Last update:
Wed Nov 8 14:14:05 MST 2023
Gábor I. Csonka and
Nam Anh Nguyen and
István Kolossváry Simple tests for density functional
methods . . . . . . . . . . . . . . . . 1534--1545
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
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
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
Mengen Chen and
Wei Yang On-the-path random walk sampling for
efficient optimization of minimum
free-energy path . . . . . . . . . . . . 1649--1653
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
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
Halvor S. Hansen and
Philippe H. Hünenberger Using the local elevation method to
construct optimized umbrella sampling
potentials: Calculation of the relative
free energies and interconversion
barriers of glucopyranose ring
conformers in water . . . . . . . . . . 1--23
Lili Xi and
Juan Du and
Shuyan Li and
Jiazhong Li and
Huanxiang Liu and
Xiaojun Yao A combined molecular modeling study on
gelatinases and their potent inhibitors 24--42
Ming-Der Su A computational study of photochemical
isomerization reactions of thiophenes 43--56
In-Ho Lee and
Seung-Yeon Kim and
Jooyoung Lee Dynamic folding pathway models of the
villin headpiece subdomain (HP-36)
structure . . . . . . . . . . . . . . . 57--65
Reza Sharifi Sedeh and
Mark Bathe and
Klaus-Jürgen Bathe The subspace iteration method in protein
normal mode analysis . . . . . . . . . . 66--74
Tamar Ansbacher and
Hemant Kumar Srivastava and
Jan M. L. Martin and
Avital Shurki Can DFT methods correctly and
efficiently predict the coordination
number of copper(I) complexes? A case
study . . . . . . . . . . . . . . . . . 75--83
Igor Zilberberg and
Sergey Ruzankin Paired orbitals for different spins
equations . . . . . . . . . . . . . . . 84--89
Maja Parac and
Markus Doerr and
Christel M. Marian and
Walter Thiel QM/MM calculation of solvent effects on
absorption spectra of guanine . . . . . 90--106
Hajime Torii and
Masaki Yoshida Properties of halogen atoms for
representing intermolecular
electrostatic interactions related to
halogen bonding and their substituent
effects . . . . . . . . . . . . . . . . 107--116
Imran S. Haque and
Vijay S. Pande PAPER --- accelerating parallel
evaluations of ROCS . . . . . . . . . . 117--132
Evgeny Krissinel Crystal contacts as nature's docking
solutions . . . . . . . . . . . . . . . 133--143
Roman I. Zubatyuk and
Leonid Gorb and
Oleg V. Shishkin and
Mo Qasim and
Jerzy Leszczynski Exploration of density functional
methods for one-electron reduction
potential of nitrobenzenes . . . . . . . 144--150
Traci Strohecker and
Herschel Rabitz Quantum control implemented as
combinatorial optimization . . . . . . . 151--153
Bong Hyun Boo and
Suk Im and
Sungyul Lee Ab initio and DFT studies of the thermal
rearrangement of
trimethylsilyl(methyl)silylene:
Remarkable rearrangements of silicon
intermediates . . . . . . . . . . . . . 154--163
Francisco J. Prado-Prado and
Florencio M. Ubeira and
Fernanda Borges and
Humberto González-Díaz Unified QSAR & network-based
computational chemistry approach to
antimicrobials. II. Multiple distance
and triadic census analysis of
antiparasitic drugs complex networks . . 164--173
Alfonso T. García-Sosa and
Csaba Hetényi and
Uko Maran Drug efficiency indices for improvement
of molecular docking scoring functions 174--184
Marie-Céline van Severen and
Christophe Gourlaouen and
Olivier Parisel Application of the topological analysis
of the electronic localization function
to archetypical [Pb(II)L$_n$ ]$^p$
complexes: the bonding of Pb$^{2+}$
revisited . . . . . . . . . . . . . . . 185--194
Yin-Feng Wang and
Zhi-Ru Li and
Di Wu and
Chia-Chung Sun and
Feng-Long Gu Excess electron is trapped in a large
single molecular cage C$_{60}$F$_{60}$ 195--203
Alexey K. Shaytan and
Victor A. Ivanov and
Konstantin V. Shaitan and
Alexei R. Khokhlov Free energy profiles of amino acid side
chain analogs near water-vapor interface
obtained via MD simulations . . . . . . 204--216
Yu-yen Ou and
Shu-an Chen and
M. Michael Gromiha Prediction of membrane spanning segments
and topology in $ \beta $-barrel
membrane proteins at better accuracy . . 217--223
Francesco Aquilante and
Luca De Vico and
Nicolas Ferré and
Giovanni Ghigo and
Per-åke Malmqvist and
Pavel Neogrády and
Thomas Bondo Pedersen and
Michal Pito\unák and
Markus Reiher and
Björn O. Roos and
Luis Serrano-Andrés and
Miroslav Urban and
Valera Veryazov and
Roland Lindh MOLCAS 7: the Next Generation . . . . . 224--247
Viwat Vchirawongkwin and
Andreas B. Pribil and
Bernd M. Rode Ab initio quantum mechanical charge
field study of hydrated bicarbonate ion:
Structural and dynamical properties . . 249--257
Hsin-Tsung Chen and
Jee-Gong Chang and
Shin-Pon Ju and
Hui-Lung Chen First-principle calculations on CO
oxidation catalyzed by a gold
nanoparticle . . . . . . . . . . . . . . 258--265
Priyanka Prakash and
Ramasubbu Sankararamakrishnan Force field dependence of phospholipid
headgroup and acyl chain properties:
Comparative molecular dynamics
simulations of DMPC bilayers . . . . . . 266--277
S. Sikander Azam and
Len Herald V. Lim and
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Hydrated germanium (II): Irregular
structural and dynamical properties
revealed by a quantum mechanical charge
field molecular dynamics study . . . . . 278--285
S. Jalili and
M. Akhavan Molecular dynamics simulation study of
association in trifluoroethanol/water
mixtures . . . . . . . . . . . . . . . . 286--294
Lionello Pogliani Model of twelve properties of a set of
organic solvents with graph-theoretical
and/or experimental parameters . . . . . 295--307
Johan Strümpfer and
Kevin J. Naidoo Computing free energy hypersurfaces for
anisotropic intermolecular associations 308--316
Irina S. Moreira and
Pedro A. Fernandes and
Maria J. Ramos Protein--protein docking dealing with
the unknown . . . . . . . . . . . . . . 317--342
Carlo Canepa A stationary-wave model of enzyme
catalysis . . . . . . . . . . . . . . . 343--350
Qi Dai and
Xiaoqing Liu and
Lihua Li and
Yuhua Yao and
Bin Han and
Lei Zhu Using Gaussian model to improve
biological sequence comparison . . . . . 351--361
Bin Li and
Tian-Shu Chu and
Ke-Li Han Non-Born--Oppenheimer dynamics
calculations using the coherent
switching with decay of mixing method 362--370
Zhongqiao Hu and
Jianwen Jiang Assessment of biomolecular force fields
for molecular dynamics simulations in a
protein crystal . . . . . . . . . . . . 371--380
Andrey A. Toropov and
Alla P. Toropova and
Emilio Benfenati and
Danuta Leszczynska and
Jerzy Leszczynski SMILES-based optimal descriptors: QSAR
analysis of fullerene-based HIV-1 PR
inhibitors by means of balance of
correlations . . . . . . . . . . . . . . 381--392
Shihai Yan and
Sunwoo Kang and
Tomoyuki Hayashi and
Shaul Mukamel and
Jin Yong Lee Computational studies on electron and
proton transfer in phenol-imidazole-base
triads . . . . . . . . . . . . . . . . . 393--402
Hui Zhang and
Gui-Ling Zhang and
Jing-Yao Liu and
Miao Sun and
Bo Liu and
Ze-Sheng Li Theoretical study and rate constants
calculation for the reactions of SiH$_3$
radical with SiH$_3$CH$_3$ and SiH$_2$
(CH$_3$ )$_2$ . . . . . . . . . . . . . 403--411
Christos Christodouleas and
Demetrios Xenides and
Theodore E. Simos Trends of the bonding effect on the
performance of DFT methods in electric
properties calculations: a pattern
recognition and metric space approach on
some XY$_2$ (X = O, S and Y = H, O, F,
S, Cl) molecules . . . . . . . . . . . . 412--420
A. V. Larin and
G. M. Zhidomirov and
D. N. Trubnikov and
D. P. Vercauteren Ion-exchanged binuclear Ca$_2$O$_x$
clusters, $ x = 1 $--4, as active sites
of selective oxidation over MOR and FAU
zeolites . . . . . . . . . . . . . . . . 421--430
Athanassios C. Tsipis and
Ioannis G. Depastas and
Efstathios E. Karagiannis and
Constantinos A. Tsipis Diagnosis of magnetoresponsive aromatic
and antiaromatic zones in three-membered
rings of $d$- and $f$-block elements . . 431--446
Tsutomu Ikegami and
Toyokazu Ishida and
Dmitri G. Fedorov and
Kazuo Kitaura and
Yuichi Inadomi and
Hiroaki Umeda and
Mitsuo Yokokawa and
Satoshi Sekiguchi Fragment molecular orbital study of the
electronic excitations in the
photosynthetic reaction center of
Blastochloris viridis . . . . . . . . . 447--454
Oleg Trott and
Arthur J. Olson AutoDock Vina: Improving the speed and
accuracy of docking with a new scoring
function, efficient optimization, and
multithreading . . . . . . . . . . . . . 455--461
Rekik Najeh and
Ghalla Houcine and
Henryk T. Flakus and
Magdalena Jablonska and
Oujia Brahim Experimental and theoretical study of
the polarized infrared spectra of the
hydrogen bond in 3-thiophenic acid
crystal . . . . . . . . . . . . . . . . 463--475
Daniel K. W. Mok and
Foo-Tim Chau and
Edmond P. F. Lee and
John M. Dyke High-level ab initio calculations on
HGeCl and the equilibrium geometry of
the $ {\rm \tilde {A}}^1 {\rm A}' $
state derived from Franck--Condon
analysis of the single-vibronic-level
emission spectra of HGeCl and DGeCl . . 476--491
Peng Cui and
Jian Wu and
Guiqing Zhang and
Russell J. Boyd A simple representation of energy matrix
elements in terms of symmetry-invariant
bases . . . . . . . . . . . . . . . . . 492--496
Masahiro Sekiya and
Takeshi Noro and
Toshikatsu Koga and
Shiro L. Saito Relativistic correlating basis sets for
$_{57}$La and $_{89}$Ac . . . . . . . . 497--499
Mohamad Akbar Ali and
B. Rajakumar Rate coefficients for the reaction of OH
with CF$_3$CH$_2$CH$_3$ (HFC-263fb)
between 200 and 400 K: ab initio, DFT,
and transition state theory calculations 500--509
Yue-Meng Ji and
Fenglei Cao and
Hui Gao and
Xiangzhi Li and
Cunyuan Zhao and
Chengyong Su and
Jing-Yao Liu and
Ze-Sheng Li On the kinetic mechanism of the hydrogen
abstraction reactions of the hydroxyl
radical with CH$_3$CF$_2$Cl and
CH$_3$CFCl$_2$: a dual level direct
dynamics study . . . . . . . . . . . . . 510--519
Jesús Gálvez and
Antonio Guirado A theoretical study of topomerization of
imine systems: Inversion, rotation or
mixed mechanisms? . . . . . . . . . . . 520--531
Yong Zhang and
Wenhua Xu and
Qiming Sun and
Wenli Zou and
Wenjian Liu Excited states of OsO$_4$: a
comprehensive time-dependent
relativistic density functional theory
study . . . . . . . . . . . . . . . . . 532--551
Angelika Baranowska and
Andrzej J. Sadlej Polarized basis sets for accurate
calculations of static and dynamic
electric properties of molecules . . . . 552--560
Pieter M. S. Hendrickx and
Francisco Corzana and
Stefaan Depraetere and
Dirk A. Tourwé and
Koen Augustyns and
José C. Martins The use of time-averaged $^3$J$_{HH}$
restrained molecular dynamics (tar-MD)
simulations for the conformational
analysis of five-membered ring systems:
Methodology and applications . . . . . . 561--572
Wolfgang Quapp and
Alraune Zech Transition state theory with Tsallis
statistics . . . . . . . . . . . . . . . 573--585
Feng Fan and
Jiagao Cheng and
Zhong Li and
Xiaoyong Xu and
Xuhong Qian Novel dimer based descriptors with
solvational computation for QSAR study
of oxadiazoylbenzoyl-ureas as novel
insect-growth regulators . . . . . . . . 586--591
Dong-Sheng Cao and
Yi-Zeng Liang and
Qing-Song Xu and
Hong-Dong Li and
Xian Chen A new strategy of outlier detection for
QSAR/QSPR . . . . . . . . . . . . . . . 592--602
Youn Jo Ko and
Won Ho Jo Chloride ion conduction without water
coordination in the pore of ClC protein 603--611
Michael Gilleßen and
Richard Dronskowski A combinatorial study of inverse Heusler
alloys by first-principles computational
methods . . . . . . . . . . . . . . . . 612--619
Jory Z. Ruscio and
Nicolas L. Fawzi and
Teresa Head-Gordon How hot? Systematic convergence of the
replica exchange method using multiple
reservoirs . . . . . . . . . . . . . . . 620--627
Tao Liu and
Bao-Hui Xia and
Qing-Chuan Zheng and
Xin Zhou and
Qing-Jiang Pan and
Hong-Xing Zhang DFT/TD-DFT investigation on Ir(III)
complexes with $N$-heterocyclic carbene
ligands: Geometries, electronic
structures, absorption, and
phosphorescence properties . . . . . . . 628--638
T. G. A. Youngs Aten --- an application for the
creation, editing, and visualization of
coordinates for glasses, liquids,
crystals, and molecules . . . . . . . . 639--648
Thierry Schüpbach and
Vincent Zoete and
Brice Tsakam-Sotché and
Olivier Michielin Fourier transform convolution integrals
applied to generalized Born molecular
volume . . . . . . . . . . . . . . . . . 649--659
Udo Feldkamp CANADA: Designing nucleic acid sequences
for nanobiotechnology applications . . . 660--663
Sebastian Schlund and
Eline M. Basílio Janke and
Klaus Weisz and
Bernd Engels Predicting the tautomeric equilibrium of
acetylacetone in solution. I. The right
answer for the wrong reason? . . . . . . 665--670
K. Vanommeslaeghe and
E. Hatcher and
C. Acharya and
S. Kundu and
S. Zhong and
J. Shim and
E. Darian and
O. Guvench and
P. Lopes and
I. Vorobyov and
A. D. Mackerell Jr. CHARMM general force field: a force
field for drug-like molecules compatible
with the CHARMM all-atom additive
biological force fields . . . . . . . . 671--690
Ramu Anandakrishnan and
Alexey V. Onufriev An $ N \log N $ approximation based on
the natural organization of biomolecules
for speeding up the computation of long
range interactions . . . . . . . . . . . 691--706
Santiago Vilar and
Joel Karpiak and
Stefano Costanzi Ligand and structure-based models for
the prediction of ligand-receptor
affinities and virtual screenings:
Development and application to the $
\beta_2 $-adrenergic receptor . . . . . 707--720
Selina C. Wang and
Peter A. Beal and
Dean J. Tantillo Covalent hydration energies for purine
analogs by quantum chemical methods . . 721--725
Julien Maupetit and
Philippe Derreumaux and
Pierre Tufféry A fast method for large-scale De Novo
peptide and miniprotein structure
prediction . . . . . . . . . . . . . . . 726--738
Nilesh R. Tawari and
Mariam S. Degani Pharmacophore mapping and electronic
feature analysis for a series of
nitroaromatic compounds with
antitubercular activity . . . . . . . . 739--751
Hanbing Rao and
Zerong Li and
Xiangyuan Li and
Xiaohua Ma and
Choongyong Ung and
Hu Li and
Xianghui Liu and
Yuzong Chen Identification of small molecule
aggregators from large compound
libraries by support vector machines . . 752--763
Vill\Ho K. Pálfi and
András Perczel Stability of the hydration layer of
tropocollagen: a QM study . . . . . . . 764--777
Hui Li and
Dmitri G. Fedorov and
Takeshi Nagata and
Kazuo Kitaura and
Jan H. Jensen and
Mark S. Gordon Energy gradients in combined fragment
molecular orbital and polarizable
continuum model (FMO/PCM) calculation 778--790
Katsumi Murata and
Naoya Nagata and
Isao Nakanishi and
Kazuo Kitaura Ligand shape emerges in solvent dipole
ordering region at ligand binding site
of protein . . . . . . . . . . . . . . . 791--796
Giulio Rastelli and
Alberto Del Rio and
Gianluca Degliesposti and
Miriam Sgobba Fast and accurate predictions of binding
free energies using MM-PBSA and MM-GBSA 797--810
Jean-François Truchon and
Anthony Nicholls and
J. Andrew Grant and
Radu I. Iftimie and
Beno\^\it Roux and
Christopher I. Bayly Using electronic polarization from the
internal continuum (EPIC) for
intermolecular interactions . . . . . . 811--824
Laibin Zhang and
Huifang Li and
Jilai Li and
Xiaohua Chen and
Yuxiang Bu Absorption and fluorescence emission
spectroscopic characters of
naphtho-homologated yy-DNA bases and
effect of methanol solution and base
pairing . . . . . . . . . . . . . . . . 825--836
Samuel Genheden and
Ulf Ryde How to obtain statistically converged
MM/GBSA results . . . . . . . . . . . . 837--846
Ling Wang and
Boris Stumm and
Volkhard Helms Graph-theoretical identification of
dissociation pathways on free energy
landscapes of biomolecular interaction 847--854
Yves Noel and
Philippe D'arco and
Raffaella Demichelis and
Claudio M. Zicovich-Wilson and
Roberto Dovesi On the use of symmetry in the ab initio
quantum mechanical simulation of
nanotubes and related materials . . . . 855--862
Guang Tao Yu and
Wei Chen and
Feng Long Gu and
Yuriko Aoki Theoretical study on nonlinear optical
properties of the Li$^+$
[calix[4]pyrrole]Li$^-$ dimer, trimer
and its polymer with diffuse excess
electrons . . . . . . . . . . . . . . . 863--870
Xiaoyan Zheng and
Xueye Wang and
Shanfeng Yi and
Nuanqing Wang and
Yueming Peng Density functional theory study of the
free and tetraprotonated spheroidal
macrotricyclic ligands and the complexes
with halide anions: F$^-$, Cl$^-$,
Br$^-$ . . . . . . . . . . . . . . . . . 871--881
Alejandro Speck Planche and
Marcus Tulius Scotti and
Vicente de Paulo Emerenciano and
América García López and
Enrique Molina Pérez and
Eugenio Uriarte Designing novel antitrypanosomal agents
from a mixed graph-theoretical
substructural approach . . . . . . . . . 882--894
Michael Springborg Book review: \booktitleComputational
Chemistry Workbook, by Thomas Heine,
Jan-Ole Joswig, and Achim Gelessus,
Wiley-VCH Verlag GmbH & Co. KGaA,
Weinheim, 2009, 250 pp. ISBN-10
3-527-32442-9 . . . . . . . . . . . . . 895--896
Hwanho Choi and
Hongsuk Kang and
Hwangseo Park New angle-dependent potential energy
function for backbone--backbone hydrogen
bond in protein--protein interactions 897--903
Benjamin D. Allen and
Stephen L. Mayo An efficient algorithm for multistate
protein design based on FASTER . . . . . 904--916
Mercedes Alonso and
Bernardo Herradón A universal scale of aromaticity for $
\pi $-organic compounds . . . . . . . . 917--928
Behnam Assadollahzadeh and
Sascha Schäfer and
Peter Schwerdtfeger Electronic properties for small tin
clusters Sn$_n$ ($ n \leq 20 $ ) from
density functional theory and the
convergence toward the solid state . . . 929--937
Chao Gao and
Hua-Qing Yang and
Jian Xu and
Song Qin and
Chang-Wei Hu Theoretical study on the gas-phase
reaction mechanism between rhodium
monoxide and methane for methanol
production . . . . . . . . . . . . . . . 938--953
Yu Takano and
Haruki Nakamura Electronic structures of heme $a$ of
cytochrome $c$ oxidase in the redox
states --- charge density migration to
the propionate groups of heme $a$ . . . 954--962
Richard Kramer Campen and
James D. Kubicki Interaction energy and the shift in OH
stretch frequency on hydrogen bonding
for the H$_2$O $ \rightarrow $ H$_2$O,
CH$_3$OH $ \rightarrow $ H$_2$O, and
H$_2$O $ \rightarrow $ CH$_3$OH dimers 963--972
Jiazhong Li and
Shuyan Li and
Beilei Lei and
Huanxiang Liu and
Xiaojun Yao and
Mancang Liu and
Paola Gramatica A new strategy to improve the predictive
ability of the local lazy regression and
its application to the QSAR study of
melanin-concentrating hormone receptor 1
antagonists . . . . . . . . . . . . . . 973--985
Zheng Guo Huang and
Lei Yu and
Yu Mei Dai An ab initio potential energy surface
and vibrational energy levels of ZnH$_2$ 986--993
An Ghysels and
Veronique Van Speybroeck and
Ewald Pauwels and
Saron Catak and
Bernard R. Brooks and
Dimitri Van Neck and
Michel Waroquier Comparative study of various normal mode
analysis techniques based on partial
Hessians . . . . . . . . . . . . . . . . 994--1007
Jason P. Holland and
Jennifer C. Green Evaluation of exchange-correlation
functionals for time-dependent density
functional theory calculations on metal
complexes . . . . . . . . . . . . . . . 1008--1014
Bogdan Lev and
Rui Zhang and
Aurélien de la Lande and
Dennis Salahub and
Sergei Yu Noskov The QM--MM interface for CHARMM--deMon 1015--1023
Karmen Condic-Jurkic and
Hendrik Zipse and
David M. Smith A compound QM/MM procedure: Comparative
performance on a pyruvate formate-lyase
model system . . . . . . . . . . . . . . 1024--1035
Chang-Sheng Wang and
Chang-Liang Sun Investigation on the individual
contributions of N H\dottedbondO C and C
H\dottedbondO C interactions to the
binding energies of $ \beta $-sheet
models . . . . . . . . . . . . . . . . . 1036--1044
Yu-Hua Yao and
Qi Dai and
Ling Li and
Xu-Ying Nan and
Ping-An He and
Yao-Zhou Zhang Similarity/dissimilarity studies of
protein sequences based on a new $2$D
graphical representation . . . . . . . . 1045--1052
Vincent Tognetti and
Pascal Le Floch and
Carlo Adamo How the choice of a computational model
could rule the chemical interpretation:
the Ni(II) catalyzed ethylene
dimerization as a case study . . . . . . 1053--1062
Noel Ferro and
Thomas Bredow Assessment of quantum-chemical methods
for electronic properties and geometry
of signaling biomolecules . . . . . . . 1063--1079
Yury N. Vorobjev Blind docking method combining search of
low-resolution binding sites with ligand
pose refinement by molecular
dynamics-based global optimization . . . 1080--1092
Michal Brylinski and
Jeffrey Skolnick Q-Dock$^{LHM}$: Low-resolution
refinement for ligand comparative
modeling . . . . . . . . . . . . . . . . 1093--1105
Simone Marsili and
Giorgio Federico Signorini and
Riccardo Chelli and
Massimo Marchi and
Piero Procacci ORAC: a molecular dynamics simulation
program to explore free energy surfaces
in biomolecular systems at the atomistic
level . . . . . . . . . . . . . . . . . 1106--1116
David Poger and
Wilfred F. Van Gunsteren and
Alan E. Mark A new force field for simulating
phosphatidylcholine bilayers . . . . . . 1117--1125
Jingyu Sun and
Yizhen Tang and
Hao Sun and
Xiujuan Jia and
Xiumei Pan and
Rongshun Wang Theoretical and kinetic study of the H +
C$_2$H$_5$CN reaction . . . . . . . . . 1126--1134
Jens Kleesiek and
Andrew E. Torda RNA secondary structure prediction using
a self-consistent mean field approach 1135--1142
Urszula Koz\lowska and
Adam Liwo and
Harold A. Scheraga Determination of side-chain-rotamer and
side-chain and backbone
virtual-bond-stretching potentials of
mean force from AM1 energy surfaces of
terminally-blocked amino-acid residues,
for coarse-grained simulations of
protein structure and folding. I. The
method . . . . . . . . . . . . . . . . . 1143--1153
Urszula Koz\lowska and
Gia G. Maisuradze and
Adam Liwo and
Harold A. Scheraga Determination of side-chain-rotamer and
side-chain and backbone
virtual-bond-stretching potentials of
mean force from AM1 energy surfaces of
terminally-blocked amino-acid residues,
for coarse-grained simulations of
protein structure and folding. II.
Results, comparison with statistical
potentials, and implementation in the
UNRES force field . . . . . . . . . . . 1154--1167
Ryota Jono and
Yuusuke Watanabe and
Kentaro Shimizu and
Tohru Terada Multicanonical ab inito QM/MM molecular
dynamics simulation of a peptide in an
aqueous environment . . . . . . . . . . 1168--1175
Angelika Baranowska and
Krzysztof Z. \L\kaczkowski and
Andrzej J. Sadlej Model studies of the optical rotation,
and theoretical determination of its
sign for $ \beta $-pinene and
trans-pinane . . . . . . . . . . . . . . 1176--1181
K. Senthil Kumar and
Archita Patnaik Intramolecular electronic communication
in a dimethylaminoazobenzene--fullerene
C$_{60}$ dyad: an experimental and
TD-DFT study . . . . . . . . . . . . . . 1182--1194
Len Herald V. Lim and
Andreas B. Pribil and
Andreas E. Ellmerer and
Bernhard R. Randolf and
Bernd M. Rode Temperature dependence of structure and
dynamics of the hydrated Ca$^{2+}$ ion
according to ab initio quantum
mechanical charge field and classical
molecular dynamics . . . . . . . . . . . 1195--1200
Xiaoqi Zheng and
Chun Li and
Jun Wang An information-theoretic approach to the
prediction of protein structural class 1201--1206
Maria Safi and
Ryan H. Lilien Restricted dead-end elimination: Protein
redesign with a bounded number of
residue mutations . . . . . . . . . . . 1207--1215
Hao Wu and
Alana Canfield and
Jhashanath Adhikari and
Shuanghong Huo Quantum mechanical studies on model $
\alpha $-pleated sheets . . . . . . . . 1216--1223
Kenneth W. Borrelli and
Benjamin Cossins and
Victor Guallar Exploring hierarchical refinement
techniques for induced fit docking with
protein and ligand flexibility . . . . . 1224--1235
Gráinne Black and
John M. Simmie Barrier heights for H-atom abstraction
by H\.O$_2$ from $n$-butanol --- a
simple yet exacting test for model
chemistries? . . . . . . . . . . . . . . 1236--1248
Xue-Gang Yang and
Wei Lv and
Yu-Zong Chen and
Ying Xue In silico prediction and screening of $
\gamma $-secretase inhibitors by
molecular descriptors and machine
learning methods . . . . . . . . . . . . 1249--1258
Ahmed Mehdi and
Legesse Adane and
Dhilon S. Patel and
Prasad V. Bharatam Electronic structure and reactivity of
guanylthiourea: a quantum chemical study 1259--1267
Peter Eastman and
Vijay S. Pande Efficient nonbonded interactions for
molecular dynamics on a graphics
processing unit . . . . . . . . . . . . 1268--1272
Anne Lopes and
Marcel Schmidt Am Busch and
Thomas Simonson Computational design of protein--ligand
binding: Modifying the specificity of
asparaginyl-tRNA synthetase . . . . . . 1273--1286
Norio Takenaka and
Yoshiyuki Koyano and
Yukinori Nakagawa and
Masataka Nagaoka An optimum strategy for solution
chemistry using semiempirical molecular
orbital method: Importance of
description of charge distribution . . . 1287--1296
Chérif F. Matta How dependent are molecular and atomic
properties on the electronic structure
method? Comparison of Hartree--Fock,
DFT, and MP2 on a biologically relevant
set of molecules . . . . . . . . . . . . 1297--1311
N. Yousfi and
M. Sekkal-Rahal and
A. Sayede and
M. Springborg Relaxed energetic maps of $ \kappa
$-carrabiose: a DFT study . . . . . . . 1312--1320
J. J. Borrás-Almenar and
S. Cardona-Serra and
J. M. Clemente-Juan and
E. Coronado and
A. V. Palii and
B. S. Tsukerblat MVPACK: a package to calculate energy
levels and magnetic properties of high
nuclearity mixed valence clusters . . . 1321--1332
Andrzej J. Rzepiela and
Lars V. Schäfer and
Nicolae Goga and
H. Jelger Risselada and
Alex H. De Vries and
Siewert J. Marrink Reconstruction of atomistic details from
coarse-grained structures . . . . . . . 1333--1343
Anonymous Journal of Computational Chemistry,
Volume 31, Number 2, January 30, 2010 1344--1344
Anonymous Computing free energy hypersurfaces for
anisotropic intermolecular associations
Trevor Cickovski and
Santanu Chatterjee and
Jacob Wenger and
Christopher R. Sweet and
Jesús A. Izaguirre MDLab: a molecular dynamics simulation
prototyping environment . . . . . . . . 1345--1356
Hisashi Okumura and
Emilio Gallicchio and
Ronald M. Levy Conformational populations of
ligand-sized molecules by replica
exchange molecular dynamics and
temperature reweighting . . . . . . . . 1357--1367
Changjun Chen and
Yi Xiao Accurate free energy calculation along
optimized paths . . . . . . . . . . . . 1368--1375
Na Qi and
Rong-Zhen Liao and
Jian-Guo Yu and
Ruo-Zhuang Liu DFT study of the asymmetric nitroaldol
(Henry) reaction catalyzed by a
dinuclear Zn complex . . . . . . . . . . 1376--1384
Tianshu Chu Quantum mechanics and quasiclassical
study of the H/D + FO $ \rightarrow $
OH/OD + F, HF/DF + O reactions: Chemical
stereodynamics . . . . . . . . . . . . . 1385--1396
Wen-Zuo Li and
Jian-Bo Cheng and
Qing-Zhong Li and
Bao-An Gong and
Jia-Zhong Sun Theoretical study on HBO$^+$ and HOB$^+$
cations using multiconfiguration
second-order perturbation theory . . . . 1397--1401
Edyta Ma\lolepsza and
Birgit Strodel and
Mey Khalili and
Semen Trygubenko and
Szilard N. Fejer and
David J. Wales Symmetrization of the AMBER and CHARMM
force fields . . . . . . . . . . . . . . 1402--1409
Xiao-Nan Jiang and
Chang-Liang Sun and
Chang-Sheng Wang A scheme for rapid prediction of
cooperativity in hydrogen bond chains of
formamides, acetamides, and
$N$-methylformamides . . . . . . . . . . 1410--1420
Yena Qu and
Kehe Su and
Xin Wang and
Yan Liu and
Qingfeng Zeng and
Laifei Cheng and
Litong Zhang Reaction pathways of propene pyrolysis 1421--1442
Amir Abbas Rafati and
Sayed Majid Hashemianzadeh and
Zabiollah Bolboli Nojini and
Negin Naghshineh Canonical Monte Carlo simulation of
adsorption of O$_2$ and N$_2$ mixture on
single walled carbon nanotube at
different temperatures and pressures . . 1443--1449
Rungtiwa Chidthong and
Supa Hannongbua Excited state properties, fluorescence
energies, and lifetimes of a
poly(fluorene-phenylene), based on
TD-DFT investigation . . . . . . . . . . 1450--1457
Xiaoyan Zheng and
Xueye Wang and
Shanfeng Yi and
Nuanqing Wang and
Yueming Peng Density functional theory study of
calix[4]arene-$N$-azacrown-5,
calix[4]arene-$N$-phenyl-azacrown-5, and
their complexes with alkali-metal
cations: Na$^+$, K$^+$, and Rb$^+$ . . . 1458--1468
Ville Weijo and
Maharavo Randrianarivony and
Helmut Harbrecht and
Luca Frediani Wavelet formulation of the polarizable
continuum model . . . . . . . . . . . . 1469--1477
Lin Zhu and
Jie Yang and
Jiang-Ning Song and
Kuo-Chen Chou and
Hong-Bin Shen Improving the accuracy of predicting
disulfide connectivity by feature
selection . . . . . . . . . . . . . . . 1478--1485
Lj. Miljacic and
D. E. Ellis Radial-template approach for accurate
density representation in computational
quantum theory . . . . . . . . . . . . . 1486--1494
J. M. C. Marques and
A. A. C. C. Pais and
P. E. Abreu Generation and characterization of
low-energy structures in atomic clusters 1495--1503
Viktor Bezugly and
Pawel Wielgus and
Miroslav Kohout and
Frank R. Wagner Electron localizability indicators
ELI--D and ELIA for highly correlated
wavefunctions of homonuclear dimers. I.
Li$_2$, Be$_2$, B$_2$, and C$_2$ . . . . 1504--1519
Yizhen Tang and
Jingyu Sun and
Xiujuan Jia and
Hao Sun and
Xiumei Pan and
Rongshun Wang Mechanistic and kinetic investigations
of N$_2$H$_4$ + OH reaction . . . . . . 1520--1527
Thomas A. Manz and
David S. Sholl A dimensionless reaction coordinate for
quantifying the lateness of transition
states . . . . . . . . . . . . . . . . . 1528--1541
Artur Gertych and
Jacek Koput Ab initio prediction of the structure
and vibration-rotation spectroscopic
properties of Na$_2$OH and K$_2$OH . . . 1542--1549
Alexey Aleksandrov and
Thomas Simonson A molecular mechanics model for imatinib
and imatinib:kinase binding . . . . . . 1550--1560
Pu Liu and
Dimitris K. Agrafiotis and
Douglas L. Theobald Fast determination of the optimal
rotational matrix for macromolecular
superpositions . . . . . . . . . . . . . 1561--1563
Hendrik Heinz Computational screening of biomolecular
adsorption and self-assembly on
nanoscale surfaces . . . . . . . . . . . 1564--1568
Clara D. Christ and
Alan E. Mark and
Wilfred F. van Gunsteren Basic ingredients of free energy
calculations: a review . . . . . . . . . 1569--1582
Asbjòrn Holt and
Jonas Boström and
Gunnar Karlström and
Roland Lindh A NEMO potential that includes the
dipole--quadrupole and
quadrupole--quadrupole polarizability 1583--1591
Ying Xiong and
Junjun Liu and
Guang-Fu Yang and
Chang-Guo Zhan Computational determination of
fundamental pathway and activation
barriers for acetohydroxyacid
synthase-catalyzed condensation
reactions of $ \alpha $-keto acids . . . 1592--1602
Elsa Sanchez-Garcia and
Markus Doerr and
Walter Thiel QM/MM study of the absorption spectra of
DsRed.M1 chromophores . . . . . . . . . 1603--1612
Michael Wessel and
Richard Dronskowski A first-principles study on the
existence and structures of the lighter
alkaline-earth pernitrides . . . . . . . 1613--1617
Xian-Yong Pang and
Bin Xing and
Li-Qin Xue and
Gui-Chang Wang Selective oxidation of styrene on an
oxygen-adsorbed Cu(111): a comparison
with Au(111) . . . . . . . . . . . . . . 1618--1624
Stephen D. Bond and
Jehanzeb Hameed Chaudhry and
Eric C. Cyr and
Luke N. Olson A first-order system least-squares
finite element method for the
Poisson--Boltzmann equation . . . . . . 1625--1635
Nathan Schmid and
Mathias Bötschi and
Wilfred F. Van Gunsteren A GPU solvent--solvent interaction
calculation accelerator for biomolecular
simulations using the GROMOS software 1636--1643
Maciej Maciejczyk and
Aleksandar Spasic and
Adam Liwo and
Harold A. Scheraga Coarse-grained model of nucleic acid
bases . . . . . . . . . . . . . . . . . 1644--1655
Nitin Wadnerkar and
Vijayanand Kalamse and
Ajay Chaudhari Hydrogen uptake capacity of C$_2$H$_4$Sc
and its ions: a density functional study 1656--1661
Qing-Zhong Li and
Xu Dong and
Bo Jing and
Wen-Zuo Li and
Jian-Bo Cheng and
Bao-An Gong and
Zhi-Wu Yu A new unconventional halogen bond
C\bondX\dottedbondH\bondM between HCCX
(X = Cl and Br) and HMH (M = Be and Mg):
an ab initio study . . . . . . . . . . . 1662--1669
G. Cilpa and
M. T. Hyvönen and
A. Koivuniemi and
M.-L. Riekkola Atomistic insight into
chondroitin-6-sulfate glycosaminoglycan
chain through quantum mechanics
calculations and molecular dynamics
simulation . . . . . . . . . . . . . . . 1670--1680
J. W. Liu and
Z. F. Liu Thermal dissociation of tripropylamine
as the first step in the growth of
carbon nanotubes inside AlPO$_4$-5
channels . . . . . . . . . . . . . . . . 1681--1688
Jun Wang and
Ray Luo Assessment of linear finite-difference
Poisson--Boltzmann solvers . . . . . . . 1689--1698
Hiroshi Takeuchi Global minimum geometries of acetylene
clusters (HCCH)$_n$ with $ n \leq 55 $
obtained by a heuristic method combined
with geometrical perturbations . . . . . 1699--1706
Polina Georgieva and
Fahmi Himo Quantum chemical modeling of enzymatic
reactions: the case of histone lysine
methyltransferase . . . . . . . . . . . 1707--1714
Li-Hua Gan and
Jian-Qiang Zhao and
Qun Hui Nonclassical fullerenes with a heptagon
violating the pentagon adjacency penalty
rule . . . . . . . . . . . . . . . . . . 1715--1721
J. Santeri Puranen and
Mikko J. Vainio and
Mark S. Johnson Accurate conformation-dependent
molecular electrostatic potentials for
high-throughput in silico drug discovery 1722--1732
Marcin Makowski and
Jacek Korchowiec and
Feng Long Gu and
Yuriko Aoki Describing electron correlation effects
in the framework of the elongation
method --- Elongation-MP2: Formalism,
implementation and efficiency . . . . . 1733--1740
Julien Preat and
Francisco Rodríguez-Ropero and
Juan Torras and
Oscar Bertran and
David Zanuy and
Carlos Alemán Parameterization of the torsional
potential for calix[4]arene-substituted
poly(thiophene)s . . . . . . . . . . . . 1741--1751
Yibo Lei and
Bingbing Suo and
Yusheng Dou and
Yubin Wang and
Zhenyi Wen New implementations of MRCI in
semiempirical frameworks . . . . . . . . 1752--1758
Guang-Yue Li and
Guang-Jiu Zhao and
Yu-Hui Liu and
Ke-Li Han and
Guo-Zhong He TD--DFT study on the sensing mechanism
of a fluorescent chemosensor for
fluoride: Excited-state proton transfer 1759--1765
Lei Chen and
Ziliang Qian and
Kaiyan Fen and
Yudong Cai Prediction of interactiveness between
small molecules and enzymes by combining
gene ontology and compound similarity 1766--1776
Anna Maria Ferrari and
Bartolomeo Civalleri and
Roberto Dovesi Ab initio periodic study of the
conformational behavior of glycine
helical homopeptides . . . . . . . . . . 1777--1784
Chinapong Kritayakornupong and
Viwat Vchirawongkwin and
Bernd M. Rode An ab initio quantum mechanical charge
field molecular dynamics simulation of a
dilute aqueous HCl solution . . . . . . 1785--1792
W. H. Eugen Schwarz Book review: \booktitleThe Periodic
Table: Its Story and Its Significance,
by Eric R. Scerri, ISBN-13:
978-0-19-530573-9 . . . . . . . . . . . 1793--1794
Weiyu Song and
Jing Wang and
Jian Meng and
Zhijian Wu Half metallic properties of LaSrVMoO$_6$ 1795--1798
Sergei Grudinin and
Stephane Redon Practical modeling of molecular systems
with symmetries . . . . . . . . . . . . 1799--1814
Santanab Giri and
Debesh Ranjan Roy and
Soma Duley and
Arindam Chakraborty and
Ramakrishnan Parthasarathi and
Munusamy Elango and
Ramadoss Vijayaraj and
Venkatesan Subramanian and
Rafael Islas and
Gabriel Merino and
Pratim Kumar Chattaraj Bonding, aromaticity, and structure of
trigonal dianion metal clusters . . . . 1815--1821
Chunzhi Ai and
Yan Li and
Yonghua Wang and
Wei Li and
Peipei Dong and
Guangbo Ge and
Ling Yang Investigation of binding features:
Effects on the interaction between
CYP2A6 and inhibitors . . . . . . . . . 1822--1831
Milan Randi\'c and
Toma\vz Pisanski and
Marjana Novi\vc and
Dejan Plav\vsi\'c Novel graph distance matrix . . . . . . 1832--1841
Benjamí Martorell and
Anna Clotet and
Jordi Fraxedas A first principle study of the
structural, vibrational and electronic
properties of tetrathiafulvalene
adsorbed on Ag(110) and Au(110) surfaces 1842--1852
Timm Lankau and
Chin-Hui Yu A model study of the efficiency of the
Asp--His--Ser triad . . . . . . . . . . 1853--1859
Richard P. Muller and
Ann E. Mattsson and
Curtis L. Janssen Calculation of chemical reaction
energies using the AM05 density
functional . . . . . . . . . . . . . . . 1860--1863
Elad Project and
Esther Nachliel and
Menachem Gutman Force field-dependant structural
divergence revealed during long time
simulations of Calbindin d9k . . . . . . 1864--1872
Janne Pesonen and
Krister O. E. Henriksson Polymer conformations in internal
(polyspherical) coordinates . . . . . . 1873--1881
Krister O. E. Henriksson and
Janne Pesonen Polymer dynamics in torsion space . . . 1882--1888
Roman Affentranger and
Xavier Daura Polypeptide folding on a
conformational-space network: Dependence
of network topology on the structural
discretization procedure . . . . . . . . 1889--1903
Erjun Zhao and
Jinping Wang and
Jian Meng and
Zhijian Wu Phase stability and mechanical
properties of rhenium borides by
first-principles calculations . . . . . 1904--1910
Jan Fuhrmann and
Alexander Rurainski and
Hans-Peter Lenhof and
Dirk Neumann A new Lamarckian genetic algorithm for
flexible ligand-receptor docking . . . . 1911--1918
Tim Geppert and
Ewgenij Proschak and
Gisbert Schneider Protein-protein docking by
shape-complementarity and property
matching . . . . . . . . . . . . . . . . 1919--1928
Efrat Noy and
Amiram Goldblum Flexible protein-protein docking based
on Best-First search algorithm . . . . . 1929--1943
Potjaman Poolmee and
Supa Hannongbua Investigation of excited-state
properties of fluorene--thiophene
oligomers by the SAC--CI theoretical
approach . . . . . . . . . . . . . . . . 1945--1955
Jingheng Wu and
Juan Mei and
Sixiang Wen and
Siyan Liao and
Jincan Chen and
Yong Shen A self-adaptive genetic
algorithm-artificial neural network
algorithm with leave-one-out cross
validation for descriptor selection in
QSAR study . . . . . . . . . . . . . . . 1956--1968
John T. Tsalavoutis and
Michael P. Sigalas Density functional investigation and
bonding analysis of pentacoordinated
iron complexes with mixed cyano and
carbonyl ligands . . . . . . . . . . . . 1969--1978
Suchaya Pongsai Combination of the Metropolis Monte
Carlo and Lattice Statics method for
geometry optimization of H-(Al)-ZSM-5 1979--1985
Júlio C. S. da Silva and
Roberta P. Dias and
Wagner B. de Almeida and
Willian R. Rocha DFT study of the full catalytic cycle
for the propene hydroformylation
catalyzed by a heterobimetallic
HPt(SnCl$_3$ )(PH$_3$ )$_2$ model
catalyst . . . . . . . . . . . . . . . . 1986--2000
Prasenjit Seal Carbondioxide rare-gas systems:
Sensitivity of basis sets and
double-hybrid density functionals . . . 2001--2007
Philip Brown and
Christopher J. Woods and
Simon McIntosh-Smith and
Frederick R. Manby A massively multicore parallelization of
the Kohn--Sham energy gradients . . . . 2008--2013
Huameng Li and
Chenglong Li Multiple ligand simultaneous docking:
Orchestrated dancing of ligands in
binding sites of protein . . . . . . . . 2014--2022
Cui-Yu Niu and
Jiao Jiao and
Bin Xing and
Gui-Chang Wang and
Xian-He Bu Reaction mechanism of methanol
decomposition on Pt-based model
catalysts: a theoretical study . . . . . 2023--2037
Zheng-Wang Qu and
Hui Zhu Do anionic titanium dioxide
nano-clusters reach bulk band gap? A
density functional theory study . . . . 2038--2045
Hasan Pa\vsali\'c and
Adélia J. A. Aquino and
Daniel Tunega and
Georg Haberhauer and
Martin H. Gerzabek and
Herbert C. Georg and
Tatiane F. Moraes and
Kaline Coutinho and
Sylvio Canuto and
Hans Lischka Thermodynamic stability of
hydrogen-bonded systems in polar and
nonpolar environments . . . . . . . . . 2046--2055
Shu-Hui Yin and
Yufang Liu and
Wei Zhang and
Ming-Xing Guo and
Peng Song Time-dependent density functional theory
study on the hydrogen bonding-induced
twisted intramolecular charge-transfer
excited states of 2-(4'-$N$,
$N$-dimethylaminophenyl)imidazo[4,5-b]pyridine 2056--2062
Xiao Zhu and
Peter Koenig and
Michael Hoffmann and
Arun Yethiraj and
Qiang Cui Establishing effective simulation
protocols for $ \beta $- and $ \alpha $
/$ \beta $-peptides. III. Molecular
mechanical model for acyclic $ \beta
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Károly Németh and
Matt Challacombe and
Michel Van Veenendaal The choice of internal coordinates in
complex chemical systems . . . . . . . . 2078--2086
Udo Schnupf and
J. L. Willett and
Frank A. Momany 27 ps DFT molecular dynamics simulation
of $ \alpha $-maltose: a reduced basis
set study . . . . . . . . . . . . . . . 2087--2097
Li-Dong Gong and
Zhong-Zhi Yang Investigation of the molecular surface
area and volume: Defined and calculated
by the molecular face theory . . . . . . 2098--2108
Xun Li and
Yan Li and
Tiejun Cheng and
Zhihai Liu and
Renxiao Wang Evaluation of the performance of four
molecular docking programs on a diverse
set of protein-ligand complexes . . . . 2109--2125
Jia-Feng Yu and
Xiao Sun Reannotation of protein-coding genes
based on an improved graphical
representation of DNA sequence . . . . . 2126--2135
Ping-An He and
Yan-Ping Zhang and
Yu-Hua Yao and
Yi-Fa Tang and
Xu-Ying Nan The graphical representation of protein
sequences based on the physicochemical
properties and its applications . . . . 2136--2142
Xiaoyan Zheng and
Xueye Wang and
Keqi Shen and
Nuanqing Wang and
Yueming Peng Molecular design of a ``molecular
syringe'' mimic for metal cations using
a 1,3-alternate calix[4]arene cavity . . 2143--2156
Rui Wang and
Ce Hao and
Peng Li and
Ning-Ning Wei and
Jingwen Chen and
Jieshan Qiu Time-dependent density functional theory
study on the electronic excited-state
hydrogen-bonding dynamics of
4-aminophthalimide (4AP) in aqueous
solution: 4AP and 4AP--(H$_2$O)$_{1, 2}$
clusters . . . . . . . . . . . . . . . . 2157--2163
Xiangqian Hu and
Hao Hu and
David N. Beratan and
Weitao Yang A gradient-directed Monte Carlo approach
for protein design . . . . . . . . . . . 2164--2168
Maarten G. Wolf and
Martin Hoefling and
Camilo Aponte-Santamaría and
Helmut Grubmüller and
Gerrit Groenhof \tt g\_membed: Efficient insertion of a
membrane protein into an equilibrated
lipid bilayer with minimal perturbation 2169--2174
Yuko Ito and
Mitsunori Ikeguchi Structural fluctuation and concerted
motions in F$_1$-ATPase: a molecular
dynamics study . . . . . . . . . . . . . 2175--2185
Kenta Hongo and
Ryo Maezono and
Kenichi Miura Random number generators tested on
quantum Monte Carlo simulations . . . . 2186--2194
Ramon Carbó-Dorca and
Luz Dary Mercado Commentaries on quantum similarity (1):
Density gradient quantum similarity . . 2195--2212
Jakub Kaminský and
Ivan Raich and
Kate\vrina Tom\vcáková and
Petr Bou\vr Conformational behavior of simple
furanosides studied by optical rotation 2213--2224
Hajime Muta and
Noriaki Hirayama Alpha sphere filter method: Application
of pseudomolecular descriptors in
virtual screening of $2$D chemical
structures . . . . . . . . . . . . . . . 2225--2232
Bisheng Tan and
Rufang Peng and
Hongbo Li and
Bo Jin and
Shijin Chu and
Xinping Long Theoretical investigation of an
energetic fullerene derivative . . . . . 2233--2237
Xian-Hui Wu and
Guo-Lin Zou and
Jun-Min Quan and
Yun-Dong Wu A theoretical study on the catalytic
mechanism of Mus musculus adenosine
deaminase . . . . . . . . . . . . . . . 2238--2247
Yong Wu and
Lu Jin and
Ying Xue and
Ik-Mo Lee and
Chan Kyung Kim Mechanisms of norbornadiene dimerization
to Binor-S using cationic Co$^I$,
Rh$^I$, and Ir$^I$ catalysts . . . . . . 2248--2257
Chin-Hung Lai and
Pi-Tai Chou A computational study on the capability
of borane-cyclic boryl anion adducts to
act as hydrogen atom donors . . . . . . 2258--2262
Xiu-Juan Jia and
You-Jun Liu and
Jing-Yu Sun and
Hao Sun and
Fang Wang and
Zhong-Min Su and
Xiu-Mei Pan and
Rong-Shun Wang Computational studies on the mechanism
and kinetics of Cl reaction with
C$_2$H$_5$I . . . . . . . . . . . . . . 2263--2272
Viktor Bezugly and
Pawel Wielgus and
Miroslav Kohout and
Frank R. Wagner Electron localizability indicators
ELI--D and ELIA for highly correlated
wavefunctions of homonuclear dimers. II.
