                                  temperatures and pressures . . . . . . . 2255--2259
               Holger Wolff and   
            Richard Dronskowski   First-principles and molecular-dynamics
                                  study of structure and bonding in
                                  perovskite-type oxynitrides ABO$_2$N (A
                                  = Ca, Sr, Ba; B = Ta, Nb)  . . . . . . . 2260--2267
      C. M. Zicovich-Wilson and   
               F. J. Torres and   
                 F. Pascale and   
               L. Valenzano and   
                 R. Orlando and   
                      R. Dovesi   Ab initio simulation of the IR spectra
                                  of pyrope, grossular, and andradite  . . 2268--2278
                Jerome Cuny and   
            Sabri Messaoudi and   
           Veronique Alonzo and   
                 Eric Furet and   
 Jean-François Halet and   
                Eric Le Fur and   
         Sharon E. Ashbrook and   
           Chris J. Pickard and   
              Regis Gautier and   
              Laurent Le Polles   DFT calculations of quadrupolar
                                  solid-state NMR properties: Some
                                  examples in solid-state inorganic
                                  chemistry  . . . . . . . . . . . . . . . 2279--2287
             Lindsay E. Roy and   
         Tomasz Durakiewicz and   
          Richard L. Martin and   
            Juan E. Peralta and   
        Gustavo E. Scuseria and   
             Cliff G. Olson and   
              John J. Joyce and   
                  Ela Guziewicz   Dispersion in the Mott insulator UO$_2$:
                                  a comparison of photoemission
                                  spectroscopy and screened hybrid density
                                  functional theory  . . . . . . . . . . . 2288--2294
           Florian Janetzko and   
              Thomas Bredow and   
            Gerald Geudtner and   
         Andreas M. Köster   Boron-doped diamond: Investigation of
                                  the stability of surface-doping versus
                                  bulk-doping using cyclic cluster model
                                  calculations . . . . . . . . . . . . . . 2295--2301
              Ilka Hegemann and   
           Andreas Schwaebe and   
                     Karin Fink   Adsorption of single Cu atoms at
                                  differently stabilized polar ZnO
                                  surfaces: an ab initio study . . . . . . 2302--2310

Journal of Computational Chemistry
Volume 29, Number 14, November 15, 2008

        Takashi Tsuchimochi and   
           Masato Kobayashi and   
               Ayako Nakata and   
             Yutaka Imamura and   
                   Hiromi Nakai   Application of the Sakurai-Sugiura
                                  projection method to core-excited-state
                                  calculation by time-dependent density
                                  functional theory  . . . . . . . . . . . 2311--2316
              Masato Morita and   
              Satoshi Yabushita   Photoionization cross sections with
                                  optimized orbital exponents within the
                                  complex basis function method  . . . . . 2317--2329
          Andreas B. Pribil and   
            Thomas S. Hofer and   
        Bernhard R. Randolf and   
                  Bernd M. Rode   Structure and dynamics of phosphate ion
                                  in aqueous solution: an ab initio QMCF
                                  MD study . . . . . . . . . . . . . . . . 2330--2334
           Daniel R. Fisher and   
           David R. Kent IV and   
        Michael T. Feldmann and   
         William A. Goddard III   An optimized initialization algorithm to
                                  ensure accuracy in quantum Monte Carlo
                                  calculations . . . . . . . . . . . . . . 2335--2343
                A. V. Larin and   
         I. K. Sakodynskaya and   
                D. N. Trubnikov   Convergence of electric field and
                                  electric field gradient versus atomic
                                  basis sets in all-siliceous and Mg
                                  substituted phillipsites . . . . . . . . 2344--2358
    Carl-Johan Högberg and   
          Alexei M. Nikitin and   
        Alexander P. Lyubartsev   Modification of the CHARMM force field
                                  for DMPC lipid bilayer . . . . . . . . . 2359--2369
               Zdenek Chval and   
               Miroslav Sip and   
              Jaroslav V. Burda   The trans effect in square-planar
                                  platinum(II) complexes --- a density
                                  functional study . . . . . . . . . . . . 2370--2381
    Paraskevas A. Karipidis and   
         Constantinos A. Tsipis   The dramatic effect of NH$_3$
                                  co-ligation on the FE$^+$-assisted
                                  activation of carbon dioxide in the gas
                                  phase: From bare metal ions to complexes 2382--2396
                 Lula Rosso and   
              Antony D. Gee and   
                   Ian R. Gould   Ab initio computational study of
                                  positron emission tomography ligands
                                  interacting with lipid molecule for the
                                  prediction of nonspecific binding  . . . 2397--2405
           Gennady N. Chuev and   
           Maxim V. Fedorov and   
              Sandro Chiodo and   
                 Nino Russo and   
                 Emilia Sicilia   Hydration of ionic species studied by
                                  the reference interaction site model
                                  with a repulsive bridge correction . . . 2406--2415
           Jens Krüger and   
            Wolfgang B. Fischer   Exploring the conformational space of
                                  Vpu from HIV-1: a versatile adaptable
                                  protein  . . . . . . . . . . . . . . . . 2416--2424
 Karmen \vCondi\'c-Jurki\'c and   
       V. Tamara Perchyonok and   
              Hendrik Zipse and   
                 David M. Smith   On the modeling of arginine-bound
                                  carboxylates: a case study with Pyruvate
                                  Formate-Lyase  . . . . . . . . . . . . . 2425--2433
            G. G. Camiletti and   
              S. F. Machado and   
                    F. E. Jorge   Gaussian basis set of double zeta
                                  quality for atoms K through Kr:
                                  Application in DFT calculations of
                                  molecular properties . . . . . . . . . . 2434--2444
     Maykel Cruz-Monteagudo and   
            Fernanda Borges and   
M. Natália D. S. Cordeiro   Desirability-based multiobjective
                                  optimization for global QSAR studies:
                                  Application to the design of novel
                                  NSAIDs with improved analgesic,
                                  antiinflammatory, and ulcerogenic
                                  profiles . . . . . . . . . . . . . . . . 2445--2459
            Carmen Herrmann and   
        Johannes Neugebauer and   
                  Markus Reiher   QM/MM vibrational mode tracking  . . . . 2460--2470
              Masato Morita and   
              Satoshi Yabushita   Photoionization cross sections of H and
                                  H$_2$ with complex Gaussian-type basis
                                  functions optimized for the
                                  frequency-dependent polarizabilities . . 2471--2478
                 Jinwoo Lee and   
              Keehyoung Joo and   
             Seung-Yeon Kim and   
                   Jooyoung Lee   Re-examination of structure optimization
                                  of off-lattice protein AB models by
                                  conformational space annealing . . . . . 2479--2484
        Asbjòrn Holt and   
          Gunnar Karlström   Erratum: Inclusion of the quadrupole
                                  moment when describing polarization. The
                                  effect of the dipole-quadrupole
                                  polarizability . . . . . . . . . . . . . 2485--2486

Journal of Computational Chemistry
Volume 29, Number 15, November 30, 2008

              Chin-Hung Lai and   
                    Ming-Der Su   Theoretical characterizations of HAsXH
                                  (X = N, P, As, Sb, and Bi) isomers in
                                  the singlet and triplet states . . . . . 2487--2499
     Juan A. Castillo-Garit and   
       Yovani Marrero-Ponce and   
          Francisco Torrens and   
Ramón García-Domenech and   
        Vicente Romero-Zaldivar   Bond-based 3D-chiral linear indices:
                                  Theory and QSAR applications to central
                                  chirality codification . . . . . . . . . 2500--2512
                  Yajun Liu and   
               Hongyan Xiao and   
                Mengtao Sun and   
                    Weihai Fang   Spin-orbit ab initio investigation of
                                  the photodissociation of dibromomethane
                                  in the gas and solution phases . . . . . 2513--2519
                    Wei Shi and   
               Edward J. Maginn   Improvement in molecule exchange
                                  efficiency in Gibbs ensemble Monte
                                  Carlo: Development and implementation of
                                  the continuous fractional component move 2520--2530
               Hirotaka Ode and   
                Yuri Matsuo and   
                Saburo Neya and   
                  Tyuji Hoshino   Force field parameters for rotation
                                  around $\chi$ torsion axis in nucleic
                                  acids  . . . . . . . . . . . . . . . . . 2531--2542
              Olgun Guvench and   
          Shannon N. Greene and   
              Ganesh Kamath and   
              John W. Brady and   
         Richard M. Venable and   
          Richard W. Pastor and   
     Alexander D. Mackerell Jr.   Additive empirical force field for
                                  hexopyranose monosaccharides . . . . . . 2543--2564
Natércia F. Brás and   
      Sara A. Moura-Tamames and   
         Pedro A. Fernandes and   
                 Maria J. Ramos   Mechanistic studies on the formation of
                                  glycosidase-substrate and
                                  glycosidase-inhibitor covalent
                                  intermediates  . . . . . . . . . . . . . 2565--2574
         Gernot Kieseritzky and   
                    E. W. Knapp   Improved $pK_a$ prediction: Combining
                                  empirical and semimicroscopic methods    2575--2581
                 P. Poulain and   
                 A. Saladin and   
                B. Hartmann and   
              C. Prévost   Insights on protein-DNA recognition by
                                  coarse grain modelling . . . . . . . . . 2582--2592
          Giovanni Grazioso and   
             Andrea Cavalli and   
             Marco De Amici and   
        Maurizio Recanatini and   
               Carlo De Micheli   Alpha7 nicotinic acetylcholine receptor
                                  agonists: Prediction of their binding
                                  affinity through a molecular mechanics
                                  Poisson--Boltzmann surface area approach 2593--2602
            Jakob Schluttig and   
           Michael Bachmann and   
                 Wolfhard Janke   Comparative molecular dynamics and Monte
                                  Carlo study of statistical properties
                                  for coarse-grained heteropolymers  . . . 2603--2612