N$_2$, O$_2$, F$_2$, and Ne$_2$ . . . . 2273--2285
Stijn Fias and
Sofie Van Damme and
Patrick Bultinck Multidimensionality of delocalization
indices and nucleus-independent chemical
shifts in polycyclic aromatic
hydrocarbons II: Proof of further
nonlocality . . . . . . . . . . . . . . 2286--2293
Milan On\vcák and
Detlef Schröder and
Petr Slaví\vcek Theoretical study of the microhydration
of mononuclear and dinuclear uranium(VI)
species derived from solvolysis of
uranyl nitrate in water . . . . . . . . 2294--2306
Benjamin Waldher and
Jadwiga Kuta and
Samuel Chen and
Neil Henson and
Aurora E. Clark ForceFit: a code to fit classical force
fields to quantum mechanical potential
energy surfaces . . . . . . . . . . . . 2307--2316
Hisashi Ishida Branch migration of Holliday junction in
RuvA tetramer complex studied by
umbrella sampling simulation using a
path-search algorithm . . . . . . . . . 2317--2329
Xiao Zhu and
Alexander D. Mackerell Jr. Polarizable empirical force field for
sulfur-containing compounds based on the
classical Drude oscillator model . . . . 2330--2341
Shuchi Nagar and
Achintya Saha Modeling of diarylalkyl-imidazole and
diarylalkyl-triazole derivatives as
potent aromatase inhibitors for
treatment of hormone-dependent cancer 2342--2353
Vali Zare-shahabadi and
Fatemeh Abbasitabar Application of ant colony optimization
in development of models for prediction
of anti-HIV-1 activity of HEPT
derivatives . . . . . . . . . . . . . . 2354--2362
Peng Tao and
H. Bernhard Schlegel A toolkit to assist ONIOM calculations 2363--2369
Sadegh Salehzadeh and
Mehdi Bayat Theoretical studies on the structure and
protonation of Cu(II) complexes of a
series of tripodal aliphatic
tetraamines: Good correlations with the
experimental data . . . . . . . . . . . 2371--2380
Hiroaki Umeda and
Yuichi Inadomi and
Toshio Watanabe and
Toru Yagi and
Takayoshi Ishimoto and
Tsutomu Ikegami and
Hiroto Tadano and
Tetsuya Sakurai and
Umpei Nagashima Parallel Fock matrix construction with
distributed shared memory model for the
FMO--MO method . . . . . . . . . . . . . 2381--2388
David Casanova and
Pere Alemany and
Santiago Alvarez Symmetry measures of the electron
density . . . . . . . . . . . . . . . . 2389--2404
Anuja P. Rahalkar and
Michio Katouda and
Shridhar R. Gadre and
Shigeru Nagase Molecular tailoring approach in
conjunction with MP2 and Ri-MP2 codes: a
comparison with fragment molecular
orbital method . . . . . . . . . . . . . 2405--2418
Zhixiong Lin and
Haiyan Liu and
Wilfred F. van Gunsteren Using one-step perturbation to predict
the effect of changing force-field
parameters on the simulated folding
equilibrium of a $ \beta $-peptide in
solution . . . . . . . . . . . . . . . . 2419--2427
Gregory Scott and
Martin Gruebele Solving the low dimensional Smoluchowski
equation with a singular value basis set 2428--2433
Cédric Grauffel and
Roland H. Stote and
Annick Dejaegere Force field parameters for the
simulation of modified histone tails . . 2434--2451
R. Carbó-Dorca and
E. Besalú Communications on quantum similarity
(2): a geometric discussion on
holographic electron density theorem and
confined quantum similarity measures . . 2452--2462
Santhosh Kannan Venkatesan and
Anil Kumar Shukla and
Vikash Kumar Dubey Molecular docking studies of selected
tricyclic and quinone derivatives on
trypanothione reductase of Leishmania
infantum . . . . . . . . . . . . . . . . 2463--2475
Bulumoni Kalita and
Ramesh C. Deka Adsorption of CO on oxygen preadsorbed
neutral and charged gas phase Pd$_4$
clusters: a density functional study . . 2476--2482
Kiyull Yang and
Young Hee Park and
Soo Gyeong Cho and
Hai Whang Lee and
Chan Kyung Kim and
Hyun-Joo Koo Theoretical studies on the formation
mechanism and explosive performance of
nitro-substituted 1,3,5-triazines . . . 2483--2492
P. González-Navarrete and
L. Gracia and
M. Calatayud and
J. AndréS Density functional theory study of the
oxidation of methanol to formaldehyde on
a hydrated vanadia cluster . . . . . . . 2493--2501
Xuewei Jiang and
Changjun Chen and
Yi Xiao Improvements of network approach for
analysis of the folding free-energy
surface of peptides and proteins . . . . 2502--2509
Antoni Aguilar-Mogas and
Xavier Giménez and
Josep Maria Bofill Implementation of an algorithm based on
the Runge--Kutta--Fehlberg technique and
the potential energy as a reaction
coordinate to locate intrinsic reaction
paths . . . . . . . . . . . . . . . . . 2510--2525
Wolfgang Quapp and
Josep Maria Bofill A comment to the nudged elastic band
method . . . . . . . . . . . . . . . . . 2526--2531
Haiying Liu and
Xiaohua Chen and
Yuxiang Bu Redox-induced configuration conversion
for thioacetamide dimer can function as
a molecular switch . . . . . . . . . . . 2533--2539
Jianwen A. Feng and
Garland R. Marshall SKATE: a docking program that decouples
systematic sampling from scoring . . . . 2540--2554
Slawomir Berski and
Zdzislaw Latajka and
Agnieszka J. Gordon Ab initio and Quantum Chemical Topology
studies on the isomerization of HONO to
HNO$_2$. Effect of the basis set in QCT 2555--2567
Kathrin Götz and
Florian Meier and
Carlo Gatti and
Asbjörn M. Burow and
Marek Sierka and
Joachim Sauer and
Martin Kaupp Modeling environmental effects on charge
density distributions in polar
organometallics: Validation of embedded
cluster models for the methyl lithium
crystal . . . . . . . . . . . . . . . . 2568--2576
Jianguo Qian and
Fuji Zhang Counting the cyclocized polyphenacenes 2577--2584
Cun-Xi Liu and
Hai-Xia Wang and
Ze-Rong Li and
Chong-Wen Zhou and
Han-Bing Rao and
Xiang-Yuan Li Accurate prediction of enthalpies of
formation for a large set of organic
compounds . . . . . . . . . . . . . . . 2585--2592
Per Larsson and
Erik Lindahl A high-performance parallel-generalized
Born implementation enabled by tabulated
interaction rescaling . . . . . . . . . 2593--2600
Ramin M. Abolfath and
Thomas Brabec DNA-backbone radio resistivity induced
by spin blockade effect . . . . . . . . 2601--2606
Fahrettin Gogtas and
Rukiye Tutuk and
Mustafa Kurban Time-dependent quantum study of H($^2$S)
$+$ FO($^2 \Pi $ ) $ \rightarrow $
OH($^2 \Pi $ ) $+$ F($^2$P) reaction on
the 1$^3$A' and 1$^3$A'' states . . . . 2607--2611
Alice Borghini and
Paolo Crotti and
Daniele Pietra and
Lucilla Favero and
Anna Maria Bianucci Chemical reactivity predictions: Use of
data mining techniques for analyzing
regioselective azidolysis of epoxides 2612--2619
Jörg Von Appen and
Bernhard Eck and
Richard Dronskowski A density-functional study of the phase
diagram of cementite-type (Fe,Mn)$_3$C
at absolute zero temperature . . . . . . 2620--2627
Yoshiyuki Koyano and
Norio Takenaka and
Yukinori Nakagawa and
Masataka Nagaoka An optimum strategy for solution
chemistry using semiempirical molecular
orbital method. II. Primary importance
of reproducing electrostatic interaction
in the QM/MM framework . . . . . . . . . 2628--2641
Esteban Vöhringer-Martinez and
Alejandro Toro-Labbé The role of water in the proton transfer
reaction mechanism in tryptophan . . . . 2642--2649
Shu-Wei Tang and
Jing-Dong Feng and
Yong-Qing Qiu and
Hao Sun and
Feng-Di Wang and
Ying-Fei Chang and
Rong-Shun Wang Electronic structures and nonlinear
optical properties of highly deformed
halofullerenes C$_{3v}$ C$_{60}$F$_{18}$
and D$_{3d}$ C$_{60}$Cl$_{30}$ . . . . . 2650--2657
Mihaly Mezei Simulaid: a simulation facilitator and
analysis program . . . . . . . . . . . . 2658--2668
Oscar Bertran and
S. B. Trickey and
Juan Torras Incorporation of deMon2k as a new
parallel quantum mechanical code for the
PUPIL system . . . . . . . . . . . . . . 2669--2676
Christopher J. R. Illingworth and
Paul D. Scott and
Kevin E. B. Parkes and
Christopher R. Snell and
Matthew P. Campbell and
Christopher A. Reynolds Connectivity and binding-site
recognition: Applications relevant to
drug design . . . . . . . . . . . . . . 2677--2688
Sree V. Chintapalli and
Boon K. Yew and
Christopher J. R. Illingworth and
Graham J. G. Upton and
Philip J. Reeves and
Kevin E. B. Parkes and
Christopher R. Snell and
Christopher A. Reynolds Closed loop folding units from
structural alignments: Experimental
foldons revisited . . . . . . . . . . . 2689--2701
Dennis M. Elking and
Lalith Perera and
Robert Duke and
Thomas Darden and
Lee G. Pedersen Atomic forces for geometry-dependent
point multipole and Gaussian multipole
models . . . . . . . . . . . . . . . . . 2702--2713
Katsumi Murata and
Naoya Nagata and
Isao Nakanishi and
Kazuo Kitaura SDOVS: a solvent dipole ordering-based
method for virtual screening . . . . . . 2714--2722
Pedro A. Valiente and
Alejandro Gil L. and
Paulo R. Batista and
Ernesto R. Caffarena and
Tirso Pons and
Pedro G. Pascutti New parameterization approaches of the
LIE method to improve free energy
calculations of PlmII-inhibitors
complexes . . . . . . . . . . . . . . . 2723--2734
Marcos Mandado and
M. Natália D. S. Cordeiro On the stability of metal--aminoacid
complexes in water based on
water--ligand exchange reactions and
electronic properties: Detailed study on
iron--glycine hexacoordinated complexes 2735--2745
Eri Sano and
Weihua Li and
Hitomi Yuki and
Xinli Liu and
Tomomi Furihata and
Kaoru Kobayashi and
Kan Chiba and
Saburo Neya and
Tyuji Hoshino Mechanism of the decrease in catalytic
activity of human cytochrome P450 2C9
polymorphic variants investigated by
computational analysis . . . . . . . . . 2746--2758
Tzong-Yi Lee and
Justin Bo-Kai Hsu and
Feng-Mao Lin and
Wen-Chi Chang and
Po-Chiang Hsu and
Hsien-Da Huang $N$-Ace: Using solvent accessibility and
physicochemical properties to identify
protein $N$-acetylation sites . . . . . 2759--2771
Hao Zhang and
Yun-Hong Zhang Ab initio investigation on the
ion-associated species and process in
Mg(NO$_3$ )$_2$ solution . . . . . . . . 2772--2782
Juan Du and
Lili Xi and
Beilei Lei and
Jing Lu and
Jiazhong Li and
Huanxiang Liu and
Xiaojun Yao Structure-based quantitative
structure-activity relationship studies
of checkpoint kinase 1 inhibitors . . . 2783--2793
Hui Zhang and
Gui-Ling Zhang and
Jing-Yao Liu and
Miao Sun and
Bo Liu and
Ze-Sheng Li Theoretical studies on the reactions
CH$_3$SCH$_3$ with OH, CF$_3$, and
CH$_3$ radicals . . . . . . . . . . . . 2794--2803
Qi Liang Lu and
Li Li Chen and
Jian Guo Wan and
Guang Hou Wang First principles studies on the
interaction of O$_2$ with X@Al$_{12}$ (X
= Al$^-$, P$^+$, C, Si) clusters . . . . 2804--2809
Volker Hähnke and
Matthias Rupp and
Mireille Krier and
Friedrich Rippmann and
Gisbert Schneider Pharmacophore alignment search tool:
Influence of canonical atom labeling on
similarity searching . . . . . . . . . . 2810--2826
Emilia L. Wu Coriolis coupling and nonadiabaticity in
chemical reaction dynamics . . . . . . . 2827--2835
Dimitrios N. Garbounis and
Athanassios C. Tsipis and
Constantinos A. Tsipis Structural, electronic, bonding,
magnetic, and optical properties of
bimetallic [Ru$_n$Au$_m$ ]$^{0 / +}$ ($
n + m \leq 3 $ ) clusters . . . . . . . 2836--2852
Ning-Ning Wei and
Ce Hao and
Zhilong Xiu and
Jingwen Chen and
Jieshan Qiu Time-dependent density functional theory
study on excited-state dihydrogen
bonding OH\dottedbondHGe of the
dihydrogen-bonded
phenol-triethylgermanium complex . . . . 2853--2858
Huan Rui and
Wonpil Im Protegrin-1 orientation and
physicochemical properties in membrane
bilayers studied by potential of mean
force calculations . . . . . . . . . . . 2859--2867
Bernhard Knapp and
Nadja Lederer and
Ulrich Omasits and
Wolfgang Schreiner vmdICE: a plug-in for rapid evaluation
of molecular dynamics simulations using
VMD . . . . . . . . . . . . . . . . . . 2868--2873
Neetha Mohan and
Kunduchi P. Vijayalakshmi and
Nobuaki Koga and
Cherumuttathu H. Suresh Comparison of aromatic NH\dottedbond$
\pi $, OH\dottedbond$ \pi $, and
CH\dottedbond$ \pi $ interactions of
alanine using MP2, CCSD, and DFT methods 2874--2882
Erjun Zhao and
Jinping Wang and
Zhijian Wu Structural stability and phase
transition in OsC and RuC . . . . . . . 2883--2888
Stewart N. Weiss and
Lulu Huang and
Lou Massa A generalized higher order kernel energy
approximation method . . . . . . . . . . 2889--2899
Seungsoo Hahn and
Orr Ashenberg and
Gevorg Grigoryan and
Amy E. Keating Identifying and reducing error in
cluster-expansion approximations of
protein energies . . . . . . . . . . . . 2900--2914
Young Kee Kang and
Byung Jin Byun Assessment of density functionals with
long-range and/or empirical dispersion
corrections for conformational energy
calculations of peptides . . . . . . . . 2915--2923
Shinji Aono and
Shigeki Kato Proton transfer in phenol--amine
complexes: Phenol electronic effects on
free energy profile in solution . . . . 2924--2931
Benedict M. Sattelle and
Andrew Almond Less is more when simulating unsulfated
glycosaminoglycan 3D-structure:
Comparison of GLYCAM06/TIP3P,
PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P
predictions with experiment . . . . . . 2932--2947
Anik Sen and
Bishwajit Ganguly What is the minimum number of water
molecules required to dissolve a
potassium chloride molecule? . . . . . . 2948--2954
Maria L. Sushko and
Peter V. Sushko and
Igor V. Abarenkov and
Alexander L. Shluger QM/MM method for metal--organic
interfaces . . . . . . . . . . . . . . . 2955--2966
Claudia Steffen and
Klaus Thomas and
Uwe Huniar and
Arnim Hellweg and
Oliver Rubner and
Alexander Schroer TmoleX --- a graphical user interface
for TURBOMOLE . . . . . . . . . . . . . 2967--2970
Subrata Mahanta and
Bijan Kumar Paul and
Rupashree Balia Singh and
Nikhil Guchhait Inequivalence of substitution pairs in
hydroxynaphthaldehyde: a theoretical
measurement by intramolecular hydrogen
bond strength, aromaticity, and
excited-state intramolecular proton
transfer reaction . . . . . . . . . . . 1--14
Qiang Hao and
Andrew C. Simmonett and
Yukio Yamaguchi and
De-Cai Fang and
Henry F. Schaefer III From acetylene complexes to vinylidene
structures: The GeC$_2$H$_2$ system . . 15--22
Oz Sharabi and
Chen Yanover and
Ayelet Dekel and
Julia M. Shifman Optimizing energy functions for
protein--protein interface design . . . 23--32
Yongbing Zhao and
Jingfa Xiao Homology modeling and molecular dynamics
simulation studies of human type 1 3$
\beta $-hydroxysteroid dehydrogenase:
Toward the understanding of cofactor
specificity . . . . . . . . . . . . . . 33--42
Jon Baker and
Krzysztof Wolinski Isomerization of stilbene using enforced
geometry optimization . . . . . . . . . 43--53
Eric J. Bylaska and
Kiril Tsemekhman and
Scott B. Baden and
John H. Weare and
Hannes Jonsson Parallel implementation of $ \gamma
$-point pseudopotential plane-wave DFT
with exact exchange . . . . . . . . . . 54--69
Shih-Hau Chiu and
Chien-Chi Chen and
Gwo-Fang Yuan and
Thy-Hou Lin Deriving the phylogenetic information
from some physicochemical properties of
protein sequences computed . . . . . . . 70--80
Annalisa Bordogna and
Alessandro Pandini and
Laura Bonati Predicting the accuracy of
protein--ligand docking on homology
models . . . . . . . . . . . . . . . . . 81--98
A. M. Tokmachev and
R. Dronskowski Hydrogen-bond networks in finite ice
nanotubes . . . . . . . . . . . . . . . 99--105
Guillaume Launay and
Thomas Simonson A large decoy set of protein--protein
complexes produced by flexible docking 106--120
Mohammad Alaghemandi and
Joachim Schulte and
Frédéric Leroy and
Florian Müller-Plathe and
Michael C. Böhm Correlation between thermal conductivity
and bond length alternation in carbon
nanotubes: a combined reverse
nonequilibrium molecular dynamics ---
crystal orbital analysis . . . . . . . . 121--133
Conrad Shyu and
F. Marty Ytreberg Accurate estimation of solvation free
energy using polynomial fitting
techniques . . . . . . . . . . . . . . . 134--141
Qingyong Meng and
Ming-Bao Huang A CAS study on S-loss and O-loss
dissociation mechanisms of the SO$_2^+$
ion in the C, D, and E states . . . . . 142--151
Chaoyang Zhang Shape and size effects in $ \pi $--$ \pi
$ interactions: Face-to-face dimers . . 152--160
Jae In Kim and
Sungsoo Na and
Kilho Eom Domain decomposition-based structural
condensation of large protein structures
for understanding their conformational
dynamics . . . . . . . . . . . . . . . . 161--169
Joseph N. Zadeh and
Conrad D. Steenberg and
Justin S. Bois and
Brian R. Wolfe and
Marshall B. Pierce and
Asif R. Khan and
Robert M. Dirks and
Niles A. Pierce NUPACK: Analysis and design of nucleic
acid systems . . . . . . . . . . . . . . 170--173
Abdul-Rahman Allouche Gabedit --- a graphical user interface
for computational chemistry softwares 174--182
Gerald R. Kneller Comment on ``Fast determination of the
optimal rotational matrix for
macromolecular superpositions'' [J.
Comp. Chem. \bf 31, 1561 (2010)] . . . . 183--184
Pu Liu and
Dimitris K. Agrafiotis and
Douglas L. Theobald Rapid communication reply to comment on:
``Fast determination of the optimal
rotational matrix for macromolecular
superpositions'' . . . . . . . . . . . . 185--186
Samuel Genheden and
Ulf Ryde A comparison of different initialization
protocols to obtain statistically
independent molecular dynamics
simulations . . . . . . . . . . . . . . 187--195
Juan R. Perilla and
Oliver Beckstein and
Elizabeth J. Denning and
Thomas B. Woolf Computing ensembles of transitions from
stable states: Dynamic importance
sampling . . . . . . . . . . . . . . . . 196--209
John W. Raymond and
Daniel D. Holsworth and
Mehran Jalaie The flexible alignment of molecular
structures using simulated annealing
with weighted Lagrangian multipliers . . 210--217
Wen-Zhi Yao and
Da-Zhi Li and
Si-Dian Li Bridging gold: B-Au-B
three-center--two-electron bonds in
electron-deficient B$_2$Au$_n^{- / 0}$
($ n = 1 $, $3$, $5$ ) and mixed
analogues . . . . . . . . . . . . . . . 218--225
Kathy L. Phillips and
Stanley I. Sandler and
Pei C. Chiu A method to calculate the one-electron
reduction potentials for nitroaromatic
compounds based on gas-phase quantum
mechanics . . . . . . . . . . . . . . . 226--239
Blandine Courcot and
Adam J. Bridgeman Optimization of a molecular mechanics
force field for polyoxometalates based
on a genetic algorithm . . . . . . . . . 240--247
Peng Bao and
Zhong-Heng Yu New procedure to evaluate aromaticity at
the density functional theory,
Hartree--Fock, and post-self-consistent
field levels . . . . . . . . . . . . . . 248--259
Suyong Re and
Takashi Imai and
Jaewoon Jung and
Seiichiro Ten-No and
Yuji Sugita Geometrically associative yet
electronically dissociative character in
the transition state of enzymatic
reversible phosphorylation . . . . . . . 260--270
Dongsheng Zou and
Zhongshi He and
Jingyuan He and
Yuxian Xia Supersecondary structure prediction
using Chou's pseudo amino acid
composition . . . . . . . . . . . . . . 271--278
Massimiliano Bartolomei and
Estela Carmona-Novillo and
Marta I. Hernández and
José Campos-Martínez and
Ramón Hernández-Lamoneda Long-range interaction for dimers of
atmospheric interest: dispersion,
induction and electrostatic
contributions for O$_2$O$_2$, N$_2$N$_2$
and O$_2$N$_2$ . . . . . . . . . . . . . 279--290
A. Otero-de-la-Roza and
Víctor Luaña A fast and accurate algorithm for QTAIM
integration in solids . . . . . . . . . 291--305
Daniel Tunega and
Ali Zaoui Understanding of bonding and mechanical
characteristics of cementitious mineral
tobermorite from first principles . . . 306--314
Carmen J. Calzado and
A. Monari and
S. Evangelisti Heisenberg behavior of some
carbon-beryllium compounds: How well
truncated-CI approaches work . . . . . . 315--324
Uttam Sinha Mahapatra and
Sudip Chattopadhyay and
Rajat K. Chaudhuri Second-order state-specific
multireference Mòller--Plesset
perturbation theory: Application to
energy surfaces of diimide, ethylene,
butadiene, and cyclobutadiene . . . . . 325--337
Shu-Ling Chen and
Dong-Xia Zhao and
Zhong-Zhi Yang An estimation method of binding free
energy in terms of ABEEM$ \sigma \pi $
/MM and continuum electrostatics fused
into LIE method . . . . . . . . . . . . 338--348
Chewook Lee and
Sihyun Ham Characterizing amyloid-beta protein
misfolding from molecular dynamics
simulations with explicit water . . . . 349--355
Luká\vs Bu\vcinský and
Stanislav Biskupi\vc and
Michal Il\vcin and
Vladimír Luke\vs and
Viliam Laurinc Relativistic effects in HgHe and HgXe
CCSD(T) ground state potential curves.
Low-density viscosity simulations of
Hg:Xe mixture . . . . . . . . . . . . . 356--367
Richard Lonsdale and
Jeremy N. Harvey and
Frederick R. Manby and
Adrian J. Mulholland Comment on ``A stationary-wave model of
enzyme catalysis'' by Carlo Canepa . . . 368--369
Carlo Canepa Reply to the comment on ``A
stationary-wave model of enzyme
catalysis'' . . . . . . . . . . . . . . 370--371
J. Oscar C. Jiménez-Halla and
Eduard Matito and
Lluís Blancafort and
Juvencio Robles and
Miquel Sol\`a Erratum: ``Tuning aromaticity in
trigonal alkaline earth metal clusters
and their alkali metal salts'' . . . . . 372--373
Anonymous Tuning aromaticity in trigonal alkaline
earth metal clusters and their alkali
metal salts . . . . . . . . . . . . . .
Brad A. Bauer and
Joseph E. Davis and
Michela Taufer and
Sandeep Patel Molecular dynamics simulations of
aqueous ions at the liquid--vapor
interface accelerated using graphics
processors . . . . . . . . . . . . . . . 375--385
Wouter Heyndrickx and
Pedro Salvador and
Patrick Bultinck and
Miquel Sol\`a and
Eduard Matito Performance of 3D-space-based
atoms-in-molecules methods for
electronic delocalization aromaticity
indices . . . . . . . . . . . . . . . . 386--395
Artem B. Mamonov and
Xin Zhang and
Daniel M. Zuckerman Rapid sampling of all-atom peptides
using a library-based polymer-growth
approach . . . . . . . . . . . . . . . . 396--405
Yuan Miao and
Xueye Wang and
Xin Jin and
Ling Yi and
Cuihuan Ren Density functional theory study of a
molecular allosteric switch for
2,2'-bipyridyl-3,3'-15-crown-5 . . . . . 406--415
Bo Yang and
Yanyan Zhu and
Yan Wang and
Guangju Chen Interaction identification of Zif268 and
TATA$_{ZF}$ proteins with GC-/AT-rich
DNA sequence: a theoretical study . . . 416--428
Matthew A. Addicoat and
Gregory F. Metha and
Tak W. Kee Density functional theory investigation
of Cu(I)- and Cu(II)-curcumin complexes 429--438
Joseph N. Zadeh and
Brian R. Wolfe and
Niles A. Pierce Nucleic acid sequence design via
efficient ensemble defect optimization 439--452
Omololu Akin-Ojo and
Feng Wang The quest for the best nonpolarizable
water model from the adaptive force
matching method . . . . . . . . . . . . 453--462
Ahmed Mutanabbi Abdula and
Reema Abu Khalaf and
Mohammad S. Mubarak and
Mutasem O. Taha Discovery of new $ \beta $-
D-galactosidase inhibitors via
pharmacophore modeling and QSAR analysis
followed by in silico screening . . . . 463--482
Burak Alakent and
Sena Baskan and
Pemra Doruker Effect of ligand binding on the
intraminimum dynamics of proteins . . . 483--496
Andres Jaramillo-Botero and
Julius Su and
An Qi and
William A. Goddard III Large-scale, long-term nonadiabatic
electron molecular dynamics for
describing material properties and
phenomena in extreme environments . . . 497--512
Timothy H. Click and
Aibing Liu and
George A. Kaminski Quality of random number generators
significantly affects results of Monte
Carlo simulations for organic and
biological systems . . . . . . . . . . . 513--524
Aravindhan Ganesan and
Feng Wang and
Chantal Falzon Intramolecular interactions of
L-phenylalanine: Valence ionization
spectra and orbital momentum
distributions of its fragment molecules 525--535
Dorota Latek and
Andrzej Kolinski CABS-NMR --- de novo tool for rapid
global fold determination from chemical
shifts, residual dipolar couplings and
sparse methyl-methyl NOEs . . . . . . . 536--544
Wenwei Zhao and
Yihong Ding and
Qiying Xia Time-dependent density functional theory
study on the absorption spectrum of
Coumarin 102 and its hydrogen-bonded
complexes . . . . . . . . . . . . . . . 545--553
Jagdish C. Patra and
Boon H. Chua Artificial neural network-based drug
design for diabetes mellitus using
flavonoids . . . . . . . . . . . . . . . 555--567
Dariusz Plewczynski and
Micha\l \La\.zniewski and
Marcin Von Grotthuss and
Leszek Rychlewski and
Krzysztof Ginalski VoteDock: Consensus docking method for
prediction of protein--ligand
interactions . . . . . . . . . . . . . . 568--581
Ramon Carbó-Dorca and
Emili Besalú and
Luz Dary Mercado Communications on quantum similarity,
part 3: a geometric-quantum similarity
molecular superposition algorithm . . . 582--599
Christian C. Gruber and
Jürgen Pleiss Systematic benchmarking of large
molecular dynamics simulations employing
GROMACS on massive multiprocessing
facilities . . . . . . . . . . . . . . . 600--606
David Curcó and
David Zanuy and
Ruth Nussinov and
Carlos Alemán A simulation strategy for the atomistic
modeling of flexible molecules
covalently tethered to rigid surfaces:
Application to peptides . . . . . . . . 607--619
Athanassios C. Tsipis and
Alexandros V. Stalikas Structural, electronic, and
magnetoresponsive properties of
triangular lanthanide clusters and their
free-standing nitrides . . . . . . . . . 620--638
Arthur N. Mayeno and
Jonathan L. Robinson and
Brad Reisfeld Rapid estimation of activation
enthalpies for cytochrome-P450-mediated
hydroxylations . . . . . . . . . . . . . 639--657
Shu-Wei Tang and
Jing-Dong Feng and
Yong-Qing Qiu and
Hao Sun and
Feng-Di Wang and
Zhong-Min Su and
Ying-Fei Chang and
Rong-Shun Wang Thermochemical stabilities, electronic
structures, and optical properties of
C$_{56}$X$_{10}$ (X = H, F, and Cl)
fullerene compounds . . . . . . . . . . 658--667
Guang-Yue Li and
Guang-Jiu Zhao and
Ke-Li Han and
Guo-Zhong He A TD-DFT study on the
cyanide-chemosensing mechanism of
8-formyl-7-hydroxycoumarin . . . . . . . 668--674
Chun Li and
Hong Ma and
Yang Zhou and
Xiaolei Wang and
Xiaoqi Zheng Similarity analysis of DNA sequences
based on the weighted pseudo-entropy . . 675--680
Juan M. Ruiz and
R. Joshua Mulder and
Célia Fonseca Guerra and
F. Matthias Bickelhaupt Steric effects on alkyl cation
affinities of maingroup-element hydrides 681--688
T. Zoboki and
I. Mayer Extremely localized nonorthogonal
orbitals by the pairing theorem . . . . 689--695
Zahid Rashid and
Joop H. van Lenthe Generation of Kekulé valence structures
and the corresponding valence bond wave
function . . . . . . . . . . . . . . . . 696--708
Matthew S. Lin and
Teresa Head-Gordon Reliable protein structure refinement
using a physical energy function . . . . 709--717
Andrzej T. Kowal Ab initio molecular geometry and
anharmonic vibrational spectra of
thiourea and thiourea-$ d_4 $ . . . . . 718--729
Shih-I Lu Computational study of static first
hyperpolarizability of donor--acceptor
substituted (E)-benzaldehyde
phenylhydrazone . . . . . . . . . . . . 730--736
Zongling Ding and
Jun Jiang and
Huaizhong Xing and
Haibo Shu and
Ruibin Dong and
Xiaoshuang Chen and
Wei Lu Transport properties of graphene
nanoribbon-based molecular devices . . . 737--741
Dariusz Plewczynski and
Micha\l \La\'zniewski and
Rafa\l Augustyniak and
Krzysztof Ginalski Can we trust docking results? Evaluation
of seven commonly used programs on
PDBbind database . . . . . . . . . . . . 742--755
Duan Chen and
Zhan Chen and
Changjun Chen and
Weihua Geng and
Guo-Wei Wei MIBPB: a software package for
electrostatic analysis . . . . . . . . . 756--770
Chang-Bin Shao and
Lin Jin and
Yi-Hong Ding A theoretical survey on the structures,
energetics, and isomerization pathways
of the B$_5$O radical . . . . . . . . . 771--777
Kenji Hori and
Toru Yamaguchi and
Keita Uezu and
Michinori Sumimoto A free-energy perturbation method based
on Monte Carlo simulations using quantum
mechanical calculations (QM/MC/FEP
method): Application to highly
solvent-dependent reactions . . . . . . 778--786
Pralay Mitra and
Debnath Pal Using correlated parameters for improved
ranking of protein--protein docking
decoys . . . . . . . . . . . . . . . . . 787--796
Hossein Farrokhpour and
Zainab Mombeini and
Mansoor Namazian and
Michelle L. Coote Intermolecular potential energy surface
for CS$_2$ dimer . . . . . . . . . . . . 797--809
Kay Hamacher Efficient quantification of the
importance of contacts for the dynamical
stability of proteins . . . . . . . . . 810--815
Adam D. Swetnam and
Michael P. Allen Improving the Wang--Landau algorithm for
polymers and proteins . . . . . . . . . 816--821
Eric A. C. Bushnell and
Edvin Erdtman and
Jorge Llano and
Leif A. Eriksson and
James W. Gauld The first branching point in porphyrin
biosynthesis: a systematic docking,
molecular dynamics and quantum
mechanical/molecular mechanical study of
substrate binding and mechanism of
uroporphyrinogen-III decarboxylase . . . 822--834
C. Weng and
J. Kouvetakis and
A. V. G. Chizmeshya A novel predictive model for formation
enthalpies of Si and Ge hydrides with
propane- and butane-like structures . . 835--853
Ramkumar Rajamani and
Yen-Lin Lin and
Jiali Gao The opsin shift and mechanism of
spectral tuning in rhodopsin . . . . . . 854--865
Tingjun Hou and
Junmei Wang and
Youyong Li and
Wei Wang Assessing the performance of the
molecular mechanics/Poisson Boltzmann
surface area and molecular
mechanics/generalized Born surface area
methods. II. The accuracy of ranking
poses generated from docking . . . . . . 866--877
Bin Lin and
B. Montgomery Pettitt Electrostatic solvation free energy of
amino acid side chain analogs:
Implications for the validity of
electrostatic linear response in water 878--885
Syed Tarique Moin and
Thomas S. Hofer and
Bernhard R. Randolf and
Bernd M. Rode Structure and dynamics of methanol in
water: a quantum mechanical charge field
molecular dynamics study . . . . . . . . 886--892
Goutam Mukherjee and
Niladri Patra and
Poranjyoti Barua and
B. Jayaram A fast empirical GAFF compatible partial
atomic charge assignment scheme for
modeling interactions of small molecules
with biomolecular targets . . . . . . . 893--907
H. Reis and
O. Loboda and
A. Avramopoulos and
M. G. Papadopoulos and
B. Kirtman and
J. M. Luis and
R. Zale\'sny Electronic and vibrational linear and
nonlinear polarizabilities of
Li@C$_{60}$ and [Li@C$_{60}$ ]$^+$ . . . 908--914
J. M. Villalba and
A. J. Barbero and
R. Diaz-Sierra and
E. Arribas and
M. J. Garcia-Meseguer and
F. Garcia-Sevilla and
M. Garcia-Moreno and
J. A. Vidal De Labra and
R. Varon Computerized evaluation of mean
residence times in multicompartmental
linear system and pharmacokinetics . . . 915--931
Takuya Okamoto and
Kenta Yamada and
Yoshiyuki Koyano and
Toshio Asada and
Nobuaki Koga and
Masataka Nagaoka A minimal implementation of the
AMBER--GAUSSIAN interface for ab initio
QM/MM-MD simulation . . . . . . . . . . 932--942
Gui-Xiang Wang and
Xue-Dong Gong and
Yan Liu and
Hong-Chen Du and
Xiao-Juan Xu and
He-Ming Xiao Looking for high energy density
compounds applicable for propellant
among the derivatives of DPO with N$_3$,
ONO$_2$, and NNO$_2$ groups . . . . . . 943--952
Yang Li and
Xiao-Nan Jiang and
Chang-Sheng Wang Rapid evaluation of the binding energies
in hydrogen-bonded amide--thymine and
amide--uracil dimers in gas phase . . . 953--966
Yue Shi and
Chuanjie Wu and
Jay W. Ponder and
Pengyu Ren Multipole electrostatics in hydration
free energy calculations . . . . . . . . 967--977
Andreas Uhe and
Sebastian Kozuch and
Sason Shaik Automatic analysis of computed catalytic
cycles . . . . . . . . . . . . . . . . . 978--985
Jie Luo and
Xiujuan Jia and
Yang Gao and
Guicai Song and
Yanbo Yu and
Rongshun Wang and
Xiumei Pan Theoretical study on the kinetics of OH
radical reactions with CH$_3$OOH and
CH$_3$CH$_2$OOH . . . . . . . . . . . . 987--997
Halvor S. Hansen and
Philippe H. Hünenberger A reoptimized GROMOS force field for
hexopyranose-based carbohydrates
accounting for the relative free
energies of ring conformers, anomers,
epimers, hydroxymethyl rotamers, and
glycosidic linkage conformers . . . . . 998--1032
Xiao-Na Li and
Zhi-Jian Wu and
Xi-Yan Li and
Hong-Jie Zhang and
Xiao-Juan Liu Theoretical study on phosphorescence
efficiency and color tuning from orange
to blue-green of Ir(III) complexes based
on substituted
2-phenylimidazo[1,2-a]pyridine ligand 1033--1042
Ivan I. Vorontsov and
Osamu Miyashita Crystal molecular dynamics simulations
to speed up MM/PB(GB)SA evaluation of
binding free energies of di-mannose
deoxy analogs with P51G-m4-Cyanovirin-N 1043--1053
Piotr De Silva and
Jacek Korchowiec Energy partitioning scheme based on
self-consistent method for subsystems:
Populational space approach . . . . . . 1054--1064
Wen-Fei Huang and
P. Raghunath and
M. C. Lin Computational study on the reactions of
H$_2$O$_2$ on TiO$_2$ anatase (101) and
rutile (110) surfaces . . . . . . . . . 1065--1081
Gerhard König and
Stefan Boresch Non-Boltzmann sampling and Bennett's
acceptance ratio method: How to profit
from bending the rules . . . . . . . . . 1082--1090
Xianfeng Li and
Robert A. Latour The temperature intervals with global
exchange of replicas empirical
accelerated sampling method: Parameter
sensitivity and extension to a complex
molecular system . . . . . . . . . . . . 1091--1100
Jee-Gong Chang and
Hsin-Tsung Chen and
Shin-Pon Ju and
Ching-Sheng Chang and
Meng-Hsiung Weng Adsorption and dissociation of NH$_3$ on
clean and hydroxylated TiO$_2$ rutile
(110) surfaces: a computational study 1101--1112
Francesco Rao Protein inherent structures by different
minimization strategies . . . . . . . . 1113--1116
Marcel Swart and
Miquel Sol\`a and
F. Matthias Bickelhaupt Inter- and intramolecular dispersion
interactions . . . . . . . . . . . . . . 1117--1127
Adam Tuer and
Serguei Krouglov and
Richard Cisek and
Danielle Tokarz and
Virginijus Barzda Three-dimensional visualization of the
first hyperpolarizability tensor . . . . 1128--1134
Steven Lettieri and
Artem B. Mamonov and
Daniel M. Zuckerman Extending fragment-based free energy
calculations with library Monte Carlo
simulation: Annealing in interaction
space . . . . . . . . . . . . . . . . . 1135--1143
Jhon Zapata-Rivera and
Rosa Caballol and
Carmen J. Calzado Electronic structure and relative
stability of 1:1 Cu-O$_2$ adducts from
difference-dedicated configuration
interaction calculations . . . . . . . . 1144--1158
Huifang Li and
Laibin Zhang and
Li Han and
Wenming Sun and
Yuxiang Bu Internucleotide $J$-couplings and
chemical shifts of the
N\bondH\dottedbondN hydrogen-bonds in
the radiation-damaged guanine-cytosine
base pairs . . . . . . . . . . . . . . . 1159--1169
Meiyan Wang and
Lin Cheng and
Jinping Wang and
Zhijian Wu Mechanism of methylacetylene
bisselenation catalyzed by palladium
complex from density functional study 1170--1177
Aurelien De La Lande and
Dennis R. Salahub and
Jacques Maddaluno and
Anthony Scemama and
Julien Pilme and
Olivier Parisel and
Helene Gerard and
Michel Caffarel and
Jean-Philip Piquemal Spin-driven activation of dioxygen in
various metalloenzymes and their
inspired models . . . . . . . . . . . . 1178--1182
Michele Seeber and
Angelo Felline and
Francesco Raimondi and
Stefanie Muff and
Ran Friedman and
Francesco Rao and
Amedeo Caflisch and
Francesca Fanelli Wordom: a user-friendly program for the
analysis of molecular structures,
trajectories, and free energy surfaces 1183--1194
Christoph van Wüllen Shared-memory parallelization of the
TURBOMOLE programs AOFORCE, ESCF, and
EGRAD: How to quickly parallelize legacy
code . . . . . . . . . . . . . . . . . . 1195--1201
Barbara Collignon and
Roland Schulz and
Jeremy C. Smith and
Jerome Baudry Task-parallel message passing interface
implementation of Autodock4 for docking
of very large databases of compounds
using high-performance super-computers 1202--1209
Shuyan Li and
Lili Xi and
Jiazhong Li and
Chengqi Wang and
Beilei Lei and
Yulin Shen and
Huanxiang Liu and
Xiaojun Yao and
Biao Li In silico prediction of deleterious
single amino acid polymorphisms from
amino acid sequence . . . . . . . . . . 1211--1216
Adélia J. A. Aquino and
Dana Nachtigallova and
Pavel Hobza and
Donald G. Truhlar and
Christof Hättig and
Hans Lischka The charge-transfer states in a stacked
nucleobase dimer complex: a benchmark
study . . . . . . . . . . . . . . . . . 1217--1227
Tsuyoshi Terakawa and
Tomoshi Kameda and
Shoji Takada On easy implementation of a variant of
the replica exchange with solute
tempering in GROMACS . . . . . . . . . . 1228--1234
Hongping Li and
Shuhui Lv and
Xiaojuan Liu and
Jian Meng First-principles investigation of A-B
intersite charge transfer and correlated
electrical and magnetic properties in
BiCu$_3$Fe$_4$O$_{12}$ . . . . . . . . . 1235--1240
Efstathios E. Karagiannis and
Christos E. Kefalidis and
Ioanna Petrakopoulou and
Constantinos A. Tsipis Density functional study of structural,
electronic, and optical properties of
small bimetallic ruthenium-copper
clusters . . . . . . . . . . . . . . . . 1241--1261
Zsófia Szalay and
János Rohonczy Fast calculation of DNMR spectra on
CUDA-enabled graphics card . . . . . . . 1262--1270
Li-Zhen Zhao and
Wan-Sheng Su and
Wen-Cai Lu and
C. Z. Wang and
K. M. Ho Competitive diamond-like and endohedral
fullerene structures of Si$_{70}$ . . . 1271--1278
Yang Liu and
Huai Sun Electronic ground states and vibrational
frequency shifts of diatomic ligands in
heme adducts . . . . . . . . . . . . . . 1279--1285
Jinzen Ikebe and
Koji Umezawa and
Narutoshi Kamiya and
Takanori Sugihara and
Yasushige Yonezawa and
Yu Takano and
Haruki Nakamura and
Junichi Higo Theory for trivial trajectory
parallelization of multicanonical
molecular dynamics and application to a
polypeptide in water . . . . . . . . . . 1286--1297
Chong Han and
Shi-Shen Yan and
Xue-Ling Lin and
Shu-Jun Hu and
Ming-Wen Zhao and
Xin-Xin Yao and
Yan-Xue Chen and
Guo-Lei Liu and
Liang-Mo Mei Effect of native defects and Co doping
on ferromagnetism in HfO$_2$:
First-principles calculations . . . . . 1298--1302
Stefan Bruckner and
Stefan Boresch Efficiency of alchemical free energy
simulations. I. A practical comparison
of the exponential formula,
thermodynamic integration, and Bennett's
acceptance ratio method . . . . . . . . 1303--1319
Stefan Bruckner and
Stefan Boresch Efficiency of alchemical free energy
simulations. II. Improvements for
thermodynamic integration . . . . . . . 1320--1333
Albert H. Ng and
Christopher D. Snow Polarizable protein packing . . . . . . 1334--1344
Hiroshi Takeuchi A theoretical investigation on optimal
structures of ethane clusters
(C$_2$H$_6$ )$_n$ with $ n \leq 25 $ and
their building-up principle . . . . . . 1345--1352
Yoshitake Sakae and
Tomoyuki Hiroyasu and
Mitsunori Miki and
Yuko Okamoto Protein structure predictions by
parallel simulated annealing molecular
dynamics using genetic crossover . . . . 1353--1360
Jun-Xian Chen and
Chang Kon Kim and
Hai Whang Lee and
Ying Xue and
Chan Kyung Kim Reexamination of the $ \pi $-bond
strengths within H$_2$C\doublebondXH$_n$
systems: a theoretical study . . . . . . 1361--1367
P. O. Fedichev and
E. G. Getmantsev and
L. I. Menshikov $ O(N \log N) $ continuous
electrostatics method for fast
calculation of solvation energies of
biomolecules . . . . . . . . . . . . . . 1368--1376
Johannes M. Dieterich and
Bernd Hartke Composition-induced structural
transitions in mixed Lennard-Jones
clusters: Global reparametrization and
optimization . . . . . . . . . . . . . . 1377--1385
Eduard S. Fomin Consideration of data load time on
modern processors for the Verlet table
and linked-cell algorithms . . . . . . . 1386--1399
Nicolas Sapay and
D. Peter Tieleman Combination of the CHARMM27 force field
with united-atom lipid force fields . . 1400--1410
Emanuel H. Rubensson and
Elias Rudberg Bringing about matrix sparsity in
linear-scaling electronic structure
calculations . . . . . . . . . . . . . . 1411--1423
Felix Hanke Sensitivity analysis and uncertainty
calculation for dispersion corrected
density functional theory . . . . . . . 1424--1430
Allyn R. Brice and
Brian N. Dominy Analyzing the robustness of the MM/PBSA
free energy calculation method:
Application to DNA conformational
transitions . . . . . . . . . . . . . . 1431--1440
Justyna Dominikowska and
Marcin Palusiak Cyclooctatetraene dianion --- an
artifact? . . . . . . . . . . . . . . . 1441--1448
Nan-Nan Wu and
Chao-Zheng He and
Xue-Mei Duan and
Jing-Yao Liu Theoretical mechanistic study on the
reaction of CN radical with HNCN . . . . 1449--1455
Stefan Grimme and
Stephan Ehrlich and
Lars Goerigk Effect of the damping function in
dispersion corrected density functional
theory . . . . . . . . . . . . . . . . . 1456--1465
Chun Wei Yap PaDEL-descriptor: an open source
software to calculate molecular
descriptors and fingerprints . . . . . . 1466--1474
Hossein Ali Karimi-Varzaneh and
Hu-Jun Qian and
Xiaoyu Chen and
Paola Carbone and
Florian Müller-Plathe IBIsCO: a molecular dynamics simulation
package for coarse-grained simulation 1475--1487
Samir Unni and
Yong Huang and
Robert M. Hanson and
Malcolm Tobias and
Sriram Krishnan and
Wilfred W. Li and
Jens E. Nielsen and
Nathan A. Baker Web servers and services for
electrostatics calculations with APBS
and PDB2PQR . . . . . . . . . . . . . . 1488--1491
Thomas M. Gilbert Testing the ONIOM G2R3 model against
donor--acceptor dissociation energies of
group 13--15 complexes: Accuracy
comparable to CCSD(T)/aug-CC-pVTZ at a
fraction of the resource cost . . . . . 1493--1499
Zheng-Wang Qu and
Hui Zhu and
Volkhard May Vibrational spectral signatures of
peptide secondary structures:
$N$-methylation and side chain hydrogen
bond in cyclosporin A . . . . . . . . . 1500--1518
Joshua A. Plumley and
J. J. Dannenberg A comparison of the behavior of
functional/basis set combinations for
hydrogen-bonding in the water dimer with
emphasis on basis set superposition
error . . . . . . . . . . . . . . . . . 1519--1527
Slawomir Berski and
Zdzislaw Latajka and
Agnieszka J. Gordon Electron localization function and
electron localizability indicator
applied to study the bonding in the
peroxynitrous acid HOONO . . . . . . . . 1528--1540
Stephen M. Long and
Tran T. Tran and
Peter Adams and
Paul Darwen and
Mark L. Smythe Conformational searching using a
population-based incremental learning
algorithm . . . . . . . . . . . . . . . 1541--1549
Stéphanie Halbert and
Carine Clavaguéra and
Guy Bouchoux The shape of gaseous $n$-butylbenzene:
Assessment of computational methods and
comparison with experiments . . . . . . 1550--1560
Dieter Ghillemijn and
Patrick Bultinck and
Dimitri Van Neck and
Paul W. Ayers A self-consistent Hirshfeld method for
the atom in the molecule based on
minimization of information loss . . . . 1561--1567
Thanisorn Yakhanthip and
Siriporn Jungsuttiwong and
Supawadee Namuangruk and
Nawee Kungwan and
Vinich Promarak and
Taweesak Sudyoadsuk and
Palita Kochpradist Theoretical investigation of novel
carbazole-fluorene based D-$ \pi $-A
conjugated organic dyes as
dye-sensitizer in dye-sensitized solar
cells (DSCs) . . . . . . . . . . . . . . 1568--1576
Le Yu and
Wensheng Bian Extensive theoretical study on
electronically excited states and
predissociation mechanisms of sulfur
monoxide including spin--orbit coupling 1577--1588
Svetlana Artemova and
Sergei Grudinin and
Stephane Redon Fast construction of assembly trees for
molecular graphs . . . . . . . . . . . . 1589--1598
Stefano Pelloni and
Raphaël Carion and
Vincent Liégeois and
Paolo Lazzeretti The ring current model of the
pentaprismane molecule . . . . . . . . . 1599--1611
Jianxiu Guo and
Nini Rao and
Guangxiong Liu and
Yong Yang and
Gang Wang Predicting protein folding rates using
the concept of Chou's pseudo amino acid
composition . . . . . . . . . . . . . . 1612--1617
Volker Hähnke and
Alexander Klenner and
Friedrich Rippmann and
Gisbert Schneider Pharmacophore alignment search tool:
Influence of the third dimension on
text-based similarity searching . . . . 1618--1634
Volker Hähnke and
Gisbert Schneider Pharmacophore alignment search tool:
Influence of scoring systems on
text-based similarity searching . . . . 1635--1647
Daniel K. W. Mok and
Edmond P. F. Lee and
Foo-Tim Chau and
John M. Dyke Franck--Condon simulation of the
photoelectron spectrum of AsCl$_2$ and
the photodetachment spectrum of AsCl
employing UCCSD(T)-F12a potential energy
functions: IE and EA of AsCl$_2$ . . . . 1648--1660
Tatsuya Ohyama and
Masato Hayakawa and
Shin Nishikawa and
Noriyuki Kurita Specific interactions between lactose
repressor protein and DNA affected by
ligand binding: Ab initio molecular
orbital calculations . . . . . . . . . . 1661--1670
Yao-Yuan Chuang and
Sheng-Min Chen Infinite basis set extrapolation for
double hybrid density functional theory
1: Effect of applying various
extrapolation functions . . . . . . . . 1671--1679
Shide Liang and
Yaoqi Zhou and
Nick Grishin and
Daron M. Standley Protein side chain modeling with
orientation-dependent atomic force
fields derived by series expansions . . 1680--1686
Hongmei Liu and
Zhenzhen Zhao and
Nan Wang and
Cui Yu and
Jianwei Zhao Can the transition from tunneling to
hopping in molecular junctions be
predicted by theoretical calculation? 1687--1693
Sen Lin and
Daiqian Xie New ab initio potential energy surfaces
for both the ground (\~X$^1$A') and
excited (Ã$^1$A'') electronic states of
HSiCl and the absorption and emission
spectra of HSiCl/DSiCl . . . . . . . . . 1694--1702
Blandine Courcot and
Adam J. Bridgeman Optimization of a molecular mechanics
force field for type-II polyoxometalates
focussing on electrostatic interactions:
a case study . . . . . . . . . . . . . . 1703--1710
Nicole Legenski and
Chenggang Zhou and
Qingfan Zhang and
Bo Han and
Jinping Wu and
Liang Chen and
Hansong Cheng and
Robert C. Forrey Force fields for metallic clusters and
nanoparticles . . . . . . . . . . . . . 1711--1720
Pawe\l Szarek and
Ludwik Komorowski Modeling the electron density kernels 1721--1724
Mohammednoor Altarawneh and
Ala'A H. Al-Muhtaseb and
Bogdan Z. Dlugogorski and
Eric M. Kennedy and
John C. Mackie Rate constants for hydrogen abstraction
reactions by the hydroperoxyl radical
from methanol, ethenol, acetaldehyde,
toluene, and phenol . . . . . . . . . . 1725--1733
Ch. Bheema Lingam and
K. Ramesh Babu and
Surya P. Tewari and
G. Vaitheeswaran Structural, electronic, bonding, and
elastic properties of NH$_3$BH$_3$: a
density functional study . . . . . . . . 1734--1742
Hannes G. Wallnoefer and
Klaus R. Liedl and
Thomas Fox A challenging system: Free energy
prediction for factor Xa . . . . . . . . 1743--1752
Zongling Ding and
Jun Jiang and
Huaizhong Xing and
Haibo Shu and
Yan Huang and
Xiaoshuang Chen and
Wei Lu The finite-size effect on the transport
properties in edge-modified graphene
nanoribbon-based molecular devices . . . 1753--1759
Chaoyang Zhang and
Xiaolin Wang and
Mingfei Zhou Isomers and isomerization reactions of
four nitro derivatives of methane . . . 1760--1768
Daniel Sheppard and
Graeme Henkelman Paths to which the nudged elastic band
converges . . . . . . . . . . . . . . . 1769--1771
Wolfgang Quapp and
Josep Maria Bofill Reply to the comment by Sheppard and
Henkelman on the nudged elastic band
method . . . . . . . . . . . . . . . . . 1772--1773
M. De La Pierre and
R. Orlando and
L. Maschio and
K. Doll and
P. Ugliengo and
R. Dovesi Performance of six functionals (LDA,
PBE, PBESOL, B3LYP, PBE0, and WC1LYP) in
the simulation of vibrational and
dielectric properties of crystalline
compounds. The case of forsterite
Mg$_2$SiO$_4$ . . . . . . . . . . . . . 1775--1784
Moshe Goldstein and
Erick Fredj and
R. Benny Gerber A new hybrid algorithm for finding the
lowest minima of potential surfaces:
Approach and application to peptides . . 1785--1800
Denise Steiner and
Chris Oostenbrink and
François Diederich and
Martina Zürcher and
Wilfred F. van Gunsteren Calculation of binding free energies of
inhibitors to plasmepsin II . . . . . . 1801--1812
Nasr Y. M. Omar and
Noorsaadah A. Rahman and
Sharifuddin Md Zain Enantioselective organocatalytic
Diels--Alder reactions: a density
functional theory and kinetic isotope
effects study . . . . . . . . . . . . . 1813--1823
Igor Ying Zhang and
Jianming Wu and
Yi Luo and
Xin Xu Accurate bond dissociation enthalpies by
using doubly hybrid XYG3 functional . . 1824--1838
Doreen Mollenhauer and
Johannes Flob and
Hans-Ulrich Reissig and
Elena Voloshina and
Beate Paulus Accurate quantum-chemical description of
gold complexes with pyridine and its
derivatives . . . . . . . . . . . . . . 1839--1845
Zhiwei Liu and
Alexey Teslja and
Vojislava Pophristic An ab initio molecular orbital study of
intramolecular hydrogen bonding in
ortho-substituted arylamides:
Implications for the parameterization of
molecular mechanics force fields . . . . 1846--1858
Jongtaek Kim and
Eunjung Yoo and
Sukbok Chang and
Yoon Sup Lee Electronic and chelation effects on the
unusual C2-methylation of
$N$-(para-substituted)phenylaziridines
with lithium organocuprates . . . . . . 1859--1868
Fabrice Avaltroni and
Clemence Corminboeuf Efficiency of random search procedures
along the silicon cluster series: Si$_n$
($ n = 5 $--$ 10 $, $ 15 $, and $ 20 $ ) 1869--1875
Francisco Rodríguez-Ropero and
Marco Fioroni Effect of Na$^+$, Mg$^{2+}$, and
Zn$^{2+}$ chlorides on the structural
and thermodynamic properties of
water/$n$-heptane interfaces . . . . . . 1876--1886
\.Zaneta Czy\.znikowska and
Wojciech Bartkowiak Physical origins of the stability of
aromatic amino acid core ring-polycyclic
hydrocarbon complexes: a
post-Hartree--Fock and density
functional study . . . . . . . . . . . . 1887--1895
Chi-Shiun Wu and
Ming-Der Su A computational study of the
reactivities of four-membered heavy
carbene systems . . . . . . . . . . . . 1896--1906
Shao-Yong Lu and
Yong-Jun Jiang and
Jing Lv and
Jian-Wei Zou and
Tian-Xing Wu Role of bridging water molecules in
GSK3$ \beta $-inhibitor complexes:
Insights from QM/MM, MD, and molecular
docking studies . . . . . . . . . . . . 1907--1918
Djurre H. De Jong and
Lars V. Schäfer and
Alex H. De Vries and
Siewert J. Marrink and
Herman J. C. Berendsen and
Helmut Grubmüller Determining equilibrium constants for
dimerization reactions from molecular
dynamics simulations . . . . . . . . . . 1919--1928
Elizabeth J. Denning and
U. Deva Priyakumar and
Lennart Nilsson and
Alexander D. Mackerell Jr. Impact of 2'-hydroxyl sampling on the
conformational properties of RNA: Update
of the CHARMM all-atom additive force
field for RNA . . . . . . . . . . . . . 1929--1943
Abdel Laoui and
Valery R. Polyakov Web services as applications'
integration tool: QikProp case study . . 1944--1951
Pieter Van der Weeën and
Jan M. Baetens and
Bernard De Baets Design and parameterization of a
stochastic cellular automaton describing
a chemical reaction . . . . . . . . . . 1952--1961
Manjaly J. Ajitha and
Cherumuttathu H. Suresh Role of stereoelectronic features of
imine and enamine in (S)-proline
catalyzed Mannich reaction of
acetaldehyde: an in silico study . . . . 1962--1970
Wenlan Liu and
Volker Settels and
Philipp H. P. Harbach and
Andreas Dreuw and
Reinhold F. Fink and
Bernd Engels Assessment of TD-DFT- and TD-HF-based
approaches for the prediction of exciton
coupling parameters, potential energy
curves, and electronic characters of
electronically excited aggregates . . . 1971--1981
Volodymyr P. Sergiievskyi and
Wolfgang Hackbusch and
Maxim V. Fedorov Multigrid solver for the reference
interaction site model of molecular
liquids theory . . . . . . . . . . . . . 1982--1992
Evgeniy Yu. Pankratyev and
Artur R. Tulyabaev and
Leonard M. Khalilov How reliable are GIAO calculations of
$^1$H and $^{13}$C NMR chemical shifts?