Journal of Computational Chemistry
Volume 29, Number 16, December, 2008

             Santiago Vilar and   
Humberto González-Díaz and   
            Lourdes Santana and   
                Eugenio Uriarte   QSAR model for alignment-free prediction
                                  of human breast cancer biomarkers based
                                  on electrostatic potentials of protein
                                  pseudofolding HP-lattice networks  . . . 2613--2622
               Yan-Hong Cui and   
              Wei Quan Tian and   
               Ji-Kang Feng and   
                     De-Li Chen   Structures, stabilities, electronic, and
                                  optical properties of C$_{64}$ fullerene
                                  isomers, anions (C and C$_{64}^{4-}$),
                                  metallofullerene Sc$_2$@C$_{64}$, and
                                  Sc$_2$C$_2$@C$_{64}$ . . . . . . . . . . 2623--2630
                   Lili Sun and   
                Shuwei Tang and   
              Yingfei Chang and   
             Zhanliang Wang and   
                  Rongshun Wang   Searching for stable hept-C$_{62}$X$_2$
                                  (X = F, Cl, and Br): Structures and
                                  stabilities of heptagon-containing
                                  C$_{62}$ halogenated derivatives . . . . 2631--2635
                Jiazhong Li and   
                 Beilei Lei and   
              Huanxiang Liu and   
                  Shuyan Li and   
                Xiaojun Yao and   
                Mancang Liu and   
                Paola Gramatica   QSAR study of malonyl-CoA decarboxylase
                                  inhibitors using GA-MLR and a new
                                  strategy of consensus modeling . . . . . 2636--2647
              Guoming Liang and   
              Xiaoguang Bao and   
                      Jiande Gu   The possibility of the decomposition of
                                  2'-deoxyribose moiety of thymidine
                                  induced by the low energy electron
                                  attachment . . . . . . . . . . . . . . . 2648--2655
             Tomonaga Ozawa and   
                 Kosuke Okazaki   CH/$\pi$ hydrogen bonds determine the
                                  selectivity of the Src homology 2 domain
                                  to tyrosine phosphotyrosyl peptides: an
                                  ab initio fragment molecular orbital
                                  study  . . . . . . . . . . . . . . . . . 2656--2666
               Mahito Chiba and   
          Dmitri G. Fedorov and   
                  Kazuo Kitaura   Polarizable continuum model with the
                                  fragment molecular orbital-based
                                  time-dependent density functional theory 2667--2676
          Karolina Kisowska and   
            Slawomir Berski and   
               Zdzislaw Latajka   The structure and chemical bonding in
                                  the N$_2$CuX and N$_2$\dottedbondXCu (X
                                  = F, Cl, Br) systems studied by means of
                                  the molecular orbital and Quantum
                                  Chemical Topology methods  . . . . . . . 2677--2692
       Valery Andrushchenko and   
                    Petr Bou\vr   Circular dichroism enhancement in large
                                  DNA aggregates simulated by a
                                  generalized oscillator model . . . . . . 2693--2703
 María Suárez and   
              Pablo Tortosa and   
             Javier Carrera and   
              Alfonso Jaramillo   Pareto optimization in computational
                                  protein design with multiple objectives  2704--2711
                Mark Pinsky and   
               Chaim Dryzun and   
             David Casanova and   
               Pere Alemany and   
                    David Avnir   Analytical methods for calculating
                                  Continuous Symmetry Measures and the
                                  Chirality Measure  . . . . . . . . . . . 2712--2721
                  N. Flocke and   
                     V. Lotrich   Efficient electronic integrals and their
                                  generalized derivatives for object
                                  oriented implementations of electronic
                                  structure calculations . . . . . . . . . 2722--2736


Journal of Computational Chemistry
Volume 30, Number 1, January 15, 2009

            Gernot Frenking and   
      Charles L. Brooks III and   
              Shigeyoshi Sakiki   Editors' note  . . . . . . . . . . . . . 1--1
            Vincenzo Barone and   
             Mirco Zerbetto and   
              Antonino Polimeno   Hydrodynamic modeling of diffusion
                                  tensor properties of flexible molecules  2--13
              Olga Yuzlenko and   
    Katarzyna Kie\'c-Kononowicz   Molecular modeling of A$_1$ and A$_{2A}$
                                  adenosine receptors: Comparison of
                                  rhodopsin- and
                                  $\beta_2$-adrenergic-based homology
                                  models through the docking studies . . . 14--32
                   Bing Niu and   
                     Lin Lu and   
                  Liang Liu and   
               Tian Hong Gu and   
               Kai-Yan Feng and   
                Wen-Cong Lu and   
                    Yu-Dong Cai   HIV-1 protease cleavage site prediction
                                  based on amino acid property . . . . . . 33--39
               Yuto Komeiji and   
           Takeshi Ishikawa and   
             Yuji Mochizuki and   
           Hiroshi Yamataka and   
                 Tatsuya Nakano   Fragment Molecular Orbital method-based
                                  Molecular Dynamics (FMO--MD) as a
                                  simulator for chemical reactions in
                                  explicit solvation . . . . . . . . . . . 40--50
                  Bryan M. Wong   Noncovalent interactions in
                                  supramolecular complexes: a study on
                                  corannulene and the double concave
                                  buckycatcher . . . . . . . . . . . . . . 51--56
        Matthew A. Addicoat and   
               Gregory F. Metha   Kick: Constraining a stochastic search
                                  procedure with molecular fragments . . . 57--64
Luká\vs Bu\vcinský and   
       Stanislav Biskupi\vc and   
             Michal Il\vcin and   
    Vladimír Luke\vs and   
                 Viliam Laurinc   On relativistic effects in ground state
                                  potential curves of Zn$_2$, Cd$_2$, and
                                  Hg$_2$ dimers. A CCSD(T) study . . . . . 65--74
            Daniel Escudero and   
           Antonio Frontera and   
     David Quiñonero and   
                 Pere M. Dey\`a   Interplay between anion-$\pi$ and
                                  hydrogen bonding interactions  . . . . . 75--82
               Wissam Helal and   
        Stefano Evangelisti and   
          Thierry Leininger and   
                  Daniel Maynau   Ab-initio multireference study of an
                                  organic mixed-valence Spiro molecular
                                  system . . . . . . . . . . . . . . . . . 83--92
               Weiyang Chen and   
                    Bo Liao and   
                    Wen Zhu and   
                    Hao Liu and   
                 Qingguang Zeng   An ant colony pairwise alignment based
                                  on the dot plots . . . . . . . . . . . . 93--97
A. Martín Pendás and   
               M. A. Blanco and   
                   E. Francisco   Steric repulsions, rotation barriers,
                                  and stereoelectronic effects: a real
                                  space perspective  . . . . . . . . . . . 98--109
              Gota Kikugawa and   
           Rossen Apostolov and   
           Narutoshi Kamiya and   
               Makoto Taiji and   
             Ryutaro Himeno and   
            Haruki Nakamura and   
             Yasushige Yonezawa   Application of MDGRAPE-3, a special
                                  purpose board for molecular dynamics
                                  simulations, to periodic biomolecular
                                  systems  . . . . . . . . . . . . . . . . 110--118
               A. S. Zyubin and   
                A. M. Mebel and   
                 M. Hayashi and   
                H. C. Chang and   
                      S. H. Lin   Quantum chemical modeling of
                                  photoadsorption properties of the
                                  nitrogen-vacancy point defect in diamond 119--131
          Michael D. Altman and   
         Jaydeep P. Bardhan and   
             Jacob K. White and   
                    Bruce Tidor   Accurate solution of multi-region
                                  continuum biomolecule electrostatic
                                  problems using the linearized
                                  Poisson--Boltzmann equation with curved
                                  boundary elements  . . . . . . . . . . . 132--153
               Nikolaj Otte and   
               Marco Bocola and   
                   Walter Thiel   Force-field parameters for the
                                  simulation of tetrahedral intermediates
                                  of serine hydrolases . . . . . . . . . . 154--162
                    Ke Chen and   
               Yingfu Jiang and   
                      Li Du and   
                  Lukasz Kurgan   Prediction of integral membrane protein
                                  type by collocated hydrophobic amino
                                  acid pairs . . . . . . . . . . . . . . . 163--172

Journal of Computational Chemistry
Volume 30, Number 2, January 30, 2009

Juan M. Ramírez-Anguita and   
\`Angels González-Lafont and   
           José M. Lluch   Formation pathways of DMSO from DMS-OH
                                  in the presence of O$_2$ and NO$_x$: a
                                  theoretical study  . . . . . . . . . . . 173--182
              Wen Lai Huang and   
                   Qingshan Zhu   DFT calculations on the electronic
                                  structures of BiOX (X = F, Cl, Br, I)
                                  photocatalysts with and without semicore
                                  Bi $5 d$ states  . . . . . . . . . . . . 183--190
         Dmitri V. Sakharov and   
                     Carmay Lim   Force fields including charge transfer
                                  and local polarization effects:
                                  Application to proteins containing
                                  multi/heavy metal ions . . . . . . . . . 191--202
             Artur Galstyan and   
             Ernst-Walter Knapp   Accurate redox potentials of mononuclear
                                  iron, manganese, and nickel model
                                  complexes* . . . . . . . . . . . . . . . 203--211
              Chris Oostenbrink   Efficient free energy calculations on
                                  small molecule host-guest systems --- a
                                  combined linear interaction
                                  energy/one-step perturbation approach    212--221
                Anmin Zheng and   
              Shang-Bin Liu and   
                      Feng Deng   $^{13}$C shielding tensors of
                                  crystalline amino acids and peptides:
                                  Theoretical predictions based on
                                  periodic structure models  . . . . . . . 222--235
                  Hui Zhang and   
             Gui-Ling Zhang and   
               Jing-Yan Liu and   
                   Miao Sun and   
                     Bo Liu and   
                    Ze-Sheng Li   Theoretical study on the reaction of
                                  SiH(CH$_3$)$_3$ with SiH$_3$ radical . . 236--242
         Alexey Aleksandrov and   
                Thomas Simonson   Molecular mechanics models for
                                  tetracycline analogs . . . . . . . . . . 243--255
                Xiaolei Zhu and   
                      Luhua Lai   A novel method for enzyme design . . . . 256--267
             Edgar Luttmann and   
           Daniel L. Ensign and   
        Vishal Vaidyanathan and   
               Mike Houston and   
                 Noam Rimon and   
         Jeppe Òland and   
          Guha Jayachandran and   
            Mark Friedrichs and   
                 Vijay S. Pande   Accelerating molecular dynamic
                                  simulation on the Cell processor and
                                  Playstation 3  . . . . . . . . . . . . . 268--274
              Albert Poater and   
       Ana Gallegos Saliner and   
   Ramon Carbó-Dorca and   
               Jordi Poater and   
              Miquel Sol\`a and   
              Luigi Cavallo and   
                Andrew P. Worth   Modeling the structure-property
                                  relationships of nanoneedles: a journey
                                  toward nanomedicine  . . . . . . . . . . 275--284
                  Chao Deng and   
               Xiao-Peng Wu and   
              Xiao-Ming Sun and   
                     Yi Ren and   
                Ying-Hong Sheng   Neutral hydrolyses of carbon disulfide:
                                  an ab initio study of water catalysis    285--294
                  Qi-Shi Du and   
                Ri-Bo Huang and   
                 Yu-Tuo Wei and   
              Zong-Wen Pang and   
                  Li-Qin Du and   
                  Kuo-Chen Chou   Fragment-based quantitative
                                  structure--activity relationship
                                  (FB-QSAR) for fragment-based drug design 295--304
                 Li-Ping Ju and   
                  Ke-Li Han and   
               John Z. H. Zhang   Global dynamics and transition state
                                  theories: Comparative study of reaction
                                  rate constants for gas-phase chemical
                                  reactions  . . . . . . . . . . . . . . . 305--316
                  Jon Baker and   
         Krzysztof Wolinski and   
           Massimo Malagoli and   
               Don Kinghorn and   
             Pawel Wolinski and   
   Gábor Magyarfalvi and   
                Svein Saebo and   
            Tomasz Janowski and   
                    Peter Pulay   Quantum chemistry in parallel with PQS   317--335