A statistical analysis and empirical
corrections at DFT (PBE/3z) level . . . 1993--1997
Eliseo Ruiz Exchange coupling constants using
density functional theory: Long-range
corrected functionals . . . . . . . . . 1998--2004
Guangtao Yu and
Xu-Ri Huang and
Wei Chen and
Chia-Chung Sun Alkali metal atom-aromatic ring: a novel
interaction mode realizes large first
hyperpolarizabilities of M@AR (M = Li,
Na, and K, AR = pyrrole, indole,
thiophene, and benzene) . . . . . . . . 2005--2011
Yin-Feng Wang and
Wei Chen and
Guang-Tao Yu and
Zhi-Ru Li and
Di Wu and
Chia-Chung Sun Evolution of lone pair of excess
electrons inside molecular cages with
the deformation of the cage in $ e_2 $
@C$_{60}$F$_{60}$ systems . . . . . . . 2012--2021
Darren J. Simpson and
Thomas Bredow and
Anand P. Chandra and
Giuseppe P. Cavallaro and
Andrea R. Gerson The effect of iron and copper impurities
on the wettability of sphalerite (110)
surface . . . . . . . . . . . . . . . . 2022--2030
Mark J. Abraham and
Jill E. Gready Optimization of parameters for molecular
dynamics simulation using smooth
particle-mesh Ewald in GROMACS 4.5 . . . 2031--2040
Mark J. Abraham Performance enhancements for GROMACS
nonbonded interactions on BlueGene . . . 2041--2046
Sanliang Ling and
Maciej Gutowski SSC: a tool for constructing libraries
for systematic screening of conformers 2047--2054
Zhaowei Huang and
Hui Sun and
Houyu Zhang and
Yue Wang and
Fei Li $ \pi $--$ \pi $ interaction of
quinacridone derivatives . . . . . . . . 2055--2063
Alexey I. Baranov and
Miroslav Kohout Electron localization and delocalization
indices for solids . . . . . . . . . . . 2064--2076
Lalitha Selvam and
Fang Fang Chen and
Feng Wang Methylation of zebularine investigated
using density functional theory
calculations . . . . . . . . . . . . . . 2077--2083
Jens Smiatek and
Andreas Heuer Calculation of free energy landscapes: a
histogram reweighted metadynamics
approach . . . . . . . . . . . . . . . . 2084--2096
R. S. Rathore and
P. Aparoy and
P. Reddanna and
A. K. Kondapi and
M. Rami Reddy Minimum MD simulation length required to
achieve reliable results in free energy
perturbation calculations: Case study of
relative binding free energies of
fructose-1,6-bisphosphatase inhibitors 2097--2103
Juan M. Ramírez-Anguita and
\`Angels González-Lafont and
José M. Lluch Variational transition-state theory
study of the rate constant of the DMS$
\cdot $OH scavenging reaction by O$_2$ 2104--2118
Hadley A. Iliff and
Diane L. Lynch and
Evangelia Kotsikorou and
Patricia H. Reggio Parameterization of Org27569: an
allosteric modulator of the cannabinoid
CB$_1$G protein-coupled receptor . . . . 2119--2126
Peng Zhang and
Peng Bao and
Jiali Gao Dipole preserving and polarization
consistent charges . . . . . . . . . . . 2127--2139
Steven K. Burger and
Paul W. Ayers Empirical prediction of protein $ p K_a
$ values with residue mutation . . . . . 2140--2148
Aurélien Grosdidier and
Vincent Zoete and
Olivier Michielin Fast docking using the CHARMM force
field with EADock DSS . . . . . . . . . 2149--2159
Stephanie B. A. De Beer and
Alice GlÄttli and
Johannes Hutzler and
Nico P. E. Vermeulen and
Chris Oostenbrink Molecular dynamics simulations and free
energy calculations on the enzyme
4-hydroxyphenylpyruvate dioxygenase . . 2160--2169
Manoj K. Kesharwani and
Bishwajit Ganguly Probing the structural and electronic
effects to stabilize nonplanar forms of
thioamide derivatives: a computational
study . . . . . . . . . . . . . . . . . 2170--2176
Frédéric Labat and
Claude Pouchan and
Carlo Adamo and
Gustavo E. Scuseria Role of nonlocal exchange in molecular
crystals: the case of two proton-ordered
phases of ice . . . . . . . . . . . . . 2177--2185
Alexander M. Silva and
Itamar Borges Jr. How to find an optimum cluster size
through topological site properties:
MoS$_x$ model clusters . . . . . . . . . 2186--2194
Liudmila Sviatenko and
Olexandr Isayev and
Leonid Gorb and
Frances Hill and
Jerzy Leszczynski Toward robust computational
electrochemical predicting the
environmental fate of organic pollutants 2195--2203
Raghuvir R. S. Pissurlenkar and
Vijay M. Khedkar and
Radhakrishnan P. Iyer and
Evans C. Coutinho Ensemble QSAR: a QSAR method based on
conformational ensembles and metric
descriptors . . . . . . . . . . . . . . 2204--2218
Flavio Forti and
Leonardo Boechi and
Dario A. Estrin and
Marcelo A. Marti Comparing and combining implicit ligand
sampling with multiple steered molecular
dynamics to study ligand migration
processes in heme proteins . . . . . . . 2219--2231
Matthew G. Seetin and
David H. Mathews Automated RNA tertiary structure
prediction from secondary structure and
low-resolution restraints . . . . . . . 2232--2244
Christoph Grebner and
Johannes Becker and
Svetlana Stepanenko and
Bernd Engels Efficiency of tabu-search-based
conformational search algorithms . . . . 2245--2253
Victor M. Anisimov and
Claudio N. Cavasotto Quantum mechanical binding free energy
calculation for phosphopeptide
inhibitors of the Lck SH2 domain . . . . 2254--2263
Yutaka Uejima and
Tomoharu Terashima and
Ryo Maezono Acceleration of a QM/MM-QMC simulation
using GPU . . . . . . . . . . . . . . . 2264--2272
Trent E. Balius and
Sudipto Mukherjee and
Robert C. Rizzo Implementation and evaluation of a
docking-rescoring method using molecular
footprint comparisons . . . . . . . . . 2273--2289
Zhixiong Lin and
Wilfred F. Van Gunsteren and
Haiyan Liu Conformational state-specific free
energy differences by one-step
perturbation: Protein secondary
structure preferences of the GROMOS 43A1
and 53A6 force fields . . . . . . . . . 2290--2297
Weihua Zhu and
Chenchen Zhang and
Tao Wei and
Heming Xiao Computational study of energetic
nitrogen-rich derivatives of 1,1'- and
5,5'-bridged ditetrazoles . . . . . . . 2298--2312
Karl A. Wilkinson and
Paul Sherwood and
Martyn F. Guest and
Kevin J. Naidoo Acceleration of the GAMESS-UK electronic
structure package on graphical
processing units . . . . . . . . . . . . 2313--2318
Naveen Michaud-Agrawal and
Elizabeth J. Denning and
Thomas B. Woolf and
Oliver Beckstein MDAnalysis: a toolkit for the analysis
of molecular dynamics simulations . . . 2319--2327
Christoph R. Jacob and
S. Maya Beyhan and
Rosa E. Bulo and
André Severo Pereira Gomes and
Andreas W. Götz and
Karin Kiewisch and
Jetze Sikkema and
Lucas Visscher PyADF --- a scripting framework for
multiscale quantum chemistry . . . . . . 2328--2338
Marie L. Laury and
Scott E. Boesch and
Ian Haken and
Pankaj Sinha and
Ralph A. Wheeler and
Angela K. Wilson Harmonic vibrational frequencies: Scale
factors for pure, hybrid, hybrid meta,
and double-hybrid functionals in
conjunction with correlation consistent
basis sets . . . . . . . . . . . . . . . 2339--2347
Yuhang Wang and
Jason A. Wallace and
Peter H. Koenig and
Jana K. Shen Molecular dynamics simulations of ionic
and nonionic surfactant micelles with a
generalized Born implicit-solvent model 2348--2358
Vincent Zoete and
Michel A. Cuendet and
Aurélien Grosdidier and
Olivier Michielin SwissParam: a fast force field
generation tool for small organic
molecules . . . . . . . . . . . . . . . 2359--2368
Robert J. Petrella A versatile method for systematic
conformational searches: Application to
CheY . . . . . . . . . . . . . . . . . . 2369--2385
Partha Pratim Roy and
Simona Kovarich and
Paola Gramatica QSAR model reproducibility and
applicability: a case study of rate
constants of hydroxyl radical reaction
models applied to polybrominated
diphenyl ethers and (benzo-)triazoles 2386--2396
Pablo A. Denis and
Federico Iribarne On the applicability of cluster models
to study the chemical reactivity of
carbon nanotubes . . . . . . . . . . . . 2397--2403
Vikas He molecular ion in a strong
time-dependent magnetic field: a
current-density functional study . . . . 2404--2413
Yi-Hsing Chung and
Arvin Huang-Te Li and
Sheng D. Chao Computer simulation of trifluoromethane
properties with ab initio force field 2414--2421
Cina Foroutan-Nejad and
Shant Shahbazian and
Ferran Feixas and
Parviz Rashidi-Ranjbar and
Miquel Sol\`a A dissected ring current model for
assessing magnetic aromaticity: a
general approach for both organic and
inorganic rings . . . . . . . . . . . . 2422--2431
Qing-Zhong Li and
Jun-Ling Zhao and
Bo Jing and
Ran Li and
Wen-Zuo Li and
Jian-Bo Cheng The structure, properties, and nature of
HArF--HOX (X = F, Cl, Br) complex: an ab
initio study and an unusual short
hydrogen bond . . . . . . . . . . . . . 2432--2440
Luc Roumen and
Bram Van Hoof and
Koen Pieterse and
Peter A. J. Hilbers and
Erica M. G. Custers and
Ralf Plate and
Marcel De Gooyer and
Ilona P. E. Beugels and
Judith M. A. Emmen and
Dirk Leysen and
Jos F. M. Smits and
Harry C. J. Ottenheijm and
J. J. Rob Hermans Application of a ligand-based
theoretical approach to derive
conversion paths and ligand
conformations in CYP11B2-mediated
aldosterone formation . . . . . . . . . 2441--2448
Stefan Boresch and
Stefan Bruckner Avoiding the van der Waals endpoint
problem using serial atomic insertion 2449--2458
Alexander V. Larin Point atomic multipole moments for
simulation of electrostatic potential
and field in all-siliceous zeolites . . 2459--2473
Qun Jing and
Hai-Bin Cao and
Gui-Xian Ge and
Yuan Xu Wang and
Hong-Xia Yan and
Zi-Ying Zhang and
Yun-Hu Liu Giant magnetic moment of the core-shell
Co$_{13}$ @Mn$_{20}$ clusters:
First-principles calculations . . . . . 2474--2478
Hossein Farrokhpour and
Fariman Fathi Theoretical study of valance
photoelectron spectra of hypoxanthine,
xanthine, and caffeine using direct
symmetry-adapted cluster/configuration
interaction methodology . . . . . . . . 2479--2491
Rafa\l A. Bachorz and
Florian A. Bischoff and
Andreas Glöß and
Christof Hättig and
Sebastian Höfener and
Wim Klopper and
David P. Tew The MP2-F12 method in the T URBOMOLE
program package . . . . . . . . . . . . 2492--2513
Ali Nekouzadeh and
Yoram Rudy Three-residue loop closure in proteins:
a new kinematic method reveals a locus
of connected loop conformations . . . . 2515--2525
Chaim Dryzun and
Amir Zait and
David Avnir Quantitative symmetry and chirality ---
a fast computational algorithm for large
structures: Proteins, macromolecules,
nanotubes, and unit cells . . . . . . . 2526--2538
Bo Liao and
Benyou Liao and
Xinguo Lu and
Zhi Cao A novel graphical representation of
protein sequences and its application 2539--2544
Futing Xia and
Hua Zhu Alkaline hydrolysis of ethylene
phosphate: an ab initio study by
supermolecule model and polarizable
continuum approach . . . . . . . . . . . 2545--2554
Han-Ying Wu and
Wan-Fei Cai and
Lai-Cai Li and
An-Min Tian and
Ning-Bew Wong Theoretical study on the ring-opening
isomerization reaction mechanism of the
ring isomers of N$_8$H$_8$ . . . . . . . 2555--2563
Mahmoud A. A. Ibrahim Molecular mechanical study of halogen
bonding in drug discovery . . . . . . . 2564--2574
Florian Fink and
Jochen Hochrein and
Vincent Wolowski and
Rainer Merkl and
Wolfram Gronwald PROCOS: Computational analysis of
protein--protein complexes . . . . . . . 2575--2586
Zheng Fu and
Xue Li and
Kenneth M. Merz Jr. Accurate assessment of the strain energy
in a protein-bound drug using QM/MM
X-ray refinement and converged quantum
chemistry . . . . . . . . . . . . . . . 2587--2597
Changsheng Zhang and
Luhua Lai SDOCK: a global protein-protein docking
program using stepwise force-field
potentials . . . . . . . . . . . . . . . 2598--2612
David Robinson and
Nicholas A. Besley and
Paul O'Shea and
Jonathan D. Hirst Water order profiles on
phospholipid/cholesterol membrane
bilayer surfaces . . . . . . . . . . . . 2613--2618
Arne Lüchow and
René Petz Single electron densities: a new tool to
analyze molecular wavefunctions . . . . 2619--2626
Adriana Pietropaolo and
Davide Branduardi and
Massimiliano Bonomi and
Michele Parrinello A chirality-based metrics for
free-energy calculations in biomolecular
systems . . . . . . . . . . . . . . . . 2627--2637
Elisabet Gregori-Puigjané and
Rut Garriga-Sust and
Jordi Mestres Indexing molecules with chemical graph
identifiers . . . . . . . . . . . . . . 2638--2646
Konstantin V. Klenin and
Frank Tristram and
Timo Strunk and
Wolfgang Wenzel Derivatives of molecular surface area
and volume: Simple and exact analytical
formulas . . . . . . . . . . . . . . . . 2647--2653
Luís Pinto Da Silva and
Joaquim C. G. Esteves Da Silva Theoretical modulation of the color of
light emitted by firefly oxyluciferin 2654--2663
Michel Masella and
Daniel Borgis and
Philippe Cuniasse Combining a polarizable force-field and
a coarse-grained polarizable solvent
model. II. Accounting for hydrophobic
effects . . . . . . . . . . . . . . . . 2664--2678
Rini Gupta and
Amalendu Chandra Nonideality in diffusion of ionic and
neutral solutes and hydrogen bond
dynamics in dimethyl
sulfoxide--chloroform mixtures of
varying composition . . . . . . . . . . 2679--2689
Giovanni Granucci and
Maurizio Persico Gradients for configuration interaction
energies with spin-orbit coupling in a
semiempirical framework . . . . . . . . 2690--2696
R. S. Dias and
P. Linse and
A. A. C. C. Pais Stepwise disproportionation in
polyelectrolyte complexes . . . . . . . 2697--2707
Ala'a H. Al-Muhtaseb and
Mohammednoor Altarawneh and
Mansour H. Almatarneh and
Raymond A. Poirier and
Niveen W. Assaf Theoretical study on the unimolecular
decomposition of thiophenol . . . . . . 2708--2715
Ka-un Lao and
Chin-hui Yu A computational study of unique
properties of pillar$ [n] $ quinones:
Self-assembly to tubular structures and
potential applications as electron
acceptors and anion recognizers . . . . 2716--2726
A. P. Toropova and
A. A. Toropov and
E. Benfenati and
G. Gini and
D. Leszczynska and
J. Leszczynski CORAL: Quantitative structure--activity
relationship models for estimating
toxicity of organic compounds in rats 2727--2733
Maciej D\lugosz and
Pawe\l Zieli\'nski and
Joanna Trylska Brownian dynamics simulations on CPU and
GPU with BD\_BOX . . . . . . . . . . . . 2734--2744
Peipei Han and
Kehe Su and
Yan Liu and
Yanli Wang and
Xin Wang and
Qingfeng Zeng and
Laifei Cheng and
Litong Zhang Reaction rate of propene pyrolysis . . . 2745--2755
Michio Katouda and
Masato Kobayashi and
Hiromi Nakai and
Shigeru Nagase Two-level hierarchical parallelization
of second-order Mòller--Plesset
perturbation calculations in
divide-and-conquer method . . . . . . . 2756--2764
Yang Li and
Chang-Sheng Wang Rapid evaluation of the binding energies
between peptide amide and DNA base . . . 2765--2773
Tomonaga Ozawa and
Kosuke Okazaki and
Kazuo Kitaura Importance of CH/$ \pi $ hydrogen bonds
in recognition of the core motif in
proline-recognition domains: An ab
initio fragment molecular orbital study 2774--2782
Pei-Kun Yang Discrepancy in the near-solute electric
dipole moment calculated from the
electric field . . . . . . . . . . . . . 2783--2799
Juan Du and
Huijun Sun and
Lili Xi and
Jiazhong Li and
Ying Yang and
Huanxiang Liu and
Xiaojun Yao Molecular modeling study of checkpoint
kinase 1 inhibitors by multiple docking
strategies and prime/MM--GBSA
calculation . . . . . . . . . . . . . . 2800--2809
Hironori Kokubo and
Toshimasa Tanaka and
Yuko Okamoto Ab initio prediction of protein--ligand
binding structures by replica-exchange
umbrella sampling simulations . . . . . 2810--2821
Giovanni Micera and
Eugenio Garribba Is the spin-orbit coupling important in
the prediction of the $^{51}$V hyperfine
coupling constants of V$^{IV}$O$^{2+}$
species? ORCA versus Gaussian
performance and biological applications 2822--2835
Jonah Z. Vilseck and
Somisetti V. Sambasivarao and
Orlando Acevedo Optimal scaling factors for CM1 and CM3
atomic charges in RM1-based aqueous
simulations . . . . . . . . . . . . . . 2836--2842
Shunzhou Wan and
Peter V. Coveney Molecular dynamics simulation reveals
structural and thermodynamic features of
kinase activation by cancer mutations
within the epidermal growth factor
receptor . . . . . . . . . . . . . . . . 2843--2852
Janus J. Eriksen and
Jógvan Magnus H. Olsen and
K\kestutis Aidas and
Hans Ågren and
Kurt V. Mikkelsen and
Jacob Kongsted Computational protocols for prediction
of solute NMR relative chemical shifts.
A case study of L-tryptophan in aqueous
solution . . . . . . . . . . . . . . . . 2853--2864
Svetlana Artemova and
Sergei Grudinin and
Stephane Redon A comparison of neighbor search
algorithms for large rigid molecules . . 2865--2877
Nathanael Weill and
Christopher R. Corbeil and
Joris W. De Schutter and
Nicolas Moitessier Toward a computational tool predicting
the stereochemical outcome of asymmetric
reactions: Development of the molecular
mechanics-based program ACE and
application to asymmetric epoxidation
reactions . . . . . . . . . . . . . . . 2878--2889
Yung-Fou Chen and
J. J. Dannenberg The effect of polarization on multiple
hydrogen-bond formation in models of
self-assembling materials . . . . . . . 2890--2895
Xiao Wei Sheng and
Lukasz Mentel and
Oleg V. Gritsenko and
Evert Jan Baerends Counterpoise correction is not useful
for short and van der Waals distances
but may be useful at long range . . . . 2896--2901
Taro Udagawa and
Shogo Sakai Ab initio molecular dynamics of
protonated water clusters by integrated
multicenter molecular-orbital method . . 2902--2908
Jennifer L. Knight and
Charles L. Brooks III Surveying implicit solvent models for
estimating small molecule absolute
hydration free energies . . . . . . . . 2909--2923
Matthieu Chavent and
Antoine Vanel and
Alex Tek and
Bruno Levy and
Sophie Robert and
Bruno Raffin and
Marc Baaden GPU-accelerated atom and dynamic bond
visualization using hyperballs: a
unified algorithm for balls, sticks, and
hyperboloids . . . . . . . . . . . . . . 2924--2935
Reed B. Jacob and
Casey W. Bullock and
Tim Andersen and
Owen M. McDougal DockoMatic: Automated peptide analog
creation for high throughput virtual
screening . . . . . . . . . . . . . . . 2936--2941
Bing Xia and
Zheng-Fu Tai and
Yu-Cheng Gu and
Bang-Jing Li and
Li-Sheng Ding and
Yan Zhou MyMolDB: a micromolecular database
solution with open source and free
components . . . . . . . . . . . . . . . 2942--2948
Robin Chaudret and
Nohad Gresh and
Olivier Parisel and
Jean-Philip Piquemal Many-body exchange-repulsion in
polarizable molecular mechanics. I.
orbital-based approximations and
applications to hydrated metal cation
complexes . . . . . . . . . . . . . . . 2949--2957
Narayan Ganesan and
Brad A. Bauer and
Timothy R. Lucas and
Sandeep Patel and
Michela Taufer Structural, dynamic, and electrostatic
properties of fully hydrated DMPC
bilayers from molecular dynamics
simulations accelerated with graphical
processing units (GPUs) . . . . . . . . 2958--2973
G. L. Gutsev and
C. A. Weatherford and
K. Pradhan and
P. Jena Density functional study of neutral and
anionic AlO$_n$ and ScO$_n$ with high
oxygen content . . . . . . . . . . . . . 2974--2982
Davide Ravelli and
Daniele Dondi and
Maurizio Fagnoni and
Angelo Albini and
Alessandro Bagno Predicting the UV spectrum of
polyoxometalates by TD-DFT . . . . . . . 2983--2987
Wojciech Plazinski Molecular basis of calcium binding by
polyguluronate chains. Revising the
egg-box model . . . . . . . . . . . . . 2988--2995
Milind M. Deshmukh and
Libero J. Bartolotti and
Shridhar R. Gadre Intramolecular hydrogen bond energy and
cooperative interactions in $ \alpha $-,
$ \beta $-, and $ \gamma $-cyclodextrin
conformers . . . . . . . . . . . . . . . 2996--3004
Urban Bor\vstnik and
Benjamin T. Miller and
Bernard R. Brooks and
Du\vsanka Jane\vzi\vc The distributed diagonal force
decomposition method for parallelizing
molecular dynamics simulations . . . . . 3005--3013
Mark A. Olson and
Sidhartha Chaudhury and
Michael S. Lee Comparison between self-guided Langevin
dynamics and molecular dynamics
simulations for structure refinement of
protein loop conformations . . . . . . . 3014--3022
Paul Mach and
Patrice Koehl Geometric measures of large
biomolecules: Surface, volume, and
pockets . . . . . . . . . . . . . . . . 3023--3038
Pablo García-Risueño and
Pablo Echenique and
J. L. Alonso Exact and efficient calculation of
Lagrange multipliers in biological
polymers with constrained bond lengths
and bond angles: Proteins and nucleic
acids as example cases . . . . . . . . . 3039--3046
Kenichi Dedachi and
Tatsuya Hirakawa and
Seiya Fujita and
Mahmud Tareq Hassan Khan and
Ingebrigt Sylte and
Noriyuki Kurita Specific interactions and binding free
energies between thermolysin and
dipeptides: Molecular simulations
combined with ab initio molecular
orbital and classical vibrational
analysis . . . . . . . . . . . . . . . . 3047--3057
Chuang Miao and
Ying Shi Reconsideration on hydrogen bond
strengthening or cleavage of
photoexcited coumarin 102 in aqueous
solvent: a DFT/TDDFT study . . . . . . . 3058--3061
Michinori Sumimoto and
Yukio Kawashima and
Daisuke Yokogawa and
Kenji Hori and
Hitoshi Fujimoto Theoretical study on the molecular
structures of X-, $ \alpha $-, and $
\beta $-types of lithium phthalocyanine
dimer . . . . . . . . . . . . . . . . . 3062--3067
Feng-Chao Cui and
Xiao-Liang Pan and
Wei Liu and
Jing-Yao Liu Elucidation of the methyl transfer
mechanism catalyzed by chalcone
O-methyltransferase: a density
functional study . . . . . . . . . . . . 3068--3074
Zhinan Ma and
Wensheng Cai and
Xueguang Shao Impact of different potentials on the
structures and energies of clusters . . 3075--3080
Taichi Inagaki and
Takeshi Yamamoto and
Shigeki Kato Proton-coupled electron transfer of the
phenoxyl/phenol couple: Effect of
Hartree--Fock exchange on transition
structures . . . . . . . . . . . . . . . 3081--3091
Kenta Yamada and
Yoshiyuki Koyano and
Takuya Okamoto and
Toshio Asada and
Nobuaki Koga and
Masataka Nagaoka Toward a new approach for determination
of solute's charge distribution to
analyze interatomic electrostatic
interactions in quantum
mechanical/molecular mechanical
simulations . . . . . . . . . . . . . . 3092--3104
Alessandra Manzin and
Oriano Bottauscio and
Domenico Patrizio Ansalone Application of the thin-shell
formulation to the numerical modeling of
Stern layer in biomolecular
electrostatics . . . . . . . . . . . . . 3105--3113
Robert Ponec Bond indices in solids: Extended
analytical model . . . . . . . . . . . . 3114--3121
Chang-wen Zhang and
Fu-bao Zheng First-principles prediction on
electronic and magnetic properties of
hydrogenated AlN nanosheets . . . . . . 3122--3128
Alexander Baldes and
Wim Klopper and
Ján \vSimunek and
Jozef Noga and
Florian Weigend Acceleration of self-consistent-field
convergence by combining conventional
diagonalization and a
diagonalization-free procedure . . . . . 3129--3134
Sunhwan Jo and
Kevin C. Song and
Heather Desaire and
Alexander D. MacKerell Jr. and
Wonpil Im Glycan reader: Automated sugar
identification and simulation
preparation for carbohydrates and
glycoproteins . . . . . . . . . . . . . 3135--3141
Blandine Courcot and
Adam J. Bridgeman Modeling the interactions between
polyoxometalates and their environment 3143--3153
Safwat Abdel-Azeim and
Xin Li and
Lung Wa Chung and
Keiji Morokuma Zinc--Homocysteine binding in
cobalamin-dependent methionine synthase
and its role in the substrate
activation: DFT, ONIOM, and QM/MM
molecular dynamics studies . . . . . . . 3154--3167
Hanna Kjær and
Stephan P. A. Sauer and
Jacob Kongsted The coupling constant polarizability and
hyperpolarizabilty of $^1$J (NH) in
$N$-methylacetamide, and its application
for the multipole spin--spin coupling
constant polarizability/reaction field
approach to solvation . . . . . . . . . 3168--3174
Jenn-Huei Lii and
Fu-Xing Liao and
Ching-Han Hu Accurate prediction of the enthalpies of
formation for xanthophylls . . . . . . . 3175--3187
Beisi Xu and
Hujun Shen and
Xiao Zhu and
Guohui Li Fast and accurate computation schemes
for evaluating vibrational entropy of
proteins . . . . . . . . . . . . . . . . 3188--3193
Alexios Grigoropoulos and
Robert K. Szilagyi In silico evaluation of proposed
biosynthetic pathways for the unique
dithiolate ligand of the H-cluster of
[FeFe]-hydrogenase . . . . . . . . . . . 3194--3206
David Kozlowski and
Julien Pilmé New insights in quantum chemical
topology studies using numerical
grid-based analyses . . . . . . . . . . 3207--3217
Shuo Chai and
Shu-Hao Wen and
Jin-Dou Huang and
Ke-Li Han Density functional theory study on
electron and hole transport properties
of organic pentacene derivatives with
electron-withdrawing substituent . . . . 3218--3225
Woong-Hee Shin and
Lim Heo and
Juyong Lee and
Junsu Ko and
Chaok Seok and
Jooyoung Lee LigDockCSA: Protein--ligand docking
using conformational space annealing . . 3226--3232
Zhao-Hui Qi and
Ling Li and
Xiao-Qin Qi Using Huffman coding method to visualize
and analyze DNA sequences . . . . . . . 3233--3240
Jie Xu and
Lei Wang and
Luoxin Wang and
Xiaolin Shen and
Weilin Xu QSPR study of Setschenow constants of
organic compounds using MLR, ANN, and
SVM analyses . . . . . . . . . . . . . . 3241--3252
Thomas Steinbrecher and
InSuk Joung and
David A. Case Soft-core potentials in thermodynamic
integration: Comparing one- and two-step
transformations . . . . . . . . . . . . 3253--3263
Fengting T. Wang and
Lei Chen and
Chuanjin J. Tian and
Yan Meng and
Zhigang G. Wang and
Ruiqin Q. Zhang and
Mingxing X. Jin and
Ping Zhang and
Dajun J. Ding Interactions between free radicals and a
graphene fragment: Physical versus
chemical bonding, charge transfer, and
deformation . . . . . . . . . . . . . . 3264--3268
Jong-Won Song and
Daoling Peng and
Kimihiko Hirao A semiempirical long-range corrected
exchange correlation functional
including a short-range Gaussian
attenuation (LCgau-B97) . . . . . . . . 3269--3275
Keju Sun and
Masanori Kohyama and
Shingo Tanaka and
Seiji Takeda A theoretical study of CO adsorption on
gold by Hückel theory and density
functional theory calculations . . . . . 3276--3282
Dennis M. Elking and
Lalith Perera and
Robert Duke and
Thomas Darden and
Lee G. Pedersen A finite field method for calculating
molecular polarizability tensors for
arbitrary multipole rank . . . . . . . . 3283--3295
Qingzhong Li and
Ran Li and
Zhenbo Liu and
Wenzuo Li and
Jianbo Cheng Interplay between halogen bond and
lithium bond in MCN--LiCN--XCCH (M = H,
Li, and Na; X = Cl, Br, and I) complex:
The enhancement of halogen bond by a
lithium bond . . . . . . . . . . . . . . 3296--3303
Jon Baker and
Krzysztof Wolinski An efficient parallel algorithm for the
calculation of unrestricted canonical
MP2 energies . . . . . . . . . . . . . . 3304--3312
Jing Wang and
Jian Meng and
Zhijian Wu Theoretical insights on the electron
doping and Curie temperature in La-doped
Sr$_2$CrWO$_6$ . . . . . . . . . . . . . 3313--3318
Anurag Prakash Sunda and
Arun Venkatnathan Molecular dynamics simulations of
triflic acid and triflate ion/water
mixtures: a proton conducting
electrolytic component in fuel cells . . 3319--3328
M. N. Bannerman and
R. Sargant and
L. Lue DynamO: a free $ O(N) $ general
event-driven molecular dynamics
simulator . . . . . . . . . . . . . . . 3329--3338
Yang Zhong and
Brad A. Bauer and
Sandeep Patel Solvation properties of $N$-acetyl-$
\beta $-glucosamine: Molecular dynamics
study incorporating electrostatic
polarization . . . . . . . . . . . . . . 3339--3353
C. Izanloo and
G. A. Parsafar and
H. Abroshan and
H. Akbarzadeh Denaturation of Drew--Dickerson DNA in a
high salt concentration medium:
Molecular dynamics simulations . . . . . 3354--3361
András Czajlik and
Ilona Hudáky and
András Perczel Local protein backbone folds determined
by calculated NMR chemical shifts . . . 3362--3382
Júlio C. S. Da Silva and
Willian R. Rocha C\bondH bond activation of methane in
aqueous solution: a hybrid quantum
mechanical/effective fragment potential
study . . . . . . . . . . . . . . . . . 3383--3392
Qi Dai and
Li Wu and
Lihua Li Improving protein structural class
prediction using novel combined sequence
information and predicted secondary
structural features . . . . . . . . . . 3393--3398
Kuan-Yu Yeh and
Michael J. Janik Density functional theory-based
electrochemical models for the oxygen
reduction reaction: Comparison of
modeling approaches for electric field
and solvent effects . . . . . . . . . . 3399--3408
Ren-Jie Lin and
Soonmin Jang and
Chen-Chang Wu and
Ya-Ling Liu and
Feng-Yin Li Site specificity of OH $ \alpha $-H
abstraction reaction for a $ \beta
$-hairpin peptide: an ab initio study 3409--3422
Jennifer L. Knight and
Charles L. Brooks III Applying efficient implicit nongeometric
constraints in alchemical free energy
simulations . . . . . . . . . . . . . . 3423--3432
Simon Leis and
Martin Zacharias Efficient inclusion of receptor
flexibility in grid-based
protein--ligand docking* . . . . . . . . 3433--3439
Hua-Qing Yang and
Chang-Wei Hu and
Chao Gao and
Meng-Yao Yang and
Fang-Ming Li and
Cai-Qin Li and
Xiang-Yuan Li Theoretical study on the gas-phase
reaction mechanism between palladium
monoxide and methane . . . . . . . . . . 3440--3455
Jan Meisner and
Judith B. Rommel and
Johannes Kästner Kinetic isotope effects calculated with
the instanton method . . . . . . . . . . 3456--3463
Léonard Jaillet and
Francesc J. Corcho and
Juan-Jesús Pérez and
Juan Cortés Randomized tree construction algorithm
to explore energy landscapes . . . . . . 3464--3474
Yu-Fang Liu and
Da-Peng Yang and
De-Heng Shi and
Jin-Feng Sun A TD-DFT study on the hydrogen bonding
of three esculetin complexes in
electronically excited states:
Strengthening and weakening . . . . . . 3475--3484
Diederik Vanfleteren and
Dieter Ghillemijn and
Dimitri Van Neck and
Patrick Bultinck and
Michel Waroquier and
Paul W. Ayers Fast density matrix-based partitioning
of the energy over the atoms in a
molecule consistent with the hirshfeld-I
partitioning of the electron density . . 3485--3496
Maria Jadraque and
Margarita Martin Charge-transfer processes in the
assembly of Si$_n$ O$_m$ neutral
clusters . . . . . . . . . . . . . . . . 3497--3504
Junmei Wang and
Tingjun Hou Application of molecular dynamics
simulations in molecular property
prediction II: Diffusion coefficient . . 3505--3519
Boran Han and
Yujun Zheng Nonadiabatic quantum dynamics in
O($^3$P) + H$_2$ $ \rightarrow $ OH + H:
a revisited study . . . . . . . . . . . 3520--3525
A. Laref Tight-binding molecular dynamics
simulation of ZnSe liquid within the
local environment dependence . . . . . . 1--10
Chengqi Wang and
Lili Xi and
Shuyan Li and
Huanxiang Liu and
Xiaojun Yao A sequence-based computational model for
the prediction of the solvent accessible
surface area for $ \alpha $-helix and $
\beta $-barrel transmembrane residues 11--17
Xiang Po Du and
Veng Cheong Lo and
Yuan Xu Wang The effect of structure and phase
transformation on the mechanical
properties of Re$_2$N and the stability
of Mn$_2$N . . . . . . . . . . . . . . . 18--24
Floris P. Buelens and
Helmut Grubmüller Linear-scaling soft-core scheme for
alchemical free energy calculations . . 25--33
Hongjiang Zhang and
Jean-Paul Malrieu and
Haibo Ma and
Jing Ma Implementation of renormalized excitonic
method at ab initio level . . . . . . . 34--43
Uppula Purushotham and
Dolly Vijay and
G. Narahari Sastry A computational investigation and the
conformational analysis of dimers,
anions, cations, and zwitterions of
L-phenylalanine . . . . . . . . . . . . 44--59
Yusuke Ootani and
Tetsuya Taketsugu Ab initio molecular dynamics approach to
tunneling splitting in polyatomic
molecules . . . . . . . . . . . . . . . 60--65
Li Wang and
Yanjie Li and
Hongqing He and
Jinglai Zhang Hydrogen abstraction reactions of OH
radicals with CH$_3$CH$_2$CH$_2$Cl and
CH$_3$CHClCH$_3$: a mechanistic and
kinetic study . . . . . . . . . . . . . 66--75
Pedro Gonnet Pairwise Verlet lists: Combining cell
lists and Verlet lists to improve memory
locality and parallelism . . . . . . . . 76--81
Hongping Li and
Shuhui Lv and
Yijia Bai and
Yanjie Xia and
Xiaojuan Liu and
Jian Meng First-principle investigation of
magnetic coupling mechanism in
hypothesized A-site-ordered perovskite
YMn$_3$Sc$_4$O$_{12}$ . . . . . . . . . 82--87
Yu Li Yan and
Yuan Xu Wang Electronic structure and low temperature
thermoelectric properties of
In$_{24}$M$_8$O$_{48}$ (M = Ge$^{4+}$,
Sn$^{4+}$, Ti$^{4+}$, and Zr$^{4+}$ ) 88--92
Xu-Geng Guo and
Jing-Lai Zhang and
Yuan Zhao Ab initio characterization of size
dependence of electronic spectra for
linear anionic carbon clusters C$_n^-$
($ n = 4 $--$ 17 $ ) . . . . . . . . . . 93--102
Chi-Shiun Wu and
Ming-Der Su Theoretical investigations of the
reactivities of four-membered
N-heterocyclic carbene analogues of the
group 13 elements . . . . . . . . . . . 103--111
Andreas Orthaber and
Alexander F. Sax and
Kevin A. Francesconi Oxygen versus sulfur: Structure and
reactivity of substituted arsine oxides
and arsine sulfides . . . . . . . . . . 112--117
Kiumars Shahrokh and
Anita Orendt and
Garold S. Yost and
Thomas E. Cheatham III Quantum mechanically derived
AMBER-compatible heme parameters for
various states of the cytochrome P450
catalytic cycle . . . . . . . . . . . . 119--133
Benjamin Helmich and
Marek Sierka Similarity recognition of molecular
structures by optimal atomic matching
and rotational superposition . . . . . . 134--140
Timothy R. Lucas and
Brad A. Bauer and
Joseph E. Davis and
Sandeep Patel Molecular dynamics simulation of
hydrated DPPC monolayers using charge
equilibration force fields . . . . . . . 141--152
Qi-Shi Du and
Si-Yu Long and
Jian-Zong Meng and
Ri-Bo Huang Empirical formulation and
parameterization of cation--$ \pi $
interactions for protein modeling . . . 153--162
Lingli Tang and
Linwei Sai and
Jijun Zhao and
Ruifeng Qiu A topological method for global
optimization of clusters: Application to
(TiO$_2$ )$_n$ ($ n = 1 $--$6$ ) . . . . 163--169
Nitin Wadnerkar and
Vijayanand Kalamse and
Shyi-Long Lee and
Ajay Chaudhari Verification of DFT-predicted hydrogen
storage capacity of VC$_3$H$_3$ complex
using molecular dynamics simulations . . 170--174
Sermsiri Chaiwongwattana and
Mayuree Phonyiem and
Viwat Vchirawongkwin and
Supakit Prueksaaroon and
Kritsana Sagarik Dynamics and mechanism of structural
diffusion in linear hydrogen bond . . . 175--188
Joseph D. Yesselman and
Daniel J. Price and
Jennifer L. Knight and
Charles L. Brooks III MATCH: an atom-typing toolset for
molecular mechanics force fields . . . . 189--202
Hui Zhang and
Liu Yang and
Jing-Yao Liu and
Ze-Sheng Li Theoretical study on the reaction CX$_3$
+ SiH(CH$_3$ )$_3$ (X = H, F) . . . . . 203--210
Nana Ma and
Chunguang Liu and
Yongqing Qiu and
Shiling Sun and
Zhongmin Su Theoretical investigation on
redox-switchable second-order nonlinear
optical responses of push--pull
Cp*CoEt$_2$C$_2$B$_4$H$_3$-expanded
(metallo)porphyrins . . . . . . . . . . 211--219
Jie Ying Gao and
Cheng Hua Zhang and
Mei Ming Luo and
Chan Kyung Kim and
Wei Chu and
Ying Xue Mechanism for the reaction of 2-naphthol
with N-methyl-N-phenyl-hydrazine
suggested by the density functional
theory investigations . . . . . . . . . 220--230
Jia-Nan Wang and
Hong-Liang Xu and
Shi-Ling Sun and
Ting Gao and
Hong-Zhi Li and
Hui Li and
Zhong-Min Su An effective method for accurate
prediction of the first
hyperpolarizability of alkalides . . . . 231--236
Wolf-D. Ihlenfeldt Letters to the editor: Comment on the
paper ``Indexing molecules with chemical
graph identifiers' by Elisabeth
Gregori-Puigjané, Rut Garriga-Sust, and
Jordi Mestres . . . . . . . . . . . . . 237--237
Elisabet Gregori-Puigjané and
Rut Garriga-Sust and
Jordi Mestres Letters to the Editor: Response to the
comment by Wolf Ihlenfeldt on the paper
``Indexing molecules with chemical graph
identifiers'' . . . . . . . . . . . . . 238--238
Hirofumi Fujimoto and
Mariko Higuchi and
Manabu Koike and
Hirotaka Ode and
Miroslav Pinak and
Juraj Kotulic Bunta and
Toshiyuki Nemoto and
Takashi Sakudoh and
Naoko Honda and
Hideaki Maekawa and
Kimiaki Saito and
Kozo Tsuchida A possible overestimation of the effect
of acetylation on lysine residues in KQ
mutant analysis . . . . . . . . . . . . 239--246
Jean-Marie Ducéré and
Anne Hemeryck and
Alain Est\`eve and
Mehdi Djafari Rouhani and
Georges Landa and
Philippe Ménini and
Cyril Tropis and
André Maisonnat and
Pierre Fau and
Bruno Chaudret A computational chemist approach to gas
sensors: Modeling the response of
SnO$_2$ to CO, O$_2$, and H$_2$O Gases 247--258
Eshel Faraggi and
Tuo Zhang and
Yuedong Yang and
Lukasz Kurgan and
Yaoqi Zhou SPINE X: Improving protein secondary
structure prediction by multistep
learning coupled with prediction of
solvent accessible surface area and
backbone torsion angles . . . . . . . . 259--267
Steven Lettieri and
Daniel M. Zuckerman Accelerating molecular Monte Carlo
simulations using distance and
orientation-dependent energy tables:
Tuning from atomistic accuracy to
smoothed ``coarse-grained'' models . . . 268--275
Shantanu Kadam and
Kumar Vanka A new approximate method for the
stochastic simulation of chemical
systems: the representative reaction
approach . . . . . . . . . . . . . . . . 276--285
Takaharu Mori and
Fumiko Ogushi and
Yuji Sugita Analysis of lipid surface area in
protein--membrane systems combining
Voronoi tessellation and Monte Carlo
integration methods . . . . . . . . . . 286--293
V. Ruiz de Angulo and
J. Cortés and
J. M. Porta Rigid-CLL: Avoiding constant-distance
computations in cell linked-lists
algorithms . . . . . . . . . . . . . . . 294--300
Xue Li and
Zheng Fu and
Kenneth M. Merz Jr. QM/MM refinement and analysis of protein
bound retinoic acid . . . . . . . . . . 301--310
Xiao-Jing Liu and
Ian Hamilton and
Robert P. Krawczyk and
Peter Schwerdtfeger The stability of small helical gold
nanorods: a relativistic density
functional study . . . . . . . . . . . . 311--318
Yulia N. Kalugina and
Victor N. Cherepanov and
Mikhail A. Buldakov and
Natalia Zvereva-Loëte and
Vincent Boudon Theoretical investigation of the
ethylene dimer: Interaction energy and
dipole moment . . . . . . . . . . . . . 319--330
Kyu Il Lee and
Sunhwan Jo and
Huan Rui and
Bernhard Egwolf and
Beno\^\it Roux and
Richard W. Pastor and
Wonpil Im Software News and Updates: Web interface
for Brownian dynamics simulation of ion
transport and its applications to
beta-barrel pores . . . . . . . . . . . 331--339
Anna-Pitschna E. Kunz and
Jane R. Allison and
Daan P. Geerke and
Bruno A. C. Horta and
Philippe H. Hünenberger and
Sereina Riniker and
Nathan Schmid and
Wilfred F. van Gunsteren Software News and Updates: New
functionalities in the GROMOS
biomolecular simulation software . . . . 340--353
Laban Bondesson and
Elias Rudberg and
Yi Luo and
Pawe\l Sa\lek Erratum: ``Basis set dependence of
solute--solvent interaction energy of
benzene in water: a HF/DFT study'' . . . 354--354
Michael Honigmann and
Robert J. Buenker and
Heinz-Peter Liebermann Complex configuration interaction
calculations of the cross section for
the dissociative electron attachment
process $ e^- $ + F$_2$ $ \rightarrow $
F $ \rightarrow $ F + F$^-$ using the
complex basis function method . . . . . 355--362
Katharina Meier and
Walter Thiel and
Wilfred F. van Gunsteren On the effect of a variation of the
force field, spatial boundary condition
and size of the QM region in QM/MM MD
simulations . . . . . . . . . . . . . . 363--378
Cui Liu and
Dong-Xia Zhao and
Zhong-Zhi Yang Direct evaluation of individual hydrogen
bond energy in situ in intra- and
intermolecular multiple hydrogen bonds
system . . . . . . . . . . . . . . . . . 379--390
Andrew J. Logsdail and
Z. Y. Li and