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

           Edmond P. F. Lee and   
           Daniel K. W. Mok and   
               Foo-Tim Chau and   
                   John M. Dyke   A combined ab initio and Franck--Condon
                                  factor simulation study on the
                                  photodetachment spectrum of ScO$_2^-$    337--345
          Ján Bu\vsa and   
              Shura Hayryan and   
                Chin-Kun Hu and   
Jaroslav Sk\vrivánek and   
                   Ming-Chya Wu   Enveloping triangulation method for
                                  detecting internal cavities in proteins
                                  and algorithm for computing their
                                  surface areas and volumes  . . . . . . . 346--357
                     Yi Ren and   
               Hiroshi Yamataka   Does $\alpha$-effect exist in E2
                                  reactions? A G2(+) investigation . . . . 358--365
                Ivo Cacelli and   
        Carlo Federico Lami and   
             Giacomo Prampolini   Force-field modeling through quantum
                                  mechanical calculations: Molecular
                                  dynamics simulations of a nematogenic
                                  molecule in its condensed phases . . . . 366--378
              A. J. C. Varandas   Mòller--Plesset perturbation energies and
                                  distances for HeC$_{20}$ extrapolated to
                                  the complete basis set limit . . . . . . 379--388
        Al Mokhtar Lamsabhi and   
           Otilia Mó and   
Soledad Gutiérrez-Oliva and   
      Patricia Pérez and   
Alejandro Toro-Labbé and   
     Manuel Yáñez   The mechanism of double proton transfer
                                  in dimers of uracil and 2-thiouracil ---
                                  the reaction force perspective . . . . . 389--398
              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
             Wan-Chun Cheng and   
               Soonmin Jang and   
              Chen-Chang Wu and   
                Ren-Jie Lin and   
               Hsiu-Feng Lu and   
                    Feng-Yin Li   Site specificity of the
                                  $^{\alpha}$C\bond H bond dissociation
                                  energy for a naturally occurring
                                  $\beta$-hairpin peptide --- an ab initio
                                  study  . . . . . . . . . . . . . . . . . 407--414
              C. Mediavilla and   
               J. Tortajada and   
                   V. G. Baonza   Modeling high pressure reactivity in
                                  unsaturated systems: Application to
                                  dimethylacetylene  . . . . . . . . . . . 415--422
              Yinglong Miao and   
              Peter J. Ortoleva   Molecular dynamics/order parameter
                                  extrapolation for bionanosystem
                                  simulations  . . . . . . . . . . . . . . 423--437
                 Li-Qin Xue and   
             Xian-Yong Pang and   
                 Gui-Chang Wang   Selective oxidation of styrene on an
                                  oxygen-adsorbed Au(111): a density
                                  functional theory study  . . . . . . . . 438--446
                Maik Goette and   
         Helmut Grubmüller   Accuracy and convergence of free energy
                                  differences calculated from
                                  nonequilibrium switching processes . . . 447--456
            Loukas Petridis and   
                Jeremy C. Smith   A molecular mechanics force field for
                                  lignin . . . . . . . . . . . . . . . . . 457--467
         Cristopher Camacho and   
            Henryk A. Witek and   
            Shigeyoshi Yamamoto   Intruder states in multireference
                                  perturbation theory: the ground state of
                                  manganese dimer  . . . . . . . . . . . . 468--478
        Stephan Frickenhaus and   
   Srinivasaraghavan Kannan and   
               Martin Zacharias   Efficient evaluation of sampling quality
                                  of molecular dynamics simulations by
                                  clustering of dihedral torsion angles
                                  and Sammon mapping . . . . . . . . . . . 479--492
                  Hao Zhang and   
             Yun-Hong Zhang and   
                      Feng Wang   Theoretical understanding on the v$_1$
                                  -SO band perturbed by the formation of
                                  magnesium sulfate ion pairs  . . . . . . 493--503

Journal of Computational Chemistry
Volume 30, Number 4, March, 2009

                  Rong Wang and   
            Jian-Sheng Wang and   
               Gui-Rong Liu and   
               Jongyoon Han and   
                   Yu-Zong Chen   Simulation of DNA electrophoresis in
                                  systems of large number of solvent
                                  particles by coarse-grained hybrid
                                  molecular dynamics approach  . . . . . . 505--513
             Daan P. Geerke and   
               Sandra Luber and   
              Koni H. Marti and   
       Wilfred F. Van Gunsteren   On the direct calculation of the free
                                  energy of quantization for molecular
                                  systems in the condensed phase . . . . . 514--523
                  Wenli Zou and   
                    Wenjian Liu   Comprehensive ab initio calculation and
                                  simulation on the low-lying electronic
                                  states of TlX (X = F, Cl, Br, I, and At) 524--539
Katalin E. Kövér and   
          Tamás Beke and   
András Lipták and   
          András Perczel   Combined NMR three-bond scalar coupling
                                  measurements and QM calculations to
                                  calculate OH-rotamer equilibrium of
                                  polyalcohols . . . . . . . . . . . . . . 540--550
Inmaculada Garíca Cuesta and   
Alfredo Sánchez De Merás and   
            Stefano Pelloni and   
               Paolo Lazzeretti   Understanding the ring current effects
                                  on magnetic shielding of hydrogen and
                                  carbon nuclei in naphthalene and
                                  anthracene . . . . . . . . . . . . . . . 551--564
                   Lei Yang and   
               Jing-Yao Liu and   
                 Su-Qin Wan and   
                    Ze-Sheng Li   Theoretical studies of the reactions of
                                  CF$_3$CHCLOCHF$_2$/CF$_3$CHFOCHF$_2$
                                  with OH radical and Cl atom and their
                                  product radicals with OH . . . . . . . . 565--580
          Darren J. Simpson and   
              Thomas Bredow and   
               Andrea R. Gerson   MSINDO study of acid promoted
                                  dissolution of planar MgO and NiO
                                  surfaces . . . . . . . . . . . . . . . . 581--588
                   Wenbo Yu and   
                  Lei Liang and   
                 Zijing Lin and   
              Sanliang Ling and   
           Maciej Haranczyk and   
                Maciej Gutowski   Comparison of some representative
                                  density functional theory and wave
                                  function theory methods for the studies
                                  of amino acids . . . . . . . . . . . . . 589--600
            Keith T. Butler and   
            F. Javier Luque and   
                  Xavier Barril   Toward accurate relative energy
                                  predictions of the bioactive
                                  conformation of drugs  . . . . . . . . . 601--610
                    Li Wang and   
               Jing-yao Liu and   
                   Hong Gao and   
                 Su-qin Wan and   
                    Ze-sheng Li   Dual-level direct dynamics studies for
                                  the reactions of OH radical with
                                  bromine-substituted ethanes  . . . . . . 611--620
           Oliver J. Clarke and   
               Martin J. Parker   Identification of amyloidogenic peptide
                                  sequences using a coarse-grained
                                  physicochemical model  . . . . . . . . . 621--630
               Zunnan Huang and   
                  Chung F. Wong   Conformational selection of protein
                                  kinase A revealed by flexible-ligand
                                  flexible-protein docking . . . . . . . . 631--644
                 Zanxia Cao and   
               Zhixiong Lin and   
                   Jun Wang and   
                     Haiyan Liu   Refining the description of peptide
                                  backbone conformations improves protein
                                  simulations using the GROMOS 53A6 force
                                  field  . . . . . . . . . . . . . . . . . 645--660
                      V. Ganesh   MeTA studio: a cross platform,
                                  programmable IDE for computational
                                  chemist  . . . . . . . . . . . . . . . . 661--672

Journal of Computational Chemistry
Volume 30, Number 5, April 15, 2009

            Andreas Vitalis and   
                 Rohit V. Pappu   ABSINTH: a new continuum solvation model
                                  for simulations of polypeptides in
                                  aqueous solutions  . . . . . . . . . . . 673--699
               Pei-Kun Yang and   
                     Carmay Lim   Strategies to model the near-solute
                                  solvent molecular density/polarization   700--709
   Alexandra T. P. Carvalho and   
         Pedro A. Fernandes and   
               Marcel Swart and   
    Joost N. P. Van Stralen and   
    F. Matthias Bickelhaupt and   
                 Maria J. Ramos   Role of the variable active site
                                  residues in the function of thioredoxin
                                  family oxidoreductases . . . . . . . . . 710--724
               Yun-Xiang Lu and   
               Jian-Wei Zou and   
                 Ji-Cai Fan and   
                Wen-Na Zhao and   
             Yong-Jun Jiang and   
                    Qing-Sen Yu   Ab initio calculations on halogen-bonded
                                  complexes and comparison with density
                                  functional methods . . . . . . . . . . . 725--732
             Jeffrey S. Tan and   
   Stephan X. M. Boerrigter and   
        Raymond P. Scaringe and   
              Kenneth R. Morris   Application of error-ranked singular
                                  value decomposition for the
                                  determination of potential-derived
                                  atomic-centered point charges  . . . . . 733--742
           Lonnie D. Crosby and   
          Shawn M. Kathmann and   
              Theresa L. Windus   Implementation of dynamical nucleation
                                  theory with quantum potentials . . . . . 743--749
   Pär Söderhjelm and   
                       Ulf Ryde   Conformational dependence of charges in
                                  protein simulations  . . . . . . . . . . 750--760
         Volker Hähnke and   
            Bettina Hofmann and   
             Tomislav Grgat and   
           Ewgenij Proschak and   
         Dieter Steinhilber and   
              Gisbert Schneider   PhAST: Pharmacophore alignment search
                                  tool . . . . . . . . . . . . . . . . . . 761--771
               Yingfu Jiang and   
              Paul Iglinski and   
                  Lukasz Kurgan   Prediction of protein folding rates from
                                  primary sequences using hybrid sequence
                                  representation . . . . . . . . . . . . . 772--783
         Victor M. Anisimov and   
          Vladislav L. Bugaenko   QM/QM docking method based on the
                                  variational finite localized molecular
                                  orbital approximation  . . . . . . . . . 784--798
               Frank Eckert and   
                  Ivo Leito and   
            Ivari Kaljurand and   
            Agnes Kütt and   
              Andreas Klamt and   
            Michael Diedenhofen   Prediction of acidity in acetonitrile
                                  solution with COSMO-RS . . . . . . . . . 799--810
             Grzegorz Mazur and   
          Rados\law W\lodarczyk   Application of the dressed
                                  time-dependent density functional theory
                                  for the excited states of linear
                                  polyenes . . . . . . . . . . . . . . . . 811--817
            Loriano Storchi and   
         Giuseppe Vitillaro and   
           Francesco Tarantelli   Implementation and use of a direct,
                                  partially integral-driven non-Dyson
                                  propagator method for molecular
                                  ionization . . . . . . . . . . . . . . . 818--825
              Hiroaki Umeda and   
             Yuichi Inadomi and   
              Hiroaki Honda and   
                Umpei Nagashima   Parallel Fock matrix construction
                                  program for molecular orbital
                                  calculation --- specific computer with a
                                  hierarchical network . . . . . . . . . . 826--831
           Sandro G. Chiodo and   
                     Nino Russo   One-electron spin-orbit contribution by
                                  effective nuclear charges  . . . . . . . 832--839

Journal of Computational Chemistry
Volume 30, Number 6, April 30, 2009

                    Hua Zhu and   
                    Daiqian Xie   N$_2$O in small para-hydrogen clusters:
                                  Structures and energetics  . . . . . . . 841--846
              Hua-Qing Yang and   
                   Song Qin and   
                   Song Qin and   
                   Chang-Wei Hu   Theoretical study on the gas-phase
                                  reaction mechanism between nickel
                                  monoxide and methane for syngas
                                  production . . . . . . . . . . . . . . . 847--863
         Mark S. Friedrichs and   
              Peter Eastman and   
        Vishal Vaidyanathan and   
               Mike Houston and   
              Scott Legrand and   
             Adam L. Beberg and   
           Daniel L. Ensign and   
       Christopher M. Bruns and   
                 Vijay S. Pande   Accelerating molecular dynamic
                                  simulation on graphics processing units  864--872
              Gwonchan Yoon and   
            Hyeong-Jin Park and   
                 Sungsoo Na and   
                      Kilho Eom   Mesoscopic model for mechanical
                                  characterization of biological protein
                                  materials  . . . . . . . . . . . . . . . 873--880
               Jason Martin and   
                  Jon Baker and   
                    Peter Pulay   Comments on the molecular geometry of
                                  ferrocene: the dangers of using quantum
                                  chemistry programs as black boxes  . . . 881--883
              Jorge A. Vila and   
   Héctor A. Baldoni and   
             Harold A. Scheraga   Performance of density functional models
                                  to reproduce observed $^{13}$C$^\alpha$
                                  chemical shifts of proteins in solution  884--892
                T. R. Walsh and   
                       T. Liang   A multipole-based water potential with
                                  implicit polarization for biomolecular
                                  simulations  . . . . . . . . . . . . . . 893--899
                  Shuyan Li and   
                    Lili Xi and   
               Chengqi Wang and   
                Jiazhong Li and   
                 Beilei Lei and   
              Huanxiang Liu and   
                    Xiaojun Yao   A novel method for protein-ligand
                                  binding affinity prediction and the
                                  related descriptors exploration  . . . . 900--909
        Amanda M. Salisburg and   
           Ashley L. Deline and   
            Katrina W. Lexa and   
          George C. Shields and   
              Karl N. Kirschner   Ramachandran-type plots for glycosidic
                                  linkages: Examples from molecular
                                  dynamic simulations using the Glycam06
                                  force field  . . . . . . . . . . . . . . 910--921
             Nitin S. Sapre and   
              Swagata Gupta and   
         Nilanjana Pancholi and   
                  Neelima Sapre   A group center overlap based approach
                                  for ``3D QSAR'' studies on TIBO
                                  derivatives  . . . . . . . . . . . . . . 922--933
            Vincenzo Barone and   
           Maurizio Casarin and   
              Daniel Forrer and   
             Michele Pavone and   
                Mauro Sambi and   
               Andrea Vittadini   Role and effective treatment of
                                  dispersive forces in materials:
                                  Polyethylene and graphite crystals as
                                  test cases . . . . . . . . . . . . . . . 934--939
                  Peng Zhou and   
                Feifei Tian and   
                   Zhicai Shang   $2$D depiction of nonbonding
                                  interactions for protein complexes . . . 940--951
                     Yi Luo and   
              Satoshi Maeda and   
                    Koichi Ohno   Automated exploration of stable isomers
                                  of H$^+$(H$_2$O)$_n$ ($n = 5$--$7$) via
                                  ab initio calculations: an application
                                  of the anharmonic downward distortion
                                  following algorithm  . . . . . . . . . . 952--961
             Hajime Okamoto and   
              Tetsuo Yamada and   
           Shuichiro Kihara and   
           Kazumasa Takechi and   
            Hiroyuki Takagi and   
               Kyozaburo Takeda   Conformational transitions of cyclic D,
                                  L-peptides . . . . . . . . . . . . . . . 962--973
       Emanuel H. Rubensson and   
              Elias Rudberg and   
                  Pawe\l Sa\lek   Truncation of small matrix elements
                                  based on the Euclidean norm for blocked
                                  data structures  . . . . . . . . . . . . 974--977
                 Guohua Gao and   
                   Xiang Xu and   
                 Hong Seok Kang   A theoretical study on
                                  fullerene-dizincocene hybrids  . . . . . 978--982
      Jakub Kaminský and   
      Ji\vrí \vSebek and   
                    Petr Bou\vr   Molecular dynamics with restrictions
                                  derived from optical spectra . . . . . . 983--991
              Sarah Remmert and   
                   Carol Parish   Energetic analyses of chair and boat
                                  conformations of maleimide substituted
                                  cyclohexane derivatives  . . . . . . . . 992--998
             Ilya V. Loksha and   
        James R. Maiolo III and   
              Cheng W. Hong and   
                  Albert Ng and   
            Christopher D. Snow   SHARPEN --- Systematic Hierarchical
                                  Algorithms for Rotamers and Proteins on
                                  an Extended Network  . . . . . . . . . . 999--1005

Journal of Computational Chemistry
Volume 30, Number 7, May, 2009

                 Cun-Xi Liu and   
                 Ze-Rong Li and   
             Chong-Wen Zhou and   
                  Xiang-Yuan Li   Accurate prediction of thermodynamic
                                  properties of alkyl peroxides by
                                  combining density functional theory
                                  calculation with least-square
                                  calibration  . . . . . . . . . . . . . . 1007--1015
            James S. Wright and   
             Hooman Shadnia and   
             Leonid L. Chepelev   Stability of carbon-centered radicals:
                                  Effect of functional groups on the
                                  energetics of addition of molecular
                                  oxygen . . . . . . . . . . . . . . . . . 1016--1026
Erika Ivonne López-Martínez and   
Luz María Rodríguez-Valdez and   
Norma Flores-Holguín and   
Alfredo Márquez-Lucero and   
         Daniel Glossman-Mitnik   Theoretical study of electronic
                                  properties of organic photovoltaic
                                  materials  . . . . . . . . . . . . . . . 1027--1037
               Shunzhou Wan and   
               Peter V. Coveney   A comparative study of the COX-1 and
                                  COX-2 isozymes bound to lipid membranes  1038--1050
                 Lixin Zhan and   
            Jeff Z. Y. Chen and   
                    Wing-Ki Liu   Comparison of predicted native
                                  structures of Met-enkephalin based on
                                  various accessible-surface-area solvent
                                  models . . . . . . . . . . . . . . . . . 1051--1058
             Xavier Periole and   
              Lucy R. Allen and   
              Kamil Tamiola and   
               Alan E. Mark and   
                  Emanuele Paci   Probing the free energy landscape of the
                                  FBP28WW domain using multiple techniques 1059--1068
        Stanislav Böhm and   
                     Otto Exner   Interaction of two functional groups
                                  through the benzene ring: Theory and
                                  experiment . . . . . . . . . . . . . . . 1069--1074
      Miguel A. F. de Souza and   
            Elizete Ventura and   
Regiane C. M. U. Araújo and   
            Mozart N. Ramos and   
             Silmar A. do Monte   CASSCF and multireference CI with
                                  singles and doubles study of low-lying
                                  valence and Rydberg states of
                                  2H-tetrazole . . . . . . . . . . . . . . 1075--1081
   Juan I. Rodríguez and   
     Andreas M. Köster and   
              Paul W. Ayers and   
           Ana Santos-Valle and   
               Alberto Vela and   
                 Gabriel Merino   An efficient grid-based scheme to
                                  compute QTAIM atomic properties without
                                  explicit calculation of zero-flux
                                  surfaces . . . . . . . . . . . . . . . . 1082--1092
                 Heiko Jacobsen   Chemical bonding in view of electron
                                  charge density and kinetic energy
                                  density descriptors  . . . . . . . . . . 1093--1102
                   Jin Wang and   
                   Jin Huai Liu   Novel bi-transition metallic
                                  encapsulated naphthalene-like Si$_{20}$
                                  prismatic cage: a DFT investigation  . . 1103--1110
             Laura R. Hofto and   
            Caroline E. Lee and   
               Mauricio Cafiero   The importance of aromatic-type
                                  interactions in serotonin synthesis:
                                  Protein--ligand interactions in
                                  tryptophan hydroxylase and aromatic
                                  amino acid decarboxylase . . . . . . . . 1111--1115
             Young Kee Kang and   
                  Nam Sook Kang   Conformational preferences of
                                  $N$-methoxycarbonyl proline dipeptide    1116--1127
              Hong-Liang Xu and   
             Fang-Fang Wang and   
                  Zhi-Ru Li and   
            Bing-Qiang Wang and   
                      Di Wu and   
                   Wei Chen and   
               Guang-Tao Yu and   
               Feng Long Gu and   
                    Yuriko Aoki   The nitrogen edge-doped effect on the
                                  static first hyperpolarizability of the
                                  supershort single-walled carbon nanotube 1128--1134
                  Ji-Lai Li and   
               Cai-Yun Geng and   
                 Yuxiang Bu and   
                Xu-Ri Huang and   
                 Chia-Chung Sun   Conformational transition pathway in the
                                  allosteric process of calcium-induced
                                  recoverin: Molecular dynamics
                                  simulations  . . . . . . . . . . . . . . 1135--1145
   Ramon Carbó-Dorca and   
               Ana Gallegos and   
 Ángel J. Sánchez   Notes on quantitative
                                  structure-properties relationships
                                  (QSPR) (1): a discussion on a QSPR
                                  dimensionality paradox (QSPR DP) and its
                                  quantum resolution . . . . . . . . . . . 1146--1159
            Daniel Seeliger and   
               Bert L. De Groot   tCONCOORD-GUI: Visually supported
                                  conformational sampling of bioactive
                                  molecules  . . . . . . . . . . . . . . . 1160--1166
          Ritwik Kavathekar and   
               Subodh Khire and   
                  V. Ganesh and   
          Anuja P. Rahalkar and   
              Shridhar R. Gadre   WebMTA: a web-interface for ab initio
                                  geometry optimization of large molecules
                                  using molecular tailoring approach . . . 1167--1173
 Zuzana Jirou\vsková and   
Radka Svobodová Va\vreková and   
              Jakub Van\uek and   
                Jaroslav Ko\vca   Software news and updates
                                  electronegativity equalization method:
                                  Parameterization and validation for
                                  organic molecules using the
                                  Merz-Kollman-Singh charge distribution
                                  scheme . . . . . . . . . . . . . . . . . 1174--1178