Roy L. Johnston Development and optimization of a novel
genetic algorithm for identifying
nanoclusters from scanning transmission
electron microscopy images . . . . . . . 391--400
Feng Yu Ab initio direct classical trajectory
investigation on the S$_N$2 reaction of
F$^-$ with NH$_2$F: Nonstatistical
central barrier recrossing dynamics . . 401--405
Marcus Lundberg Understanding cross-boundary events in
ONIOM QM:QM' calculations . . . . . . . 406--415
Gennady L. Gutsev and
Charles A. Weatherford and
Lewis E. Johnson and
Purusottam Jena Structure and properties of the aluminum
borates Al(BO$_2$ )$_n$ and Al(BO$_2$
)$_n^-$, ($ n = 1 $--$4$ ) . . . . . . . 416--424
Sudip Pan and
Santanab Giri and
Pratim K. Chattaraj A computational study on the hydrogen
adsorption capacity of various
lithium-doped boron hydrides . . . . . . 425--434
Alexandra Vardi-Kilshtain and
Asaf Azuri and
Dan Thomas Major Path-integral calculations of heavy atom
kinetic isotope effects in condensed
phase reactions using higher-order
Trotter factorizations . . . . . . . . . 435--441
J. M. C. Marques and
A. A. C. C. Pais and
P. E. Abreu On the use of big-bang method to
generate low-energy structures of atomic
clusters modeled with pair potentials of
different ranges . . . . . . . . . . . . 442--452
Fangqiang Zhu and
Gerhard Hummer Convergence and error estimation in free
energy calculations using the weighted
histogram analysis method . . . . . . . 453--465
Wei Quan Tian Modeling nonlinear optics of nanosystems
with sum-over-states model . . . . . . . 466--470
Francois Berenger and
Rojan Shrestha and
Yong Zhou and
David Simoncini and
Kam Y. J. Zhang Software News and Updates: Durandal:
Fast exact clustering of protein decoys 471--474
Francesco Rao and
Martin Spichty Thermodynamics and kinetics of
large-time-step molecular dynamics . . . 475--483
Bu-Tong Li and
Lu-Lin Li and
Hai-Shun Wu Theoretical calculation about the
valence and Rydberg excited states of
hydrogen cyanide . . . . . . . . . . . . 484--489
Wenming Sun and
Yuxiang Bu and
Yixuan Wang Interaction and protection mechanism
between li@C$_{60}$ and nucleic acid
bases (NABs): Performance of PM6-DH2 on
noncovalent interaction of NABs-Li@C60 490--501
Fabrice Avaltroni and
Clemence Corminboeuf Identifying clusters as low-lying minima
--- efficiency of stochastic and genetic
algorithms using inexpensive electronic
structure levels . . . . . . . . . . . . 502--508
Israel Fernández and
F. Matthias Bickelhaupt Alder-ene reaction: Aromaticity and
activation-strain analysis . . . . . . . 509--516
Shuming Zhang A reliable and efficient first
principles-based method for predicting
pK$_a$ values. III. Adding explicit
water molecules: Can the theoretical
slope be reproduced and pK$_a$ values
predicted more accurately? . . . . . . . 517--526
Weiwei Xue and
Huanxiang Liu and
Xiaojun Yao Molecular mechanism of HIV-1
integrase--vDNA interactions and strand
transfer inhibitor action: a molecular
modeling perspective . . . . . . . . . . 527--536
Hua Dong and
Bo-Zhen Chen and
Ming-Bao Huang and
Roland Lindh The Bergman cyclizations of the enediyne
and its N-substituted analogs using
multiconfigurational second-order
perturbation theory . . . . . . . . . . 537--549
Shuntaro Chiba and
Yuich Harano and
Roland Roth and
Masahiro Kinoshita and
Minoru Sakurai Evaluation of protein-ligand binding
free energy focused on its entropic
components . . . . . . . . . . . . . . . 550--560
Stefano Costanzi and
Santiago Vilar In Silico screening for agonists and
blockers of the $ \beta_2 $ adrenergic
receptor: Implications of inactive and
activated state structures . . . . . . . 561--572
Tim Geppert and
Felix Reisen and
Max Pillong and
Volker Hähnke and
Yusuf Tanrikulu and
Christian P. Koch and
Anna Maria Perna and
Tatiana Batista Perez and
Petra Schneider and
Gisbert Schneider Virtual screening for compounds that
mimic protein--protein interface
epitopes . . . . . . . . . . . . . . . . 573--579
Tian Lu and
Feiwu Chen Software News and Updates: Multiwfn: a
multifunctional wavefunction analyzer 580--592
D. Heringer and
T. A. Niehaus and
M. Wanko and
Th. Frauenheim Erratum: ``Analytical excited state
forces for the time-dependent
density-functional tight-binding
method'' [J. Comp. Chem. \bf 28, 2589] 593--593
Jun-Xi Liang and
Zhi-Yuan Geng and
Yong-Cheng Wang Density functional study of S$_N$2
substitution reactions for CH$_3$Cl +
CX$^1$X$^{2 \bullet -}$ (X$^1$ X$^2$ =
HH, HF, HCl, HBr, HI, FF, ClCl, BrBr,
and II) . . . . . . . . . . . . . . . . 595--606
Florent Barbault and
François Maurel Is inhibition process better described
with MD(QM/MM) simulations? The case of
urokinase type plasminogen activator
inhibitors . . . . . . . . . . . . . . . 607--616
Milind M. Deshmukh and
Shigeyoshi Sakaki Two-step evaluation of binding energy
and potential energy surface of van der
Waals complexes . . . . . . . . . . . . 617--628
Soumya Ganguly Neogi and
Pinaki Chaudhury Structure and spectroscopy of
water-fluoride microclusters: a combined
genetic algorithm and DFT-based study 629--639
Niels Hansen and
Jo\vzica Dolenc and
Matthias Knecht and
Sereina Riniker and
Wilfred F. van Gunsteren Assessment of enveloping distribution
sampling to calculate relative free
enthalpies of binding for eight
netropsin--DNA duplex complexes in
aqueous solution . . . . . . . . . . . . 640--651
M. Kaukonen and
A. Gulans and
P. Havu and
E. Kauppinen Lennard-Jones parameters for small
diameter carbon nanotubes and water for
molecular mechanics simulations from van
der Waals density functional
calculations . . . . . . . . . . . . . . 652--658
Cen Gao and
J. Martin Herold and
Dmitri Kireev Assessment of free energy predictors for
ligand binding to a methyllysine histone
code reader . . . . . . . . . . . . . . 659--665
Jinliang Li and
Zhenzhen Zhao and
Cui Yu and
Hongbo Wang and
Jianwei Zhao Theoretical investigation on the
transportation behavior of molecular
wires with redox reaction . . . . . . . 666--672
A. Laref and
S. Laref and
S. Bin-Omran Electronic structure, X-ray absorption,
and optical spectroscopy of LaCoO$_3$ in
the ground-state and excited-states . . 673--684
Hui Zhang and
Yang Liu and
Jing-Yao Liu and
Ze-Sheng Li Theoretical study and rate constants
calculation for the reactions X +
CF$_3$CH$_2$OCF$_3$ (X = F, Cl, Br) . . 685--690
Jan \vRezá\vc and
Kevin E. Riley and
Pavel Hobza Evaluation of the performance of
post-Hartree--Fock methods in terms of
intermolecular distance in noncovalent
complexes . . . . . . . . . . . . . . . 691--694
Katrin Tonigold and
Axel Groß Dispersive interactions in water
bilayers at metallic surfaces: a
comparison of the PBE and RPBE
functional including semiempirical
dispersion corrections . . . . . . . . . 695--701
M. Randi\'c Very Efficient Search for Protein
Alignment --- VESPA . . . . . . . . . . 702--707
Sergio Rampino and
Noelia Faginas Lago and
Antonio Lagan\`a and
Fermin Huarte-Larrañaga Software News and Updates: An extension
of the grid empowered molecular
simulator to quantum reactive scattering 708--714
Wenjing Zhang and
Yanyan Zhu and
Donghui Wei and
Mingsheng Tang Reviews: Mechanisms of the cascade
synthesis of substituted
4-amino-1,2,4-triazol-3-one from huisgen
zwitterion and aldehyde hydrazone: a DFT
study . . . . . . . . . . . . . . . . . 715--722
Michael E. Lasinski and
Nichols A. Romero and
Shawn T. Brown and
Jean-Philippe Blaudeau Recent performance improvements to the
DFT and TDDFT in GAMESS . . . . . . . . 723--731
Abolghasem Beheshti and
Siavash Riahi and
Mohammad Reza Ganjali and
Parviz Norouzi Highlighting and trying to overcome a
serious drawback with QSPR studies; data
collection in different experimental
conditions (mixed-QSPR) . . . . . . . . 732--747
J. Andrés and
S. Berski and
L. R. Domingo and
P. González-Navarrete Nature of the ring-closure process along
the rearrangement of
octa-1,3,5,7-tetraene to
cycloocta-1,3,5-triene from the
perspective of the electron localization
function and catastrophe theory . . . . 748--756
Franziska Hess and
Attila Farkas and
Ari P. Seitsonen and
Herbert Over ``First-Principles'' kinetic Monte Carlo
simulations revisited: CO oxidation over
RuO$_2$(110) . . . . . . . . . . . . . . 757--766
Vladimír Sládek and
Vladimír Luke\vs and
Michal Il\vcin and
Stanislav Biskupi\vc Ab initio calculation of structure and
transport properties of He\ldotsX (X =
Zn, Cd, Hg) van der Waals complexes . . 767--778
Mäel Bosson and
Caroline Richard and
Antoine Plet and
Sergei Grudinin and
Stephane Redon Interactive quantum chemistry: a
divide-and-conquer ASED-MO method . . . 779--790
Sampath Koppole and
Michael Schaefer A discriminative Ramachandran potential
of mean force aimed at minimizing
secondary structure bias . . . . . . . . 791--799
Truong Ba Tai and
Minh Tho Nguyen Electronic structure and thermochemical
properties of silicon-doped lithium
clusters Li$_n$Si$^{0 \slash +}$, $ n =
1 $--$8$: New insights on their
stability . . . . . . . . . . . . . . . 800--809
Philipp Plessow and
Florian Weigend Software News and Updates: Seminumerical
calculation of the Hartree--Fock
exchange matrix: Application to
two-component procedures and efficient
evaluation of local hybrid density
functionals . . . . . . . . . . . . . . 810--816
Jiande Gu and
Jing Wang and
Yaoming Xie and
Jerzy Leszczynski and
Henry F. Schaefer III Structural and electronic property
responses to the arsenic/phosphorus
exchange in GC-related DNA of the
$B$-form . . . . . . . . . . . . . . . . 817--821
Alessandro Erba and
Cesare Pisani Evaluation of the electron momentum
density of crystalline systems from ab
initio linear combination of atomic
orbitals calculations . . . . . . . . . 822--831
Yury N. Vorobjev Potential of mean force of water--proton
bath and molecular dynamic simulation of
proteins at constant pH . . . . . . . . 832--842
Debashree Chakraborty and
Amalendu Chandra Voids and necks in liquid ammonia and
their roles in diffusion of ions of
varying size . . . . . . . . . . . . . . 843--852
Barbara Logan Mooney and
L. René Corrales and
Aurora E. Clark MoleculaRnetworks: an integrated graph
theoretic and data mining tool to
explore solvent organization in
molecular simulation . . . . . . . . . . 853--860
Cai-Hua Zhou and
Xiang Zhao Chemically modified fullerene
derivatives as photosensitizers in
photodynamic therapy: a first-principles
study . . . . . . . . . . . . . . . . . 861--867
Ying Zhao and
Antonio De Nicola and
Toshihiro Kawakatsu and
Giuseppe Milano Software News and Updates: Hybrid
particle-field molecular dynamics
simulations: Parallelization and
benchmarks . . . . . . . . . . . . . . . 868--880
Arnim Hellweg and
Michael Diedenhofen and
Uwe Huniar Software News and Updates: \tt
thermocalc --- a poor man's approach to
computational thermochemistry . . . . . 881--886
R. Thomas Ullmann and
G. Matthias Ullmann Software News and Updates: GMCT: a Monte
Carlo simulation package for
macromolecular receptors . . . . . . . . 887--900
André A. S. T. Ribeiro and
Ricardo B. de Alencastro Software News and Updates: Mixed Monte
Carlo/molecular dynamics simulations in
explicit solvent . . . . . . . . . . . . 901--905
Ilya A. Balabin and
Xiangqian Hu and
David N. Beratan Software News and Updates: Exploring
biological electron transfer pathway
dynamics with the Pathways Plugin for
VMD . . . . . . . . . . . . . . . . . . 906--910
J. H. van Lenthe and
H. B. Broer-Braam and
Z. Rashid Letters to the Editor: On the efficiency
of VBSCF algorithms, a comment on ``An
efficient algorithm for energy gradients
and orbital optimization in valence bond
theory'' . . . . . . . . . . . . . . . . 911--913
Wei Wu and
Yirong Mo Letters to the Editor: Reply to comment
on the paper ``An Efficient Algorithm
for Energy Gradients and Orbital
Optimization in Valence Bond Theory'' 914--915
Gleb Y. Solomentsev and
Niall J. English and
Damian A. Mooney Effects of external electromagnetic
fields on the conformational sampling of
a short alanine peptide . . . . . . . . 917--923
Kazuhiro Ishida Fourier transform general formula for
systematic potentials . . . . . . . . . 924--936
Olga Bezkorovaynaya and
Alexander Lukyanov and
Kurt Kremer and
Christine Peter Multiscale simulation of small peptides:
Consistent conformational sampling in
atomistic and coarse-grained models . . 937--949
Jeffrey S. Tan and
Stephan X. M. Boerrigter and
Raymond P. Scaringe and
Kenneth R. Morris Core-shell potential-derived point
charges . . . . . . . . . . . . . . . . 950--957
Gustavo L. C. Moura and
Alfredo M. Simas Quantum molecular mechanics --- a
noniterative procedure for the fast ab
initio calculation of closed shell
systems . . . . . . . . . . . . . . . . 958--969
P. Nuno Palma and
Maria João Bonifácio and
Ana Isabel Loureiro and
Patrício Soares-da-Silva Computation of the binding affinities of
catechol-O-methyltransferase inhibitors:
Multisubstate relative free energy
calculations . . . . . . . . . . . . . . 970--986
Ch. Bheema Lingam and
K. Ramesh Babu and
Surya P. Tewari and
G. Vaitheeswaran Density functional study of
electronic,bonding, and vibrational
properties of Ca(NH$_2$BH$_3$ )$_2$ . . 987--997
Shi-Bao Wang and
Arvin Huang-Te Li and
Sheng D. Chao Liquid properties of dimethyl ether from
molecular dynamics simulations using ab
initio force fields . . . . . . . . . . 998--1003
Hannes Kopitz and
Daniel A. Cashman and
Stefania Pfeiffer-Marek and
Holger Gohlke Influence of the solvent representation
on vibrational entropy calculations:
Generalized Born versus
distance-dependent dielectric model . . 1004--1013
Valentina Cantatore and
Giovanni Granucci and
Maurizio Persico Stochastic model for photoinduced
anisotropy . . . . . . . . . . . . . . . 1015--1022
K. V. Turcheniuk and
A. B. Rozhenko $ (\sigma^3, \lambda^5) $-phosphoranes
versus $ (\sigma^3, \lambda^3)
$-thiaphosphiranes: Quantum chemical
investigation of products of
phosphaalkene sulfurization . . . . . . 1023--1028
Antonio Ricci and
Andrea Brancale Density functional theory calculation of
cyclic carboxylic phosphorus mixed
anhydrides as possible intermediates in
biochemical reactions: Implications for
the Pro-Tide approach . . . . . . . . . 1029--1037
Qi Cao and
Jing Wang and
Zhao-Shuo Tian and
Zai-Feng Xie and
Fu-Quan Bai Theoretical investigation on the
photophysical properties of
N-heterocyclic carbene iridium (III)
complexes (fpmb)$_x$ Ir(bptz)$_{3 - x}$
($ x = 1 $--$2$ ) . . . . . . . . . . . 1038--1046
Sambath Baskaran and
Masilamani Tamizmani and
Thanigachalam Mahalakshmi and
Chinnappan Sivasankar A [Fe(CB$_6$ )] platform for binding of
small molecules: Insights from DFT
calculations . . . . . . . . . . . . . . 1047--1054
Ivo Cacelli and
Antonella Cimoli and
Paolo Roberto Livotto and
Giacomo Prampolini An automated approach for the
parameterization of accurate
intermolecular force-fields: Pyridine as
a case study . . . . . . . . . . . . . . 1055--1067
Emmanuel N. Koukaras and
Aristides D. Zdetsis and
Panaghiotis Karamanis and
Claude Pouchan and
Aggelos Avramopoulos and
Manthos G. Papadopoulos Structural and static electric response
properties of highly symmetric lithiated
silicon cages: Theoretical predictions 1068--1079
Martin Dra\vcínský and
Petr Bou\vr Vibrational averaging of the chemical
shift in crystalline $ \alpha $-glycine 1080--1089
Angelo Domenico Quartarolo and
Sandro Giuseppe Chiodo and
Nino Russo A TDDFT investigation of bay substituted
perylenediimides: Absorption and
intersystem crossing . . . . . . . . . . 1091--1100
Riguang Zhang and
Luzhi Song and
Baojun Wang and
Zhong Li A density functional theory
investigation on the mechanism and
kinetics of dimethyl carbonate formation
on Cu$_2$O catalyst . . . . . . . . . . 1101--1110
Milan Randi\'c and
Damir Vuki\vcevi\'c and
Alexandru T. Balaban and
Marjan Vra\vcko and
Dejan Plav\vsi\'c Conjugated circuits currents in
hexabenzocoronene and its derivatives
formed by joining proximal carbons . . . 1111--1122
Robert A. Evarestov and
Andrei V. Bandura First-principles calculations on the
four phases of BaTiO$_3$ . . . . . . . . 1123--1130
Asit K. Chandra and
Thér\`ese Zeegers-Huyskens A theoretical investigation of the
interaction between substituted carbonyl
derivatives and water: Open or cyclic
complexes? . . . . . . . . . . . . . . . 1131--1141
Timothy H. Click and
Sergei Y. Ponomarev and
George A. Kaminski Importance of electrostatic
polarizability in calculating cysteine
acidity constants and copper(I) binding
energy of \em Bacillus subtilis CopZ . . 1142--1151
Alexander H. Boschitsch and
Pavel V. Danilov Formulation of a new and simple
nonuniform size-modified
Poisson--Boltzmann description . . . . . 1152--1164
Supriya Saha and
Sougata Pal and
Pranab Sarkar and
A. L. Rosa and
Th. Frauenheim A complete set of self-consistent charge
density-functional tight-binding
parametrization of zinc chalcogenides
(ZnX; X = O, S, Se, and Te) . . . . . . 1165--1178
Paulius Mikulskis and
Samuel Genheden and
Karin Wichmann and
Ulf Ryde A semiempirical approach to
ligand-binding affinities: Dependence on
the Hamiltonian and corrections . . . . 1179--1189
Patrick Laflamme and
Alexandre Beaudoin and
Thomas Chapaton and
Claude Spino and
Armand Soldera Simulated infrared spectra of triflic
acid during proton dissociation . . . . 1190--1196
Tibor András Rokob and
Lubomír Rulí\vsek Curvature correction for microiterative
optimizations with QM/MM electronic
embedding . . . . . . . . . . . . . . . 1197--1206
René Pool and
Jaap Heringa and
Martin Hoefling and
Roland Schulz and
Jeremy C. Smith and
K. Anton Feenstra Software News and Updates: Enabling
grand-canonical Monte Carlo: Extending
the flexibility of GROMACS through the
GromPy Python interface module . . . . . 1207--1214
Markus Wagener and
Jacob de Vlieg and
Sander B. Nabuurs Software News and Updates: Flexible
protein-ligand docking using the Fleksy
protocol . . . . . . . . . . . . . . . . 1215--1217
A. P. Toropova and
A. A. Toropov and
A. Lombardo and
A. Roncaglioni and
E. Benfenati and
G. Gini Software News and Updates: Coral: QSAR
models for acute toxicity in fathead
minnow (\em Pimephales promelas) . . . . 1218--1223
You Lu and
Zhenggang Lan and
Walter Thiel Monomeric adenine decay dynamics
influenced by the DNA environment . . . 1225--1235
Marta González and
Roi Álvarez Rodríguez and
Maria Magdalena Cid and
Carlos Silva López A stepwise retro-imino-ene as a key step
in the mechanism of allene formation via
the Crabbé acetylene homologation . . . . 1236--1239
Nicolás Otero and
Marcos Mandado Chemical reactivity in the framework of
pair density functional theories . . . . 1240--1251
Deok-Soo Kim and
Joonghyun Ryu and
Hayong Shin and
Youngsong Cho Beta-decomposition for the volume and
area of the union of three-dimensional
balls and their offsets . . . . . . . . 1252--1273
Jyh Shing Lin and
Shao-Yu Lu and
Po-Jung Tseng and
Wen-Chi Chou Temperature dependence of vibrational
modes of CH$_3$CC$_{(ads)}$ and
I$_{(ads)}$ coadsorbed on Ag(111): ab
initio molecular dynamics approach . . . 1274--1283
Uttam Sinha Mahapatra and
Sudip Chattopadhyay Diagnosis of the performance of the
state-specific multireference
coupled-cluster method with different
truncation schemes . . . . . . . . . . . 1285--1303
Peter Deglmann and
Stephan Schenk Thermodynamics of chemical reactions
with COSMO-RS: the extreme case of
charge separation or recombination . . . 1304--1320
Yanli Zeng and
Min Zhu and
Xiaoyan Li and
Shijun Zheng and
Lingpeng Meng Assessment of intermolecular
interactions at three sites of the
arylalkyne in phenylacetylene-containing
lithium-bonded complexes: ab initio and
QTAIM studies . . . . . . . . . . . . . 1321--1327
Guosheng Shi and
Yihong Ding and
Haiping Fang Unexpectedly strong anion--$ \pi $
interactions on the graphene flakes . . 1328--1337
Thiago C. F. Gomes and
Munir S. Skaf Software News and Updates:
Cellulose-Builder: a toolkit for
building crystalline structures of
cellulose . . . . . . . . . . . . . . . 1338--1346
Feng Yu Assessment of ab initio MP2 and density
functionals for characterizing the
potential energy profiles of the S$_N$2
reactions at N center . . . . . . . . . 1347--1352
Shanshan Tang and
Jingping Zhang Design of donors with broad absorption
regions and suitable frontier molecular
orbitals to match typical acceptors via
substitution on
oligo(thienylenevinylene) toward solar
cells . . . . . . . . . . . . . . . . . 1353--1363
Jennifer M. Kashmirian and
Alfred Uhlherr and
Alan Dorin and
David G. Green Molecular dynamics extended for
fluctuating networks: Application to
water . . . . . . . . . . . . . . . . . 1364--1373
Ye Mei and
Yong L. Li and
Juan Zeng and
John Z. H. Zhang Electrostatic polarization is critical
for the strong binding in
streptavidin-biotin system . . . . . . . 1374--1382
David J. Huggins Benchmarking the thermodynamic analysis
of water molecules around a model beta
sheet . . . . . . . . . . . . . . . . . 1383--1392
William B. Sherman Software News and Updates: HolT Hunter:
Software for identifying and
characterizing low-strain DNA Holliday
triangles . . . . . . . . . . . . . . . 1393--1405
Jhon Zapata-Rivera and
Rosa Caballol and
Carmen J. Calzado The role of macrocyclic ligands in the
peroxo/superoxo nature of Ni--O$_2$
biomimetic complexes . . . . . . . . . . 1407--1415
Chang G. Ji and
John Z. H. Zhang Effect of interprotein polarization on
protein--protein binding energy . . . . 1416--1420
Anan Wu and
Xin Xu DCMB that combines divide-and-conquer
and mixed-basis set methods for accurate
geometry optimizations, total energies,
and vibrational frequencies of large
molecules . . . . . . . . . . . . . . . 1421--1432
Shuhui Lv and
Xiaojuan Liu and
Hongping Li and
Lin Han and
Zhongchang Wang and
Jian Meng Insulator--metal transition driven by
pressure and B-site disorder in double
perovskite La$_2$CoMnO$_6$ . . . . . . . 1433--1439
Christopher J. R. Illingworth and
Sree V. Chintipalli and
Stefano A. Serapian and
Andrew D. Miller and
Vaclav Veverka and
Mark D. Carr and
Christopher A. Reynolds The statistical significance of selected
sense--antisense peptide interactions 1440--1447
Hao Tang and
Zhuo Li and
Yu-Hong Yang and
Ying Zhao and
Su-Qin Wan and
Hui-Ling Liu and
Xu-Ri Huang Comparison of the FeO$^{2+}$ and
FeS$^{2+}$ complexes in the cyanide and
isocyanide ligand environment for
methane hydroxylation . . . . . . . . . 1448--1457
Pradip K. Biswas and
Nadeem A. Vellore and
Jeremy A. Yancey and
Tugba G. Kucukkal and
Galen Collier and
Bernard R. Brooks and
Steven J. Stuart and
Robert A. Latour Simulation of multiphase systems
utilizing independent force fields to
control intraphase and interphase
behavior . . . . . . . . . . . . . . . . 1458--1466
Denise Steiner and
Chris Oostenbrink and
Wilfred F. van Gunsteren Calculation of the relative free energy
of oxidation of azurin at pH 5 and pH 9 1467--1477
Sergey Gusarov and
Bhalchandra S. Pujari and
Andriy Kovalenko Efficient treatment of solvation shells
in $3$D molecular theory of solvation 1478--1494
Alexander F. Sax Localization of molecular orbitals on
fragments . . . . . . . . . . . . . . . 1495--1510
Pablo A. Denis Interaction between alkyl radicals and
single wall carbon nanotubes . . . . . . 1511--1516
Siriporn Jungsuttiwong and
Thanisorn Yakhanthip and
Yaowarat Surakhot and
Janeeya Khunchalee and
Taweesak Sudyoadsuk and
Vinich Promarak and
Nawee Kungwan and
Supawadee Namuangruk The effect of conjugated spacer on novel
carbazole derivatives for dye-sensitized
solar cells: Density functional
theory/time-dependent density functional
theory study . . . . . . . . . . . . . . 1517--1523
Anonymous Retracted: ``Prediction of
posttranslational modification sites
from sequences with kernel methods'' by
Xiaobo Wang, Yongcui Wang, Yingjie Tian,
Xiaojian Shao, Ling-Yun Wu, and Naiyang
Deng, published online on 21 April 2010 1524--1524
David Gfeller and
Olivier Michielin and
Vincent Zoete Expanding molecular modeling and design
tools to non-natural sidechains . . . . 1525--1535
Daniel J. Sindhikara and
Norio Yoshida and
Fumio Hirata Placevent: an algorithm for prediction
of explicit solvent atom distribution
--- application to HIV-1 protease and
F-ATP synthase . . . . . . . . . . . . . 1536--1543
Volker Settels and
Wenlan Liu and
Jens Pflaum and
Reinhold F. Fink and
Bernd Engels Comparison of the electronic structure
of different perylene-based
dye-aggregates . . . . . . . . . . . . . 1544--1553
Andrei V. Bandura and
Robert A. Evarestov First-principles calculations on
thermodynamic properties of BaTiO$_3$
rhombohedral phase . . . . . . . . . . . 1554--1563
Keda Yang and
Jiaye Su and
Hongxia Guo GPU accelerated numerical simulations of
viscoelastic phase separation model . . 1564--1571
Jussi Lehtola and
Mikko Hakala and
Arto Sakko and
Keijo Hämäläinen Software News and Updates: ERKALE --- a
flexible program package for X-ray
properties of atoms and molecules . . . 1572--1585
Jing Wang and
Jiande Gu and
Jerzy Leszczynski The electronic spectra and the H-bonding
pattern of the sulfur and selenium
substituted guanines . . . . . . . . . . 1587--1593
Robert J. Buenker and
Heinz-Peter Liebermann Ab initio study of the positronation of
the CaO and SrO molecules including
calculation of annihilation rates . . . 1594--1602
Tomasz Bere\'zniak and
Andres Jäschke and
Jeremy C. Smith and
Petra Imhof Stereoselection in the Diels--Alderase
ribozyme: a molecular dynamics study . . 1603--1614
John Kendrick and
Frank J. J. Leusen and
Marcus A. Neumann Empirical van der Waals corrections to
solid-state density functional theory:
Iodine and phosphorous containing
molecular crystals . . . . . . . . . . . 1615--1622
Chiara Panosetti and
Werner A. Hofer Adsorption of metadiiodobenzene on
Cu(110): a theoretical study . . . . . . 1623--1631
Semen O. Yesylevskyy Software News and Updates: Pteros: Fast
and easy to use open-source C++ library
for molecular analysis . . . . . . . . . 1632--1636
R. Jeffrey Largent and
William F. Polik and
J. R. Schmidt Software News and Updates: Symmetrizer:
Algorithmic determination of point
groups in nearly symmetric molecules . . 1637--1642
Benjamin P. Roberts and
Gustavo M. Seabra and
Adrian E. Roitberg and
Kenneth M. Merz and
Erik Deumens and
Juan Torras and
Samuel B. Trickey Software News and Updates: Commentary:
Comment on ``A minimal implementation of
the AMBER--GAUSSIAN interface for Ab
Initio QM/MM-MD simulation'' . . . . . . 1643--1644
Daniel W. Kulp and
Sabareesh Subramaniam and
Jason E. Donald and
Brett T. Hannigan and
Benjamin K. Mueller and
Gevorg Grigoryan and
Alessandro Senes Structural informatics, modeling, and
design with an open-source Molecular
Software Library (MSL) . . . . . . . . . 1645--1661
Hyun Woo Kim and
Young Min Rhee Molecule-specific determination of
atomic polarizabilities with the
polarizable atomic multipole model . . . 1662--1672
Christian Kramer and
Peter Gedeck and
Markus Meuwly Atomic multipoles: Electrostatic
potential fit, local reference axis
systems, and conformational dependence 1673--1688
Christos E. Kefalidis and
Constantinos A. Tsipis DFT study of the mechanism of
hydroamination of ethylene with ammonia
catalyzed by diplatinum(II) complexes:
Inner- or outer-sphere? . . . . . . . . 1689--1700
Xue-Fang Yu and
Shohei Yamazaki and
Tetsuya Taketsugu Theoretical study of the excited-state
double proton transfer in the
(3-methyl-7-azaindole)-(7-azaindole)
heterodimer . . . . . . . . . . . . . . 1701--1708
Wojciech Plazinski and
Mateusz Drach The dynamics of the calcium-induced
chain--chain association in the
polyuronate systems . . . . . . . . . . 1709--1715
Pieter Chys and
Pablo Chacón Spinor product computations for protein
conformations . . . . . . . . . . . . . 1717--1729
Jens Antony and
Stefan Grimme Fully ab initio protein-ligand
interaction energies with dispersion
corrected density functional theory . . 1730--1739
Nikhil Taxak and
Prashant V. Desai and
Bhargav Patel and
Michael Mohutsky and
Valentine J. Klimkowski and
Vijay Gombar and
Prasad V. Bharatam Metabolic-intermediate complex formation
with cytochrome P450: Theoretical
studies in elucidating the reaction
pathway for the generation of reactive
nitroso intermediate . . . . . . . . . . 1740--1747
Zahra Tabookht and
Xavier López and
Coen de Graaf and
Nathalie Guihéry and
Nicolas Suaud and
Nadia Benamor Rationalization of the behavior of M$_2$
(CH$_3$CS$_2$ )$_4$I (M = Ni, Pt) chains
at room temperature from periodic
density functional theory and ab initio
cluster calculations . . . . . . . . . . 1748--1761
D. Koley and
E. Arunan and
S. Ramakrishnan Computational investigations on covalent
dimerization/oligomerization of
polyacenes: Is it relevant to soot
formation? . . . . . . . . . . . . . . . 1762--1772
Hongfang Yang and
Qisheng Song and
Xinyu Song and
Yuxiang Bu Multi-zinc-expanded graphene patches:
Tetraradical versus diradical character 1773--1780
Weihua Zhu and
Qingli Yan and
Jinshan Li and
Bibo Cheng and
Yuling Shao and
Xuelan Xia and
Heming Xiao Prediction of the properties and
thermodynamics of formation for
energetic nitrogen-rich salts composed
of triaminoguanidinium cation and
5-nitroiminotetrazolate-based anions . . 1781--1789
Hui Liu and
Fang Wang and
Gui-Xiang Wang and
Xue-Dong Gong Theoretical investigations on structure,
density, detonation properties, and
sensitivity of the derivatives of PYX 1790--1796
Andreas Dreuw and
Matthias A. Polkehn and
Robert Binder and
Alexander Heckel and
Stefan Knippenberg Computational design of improved
two-photon active caging compounds based
on nitrodibenzofuran . . . . . . . . . . 1797--1805
Massimiliano Bartolomei and
Fernando Pirani and
Antonio Lagan\`a and
Andrea Lombardi A full dimensional grid empowered
simulation of the CO$_2$ + CO$_2$
processes . . . . . . . . . . . . . . . 1806--1819
Fang Wang and
Hong-Chen Du and
Hui Liu and
Xue-Dong Gong Density functional theory study of
high-pressure effect on crystalline
4,4',6,6'-tetra(azido)hydrazo-1,3,5-triazine 1820--1830
Luis F. Pacios and
Cristina Gómez-Casado and
Leticia Tordesillas and
Arantxa Palacín and
Rosa Sánchez-Monge and
Araceli Díaz-Perales Computational study of ligand binding in
lipid transfer proteins: Structures,
interfaces, and free energies of
protein-lipid complexes . . . . . . . . 1831--1844
Hanna Kjær and
Monia R. Nielsen and
Gabriel I. Pagola and
Marta B. Ferraro and
Paolo Lazzeretti and
Stephan P. A. Sauer Nuclear magnetic resonance $J$ coupling
constant polarizabilities of hydrogen
peroxide: a basis set and correlation
study . . . . . . . . . . . . . . . . . 1845--1853
Guangfen Wu and
Mingli Yang and
Xingyu Guo and
Jinlan Wang Comparative DFT study of N$_2$ and no
adsorption on vanadium clusters V$_n$ ($
n = 2 $--$ 13 $ ) . . . . . . . . . . . 1854--1861
Qunyan Wu and
Chunmei Deng and
Qian Peng and
Yingli Niu and
Zhigang Shuai Quantum chemical insights into the
aggregation induced emission phenomena:
a QM/MM study for pyrazine derivatives 1862--1869
Yulei Guan and
Bolun Yang Kinetics for the hydrogen-abstraction of
CH$_4$ with NO$_2$ . . . . . . . . . . . 1870--1879
Theresa J. Foster and
Alexander D. MacKerell Jr. and
Olgun Guvench Balancing target flexibility and target
denaturation in computational
fragment-based inhibitor discovery . . . 1880--1891
Malin Uppsten and
Bo Durbeej Quantum chemical comparison of vertical,
adiabatic, and $0$--$0$ excitation
energies: The PYP and GFP chromophores 1892--1901
A. A. Toropov and
A. P. Toropova and
B. F. Rasulev and
E. Benfenati and
G. Gini and
D. Leszczynska and
J. Leszczynski Software News and Updates: Coral: QSPR
modeling of rate constants of reactions
between organic aromatic pollutants and
hydroxyl radical . . . . . . . . . . . . 1902--1906
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 23 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 23 . . . . i--ii
Bruno A. C. Horta and
Zhixiong Lin and
Wei Huang and
Sereina Riniker and
Wilfred F. van Gunsteren and
Philippe H. Hünenberger Reoptimized interaction parameters for
the peptide-backbone model compound
N-methylacetamide in the GROMOS force
field: Influence on the folding
properties of two beta-peptides in
methanol . . . . . . . . . . . . . . . . 1907--1917
Paola Antoniotti and
Elena Bottizzo and
Stefano Borocci and
Maria Giordani and
Felice Grandinetti Gas-phase reactions of SiH$_n^+$ ($ n =
1, 2 $ ) with NF$_3$: a computational
investigation on the detailed
mechanistic aspects . . . . . . . . . . 1918--1926
Tae-Rae Kim and
Sangho Oh and
Joshua SungWoo Yang and
Sanghyuk Lee and
Seokmin Shin and
Jinhyuk Lee A simplified homology-model builder
toward highly protein-like structures:
an inspection of restraining potentials 1927--1935
Vinzenz Bachler A quantum chemical calculation on
Fe(CO)$_5$ revealing the operation of
the Dewar--Chatt--Duncanson model . . . 1936--1947
Conchín Meliá and
Silvia Ferrer and
Vicent Moliner and
Iñaki Tuñón and
Juan Bertrán Computational study on hydrolysis of
cefotaxime in gas phase and in aqueous
solution . . . . . . . . . . . . . . . . 1948--1959
Chuan Li and
Lin Li and
Jie Zhang and
Emil Alexov Software News and Updates: Highly
efficient and exact method for
parallelization of grid-based algorithms
and its implementation in DelPhi . . . . 1960--1966
Kameron R. Jorgensen and
Angela K. Wilson Letters to the Editor: Comment on the
paper ``Extensive Theoretical Studies of
a New Energetic Material:
Tetrazino-Tetrazine-Tetraoxide (TTTO)''
by Xinli Song, Jicun Li, Hua Hou, and
Baoshan Wang . . . . . . . . . . . . . . 1967--1968
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 24 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 24 . . . . i--ii
Lu Zhang and
Daniel-Adriano Silva and
YiJing Yan and
Xuhui Huang Force field development for cofactors in
the photosystem II . . . . . . . . . . . 1969--1980
Nail A. Gumerov and
Konstantin Berlin and
David Fushman and
Ramani Duraiswami A hierarchical algorithm for fast Debye
summation with applications to small
angle scattering . . . . . . . . . . . . 1981--1996
Vishal Maingi and
Vaibhav Jain and
Prasad V. Bharatam and
Prabal K. Maiti Dendrimer building toolkit: Model
building and characterization of various
dendrimer architectures . . . . . . . . 1997--2011
Janus J. Eriksen and
Stephan P. A. Sauer and
Kurt V. Mikkelsen and
Hans J. Aa. Jensen and
Jacob Kongsted On the importance of excited state
dynamic response electron correlation in
polarizable embedding methods . . . . . 2012--2022
Werner Reckien and
Florian Janetzko and
Michael F. Peintinger and
Thomas Bredow Implementation of empirical dispersion
corrections to density functional theory
for periodic systems . . . . . . . . . . 2023--2031
Brent R. Wilson and
Nathan J. DeYonker and
Angela K. Wilson Prediction of hydrocarbon enthalpies of
formation by various thermochemical
schemes . . . . . . . . . . . . . . . . 2032--2042
Konrad Hinsen and
Eric Pellegrini and
S\lawomir Stachura and
Gerald R. Kneller Software News and Updates: n Moldyn 3:
Using task farming for a parallel
spectroscopy-oriented analysis of
molecular dynamics simulations . . . . . 2043--2048
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 25 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 25 . . . . i--ii
Otello M. Roscioni and
Edmond P. F. Lee and
John M. Dyke Development and testing of a compact
basis set for use in effective core
potential calculations on rhodium
complexes . . . . . . . . . . . . . . . 2049--2057
V. N. Glushkov and
X. Assfeld On orthogonality constrained multiple
core-hole states and optimized effective
potential method . . . . . . . . . . . . 2058--2066
Tobias Schwabe Accurate and fast treatment of large
molecular systems: Assessment of CEPA
and pCCSD within the local pair natural
orbital approximation . . . . . . . . . 2067--2072
Pradeep R. Varadwaj and
Arpita Varadwaj and
Gilles H. Peslherbe An electronic structure theory
investigation of the physical chemistry
of the intermolecular complexes of
cyclopropenylidene with hydrogen halides 2073--2082
F. Rabilloud Structure and stability of coinage metal
fluoride and chloride clusters
(M$_n$F$_n$ and M$_n$Cl$_n$, M = Cu, Ag,
or Au; $ n = 1 $--$6$ ) . . . . . . . . 2083--2091
Zden\uek Futera and
James A. Platts and
Jaroslav V. Burda Binding of piano-stool Ru(II) complexes
to DNA; QM/MM study . . . . . . . . . . 2092--2101
C. Wessel and
C. Reimann and
A. Müller and
D. Weber and
M. Lerch and
T. Ressler and
T. Bredow and
R. Dronskowski Electronic structure and thermodynamics
of V$_2$O$_3$ polymorphs . . . . . . . . 2102--2107
Katharina Meier and
Nathan Schmid and
Wilfred F. van Gunsteren Interfacing the GROMOS (bio)molecular
simulation software to quantum-chemical
program packages . . . . . . . . . . . . 2108--2117
Luís Pinto da Silva and
Joaquim C. G. Esteves da Silva Density functional theory study of
1,2-dioxetanone decomposition in
condensed phase . . . . . . . . . . . . 2118--2123
Daniel Roca-Sanjuán and
Marcus Lundberg and
David A. Mazziotti and
Roland Lindh Letters to the Editor: Comment on
``Density functional theory study of
1,2-dioxetanone decomposition in
condensed phase'' . . . . . . . . . . . 2124--2126
Luís Pinto da Silva and
Joaquim C. G. Esteves da Silva Letters to the Editor: Response to
``Comment on density functional theory
study of 1,2-dioxetanone decomposition
in condensed phase'' . . . . . . . . . . 2127--2130
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 26 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 26 . . . . i--ii
Patrick Marais and
Julian Kenwood and
Keegan Carruthers Smith and
Michelle M. Kuttel and
James Gain Efficient compression of molecular
dynamics trajectory files . . . . . . . 2131--2141
Wenping Guo and
Anan Wu and
Igor Ying Zhang and
Xin Xu XO: an extended ONIOM method for
accurate and efficient modeling of large
systems . . . . . . . . . . . . . . . . 2142--2160
Ruairidh S. Hunter and
Tanja van Mourik DNA base stacking: the stacked
uracil/uracil and thymine/thymine minima 2161--2172
Sergey P. Gavrish Approximate expressions and the
relationship between pyramidalization
(out-of-plane deformation)
characteristics of trigonal centers . . 2173--2179
Mario Ulises Delgado-Jaime and
Serena DeBeer Software News and Updates: Expedited
analysis of DFT outputs: Introducing
moanalyzer . . . . . . . . . . . . . . . 2180--2185
Thomas Weymuth and
Moritz P. Haag and
Karin Kiewisch and
Sandra Luber and
Stephan Schenk and
Christoph R. Jacob and
Carmen Herrmann and
Johannes Neugebauer and
Markus Reiher Software News and Updates: \sc MoViPac:
Vibrational spectroscopy with a robust
meta-program for massively parallel
standard and inverse calculations . . . 2186--2198
Janez Konc and
Matja\vz Depolli and
Roman Trobec and
Kati Rozman and
Du\vsanka Jane\vzi\vc Software News and Updates:
Parallel-ProBiS: Fast parallel algorithm
for local structural comparison of
protein structures and binding sites . . 2199--2203
Giovanni Garberoglio Software News and Updates: OBGMX: a
Web-based generator of GROMACS
topologies for molecular and periodic
systems using the universal force field 2204--2208
Edyta Ma\lolepsza and
Birgit Strodel and
Mey Khalili and
Semen Trygubenko and
Szilard Fejer and
Joanne M. Carr and
David J. Wales Erratum: ``Symmetrization of the AMBER
and CHARMM force fields'' [J. Comp.
Chem. \bf 31, 1402] . . . . . . . . . . 2209--2209
Shuntaro Chiba and
Yuichi Harano and
Roland Roth and
Masahiro Kinoshita and
Minoru Sakurai Errata: ``Evaluation of protein-ligand
binding free energy focused on its
entropic components'' [J. Comp. Chem.
\bf 33, 550--560] . . . . . . . . . . . 2210--2210
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 27 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 27 . . . . i--ii
Chanda-Malis Ouk and
Natalia Zvereva-Loëte and
Yohann Scribano and
Béatrice Bussery-Honvault Transition state theory thermal rate
constants and RRKM-based branching
ratios for the N($^2$D) + CH$_4$
reaction based on multi-state and
multi-reference ab initio calculations
of interest for the Titan's chemistry 2211--2224
Maarten G. Wolf and
Gerrit Groenhof Evaluating nonpolarizable nucleic acid
force fields: a systematic comparison of
the nucleobases hydration free energies
and chloroform-to-water partition
coefficients . . . . . . . . . . . . . . 2225--2232
Jan P. Götze and
Claudio Greco and
Roland Mitri\'c and
Vlasta Bona\vci\'c-Koutecký and
Peter Saalfrank BLUF hydrogen network dynamics and
UV/Vis spectra: a combined molecular
dynamics and quantum chemical study . . 2233--2242
Jian Wang and
Yu Wang and
Jesus M. Ugalde Electron-pair density decomposition for
core--valence separable systems . . . . 2243--2249
An Ghysels and
Benjamin T. Miller and
Frank C. Pickard IV and
Bernard R. Brooks Comparing normal modes across different
models and scales: Hessian reduction
versus coarse-graining . . . . . . . . . 2250--2275
Roberto Orlando and
Massimo Delle Piane and
Ian J. Bush and
Piero Ugliengo and
Matteo Ferrabone and
Roberto Dovesi Software News and Updates: a new
massively parallel version of CRYSTAL
for large systems on high performance
computing architectures . . . . . . . . 2276--2284
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 28 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 28 . . . . i--ii
Orsolya Gereben and
László Pusztai RMC\_POT: a computer code for reverse
Monte Carlo modeling the structure of
disordered systems containing molecules
of arbitrary complexity . . . . . . . . 2285--2291
Diego Paschoal and
Bruna L. Marcial and
Juliana Fedoce Lopes and
Wagner B. De Almeida and
Hélio F. Dos Santos The role of the basis set and the level
of quantum mechanical theory in the
prediction of the structure and
reactivity of cisplatin . . . . . . . . 2292--2302
M. V. Vener and
A. N. Egorova and
A. V. Churakov and
V. G. Tsirelson Intermolecular hydrogen bond energies in
crystals evaluated using electron
density properties: DFT computations
with periodic boundary conditions . . . 2303--2309
Ji\vrí Kessler and
Milan Jakubek and
Bohumil Dolenský and
Petr Bou\vr Binding energies of five molecular
pincers calculated by explicit and
implicit solvent models . . . . . . . . 2310--2317
Athanassios C. Tsipis and
Dimitrios N. Gkarmpounis Probing the electronic structure,
chemical bonding, and excitation spectra
of [CuE]$^{+ / 0 / -}$ (E = 14 group
element) diatomics employing DFT and ab
initio methods . . . . . . . . . . . . . 2318--2331
Emanuele Coccia and
Leonardo Guidoni Quantum Monte Carlo study of the retinal
minimal model C$_5$H$_6$NH$_2^+$ . . . . 2332--2339
Sushil Kumar Mishra and
Johan Sund and
Johan Åqvist and
Jaroslav Ko\vca Computational prediction of
monosaccharide binding free energies to
lectins with linear interaction energy
models . . . . . . . . . . . . . . . . . 2340--2350
Siegfried Höfinger and
Angela Acocella and
Sergiu C. Pop and
Tetsu Narumi and
Kenji Yasuoka and
Titus Beu and
Francesco Zerbetto GPU-accelerated computation of electron
transfer . . . . . . . . . . . . . . . . 2351--2356
Damien Farrell and
Jens Erik Nielsen Software News and Updates: DataPipeline:
Automated importing and fitting of large
amounts of biophysical data . . . . . . 2357--2362
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 29 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 29 . . . . i--ii
Frank Weinhold Natural bond orbital analysis: a
critical overview of relationships to
alternative bonding perspectives . . . . 2363--2379
Marie L. Laury and
Matthew J. Carlson and
Angela K. Wilson Vibrational frequency scale factors for
density functional theory and the
polarization consistent basis sets . . . 2380--2387
Ity Sharma and
George A. Kaminski Calculating pK$_a$ values for
substituted phenols and hydration
energies for other compounds with the
first-order fuzzy-border continuum
solvation model . . . . . . . . . . . . 2388--2399
Patricio González-Navarrete and
Luis R. Domingo and
Juan Andrés and
Slawomir Berski and
Bernard Silvi Electronic fluxes during Diels--Alder
reactions involving 1,2-benzoquinones:
mechanistic insights from the analysis
of electron localization function and
catastrophe theory . . . . . . . . . . . 2400--2411
Ilia A. Solov'yov and
Alexander V. Yakubovich and
Pavel V. Nikolaev and
Ilya Volkovets and
Andrey V. Solov'yov MesoBioNano explorer --- a universal
program for multiscale computer
simulations of complex molecular
structure and dynamics . . . . . . . . . 2412--2439
Frank Weinhold Software News and Updates: Natural bond
critical point analysis: Quantitative
relationships between natural bond
orbital-based and QTAIM-based
topological descriptors of chemical
bonding . . . . . . . . . . . . . . . . 2440--2449
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 30 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 30 . . . . i--ii
Wenbo Yu and
Xibing He and
Kenno Vanommeslaeghe and
Alexander D. MacKerell Jr. Extension of the CHARMM general force
field to sulfonyl-containing compounds
and its utility in biomolecular
simulations . . . . . . . . . . . . . . 2451--2468
Shuming Zhang A reliable and efficient first
principles-based method for predicting
pK$_a$ values. 4. organic bases . . . . 2469--2482
Michael D. Tyka and
Kenneth Jung and
David Baker Efficient sampling of protein
conformational space using fast loop
building and batch minimization on
highly parallel computers . . . . . . . 2483--2491
Abu Md. Asaduzzaman and
Guy A. G. Chappellaz and
Georg Schreckenbach Relationship between dye--iodine binding
and cell voltage in dye-sensitized solar
cells: a quantum-mechanical look . . . . 2492--2497
Bu-Tong Li and
Zi-Zhang Wei and
Hai-Shun Wu The valence and Rydberg excited states
of CH$_2$: a theoretical exploration . . 2498--2503
Johannes Flick and
Frank Tristram and
Wolfgang Wenzel Modeling loop backbone flexibility in
receptor-ligand docking simulations . . 2504--2515
Yunqing Han and
Tianxiang Li and
Kozo Saito Comprehensive method based on model free
method and IKP method for evaluating
kinetic parameters of solid state
reactions . . . . . . . . . . . . . . . 2516--2525
David Vega and
Yosslen Aray and
Jesús Rodríguez Software News and Updates: C library for
topological study of the electronic
charge density . . . . . . . . . . . . . 2526--2531
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 31 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 31 . . . . i--ii
David Ferro-Costas and
Nicolás Otero and
Ana M. Graña and
Ricardo A. Mosquera A QTAIM-based energy partitioning for
understanding the physical origin of
conformational preferences: Application
to the Z effect in
O\doublebondC\bondX\bondR and related
units . . . . . . . . . . . . . . . . . 2533--2543
Yulia N. Kalugina and
Mikhail A. Buldakov and
Victor N. Cherepanov Static hyperpolarizability of the van
der Waals complex CH$_4$N$_2$ . . . . . 2544--2553
Lennart Heinzerling and
Robert Klein and
Matthias Rarey Fast force field-based optimization of
protein--ligand complexes with graphics
processor . . . . . . . . . . . . . . . 2554--2565
Daniel P. Oehme and
Robert T. C. Brownlee and
David J. D. Wilson Effect of atomic charge, solvation,
entropy, and ligand protonation state on
MM-PB(GB)SA binding energies of HIV
protease . . . . . . . . . . . . . . . . 2566--2580
Mohamed Hacene and
Ani Anciaux-Sedrakian and
Xavier Rozanska and
Diego Klahr and
Thomas Guignon and
Paul Fleurat-Lessard Accelerating VASP electronic structure
calculations using graphic processing
units . . . . . . . . . . . . . . . . . 2581--2589
Amanda G. Riojas and
Joshua R. John and
T. Gavin Williams and
Angela K. Wilson Proton affinities of
deoxyribonucleosides via the ONIOM-ccCA
methodology . . . . . . . . . . . . . . 2590--2601
T. Strunk and
M. Wolf and
M. Brieg and
K. Klenin and
A. Biewer and
F. Tristram and
M. Ernst and
P. J. Kleine and
N. Heilmann and
I. Kondov and
W. Wenzel Software News and Updates: SIMONA 1.0:
an efficient and versatile framework for
stochastic simulations of molecular and
nanoscale systems . . . . . . . . . . . 2602--2613
Jianxiu Guo and
Nini Rao and
Guangxiong Liu and
Yong Yang and
Gang Wang Retracted: Predicting protein folding
rates using the concept of Chou's pseudo
amino acid composition . . . . . . . . . 2614--2614
Anonymous Cover Image: Inside Cover, Volume 33,
Issue 32 . . . . . . . . . . . . . . . . iii--iv
Anonymous Cover Image, Volume 33, Issue 32 . . . . i--ii
Anonymous Cover Image, Volume 34, Issue 1 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 1 . . . . . . . . . . . . . . . . iii--iv
Charles L. Brooks III and
Masahiro Ehara and
Gernot Frenking and
Peter R. Schreiner Editorials: New paint and a new engine 1--1
Mark Pinsky and
Amir Zait and
Maayan Bonjack and
David Avnir Continuous symmetry analyses: C$_{nv}$
and D$_n$ measures of molecules,
complexes, and proteins . . . . . . . . 2--9
Susanne Pape and
Franziska Hoffgaard and
Mirjam Dür and
Kay Hamacher Distance dependency and minimum amino
acid alphabets for decoy scoring
potentials . . . . . . . . . . . . . . . 10--20
Toru Matsui and
Yasutaka Kitagawa and
Mitsutaka Okumura and
Yasuteru Shigeta and
Shigeyoshi Sakaki Consistent scheme for computing standard
hydrogen electrode and redox potentials 21--26
Andriy Samsonyuk and
Christoph Scheurer Configuration space partitioning and
matrix buildup scaling for the
vibrational configuration interaction
method . . . . . . . . . . . . . . . . . 27--37
Jinshuai Song and
Zhenhua Chen and
Sason Shaik and
Wei Wu An efficient algorithm for complete
active space valence bond
self-consistent field calculation . . . 38--48
J. Drujon and
Y. Carissan Pseudopotentials for hybridized carbon
atoms . . . . . . . . . . . . . . . . . 49--59
Jin Yang and
Paul J. Dauenhauer and
Ashwin Ramasubramaniam The role of water in the adsorption of
oxygenated aromatics on Pt and Pd . . . 60--66
Yu Liu and
Lei Zhao and
Wentao Li and
Dongyu Zhao and
Miao Song and
Yongliang Yang FIPSDock: a new molecular docking
technique driven by fully informed swarm
optimization algorithm . . . . . . . . . 67--75
Anonymous Cover Image, Volume 34, Issue 2 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 2 . . . . . . . . . . . . . . . . iii--iv
Milan Randi\'c Very efficient search for nucleotide
alignments . . . . . . . . . . . . . . . 77--82
Yutaka Uejima and
Ryo Maezono GPGPU for orbital function evaluation
with a new updating scheme . . . . . . . 83--94
Yutong Zhao and
Fu Kit Sheong and
Jian Sun and
Pedro Sander and
Xuhui Huang A fast parallel clustering algorithm for
molecular simulation trajectories . . . 95--104
Paul Mach and
Patrice Koehl An analytical method for computing
atomic contact areas in biomolecules . . 105--120
Yuan Liu and
Jijun Zhao and
Fengyu Li and
Zhongfang Chen Appropriate description of
intermolecular interactions in the
methane hydrates: an assessment of DFT
methods . . . . . . . . . . . . . . . . 121--131
Yannick G. Spill and
Guillaume Bouvier and
Michael Nilges A convective replica-exchange method for
sampling new energy basins . . . . . . . 132--140
Eric A. C. Bushnell and
James W. Gauld An assessment of pure, hybrid, meta, and
hybrid-meta GGA density functional
theory methods for open-shell systems:
the case of the nonheme iron enzyme
8R--LOX . . . . . . . . . . . . . . . . 141--148
Kenta Yamada and
Nobuaki Koga Variationally determined electronic
states for the theoretical analysis of
intramolecular interaction. II.
Qualitative nature of the P\bondO bond
in phosphine oxides . . . . . . . . . . 149--161
Anonymous Cover Image, Volume 34, Issue 3 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 3 . . . . . . . . . . . . . . . . iii--iv
Yang Zhong and
Sandeep Patel Binding structures of tri-N-acetyl-$
\beta $-glucosamine in hen egg white
lysozyme using molecular dynamics with a
polarizable force field . . . . . . . . 163--174
Robert A. Evarestov and
Andrei V. Bandura and
Dmitrii D. Kuruch BaTiO$_3$-based nanolayers and
nanotubes: First-principles calculations 175--186
Joakim P. M. Jämbeck and
Francesca Mocci and
Alexander P. Lyubartsev and
Aatto Laaksonen Partial atomic charges and their impact
on the free energy of solvation . . . . 187--197
Hiroshi Watanabe and
Marcus Elstner and
Thomas Steinbrecher Rotamer decomposition and protein
dynamics: Efficiently analyzing dihedral
populations from molecular dynamics . . 198--205
Pavel M. Polestshuk Accurate integration over atomic regions
bounded by zero-flux surfaces . . . . . 206--219
Christopher Pfleger and
Sebastian Radestock and
Elena Schmidt and
Holger Gohlke Global and local indices for
characterizing biomolecular flexibility
and rigidity . . . . . . . . . . . . . . 220--233
Josep M. Porta and
Léonard Jaillet Exploring the energy landscapes of
flexible molecular loops using
higher-dimensional continuation . . . . 234--244
Elijah Roberts and
John E. Stone and
Zaida Luthey-Schulten Lattice microbes: High-performance
stochastic simulation method for the
reaction-diffusion master equation . . . 245--255
Christopher J. R. Illingworth and
Sree V. Chintapalli and
Stefano A. Serapian and
Andrew D. Miller and
Vaclav Veverka and
Mark D. Carr and
Christopher A. Reynolds Erratum: The statistical significance of
selected sense--antisense peptide
interactions [J. Comp. Chem. \bf 33,
1440--1447] . . . . . . . . . . . . . . 256--256
Paola Antoniotti and
Elena Bottizzo and
Stefano Borocci and
Maria Giordani and
Felice Grandinetti Erratum: Gas-phase reactions of
SiH$_n^+$ ($ n = 1, 2 $ ) with NF$_3$: a
computational investigation on the
detailed mechanistic aspects [J. Comp.
Chem. 33, 1918--1926] . . . . . . . . . 257--257
Anonymous Cover Image, Volume 34, Issue 4 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 4 . . . . . . . . . . . . . . . . iii--iv
Stephen J. Barigye and
Yovani Marrero-Ponce and
Yoan Martínez-López and
Francisco Torrens and
Luis Manuel Artiles-Martínez and
Ricardo W. Pino-Urias and
Oscar Martínez-Santiago Relations frequency hypermatrices in
mutual, conditional and joint
entropy-based information indices . . . 259--274
Angelika Baranowska-\L\kaczkowska and
Berta Fernández and
Robert Zale\'sny New basis sets for the evaluation of
interaction-induced electric properties
in hydrogen-bonded complexes . . . . . . 275--283
Li Yang and
Alauddin Ahmed and
Stanley I. Sandler Comparison of two simulation methods to
compute solvation free energies and
partition coefficients . . . . . . . . . 284--293
\Lukasz Pi\kEko\'s and
Mariusz Pawe\l Mitoraj Theoretical description of
dihydrogen/hydride and trihydride
molybdocene complexes: an insight from
static and molecular dynamics
simulations . . . . . . . . . . . . . . 294--304
Hongguang Liu and
Jin Yong Lee Electric field assisted oxygen removal
from the basal plane of the graphitic
material . . . . . . . . . . . . . . . . 305--310
Sheng-You Huang and
Xiaoqin Zou A nonredundant structure dataset for
benchmarking protein-RNA computational
docking . . . . . . . . . . . . . . . . 311--318
Alexander V. Popov and
Yury N. Vorobjev and
Dmitry O. Zharkov Software News and Updates: MDTRA: a
molecular dynamics trajectory analyzer
with a graphical user interface . . . . 319--325
Xuchang Ouyang and
Shuo Zhou and
Chinh Tran To Su and
Zemei Ge and
Runtao Li and
Chee Keong Kwoh Software News and Updates: CovalentDock:
Automated covalent docking with
parameterized covalent linkage energy
estimation and molecular geometry
constraints . . . . . . . . . . . . . . 326--336
Anonymous Cover Image, Volume 34, Issue 5 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 5 . . . . . . . . . . . . . . . . iii--iv
Pawe\l Ma\lyszek and
Jacek Koput Accurate Ab initio potential energy
surface and vibration-rotation energy
levels of hydrogen peroxide . . . . . . 337--345
Alessandro Erba and
Matteo Ferrabone and
Roberto Orlando and
Roberto Dovesi Accurate dynamical structure factors
from ab initio lattice dynamics: the
case of crystalline silicon . . . . . . 346--354
Gonzalo Astray and
Juan F. Gálvez and
Juan C. Mejuto and
Oscar A. Moldes and
Iago Montoya Esters flash point prediction using
artificial neural networks . . . . . . . 355--359
Hongmei Liu and
Hongbo Wang and
Jianwei Zhao and
Manabu Kiguchi Molecular rectification in triangularly
shaped graphene nanoribbons . . . . . . 360--365
Ji\vrí Kessler and
Martin Dra\vcínský and
Petr Bou\vr Parallel variable selection of molecular
dynamics clusters as a tool for
calculation of spectroscopic properties 366--371
Binju Wang and
Zexing Cao How water molecules modulate the
hydration of CO$_2$ in water solution:
Insight from the cluster-continuum model
calculations . . . . . . . . . . . . . . 372--378
Raman K. Singh and
Takao Tsuneda Reaction energetics on long-range
corrected density functional theory:
Diels--Alder reactions . . . . . . . . . 379--386
Zhixiong Lin and
Wilfred F. van Gunsteren On the choice of a reference state for
one-step perturbation calculations
between polar and nonpolar molecules in
a polar environment . . . . . . . . . . 387--393
Shantanu Kadam and
Kumar Vanka Solving the problem of negative
populations in approximate accelerated
stochastic simulations using the
representative reaction approach . . . . 394--404
Danny E. P. Vanpoucke and
Patrick Bultinck and
Isabel Van Driessche Extending Hirshfeld-I to bulk and
periodic materials . . . . . . . . . . . 405--417
Thomas A. Manz Letters to the Editor: Comment on
``Extending Hirshfeld-I to bulk and
periodic materials'' . . . . . . . . . . 418--421
Danny E. P. Vanpoucke and
Isabel Van Driessche and
Patrick Bultinck Letters to the Editor: Reply to `Comment
on ``Extending Hirshfeld-I to bulk and
periodic materials''' . . . . . . . . . 422--427
Anonymous Cover Image, Volume 34, Issue 6 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 6 . . . . . . . . . . . . . . . . iii--iv
Louis P. Lee and
Daniel J. Cole and
Mike C. Payne and
Chris-Kriton Skylaris Natural bond orbital analysis in the
ONETEP code: Applications to large
protein systems . . . . . . . . . . . . 429--444
Mohsen Chitsaz and
Stephen L. Mayo GRID: a high-resolution protein
structure refinement algorithm . . . . . 445--450
Michael F. Peintinger and
Daniel Vilela Oliveira and
Thomas Bredow Consistent Gaussian basis sets of
triple-zeta valence with polarization
quality for solid-state calculations . . 451--459
János Pipek and
Szilvia Nagy An economic prediction of refinement
coefficients in wavelet-based adaptive
methods for electron structure
calculations . . . . . . . . . . . . . . 460--465
Jack Yang and
Mark P. Waller Revealing noncovalent interactions in
quantum crystallography: Taurine
revisited . . . . . . . . . . . . . . . 466--470
Soumya Ganguly Neogi and
Pinaki Chaudhury Structure and spectroscopic aspects of
water-halide ion clusters: a study based
on a conjunction of stochastic and
quantum chemical methods . . . . . . . . 471--491
Maël Bosson and
Sergei Grudinin and
Stephane Redon Block-adaptive quantum mechanics: an
adaptive divide-and-conquer approach to
interactive quantum chemistry . . . . . 492--504
Jorge M. C. Marques and
Francisco B. Pereira A detailed investigation on the global
minimum structures of mixed rare-gas
clusters: Geometry, energetics, and site
occupancy . . . . . . . . . . . . . . . 505--517
David D. Jenkins and
Jason B. Harris and
Elizabeth E. Howell and
Robert J. Hinde and
Jerome Baudry Software News and Updates: STAAR:
Statistical analysis of aromatic rings 518--522
Anonymous Cover Image, Volume 34, Issue 7 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 7 . . . . . . . . . . . . . . . . iii--iv
Ananth P. Kaushik and
Paulette Clancy Solvent-driven symmetry of
self-assembled nanocrystal superlattices
--- a computational study . . . . . . . 523--532
Vladimir V. Rybkin and
Anton O. Simakov and
Vebjòrn Bakken and
Simen Reine and
Thomas Kjærgaard and
Trygve Helgaker and
Einar Uggerud Insights into the dynamics of
evaporation and proton migration in
protonated water clusters from
large-scale Born--Oppenheimer direct
dynamics . . . . . . . . . . . . . . . . 533--544
Maggie Ng and
Daniel K. W. Mok and
Edmond P. F. Lee and
John M. Dyke Rate coefficients of the CF$_3$CHFCF$_3$
$+$ H $ \rightarrow $ CF$_3$CFCF$_3$ $+$
H$_2$ reaction at different temperatures
calculated by transition state theory
with ab initio and DFT reaction paths 545--557
Shelley A. Smith and
Karen E. Hand and
Melissa L. Love and
Glake Hill and
David H. Magers Conventional strain energies of
azetidine and phosphetane: Can density
functional theory yield reliable
results? . . . . . . . . . . . . . . . . 558--565
Jia-Nan Wang and
Jun-Ling Jin and
Yun Geng and
Shi-Ling Sun and
Hong-Liang Xu and
Ying-Hua Lu and
Zhong-Min Su An accurate and efficient method to
predict the electronic excitation
energies of BODIPY fluorescent dyes . . 566--575
Bradley Scott Perrin Jr. and
Shuqiang Niu and
Toshiko Ichiye Calculating standard reduction
potentials of [4Fe--4S] proteins . . . . 576--582
Mingyue Zheng and
Yanlian Li and
Bing Xiong and
Hualiang Jiang and
Jingkang Shen Water PMF for predicting the properties
of water molecules in protein binding
site . . . . . . . . . . . . . . . . . . 583--592
Jihyun Shim and
Xiao Zhu and
Robert B. Best and
Alexander D. MacKerell Jr. (Ala)$_4$ -X-(Ala)$_4$ as a model system
for the optimization of the $\chi_1$ and
$\chi_2$ amino acid side-chain dihedral
empirical force field parameters . . . . 593--603
Yuye He and
Chin Yee Liew and
Nitin Sharma and
Sze Kwang Woo and
Yi Ting Chau and
Chun Wei Yap Software News and Updates:
PaDEL-DDPredictor: Open-source software
for PD-PK-T prediction . . . . . . . . . 604--610
Anonymous Cover Image, Volume 34, Issue 8 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 8 . . . . . . . . . . . . . . . . iii--iv
Marcus V. P. dos Santos and
Eduardo C. Aguiar and
João Bosco P. da Silva and
Ricardo L. Longo PICVib: an accurate, fast, and simple
procedure to investigate selected
vibrational modes at high theoretical
levels . . . . . . . . . . . . . . . . . 611--621
Satoru G. Itoh and
Hisashi Okumura Coulomb replica-exchange method:
Handling electrostatic attractive and
repulsive forces for biomolecules . . . 622--639
Ning Ma and
Ying-Hua Chung and
Arjan van der Vaart Free energy simulation of helical
transitions . . . . . . . . . . . . . . 640--645
Goran Kovacevic and
Aleksandar Sabljic Theoretical study on the mechanism and
kinetics of addition of hydroxyl
radicals to fluorobenzene . . . . . . . 646--655
Drahomír Hnyk and
Elambalassery G. Jayasree Cationic Closo-carboranes 2. Do computed
$^{11}$B and $^{13}$C NMR chemical
shifts support their experimental
availability? . . . . . . . . . . . . . 656--661
Soumen Saha and
Rituparna Bhattacharjee and
Ram Kinkar Roy Hardness potential derivatives and their
relation to Fukui indices . . . . . . . 662--672
Jian-Dong Zhang and
Shu-Jin Li and
Fu-Ming Tao Ab initio calculations of the Ar--ethane
intermolecular potential energy surface
using bond function basis sets . . . . . 673--680
Juan I. Rodríguez An efficient method for computing the
QTAIM topology of a scalar field: the
electron density case . . . . . . . . . 681--686
Dennis G. Thomas and
Jaehun Chun and
Zhan Chen and
Guowei Wei and
Nathan A. Baker Parameterization of a geometric flow
implicit solvation model . . . . . . . . 687--695
Halina Szaty\lowicz and
Tadeusz M. Krygowski and
Célia Fonseca Guerra and
F. Matthias Bickelhaupt Complexes of 4-substituted phenolates
with HF and HCN: Energy decomposition
and electronic structure analyses of
hydrogen bonding . . . . . . . . . . . . 696--705
Anonymous Cover Image, Volume 34, Issue 9 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 9 . . . . . . . . . . . . . . . . iii--iv
Florent Réal and
Michael Trumm and
Bernd Schimmelpfennig and
Michel Masella and
Valérie Vallet Further insights in the ability of
classical nonadditive potentials to
model actinide ion--water interactions 707--719
David Casanova Efficient implementation of restricted
active space configuration interaction
with the hole and particle approximation 720--730
Olga Yuzlenko and
Themis Lazaridis Membrane protein native state
discrimination by implicit membrane
models . . . . . . . . . . . . . . . . . 731--738
Jin Yu Xiang and
Jay W. Ponder A valence bond model for aqueous Cu(II)
and Zn(II) ions in the AMOEBA
polarizable force field . . . . . . . . 739--749
Marcin Nowosielski and
Marcin Hoffmann and
Aneta Kuron and
Ma\lgorzata Korycka-Machala and
Jaros\law Dziadek The MM2QM tool for combining docking,
molecular dynamics, molecular mechanics,
and quantum mechanics . . . . . . . . . 750--756
Jia-Lin Chang and
Cyong-Huei Huang and
Sue-Chang Chen and
Tsung-Hao Yin and
Yi-Tsung Chen An analytical approach for computing
Franck--Condon integrals of harmonic
oscillators with arbitrary dimensions 757--765
Ramon Carbó-Dorca Notes on quantitative
structure--property relationships
(QSPR), part 3: Density functions origin
shift as a source of quantum QSPR
algorithms in molecular spaces . . . . . 766--779
Ignacio Viciano and
Slawomir Berski and
Sergio Martí and
Juan Andrés New insight into the electronic
structure of iron(IV)-oxo porphyrin
compound I. A quantum chemical
topological analysis . . . . . . . . . . 780--789
Nikola Minovski and
Andrej Perdih and
Marjana Novic and
Tom Solmajer Cluster-based molecular docking study
for in silico identification of novel
6-fluoroquinolones as potential
inhibitors against mycobacterium
tuberculosis . . . . . . . . . . . . . . 790--801
Anonymous Cover Image, Volume 34, Issue 10 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 10 . . . . . . . . . . . . . . . . iii--iv
Ardita Shkurti and
Mario Orsi and
Enrico Macii and
Elisa Ficarra and
Andrea Acquaviva Acceleration of coarse grain molecular
dynamics on GPU architectures . . . . . 803--818
Angelika Baranowska-\L\kaczkowska and
Wojciech Bartkowiak and
Robert W. Góra and
Filip Paw\lowski and
Robert Zale\'sny On the performance of
long-range-corrected density functional
theory and reduced-size polarized
LPol-$n$ basis sets in computations of
electric dipole (hyper)polarizabilities
of $ \pi $-conjugated molecules . . . . 819--826
Ole Schütt and
Daniel Sebastiani Spectroscopic fingerprints of toroidal
nuclear quantum delocalization via ab
initio path integral simulations . . . . 827--835
Thomas Simonson and
Priyadarshi Satpati Simulating GTP:Mg and GDP:Mg with a
simple force field: a structural and
thermodynamic analysis . . . . . . . . . 836--846
Juan Zeng and
LiLi Duan and
John Z. H. Zhang and
Ye Mei A numerically stable restrained
electrostatic potential charge fitting
method . . . . . . . . . . . . . . . . . 847--853
György G. Ferenczy Calculation of wave-functions with
frozen orbitals in mixed quantum
mechanics/molecular mechanics methods.
Part I. Application of the Huzinaga
equation . . . . . . . . . . . . . . . . 854--861
György G. Ferenczy Calculation of wave-functions with
frozen orbitals in mixed quantum
mechanics/molecular mechanics methods.
II. Application of the local basis
equation . . . . . . . . . . . . . . . . 862--869
Andranik Kazaryan and
Evert Jan Baerends Assessment of density functional methods
for reaction energetics:
Iridium-catalyzed water oxidation as
case study . . . . . . . . . . . . . . . 870--878
Yoonjoo Choi and
Karl E. Griswold and
Chris Bailey-Kellogg Structure-based redesign of proteins for
minimal T-cell epitope content . . . . . 879--891
Anonymous Cover Image, Volume 34, Issue 11 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 11 . . . . . . . . . . . . . . . . iii--iv
Jennifer L. Knight and
Joseph D. Yesselman and
Charles L. Brooks III Assessing the quality of absolute
hydration free energies among
CHARMM-compatible ligand
parameterization schemes . . . . . . . . 893--903
Jeffrey R. Wagner and
Gouthaman S. Balaraman and
Michiel J. M. Niesen and
Adrien B. Larsen and
Abhinandan Jain and
Nagarajan Vaidehi Advanced techniques for constrained
internal coordinate molecular dynamics 904--914
Xiaohua Zhang and
Sergio E. Wong and
Felice C. Lightstone Message passing interface and
multithreading hybrid for parallel
molecular docking of large databases on
petascale high performance computing
machines . . . . . . . . . . . . . . . . 915--927
Robert J. Buenker and
Heinz-Peter Liebermann and
Yu Zhang and
Yong Wu and
Lingling Yan and
Chunhua Liu and
Yizhi Qu and
Jianguo Wang Adjustment of Born--Oppenheimer
electronic wave functions to simplify
close coupling calculations . . . . . . 928--937
Anthony Scemama and
Michel Caffarel and
Emmanuel Oseret and
William Jalby Quantum Monte Carlo for large chemical
systems: Implementing efficient
strategies for petascale platforms and
beyond . . . . . . . . . . . . . . . . . 938--951
Heng-Qing Wu and
Rong-Lin Zhong and
Yu-He Kan and
Shi-Ling Sun and
Min Zhang and
Hong-Liang Xu and
Zhong-Min Su After the electronic field: Structure,
bonding, and the first
hyperpolarizability of HArF . . . . . . 952--957
Rahul Kar and
Jong-Won Song and
Kimihiko Hirao Long-range corrected functionals satisfy
Koopmans' theorem: Calculation of
correlation and relaxation energies . . 958--964
Nadine Homeyer and
Holger Gohlke Software News and Updates: FEW: a
workflow tool for free energy
calculations of ligand binding . . . . . 965--973
Dong-Jun Yu and
Jun Hu and
Yan Huang and
Hong-Bin Shen and
Yong Qi and
Zhen-Min Tang and
Jing-Yu Yang Software News and Updates:
TargetATPsite: a template-free method
for ATP-binding sites prediction with
residue evolution image sparse
representation and classifier ensemble 974--985
Anonymous Cover Image, Volume 34, Issue 12 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 12 . . . . . . . . . . . . . . . . iii--iv
Karina Kornobis and
Neeraj Kumar and
Piotr Lodowski and
Maria Jaworska and
Piotr Piecuch and
Jesse J. Lutz and
Bryan M. Wong and
Pawel M. Kozlowski Electronic structure of the $ S_1 $
state in methylcobalamin: Insight from
CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT
calculations . . . . . . . . . . . . . . 987--1004
Yanliang Ren and
Bo Chi and
Osama Melhem and
Ke Wei and
Lingling Feng and
Yongjian Li and
Xinya Han and
Ding Li and
Ying Zhang and
Jian Wan and
Xin Xu and
Minghui Yang Understanding the electronic energy
transfer pathways in the trimeric and
hexameric aggregation state of
cyanobacteria phycocyanin within the
framework of förster theory . . . . . . . 1005--1012
Terutaka Yoshizawa and
Shigeyoshi Sakaki NMR shielding constants of CuX, AgX, and
AuX (X = F, Cl, Br, and I) investigated
by density functional theory based on
the Douglas--Kroll--Hess Hamiltonian . . 1013--1023
Anita de Ruiter and
Stefan Boresch and
Chris Oostenbrink Comparison of thermodynamic integration
and Bennett's acceptance ratio for
calculating relative protein-ligand
binding free energies . . . . . . . . . 1024--1034
M. Rohrmüller and
S. Herres-Pawlis and
M. Witte and
W. G. Schmidt Bis-$ \mu $-oxo and $ \mu $-$ \eta^2 $:$
\eta^2 $-peroxo dicopper complexes
studied within (time-dependent)
density-functional and many-body
perturbation theory . . . . . . . . . . 1035--1045
Zhanghui Chen and
Xiangwei Jiang and
Jingbo Li and
Shushen Li and
Linwang Wang PDECO: Parallel differential evolution
for clusters optimization . . . . . . . 1046--1059
Debashree Ghosh and
Dmytro Kosenkov and
Vitalii Vanovschi and
Joanna Flick and
Ilya Kaliman and
Yihan Shao and
Andrew T. B. Gilbert and
Anna I. Krylov and
Lyudmila V. Slipchenko Effective fragment potential method in
Q-CHEM: a guide for users and developers 1060--1070
Kunal Roy and
Pratim Chakraborty and
Indrani Mitra and
Probir Kumar Ojha and
Supratik Kar and
Rudra Narayan Das Software News and Updates: Some case
studies on application of ``$ r_m^2 $''
metrics for judging quality of
quantitative structure--activity
relationship predictions: Emphasis on
scaling of response data . . . . . . . . 1071--1082
Anonymous Cover Image, Volume 34, Issue 13 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 13 . . . . . . . . . . . . . . . . iii--iv
Jeremy P. Coe and
Daniel J. Taylor and
Martin J. Paterson Monte Carlo configuration interaction
applied to multipole moments, ionisation
energies and electron affinities . . . . 1083--1093
Liudmyla K. Sviatenko and
Leonid Gorb and
Frances C. Hill and
Jerzy Leszczynski Theoretical study of ionization and
one-electron oxidation potentials of
N-heterocyclic compounds . . . . . . . . 1094--1100
Rui Yang and
Alistair P. Rendell First principles study of gallium
cleaning for hydrogen-contaminated $
\alpha $-Al$_2$O$_3$ (0001) surfaces . . 1101--1111
Michel Masella and
Daniel Borgis and
Philippe Cuniasse A multiscale coarse-grained polarizable
solvent model for handling long tail
bulk electrostatics . . . . . . . . . . 1112--1124
Krystel El Hage and
Jean-Philip Piquemal and
Zeina Hobaika and
Richard G. Maroun and
Nohad Gresh Could an anisotropic molecular
mechanics/dynamics potential account for
sigma hole effects in the complexes of
halogenated compounds? . . . . . . . . . 1125--1135
Xue X. Yao and
Chang G. Ji and
Dai Q. Xie and
John Z. H. Zhang Molecular dynamics study of DNA binding
by INT-DBD under a polarized force field 1136--1142
E. Iype and
M. Hütter and
A. P. J. Jansen and
S. V. Nedea and
C. C. M. Rindt Parameterization of a reactive force
field using a Monte Carlo algorithm . . 1143--1154
Torsten Kerber and
Rachel Nathaniel Kerber and
Xavier Rozanska and
Philippe Sautet and
Paul Fleurat-Lessard Software news and updates: QMX: a
versatile environment for hybrid
calculations applied to the grafting of
Al$_2$Cl$_3$Me$_3$ on a silica surface 1155--1163
Nicholas F. Chilton and
Russell P. Anderson and
Lincoln D. Turner and
Alessandro Soncini and
Keith S. Murray Software News and Updates: PHI: a
powerful new program for the analysis of
anisotropic monomeric and
exchange-coupled polynuclear $d$- and
$f$-block complexes . . . . . . . . . . 1164--1175
Anonymous Cover Image, Volume 34, Issue 14 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 14 . . . . . . . . . . . . . . . . iii--iv
Claudia R. Herbers and
Chunli Li and
Nico F. A. van der Vegt Reviews: Grand challenges in
quantum-classical modeling of
molecule--surface interactions . . . . . 1177--1188
Jenna A. Bilbrey and
Arianna H. Kazez and
Jason Locklin and
Wesley D. Allen Exact ligand cone angles . . . . . . . . 1189--1197
Sandra C. C. Nunes and
P. Pinto and
A. A. C. C. Pais Nonrandom adsorption of polyelectrolyte
chains on finite regularly charged
surfaces . . . . . . . . . . . . . . . . 1198--1209
Daniel Strobusch and
Mathias Nest and
Christoph Scheurer The adaptive hierarchical expansion of
the kinetic energy operator . . . . . . 1210--1217
Yutaka Imamura and
Rie Kobayashi and
Hiromi Nakai Linearity condition for orbital energies
in density functional theory (III):
Benchmark of total energies . . . . . . 1218--1225
Trent E. Balius and
William J. Allen and
Sudipto Mukherjee and
Robert C. Rizzo Grid-based molecular footprint
comparison method for docking and de
novo design: Application to HIVgp41 . . 1226--1240
Xinbi Li and
Sergei Y. Ponomarev and
Qina Sa and
Daniel L. Sigalovsky and
George A. Kaminski Polarizable simulations with second
order interaction model (POSSIM) force
field: Developing parameters for protein
side-chain analogues . . . . . . . . . . 1241--1250
Le Chang and
Takeshi Ishikawa and
Kazuo Kuwata and
Shoji Takada Protein-specific force field derived
from the fragment molecular orbital
method can improve protein--ligand
binding interactions . . . . . . . . . . 1251--1257
Marcel Schumann and
Roger S. Armen Systematic and efficient side chain
optimization for molecular docking using
a cheapest-path procedure . . . . . . . 1258--1269
Anonymous Cover Image, Volume 34, Issue 15 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 15 . . . . . . . . . . . . . . . . iii--iv
Yao Wu and
Xiaodong Dai and
Niu Huang and
Lifeng Zhao A partition function-based weighting
scheme in force field parameter
development using ab initio calculation
results in global configurational space 1271--1282
Maria Ana Castro and
Adrian E. Roitberg and
Fabio D. Cukiernik Simulation of mesogenic diruthenium
tetracarboxylates: Development of a
force field for coordination polymers of
the MMX type . . . . . . . . . . . . . . 1283--1290
Kalipada Adhikari and
Sudip Chattopadhyay and
Barin Kumar De and
Amitava Sharma and
Ranendu Kumar Nath and
Dhiman Sinha Search of truncation of $ (N - 1) $
electron basis containing full connected
triple excitations in computing main and
satellite ionization potentials via
Fock-space coupled cluster approach . . 1291--1310
Ida-Marie Hòyvik and
Branislav Jansik and
Kasper Kristensen and
Poul Jòrgensen Local Hartree--Fock orbitals using a
three-level optimization strategy for
the energy . . . . . . . . . . . . . . . 1311--1320
David Casanova and
Pere Alemany and
Andrés Falceto and
Abel Carreras and
Santiago Alvarez Pseudosymmetry analysis of molecular
orbitals . . . . . . . . . . . . . . . . 1321--1331
Sven Jakobtorweihen and
Thomas Ingram and
Irina Smirnova Combination of COSMOmic and molecular
dynamics simulations for the calculation
of membrane-water partition coefficients 1332--1340
Karunakaran Remya and
Cherumuttathu H. Suresh Which density functional is close to
CCSD accuracy to describe geometry and
interaction energy of small non-covalent
dimers? A benchmark study using \tt
gaussian09 . . . . . . . . . . . . . . . 1341--1353
Silvia A. Martins and
Sergio F. Sousa Comparative assessment of computational
methods for the determination of
solvation free energies in alcohol-based
molecules . . . . . . . . . . . . . . . 1354--1362
Anonymous Cover Image, Volume 34, Issue 16 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 16 . . . . . . . . . . . . . . . . iii--iv
Olle Falklöf and
Bo Durbeej Modeling of phytochrome absorption
spectra . . . . . . . . . . . . . . . . 1363--1374
Tetsuya Morishita and
Satoru G. Itoh and
Hisashi Okumura and
Masuhiro Mikami On-the-fly reconstruction of free-energy
profiles using logarithmic mean-force
dynamics . . . . . . . . . . . . . . . . 1375--1384
Paul M. Zimmerman Automated discovery of chemically
reasonable elementary reaction steps . . 1385--1392
Axel Schild and
Beate Paulus Multireference calculations for ring
inversion and double bond shifting in
cyclooctatetraene . . . . . . . . . . . 1393--1397
Jose Antonio Garate and
Chris Oostenbrink Free-energy differences between states
with different conformational ensembles 1398--1408
Milan Randi\'c and
Marjana Novi\vc and
Dejan Plav\vsi\'c Common vertex matrix: a novel
characterization of molecular graphs by
counting . . . . . . . . . . . . . . . . 1409--1419
Mark P. Waller and
Thomas Dresselhaus and
Jack Yang Software News and Updates: JACOB: an
enterprise framework for computational
chemistry . . . . . . . . . . . . . . . 1420--1428
Eric D. Glendening and
Clark R. Landis and
Frank Weinhold Software News and Updates: NBO 6.0:
Natural bond orbital analysis program 1429--1437
Anonymous Cover Image, Volume 34, Issue 17 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 17 . . . . . . . . . . . . . . . . iii--iv
Ivana Antol Photodeactivation paths in norbornadiene 1439--1445
Aggelos Avramopoulos and
Heribert Reis and
Josep M. Luis and
Manthos G. Papadopoulos On the vibrational linear and nonlinear
optical properties of compounds
involving noble gas atoms: HXeOXeH,
HXeOXeF, and FXeOXeF . . . . . . . . . . 1446--1455
Ida-Marie Hòyvik and
Branislav Jansik and
Poul Jòrgensen Pipek--Mezey localization of occupied
and virtual orbitals . . . . . . . . . . 1456--1462
Yi He and
Lidia Prieto and
Themis Lazaridis Modeling peptide binding to anionic
membrane pores . . . . . . . . . . . . . 1463--1475
Marco De La Pierre and
Cédric Carteret and
Roberto Orlando and
Roberto Dovesi Use of ab initio methods for the
interpretation of the experimental IR
reflectance spectra of crystalline
compounds . . . . . . . . . . . . . . . 1476--1485
Patrick Merlot and
Thomas Kjærgaard and
Trygve Helgaker and
Roland Lindh and
Francesco Aquilante and
Simen Reine and
Thomas Bondo Pedersen Attractive electron--electron
interactions within robust local fitting
approximations . . . . . . . . . . . . . 1486--1496
Ahmed A. K. Mohammed and
Peter A. Limacher and
Beno\^\it Champagne Finding optimal finite field strengths
allowing for a maximum of precision in
the calculation of polarizabilities and
hyperpolarizabilities . . . . . . . . . 1497--1507
Peter Schwerdtfeger and
Lukas Wirz and
James Avery Software News and Updates: Program
Fullerene: a software package for
constructing and analyzing structures of
regular fullerenes . . . . . . . . . . . 1508--1526
Anonymous Cover Image, Volume 34, Issue 18 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 18 . . . . . . . . . . . . . . . . iii--iv
Marat R. Talipov and
Dmitry G. Khomyakov and
Ming Xian and
Qadir K. Timerghazin Computational design of S-nitrosothiol
``click'' reactions . . . . . . . . . . 1527--1530
Petr \vSt\vepánek and
Petr Bou\vr Computation of magnetic circular
dichroism by sum-over-states summations 1531--1539
Alexandra T. P. Carvalho and
Ana F. S. Teixeira and
Maria J. Ramos Parameters for molecular dynamics
simulations of iron-sulfur proteins . . 1540--1548
Azaria Solomon Eisenberg and
Laura J. Juszczak Relating Trp-Glu dipeptide fluorescence
to molecular conformation: the role of
the discrete chi 1 and chi 2 angles . . 1549--1560
Paolo Nicolini and
Diego Frezzato and
Cristina Gellini and
Marco Bizzarri and
Riccardo Chelli Toward quantitative estimates of binding
affinities for protein--ligand systems
involving large inhibitor compounds: a
steered molecular dynamics simulation
route . . . . . . . . . . . . . . . . . 1561--1576
Sonam Bhatia and
Yogesh J. Malkhede and
Prasad V. Bharatam Existence of dynamic tautomerism and
divalent N(I) character in
N-(pyridin-2-yl)thiazol-2-amine . . . . 1577--1588
Han Myoung Lee and
Kwang S. Kim Dynamics and structural changes of small
water clusters on ionization . . . . . . 1589--1597
Peter Comba and
Bodo Martin and
Avik Sanyal An efficient fluctuating charge model
for transition metal complexes . . . . . 1598--1608
Yannick G. Spill and
Guillaume Bouvier and
Michael Nilges Erratum: A convective replica-exchange
method for sampling new energy basins 1609--1609
Anonymous Cover Image, Volume 34, Issue 19 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 19 . . . . . . . . . . . . . . . . iii--iv
Yu-Ai Duan and
Yun Geng and
Hai-Bin Li and
Jun-Ling Jin and
Yong Wu and
Zhong-Min Su Theoretical characterization and design
of small molecule donor material
containing naphthodithiophene central
unit for efficient organic solar cells 1611--1619
Xueqin Pang and
Keli Han and
Qiang Cui A simple but effective modeling strategy
for structural properties of non-heme
Fe(II) sites in proteins: Test of force
field models and application to proteins
in the AlkB family . . . . . . . . . . . 1620--1635
Li Rao and
Igor Ying Zhang and
Wenping Guo and
Li Feng and
Eric Meggers and
Xin Xu Nonfitting protein--ligand interaction
scoring function based on
first-principles theoretical chemistry
methods: Development and application on
kinase inhibitors . . . . . . . . . . . 1636--1646
Justin E. Elenewski and
John C. Hackett Cytochrome P450 compound I in the plane
wave pseudopotential framework: GGA
electronic and geometric structure of
thiolate-ligated iron(IV)--oxo porphyrin 1647--1660
Brajesh K. Rai and
Gregory A. Bakken Fast and accurate generation of ab
initio quality atomic charges using
nonparametric statistical regression . . 1661--1671
Rebecca Sure and
Stefan Grimme Corrected small basis set Hartree--Fock
method for large systems . . . . . . . . 1672--1685
Yongqing Li and
Jiuchuang Yuan and
Maodu Chen and
Fengcai Ma and
Mengtao Sun Accurate double many-body expansion
potential energy surface by
extrapolation to the complete basis set
limit and dynamics calculations for
ground state of NH$_2$ . . . . . . . . . 1686--1696
Wouter Boomsma and
Jes Frellsen and
Tim Harder and
Sandro Bottaro and
Kristoffer E. Johansson and
Pengfei Tian and
Kasper Stòvgaard and
Christian Andreetta and
Simon Olsson and
Jan B. Valentin and
Lubomir D. Antonov and
Anders S. Christensen and
Mikael Borg and
Jan H. Jensen and
Kresten Lindorff-Larsen and
Jesper Ferkinghoff-Borg and
Thomas Hamelryck Software News and Updates: PHAISTOS: a
framework for Markov chain Monte Carlo
simulation and inference of protein
structure . . . . . . . . . . . . . . . 1697--1705
Anonymous Cover Image, Volume 34, Issue 20 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 20 . . . . . . . . . . . . . . . . iii--iv
Ranieri V. de Carvalho and
Daniel Lopez-Ferrer and
Katia S. Guimarães and
Roberto D. Lins IMSPeptider: a computational peptide
collision cross-section area calculator
based on a novel molecular dynamics
simulation protocol . . . . . . . . . . 1707--1718
Christiane Regina Soares Brasil and
Alexandre Claudio Botazzo Delbem and
Fernando Luís Barroso da Silva Multiobjective evolutionary algorithm
with many tables for purely ab initio
protein structure prediction . . . . . . 1719--1734
Ruifeng Lu and
Yunhui Wang and
Kaiming Deng Quantum wave packet and quasiclassical
trajectory studies of the reaction
H($^2$S) + CH(X$^2 \Pi $ ); $ v = 0 $, j
= 1 $ \rightarrow $ C($^1$ D) + H$_2$
(X$^1 \Sigma $ g+): Coriolis coupling
effects and stereodynamics . . . . . . . 1735--1742
Victoria A. Roberts and
Elaine E. Thompson and
Michael E. Pique and
Martin S. Perez and
L. F. Ten Eyck DOT2: Macromolecular docking with
improved biophysical models . . . . . . 1743--1758
Neil Qiang Su and
Igor Ying Zhang and
Xin Xu Analytic derivatives for the XYG3 type
of doubly hybrid density functionals:
Theory, implementation, and assessment 1759--1774
Ireneusz W. Bulik and
Robert Zale\'sny and
Wojciech Bartkowiak and
Josep M. Luis and
Bernard Kirtman and
Gustavo E. Scuseria and
Aggelos Avramopoulos and
Heribert Reis and
Manthos G. Papadopoulos Performance of density functional theory
in computing nonresonant vibrational
(hyper)polarizabilities . . . . . . . . 1775--1784
Mark A. Olson and
Michael S. Lee Application of replica exchange umbrella
sampling to protein structure refinement
of nontemplate models . . . . . . . . . 1785--1793
Sierra Rayne Letters to the Editor: Comment on ``QSAR
model reproducibility and applicability:
a case study of rate constants of
hydroxyl radical reaction models applied
to polybrominated diphenyl ethers and
(benzo-)triazoles'' . . . . . . . . . . 1794--1795
Paola Gramatica and
Simona Kovarich and
Partha Pratim Roy Letters to the Editor: Reply to the
comment of S. Rayne on ``QSAR model
reproducibility and applicability: a
case study of rate constants of hydroxyl
radical reaction models applied to
polybrominated diphenyl ethers and
(benzo-)triazoles'' . . . . . . . . . . 1796--1796
Anonymous Cover Image, Volume 34, Issue 21 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 21 . . . . . . . . . . . . . . . . iii--iv
Wiktor Beker and
Karol M. Langner and
Edyta Dyguda-Kazimierowicz and
Miko\laj Feliks and
W. Andrzej Sokalski Low cost prediction of relative
stabilities of hydrogen bonded complexes