Journal of Computational Chemistry
Volume 30, Number 8, June, 2009

              Ahmed Dkhissi and   
Jean Marie Ducéré and   
               Ralf Blossey and   
                 Claude Pouchan   Can the hybrid meta GGA and DFT-D
                                  methods describe the stacking
                                  interactions in conjugated polymers? . . 1179--1184
                 K. S. Kang and   
            J. W. Davenport and   
                   J. Glimm and   
                D. E. Keyes and   
                    M. McGuigan   Linear augmented Slater-type orbital
                                  method for free standing clusters  . . . 1185--1193
             Oana Cramariuc and   
            Terttu I. Hukka and   
           Tapio T. Rantala and   
              Helge Lemmetyinen   Ab initio description of photoabsorption
                                  and electron transfer in a doubly-linked
                                  porphyrin-fullerene dyad . . . . . . . . 1194--1201
              Xue-Gang Yang and   
                  Duan Chen and   
                   Min Wang and   
                   Ying Xue and   
                   Yu-Zong Chen   Prediction of antibacterial compounds by
                                  machine learning approaches  . . . . . . 1202--1211
     M. Fernanda Rey-Stolle and   
               Marta Enciso and   
                    Antonio Rey   Topology-based models and NMR structures
                                  in protein folding simulations . . . . . 1212--1219
                Pedro A. Derosa   A combined semiempirical-DFT study of
                                  oligomers within the finite-chain
                                  approximation, evolution from oligomers
                                  to polymers  . . . . . . . . . . . . . . 1220--1228
              Miguel Arenas and   
       M. Carmen Villaverde and   
                  Fredy Sussman   Prediction and analysis of binding
                                  affinities for chemically diverse HIV-1
                                  PR inhibitors by the modified SAFE\_p
                                  approach . . . . . . . . . . . . . . . . 1229--1240
            Aneta Jezierska and   
             Jaros\law J. Panek   Investigations of an OH\dottedbondS
                                  hydrogen bond via Car--Parrinello and
                                  path integral molecular dynamics . . . . 1241--1250
                  Yan Zhang and   
               Chang-Sheng Wang   Estimation on the intramolecular
                                  10-membered ring N H\dottedbondO C
                                  hydrogen-bonding energies in glycine and
                                  alanine peptides . . . . . . . . . . . . 1251--1260
    Vincent Liégeois and   
            Beno\^\it Champagne   Vibrational Raman optical activity of
                                  $\pi$-conjugated helical systems:
                                  Hexahelicene and heterohelicenes . . . . 1261--1278
                    Lin Jin and   
                   Yi-Hong Ding   Stability of $N$-based sandwich-like
                                  energetic complexes
                                  [N$_4$TiN$_4$]$^{2-}$: Effect of spins
                                  and counterions  . . . . . . . . . . . . 1279--1289
     Michael Gilleßen and   
            Richard Dronskowski   A combinatorial study of full Heusler
                                  alloys by first-principles computational
                                  methods  . . . . . . . . . . . . . . . . 1290--1299
           Michael Devereux and   
        Paul L. A. Popelier and   
                  Iain M. McLay   Toward an ab initio fragment database
                                  for bioisosterism: Dependence of QCT
                                  properties on level of theory,
                                  conformation, and chemical environment   1300--1318
               Celestino Angeli   On the nature of the $\pi$ $\rightarrow$
                                  $\pi^*$ ionic excited states: the $V$
                                  state of ethene as a prototype . . . . . 1319--1333
                Jinhyuk Lee and   
                 Sihyun Ham and   
                      Wonpil Im   Beta-hairpin restraint potentials for
                                  calculations of potentials of mean force
                                  as a function of beta-hairpin tilt,
                                  rotation, and distance . . . . . . . . . 1334--1343
              Jian-Ding Qiu and   
                San-Hua Luo and   
             Jian-Hua Huang and   
                  Ru-Ping Liang   Using support vector machines for
                                  prediction of protein structural classes
                                  based on discrete wavelet transform  . . 1344--1350
             Yasuomi Kiyota and   
            Jun-Ya Hasegawa and   
          Kazuhiro Fujimoto and   
                 Ben Swerts and   
              Hiroshi Nakatsuji   A multicore QM/MM approach for the
                                  geometry optimization of chromophore
                                  aggregate in protein . . . . . . . . . . 1351--1359

Journal of Computational Chemistry
Volume 30, Number 9, July 15, 2009

                Liuming Yan and   
               Changle Shao and   
                      Xiaobo Ji   Evaluation of electroosmotic drag
                                  coefficient of water in hydrated sodium
                                  perfluorosulfonate electrolyte polymer   1361--1370
               Jan Fuhrmann and   
        Alexander Rurainski and   
          Hans-Peter Lenhof and   
                   Dirk Neumann   A new method for the gradient-based
                                  optimization of molecular complexes  . . 1371--1378
            Anatoliy Volkov and   
         Tibor Koritsanszky and   
         Michal Chodkiewicz and   
                  Harry F. King   On the basis-set dependence of local and
                                  integrated electron density properties:
                                  Application of a new computer program
                                  for quantum-chemical density analysis    1379--1391
    Cherumuttathu H. Suresh and   
               Neetha Mohan and   
    K. Periya Vijayalakshmi and   
            Renjumon George and   
               Janice M. Mathew   Typical aromatic noncovalent
                                  interactions in proteins: a theoretical
                                  study using phenylalanine  . . . . . . . 1392--1404
              Arghya Barman and   
                Woody Taves and   
               Rajeev Prabhakar   Insights into the mechanism of
                                  methionine oxidation catalyzed by metal
                                  (Cu$^{2+}$, Zn$^{2+}$, and Fe$^{3+}$)
                                  --- Amyloid beta (A$\beta$) peptide
                                  complexes: a computational study . . . . 1405--1413
                  Xuan Xiao and   
                    Pu Wang and   
                  Kuo-Chen Chou   GPCR-CA: a cellular automaton image
                                  approach for predicting
                                  G-protein--coupled receptor functional
                                  classes  . . . . . . . . . . . . . . . . 1414--1423
                Jianming Wu and   
                         Xin Xu   Accurate prediction of heats of
                                  formation by a combined method of B3LYP
                                  and neural network correction  . . . . . 1424--1444
                Sandor Kristyan   Interesting properties of Thomas--Fermi
                                  kinetic and Parr
                                  electron--electron-repulsion DFT energy
                                  functional generated compact
                                  one-electron density approximation for
                                  ground-state electronic energy of
                                  molecular systems  . . . . . . . . . . . 1445--1453
     Johannes Schwöbel and   
             Ralf-Uwe Ebert and   
           Ralph Kühne and   
    Gerrit Schüürmann   Modeling the H bond donor strength of
                                  OH, NH, and CH sites by local molecular
                                  parameters . . . . . . . . . . . . . . . 1454--1464
                    F. Iori and   
               R. Di Felice and   
                E. Molinari and   
                       S. Corni   GolP: an atomistic force-field to
                                  describe the interaction of proteins
                                  with Au(111) surfaces in water . . . . . 1465--1476
Juan M. Ramírez-Anguita and   
\`Angels González-Lafont and   
           José M. Lluch   Formation pathways of DMSO$_2$ in the
                                  addition channel of the OH-initiated DMS
                                  oxidation: a theoretical study . . . . . 1477--1489
                Lennart Nilsson   Efficient table lookup without inverse
                                  square roots for calculation of pair
                                  wise atomic interactions in classical
                                  simulations  . . . . . . . . . . . . . . 1490--1498
        Alexander Rurainski and   
        Andreas Hildebrandt and   
              Hans-Peter Lenhof   A consensus line search algorithm for
                                  molecular potential energy functions . . 1499--1509
             Riccardo Concu and   
               Gianni Podda and   
            Eugenio Uriarte and   
Humberto González-Díaz   Computational chemistry study of
                                  3D-structure-function relationships for
                                  enzymes based on Markov models for
                                  protein electrostatic, HINT, and van der
                                  Waals potentials . . . . . . . . . . . . 1510--1520
                Meiyan Wang and   
                  Lin Cheng and   
                    Bo Hong and   
                     Zhijian Wu   Reaction mechanism of
                                  palladium-catalyzed silastannation of
                                  allenes by density functional theory . . 1521--1531
            Dray-Ming Shien and   
               Tzong-Yi Lee and   
              Wen-Chi Chang and   
          Justin Bo-Kai Hsu and   
          Jorng-Tzong Horng and   
              Po-Chiang Hsu and   
             Ting-Yuan Wang and   
                 Hsien-Da Huang   Incorporating structural characteristics
                                  for identification of protein
                                  methylation sites  . . . . . . . . . . . 1532--1543