from atomic multipole moments for overly
short intermolecular distances . . . . . 1797--1799
Rafael López and
Guillermo Ramírez and
Ignacio Ema and
Jaime Fernández Rico Improved partition--expansion of
two-center distributions involving
Slater functions . . . . . . . . . . . . 1800--1809
Christoph Grebner and
Lukas P. Pason and
Bernd Engels PathOpt --- A global transition state
search approach: Outline of algorithm 1810--1818
Mirko Franchini and
Pierre Herman Theodoor Philipsen and
Lucas Visscher The Becke Fuzzy Cells Integration Scheme
in the Amsterdam Density Functional
Program Suite . . . . . . . . . . . . . 1819--1827
Atsushi Ishikawa and
Hiroshi Nakatsuji XPS of oxygen atoms on Ag(111) and
Ag(110) surfaces: Accurate study with
SAC/SAC-CI combined with dipped
adcluster model . . . . . . . . . . . . 1828--1834
Arnim Hellweg Heuristic control of kinetic energy in
dynamic reaction coordinate calculations 1835--1841
Vladimir V. Rybkin and
Ulf Ekström and
Trygve Helgaker Internal-to-Cartesian back
transformation of molecular geometry
steps using high-order geometric
derivatives . . . . . . . . . . . . . . 1842--1849
Shaun M. Kandathil and
Timothy L. Fletcher and
Yongna Yuan and
Joshua Knowles and
Paul L. A. Popelier Accuracy and tractability of a kriging
model of intramolecular polarizable
multipolar electrostatics and its
application to histidine . . . . . . . . 1850--1861
Birgit Hischenhuber and
Hans Havlicek and
Jelena Todoric and
Sonja Höllrigl-Binder and
Wolfgang Schreiner and
Bernhard Knapp Software News and Updates: Differential
geometric analysis of alterations in MH$
\alpha $-helices . . . . . . . . . . . . 1862--1879
Anonymous Cover Image, Volume 34, Issue 22 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 22 . . . . . . . . . . . . . . . . iii--iv
Benjamin L. Moore and
Lawrence A. Kelley and
James Barber and
James W. Murray and
James T. MacDonald High-quality protein backbone
reconstruction from alpha carbons using
Gaussian mixture models . . . . . . . . 1881--1889
Stanislav Standara and
Petr Kulhánek and
Radek Marek and
Michal Straka $^{129}$Xe NMR chemical shift in
Xe@C$_{60}$ calculated at experimental
conditions: Essential role of the
relativity, dynamics, and explicit
solvent . . . . . . . . . . . . . . . . 1890--1898
Zhixiong Lin and
Wilfred F. van Gunsteren Influence of variation of a side chain
on the folding equilibrium of a $ \beta
$-peptide: Limitations of one-step
perturbation . . . . . . . . . . . . . . 1899--1906
Chandan Sahu and
Kaushik Sen and
Srimanta Pakhira and
Bhaskar Mondal and
Abhijit K. Das Binding affinity of substituted
ureido-benzenesulfonamide ligands to the
carbonic anhydrase receptor: a
theoretical study of enzyme inhibition 1907--1916
Anton S. Nizovtsev Activation of C--H bond in methane by Pd
atom from the bonding evolution theory
perspective . . . . . . . . . . . . . . 1917--1924
Priyanka Dhingra and
Bhyravabhotla Jayaram A homology/ab initio hybrid algorithm
for sampling near-native protein
conformations . . . . . . . . . . . . . 1925--1936
Steven Vancoillie and
Mickaël G. Delcey and
Roland Lindh and
Victor Vysotskiy and
Per-Åke Malmqvist and
Valera Veryazov Parallelization of a
multiconfigurational perturbation theory 1937--1948
Chuan Li and
Marharyta Petukh and
Lin Li and
Emil Alexov Continuous development of schemes for
parallel computing of the electrostatics
in biological systems: Implementation in
DelPhi . . . . . . . . . . . . . . . . . 1949--1960
José J. Baldoví and
Salvador Cardona-Serra and
Juan M. Clemente-Juan and
Eugenio Coronado and
Alejandro Gaita-Ariño and
Andrew Palii Software News and Updates: SIMPRE: a
software package to calculate crystal
field parameters, energy levels, and
magnetic properties on mononuclear
lanthanoid complexes based on charge
distributions . . . . . . . . . . . . . 1961--1967
Anonymous Cover Image, Volume 34, Issue 23 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 23 . . . . . . . . . . . . . . . . iii--iv
Yuichi Harano and
Roland Roth and
Shuntaro Chiba A morphometric approach for the accurate
solvation thermodynamics of proteins and
ligands . . . . . . . . . . . . . . . . 1969--1974
Daniel A. Götz and
Rolf Schäfer and
Peter Schwerdtfeger The performance of density functional
and wavefunction-based methods for $2$D
and $3$D structures of Au$_{10}$ . . . . 1975--1981
Takahiro Yamada and
Donald K. Phelps and
Adri C. T. van Duin First principle and ReaxFF molecular
dynamics investigations of formaldehyde
dissociation on Fe(100) surface . . . . 1982--1996
Yi Ren and
Xi-Guang Wei and
Si-Jia Ren and
Kai-Chung Lau and
Ning-Bew Wong and
Wai-Kee Li The $ \alpha $-effect exhibited in
gas-phase S$_N$2@N and S$_N$2@C
reactions . . . . . . . . . . . . . . . 1997--2005
Angelika Baranowska-\L\kaczkowska and
Krzysztof Z. \L\kaczkowski The ORP basis set designed for optical
rotation calculations . . . . . . . . . 2006--2013
Alexander V. Mitin Polarization functions for the modified
m6-31G basis sets for atoms Ga through
Kr . . . . . . . . . . . . . . . . . . . 2014--2019
Ringo Rey-Villaverde and
Hubert Cybulski and
Jesús R. Flores and
Berta Fernández A high-accuracy theoretical study of the
CH$_n$P systems $ n = 1 $--$3$ . . . . . 2020--2031
Likai Du and
Jun Gao and
Fuzhen Bi and
Lili Wang and
Chengbu Liu A polarizable ellipsoidal force field
for halogen bonds . . . . . . . . . . . 2032--2040
Ernesto Suárez and
Natalia Díaz and
Jefferson Méndez and
Dimas Suárez Software News and Updates: CENCALC: a
computational tool for conformational
entropy calculations from molecular
simulations . . . . . . . . . . . . . . 2041--2054
Anonymous Cover Image, Volume 34, Issue 24 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 24 . . . . . . . . . . . . . . . . iii--iv
Ge-Fei Hao and
Sheng-Gang Yang and
Guang-Fu Yang and
Chang-Guo Zhan Computational gibberellin-binding
channel discovery unraveling the
unexpected perception mechanism of
hormone signal by gibberellin receptor 2055--2064
Bin Tu and
Minxin Chen and
Yan Xie and
Linbo Zhang and
Bob Eisenberg and
Benzhuo Lu A parallel finite element simulator for
ion transport through three-dimensional
ion channel systems . . . . . . . . . . 2065--2078
Sérgio F. Sousa and
Gaspar R. P. Pinto and
António J. M. Ribeiro and
João T. S. Coimbra and
Pedro A. Fernandes and
Maria João Ramos Comparative analysis of the performance
of commonly available density
functionals in the determination of
geometrical parameters for copper
complexes . . . . . . . . . . . . . . . 2079--2090
Riadh Dardouri and
Héla Habli and
Brahim Oujia and
Florent Xavier Gadéa Ab Initio Diabatic energies and dipole
moments of the electronic states of RbLi
molecule . . . . . . . . . . . . . . . . 2091--2099
Xin Feng and
Kelin Xia and
Zhan Chen and
Yiying Tong and
Guo-Wei Wei Multiscale geometric modeling of
macromolecules II: Lagrangian
representation . . . . . . . . . . . . . 2100--2120
Paola Gramatica and
Nicola Chirico and
Ester Papa and
Stefano Cassani and
Simona Kovarich Software News and Updates: QSARINS: a
new software for the development,
analysis, and validation of QSAR MLR
models . . . . . . . . . . . . . . . . . 2121--2132
Kalipada Adhikari and
Sudip Chattopadhyay and
Barin Kumar De and
Amitava Sharma and
Ranendu Kumar Nath and
Dhiman Sinha Erratum: Search of truncation of $ (N -
1) $ electron basis containing full
connected triple excitations in
computing main and satellite ionization
potentials via Fock space coupled
cluster approach . . . . . . . . . . . . 2133--2133
Eric D. Glendening and
Clark R. Landis and
Frank Weinhold Erratum: NBO 6.0: Natural bond orbital
analysis program . . . . . . . . . . . . 2134--2134
Anonymous Cover Image, Volume 34, Issue 25 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 25 . . . . . . . . . . . . . . . . iii--iv
Jing Huang and
Alexander D. MacKerell Jr. CHARMM36 all-atom additive protein force
field: Validation based on comparison to
NMR data . . . . . . . . . . . . . . . . 2135--2145
Betsy M. Rice and
Edward F. C. Byrd Evaluation of electrostatic descriptors
for predicting crystalline density . . . 2146--2151
Shigeki Yamamoto and
Petr Bou\vr Transition polarizability model of
induced resonance Raman optical activity 2152--2158
Henry A. Boateng and
Robert Krasny Comparison of treecodes for computing
electrostatic potentials in charged
particle systems with disjoint targets
and sources . . . . . . . . . . . . . . 2159--2167
J. Grant Hill Auxiliary basis sets for density-fitting
second-order Mòller--Plesset perturbation
theory: Weighted core-valence
correlation consistent basis sets for
the $ 4 d $ elements Y--Pd . . . . . . . 2168--2177
Henrik R. Larsson and
Adri C. T. van Duin and
Bernd Hartke Global optimization of parameters in the
reactive force field ReaxFF for SiOH . . 2178--2189
José Fernando R. Bachega and
Luís Fernando S. M. Timmers and
Lucas Assirati and
Leonardo R. Bachega and
Martin J. Field and
Troy Wymore Software News and Updates: GTKDynamo: A
PyMOL plug-in for QC/MM hybrid potential
simulations . . . . . . . . . . . . . . 2190--2196
You-Liang Zhu and
Hong Liu and
Zhan-Wei Li and
Hu-Jun Qian and
Giuseppe Milano and
Zhong-Yuan Lu Software News and Updates: GALAMOST:
GPU-accelerated large-scale molecular
simulation toolkit . . . . . . . . . . . 2197--2211
Sally R. Ellingson and
Jeremy C. Smith and
Jerome Baudry Software News and Updates: VinaMPI:
Facilitating multiple receptor
high-throughput virtual docking on
high-performance computers . . . . . . . 2212--2221
Anonymous Cover Image, Volume 34, Issue 26 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 26 . . . . . . . . . . . . . . . . iii--iv
Tao Yang and
Xiang Zhao and
Shigeru Nagase 1,3-Dipolar cycloadditions of
Stone--Wales defective single-walled
carbon nanotubes: a theoretical study 2223--2232
Hyungjun Kim and
Joungwon Park and
Yoon Sup Lee A protocol to evaluate one electron
redox potential for iron complexes . . . 2233--2241
Laetitia Bomble and
Stephan N. Steinmann and
Nancy Perez-Peralta and
Gabriel Merino and
Clemence Corminboeuf Bonding analysis of planar
hypercoordinate atoms via the
generalized BLW-LOL . . . . . . . . . . 2242--2248
Athanasios Anthopoulos and
Ian Grimstead and
Andrea Brancale GPU-accelerated molecular mechanics
computations . . . . . . . . . . . . . . 2249--2260
Anna Stachowicz and
Jacek Korchowiec Bond detectors for molecular dynamics
simulations, Part I: Hydrogen bonds . . 2261--2269
Subha Kalyaanamoorthy and
Yi-Ping Phoebe Chen Ligand release mechanisms and channels
in histone deacetylases . . . . . . . . 2270--2283
Ilya A. Kaliman and
Lyudmila V. Slipchenko Software News and Updates: LIBEFP: a new
parallel implementation of the effective
fragment potential method as a portable
software library . . . . . . . . . . . . 2284--2292
Evgeny Epifanovsky and
Michael Wormit and
Tomasz Ku\'s and
Arie Landau and
Dmitry Zuev and
Kirill Khistyaev and
Prashant Manohar and
Ilya Kaliman and
Andreas Dreuw and
Anna I. Krylov Software News and Updates: New
implementation of high-level correlated
methods using a general block tensor
library for high-performance electronic
structure calculations . . . . . . . . . 2293--2309
Panagiotis I. Koukos and
Nicholas M. Glykos Software News and Updates: Grcarma: a
fully automated task-oriented interface
for the analysis of molecular dynamics
trajectories . . . . . . . . . . . . . . 2310--2312
Anonymous Cover Image, Volume 34, Issue 27 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 27 . . . . . . . . . . . . . . . . iii--iv
Steven K. Burger and
G. Andrés Cisneros Efficient optimization of van der Waals
parameters from bulk properties . . . . 2313--2319
Volker L. Deringer and
Marck Lumeij and
Ralf P. Stoffel and
Richard Dronskowski Ab initio study of the high-temperature
phase transition in crystalline GeO$_2$ 2320--2326
Sebastian Kozuch and
Jan M. L. Martin Spin-component-scaled double hybrids: an
extensive search for the best fifth-rung
functionals blending DFT and
perturbation theory . . . . . . . . . . 2327--2344
Tomoya Inui and
Yasuteru Shigeta and
Katsuki Okuno and
Takeshi Baba and
Ryohei Kishi and
Masayoshi Nakano Finite-field method with unbiased
polarizable continuum model for
evaluation of the second
hyperpolarizability of an open-shell
singlet molecule in solvents . . . . . . 2345--2352
Rahul Kar and
Jong-Won Song and
Takeshi Sato and
Kimihiko Hirao Long-range corrected density functionals
combined with local response dispersion:
a promising method for weak interactions 2353--2359
Camilo Velez-Vega and
Michael K. Gilson Overcoming dissipation in the
calculation of standard binding free
energies by ligand extraction . . . . . 2360--2371
Tiago Quevedo Teodoro and
Roberto Luiz Andrade Haiduke Accurate relativistic adapted Gaussian
basis sets for francium through
ununoctium without variational prolapse
and to be used with both uniform sphere
and Gaussian nucleus models . . . . . . 2372--2379
Yingdi Jin and
Erin R. Johnson and
Xiangqian Hu and
Weitao Yang and
Hao Hu Contributions of Pauli repulsions to the
energetics and physical properties
computed in QM/MM methods . . . . . . . 2380--2388
Rong-Zhen Liao and
Walter Thiel Convergence in the QM-only and QM/MM
modeling of enzymatic reactions: a case
study for acetylene hydratase . . . . . 2389--2397
Neil Qiang Su and
Igor Ying Zhang and
Xin Xu Erratum: Analytic derivatives for the
XYG3 type of doubly hybrid density
functionals: Theory, implementation, and
assessment . . . . . . . . . . . . . . . 2398--2399
M. E. Chen and
W. Yang Erratum: On-the-path random walk
sampling for efficient optimization of
minimum free energy path . . . . . . . . 2400--2400
M. Swart and
M. Sol\`a and
F. M. Bickelhaupt Corrigendum: Inter- and intramolecular
dispersion interactions . . . . . . . . 2401--2402
Anonymous Cover Image, Volume 34, Issue 28 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 28 . . . . . . . . . . . . . . . . iii--iv
Masashi Daido and
Yukio Kawashima and
Masanori Tachikawa Nuclear quantum effect and temperature
dependency on the hydrogen-bonded
structure of base pairs . . . . . . . . 2403--2411
Jaewoon Jung and
Takaharu Mori and
Yuji Sugita Efficient lookup table using a linear
function of inverse distance squared . . 2412--2420
Patrick Bultinck and
Sofie Van Damme and
Andrés Cedillo Bond Fukui indices: Comparison of frozen
molecular orbital and finite differences
through Mulliken populations . . . . . . 2421--2429
Annia Galano and
Juan Raúl Alvarez-Idaboy A computational methodology for accurate
predictions of rate constants in
solution: Application to the assessment
of primary antioxidant activity . . . . 2430--2445
Karl Wilkinson and
Chris-Kriton Skylaris Porting ONETEP to graphical processing
unit-based coprocessors. 1. FFT box
operations . . . . . . . . . . . . . . . 2446--2459
Erix Wiliam Hernández-Rodríguez and
Ana Lilian Montero-Alejo and
Rafael López and
Elsa Sánchez-García and
Luis Alberto Montero-Cabrera and
José Manuel García de la Vega Electron density deformations provide
new insights into the spectral shift of
rhodopsins . . . . . . . . . . . . . . . 2460--2471
Thomas Simonson and
Thomas Gaillard and
David Mignon and
Marcel Schmidt am Busch and
Anne Lopes and
Najette Amara and
Savvas Polydorides and
Audrey Sedano and
Karen Druart and
Georgios Archontis Computational protein design: the
Proteus software and selected
applications . . . . . . . . . . . . . . 2472--2484
Thorsten Will and
Michael C. Hutter and
Johann Jauch and
Volkhard Helms Software News and Updates: Batch
tautomer generation with MolTPC . . . . 2485--2492
Anonymous Cover Image, Volume 34, Issue 29 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 29 . . . . . . . . . . . . . . . . iii--iv
Satoru G. Itoh and
Hisashi Okumura Hamiltonian replica-permutation method
and its applications to an alanine
dipeptide and amyloid-$ \beta $ (29--42)
peptides . . . . . . . . . . . . . . . . 2493--2497
Masahiro Ehara and
Ryoichi Fukuda and
Carlo Adamo and
Ilaria Ciofini Chemically intuitive indices for
charge-transfer excitation based on
SAC-CI and TD-DFT calculations . . . . . 2498--2501
Carlos Campañá and
Ronald E. Miller Transiting the molecular potential
energy surface along low energy
pathways: The TRREAT algorithm . . . . . 2502--2513
Milan Randi\'c and
Marjana Novi\vc and
Marjan Vra\vcko and
Dejan Plav\vsi\'c On the centrality of vertices of
molecular graphs . . . . . . . . . . . . 2514--2523
Liang Xu and
Xiaojuan Wang and
Shengsheng Shan and
Xicheng Wang Characterization of the polymorphic
states of copper(II)-bound A$ \beta $
(1-16) peptides by computational
simulations . . . . . . . . . . . . . . 2524--2536
Otilia Mó and
Al Mokhtar Lamsabhi and
Manuel Yáñez and
Gavin S. Heverly-Coulson and
Russell J. Boyd Dramatic substituent effects on the
mechanisms of nucleophilic attack on
Se---S bridges . . . . . . . . . . . . . 2537--2547
José Rogan and
Alejandro Varas and
Juan Alejandro Valdivia and
Miguel Kiwi A strategy to find minimal energy
nanocluster structures . . . . . . . . . 2548--2556
Stefan Maintz and
Volker L. Deringer and
Andrei L. Tchougréeff and
Richard Dronskowski Analytic projection from plane-wave and
PAW wavefunctions and application to
chemical-bonding analysis in solids . . 2557--2567
Masato Tanaka and
Michio Katouda and
Shigeru Nagase Optimization of RI-MP2 Auxiliary Basis
Functions for 6-31G** and 6-311G** Basis
Sets for First-, Second-, and Third-Row
Elements . . . . . . . . . . . . . . . . 2568--2575
Anonymous Cover Image, Volume 34, Issue 30 . . . . i--ii
Anonymous Cover Image, Volume 34, Issue 30 . . . . iii--iv
Ol'ha O. Brovarets' and
Dmytro M. Hovorun Atomistic understanding of the C$ \cdot
$T mismatched DNA base pair
tautomerization via the DPT: QM and
QTAIM computational approaches . . . . . 2577--2590
Matthew A. Addicoat and
Syou Fukuoka and
Alister J. Page and
Stephan Irle Stochastic structure determination for
conformationally flexible heterogeneous
molecular clusters: Application to ionic
liquids . . . . . . . . . . . . . . . . 2591--2600
Hironori Kokubo and
Toshimasa Tanaka and
Yuko Okamoto Two-dimensional replica-exchange method
for predicting protein--ligand binding
structures . . . . . . . . . . . . . . . 2601--2614
Yu. D. Fomin Molecular dynamics simulation of benzene
in graphite and amorphous carbon slit
pores . . . . . . . . . . . . . . . . . 2615--2624
David Robinson Splitting multiple bonds: a comparison
of methodologies on the accuracy of bond
dissociation energies . . . . . . . . . 2625--2634
Mahesh R. Borkar and
Raghuvir R. S. Pissurlenkar and
Evans C. Coutinho HomoSAR: Bridging comparative protein
modeling with quantitative structural
activity relationship to design new
peptides . . . . . . . . . . . . . . . . 2635--2646
Woong-Hee Shin and
Jae-Kwan Kim and
Deok-Soo Kim and
Chaok Seok GalaxyDock2: Protein--ligand docking
using beta-complex and global
optimization . . . . . . . . . . . . . . 2647--2656
Victor P. Vysotskiy and
Jonas Boström and
Valera Veryazov Software News and Updates: a new module
for constrained multi-fragment geometry
optimization in internal coordinates
implemented in the MOLCAS package . . . 2657--2665
Anonymous Cover Image, Volume 34, Issue 31 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 31 . . . . . . . . . . . . . . . . iii--iv
Pekka Pyykkö The RTAM electronic bibliography,
version 17.0, on relativistic theory of
atoms and molecules . . . . . . . . . . 2667--2667
Leonardo Pacifici and
Marco Verdicchio and
Noelia Faginas Lago and
Andrea Lombardi and
Alessandro Costantini A high-level ab initio study of the
N$_2$ + N$_2$ reaction channel . . . . . 2668--2676
Juan Zeng and
Xiangyu Jia and
John Z. H. Zhang and
Ye Mei The F130L mutation in streptavidin
reduces its binding affinity to biotin
through electronic polarization effect 2677--2686
Marina \'Cendi\'c and
Zoran D. Matovi\'c and
Robert J. Deeth Molecular modeling for
Cu(II)-aminopolycarboxylate complexes:
Structures, conformational energies, and
ligand binding affinities . . . . . . . 2687--2696
Yung Ting Lee and
Jyh Shing Lin Ab Initio molecular dynamics study of
ethylene adsorption onto Si(001)
surface: Short-time Fourier transform
analysis of structural coordinate
autocorrelation function . . . . . . . . 2697--2706
Stella Nickerson and
Denzil S. Frost and
Harrison Phelan and
Lenore L. Dai Comparison of the capillary wave method
and pressure tensor route for
calculation of interfacial tension in
molecular dynamics simulations . . . . . 2707--2715
Tobias Neumann and
Denis Danilov and
Christian Lennartz and
Wolfgang Wenzel Modeling disordered morphologies in
organic semiconductors . . . . . . . . . 2716--2725
Gevorg Grigoryan Absolute free energies of biomolecules
from unperturbed ensembles . . . . . . . 2726--2741
Savvas Polydorides and
Thomas Simonson Monte Carlo simulations of proteins at
constant pH with generalized Born
solvent, flexible sidechains, and an
effective dielectric boundary . . . . . 2742--2756
Anonymous Cover Image, Volume 34, Issue 32 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 34,
Issue 32 . . . . . . . . . . . . . . . . iii--iv
Christopher G. Mayne and
Jan Saam and
Klaus Schulten and
Emad Tajkhorshid and
James C. Gumbart Rapid parameterization of small
molecules using the force field toolkit 2757--2770
David Schmidling A new set of bending T$_d$ symmetry
coordinates for MX$_4$ molecules . . . . 2771--2773
Vincent Hall and
Anthony Nash and
Evor Hines and
Alison Rodger Elucidating protein secondary structure
with circular dichroism and a neural
network . . . . . . . . . . . . . . . . 2774--2786
Yutaka Imamura and
Jun Suzuki and
Hiromi Nakai Kinetic energy decomposition scheme
based on information theory . . . . . . 2787--2795
Zhixiong Lin and
Wilfred F. van Gunsteren Refinement of the application of the
GROMOS 54A7 force field to $ \beta
$-peptides . . . . . . . . . . . . . . . 2796--2805
Jen-Ping Su and
Yung-Ting Lee and
Shao-Yu Lu and
Jyh Shing Lin Chemical mechanism of surface-enhanced
Raman scattering spectrum of pyridine
adsorbed on Ag cluster: Ab initio
molecular dynamics approach . . . . . . 2806--2815
Nandun M. Thellamurege and
Dejun Si and
Fengchao Cui and
Hongbo Zhu and
Rui Lai and
Hui Li Software News and Updates: QuanPol: a
full spectrum and seamless QM/MM program 2816--2833
B. Hischenhuber and
H. Havlicek and
J. Todoric and
S. Höllrigl-Binder and
W. Schreiner and
B. Knapp Corrigendum: Differential geometric
analysis of alterations in MH$ \alpha
$-helices . . . . . . . . . . . . . . . 2834--2834
Anonymous Cover Image, Volume 35, Issue 1 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 1 . . . . iii--iv
Anton Jesser and
Martin Rohrmüller and
Wolf Gero Schmidt and
Sonja Herres-Pawlis Geometrical and optical benchmarking of
copper guanidine--quinoline complexes:
Insights from TD-DFT and many-body
perturbation theory . . . . . . . . . . 1--17
Franziska D. Hofmann and
Michael Devereux and
Andreas Pfaltz and
Markus Meuwly Toward force fields for atomistic
simulations of iridium-containing
complexes . . . . . . . . . . . . . . . 18--29
Francesco Fracchia and
Claudia Filippi and
Claudio Amovilli Multi-level quantum Monte Carlo wave
functions for complex reactions: the
decomposition of $ \alpha
$-hydroxy-dimethylnitrosamine . . . . . 30--38
Jinzen Ikebe and
Shun Sakuraba and
Hidetoshi Kono Adaptive lambda square dynamics
simulation: an efficient conformational
sampling method for biomolecules . . . . 39--50
Soumya Ganguly Neogi and
Pinaki Chaudhury Structural, spectroscopic aspects, and
electronic properties of (TiO$_2$ )$_n$
clusters: a study based on the use of
natural algorithms in association with
quantum chemical methods . . . . . . . . 51--61
Pei-Kun Yang Incorporating the excluded solvent
volume and surface charges for computing
solvation free energy . . . . . . . . . 62--69
Zhijun Xu and
Yang Yang and
Ziqiu Wang and
Donald Mkhonto and
Cheng Shang and
Zhi-Pan Liu and
Qiang Cui and
Nita Sahai Small molecule-mediated control of
hydroxyapatite growth: Free energy
calculations benchmarked to density
functional theory . . . . . . . . . . . 70--81
Sébastien Canneaux and
Frédéric Bohr and
Eric Henon Software News and Updates: KiSThelP: a
program to predict thermodynamic
properties and rate constants from
quantum chemistry results . . . . . . . 82--93
Anonymous Cover Image, Volume 35, Issue 2 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 2 . . . . iii--iv
Andreas W. Götz and
Matthew A. Clark and
Ross C. Walker An extensible interface for QM/MM
molecular dynamics simulations with
AMBER . . . . . . . . . . . . . . . . . 95--108
Panwang Zhou and
Jianyong Liu and
Keli Han and
Guozhong He The photoisomerization of 11-cis-retinal
protonated Schiff base in gas phase:
Insight from spin-flip density
functional theory . . . . . . . . . . . 109--120
Feiwu Chen and
Zhihui Fan A new size extensive multireference
perturbation theory . . . . . . . . . . 121--129
Fabien Cailliez and
Arnaud Bourasseau and
Pascal Pernot Calibration of forcefields for molecular
simulation: Sequential design of
computer experiments for building
cost-efficient kriging metamodels . . . 130--149
Katja Ostermeir and
Martin Zacharias Hamiltonian replica-exchange simulations
with adaptive biasing of peptide
backbone and side chain dihedral angles 150--158
Shuai Jiang and
Yi-Rong Liu and
Teng Huang and
Hui Wen and
Kang-Ming Xu and
Wei-Xiong Zhao and
Wei-Jun Zhang and
Wei Huang Study of Cl$^-$ (H$_2$O)$_n$ ($n$ =
1--4) using basin-hopping method coupled
with density functional theory . . . . . 159--165
Satoshi Maeda and
Tetsuya Taketsugu and
Keiji Morokuma Exploring transition state structures
for intramolecular pathways by the
artificial force induced reaction method 166--173
Wenliang Li and
Jingping Zhang Multiscale simulation of pollution gases
adsorption in porous organic cage CC3 174--180
Anonymous Cover Image, Volume 35, Issue 3 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 3 . . . . iii--iv
Ivan Welsh and
Matthias Lein Accurate density functional theory
description of binding constants and NMR
chemical shifts of weakly interacting
complexes of C$_{60}$ with
corannulene-based molecular bowls . . . 181--191
Elisabeth Ortega-Carrasco and
Agusti Lledós and
Jean-Didier Maréchal Assessing protein--ligand docking for
the binding of organometallic compounds
to proteins . . . . . . . . . . . . . . 192--198
Angelika Baranowska-\L\kaczkowska and
Berta Fernández Basis sets for the evaluation of van der
Waals complex interaction energies:
Ne--N$_2$ intermolecular potential and
microwave spectrum . . . . . . . . . . . 199--203
Edoardo Fertitta and
Elena Voloshina and
Beate Paulus Adsorption of multivalent alkylthiols on
Au(111) surface: Insights from DFT . . . 204--213
Vishwesh Venkatraman and
Per-Olof Åstrand and
Bjòrn Kåre Alsberg Quantitative structure--property
relationship modeling of Grätzel solar
cell dyes . . . . . . . . . . . . . . . 214--226
Maria M. Reif and
Chris Oostenbrink Net charge changes in the calculation of
relative ligand-binding free energies
via classical atomistic molecular
dynamics simulation . . . . . . . . . . 227--243
Mahdi Shirazi and
Simon D. Elliott Atomistic kinetic Monte Carlo study of
atomic layer deposition derived from
density functional theory . . . . . . . 244--259
Magnus Lundborg and
Rossen Apostolov and
Daniel Spångberg and
Anders Gärdenäs and
David van der Spoel and
Erik Lindahl Software News and Updates: An efficient
and extensible format, library, and API
for binary trajectory data from
molecular simulations . . . . . . . . . 260--269
Anonymous Cover Image, Volume 35, Issue 4 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 4 . . . . iii--iv
Taro Udagawa and
Masanori Tachikawa Why is N\dottedbondBe distance of
NH$_3$H$^+$\dottedbondDBeH shorter than
that of NH$_3$D$^+$\dottedbondHBeH?
Paradoxical geometrical isotope effects
for partially isotope-substituted
dihydrogen-bonded isotopomers . . . . . 271--274
Marco Heinen and
Elshad Allahyarov and
Hartmut Löwen Highly asymmetric electrolytes in the
primitive model: Hypernetted chain
solution in arbitrary spatial dimensions 275--289
Otávio Beruski and
Luciano N. Vidal Algorithms for computer detection of
symmetry elements in molecular systems 290--299
Pai-Chi Li and
Naoyuki Miyashita and
Wonpil Im and
Satoshi Ishido and
Yuji Sugita Multidimensional umbrella sampling and
replica-exchange molecular dynamics
simulations for structure prediction of
transmembrane helix dimers . . . . . . . 300--308
Jorge A. Vila and
Yelena A. Arnautova and
Osvaldo A. Martin and
Harold A. Scheraga Are accurate computations of the
$^{13}$C' shielding feasible at the DFT
level of theory? . . . . . . . . . . . . 309--312
Vitaly N. Glushkov and
Xavier Assfeld Multireference space without first
solving the configuration interaction
problem . . . . . . . . . . . . . . . . 313--323
Dimas Suárez and
Natalia Díaz and
Ramón López A combined semiempirical and DFT
computational protocol for studying
bioorganometallic complexes: Application
to molybdocene--cysteine complexes . . . 324--334
Shide Liang and
Chi Zhang and
Yaoqi Zhou LEAP: Highly accurate prediction of
protein loop conformations by
integrating coarse-grained sampling and
optimized energy scores with all-atom
refinement of backbone and side chains 335--341
Anonymous Cover Image, Volume 35, Issue 5 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 5 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 5 . . . . v--vi
Yongna Yuan and
Matthew J. L. Mills and
Paul L. A. Popelier Multipolar electrostatics for proteins:
Atom--atom electrostatic energies in
crambin . . . . . . . . . . . . . . . . 343--359
Dina T. Mirijanian and
Ranjan V. Mannige and
Ronald N. Zuckermann and
Stephen Whitelam Development and use of an atomistic
CHARMM-based forcefield for peptoid
simulation . . . . . . . . . . . . . . . 360--370
Israel Fernández and
F. Matthias Bickelhaupt Origin of the ``endo rule'' in
Diels--Alder reactions . . . . . . . . . 371--376
David J. Huggins Comparing distance metrics for rotation
using the $k$-nearest neighbors
algorithm for entropy estimation . . . . 377--385
Alessandra Forni and
Stefano Pieraccini and
Stefano Rendine and
Maurizio Sironi Halogen bonds with benzene: an
assessment of DFT functionals . . . . . 386--394
Andrei V. Bandura and
Robert A. Evarestov TiS$_2$ and ZrS$_2$ single- and
double-wall nanotubes: First-principles
study . . . . . . . . . . . . . . . . . 395--405
Antti-Pekka Hynninen and
Michael F. Crowley Software News and Updates: New faster
CHARMM molecular dynamics engine . . . . 406--413
Anonymous Cover Image, Volume 35, Issue 6 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 6 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 6 . . . . v--vi
Shu-Shi Li and
Cui-Ying Huang and
Jiao-Jiao Hao and
Chang-Sheng Wang A polarizable dipole--dipole interaction
model for evaluation of the interaction
energies for NH\dottedbondOC and
CH\dottedbondOC hydrogen-bonded
complexes . . . . . . . . . . . . . . . 415--426
Pablo García-Risueño and
Joseba Alberdi-Rodriguez and
Micael J. T. Oliveira and
Xavier Andrade and
Michael Pippig and
Javier Muguerza and
Agustin Arruabarrena and
Angel Rubio A survey of the parallel performance and
accuracy of Poisson solvers for
electronic structure calculations . . . 427--444
Jie Chen and
Yulong Xu and
Dunyou Wang A multilayered representation, quantum
mechanical and molecular mechanics study
of the CH$_3$F $+$ OH$^-$ reaction in
water . . . . . . . . . . . . . . . . . 445--450
Ol'ha O. Brovarets' and
Roman O. Zhurakivsky and
Dmytro M. Hovorun Is the DPT tautomerization of the long
A$\cdot$G Watson--Crick DNA base mispair
a source of the adenine and guanine
mutagenic tautomers? A QM and QTAIM
response to the biologically important
question . . . . . . . . . . . . . . . . 451--466
Tonghao Shen and
Neil Qiang Su and
Anan Wu and
Xin Xu Perturbative treatment of anharmonic
vibrational effects on bond distances:
an extended Langevin dynamics method . . 467--478
Eric Van Dornshuld and
Gregory S. Tschumper Characterization of the potential energy
surfaces of two small but challenging
noncovalent dimers: (P$_2$)$_2$ and
(PCCP)$_2$ . . . . . . . . . . . . . . . 479--487
Leslie Sánchez and
Gonzalo A. Jaña and
Eduardo J. Delgado A QM/MM study on the reaction pathway
leading to $2$-Aceto-$2$-hydroxybutyrate
in the catalytic cycle of AHAS . . . . . 488--494
Abdullah Ozkanlar and
Aurora E. Clark Software News and Updates: ChemNetworks:
a complex network analysis tool for
chemical systems . . . . . . . . . . . . 495--505
Anonymous Cover Image, Volume 35, Issue 7 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 7 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 7 . . . . iv--v
Luís P. Viegas and
António J. C. Varandas Coupled-cluster reaction barriers of
HO$_2$ + H$_2$O + O$_3$: an application
of the coupled-cluster/Kohn--Sham
density functional theory model
chemistry . . . . . . . . . . . . . . . 507--517
Mateusz Maciejewski and
Paul N. Barlow and
Nico Tjandra Decoding the components of dynamics in
three-domain proteins . . . . . . . . . 518--525
Anita K. Nivedha and
Spandana Makeneni and
Bethany Lachele Foley and
Matthew B. Tessier and
Robert J. Woods Importance of ligand conformational
energies in carbohydrate docking:
Sorting the wheat from the chaff . . . . 526--539
Travis V. Harris and
Robert K. Szilagyi Iron--sulfur bond covalency from
electronic structure calculations for
classical iron--sulfur clusters . . . . 540--552
Katharina Krause and
Thomas Bredow Conductor-like screening model for
relaxed excited states: Implementation
in the semiempirical method MSINDO . . . 553--564
Alexey I. Baranov Electron localizability indicators from
spinor wavefunctions . . . . . . . . . . 565--585
Talapunur Vikramaditya and
Kanakamma Sumithra Effect of substitutionally boron-doped
single-walled semiconducting zigzag
carbon nanotubes on ammonia adsorption 586--594
Anonymous Cover Image, Volume 35, Issue 8 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 8 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 8 . . . . v--vi
Uppula Purushotham and
G. Narahari Sastry A comprehensive conformational analysis
of tryptophan, its ionic and dimeric
forms . . . . . . . . . . . . . . . . . 595--610
Elda Rossi and
Stefano Evangelisti and
Antonio Lagan\`a and
Antonio Monari and
Sergio Rampino and
Marco Verdicchio and
Kim K. Baldridge and
Gian Luigi Bendazzoli and
Stefano Borini and
Renzo Cimiraglia and
Celestino Angeli and
Peter Kallay and
Hans P. Lüthi and
Kenneth Ruud and
José Sanchez-Marin and
Anthony Scemama and
Peter G. Szalay and
Attila Tajti Code interoperability and standard data
formats in quantum chemistry and quantum
dynamics: The Q5/D5Cost data model . . . 611--621
Magnus Ringholm and
Dan Jonsson and
Kenneth Ruud A general, recursive, and open-ended
response code . . . . . . . . . . . . . 622--633
Tony Anacker and
Joachim Friedrich New accurate benchmark energies for
large water clusters: DFT is better than
expected . . . . . . . . . . . . . . . . 634--643
Kevin J. Maurice SSThread: Template-free protein
structure prediction by threading pairs
of contacting secondary structures
followed by assembly of overlapping
pairs . . . . . . . . . . . . . . . . . 644--656
Maarten G. Wolf and
Gerrit Groenhof Software News and Updates: Explicit
proton transfer in classical molecular
dynamics simulations . . . . . . . . . . 657--671
Kliment Olechnovi\vc and
\vCeslovas Venclovas Software News and Updates: Voronota: a
fast and reliable tool for computing the
vertices of the Voronoi diagram of
atomic balls . . . . . . . . . . . . . . 672--681
Anonymous Cover Image, Volume 35, Issue 9 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 9 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 9 . . . . v--vi
Sateesh Bandaru and
Niall J. English and
J. M. D. MacElroy Implicit and explicit solvent models for
modeling a bifunctional arene ruthenium
hydrogen-storage catalyst: a classical
and ab initio molecular simulation study 683--691
Hugh S. C. Martin and
Shantenu Jha and
Peter V. Coveney Comparative analysis of nucleotide
translocation through protein nanopores
using steered molecular dynamics and an
adaptive biasing force . . . . . . . . . 692--702
Kun Liu and
Yu-Xue Li and
Jia-Ling Su and
Bin Wang The reliability of DFT methods to
predict electronic structures and
minimum energy crossing point for
[Fe$^{IV}$O](OH)$_2$ models: a
comparison study with MCQDPT method . . 703--710
Pablo M. De Biase and
Suren Markosyan and
Sergei Noskov Microsecond simulations of DNA and ion
transport in nanopores with novel
ion--ion and ion--nucleotides effective
potentials . . . . . . . . . . . . . . . 711--721
Alexander Kurnosov and
Mario Cacciatore and
Antonio Lagan\`a and
Fernando Pirani and
Massimiliano Bartolomei and
Ernesto Garcia The effect of the intermolecular
potential formulation on the
state-selected energy exchange rate
coefficients in N$_2$--N$_2$ collisions 722--736
Xiangyu Jia and
Juan Zeng and
John Z. H. Zhang and
Ye Mei Accessing the applicability of polarized
protein-specific charge in linear
interaction energy analysis . . . . . . 737--747
Chaim Dryzun Continuous symmetry measures for complex
symmetry group . . . . . . . . . . . . . 748--755
Bruce M. Allen and
Paul K. Predecki and
Maciej Kumosa Software News and Updates: Integrating
open-source software applications to
build molecular dynamics systems . . . . 756--764
Anonymous Cover Image, Volume 35, Issue 10 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 10 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 10 . . . . v--vi
Anna K. Hildebrandt and
Matthias Dietzen and
Thomas Lengauer and
Hans-Peter Lenhof and
Ernst Althaus and
Andreas Hildebrandt Efficient computation of root mean
square deviations under rigid
transformations . . . . . . . . . . . . 765--771
José Diogo L. Dutra and
Thiago D. Bispo and
Ricardo O. Freire LUMPAC lanthanide luminescence software:
Efficient and user friendly . . . . . . 772--775
Tsvetan K. Zahariev and
Radomir I. Slavchov and
Alia V. Tadjer and
Anela N. Ivanova Fully atomistic molecular-mechanical
model of liquid alkane oils:
Computational validation . . . . . . . . 776--788
Oliwia M. Szklarczyk and
Stephan J. Bachmann and
Wilfred F. van Gunsteren A polarizable empirical force field for
molecular dynamics simulation of liquid
hydrocarbons . . . . . . . . . . . . . . 789--801
Gian Luigi Bendazzoli and
Muammar El Khatib and
Stefano Evangelisti and
Thierry Leininger The total Position Spread in
mixed-valence compounds: a study on the
H4+ model system . . . . . . . . . . . . 802--808
Cheng-chau Chiu and
Georgi N. Vayssilov and
Alexander Genest and
Armando Borgna and
Notker Rösch Predicting adsorption enthalpies on
silicalite and HZSM-5: a benchmark study
on DFT strategies addressing dispersion
interactions . . . . . . . . . . . . . . 809--819
Eric Iván Sánchez-Flores and
Rodrigo Chávez-Calvillo and
Todd A. Keith and
Gabriel Cuevas and
Tomás Rocha-Rinza and
Fernando Cortés-Guzmán Properties of atoms in electronically
excited molecules within the formalism
of TDDFT . . . . . . . . . . . . . . . . 820--828
Anonymous Cover Image, Volume 35, Issue 11 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 11 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 11 . . . . v--vi
Panaghiotis Karamanis and
Nicolás Otero and
Claude Pouchan and
Juan José Torres and
William Tiznado and
Aggelos Avramopoulos and
Manthos G. Papadopoulos Significant nonlinear-optical switching
capacity in atomic clusters built from
silicon and lithium: a combined ab
initio and density functional study . . 829--838
Michael F. Peintinger and
Thomas Bredow The cyclic cluster model at
Hartree--Fock level . . . . . . . . . . 839--846
Toshiaki Kawamura and
Minori Abe and
Masaichi Saito and
Masahiko Hada Quantum-chemical analyses of
aromaticity, UV spectra, and NMR
chemical shifts in
plumbacyclopentadienylidenes stabilized
by Lewis bases . . . . . . . . . . . . . 847--853
Arne Lüchow Maxima of |$ \Psi $ |2: a connection
between quantum mechanics and Lewis
structures . . . . . . . . . . . . . . . 854--864
Kazuaki Z. Takahashi Design of a reaction field using a
linear-combination-based isotropic
periodic sum method . . . . . . . . . . 865--875
Anita Plazinska and
Wojciech Plazinski and
Krzysztof Jozwiak Fast, metadynamics-based method for
prediction of the
stereochemistry-dependent relative free
energies of ligand--receptor
interactions . . . . . . . . . . . . . . 876--882
Ana E. Torres and
Guadalupe Castro and
Ricardo Pablo-Pedro and
Fernando Colmenares A two-step reaction scheme leading to
singlet carbene species that can be
detected under matrix conditions for the
reaction of Zr($^3$ F) with either
CH$_3$F or CH$_3$CN . . . . . . . . . . 883--890
Anonymous Cover Image, Volume 35, Issue 12 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 12 . . . . iii--iv
Anonymous Cover Image, Volume 35, Issue 12 . . . . v--vi
Sateesh Bandaru and
Niall J. English and
Andrew D. Phillips and
J. M. D. MacElroy Towards the design of novel boron- and
nitrogen-substituted ammonia-borane and
bifunctional arene ruthenium catalysts
for hydrogen storage . . . . . . . . . . 891--903
Yi-Quan Zhang and
Cheng-Lin Luo and
Qiang Zhang Exchange coupling and magnetic
anisotropy in a family of bipyrimidyl
radical-bridged dilanthanide complexes:
Density functional theory and ab initio
calculations . . . . . . . . . . . . . . 904--909
Karunakaran Remya and
Cherumuttathu H. Suresh Cooperativity and cluster growth
patterns in acetonitrile: a DFT study 910--922
Xinying Li Metalophilic interaction in gold halide:
Quantum chemical study of AuX (X =
F--At) . . . . . . . . . . . . . . . . . 923--931
Sam Z. Grinter and
Xiaoqin Zou A Bayesian statistical approach of
improving knowledge-based scoring
functions for protein--ligand
interactions . . . . . . . . . . . . . . 932--943
David Casanova How much tetraradical character is
present in the Si$_6$ Ge$_9$ cluster? 944--949
Petr Popov and
Sergei Grudinin Software News and Updates: Rapid
determination of RMSDs corresponding to
macromolecular rigid body motions . . . 950--956
Jong Cheol Jeong and
Sunhwan Jo and
Emilia L. Wu and
Yifei Qi and
Viviana Monje-Galvan and
Min Sun Yeom and
Lev Gorenstein and
Feng Chen and
Jeffery B. Klauda and
Wonpil Im Software News and Updates: ST-analyzer:
a Web-based user interface for
simulation trajectory analysis . . . . . 957--963
Anonymous Cover Image, Volume 35, Issue 13 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 13 . . . . iii--iv
Dong-Xia Zhao and
Zhong-Zhi Yang Investigation of the distinction between
van der Waals interaction and chemical
bonding based on the PAEM-MO diagram . . 965--977
David Ferro-Costas and
Ignacio Pérez-Juste and
Ricardo A. Mosquera Electronegativity estimator built on
QTAIM-based domains of the bond electron
density . . . . . . . . . . . . . . . . 978--985
Doreen Mollenhauer and
Nicola Gaston A balanced procedure for the treatment
of cluster--ligand interactions on gold
phosphine systems in catalysis . . . . . 986--997
Zhi Sun and
Henry F. Schaefer III and
Yaoming Xie and
Yongdong Liu and
Rugang Zhong The reactions of Cr(CO)$_6$, Fe(CO)$_5$,
and Ni(CO)$_4$ with O$_2$ yield viable
oxo-metal carbonyls . . . . . . . . . . 998--1009
Gennady N. Chuev and
Ivan Vyalov and
Nikolaj Georgi Extraction of site--site bridge
functions and effective pair potentials
from simulations of polar molecular
liquids . . . . . . . . . . . . . . . . 1010--1023
Georgios C. Boulougouris Free energy calculations, enhanced by a
Gaussian ansatz, for the ``chemical
work'' distribution . . . . . . . . . . 1024--1035
Paola Gramatica and
Stefano Cassani and
Nicola Chirico Software News and Updates: QSARINS-chem:
Insubria datasets and new QSAR/QSPR
models for environmental pollutants in
QSARINS . . . . . . . . . . . . . . . . 1036--1044
Anonymous Cover Image, Volume 35, Issue 14 . . . . i--ii
Anonymous Cover Image: Inside Cover, Volume 35,
Issue 14 . . . . . . . . . . . . . . . . iii--iv
Marc Raupach and
Stefanie Dehnen and
Ralf Tonner Quantitative investigation of bonding
characteristics in ternary Zintl anions:
Charge and energy analysis of [Sn$_2$
E$^{15}_2$ (ZnPh)]$^-$ (E$^{15}$ = Sb,
Bi) and [Sn$_2$ Sb$_5$
(ZnPh)$_2$]$^{3-}$ . . . . . . . . . . . 1045--1057
Haining Liu and
C. Heath Turner Oxygen adsorption characteristics on
hybrid carbon and boron-nitride
nanotubes . . . . . . . . . . . . . . . 1058--1063
Jaewoon Jung and
Takaharu Mori and
Yuji Sugita Midpoint cell method for hybrid (MPI +
OpenMP) parallelization of molecular
dynamics simulations . . . . . . . . . . 1064--1072
Emine Soyda\cs and
U\ugur Bozkaya Assessment of the orbital-optimized
coupled-electron pair theory for
thermochemistry and kinetics: Improving
on CCSD and CEPA(1) . . . . . . . . . . 1073--1081
Po-Jen Hsu A new perspective of shape recognition
to discover the phase transition of
finite-size clusters . . . . . . . . . . 1082--1092
Takao Tsuneda and
Raman K. Singh Reactivity index based on orbital
energies . . . . . . . . . . . . . . . . 1093--1100
Biao Fu and
Aleksandr B. Sahakyan and
Carlo Camilloni and
Gian Gaetano Tartaglia and
Emanuele Paci and
Amedeo Caflisch and
Michele Vendruscolo and
Andrea Cavalli Software News and Updates: ALMOST: an
all atom molecular simulation toolkit
for protein structure determination . . 1101--1105
Anonymous Cover Image, Volume 35, Issue 15 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 15 . . . . iii--iv
Hui Zhu and
Zheng-Wang Qu Toward product control in ring-opening
oligomerization of 9H-9-borafluorenes 1107--1110
Fei Xia and
Dudu Tong and
Lifeng Yang and
Dayong Wang and
Steven C. H. Hoi and
Patrice Koehl and
Lanyuan Lu Identifying essential pairwise
interactions in elastic network model
using the alpha shape theory . . . . . . 1111--1121
Xin Yan and
Jiabo Li and
Qiong Gu and
Jun Xu gWEGA: GPU-accelerated WEGA for
molecular superposition and shape
comparison . . . . . . . . . . . . . . . 1122--1130
Ad\`ele D. Laurent and
Vitaly N. Glushkov and
Thibaut Very and
Xavier Assfeld Toward the understanding of the
environmental effects on core
ionizations . . . . . . . . . . . . . . 1131--1139
Shinichi Yamabe and
Guixiang Zeng and
Wei Guan and
Shigeyoshi Sakaki S$_N$1--S$_N$2 and S$_N$2--S$_N$3
mechanistic changes revealed by
transition states of the hydrolyses of
benzyl chlorides and benzenesulfonyl
chlorides . . . . . . . . . . . . . . . 1140--1148
Martin Carlsen Using operators to expand the block
matrices forming the Hessian of a
molecular potential . . . . . . . . . . 1149--1158
Solen Ekesan and
Seyit Kale and
Judith Herzfeld Transferable pseudoclassical electrons
for aufbau of atomic ions . . . . . . . 1159--1164
Anonymous Cover Image, Volume 35, Issue 16 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 16 . . . . iii--iv
Chérif F. Matta Modeling biophysical and biological
properties from the characteristics of
the molecular electron density, electron
localization and delocalization
matrices, and the electrostatic
potential . . . . . . . . . . . . . . . 1165--1198
Nicodemo Di Pasquale and
Richard J. Gowers and
Paola Carbone A multiple time step scheme for
multiresolved models of macromolecules 1199--1207
Alexander Mirzoev and
Alexander P. Lyubartsev Systematic implicit solvent coarse
graining of
dimyristoylphosphatidylcholine lipids 1208--1218
Alexey Savelyev and
Alexander D. MacKerell Jr. All-atom polarizable force field for DNA
based on the classical Drude oscillator
model . . . . . . . . . . . . . . . . . 1219--1239
Takeshi Baba and
Ryuhei Harada and
Masayoshi Nakano and
Yasuteru Shigeta On the induced-fit mechanism of
substrate-enzyme binding structures of
nylon-oligomer hydrolase . . . . . . . . 1240--1247
Phillip V. Smith and
Marian W. Radny and
G. Ali Shah Surface electronic structure
calculations using the MBJLDA potential:
Application to Si(111)2 $ \times $ 1 . . 1248--1254
Bingjie Hu and
Markus A. Lill Software News and Updates: WATsite:
Hydration site prediction program with
PyMOL interface . . . . . . . . . . . . 1255--1260
Anonymous Cover Image, Volume 35, Issue 17 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 17 . . . . iii--iv
Marcos Mandado and
Nicolás Ramos-Berdullas Analyzing the electric response of
molecular conductors using ``electron
deformation'' orbitals and
occupied-virtual electron transfer . . . 1261--1269
Olga E. Glukhova and
Anna S. Kolesnikova and
Michael M. Slepchenkov and
Vladislav V. Shunaev Moving of fullerene between potential
wells in the external icosahedral shell 1270--1277
Olivia Wise and
Orkid Coskuner New force field parameters for
metalloproteins I: Divalent copper ion
centers including three histidine
residues and an oxygen-ligated amino
acid residue . . . . . . . . . . . . . . 1278--1289
Alba Campo-Cacharrón and
Enrique M. Cabaleiro-Lago and
Jorge A. Carrazana-García and
Jesús Rodríguez-Otero Interaction of aromatic units of amino
acids with guanidinium cation: the
interplay of $ \pi \cdots \pi $, XH$
\cdots \pi $ and M$^+ \cdots \pi$
contacts . . . . . . . . . . . . . . . . 1290--1301
Kin-Yiu Wong and
Yuqing Xu and
Darrin M. York Ab initio path-integral calculations of
kinetic and equilibrium isotope effects
on base-catalyzed RNA
transphosphorylation models . . . . . . 1302--1316
Mikhail Panshenskov and
Ilia A. Solov'yov and
Andrey V. Solov'yov Software News and Updates: Efficient
$3$D kinetic Monte Carlo method for
modeling of molecular structure and
dynamics . . . . . . . . . . . . . . . . 1317--1329
César Mogo and
João Brandão Software News and Updates: The READY
program: Building a global potential
energy surface and reactive dynamic
simulations for the hydrogen combustion 1330--1337
Anonymous Cover Image, Volume 35, Issue 18 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 18 . . . . iii--iv
Ariadna Blanca Romero and
Piotr M. Kowalski and
George Beridze and
Hartmut Schlenz and
Dirk Bosbach Performance of DFT+ U method for
prediction of structural and
thermodynamic parameters of
monazite-type ceramics . . . . . . . . . 1339--1346
Yutaka Maruyama and
Norio Yoshida and
Hiroto Tadano and
Daisuke Takahashi and
Mitsuhisa Sato and
Fumio Hirata Massively parallel implementation of
$3$D-RISM calculation with volumetric
$3$D-FFT . . . . . . . . . . . . . . . . 1347--1355
Emilio San-Fabián and
Federico Moscardó Cyclobutadiene automerization and
rotation of ethylene: Energetics of the
barriers by using spin-polarized wave
functions . . . . . . . . . . . . . . . 1356--1363
Song-Ho Chong and
Sihyun Ham Site-directed analysis on protein
hydrophobicity . . . . . . . . . . . . . 1364--1370
Thomas Gaillard and
Thomas Simonson Pairwise decomposition of an MMGBSA
energy function for computational
protein design . . . . . . . . . . . . . 1371--1387
Gregory K. Pierens $^1$H and $^{13}$C NMR scaling factors
for the calculation of chemical shifts
in commonly used solvents using density
functional theory . . . . . . . . . . . 1388--1394
César R. García-Jacas and
Yovani Marrero-Ponce and
Liesner Acevedo-Martínez and
Stephen J. Barigye and
José R. Valdés-Martiní and
Ernesto Contreras-Torres Software News and Updates:
QuBiLS--MIDAS: a parallel free-software
for molecular descriptors computation
based on multilinear algebraic maps . . 1395--1409
Anonymous Cover Image, Volume 35, Issue 19 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 19 . . . . iii--iv
Daniel Roston and
Amnon Kohen and
Dvir Doron and
Dan T. Major Simulations of remote mutants of
dihydrofolate reductase reveal the
nature of a network of residues coupled
to hydride transfer . . . . . . . . . . 1411--1417
Roberta P. Dias and
Lin Li and
Thereza A. Soares and
Emil Alexov Modeling the electrostatic potential of
asymmetric lipopolysaccharide membranes:
The MEMPOT algorithm implemented in
DelPhi . . . . . . . . . . . . . . . . . 1418--1429
Hsin-Lin Chiang and
Chun-Jung Chen and
Hisashi Okumura and
Chin-Kun Hu Transformation between $ \alpha $-helix
and $ \beta $-sheet structures of one
and two polyglutamine peptides in
explicit water molecules by
replica-exchange molecular dynamics
simulations . . . . . . . . . . . . . . 1430--1437
Steven K. Burger and
Paul W. Ayers and
Jeremy Schofield Efficient parameterization of torsional
terms for force fields . . . . . . . . . 1438--1445
Zden\vek Futera and
Jaroslav V. Burda Reaction mechanism of Ru(II) piano-stool
complexes: Umbrella sampling QM/MM MD
study . . . . . . . . . . . . . . . . . 1446--1456
Frans T. I. Marx and
Johan H. L. Jordaan and
Gerhard Lachmann and
Hermanus C. M. Vosloo A Molecular modeling study of the
changes of some steric properties of the
precatalysts during the olefin
metathesis reaction . . . . . . . . . . 1457--1463
Frans T. I. Marx and
Johan H. L. Jordaan and
Gerhard Lachmann and
Hermanus C. M. Vosloo A comparison of low and high activity
precatalysts: Do the calculated energy
barriers during the self-metathesis
reaction of 1-Octene correlate with the
precatalyst metathesis activity? . . . . 1464--1471
Anonymous Cover Image, Volume 35, Issue 20 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 20 . . . . iii--iv
Masaki Okoshi and
Hiromi Nakai Acceleration of self-consistent field
convergence in ab initio molecular
dynamics simulation with
multiconfigurational wave function . . . 1473--1480
Lewis C. Smeeton and
Mark T. Oakley and
Roy L. Johnston Visualizing energy landscapes with
metric disconnectivity graphs . . . . . 1481--1490
Hao Hu and
Lin Shen In silico concurrent multisite pH
titration in proteins . . . . . . . . . 1491--1498
Frank Weinhold and
Paul von Ragué Schleyer and
William Chadwick McKee Bay-type H$ \cdots $H ``bonding'' in
cis-$2$-butene and related species:
QTAIM versus NBO description . . . . . . 1499--1508
Tobias Risthaus and
Marc Steinmetz and
Stefan Grimme Implementation of nuclear gradients of
range-separated hybrid density
functionals and benchmarking on
rotational constants for organic
molecules . . . . . . . . . . . . . . . 1509--1516
Masao Hayami and
Junji Seino and
Hiromi Nakai Extension of accompanying coordinate
expansion and recurrence relation method
for general-contraction basis sets . . . 1517--1527
Hung Dien and
Charlotte M. Deane and
Bernhard Knapp Software News and Updates: Gro2mat: a
package to efficiently read \tt gromacs
output in MATLAB . . . . . . . . . . . . 1528--1531
Anonymous Cover Image, Volume 35, Issue 21 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 21 . . . . iii--iv
Alba Campo-Cacharrón and
Enrique M. Cabaleiro-Lago and
Jesús Rodríguez-Otero Interaction between ions and substituted
buckybowls: a comprehensive
computational study . . . . . . . . . . 1533--1544
Ahmed A. K. Mohammed and
Steven K. Burger and
Paul W. Ayers Drug release by pH-responsive molecular
tweezers: Atomistic details from
molecular modeling . . . . . . . . . . . 1545--1551
Ji\vrí Kessler and
Petr Bou\vr Molecular dynamics with helical periodic
boundary conditions . . . . . . . . . . 1552--1559
Po-Chun Liu and
Wei-Ping Hu The MC-DFT approach including the
SCS-MP2 energies to the new
minnesota-type functionals . . . . . . . 1560--1567
Gurpreet Kaur and
Vikas On the mechanism of intramolecular
nitrogen-atom hopping in the carbon
chain of C$_6$N radical: a plausible
3c--4e crossover $ \pi $--long-bond . . 1568--1576
Mike Devereux and
Nohad Gresh and
Jean-Philip Piquemal and
Markus Meuwly A supervised fitting approach to force
field parametrization with application
to the SIBFA polarizable force field . . 1577--1591
Shun Sakuraba and
Nobuyuki Matubayasi Software News and Updates: Ermod: Fast
and versatile computation software for
solvation free energy with approximate
theory of solutions . . . . . . . . . . 1592--1608
Anonymous Cover Image, Volume 35, Issue 22 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 22 . . . . iii--iv
Pooria Farahani and
Daniel Roca-Sanjuán and
Francesco Aquilante Review: a two-scale approach to electron
correlation in multiconfigurational
perturbation theory . . . . . . . . . . 1609--1617
Johannes M. Dieterich and
Bernd Hartke A graph-based short-cut to low-energy
structures . . . . . . . . . . . . . . . 1618--1620
Sergio A. Hassan Implicit treatment of solvent dispersion
forces in protein simulations . . . . . 1621--1629
My-Phuong Pham and
Buu Q. Pham and
Lam K. Huynh and
Ha Q. Pham and
Maurice J. Marks and
Thanh N. Truong Density functional theory study on
mechanisms of epoxy-phenol curing
reaction . . . . . . . . . . . . . . . . 1630--1640
Maxim R. Ryzhikov and
Vladimir A. Slepkov and
Svetlana G. Kozlova and
Svyatoslav P. Gabuda Evolution of chemical bonding and
electron density rearrangements during
D$_{3h}$ D$_{3d}$ reaction in
monolayered TiS$_2$: a QTAIM and ELF
study . . . . . . . . . . . . . . . . . 1641--1645
Yunju Zhang and
Jingyu Sun and
Wanqiao Zhang and
Yizhen Tang and
Rongshun Wang Theoretical study on the gas phase
reaction of propargyl alcohol with
hydroxyl radical . . . . . . . . . . . . 1646--1656
Pei Zhao and
Tao Yang and
Yi-Jun Guo and
Jing-Shuang Dang and
Xiang Zhao and
Shigeru Nagase Dimetallic sulfide endohedral
metallofullerene Sc$_2$S@C$_{76}$:
Density functional theory
characterization . . . . . . . . . . . . 1657--1663
Xinying Li Erratum: Metalophilic interaction in
gold halide: Quantum chemical study of
AuX (X = F--At) . . . . . . . . . . . . 1664--1664
Anonymous Cover Image, Volume 35, Issue 23 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 23 . . . . iii--iv
Mariano Spivak and
Celestino Angeli and
Carmen J. Calzado and
Coen de Graaf Improving the calculation of magnetic
coupling constants in MRPT methods . . . 1665--1671
Kirill Zinovjev and
Iñaki Tuñón Exploring chemical reactivity of complex
systems with path-based coordinates:
Role of the distance metric . . . . . . 1672--1681
Weihong Zhang and
Jianhan Chen Replica exchange with guided annealing
for accelerated sampling of disordered
protein conformations . . . . . . . . . 1682--1689
Zhong-Zhi Yang and
Jian-Jiang Wang and
Dong-Xia Zhao Valence state parameters of all
transition metal atoms in
metalloproteins --- development of
ABEEM$ \sigma \pi $ fluctuating charge
force field . . . . . . . . . . . . . . 1690--1706
Soran Jahangiri and
Lemin Cai and
Gilles H. Peslherbe Performance of density-functional
tight-binding models in describing
hydrogen-bonded anionic-water clusters 1707--1715
Sebastian Höfener Coupled-cluster frozen-density embedding
using resolution of the identity methods 1716--1724
Marcela Hrdá and
Tomá\vs Kulich and
Michal Repiský and
Jozef Noga and
Olga L. Malkina and
Vladimir G. Malkin Software News and Updates:
Implementation of the
diagonalization-free algorithm in the
self-consistent field procedure within
the four-component relativistic scheme 1725--1737
Anonymous Cover Image, Volume 35, Issue 24 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 24 . . . . iii--iv
Miros\law Jab\lo\'nski Red and blue shifted hydridic bonds . . 1739--1747
Laura J. Kingsley and
Markus A. Lill Including ligand-induced protein
flexibility into protein tunnel
prediction . . . . . . . . . . . . . . . 1748--1756
Sean M. Law and
Aaron T. Frank and
Charles L. Brooks III PCASSO: a fast and efficient
C$\alpha$-based method for accurately
assigning protein secondary structure
elements . . . . . . . . . . . . . . . . 1757--1761
Athanassios C. Tsipis DFT assessment of the spectroscopic
constants and absorption spectra of
neutral and charged diatomic species of
group 11 and 14 elements . . . . . . . . 1762--1777
Soroosh Pezeshki and
Hai Lin Molecular dynamics simulations of ion
solvation by flexible-boundary QM/MM:
On-the-fly partial charge transfer
between QM and MM subsystems . . . . . . 1778--1788
Marco Lorenz and
Bartolomeo Civalleri and
Lorenzo Maschio and
Mauro Sgroi and
Daniele Pullini Benchmarking dispersion and geometrical
counterpoise corrections for
cost-effective large-scale DFT
calculations of water adsorption on
graphene . . . . . . . . . . . . . . . . 1789--1800
Christoph Grebner and
Johannes Becker and
Daniel Weber and
Daniel Bellinger and
Maxim Tafipolski and
Charlotte Brückner and
Bernd Engels Software News and Updates: CAST: a new
program package for the accurate
characterization of large and flexible
molecular systems . . . . . . . . . . . 1801--1807
Anonymous Cover Image, Volume 35, Issue 25 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 25 . . . . iii--iv
Morten N. Pedersen and
Erik D. Hedegård and
Jacob Kongsted Basis set error estimation for DFT
calculations of electronic g-tensors for
transition metal complexes . . . . . . . 1809--1814
Stefano Pelloni and
Inmaculada García Cuesta CCSD--CTOCD static dipole shielding
polarizability for quantification of the
chiral NMR effects in oxaziridine
derivatives . . . . . . . . . . . . . . 1815--1823
David Ryan Koes and
Carlos J. Camacho Shape-based virtual screening with
volumetric aligned molecular shapes . . 1824--1834
Tatsuki Negami and
Kentaro Shimizu and
Tohru Terada Coarse-grained molecular dynamics
simulations of protein--ligand binding 1835--1845
Carlos T. Nieto and
David Díez and
Narciso M. Garrido To be or not to be butterfly: New
mechanistic insights in the Aza--Michael
asymmetric addition of lithium
(R)-N-benzyl-N-($ \alpha
$-methylbenzyl)amide . . . . . . . . . . 1846--1853
Pablo G. Garay and
Osvaldo A. Martin and
Harold A. Scheraga and
Jorge A. Vila Factors affecting the computation of the
$^{13}$C shielding in disaccharides . . 1854--1864
Mirco Zerbetto and
Andrea Piserchia and
Diego Frezzato Looking for some free energy? Call
JEFREE (\ldots) . . . . . . . . . . . . 1865--1881
Anonymous Cover Image, Volume 35, Issue 26 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 26 . . . . iii--iv
Kiamars Eskandari and
Christian Van Alsenoy Hydrogen--hydrogen interaction in planar
biphenyl: a theoretical study based on
the interacting quantum atoms and
Hirshfeld atomic energy partitioning
methods . . . . . . . . . . . . . . . . 1883--1889
Thong Nguyen-Minh Le and
Bin Liu and
Lam K. Huynh SurfKin: an ab initio kinetic code for
modeling surface reactions . . . . . . . 1890--1899
Jan Wenzel and
Michael Wormit and
Andreas Dreuw Calculating core-level excitations and
X-ray absorption spectra of medium-sized
closed-shell molecules with the
algebraic--diagrammatic construction
scheme for the polarization propagator 1900--1915
Mohammad Reza Rezapour and
Arunkumar Chitteth Rajan and
Kwang S. Kim Molecular sensing using armchair
graphene nanoribbon . . . . . . . . . . 1916--1920
Ivana Matanovi\'c and
Plamen Atanassov and
Boris Kiefer and
Fernando H. Garzon and
Neil J. Henson Applicability of density functional
theory in reproducing accurate
vibrational spectra of surface bound
species . . . . . . . . . . . . . . . . 1921--1929
José J. Baldoví and
Juan M. Clemente-Juan and
Eugenio Coronado and
Alejandro Gaita-Ariño and
Andrew Palii Letters to the Editor: An updated
version of the computational package
SIMPRE that uses the standard
conventions for Stevens crystal field
parameters . . . . . . . . . . . . . . . 1930--1934
Miros\law Karbowiak and
Czes\law Rudowicz Letters to the Editor: Software package
SIMPRE --- Revisited . . . . . . . . . . 1935--1941
Anonymous Cover Image, Volume 35, Issue 27 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 27 . . . . iii--iv
Alexander Hoffmann and
Richard Grunzke and
Sonja Herres-Pawlis Insights into the influence of
dispersion correction in the theoretical
treatment of guanidine--quinoline
copper(I) complexes . . . . . . . . . . 1943--1950
Chanin Nantasenamat and
Saw Simeon and
Wiwat Owasirikul and
Napat Songtawee and
Maris Lapins and
Virapong Prachayasittikul and
Jarl E. S. Wikberg Illuminating the origins of spectral
properties of green fluorescent proteins
via proteochemometric and molecular
modeling . . . . . . . . . . . . . . . . 1951--1966
Xiao-Jing Liu and
Ian Hamilton Adsorption of small molecules on helical
gold nanorods: a relativistic density
functional study . . . . . . . . . . . . 1967--1976
Manoj K. Shukla and
Frances Hill Plane-wave density functional theory
investigation of adsorption of
2,4,6-trinitrotoluene on Al-hydroxylated
(0001) surface of ($ 4 \times 4$) $
\alpha $-alumina . . . . . . . . . . . . 1977--1985
Wei Chen and
Jana K. Shen Effects of system net charge and
electrostatic truncation on all-atom
constant pH molecular dynamics . . . . . 1986--1996
Emilia L. Wu and
Xi Cheng and
Sunhwan Jo and
Huan Rui and
Kevin C. Song and
Eder M. Dávila-Contreras and
Yifei Qi and
Jumin Lee and
Viviana Monje-Galvan and
Richard M. Venable and
Jeffery B. Klauda and
Wonpil Im Software News and Updates: CHARMM--GUI
Membrane Builder toward realistic
biological membrane simulations . . . . 1997--2004
Alessandro Di Domizio and
Alessandro Vitriolo and
Giulio Vistoli and
Alessandro Pedretti Software News and Updates: SPILLO--PBSS:
Detecting hidden binding sites within
protein $3$D-structures through a
flexible structure-based approach . . . 2005--2017
Anonymous Cover Image, Volume 35, Issue 28 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 28 . . . . iii--iv
Annia Galano and
Juan Raúl Alvarez-Idaboy Kinetics of radical-molecule reactions
in aqueous solution: a benchmark study
of the performance of density functional
methods . . . . . . . . . . . . . . . . 2019--2026
Julia Setzler and
Carolin Seith and
Martin Brieg and
Wolfgang Wenzel SLIM: an improved generalized Born
implicit membrane model . . . . . . . . 2027--2039
James Lyons and
Abdollah Dehzangi and
Rhys Heffernan and
Alok Sharma and
Kuldip Paliwal and
Abdul Sattar and
Yaoqi Zhou and
Yuedong Yang Predicting backbone C$ \alpha $ angles
and dihedrals from protein sequences by
stacked sparse auto-encoder deep neural
network . . . . . . . . . . . . . . . . 2040--2046
Minhajul Arfeen and
Dhilon S. Patel and
Sheenu Abbat and
Nikhil Taxak and
Prasad V. Bharatam Importance of cytochromes in cyclization
reactions: Quantum chemical study on a
model reaction of proguanil to
cycloguanil . . . . . . . . . . . . . . 2047--2055
Taweetham Limpanuparb and
Josh Milthorpe and
Alistair P. Rendell Resolutions of the Coulomb operator:
VIII. Parallel implementation using the
modern programming language X10 . . . . 2056--2069
Martin P. Andersson and
Susan L. S. Stipp Predicting hydration energies for
multivalent ions . . . . . . . . . . . . 2070--2075
Saleh Riahi and
Christopher N. Rowley Software News and Updates: The
CHARMM--TURBOMOLE interface for
efficient and accurate QM/MM molecular
dynamics, free energies, and excited
state properties . . . . . . . . . . . . 2076--2086
Anonymous Cover Image, Volume 35, Issue 29 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 29 . . . . iii--iv
Laercio Pol-Fachin and
Hugo Verli and
Roberto D. Lins Extension and validation of the GROMOS
53A6$_{glyc}$ parameter set for
glycoproteins . . . . . . . . . . . . . 2087--2095
Nohad Gresh and
Krystel El Hage and
David Perahia and
Jean-Philip Piquemal and
Catherine Berthomieu and
Dorothée Berthomieu Polarizable molecular mechanics studies
of Cu(I)/Zn(II) superoxide dismutase:
Bimetallic binding site and structured
waters . . . . . . . . . . . . . . . . . 2096--2106
Marta E. Alberto and
Gloria Mazzone and
Angelo D. Quartarolo and
Flavio Fortes Ramos Sousa and
Emilia Sicilia and
Nino Russo Electronic spectra and intersystem
spin-orbit coupling in 1,2- and
1,3-squaraines . . . . . . . . . . . . . 2107--2113
Xavier Lucas and
Stefan Günther Using chiral molecules as an approach to
address low-druggability recognition
sites . . . . . . . . . . . . . . . . . 2114--2121
Oliver Sala and
Hans Peter Lüthi and
Antonio Togni The solvent effect on two competing
reaction mechanisms involving
hypervalent iodine reagents ($
\lambda^3$-iodanes): Facing the limit of
the stationary quantum chemical approach 2122--2131
Junya Yamagishi and
Noriaki Okimoto and
Gentaro Morimoto and
Makoto Taiji A new set of atomic radii for accurate
estimation of solvation free energy by
Poisson--Boltzmann solvent model . . . . 2132--2139
Israel Fernández and
Lando P. Wolters and
F. Matthias Bickelhaupt Controlling the oxidative addition of
aryl halides to Au(I) . . . . . . . . . 2140--2145
Alexander Hoffmann and
Martin Rohrmüller and
Anton Jesser and
Ines dos Santos Vieira and
Wolf Gero Schmidt and
Sonja Herres-Pawlis Geometrical and optical benchmarking of
copper(II) guanidine--quinoline
complexes: Insights from TD--DFT and
many-body perturbation theory (part II) 2146--2161
Anonymous Cover Image, Volume 35, Issue 30 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 30 . . . . iii--iv
Ryoichi Fukuda and
Masahiro Ehara Efficiency of perturbation-selection and
its orbital dependence in the SAC--CI
calculations for valence excitations of
medium-size molecules . . . . . . . . . 2163--2176
Huiying Zhao and
Yuedong Yang and
Mark von Itzstein and
Yaoqi Zhou Carbohydrate-binding protein
identification by coupling structural
similarity searching with binding
affinity prediction . . . . . . . . . . 2177--2183
Olle Falklöf and
Bo Durbeej Distinguishing between keto--enol and
acid--base forms of firefly oxyluciferin
through calculation of excited-state
equilibrium constants . . . . . . . . . 2184--2194
Shinichi Yamabe and
Guixiang Zeng and
Wei Guan and
Shigeyoshi Sakaki A DFT study on proton transfers in
hydrolysis reactions of phosphate
dianion and sulfate monoanion . . . . . 2195--2204
Yonaton Heit and
Gregory J. O. Beran Exploiting space-group symmetry in
fragment-based molecular crystal
calculations . . . . . . . . . . . . . . 2205--2214
Vincent A. Voelz and
Guangfeng Zhou Bayesian inference of conformational
state populations from computational
models and sparse experimental
observables . . . . . . . . . . . . . . 2215--2224
Dan Berco and
Chin-Kun Hu A spherical harmonic transform spectral
analysis of a localized surface plasmon
on a gold nano shell . . . . . . . . . . 2225--2230
Anonymous Cover Image, Volume 35, Issue 31 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 31 . . . . iii--iv
Bing Fu and
Li Chen and
Feifei Wang and
Yiqun Xie and
Xiang Ye Melting of icosahedral nickel clusters
under hydrostatic pressure . . . . . . . 2231--2238
Jörg von Appen and
Richard Dronskowski and
Aurab Chakrabarty and
Tilmann Hickel and
Robert Spatschek and
Jörg Neugebauer Impact of Mn on the solution enthalpy of
hydrogen in austenitic Fe--Mn alloys: a
first-principles study . . . . . . . . . 2239--2244
Adrien B. Larsen and
Jeffrey R. Wagner and
Saugat Kandel and
Romelia Salomon-Ferrer and
Nagarajan Vaidehi and
Abhinandan Jain GneimoSim: a modular internal
coordinates molecular dynamics
simulation package . . . . . . . . . . . 2245--2255
Fabian Zeller and
Martin Zacharias Efficient calculation of relative
binding free energies by umbrella
sampling perturbation . . . . . . . . . 2256--2262
Damien J. Carter and
Andrew L. Rohl van der Waals corrected density
functional calculations of the
adsorption of benzene on the Cu (111)
surface . . . . . . . . . . . . . . . . 2263--2271
Raymundo Hernández-Esparza and
Sol-Milena Mejía-Chica and
Andy D. Zapata-Escobar and
Alfredo Guevara-García and
Apolinar Martínez-Melchor and
Julio-M. Hernández-Pérez and
Rubicelia Vargas and
Jorge Garza Grid-based algorithm to search critical
points, in the electron density,
accelerated by graphics processing units 2272--2278
Anonymous Cover Image, Volume 35, Issue 32 . . . . i--ii
Anonymous Cover Image, Volume 35, Issue 32 . . . . iii--iv
Charleen G. Don and
Sereina Riniker Review: Scents and sense: In silico
perspectives on olfactory receptors . . 2279--2287
Rafael Grande-Aztatzi and
Paulina R. Martínez-Alanis and
José Luis Cabellos and
Edison Osorio and
Ana Martínez and
Gabriel Merino Structural evolution of small gold
clusters doped by one and two boron
atoms . . . . . . . . . . . . . . . . . 2288--2296
Aleksandra Karolak and
Arjan van der Vaart Enhanced sampling simulations of DNA
step parameters . . . . . . . . . . . . 2297--2304
Tod D. Romo and
Nicholas Leioatts and
Alan Grossfield Lightweight object oriented structure
analysis: Tools for building tools to
analyze molecular dynamics simulations 2305--2318
Maria M. Reif and
Chris Oostenbrink Molecular dynamics simulation of
configurational ensembles compatible
with experimental FRET efficiency data
through a restraint on instantaneous
FRET efficiencies . . . . . . . . . . . 2319--2332
Natalja Vogt and
Jean Demaison and
Jürgen Vogt and
Heinz Dieter Rudolph Why it is sometimes difficult to
determine the accurate position of a
hydrogen atom by the semiexperimental
method: Structure of molecules
containing the OH or the CH$_3$ group 2333--2342
Anonymous Cover Image, Volume 36, Issue 1 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 1 . . . . iii--iv
Lorenzo Rovigatti and
Petr \vSulc and
István Z. Reguly and
Flavio Romano A comparison between parallelization
approaches in molecular dynamics
simulations on GPUs . . . . . . . . . . 1--8
Chiara Ricca and
Armelle Ringuedé and
Michel Cassir and
Carlo Adamo and
Frederic Labat A comprehensive DFT investigation of
bulk and low-index surfaces of ZrO$_2$
polymorphs . . . . . . . . . . . . . . . 9--21
Qi Song and
Zhenyi Jiang and
Zhiyong Zhang and
Yuqing Hou and
Xiaodong Zhang From orientation disordered to ordered
--- an ab initio simulation on ammonia
borane phase transition within van der
Waals corrections . . . . . . . . . . . 22--32
Hyungjun Kim and
Joungwon Park and
Yoon Sup Lee Prediction of the reduction potential of
tris(2,2$^\prime
$-bipyridinyl)iron(III/II) derivatives 33--41
Andrey A. Kirilchuk and
Aleksandr A. Yurchenko and
Aleksandr N. Kostyuk and
Alexander B. Rozhenko 1,2-migration in $N$-phosphano
functionalized $N$-heterocyclic carbenes 42--48
Chengfei Yan and
Xiaoqin Zou Predicting peptide binding sites on
protein surfaces by clustering chemical
interactions . . . . . . . . . . . . . . 49--61
Iwona E. Weidlich and
Yuri Pevzner and
Benjamin T. Miller and
Igor V. Filippov and
H. Lee Woodcock and
Bernard R. Brooks Software News and Updates: Development
and implementation of (Q)SAR modeling
within the CHARMMing web-user interface 62--67
Anonymous Cover Image, Volume 36, Issue 2 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 2 . . . . iii--iv
Anonymous Cover Image, Volume 36, Issue 2 . . . . v--vi
Gegham Galstyan and
Ernst-Walter Knapp Computing pK$_A$ values of hexa-aqua
transition metal complexes . . . . . . . 69--78
Robin M. Betz and
Ross C. Walker Paramfit: Automated optimization of
force field parameters for molecular
dynamics simulations . . . . . . . . . . 79--87
Rebecca Sure and
Ralf Tonner and
Peter Schwerdtfeger A systematic study of rare gas atoms
encapsulated in small fullerenes using
dispersion corrected density functional
theory . . . . . . . . . . . . . . . . . 88--96
Ryuhei Harada and
Tomotake Nakamura and
Yu Takano and
Yasuteru Shigeta Protein folding pathways extracted by
OFLOOD: Outlier FLOODing method . . . . 97--102
Peter Clote Expected degree for RNA secondary
structure networks . . . . . . . . . . . 103--117
Shabbir Muhammad and
Ahmad Irfan and
Mohd Shkir and
Aijaz R. Chaudhry and
Abul Kalam and
Salem AlFaify and
Abdullah G. Al-Sehemi and
A. E. Al-Salami and
I. S. Yahia and
Hong-Liang Xu and
Zhong-Min Su How does hybrid bridging core
modification enhance the nonlinear
optical properties in donor-$ \pi
$-acceptor configuration? A case study
of dinitrophenol derivatives . . . . . . 118--128
Ilya A. Kaliman and
Lyudmila V. Slipchenko Software News and Updates: Hybrid
MPI/OpenMP parallelization of the
effective fragment potential method in
the \tt libefp software library . . . . 129--135
Anonymous Erratum: Corrigendum: A spherical
harmonic transform spectral analysis of
a localized surface plasmon on a gold
nano shell . . . . . . . . . . . . . . . 136--136
Anonymous Cover Image, Volume 36, Issue 3 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 3 . . . . iii--iv
Yanliang Ren and
Osama Melhem and
Yongjian Li and
Bo Chi and
Xinya Han and
Hao Zhu and
Lingling Feng and
Jian Wan and
Xin Xu Clarifying and illustrating the
electronic energy transfer pathways in
trimeric and hexameric aggregation state
of cyanobacteria allophycocyanin within
the framework of Förster theory . . . . . 137--145
Timothy J. Fuhrer and
Angel M. Lambert Isolated pentagon rule violating
endohedral metallofullerenes explained
using the Hückel rule: a statistical
mechanical study of the C$_{84}$
Isomeric Set . . . . . . . . . . . . . . 146--150
Jing Huang and
Likai Du and
Deping Hu and
Zhenggang Lan Theoretical analysis of excited states
and energy transfer mechanism in
conjugated dendrimers . . . . . . . . . 151--163
Takeshi Yoshikawa and
Hiromi Nakai Linear-scaling self-consistent field
calculations based on divide-and-conquer
method using resolution-of-identity
approximation on graphical processing
units . . . . . . . . . . . . . . . . . 164--170
Mariusz P. Mitoraj and
Goran V. Janji\'c and
Vesna B. Medakovi\'c and
Du\vsan \vZ. Veljkovi\'c and
Artur Michalak and
Sne\vzana D. Zari\'c and
Milo\vs K. Mil\vci\'c Nature of the water/aromatic parallel
alignment interactions . . . . . . . . . 171--180
Nick M. Vandewiele and
Ruben Van de Vijver and
Kevin M. Van Geem and
Marie-Françoise Reyniers and
Guy B. Marin Symmetry calculation for molecules and
transition states . . . . . . . . . . . 181--192
Andrii Shyichuk and
Marcin Runowski and
Stefan Lis and
Jakub Kaczkowski and
Andrzej Jezierski Semiempirical and DFT computations of
the influence of Tb(III) dopant on unit
cell dimensions of cerium(III) fluoride 193--199
Anonymous Cover Image, Volume 36, Issue 4 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 4 . . . . iii--iv
Jonny Proppe and
Carmen Herrmann Communication through molecular bridges:
Different bridge orbital trends result
in common property trends . . . . . . . 201--209
Krystel El Hage and
Jean-Philip Piquemal and
Zeina Hobaika and
Richard G. Maroun and
Nohad Gresh Could the ``Janus-like'' properties of
the halobenzene CX bond (X = Cl, Br) be
leveraged to enhance molecular
recognition? . . . . . . . . . . . . . . 210--221
Emilio Martínez-Núñez An automated method to find transition
states using chemical dynamics
simulations . . . . . . . . . . . . . . 222--234
Marcia O. Fenley and
Robert C. Harris and
Travis Mackoy and
Alexander H. Boschitsch Features of CPB: a Poisson--Boltzmann
solver that uses an adaptive cartesian
grid . . . . . . . . . . . . . . . . . . 235--243
Elaine Limé and
Per-Ola Norrby Improving the Q2MM method for transition
state force field modeling . . . . . . . 244--250
Robert J. Pantazes and
Matthew J. Grisewood and
Tong Li and
Nathanael P. Gifford and
Costas D. Maranas Software News and Updates: The Iterative
Protein Redesign and Optimization (IPRO)
suite of programs . . . . . . . . . . . 251--263
Pablo M. De Biase and
Suren Markosyan and
Sergei Noskov Software News and Updates: BROMOC suite:
Monte Carlo/Brownian dynamics suite for
studies of ion permeation and DNA
transport in biological and artificial
pores with effective potentials . . . . 264--271
Alexander Hoffmann and
Martin Rohrmüller and
Anton Jesser and
Ines dos Santos Vieira and
Wolf Gero Schmidt and
Sonja Herres-Pawlis Errata: Corrigendum: Geometrical and
optical benchmarking of copper(II)
guanidine--quinoline complexes: Insights
from TD-DFT and many-body perturbation
theory (Part II) . . . . . . . . . . . . 272--272
Anonymous Cover Image, Volume 36, Issue 5 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 5 . . . . iii--iv
Anonymous Cover Image, Volume 36, Issue 5 . . . . v--vi
Dmitry Zuev and
Eugene Vecharynski and
Chao Yang and
Natalie Orms and
Anna I. Krylov New algorithms for iterative matrix-free
eigensolvers in quantum chemistry . . . 273--284
Todor Dudev and
Mike Devereux and
Markus Meuwly and
Carmay Lim and
Jean-Philip Piquemal and
Nohad Gresh Quantum-chemistry based calibration of
the alkali metal cation series
(Li$^+$Cs$^+$) for large-scale
polarizable molecular mechanics/dynamics
simulations . . . . . . . . . . . . . . 285--302
Yasuhiro Ikabata and
Yusuke Tsukamoto and
Yutaka Imamura and
Hiromi Nakai Local response dispersion method in
periodic systems: Implementation and
assessment . . . . . . . . . . . . . . . 303--311
Igor Schapiro and
Daniel Roca-Sanjuán and
Roland Lindh and
Massimo Olivucci A surface hopping algorithm for
nonadiabatic minimum energy path
calculations . . . . . . . . . . . . . . 312--320
Daniele Licari and
Alberto Baiardi and
Ma\lgorzata Biczysko and
Franco Egidi and
Camille Latouche and
Vincenzo Barone Software News and Updates:
Implementation of a graphical user
interface for the virtual multifrequency
spectrometer: The VMS-Draw tool . . . . 321--334
Susi Lehtola Software News and Updates: Automatic
algorithms for completeness-optimization
of Gaussian basis sets . . . . . . . . . 335--347
Vytautas Gapsys and
Servaas Michielssens and
Daniel Seeliger and
Bert L. de Groot Software News and Updates: \tt pmx:
Automated protein structure and topology
generation for alchemical perturbations 348--354
Anonymous Cover Image, Volume 36, Issue 6 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 6 . . . . iii--iv
Jing Xu and
Yi-hong Ding Pentaatomic planar tetracoordinate
silicon with 14 valence electrons: a
large-scale global search of
SiX$_n$Y$_m^q$ ($ n + m = 4$; $ q = 0,
\pm 1, - 2$; X, Y = main group elements
from H to Br) . . . . . . . . . . . . . 355--360
Víctor Duarte Alaniz and
Tomás Rocha-Rinza and
Gabriel Cuevas Assessment of hydrophobic interactions
and their contributions through the
analysis of the methane dimer . . . . . 361--375
Siyan Chen and
Shasha Yi and
Wenmei Gao and
Chuncheng Zuo and
Zhonghan Hu Force field development for organic
molecules: Modifying dihedral and $ 1 -
n $ pair interaction parameters . . . . 376--384
\.Iskender Muz and
Osman Canko and
Murat Ati\cs and
Erdem Kamil Yìldìrìm Search for the global minimum structures
of AlB$_3$H$_2$$_n$ ($ n = 0$--$6$)
clusters . . . . . . . . . . . . . . . . 385--391
Tibor Dubaj and
Zuzana Cibulková and
Peter \vSimon An incremental isoconversional method
for kinetic analysis based on the
orthogonal distance regression . . . . . 392--398
Maira D'Alessando and
Andrea Amadei and
Mauro Stener and
Massimiliano Aschi Essential dynamics for the study of
microstructures in liquids . . . . . . . 399--407
Kelin Xia and
Xin Feng and
Yiying Tong and
Guo Wei Wei Persistent homology for the quantitative
prediction of fullerene stability . . . 408--422
Anonymous Cover Image, Volume 36, Issue 7 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 7 . . . . iii--iv
Anonymous Obituary: Paul Schleyer 1930--2014 . . . 423--423
Gustavo Pierdominici-Sottile and
Juliana Palma New insights into the meaning and
usefulness of principal component
analysis of concatenated trajectories 424--432
Hamed Akbarzadeh and
Amir Nasser Shamkhali H$_2$ adsorption on Ag-nanocluster
single-walled carbon nanotube
composites: a molecular dynamics study
on the effects of nanocluster size,
diameter, and chirality of nanotube . . 433--440
Fang Liu and
Likai Du and
Jun Gao and
Lili Wang and
Bo Song and
Chengbu Liu Application of polarizable ellipsoidal
force field model to pnicogen bonds . . 441--448
Wen-Xin Ji and
Wei Xu and
W. H. Eugen Schwarz and
Shu-Guang Wang Ionic bonding of lanthanides, as
influenced by $d$- and $f$-atomic
orbitals, by core-shells and by
relativity . . . . . . . . . . . . . . . 449--458
Yusuke Ootani and
Yoshinobu Akinaga and
Takahito Nakajima Theoretical investigation of
enantioselectivity of cage-like
supramolecular assembly: the insights
into the shape complementarity and
host--guest interaction . . . . . . . . 459--466
Sta\vs Bevc and
Christoph Junghans and
Matej Praprotnik Software News and Updates: STOCK:
Structure mapper and online
coarse-graining kit for molecular
simulations . . . . . . . . . . . . . . 467--477
Hiram Ponce and
Pedro Ponce and
Arturo Molina Software News and Updates: The
development of an artificial organic
networks toolkit for LabVIEW . . . . . . 478--492
Anonymous Cover Image, Volume 36, Issue 8 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 8 . . . . iii--iv
Abraham Yosipof and
Hanoch Senderowitz $k$-Nearest neighbors optimization-based
outlier removal . . . . . . . . . . . . 493--506
Pin-Kuang Lai and
Shiang-Tai Lin Internal coordinate density of state
from molecular dynamics simulation . . . 507--517
Kun Yuan and
Jing-Shuang Dang and
Yi-Jun Guo and
Xiang Zhao Theoretical prediction of the
host--guest interactions between novel
photoresponsive nanorings and C$_{60}$:
a strategy for facile encapsulation and
release of fullerene . . . . . . . . . . 518--528
Bhaskar Sharma and
Hemant Kumar Srivastava and
Gaddamanugu Gayatri and
Garikapati Narahari Sastry Energy decomposition analysis of
cation--$ \pi $, metal ion--lone pair,
hydrogen bonded, charge-assisted
hydrogen bonded, and $ \pi $--$ \pi $
interactions . . . . . . . . . . . . . . 529--538
Siladitya Padhi and
Siddabattula Ramakrishna and
U. Deva Priyakumar Prediction of the structures of helical
membrane proteins based on a minimum
unfavorable contacts approach . . . . . 539--552
Martin T. Stiebritz MetREx: a protein design approach for
the exploration of sequence-reactivity
relationships in metalloenzymes . . . . 553--563
Elixabete Rezabal and
Gilles Frison Estimating $ \pi $ binding energy of
$N$-heterocyclic carbenes: the role of
polarization . . . . . . . . . . . . . . 564--572
Andrew J. Schultz and
David A. Kofke Software News and Updates: Etomica: an
object-oriented framework for molecular
simulation . . . . . . . . . . . . . . . 573--583
Anonymous Cover Image, Volume 36, Issue 9 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 9 . . . . iii--iv
Federico Fogolari and
Alessandra Corazza and
Gennaro Esposito Accuracy assessment of the linear
Poisson--Boltzmann equation and
reparametrization of the OBC generalized
Born model for nucleic acids and nucleic
acid--protein complexes . . . . . . . . 585--596
Caleb Carlin and
Mark S. Gordon Ab initio calculation of anion proton
affinity and ionization potential for
energetic ionic liquids . . . . . . . . 597--600
Paul M. Zimmerman Single-ended transition state finding
with the growing string method . . . . . 601--611
Topi Karilainen and
Oana Cramariuc and
Mikael Kuisma and
Kirsi Tappura and
Terttu I. Hukka van der Waals interactions are critical
in Car--Parrinello molecular dynamics
simulations of porphyrin--fullerene
dyads . . . . . . . . . . . . . . . . . 612--621
Amir Karton and
Lars Goerigk Accurate reaction barrier heights of
pericyclic reactions: Surprisingly large
deviations for the CBS-QB3 composite
method and their consequences in DFT
benchmark studies . . . . . . . . . . . 622--632
Letif Mones and
Andrew Jones and
Andreas W. Götz and
Teodoro Laino and
Ross C. Walker and
Ben Leimkuhler and
Gábor Csányi and
Noam Bernstein The adaptive buffered force QM/MM method
in the CP2K and AMBER software packages 633--648
Vincent Tognetti and
Christophe Morell and
Laurent Joubert Quantifying electro/nucleophilicity by
partitioning the dual descriptor . . . . 649--659
Simone Morpurgo A DFT study on Cu(I) coordination in
Cu-ZSM-5: Effects of the functional
choice and tuning of the ONIOM approach 660--669
Avijit Sen and
Sangita Sen and
Pradipta Kumar Samanta and
Debashis Mukherjee Unitary group adapted state specific
multireference perturbation theory:
Formulation and pilot applications . . . 670--688
Alexander A. Kantardjiev Software News and Updates:
irGPU.proton.Net: Irregular strong
charge interaction networks of
protonatable groups in protein molecules
--- a GPU solver using the fast
multipole method and statistical
thermodynamics . . . . . . . . . . . . . 689--693
Anonymous Cover Image, Volume 36, Issue 10 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 10 . . . . iii--iv
Anonymous Cover Image, Volume 36, Issue 10 . . . . v--vi
Jin-Dou Huang and
Wen-Liang Li and
Shu-Hao Wen and
Bin Dong Electronic structure and microscopic
charge-transport properties of a
new-type diketopyrrolopyrrole-based
material . . . . . . . . . . . . . . . . 695--706
Paolo Della Porta and
Riccardo Zanasi and
Guglielmo Monaco Hydrogen--hydrogen bonding: the current
density perspective . . . . . . . . . . 707--716
Xiao Wang and
Juan Yang and
Ruoming Li and
Hong Jiang and
Yan Li Deformation of single-walled carbon
nanotubes by interaction with graphene:
a first-principles study . . . . . . . . 717--722
Petr \vSt\vepánek and
Petr Bou\vr Origin-independent sum over states
simulations of magnetic and electronic
circular dichroism spectra via the
localized orbital/local origin method 723--730
Haiyan Yuan and
Yiying Zheng and
Bo Li and
Wenliang Li and
Jingping Zhang The multieffects of DMF and DBU on the $
[5 + 1] $ benzannulation of nitroethane
and $ \alpha $-alkenoyl
ketene-(S,S)-acetals: Hydrogen bonding
and electrostatic interactions . . . . . 731--738
Hanne S. Antila and
Emppu Salonen On combining Thole's induced point
dipole model with fixed charge
distributions in molecular mechanics
force fields . . . . . . . . . . . . . . 739--750
Andrzej Eilmes and
Piotr Kubisiak Stability of ion triplets in ionic
liquid/lithium salt solutions: Insights
from implicit and explicit solvent
models and molecular dynamics
simulations . . . . . . . . . . . . . . 751--762
Ryuhei Harada and
Yu Takano and
Yasuteru Shigeta Enhanced conformational sampling method
for proteins based on the TaBoo SeArch
algorithm: Application to the folding of
a mini-protein, chignolin . . . . . . . 763--772
Adelene Y. L. Sim and
Chandra Verma How does a hydrocarbon staple affect
peptide hydrophobicity? . . . . . . . . 773--784
Anonymous Cover Image, Volume 36, Issue 11 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 11 . . . . iii--iv
Anonymous Cover Image, Volume 36, Issue 11 . . . . v--vi
Oliver Sala and
Hans Peter Lüthi and
Antonio Togni and
Marcella Iannuzzi and
Jürg Hutter Dividing a complex reaction involving a
hypervalent iodine reagent into three
limiting mechanisms by ab initio
molecular dynamics . . . . . . . . . . . 785--794
Nishamol Kuriakose and
Kumar Vanka Can substituted allenes be highly
efficient leaving groups in catalytic
processes? A computational investigation 795--804
Nguyen Minh Tam and
Tran Dieu Hang and
Hung Tan Pham and
Huyen Thi Nguyen and
My Phuong Pham-Ho and
Pablo A. Denis and
Minh Tho Nguyen Bonding and singlet--triplet gap of
silicon trimer: Effects of protonation
and attachment of alkali metal cations 805--815
Keisuke Nemoto and
Minori Abe and
Junji Seino and
Masahiko Hada An ab initio study of nuclear volume
effects for isotope fractionations using
two-component relativistic methods . . . 816--820
Wiktor Zierkiewicz and
Dariusz C. Bie\'nko and
Danuta Michalska and
Thér\`ese Zeegers-Huyskens Theoretical investigation of the halogen
bonded complexes between carbonyl bases
and molecular chlorine . . . . . . . . . 821--832
Marcos Menéndez and
Roberto Álvarez Boto and
Evelio Francisco and
Ángel Martín Pendás One-electron images in real space:
Natural adaptive orbitals . . . . . . . 833--843
Wen-Yang Zhao and
Jie Yu and
Si-Jia Ren and
Xi-Guang Wei and
Fang-Zhou Qiu and
Peng-Hui Li and
He Li and
Yi-Peng Zhou and
Chang-Zhen Yin and
An-Pu Chen and
Hao Li and
Lei Zhang and
Jun Zhu and
Yi Ren and
Kai-Chung Lau Probing the reactivity of microhydrated
$ \alpha $-nucleophile in the anionic
gas-phase S$_N$ 2 reaction . . . . . . . 844--852
Nils Middendorf and
Katharina Krause and
Sebastian Höfener Solvatochromic shifts of Br$_2$ and
I$_2$ in water cages of type $ 5^{12}$,
$ 5^{12}$ $ 6^2$, $ 5^{12}$ $ 6^3$, and
$ 5^{12}$ $ 6^4$ . . . . . . . . . . . . 853--860
Alex Domingo and
Celestino Angeli and
Coen de Graaf and
Vincent Robert Electronic reorganization triggered by
electron transfer: the intervalence
charge transfer of a Fe$^{3+}$
/Fe$^{2+}$ bimetallic complex . . . . . 861--869
Anonymous Cover Image, Volume 36, Issue 12 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 12 . . . . iii--iv
Bun Chan and
Jong-Won Song and
Yukio Kawashima and
Kimihiko Hirao Toward the complete range separation of
non-hybrid exchange--correlation
functional . . . . . . . . . . . . . . . 871--877
Polina V. Banushkina and
Sergei V. Krivov Fep1d: a script for the analysis of
reaction coordinates . . . . . . . . . . 878--882
Jan Dillen The topology of the Ehrenfest force
density revisited. A different
perspective based on Slater-type
orbitals . . . . . . . . . . . . . . . . 883--890
Xu Zhang and
Xiaodi Yang and
Hua Geng and
Guangjun Nan and
Xingwen Sun and
Jinyang Xi and
Xin Xu Theoretical comparative studies on
transport properties of pentacene,
pentathienoacene, and
6,13-dichloropentacene . . . . . . . . . 891--900
Yury D. Fomin and
Elena N. Tsiok and
Valentin N. Ryzhov The behavior of benzene confined in a
single wall carbon nanotube . . . . . . 901--906
Sudip Chattopadhyay and
Rajat K. Chaudhuri and
Uttam Sinha Mahapatra State-specific multireference
perturbation theory with improved
virtual orbitals: Taming the ground
state of F$_2$, Be$_2$, and N$_2$ . . . 907--925
Russell Thackston and
Ryan C. Fortenberry The performance of low-cost commercial
cloud computing as an alternative in
computational chemistry . . . . . . . . 926--933
Matthew Welborn and
Jiahao Chen and
Lee-Ping Wang and
Troy Van Voorhis Why many semiempirical molecular orbital
theories fail for liquid water and how
to fix them . . . . . . . . . . . . . . 934--939
Adam K. Sieradzan Software News and Updates: Introduction
of periodic boundary conditions into
UNRES force field . . . . . . . . . . . 940--946
Anonymous Cover Image, Volume 36, Issue 13 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 13 . . . . iii--iv
Anna Stachiewicz and
Andrzej Molski A coarse-grained MARTINI-like force
field for DNA unzipping in nanopores . . 947--956
Robert A. Evarestov and
Andrej I. Panin Symmetry classification of electron and
phonon states in TiO$_2$-based nanowires
and nanotubes . . . . . . . . . . . . . 957--969
Maria T. Panteva and
George M. Giambasu and
Darrin M. York Comparison of structural, thermodynamic,
kinetic and mass transport properties of
Mg$^{2+}$ ion models commonly used in
biomolecular simulations . . . . . . . . 970--982
Antonio Cardone and
Aaron Bornstein and
Harish C. Pant and
Mary Brady and
Ram Sriram and
Sergio A. Hassan Detection and characterization of
nonspecific, sparsely populated binding
modes in the early stages of
complexation . . . . . . . . . . . . . . 983--995
Elmar Krieger and
Gert Vriend New ways to boost molecular dynamics
simulations . . . . . . . . . . . . . . 996--1007
Yi Wang and
William Yi Wang and
Long-Qing Chen and
Zi-Kui Liu Bonding charge density from atomic
perturbations . . . . . . . . . . . . . 1008--1014
Louis Vanduyfhuys and
Steven Vandenbrande and
Toon Verstraelen and
Rochus Schmid and
Michel Waroquier and
Veronique Van Speybroeck Software News and Updates: QuickFF: a
program for a quick and easy derivation
of force fields for metal-organic
frameworks from ab initio input . . . . 1015--1027