Journal of Computational Chemistry
Volume 30, Number 10, July 30, 2009

               B. R. Brooks and   
           C. L. Brooks III and   
        A. D. Mackerell Jr. and   
                 L. Nilsson and   
             R. J. Petrella and   
                    B. Roux and   
                     Y. Won and   
               G. Archontis and   
                 C. Bartels and   
                 S. Boresch and   
                A. Caflisch and   
                   L. Caves and   
                     Q. Cui and   
               A. R. Dinner and   
                    M. Feig and   
                 S. Fischer and   
                     J. Gao and   
                M. Hodoscek and   
                      W. Im and   
                 K. Kuczera and   
               T. Lazaridis and   
                      J. Ma and   
             V. Ovchinnikov and   
                    E. Paci and   
               R. W. Pastor and   
                 C. B. Post and   
                   J. Z. Pu and   
                M. Schaefer and   
                   B. Tidor and   
              R. M. Venable and   
             H. L. Woodcock and   
                      X. Wu and   
                    W. Yang and   
                 D. M. York and   
                     M. Karplus   CHARMM: the biomolecular simulation
                                  program  . . . . . . . . . . . . . . . . 1545--1614

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

                  M. Bonomi and   
                A. Barducci and   
                  M. Parrinello   Reconstructing the equilibrium Boltzmann
                                  distribution from well-tempered
                                  metadynamics . . . . . . . . . . . . . . 1615--1621
                  Wonpil Im and   
                Jinhyuk Lee and   
                Taehoon Kim and   
                       Huan Rui   Novel free energy calculations to
                                  explore mechanisms and energetics of
                                  membrane protein structure and function  1622--1633
                Edina Rosta and   
            H. Lee Woodcock and   
          Bernard R. Brooks and   
                 Gerhard Hummer   Artificial reaction coordinate
                                  ``tunneling'' in free-energy
                                  calculations: the catalytic reaction of
                                  RNase H  . . . . . . . . . . . . . . . . 1634--1641
              Jan H. Meinke and   
          Ulrich H. E. Hansmann   Free-energy-driven folding and
                                  thermodynamics of the 67-residue protein
                                  GS-$\alpha_3$W --- a large-scale Monte
                                  Carlo study  . . . . . . . . . . . . . . 1642--1648
                Mengen Chen and   
                       Wei Yang   On-the-path random walk sampling for
                                  efficient optimization of minimum
                                  free-energy path . . . . . . . . . . . . 1649--1653
                  Payel Das and   
                Jingyuan Li and   
            Ajay K. Royyuru and   
                    Ruhong Zhou   Free energy simulations reveal a double
                                  mutant avian H5N1 virus hemagglutinin
                                  with altered receptor binding
                                  specificity  . . . . . . . . . . . . . . 1654--1663
            Clara D. Christ and   
       Wilfred F. Van Gunsteren   Comparison of three enveloping
                                  distribution sampling Hamiltonians for
                                  the estimation of multiple free energy
                                  differences from a single simulation . . 1664--1679
                  Xin Zhang and   
           Artem B. Mamonov and   
            Daniel M. Zuckerman   Absolute free energies estimated by
                                  combining precalculated molecular
                                  fragment libraries . . . . . . . . . . . 1680--1691
         Jennifer L. Knight and   
          Charles L. Brooks III   $\lambda$-Dynamics free energy
                                  simulation methods . . . . . . . . . . . 1692--1700
                  Dian Jiao and   
              Jiajing Zhang and   
             Robert E. Duke and   
                  Guohui Li and   
      Michael J. Schnieders and   
                     Pengyu Ren   Trypsin-ligand binding free energies
                                  from explicit and implicit solvent
                                  simulations with polarizable potential   1701--1711
         Gerhard König and   
            Stefan Bruckner and   
                 Stefan Boresch   Unorthodox uses of Bennett's acceptance
                                  ratio method . . . . . . . . . . . . . . 1712--1718
              Mikolai Fajer and   
            Robert V. Swift and   
             J. Andrew McCammon   Using multistate free energy techniques
                                  to improve the efficiency of replica
                                  exchange accelerated molecular dynamics  1719--1725
           Harald Oberhofer and   
              Christoph Dellago   Efficient extraction of free energy
                                  profiles from nonequilibrium experiments 1726--1736
            Eric Vanden-Eijnden   Some recent techniques for free energy
                                  calculations . . . . . . . . . . . . . . 1737--1747

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

            Sofie Van Damme and   
               Patrick Bultinck   Conceptual DFT properties-based 3D QSAR:
                                  Analysis of inhibitors of the nicotine
                                  metabolizing CYP2A6 enzyme . . . . . . . 1749--1757
            Zden\uek Futera and   
               Julia Klenko and   
          Judit E. \vSponer and   
     Ji\vrí \vSponer and   
              Jaroslav V. Burda   Interactions of the ``piano-stool''
                                  [ruthenium(II)
                                  ($\eta^6$-arene)(en)CL]$^+$ complexes
                                  with water and nucleobases; ab initio
                                  and DFT study  . . . . . . . . . . . . . 1758--1770
                Adri\`a Gil and   
             Mariona Sodupe and   
                   Juan Bertran   Influence of ionization on the
                                  conformational preferences of peptide
                                  models. Ramachandran surfaces of
                                  $N$-formyl-glycine amide and
                                  $N$-formyl-alanine amide radical cations 1771--1784
               Guo-Xu Zhang and   
                   Ying Xie and   
                 Hai-Tao Yu and   
                   Hong-Gang Fu   First-principles calculations of the
                                  stability and electronic properties of
                                  the PbTiO$_3$ (110) polar surface  . . . 1785--1798
    Séverine Queyroy and   
            Haruki Nakamura and   
                    Ikuo Fukuda   Numerical examination of the extended
                                  phase-space volume-preserving integrator
                                  by the Nosé--Hoover molecular dynamics
                                  equations  . . . . . . . . . . . . . . . 1799--1815
                 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
          Pedro E. M. Lopes and   
        Guillaume Lamoureux and   
     Alexander D. Mackerell Jr.   Polarizable empirical force field for
                                  nitrogen-containing heteroaromatic
                                  compounds based on the classical Drude
                                  oscillator . . . . . . . . . . . . . . . 1821--1838
              Shih-Wei Chao and   
          Arvin Huang-Te Li and   
                  Sheng D. Chao   Molecular dynamics simulations of fluid
                                  methane properties using ab initio
                                  intermolecular interaction potentials    1839--1849
              Shun Sakuraba and   
                     Akio Kitao   Multiple Markov transition matrix
                                  method: Obtaining the stationary
                                  probability distribution from multiple
                                  simulations  . . . . . . . . . . . . . . 1850--1858
             Kai Lüder and   
           Lennart Lindfors and   
             Jan Westergren and   
             Sture Nordholm and   
             Rasmus Persson and   
               Mikaela Pedersen   In silico prediction of drug solubility:
                                  4. Will simple potentials suffice? . . . 1859--1871
                  Ujjal Das and   
          Krishnan Raghavachari   Predicting PH vibrations of gas phase
                                  molecules and surface-adsorbed species
                                  using bond length-frequency correlations 1872--1881
                  Wen Lai Huang   Electronic structures and optical
                                  properties of BiOX (X = F, Cl, Br, I)
                                  via DFT calculations . . . . . . . . . . 1882--1891
                Huaiyong Li and   
               Siyuan Zhang and   
               Shihong Zhou and   
                   Xueqiang Cao   Investigation of chemical bond
                                  characteristics, thermal expansion
                                  coefficients and bulk moduli of
                                  $\alpha$-R$_2$MoO$_6$ and
                                  R$_2$Mo$_2$O$_7$ (R = rare earths) by
                                  using a dielectric chemical bond method  1892--1898
               Max K. Leong and   
              Yen-Ming Chen and   
                 Tzu-Hsien Chen   Prediction of human cytochrome P450
                                  2B6-substrate interactions using
                                  hierarchical support vector regression
                                  approach . . . . . . . . . . . . . . . . 1899--1909
              Robert Grybos and   
              Lubomir Benco and   
              Tomas Bu\vcko and   
             Jürgen Hafner   Interaction of NO molecules with Pd
                                  clusters: Ab initio density--functional
                                  study  . . . . . . . . . . . . . . . . . 1910--1922
              Eun-Jong Hong and   
            Shaun M. Lippow and   
                Bruce Tidor and   
Tomás Lozano-Pérez   Rotamer optimization for protein design
                                  through MAP estimation and problem-size
                                  reduction  . . . . . . . . . . . . . . . 1923--1945
               Frederik Tielens   Exploring the reactivity of framework
                                  vanadium, niobium, and tantalum sites in
                                  zeolitic materials using DFT reactivity
                                  descriptors  . . . . . . . . . . . . . . 1946--1951
           William J. Allen and   
           Justin A. Lemkul and   
                 David R. Bevan   GridMAT-MD: a grid-based membrane
                                  analysis tool for use with molecular
                                  dynamics . . . . . . . . . . . . . . . . 1952--1958

Journal of Computational Chemistry
Volume 30, Number 13, October, 2009

                Shuang Chen and   
                        Jing Ma   Charge transport in stacking metal and
                                  metal-free phthalocyanine iodides.
                                  Effects of packing, dopants, external
                                  electric field, central metals, core
                                  modification, and substitutions  . . . . 1959--1972
                 Seonah Kim and   
            Anita M. Orendt and   
           Marta B. Ferraro and   
               Julio C. Facelli   Crystal structure prediction of flexible
                                  molecules using parallel genetic
                                  algorithms with a standard force field   1973--1985
                Junmeng Cai and   
                      Siyu Chen   A new iterative linear integral
                                  isoconversional method for the
                                  determination of the activation energy
                                  varying with the conversion degree . . . 1986--1991
                     Xia Wu and   
               Wensheng Cai and   
                  Xueguang Shao   Optimization of bimetallic Cu--Au and
                                  Ag--Au clusters by using a modified
                                  adaptive immune optimization algorithm   1992--2000
       Bahram Hemmateenejad and   
         Ahmad R. Mehdipour and   
                 Ramin Miri and   
              Mojtaba Shamsipur   Application of MOLMAP approach for QSAR
                                  modeling of various biological
                                  activities using substituent electronic
                                  descriptors  . . . . . . . . . . . . . . 2001--2009
            Konrad H. Marti and   
                  Markus Reiher   Haptic quantum chemistry . . . . . . . . 2010--2020
 Aurélien Grosdidier and   
              Vincent Zoete and   
              Olivier Michielin   Blind docking of 260 protein--ligand
                                  complexes with EADock 2.0  . . . . . . . 2021--2030
               Weiyang Chen and   
                    Bo Liao and   
                    Wen Zhu and   
                     Xuyu Xiang   Multiple sequence alignment algorithm
                                  based on a dispersion graph and ant
                                  colony algorithm . . . . . . . . . . . . 2031--2038
              Michio Iwaoka and   
               Naoki Kimura and   
             Daisuke Yosida and   
               Toshiya Minezaki   The SAAP force field: Development of the
                                  single amino acid potentials for 20
                                  proteinogenic amino acids and Monte
                                  Carlo molecular simulation for short
                                  peptides . . . . . . . . . . . . . . . . 2039--2055
                   Jian Lin and   
                  Kechen Wu and   
                  Mingxin Zhang   A new hybrid DFT approach to electronic
                                  excitation and first
                                  hyperpolarizabilities of transition
                                  metal complexes  . . . . . . . . . . . . 2056--2063
      Brecht M. R. Donckels and   
         Dirk J. W. De Pauw and   
      Peter A. Vanrolleghem and   
               Bernard De Baets   A kernel-based method to determine
                                  optimal sampling times for the
                                  simultaneous estimation of the
                                  parameters of rival mathematical models  2064--2077
                   M. Piris and   
                   J. M. Ugalde   Iterative diagonalization for orbital
                                  optimization in natural orbital
                                  functional theory  . . . . . . . . . . . 2078--2086
                Vinzenz Bachler   Time-dependent density functional
                                  calculations on the electronic spectra
                                  of the neutral nickel complex
                                  [Ni(L$^{ISQ}$)$_2$] (L$^{ISQ}$ =
                                  3,5-di-tert-butyl-o-diiminobenzosemiquinonate(1$^-$)) and its monoanion and dication 2087--2098
   Ramon Carbó-Dorca and   
           Ana Gallegos Saliner   Notes on quantitative
                                  structure-properties relationships
                                  (QSPR) part 2: the role of the number of
                                  atoms as a molecular descriptor  . . . . 2099--2104
                   Wenbo Yu and   
                    Xuee Xu and   
                 Hongbao Li and   
                   Rui Pang and   
                   Kun Fang and   
                     Zijing Lin   Extensive conformational searches of 13
                                  representative dipeptides and an
                                  efficient method for dipeptide structure
                                  determinations based on amino acid
                                  conformers . . . . . . . . . . . . . . . 2105--2121
                      Yang Wang   Perfect planar tetracoordinate carbon in
                                  neutral unsaturated hydrocarbon cages: a
                                  new strategy utilizing three-dimensional
                                  electron delocalization  . . . . . . . . 2122--2126
                      Yi He and   
                    Yi Xiao and   
                  Adam Liwo and   
             Harold A. Scheraga   Exploring the parameter space of the
                                  coarse-grained UNRES force field by
                                  random search: Selecting a transferable
                                  medium-resolution force field  . . . . . 2127--2135
               Yongqi Huang and   
                 Huifang Li and   
                     Yuxiang Bu   Molecular dynamics simulation
                                  exploration of cooperative migration
                                  mechanism of calcium ions in
                                  sarcoplasmic reticulum Ca$^{2+}$-ATPase  2136--2145
           Nigel J. Brookes and   
            David C. Graham and   
            Gemma Christian and   
            Robert Stranger and   
                 Brian F. Yates   The influence of peripheral ligand bulk
                                  on nitrogen activation by
                                  three-coordinate molybdenum complexes
                                  --- a theoretical study using the ONIOM
                                  method . . . . . . . . . . . . . . . . . 2146--2156
         L. Martínez and   
                 R. Andrade and   
               E. G. Birgin and   
          J. M. Martínez   \sc Packmol: a package for building
                                  initial configurations for molecular
                                  dynamics simulations . . . . . . . . . . 2157--2164

Journal of Computational Chemistry
Volume 30, Number 14, November 15, 2009

               Zhigang Zhou and   
                 Yanli Wang and   
              Stephen H. Bryant   Computational analysis of the cathepsin
                                  B inhibitors activities through
                                  LR-MMPBSA binding affinity calculation
                                  based on docked complex  . . . . . . . . 2165--2175
                      Shih-I Lu   Gibbs energy of activation for thermal
                                  isomerization of (1Z)-acetaldehyde
                                  hydrazone and (1Z)-acetaldehyde
                                  N,N-dimethylhydrazone by Gaussian-4
                                  theory and CCSD(T)/CBS computations  . . 2176--2180
                   Gab-Yong Lee   Substituent effect on electron affinity,
                                  gas-phase basicity, and structure of
                                  monosubstituted propynyl radicals and
                                  their anions: a theoretical study  . . . 2181--2186
          C. David Sherrill and   
           Bobby G. Sumpter and   
       Mutasem O. Sinnokrot and   
        Michael S. Marshall and   
       Edward G. Hohenstein and   
             Ross C. Walker and   
                   Ian R. Gould   Assessment of standard force field
                                  models against high-quality ab initio
                                  potential curves for prototypes of
                                  $\pi$\doublebond$\pi$, CH\slash$\pi$,
                                  and SH/$\pi$ interactions  . . . . . . . 2187--2193
               Hong-Xia Liu and   
                  Ying Wang and   
                   Lei Yang and   
               Jing-Yao Liu and   
                   Hong Gao and   
                Ze-Sheng Li and   
                 Chia-Chung Sun   CH$_3$NHNH$_2$ + OH reaction: Mechanism
                                  and dynamics studies . . . . . . . . . . 2194--2204
                    Bo Liao and   
               Weiyang Chen and   
               Xingming Sun and   
                        Wen Zhu   A binary coding method of RNA secondary
                                  structure and its application  . . . . . 2205--2212
             Masanori Miura and   
                    Yuriko Aoki   Ab initio theory for treating local
                                  electron excitations in molecules and
                                  its performance for computing optical
                                  properties . . . . . . . . . . . . . . . 2213--2230
                 Yifan Song and   
                 Junjun Mao and   
                   M. R. Gunner   MCCE2: Improving protein $pK_a$
                                  calculations with extensive side chain
                                  rotamer sampling . . . . . . . . . . . . 2231--2247
                   Lei Chen and   
                     Lin Lu and   
                Kairui Feng and   
                  Wenjin Li and   
                   Jie Song and   
                 Lulu Zheng and   
               Youlang Yuan and   
               Zhenbin Zeng and   
                Kaiyan Feng and   
                 Wencong Lu and   
                     Yudong Cai   Multiple classifier integration for the
                                  prediction of protein structural classes 2248--2254
             Chenggang Zhou and   
                 Jinping Wu and   
                 Liang Chen and   
                  Yang Wang and   
              Hansong Cheng and   
               Robert C. Forrey   Force field for copper clusters and
                                  nanoparticles  . . . . . . . . . . . . . 2255--2266
               Yumi N. Imai and   
            Yoshihisa Inoue and   
             Isao Nakanishi and   
                  Kazuo Kitaura   Amide-$\pi$ interactions between
                                  formamide and benzene  . . . . . . . . . 2267--2276
              Dongsheng Zou and   
                Zhongshi He and   
                    Jingyuan He   $\beta$-Hairpin prediction with
                                  quadratic discriminant analysis using
                                  diversity measure  . . . . . . . . . . . 2277--2284
              Matthias Rupp and   
            Petra Schneider and   
              Gisbert Schneider   Distance phenomena in high-dimensional
                                  chemical descriptor spaces: Consequences
                                  for similarity-based approaches  . . . . 2285--2296
                Conrad Shyu and   
              F. Marty Ytreberg   Reducing the bias and uncertainty of
                                  free energy estimates by using
                                  regression to fit thermodynamic
                                  integration data . . . . . . . . . . . . 2297--2304
         Ute F. Röhrig and   
 Aurélien Grosdidier and   
              Vincent Zoete and   
              Olivier Michielin   Docking to heme proteins . . . . . . . . 2305--2315
               Pablo Rivero and   
          Christoph Loschen and   
Ibério De P. R. Moreira and   
                 Francesc Illas   Performance of plane-wave-based LDA + U
                                  and GGA + U approaches to describe
                                  magnetic coupling in molecular systems   2316--2326
     Mikaël Kepenekian and   
             Vincent Robert and   
           Boris Le Guennic and   
                  Coen De Graaf   Energetics of [Fe(NCH)$_6$]$^{2+}$ via
                                  CASPT2 calculations: a spin-crossover
                                  perspective  . . . . . . . . . . . . . . 2327--2333
                    Wei Kan and   
                  Hua Zhong and   
                     Hai-Tao Yu   Theoretical prediction regarding
                                  structural and thermodynamical
                                  characteristics of stable CH$_3$PO$_2$
                                  isomers and unimolecular decomposition
                                  mechanisms of species
                                  CH$_3$P(\doublebondO)$_2$,
                                  CH$_3$O\bondP\doublebondO, and
                                  CH$_2$\doublebondP(\doublebondO)OH . . . 2334--2350
               Tetsu Narumi and   
              Kenji Yasuoka and   
               Makoto Taiji and   
        Siegfried Höfinger   Current performance gains from utilizing
                                  the GPU or the ASIC MDGRAPE-3 within an
                                  enhanced Poisson Boltzmann approach  . . 2351--2357
                 Erjun Zhao and   
                    Bo Hong and   
                  Jian Meng and   
                     Zhijian Wu   First principles investigation on the
                                  ultra-incompressible and hard TaN  . . . 2358--2363
        Adam Górecki and   
           Marcin Szypowski and   
            Maciej D\lugosz and   
                 Joanna Trylska   RedMD --- reduced molecular dynamics
                                  package  . . . . . . . . . . . . . . . . 2364--2373

Journal of Computational Chemistry
Volume 30, Number 15, November 30, 2009

          Olivier Delalande and   
       Nicolas Férey and   
            Gilles Grasseau and   
                    Marc Baaden   Complex molecular assemblies at hand via
                                  interactive simulations  . . . . . . . . 2375--2387
                  Xin Zhang and   
                   Ruibo Wu and   
              Lingchun Song and   
                 Yuchun Lin and   
                Menghai Lin and   
                 Zexing Cao and   
                     Wei Wu and   
                      Yirong Mo   Molecular dynamics simulations of the
                                  detoxification of paraoxon catalyzed by
                                  phosphotriesterase . . . . . . . . . . . 2388--2401
             James R. Apgar and   
              Seungsoo Hahn and   
           Gevorg Grigoryan and   
                 Amy E. Keating   Cluster expansion models for
                                  flexible-backbone protein energetics . . 2402--2413
          Gergely Gidofalvi and   
                    Ron Shepard   Computation of determinant expansion
                                  coefficients within the graphically
                                  contracted function method . . . . . . . 2414--2419
             Luis F. Pacios and   
    Víctor M. Campos and   
               Irene Merino and   
              Luis Gómez   Structures and thermodynamics of
                                  biphenyl dihydrodiol stereoisomers and
                                  their metabolites in the enzymatic
                                  degradation of arene xenobiotics . . . . 2420--2432
            Hsin-Tsung Chen and   
             Jee-Gong Chang and   
              Hui-Lung Chen and   
                    Shin-Pon Ju   Identifying the O$_2$ diffusion and
                                  reduction mechanisms on CeO$_2$
                                  electrolyte in solid oxide fuel cells: a
                                  DFT + U study  . . . . . . . . . . . . . 2433--2442
           Jacopo Sgrignani and   
          Claudia Bonaccini and   
          Giovanni Grazioso and   
          Matteo Chioccioli and   
             Andrea Cavalli and   
                 Paola Gratteri   Insights into docking and scoring
                                  neuronal $\alpha$4$\beta$2 nicotinic
                                  receptor agonists using molecular
                                  dynamics simulations and QM/MM
                                  calculations . . . . . . . . . . . . . . 2443--2454
            Hassan Golmohammadi   Prediction of octanol--water partition
                                  coefficients of organic compounds by
                                  multiple linear regression, partial
                                  least squares, and artificial neural
                                  network  . . . . . . . . . . . . . . . . 2455--2465
   N. M. F. S. A. Cerqueira and   
             P. J. Gonzalez and   
             C. D. Brondino and   
         M. J. Romão and   
         C. C. Romão and   
                   I. Moura and   
                 J. J. G. Moura   The effect of the sixth sulfur ligand in
                                  the catalytic mechanism of periplasmic
                                  nitrate reductase  . . . . . . . . . . . 2466--2484
               A. G. Bailey and   
                     C. P. Lowe   MILCH SHAKE: an efficient method for
                                  constraint dynamics applied to alkanes   2485--2493
           Jagdish C. Patra and   
                    Onkar Singh   Artificial neural networks-based
                                  approach to design ARIs using QSAR for
                                  diabetes mellitus  . . . . . . . . . . . 2494--2508
                    Lu Wang and   
                 Jijun Zhao and   
                  Zhen Zhou and   
                S. B. Zhang and   
                 Zhongfang Chen   First-principles study of molecular
                                  hydrogen dissociation on doped
                                  Al$_{12}$X (X = B, Al, C, Si, P, Mg, and
                                  Ca) clusters . . . . . . . . . . . . . . 2509--2514
           Jacek Korchowiec and   
          Jakub Lewandowski and   
            Marcin Makowski and   
               Feng Long Gu and   
                    Yuriko Aoki   Elongation cutoff technique armed with
                                  quantum fast multipole method for linear
                                  scaling  . . . . . . . . . . . . . . . . 2515--2525
              Wen-Chi Chang and   
               Tzong-Yi Lee and   
            Dray-Ming Shien and   
          Justin Bo-Kai Hsu and   
          Jorng-Tzong Horng and   
              Po-Chiang Hsu and   
             Ting-Yuan Wang and   
             Hsien-Da Huang and   
                  Rong-Long Pan   Incorporating support vector machine for
                                  identifying protein tyrosine sulfation
                                  sites  . . . . . . . . . . . . . . . . . 2526--2537
        Oscar Gálvez and   
      Pedro C. Gómez and   
                 Luis F. Pacios   Characterization of two types of
                                  intermolecular interactions on halogen
                                  monoxide monohydrates  . . . . . . . . . 2538--2549
         Terutaka Yoshizawa and   
                  Masahiko Hada   Relativistic and electron-correlation
                                  effects on magnetizabilities
                                  investigated by the Douglas-Kroll-Hess
                                  method and the second-order
                                  Mòller--Plesset perturbation theory . . . 2550--2566
            Chang-Liang Sun and   
             Xiao-Nan Jiang and   
               Chang-Sheng Wang   An analytic potential energy function
                                  for the amide--amide and amide--water
                                  intermolecular hydrogen bonds in
                                  peptides . . . . . . . . . . . . . . . . 2567--2575
          Andrey A. Toropov and   
           Alla P. Toropova and   
           Emilio Benfenati and   
              Alberto Manganaro   QSPR modeling of enthalpies of formation
                                  for organometallic compounds by
                                  SMART-based optimal descriptors  . . . . 2576--2582

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

               Ayako Nakata and   
              Takao Tsuneda and   
                 Kimihiko Hirao   Modified regional self-interaction
                                  corrected time-dependent density
                                  functional theory for core excited-state
                                  calculations . . . . . . . . . . . . . . 2583--2593
           Takeshi Ishikawa and   
          Takakazu Ishikura and   
                   Kazuo Kuwata   Theoretical study of the prion protein
                                  based on the fragment molecular orbital
                                  method . . . . . . . . . . . . . . . . . 2594--2601
              Satoshi Omori and   
           Sotaro Fuchigami and   
         Mitsunori Ikeguchi and   
                 Akinori Kidera   Linear response theory in dihedral angle
                                  space for protein structural change upon
                                  ligand binding . . . . . . . . . . . . . 2602--2608
                 Art E. Cho and   
                  David Rinaldo   Extension of QM/MM docking and its
                                  applications to metalloproteins  . . . . 2609--2616
                    Yin Wei and   
            Bandaru Sateesh and   
             Boris Maryasin and   
               G. N. Sastry and   
                  Hendrik Zipse   The performance of computational
                                  techniques in locating the charge
                                  separated intermediates in
                                  organocatalytic transformations  . . . . 2617--2624
           Takashi Nakamura and   
            Azusa Yamaguchi and   
             Hirotaka Kondo and   
          Hirofumi Watanabe and   
            Tatsuo Kurihara and   
            Nobuyoshi Esaki and   
             Shuichi Hirono and   
               Shigenori Tanaka   Roles of K151 and D180 in L-2-haloacid
                                  dehalogenase from Pseudomonas sp. YL:
                                  Analysis by molecular dynamics and ab
                                  initio fragment molecular orbital
                                  calculations . . . . . . . . . . . . . . 2625--2634
      Mehdi Bagheri Hamaneh and   
                  Matthias Buck   Refinement of the primary hydration
                                  shell model for molecular dynamics
                                  simulations of large proteins  . . . . . 2635--2644
            R. A. Evarestov and   
                    M. V. Losev   All-electron LCAO calculations of the
                                  LiF crystal phonon spectrum: Influence
                                  of the basis set, the
                                  exchange-correlation functional, and the
                                  supercell size . . . . . . . . . . . . . 2645--2655
               Minoru Saito and   
                   Isao Okazaki   Force-field parameters of the $\Psi$ and
                                  $\Phi$ around glycosidic bonds to oxygen
                                  and sulfur atoms . . . . . . . . . . . . 2656--2665
            Thomas Sandberg and   
                  Matti Hotokka   Conformational analysis of
                                  hydroxymatairesinol in aqueous solution
                                  with molecular dynamics  . . . . . . . . 2666--2673
              Xiaoyan Zheng and   
                 Xueye Wang and   
                Shanfeng Yi and   
              Nuanqing Wang and   
                   Yueming Peng   DFT study of the carbon- and
                                  nitrogen-pivot lariat crown ethers and
                                  their complexes with alkali metal
                                  cations: Na$^+$, K$^+$ . . . . . . . . . 2674--2683
                  Wen Lai Huang   First-principles calculations on the
                                  energetics, electronic structures and
                                  magnetism of SrFeO$_2$ . . . . . . . . . 2684--2693
               Xiaohua Chen and   
             Dianxiang Xing and   
                Liang Zhang and   
           Robert I. Cukier and   
                     Yuxiang Bu   Effect of metal ions on radical type and
                                  proton-coupled electron transfer
                                  channel: $\sigma$-Radical vs
                                  $\pi$-radical and $\sigma$-channel vs
                                  $\pi$-channel in the imide units . . . . 2694--2705
                  Han Zheng and   
             Shenglong Wang and   
                  Yingkai Zhang   Increasing the time step with mass
                                  scaling in Born--Oppenheimer ab initio
                                  QM/MM molecular dynamics simulations . . 2706--2711
              Indrani Mitra and   
                  Kunal Roy and   
                  Achintya Saha   QSAR of antilipid peroxidative activity
                                  of substituted benzodioxoles using
                                  chemometric tools  . . . . . . . . . . . 2712--2722
                 Yufang Liu and   
                Junxia Ding and   
               Ruiqiong Liu and   
                 Deheng Shi and   
                    Jinfeng Sun   Time-dependent density functional theory
                                  study on the electronic excited-state
                                  geometric structure, infrared spectra,
                                  and hydrogen bonding of a doubly
                                  hydrogen-bonded complex  . . . . . . . . 2723--2727
                Akifumi Oda and   
          Noriyuki Yamaotsu and   
                 Shuichi Hirono   Evaluation of the searching abilities of
                                  HBOP and HBSITE for binding pocket
                                  detection  . . . . . . . . . . . . . . . 2728--2737
                  Peng Zhou and   
                Jianwei Zou and   
                Feifei Tian and   
                   Zhicai Shang   Geometric similarity between
                                  protein--RNA interfaces  . . . . . . . . 2738--2751
     Sérgio F. Sousa and   
       Emanuela S. Carvalho and   
          Diana M. Ferreira and   
          Isabel S. Tavares and   
         Pedro A. Fernandes and   
    Maria João Ramos and   
     José A. N. F. Gomes   Comparative analysis of the performance
                                  of commonly available density
                                  functionals in the determination of
                                  geometrical parameters for zinc
                                  complexes  . . . . . . . . . . . . . . . 2752--2763
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
     Chinapong Kritayakornupong   Structural and dynamical properties of
                                  the V$^{3+}$ ion in dilute aqueous
                                  solution: an ab initio QM/MM molecular
                                  dynamics simulation  . . . . . . . . . . 2777--2783
        F. Matthias Bickelhaupt   Book Review: \booktitleA chemist's guide
                                  to valence bond theory, by Sason S.
                                  Shaik and Philippe C. Hiberty, John
                                  Wiley & Sons, Inc., Hoboken, New Jersey,
                                  2008, 311 pp. ISBN-10 0-470-03735-0  . . 2784--2784
          Garrett M. Morris and   
                  Ruth Huey and   
          William Lindstrom and   
           Michel F. Sanner and   
           Richard K. Belew and   
          David S. Goodsell and   
                Arthur J. Olson   AutoDock4 and AutoDockTools4: Automated
                                  docking with selective receptor
                                  flexibility  . . . . . . . . . . . . . . 2785--2791


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

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


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

            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 5, February 15, 2012

                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 8, March 30, 2012

           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 24, September 15, 2012

       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


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

                 M. E. Chen and   
                        W. Yang   Erratum: On-the-path random walk
                                  sampling for efficient optimization of
                                  minimum free energy path . . . . . . . . 2400--2400