Anonymous Cover Image, Volume 36, Issue 14 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 14 . . . . iii--iv
Liudmyla K. Sviatenko and
Olexandr Isayev and
Leonid Gorb and
Frances C. Hill and
Danuta Leszczynska and
Jerzy Leszczynski Are the reduction and oxidation
properties of nitrocompounds dissolved
in water different from those produced
when adsorbed on a silica surface? A DFT
M05-2X computational study . . . . . . . 1029--1035
Hongzhi Li and
Ziyan Zhong and
Lin Li and
Rui Gao and
Jingxia Cui and
Ting Gao and
Li Hong Hu and
Yinghua Lu and
Zhong-Min Su and
Hui Li A cascaded QSAR model for efficient
prediction of overall power conversion
efficiency of all-organic dye-sensitized
solar cells . . . . . . . . . . . . . . 1036--1046
Shenggao Zhou and
Li-Tien Cheng and
Hui Sun and
Jianwei Che and
Joachim Dzubiella and
Bo Li and
J. Andrew McCammon LS--VISM: a software package for
analysis of biomolecular solvation . . . 1047--1059
Tirtharaj Dash and
Prabhat K. Sahu Gradient gravitational search: an
efficient metaheuristic algorithm for
global optimization . . . . . . . . . . 1060--1068
Milan Randi\'c and
Tomaz Pisanski Protein alignment: Exact versus
approximate. An illustration . . . . . . 1069--1074
Masaki Okoshi and
Teruo Atsumi and
Hiromi Nakai Revisiting the extrapolation of
correlation energies to complete basis
set limit . . . . . . . . . . . . . . . 1075--1082
Kenno Vanommeslaeghe and
Mingjun Yang and
Alexander D. MacKerell Jr. Robustness in the fitting of molecular
mechanics parameters . . . . . . . . . . 1083--1101
Anonymous Cover Image, Volume 36, Issue 15 . . . . i--ii
Hujun Shen and
Yan Li and
Peijun Xu and
Xiaofang Li and
Huiying Chu and
Dinglin Zhang and
Guohui Li An anisotropic coarse-grained model
based on Gay--Berne and electric
multipole potentials and its application
to simulate a DMPC bilayer in an
implicit solvent model . . . . . . . . . 1103--1113
Claudia Loerbroks and
Andreas Heimermann and
Walter Thiel Solvents effects on the mechanism of
cellulose hydrolysis: A QM/MM study . . 1114--1123
Robert Zale\'sny and
Guangjun Tian and
Christof Hättig and
Wojciech Bartkowiak and
Hans Ågren Toward assessment of density functionals
for vibronic coupling in two-photon
absorption: a case study of
$4$-nitroaniline . . . . . . . . . . . . 1124--1131
William J. Allen and
Trent E. Balius and
Sudipto Mukherjee and
Scott R. Brozell and
Demetri T. Moustakas and
P. Therese Lang and
David A. Case and
Irwin D. Kuntz and
Robert C. Rizzo DOCK 6: Impact of new features and
current docking performance . . . . . . 1132--1156
Adam B. Birkholz and
H. Bernhard Schlegel Using bonding to guide transition state
optimization . . . . . . . . . . . . . . 1157--1166
Benoit de Courcy and
Etienne Derat and
Jean-Philip Piquemal Bridging organometallics and quantum
chemical topology: Understanding
electronic relocalisation during
palladium-catalyzed reductive
elimination . . . . . . . . . . . . . . 1167--1175
Sadanandam Namsani and
Nisanth N. Nair and
Jayant K. Singh Interaction potential models for bulk
Zns, Zns nanoparticle, and Zns
nanoparticle-PMMA from first principles 1176--1186
Anonymous Cover Image, Volume 36, Issue 16 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 16 . . . . iii--iv
David Z. Gao and
Filippo Federici Canova and
Matthew B. Watkins and
Alexander L. Shluger Efficient parametrization of complex
molecule--surface force fields . . . . . 1187--1195
Shu-Ching Ou and
Di Cui and
Matthew Wezowicz and
Michela Taufer and
Sandeep Patel Free energetics of carbon nanotube
association in aqueous inorganic NaI
salt solutions: Temperature effects
using all-atom molecular dynamics
simulations . . . . . . . . . . . . . . 1196--1212
Frédéric Cazals and
Tom Dreyfus and
Dorian Mazauric and
Christine-Andrea Roth and
Charles H. Robert Conformational ensembles and sampled
energy landscapes: Analysis and
comparison . . . . . . . . . . . . . . . 1213--1231
Xun Zhu and
Yuriko Aoki Development of minimized mixing
molecular orbital method for designing
organic ferromagnets . . . . . . . . . . 1232--1239
Hiroo Nozaki and
Yuji Ikeda and
Kazuhide Ichikawa and
Akitomo Tachibana Electronic stress tensor analysis of
molecules in gas phase of CVD process
for GeSbTe alloy . . . . . . . . . . . . 1240--1251
Ayman Farhat and
Saleh N. Abdul-Al Ab initio calculations of the ground and
excited states of the ZrN molecule
including spin-orbit effects . . . . . . 1252--1258
Re\vs\vci\vc Jurij and
Linse Per Software News and Updates: MOLSIM: a
modular molecular simulation software 1259--1274
Anonymous Cover Image, Volume 36, Issue 17 . . . . i--ii
Justin A. Drake and
B. Montgomery Pettitt Force field-dependent solution
properties of glycine oligomers . . . . 1275--1285
Jacek Koput Ab initio ground-state potential energy
function and vibration-rotation energy
levels of imidogen, NH . . . . . . . . . 1286--1294
Haiyan Yuan and
Jingping Zhang [DBU-H]$^+$ and H$_2$O as effective
catalyst form for
2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-ones: a DFT study 1295--1303
Thomas Long and
Owen M. McDougal and
Tim Andersen GAMPMS: Genetic algorithm managed
peptide mutant screening . . . . . . . . 1304--1310
Oliwia M. Szklarczyk and
Eirini Arvaniti and
Wilfred F. van Gunsteren Polarizable coarse-grained models for
molecular dynamics simulation of liquid
cyclohexane . . . . . . . . . . . . . . 1311--1321
Sandro Marmitt and
Paulo F. B. Gonçalves A DFT study on the insertion of CO$_2$
into styrene oxide catalyzed by
$1$-butyl-$3$-methyl-Imidazolium bromide
ionic liquid . . . . . . . . . . . . . . 1322--1333
Athanassios C. Tsipis and
Alexandros V. Stalikas Electronic, bonding, and optical
properties of $1$ d [CuCN]$_n$ ($ n =
1$--$ 10$) chains, $ 24 $ d [Cu CN]$_n$
($ n = 2$ -- $ 10$) nanorings, and $3$ d
[Cu$_n$ (CN)$_n$]$_m$ ($ n = 4$, $ m =
2, 3$; $ n = 10$, $ m = 2$) tubes
studied by DFT /TD--DFT methods . . . . 1334--1347
Anonymous Cover Image, Volume 36, Issue 18 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 18 . . . . iii--iv
Wei Li and
Yanli Zeng and
Xiaoyan Li and
Zheng Sun and
Lingpeng Meng The competition of Y $ \cdot $ O and X $
\cdot $ N halogen bonds to enhance the
group V $ \sigma $-hole interaction in
the NCY $ \cdot $ o PH$_3$ $ \cdot $ NCX
and O PH$_3$ $ \cdot $ NCX $ \cdot $ NCY
(X, Y F, Cl, and Br) complexes . . . . . 1349--1358
Tomonari Sumi and
Ayori Mitsutake and
Yutaka Maruyama A solvation-free-energy functional: a
reference-modified density functional
formulation . . . . . . . . . . . . . . 1359--1369
Ming Huang and
Timothy J. Giese and
Darrin M. York Nucleic acid reactivity: Challenges for
next-generation semiempirical quantum
models . . . . . . . . . . . . . . . . . 1370--1389
Alexander K. H. Weiss and
Christian Ochsenfeld A rigorous and optimized strategy for
the evaluation of the Boys function
kernel in molecular electronic structure
theory . . . . . . . . . . . . . . . . . 1390--1398
Kyle D. Fernandes and
C. Alicia Renison and
Kevin J. Naidoo Quantum supercharger library:
Hyper-parallelism of the Hartree--Fock
method . . . . . . . . . . . . . . . . . 1399--1409
C. Alicia Renison and
Kyle D. Fernandes and
Kevin J. Naidoo Quantum supercharger library:
Hyper-parallel integral derivatives
algorithms for ab initio QM\slash MM
dynamics . . . . . . . . . . . . . . . . 1410--1419
Carsten Müller and
Daniel Spångberg Calculation of the stability of
nonperiodic solids using classical force
fields and the method of increments:
N$_2$O as an example . . . . . . . . . . 1420--1427
Anonymous Cover Image, Volume 36, Issue 19 . . . . i--ii
Maike Bergeler and
Carmen Herrmann and
Markus Reiher Mode-tracking based stationary-point
optimization . . . . . . . . . . . . . . 1429--1438
Raffaella Demichelis and
Marco Bruno and
Francesco R. Massaro and
Mauro Prencipe and
Marco De La Pierre and
Fabrizio Nestola First-principle modelling of forsterite
surface properties: Accuracy of methods
and basis sets . . . . . . . . . . . . . 1439--1445
Raimondas Galvelis and
Yuji Sugita Replica state exchange metadynamics for
improving the convergence of free energy
estimates . . . . . . . . . . . . . . . 1446--1455
Alonso Ramirez-Manzanares and
Joaquin Peña and
Jon M. Azpiroz and
Gabriel Merino A hierarchical algorithm for molecular
similarity (H-FORMS) . . . . . . . . . . 1456--1466
Kim Julia Hintze and
Arne Lützen and
Thomas Bredow Structure and stability of
supramolecular crown ether complexes . . 1467--1472
Justin A. Lemkul and
Beno\^\it Roux and
David van der Spoel and
Alexander D. MacKerell Jr. Software News and Updates:
Implementation of extended Lagrangian
dynamics in GROMACS for polarizable
simulations using the classical Drude
oscillator model . . . . . . . . . . . . 1473--1479
Semen O. Yesylevskyy Software News and Updates: Pteros 2.0:
Evolution of the fast parallel molecular
analysis library for C++ and Python . . 1480--1488
Anonymous Cover Image, Volume 36, Issue 20 . . . . i--ii
Junichi Higo and
Bhaskar Dasgupta and
Tadaaki Mashimo and
Kota Kasahara and
Yoshifumi Fukunishi and
Haruki Nakamura Virtual-system-coupled adaptive umbrella
sampling to compute free-energy
landscape for flexible molecular docking 1489--1501
Kelin Xia and
Guo-Wei Wei Multidimensional persistence in
biomolecular data . . . . . . . . . . . 1502--1520
Luká\vs Grajciar Low-memory iterative density fitting . . 1521--1535
Yinglong Miao and
Ferran Feixas and
Changsun Eun and
J. Andrew McCammon Accelerated molecular dynamics
simulations of protein folding . . . . . 1536--1549
Mark Dittner and
Julian Müller and
Hasan Metin Aktulga and
Bernd Hartke Efficient global optimization of
reactive force-field parameters . . . . 1550--1561
Sudhir K. Sahoo and
Nisanth N. Nair A potential with low point charges for
pure siliceous zeolites . . . . . . . . 1562--1567
Bing Xia and
Artem Mamonov and
Seppe Leysen and
Karen N. Allen and
Sergei V. Strelkov and
Ioannis Ch. Paschalidis and
Sandor Vajda and
Dima Kozakov Software News and Updates: Accounting
for observed small angle X-ray
scattering profile in the
protein--protein docking server cluspro 1568--1572
Anonymous Cover Image, Volume 36, Issue 21 . . . . i--ii
Joseelyne G. Hernández-Lima and
Jose E. Barquera-Lozada and
Gabriel Cuevas and
Fernando Cortés-Guzmán The role of induced current density in
steroelectronic effects: Perlin effect 1573--1578
Sandra C. C. Nunes and
Marie Skepö and
Alberto A. C. C. Pais Confined polyelectrolytes: the
complexity of a simple system . . . . . 1579--1586
Benjamin D. Jensen and
Kristopher E. Wise and
Gregory M. Odegard The effect of time step, thermostat, and
strain rate on ReaxFF simulations of
mechanical failure in diamond, graphene,
and carbon nanotube . . . . . . . . . . 1587--1596
Jakub Gunera and
Peter Kolb Fragment-based similarity searching with
infinite color space . . . . . . . . . . 1597--1608
Felix Plasser and
Benjamin Thomitzni and
Stefanie A. Bäppler and
Jan Wenzel and
Dirk R. Rehn and
Michael Wormit and
Andreas Dreuw Statistical analysis of electronic
excitation processes: Spatial location,
compactness, charge transfer, and
electron-hole correlation . . . . . . . 1609--1620
Tatiana Vasilevskaya and
Maria G. Khrenova and
Alexander V. Nemukhin and
Walter Thiel Mechanism of proteolysis in matrix
metalloproteinase-2 revealed by QM/MM
modeling . . . . . . . . . . . . . . . . 1621--1630
Michael Martinez and
Neil J. Bruce and
Julia Romanowska and
Daria B. Kokh and
Musa Ozboyaci and
Xiaofeng Yu and
Mehmet Ali Öztürk and
Stefan Richter and
Rebecca C. Wade Software News and Updates: SDA 7: a
modular and parallel implementation of
the simulation of diffusional
association software . . . . . . . . . . 1631--1645
Anonymous Cover Image, Volume 36, Issue 22 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 22 . . . . iii--iv
Taro Udagawa and
Masanori Tachikawa H/D isotope effect on charge-inverted
hydrogen-bonded systems: Systematic
classification of three different types
in H$_3$ $X$H\dottedbond $Y$H$_3$ ($X$ =
C, Si, or Ge, and $Y$ = B, Al, or Ga)
with multicomponent calculation . . . . 1647--1654
Yuichi Tanaka and
Norio Yoshida and
Haruyuki Nakano Three-dimensional reference interaction
site model self-consistent field
analysis of solvent and substituent
effects on the absorption spectra of
Brooker's merocyanine . . . . . . . . . 1655--1663
Qiming Sun Libcint: an efficient general integral
library for Gaussian basis functions . . 1664--1671
Martin Rohrmüller and
Alexander Hoffmann and
Christian Thierfelder and
Sonja Herres-Pawlis and
Wolf Gero Schmidt The Cu$_2$ O$_2$ torture track for a
real-life system: [Cu$_2$
(btmgp)$_2$O$_2$]$^{2+}$ oxo and peroxo
species in density functional
calculations . . . . . . . . . . . . . . 1672--1685
Noah S. Bieler and
Philippe H. Hünenberger Orthogonal sampling in free-energy
calculations of residue mutations in a
tripeptide: TI versus $\lambda$-LEUS . . 1686--1697
Michael Stenrup and
Roland Lindh and
Ignacio Fdez. Galván Constrained numerical gradients and
composite gradients: Practical tools for
geometry optimization and potential
energy surface navigation . . . . . . . 1698--1708
Takakazu Ishikura and
Yuki Iwata and
Tatsuro Hatano and
Takahisa Yamato Energy exchange network of inter-residue
interactions within a thermally
fluctuating protein molecule: a
computational study . . . . . . . . . . 1709--1718
Anonymous Cover Image, Volume 36, Issue 23 . . . . i--ii
X. W. Zhou and
D. K. Ward and
M. E. Foster An analytical bond-order potential for
carbon . . . . . . . . . . . . . . . . . 1719--1735
Ignacio Viciano and
Raquel Castillo and
Sergio Martí QM/MM modeling of the hydroxylation of
the androstenedione substrate catalyzed
by cytochrome P450 aromatase (CYP19A1) 1736--1747
Stephen J. Barigye and
Matheus P. Freitas Is molecular alignment an indispensable
requirement in the MIA-QSAR method? . . 1748--1755
Yury Yu. Rusakov and
Leonid B. Krivdin Four-component relativistic DFT
calculations of $^{77}$Se NMR chemical
shifts: a gateway to a reliable
computational scheme for the
medium-sized organoselenium molecules 1756--1762
Weizhou Wang and
Tao Sun and
Yu Zhang and
Yi-Bo Wang Benchmark calculations of the adsorption
of aromatic molecules on graphene . . . 1763--1771
Junchao Xia and
William F. Flynn and
Emilio Gallicchio and
Bin W. Zhang and
Peng He and
Zhiqiang Tan and
Ronald M. Levy Large-scale asynchronous and distributed
multidimensional replica exchange
molecular simulations and efficiency
analysis . . . . . . . . . . . . . . . . 1772--1785
Anonymous Cover Image, Volume 36, Issue 24 . . . . i--ii
Sergey Kazachenko and
Mark Giovinazzo and
Kyle Wm. Hall and
Natalie M. Cann Algorithms for GPU-based molecular
dynamics simulations of complex fluids:
Applications to water, mixtures, and
liquid crystals . . . . . . . . . . . . 1787--1804
Manuel Hochheim and
Thomas Bredow Adsorption-induced changes of
intramolecular optical transitions:
PTCDA/NaCl and PTCDA/KCl . . . . . . . . 1805--1811
Norah Heinz and
Michael Dolg and
Albrecht Berkessel A theoretical study of imine
hydrocyanation catalyzed by
halogen-bonding . . . . . . . . . . . . 1812--1817
Murugesan Thenraj and
Ashoka G. Samuelson Contrasting electronic requirements for
C H binding and C H activation in $ d^6
$ half-sandwich complexes of rhenium and
tungsten . . . . . . . . . . . . . . . . 1818--1830
Nicolás Otero and
Christian Van Alsenoy and
Claude Pouchan and
Panaghiotis Karamanis Hirshfeld-based intrinsic polarizability
density representations as a tool to
analyze molecular polarizability . . . . 1831--1843
Timothy J. Hughes and
Salvatore Cardamone and
Paul L. A. Popelier Realistic sampling of amino acid
geometries for a multipolar polarizable
force field . . . . . . . . . . . . . . 1844--1857
Jing Huang and
Likai Du and
Deping Hu and
Zhenggang Lan Erratum: Theoretical analysis of excited
states and energy transfer mechanism in
conjugated dendrimers . . . . . . . . . 1858--1858
Anonymous Cover Image, Volume 36, Issue 25 . . . . i--ii
Pin-Chih Su and
Cheng-Chieh Tsai and
Shahila Mehboob and
Kirk E. Hevener and
Michael E. Johnson Comparison of radii sets, entropy, QM
methods, and sampling on MM--PBSA,
MM--GBSA, and QM/MM--GBSA ligand binding
energies of \em F. tularensis enoyl-ACP
reductase (FabI) . . . . . . . . . . . . 1859--1873
Marie Zgarbová and
Andreana M. Rosnik and
F. Javier Luque and
Carles Curutchet and
Petr Jure\vcka Transferability and additivity of
dihedral parameters in polarizable and
nonpolarizable empirical force fields 1874--1884
Rui Duan and
Raudah Lazim and
Dawei Zhang Understanding the basis of I50V-induced
affinity decrease in HIV-1 protease via
molecular dynamics simulations using
polarized force field . . . . . . . . . 1885--1892
M. Luz Sánchez and
José C. Corchado and
M. Elena Martín and
Ignacio Fdez. Galván and
Rute Barata-Morgado and
Manuel A. Aguilar A new QM/MM method oriented to the study
of ionic liquids . . . . . . . . . . . . 1893--1901
Liangxiao Zhang and
Peiwu Li and
Jin Mao and
Fei Ma and
Xiaoxia Ding and
Qi Zhang An enhanced Monte Carlo outlier
detection method . . . . . . . . . . . . 1902--1906
Italo Curvelo Anjos and
Gerd Bruno Rocha A topological assessment of the
electronic structure of mesoionic
compounds . . . . . . . . . . . . . . . 1907--1918
Haisheng Li and
Weiguang Chen and
Xiaoyu Han and
Liben Li and
Qiang Sun and
Zhengxiao Guo and
Yu Jia Van der Waals Effects on semiconductor
clusters . . . . . . . . . . . . . . . . 1919--1927
Anonymous Cover Image, Volume 36, Issue 26 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 26 . . . . iii--iv
Manuel Hitzenberger and
Thomas S. Hofer Probing the range of applicability of
structure- and energy-adjusted QM/MM
link bonds . . . . . . . . . . . . . . . 1929--1939
Silvia Casassa and
Alessandro Erba and
Jacopo Baima and
Roberto Orlando Electron density analysis of large
(molecular and periodic) systems: a
parallel implementation . . . . . . . . 1940--1946
Joshua J. Eller and
Karen Downey Computational assessment of electron
density in metallo-organic nickel pincer
complexes for formation of P C bonds . . 1947--1953
Anirban Ghosh and
Rajat K. Chaudhuri and
Sudip Chattopadhyay and
Uttam Sinha Mahapatra Relativistic state-specific
multireference perturbation theory
incorporating improved virtual orbitals:
Application to the ground state
single-bond dissociation . . . . . . . . 1954--1972
Arina Afanasyeva and
Sergey Izmailov and
Michel Grigoriev and
Michael Petukhov Software News and Updates: AquaBridge: a
novel method for systematic search of
structural water molecules within the
protein active sites . . . . . . . . . . 1973--1977
Tomá\vs Kuba\vr and
Kai Welke and
Gerrit Groenhof Software News and Updates: New QM/MM
implementation of the DFTB3 method in
the \tt gromacs package . . . . . . . . 1978--1989
Carsten Kutzner and
Szilárd Páll and
Martin Fechner and
Ansgar Esztermann and
Bert L. de Groot and
Helmut Grubmüller Software News and Updates: Best bang for
your buck: GPU nodes for GROMACS
biomolecular simulations . . . . . . . . 1990--2008
Tomonari Sumi and
Ayori Mitsutake and
Yutaka Maruyama Erratum: ``A solvation-free-energy
functional: a reference-modified density
functional formulation'' [J. Comput.
Chem. 2015, \bf 36, 1359--1369] . . . . 2009--2011
Anonymous Cover Image, Volume 36, Issue 27 . . . . i--ii
Yun Ding and
Ye Fang and
Wei P. Feinstein and
Jagannathan Ramanujam and
David M. Koppelman and
Juana Moreno and
Michal Brylinski and
Mark Jarrell GeauxDock: a novel approach for
mixed-resolution ligand docking using a
descriptor-based force field . . . . . . 2013--2026
Railton Barbosa de Andrade and
Ezequiel Fragoso Vieira Leitão and
Miguel Angelo Fonseca de Souza and
Elizete Ventura and
Silmar Andrade do Monte Effect of methylation on relative
energies of tautomers and on the
intramolecular proton transfer barriers
of protonated nitrosamine: a MR--CISD
study . . . . . . . . . . . . . . . . . 2027--2036
Sergei F. Vyboishchikov Modeling exact exchange potential in
spherically confined atoms . . . . . . . 2037--2043
Guillaume Chevrot and
Eudes Eterno Fileti and
Vitaly V. Chaban Enhanced stability of the model
mini-protein in amino acid ionic liquids
and their aqueous solutions . . . . . . 2044--2051
Anna Pavlova and
James C. Gumbart Parametrization of macrolide antibiotics
using the force field toolkit . . . . . 2052--2063
Jonah Z. Vilseck and
Jakub Kostal and
Julian Tirado-Rives and
William L. Jorgensen Application of a BOSS-Gaussian interface
for QM/MM simulations of Henry and
methyl transfer reactions . . . . . . . 2064--2074
Arnaud Fihey and
Christian Hettich and
Jérémy Touzeau and
François Maurel and
Aurélie Perrier and
Christof Köhler and
Bálint Aradi and
Thomas Frauenheim SCC--DFTB parameters for simulating
hybrid gold-thiolates compounds . . . . 2075--2087
Anonymous Cover Image, Volume 36, Issue 28 . . . . i--ii
Holger Vach and
Lena V. Ivanova and
Qadir K. Timerghazin and
Fatme Jardali and
Ha-Linh Thi Le A deeper insight into strain for the
sila-bi[6]prismane (Si$_{18}$H$_{12}$)
cluster with its endohedrally trapped
silicon atom, Si$_{19}$H$_{12}$ . . . . 2089--2094
Grygoriy A. Dolgonos and
Koshka Mekalka Strain in nonclassical silicon hydrides:
an insight into the ``ultrastability''
of sila-bi[6]prismane (Si$_{18}$
H$_{12}$) cluster with the endohedrally
trapped silicon atom, Si$_{19}$ H$_{12}$ 2095--2102
Yuuichi Orimoto and
Kai Liu and
Yuriko Aoki Elongation method for electronic
structure calculations of random DNA
sequences . . . . . . . . . . . . . . . 2103--2113
Samuel Genheden and
Ulf Ryde and
Pär Söderhjelm Binding affinities by alchemical
perturbation using QM\slash MM with a
large QM system and polarizable MM model 2114--2124
Régis Tadeu Santiago and
Roberto Luiz Andrade Haiduke New density functional parameterizations
to accurate calculations of electric
field gradient variations among
compounds . . . . . . . . . . . . . . . 2125--2130
Maxim R. Ryzhikov and
Vladimir A. Slepkov and
Svetlana G. Kozlova and
Svyatoslav P. Gabuda and
Vladimir E. Fedorov Solid-state reaction as a mechanism of
1T $ \leftrightarrow $ 2H transformation
in MoS$_2$ monolayers . . . . . . . . . 2131--2134
Al Mokhtar Lamsabhi and
Soledad Gutiérrez-Oliva and
Otilia Mó and
Alejandro Toro-Labbé and
Manuel Yáñez Effects of the ionization in the
tautomerism of uracil: a reaction
electronic flux perspective . . . . . . 2135--2145
Anonymous Cover Image, Volume 36, Issue 29 . . . . i--ii
Ilkay Sakalli and
Ernst-Walter Knapp pK$_A$ in proteins solving the
Poisson--Boltzmann equation with finite
elements . . . . . . . . . . . . . . . . 2147--2157
Kestutis Aidas and
Kiril Lanevskij and
Rytis Kubilius and
Liutauras Juska and
Daumantas Petkevicius and
Pranas Japertas Aqueous acidities of primary
benzenesulfonamides: Quantum chemical
predictions based on density functional
theory and SMD . . . . . . . . . . . . . 2158--2167
Sudip Pan and
Ashutosh Gupta and
Ranajit Saha and
Gabriel Merino and
Pratim K. Chattaraj A coupled-cluster study on the noble gas
binding ability of metal cyanides versus
metal halides (metal = Cu, Ag, Au) . . . 2168--2176
Krishnakanta Mondal and
Arup Banerjee and
Alessandro Fortunelli and
Tapan K. Ghanty Does enhanced oxygen activation always
facilitate CO oxidation on gold
clusters? . . . . . . . . . . . . . . . 2177--2187
Pouya Partovi-Azar and
Thomas D. Kühne Efficient ``On-the-Fly'' calculation of
Raman Spectra from Ab-Initio molecular
dynamics: Application to
hydrophobic/hydrophilic solutes in bulk
water . . . . . . . . . . . . . . . . . 2188--2192
Olga A. Gapurenko and
Andrey G. Starikov and
Ruslan M. Minyaev and
Vladimir I. Minkin Germanium, carbon-germanium, and
silicon-germanium triangulenes . . . . . 2193--2199
Marat Sibaev and
Deborah L. Crittenden Software News and Updates: The PyPES
library of high quality semi-global
potential energy surfaces . . . . . . . 2200--2207
Jing Huang and
Likai Du and
Deping Hu and
Zhenggang Lan Erratum: Theoretical analysis of excited
states and energy transfer mechanism in
conjugated dendrimers . . . . . . . . . 2208--2208
Anonymous Cover Image, Volume 36, Issue 30 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 30 . . . . iii--iv
Takao Otsuka and
Noriaki Okimoto and
Makoto Taiji Assessment and acceleration of binding
energy calculations for protein-ligand
complexes by the fragment molecular
orbital method . . . . . . . . . . . . . 2209--2218
Jacek Koput Ab Initio spectroscopic characterization
of borane, BH, in its X $^1 \Sigma^+$
electronic state . . . . . . . . . . . . 2219--2227
Wenjing Gong and
Ruibo Wu and
Yingkai Zhang Thiol versus hydroxamate as zinc binding
group in HDAC inhibition: An Ab initio
QM/MM molecular dynamics study . . . . . 2228--2235
Tobias Neumann and
Denis Danilov and
Wolfgang Wenzel Multiparticle moves in acceptance rate
optimized Monte Carlo . . . . . . . . . 2236--2245
Roberto Cammi A new extension of the polarizable
continuum model: Toward a quantum
chemical description of chemical
reactions at extreme high pressure . . . 2246--2259
Lucas Modesto-Costa and
Elmar Uhl and
Itamar Borges Jr Water solvent effects using continuum
and discrete models: the nitromethane
molecule, CH$_3$ NO$_2$ . . . . . . . . 2260--2269
Anonymous Erratum to Csonka, G. I., Nguyen, N. A.,
& Kolossváry, I. (1997). Simple tests for
density functional methods. Journal of
Computational Chemistry, 18 (12),
1534--1545. (DOI: \urlc7rfjv) . . . . . 2270--2270
Anonymous Cover Image, Volume 36, Issue 31 . . . . i--ii
Anonymous Cover Image, Volume 36, Issue 31 . . . . iii--iv
Anonymous Cover Image, Volume 36, Issue 31 . . . . v--vi
Ivan Carnimeo and
Chiara Cappelli and
Vincenzo Barone Analytical gradients for MP2, double
hybrid functionals, and TD-DFT with
polarizable embedding described by
fluctuating charges . . . . . . . . . . 2271--2290
M. Bartolomei and
F. Pirani and
J. M. C. Marques Low-energy structures of benzene
clusters with a novel accurate potential
surface . . . . . . . . . . . . . . . . 2291--2301
Dan Fraenkel Ion strength limit of computed excess
functions based on the linearized
Poisson--Boltzmann equation . . . . . . 2302--2316
Guo-Liang Fan and
Xiao-Yan Zhang and
Yan-Ling Liu and
Yi Nang and
Hui Wang DSPMP: Discriminating secretory proteins
of malaria parasite by hybridizing
different descriptors of Chou's pseudo
amino acid patterns . . . . . . . . . . 2317--2327
Pradeep R. Varadwaj and
Arpita Varadwaj and
Bih-Yaw Jin Hexahalogenated and their mixed benzene
derivatives as prototypes for the
understanding of halogen$ \cdots $
halogen intramolecular interactions: New
insights from combined DFT, QTAIM-, and
RDG-based NCI analyses . . . . . . . . . 2328--2343
Yoshiharu Mori and
Hisashi Okumura Simulated tempering based on global
balance or detailed balance conditions:
Suwa--Todo, heat bath, and Metropolis
algorithms . . . . . . . . . . . . . . . 2344--2349
Anmol Kumar and
Sachin D. Yeole and
Shridhar R. Gadre and
Rafael López and
Jaime F. Rico and
Guillermo Ramírez and
Ignacio Ema and
David Zorrilla Software News and Updates: DAMQT 2.1.0:
a new version of the DAMQT package
enabled with the topographical analysis
of electron density and electrostatic
potential in molecules . . . . . . . . . 2350--2359
Anonymous Cover Image, Volume 36, Issue 32 . . . . i--ii
Salvatore Cardamone and
Paul L. A. Popelier Prediction of conformationally dependent
atomic multipole moments in
carbohydrates . . . . . . . . . . . . . 2361--2373
Yuanyuan Li and
Li Wang and
Xugeng Guo and
Jinglai Zhang A CASSCF/CASPT2 insight into
excited-state intramolecular proton
transfer of four imidazole derivatives 2374--2380
Marharyta Petukh and
Min Zhang and
Emil Alexov Statistical investigation of surface
bound ions and further development of
BION server to include pH and salt
dependence . . . . . . . . . . . . . . . 2381--2393
Matti Hellström and
Daniel Spångberg and
Kersti Hermansson Treatment of delocalized electron
transfer in periodic and embedded
cluster DFT calculations: the case of Cu
on ZnO (10$ \bar 1 $0) . . . . . . . . . 2394--2405
Takuma Nozawa and
Kazuaki Z. Takahashi and
Tetsu Narumi and
Kenji Yasuoka Comparison of the accuracy of periodic
reaction field methods in molecular
dynamics simulations of a model liquid
crystal system . . . . . . . . . . . . . 2406--2411
Sirous Yourdkhani and
Tatiana Korona and
Nasser L. Hadipour Interplay between tetrel and triel bonds
in RC$_6$H$_4$CN$ \cdot $MF$_3$ CN$
\cdot $BX$_3$ complexes: a combined
symmetry-adapted perturbation theory,
Mòller--Plesset, and quantum theory of
atoms-in-molecules study . . . . . . . . 2412--2428
Eric Iván Sánchez-Flores and
Rodrigo Chávez-Calvillo and
Todd A. Keith and
Gabriel Cuevas and
Tomás Rocha-Rinza and
Fernando Cortés-Guzmán Erratum: Properties of atoms in
electronically excited molecules within
the formalism of TDDFT [J. Comput Chem.
2014, \bf 35, 820--828] . . . . . . . . 2429--2429
Anonymous Cover Image, Volume 37, Issue 1 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 1 . . . . ii--ii
Anonymous Cover Image, Volume 37, Issue 1 . . . . iii--iii
Anonymous Issue Information --- Coming Soon,
Volume 37, Issue 1 . . . . . . . . . . . 1--1
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37, Issue 1 . . . . . . . . . . . . . . 2--2
Anonymous Issue Information -- Editorial Board,
Volume 37, Issue 1 . . . . . . . . . . . 3--3
Anonymous Issue Information --- Table of Contents
Volume 37, Issue 1 . . . . . . . . . . . 4--8
Anonymous Editorial: Paul Von Ragué Schleyer
(1930--2014) . . . . . . . . . . . . . . 9--9
Lukas N. Wirz and
Ralf Tonner and
Andreas Hermann and
Rebecca Sure and
Peter Schwerdtfeger From small fullerenes to the graphene
limit: a harmonic force-field method for
fullerenes and a comparison to density
functional calculations for
Goldberg--Coxeter fullerenes up to
C$_{980}$ . . . . . . . . . . . . . . . 10--17
Andreas J. Achazi and
Larissa K. S. von Krbek and
Christoph A. Schalley and
Beate Paulus Theoretical and experimental
investigation of crown/ammonium
complexes in solution . . . . . . . . . 18--24
Rodrigo A. Cormanich and
Roberto Rittner and
David O'Hagan and
Michael Bühl Inter- and intramolecular CF$ \cdots
$C\doublebond O interactions on
aliphatic and cyclohexane carbonyl
derivatives . . . . . . . . . . . . . . 25--33
Changwei Wang and
Liangyu Guan and
David Danovich and
Sason Shaik and
Yirong Mo The origins of the directionality of
noncovalent intermolecular interactions 34--45
Yunfei Zhou and
Xiaoguang Bao and
Weston Thatcher Borden Nucleus-independent chemical shift
analysis of the electronic states of the
(CO)$_4$, (CS)$_4$, and (CSe)$_4$
molecules . . . . . . . . . . . . . . . 46--48
Amir Karton and
Peter R. Schreiner and
Jan M. L. Martin Heats of formation of platonic
hydrocarbon cages by means of high-level
thermochemical procedures . . . . . . . 49--58
Megha Anand and
Israel Fernández and
Henry F. Schaefer III and
Judy I-Chia Wu Hydrogen bond--aromaticity cooperativity
in self-assembling $4$-pyridone chains 59--63
Alexandru Lupan and
R. Bruce King Molybdatricarbaboranes as examples of
isocloso metallaborane deltahedra with
three carbon vertices . . . . . . . . . 64--69
George A. Olah and
G. K. Surya Prakash and
Golam Rasul Ab initio /GIAO-CCSD(T)$^{13}$ C NMR
study of the rearrangement and dynamic
aspects of rapidly equilibrating
tertiary carbocations, C$_6$H$_{13}^+$
and C$_7$H$_{15}^+$ . . . . . . . . . . 70--77
Ramon Carbó-Dorca Aromaticity, quantum multimolecular
polyhedra, and quantum QSPR fundamental
equation . . . . . . . . . . . . . . . . 78--82
Riccardo Petraglia and
Adrien Nicola\"\i and
Matthew D. Wodrich and
Michele Ceriotti and
Clemence Corminboeuf Beyond static structures: Putting forth
REMD as a tool to solve problems in
computational organic chemistry . . . . 83--92
Martin Kaupp and
Simon Gückel and
Manuel Renz and
Sascha Klawohn and
Kolja Theilacker and
Matthias Parthey and
Christoph Lambert Electron transfer pathways in
mixed-valence paracyclophane-bridged
bis-triarylamine radical cations . . . . 93--102
Xiaohu Yu and
Artem R. Oganov and
Ivan A. Popov and
Alexander I. Boldyrev d-AO spherical aromaticity in
Ce$_6$O$_8$ . . . . . . . . . . . . . . 103--109
Klara Edel and
Reinhold F. Fink and
Holger F. Bettinger Isomerization and fragmentation pathways
of 1,2-azaborine . . . . . . . . . . . . 110--116
Brian J. Levandowski and
Lufeng Zou and
K. N. Houk Schleyer hyperconjugative aromaticity
and Diels--Alder reactivity of
$5$-substituted cyclopentadienes . . . . 117--123
Jenn-Huei Lii and
Norman L. Allinger and
Ching-Han Hu and
Henry F. Schaefer III Catenanes: a molecular mechanics
analysis of the (C$_{13}$H$_{26}$)$_2$
Structure 13-13 D2 . . . . . . . . . . . 124--129
Elfi Kraka and
Dani Setiawan and
Dieter Cremer Re-evaluation of the bond length--bond
strength rule: the stronger bond is not
always the shorter bond . . . . . . . . 130--142
Chérif F. Matta and
Seyed Abdolreza Sadjadi and
Dale A. Braden and
Gernot Frenking The barrier to the methyl rotation in
Cis-$2$-butene and its isomerization
energy to Trans-$2$-butene, revisited 143--154
Anonymous Cover Image, Volume 37, Issue 2 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 2 . . . . ii--ii
Anonymous Issue Information --- Coming Soon,
Volume 37, Issue 2 . . . . . . . . . . . 155--155
Anonymous Issue Information --- Copyright, Volume
37, Issue 2 . . . . . . . . . . . . . . 156--156
Anonymous Issue Information --- Editorial Board,
Volume 37, Issue 2 . . . . . . . . . . . 157--157
Anonymous Issue Information --- Table of Contents,
Volume 37, Issue 2 . . . . . . . . . . . 158--161
Jose L. Mendoza-Cortes and
Qi An and
William A. Goddard III and
Caichao Ye and
Sergey Zybin Prediction of the crystal packing of
di-tetrazine-tetroxide (DTTO) energetic
material . . . . . . . . . . . . . . . . 163--167
Haijun Jiao and
Kathrin Junge and
Elisabetta Alberico and
Matthias Beller A comparative computationally study
about the defined m(II) pincer
hydrogenation catalysts (m = FE, Ru, Os) 168--176
Guoliang Li and
Hui Wang and
Qian-Shu Li and
Yaoming Xie and
Henry F. Schaefer III The Reaction between Bromine and the
Water Dimer and the Highly Exothermic
Reverse Reaction . . . . . . . . . . . . 177--182
Bun Chan and
Lars Goerigk and
Leo Radom On the inclusion of post-MP2
contributions to double-Hybrid density
functionals . . . . . . . . . . . . . . 183--193
Habib U. Rehman and
Nida A. McKee and
Michael L. McKee Saturn Systems . . . . . . . . . . . . . 194--209
Andrey V. Shernyukov and
Alexander M. Genaev and
George E. Salnikov and
Henry S. Rzepa and
Vyacheslav G. Shubin Noncatalytic bromination of benzene: a
combined computational and experimental
study . . . . . . . . . . . . . . . . . 210--225
Sudip Pan and
Diego Moreno and
Sreyan Ghosh and
Pratim K. Chattaraj and
Gabriel Merino Structure and stability of noble gas
bound EX$_3^+$ compounds (E = C, Ge, Sn,
Pb; X = H, F, Cl, Br) . . . . . . . . . 226--236
C. R. Landis and
F. Weinhold $ 18$-electron rule and the 3c/4e
hyperbonding saturation limit . . . . . 237--241
Masahiro Ehara and
Ryoichi Fukuda and
Thomas Sommerfeld Projected CAP/SAC-CI method with smooth
Voronoi potential for calculating
resonance states . . . . . . . . . . . . 242--249
Hongyan Wang and
Hui Wang and
R. Bruce King and
Henry F. Schaefer III Bis(azulene) ``submarine'' metal dimer
sandwich compounds (C$_{10}$H$_8$)$_2$
M$_2$ (M = Ti, V, Cr, Mn, Fe, Co, Ni):
Parallel and opposed orientations . . . 250--260
Xue-Feng Zhao and
Haixia Li and
Cai-Xia Yuan and
Yan-Qin Li and
Yan-Bo Wu and
Zhi-Xiang Wang Linear, planar, and tubular molecular
structures constructed by double planar
tetracoordinate carbon D$_{2h}$ C$_2$
(BeH)$_4$ species via hydrogen-bridged
BeH$_2$Be bonds . . . . . . . . . . . . 261--269
Jyothish Joy and
Anex Jose and
Eluvathingal D. Jemmis Continuum in the X--Z---Y weak bonds: Z
= main group elements . . . . . . . . . 270--279
Berit Heggen and
Mahendra Patil and
Walter Thiel Cyclization of an $ \alpha $, $ \beta
$-Unsaturated hydrazone catalyzed by a
BINOL-phosphoric acid: Pericyclic or
not? . . . . . . . . . . . . . . . . . . 280--285
Arkajyoti Sengupta and
Raghunath O. Ramabhadran and
Krishnan Raghavachari Breaking a bottleneck: Accurate
extrapolation to ``gold standard''
CCSD(T) energies for large open shell
organic radicals at reduced
computational cost . . . . . . . . . . . 286--295
Xue-Feng Zhao and
Cai-Xia Yuan and
Xiang Wang and
Jia-Jia Li and
Yan-Bo Wu and
Xiaotai Wang Computational design of organometallic
oligomers featuring 1,3-metal-carbon
bonding and planar tetracoordinate
carbon atoms . . . . . . . . . . . . . . 296--303
Joshua R. Mulder and
Célia Fonseca Guerra and
J. Chris Slootweg and
Koop Lammertsma and
F. Matthias Bickelhaupt Substituent effects on the optical
properties of naphthalenediimides: a
frontier orbital analysis across the
periodic table . . . . . . . . . . . . . 304--313
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Volume 37, Issue 3 . . . . . . . . . . . 318--319
Yingdi Jin and
Neil Qiang Su and
Xin Xu and
Hao Hu Self-consistent field for fragmented
quantum mechanical model of large
molecular systems . . . . . . . . . . . 321--326
Arifin and
Maneeporn Puripat and
Daisuke Yokogawa and
Vudhichai Parasuk and
Stephan Irle Glucose transformation to
$5$-hydroxymethylfurfural in acidic
ionic liquid: a quantum mechanical study 327--335
Li Rao and
Bo Chi and
Yanliang Ren and
Yongjian Li and
Xin Xu and
Jian Wan DOX: a new computational protocol for
accurate prediction of the
protein--ligand binding structures . . . 336--344
Dilan Yildiz and
U\ugur Bozkaya Assessment of the extended Koopmans'
theorem for the chemical reactivity:
Accurate computations of chemical
potentials, chemical hardnesses, and
electrophilicity indices . . . . . . . . 345--353
Wojciech Plazinski and
Alice Lonardi and
Philippe H. Hünenberger Revision of the GROMOS 56A6$_{CARBO}$
force field: Improving the description
of ring-conformational equilibria in
hexopyranose-based carbohydrates chains 354--365
M. Althaf Hussain and
Dolly Vijay and
G. Narahari Sastry Buckybowls as adsorbents for CO$_2$,
CH$_4$, and C$_2$H$_2$: Binding and
structural insights from computational
study . . . . . . . . . . . . . . . . . 366--377
Sheng-Chun Yang and
Yong-Lei Wang and
Gui-Sheng Jiao and
Hu-Jun Qian and
Zhong-Yuan Lu Software News and Updates: Accelerating
electrostatic interaction calculations
with graphical processing units based on
new developments of Ewald method using
non-uniform Fast Fourier Transform . . . 378--387
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Volume 37, Issue 4 . . . . . . . . . . . 391--391
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Volume 37, Issue 4 . . . . . . . . . . . 392--393
Marzena Jankowska and
Teobald Kupka and
Leszek Stobi\'nski and
Rasmus Faber and
Evanildo G. Lacerda Jr. and
Stephan P. A. Sauer Spin-orbit ZORA and four-component
Dirac--Coulomb estimation of
relativistic corrections to isotropic
nuclear shieldings and chemical shifts
of noble gas dimers . . . . . . . . . . 395--403
Karen Druart and
Zoltan Palmai and
Eyaz Omarjee and
Thomas Simonson Protein:Ligand binding free energies: a
stringent test for computational protein
design . . . . . . . . . . . . . . . . . 404--415
Sirish Kaushik Lakkaraju and
Justin A. Lemkul and
Jing Huang and
Alexander D. MacKerell Jr. DIRECT--ID: an automated method to
identify and quantify conformational
variations --- application to $
\beta_2$-adrenergic GPCR . . . . . . . . 416--425
Ngaam J. Cheung and
Xue-Ming Ding and
Hong-Bin Shen Protein folds recognized by an
intelligent predictor based-on
evolutionary and structural information 426--436
Vincent Zoete and
Thierry Schuepbach and
Christophe Bovigny and
Prasad Chaskar and
Antoine Daina and
Ute F. Röhrig and
Olivier Michielin Attracting cavities for docking.
Replacing the rough energy landscape of
the protein by a smooth attracting
landscape . . . . . . . . . . . . . . . 437--447
Murat Keçeli and
Hong Zhang and
Peter Zapol and
David A. Dixon and
Albert F. Wagner Shift-and-invert parallel spectral
transformation eigensolver: Massively
parallel performance for
density-functional based tight-binding 448--459
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Volume 37, Issue 5 . . . . . . . . . . . 464--465
Anna Stachiewicz and
Andrzej Molski Diffusive dynamics of DNA unzipping in a
nanopore . . . . . . . . . . . . . . . . 467--476
Rahul V. Pinjari and
Mickaël G. Delcey and
Meiyuan Guo and
Michael Odelius and
Marcus Lundberg Cost and sensitivity of restricted
active-space calculations of metal
L-edge X-ray absorption spectra . . . . 477--486
Yu Harabuchi and
Yuriko Ono and
Satoshi Maeda and
Tetsuya Taketsugu and
Kristopher Keipert and
Mark S. Gordon Nontotally symmetric trifurcation of an
S$_N$2 reaction pathway . . . . . . . . 487--493
Christophe Narth and
Louis Lagard\`ere and
Étienne Polack and
Nohad Gresh and
Qiantao Wang and
David R. Bell and
Joshua A. Rackers and
Jay W. Ponder and
Pengyu Y. Ren and
Jean-Philip Piquemal Scalable improvement of SPME multipolar
electrostatics in anisotropic
polarizable molecular mechanics using a
general short-range penetration
correction up to quadrupoles . . . . . . 494--506
Francesco Aquilante and
Jochen Autschbach and
Rebecca K. Carlson and
Liviu F. Chibotaru and
Mickaël G. Delcey and
Luca De Vico and
Ignacio Fdez. Galván and
Nicolas Ferré and
Luis Manuel Frutos and
Laura Gagliardi and
Marco Garavelli and
Angelo Giussani and
Chad E. Hoyer and
Giovanni Li Manni and
Hans Lischka and
Dongxia Ma and
Per Åke Malmqvist and
Thomas Müller and
Artur Nenov and
Massimo Olivucci and
Thomas Bondo Pedersen and
Daoling Peng and
Felix Plasser and
Ben Pritchard and
Markus Reiher and
Ivan Rivalta and
Igor Schapiro and
Javier Segarra-Martí and
Michael Stenrup and
Donald G. Truhlar and
Liviu Ungur and
Alessio Valentini and
Steven Vancoillie and
Valera Veryazov and
Victor P. Vysotskiy and
Oliver Weingart and
Felipe Zapata and
Roland Lindh Software News and Updates: Molcas 8: New
capabilities for multiconfigurational
quantum chemical calculations across the
periodic table . . . . . . . . . . . . . 506--541
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Volume 37, Issue 6 . . . . . . . . . . . 545--545
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Volume 37, Issue 6 . . . . . . . . . . . 546--548
Wei Yang Editorial: Advanced Sampling for
Molecular Simulation is Coming of Age 549--549
Kuo Hao Lee and
Jianhan Chen Multiscale enhanced sampling of
intrinsically disordered protein
conformations . . . . . . . . . . . . . 550--557
Gregory R. Bowman Accurately modeling nanosecond protein
dynamics requires at least microseconds
of simulation . . . . . . . . . . . . . 558--566
Chao Lv and
Erick W. Aitchison and
Dongsheng Wu and
Lianqing Zheng and
Xiaolin Cheng and
Wei Yang Comparative exploration of hydrogen
sulfide and water transmembrane free
energy surfaces via orthogonal space
tempering free energy sampling . . . . . 567--574
Davide Branduardi and
Fabrizio Marinelli and
José D. Faraldo-Gómez Atomic-resolution dissection of the
energetics and mechanism of
isomerization of hydrated ATP-Mg$^{2+}$
through the SOMA string method . . . . . 575--586
Alex Dickson and
Logan S. Ahlstrom and
Charles L. Brooks III Coupled folding and binding with 2D
Window-Exchange Umbrella Sampling . . . 587--594
Xiongwu Wu and
Bernard R. Brooks and
Eric Vanden-Eijnden Self-guided Langevin dynamics via
generalized Langevin equation . . . . . 595--601
Juan M. Bello-Rivas and
Ron Elber Simulations of thermodynamics and
kinetics on rough energy landscapes with
milestoning . . . . . . . . . . . . . . 602--613
Xiangda Peng and
Yuebin Zhang and
Huiying Chu and
Guohui Li Free energy simulations with the AMOEBA
polarizable force field and metadynamics
on GPU platform . . . . . . . . . . . . 614--622
Raimondas Galvelis and
Yuji Sugita The Following Articles were Published in
Past Issues of the \booktitleJournal of
Computational Chemistry: Replica State
Exchange Metadynamics for Improving the
Convergence of Free Energy Estimates . .
Yinglong Miao and
Ferran Feixas and
Changsun Eun and
J. Andrew McCammon The Following Articles were Published in
Past Issues of the \booktitleJournal of
Computational Chemistry: Accelerated
Molecular Dynamics Simulations of
Protein Folding . . . . . . . . . . . .
Junchao Xia and
William F. Flynn and
Emilio Gallicchio and
Bin W. Zhang and
Peng He and
Zhiqiang Tan and
Ronald M. Levy The Following Articles were Published in
Past Issues of the \booktitleJournal of
Computational Chemistry: Large-Scale
Asynchronous and Distributed
Multidimensional Replica Exchange
Molecular Simulations and Efficiency
Analysis . . . . . . . . . . . . . . . .
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Volume 37, Issue 7 . . . . . . . . . . . 626--627
Alexander Cumberworth and
Jennifer M. Bui and
Jörg Gsponer Free energies of solvation in the
context of protein folding: Implications
for implicit and explicit solvent models 629--640
Andrei V. Bandura and
Vitaly V. Porsev and
Robert A. Evarestov Application of zone-folding approach to
the first-principles estimation of
thermodynamic properties of carbon and
ZrS$_2$-based nanotubes . . . . . . . . 641--652
Zhao Jin and
Chunwei Yang and
Fenglei Cao and
Feng Li and
Zhifeng Jing and
Long Chen and
Zhe Shen and
Liang Xin and
Sijia Tong and
Huai Sun Hierarchical atom type definitions and
extensible all-atom force fields . . . . 653--664
Arne Scherrer and
Daniel Sebastiani Moment expansion of the linear
density-density response function . . . 665--674
Gessenildo Pereira Rodrigues and
Elizete Ventura and
Silmar Andrade do Monte and
Mario Barbatti UV-photoexcitation and ultrafast
dynamics of HCFC-132b (CF$_2$ ClCH$_2$
Cl) . . . . . . . . . . . . . . . . . . 675--683
Haitao Sun and
Shian Zhang and
Cheng Zhong and
Zhenrong Sun Theoretical study of excited states of
DNA base dimers and tetramers using
optimally tuned range-separated density
functional theory . . . . . . . . . . . 684--693
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Volume 37, Issue 8 . . . . . . . . . . . 697--697
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Volume 37, Issue 8 . . . . . . . . . . . 698--699
Miguel A. F. de Souza and
Elizete Ventura and
Silmar A. do Monte and
José M. Riveros and
Ricardo L. Longo Revisiting the concept of the
(a)synchronicity of Diels--Alder
reactions based on the dynamics of
quasiclassical trajectories . . . . . . 701--711
Hiraku Oshima and
Masahiro Kinoshita A highly efficient hybrid method for
calculating the hydration free energy of
a protein . . . . . . . . . . . . . . . 712--723
Ryuhei Harada and
Tomotake Nakamura and
Yasuteru Shigeta Sparsity-weighted outlier FLOODing
(OFLOOD) method: Efficient rare event
sampling method using sparsity of
distribution . . . . . . . . . . . . . . 724--738
Christine-Andrea Roth and
Tom Dreyfus and
Charles H. Robert and
Frédéric Cazals Hybridizing rapidly exploring random
trees and basin hopping yields an
improved exploration of energy
landscapes . . . . . . . . . . . . . . . 739--752
Jessica K. Gagnon and
Sean M. Law and
Charles L. Brooks III Flexible CDOCKER: Development and
application of a pseudo-explicit
structure-based docking method within
CHARMM . . . . . . . . . . . . . . . . . 753--762
Simon W. L. Hogan and
Tanja van Mourik Competition between hydrogen and halogen
bonding in halogenated
1-methyluracil:water systems . . . . . . 763--770
Julien Racine and
Denis Hagebaum-Reignier and
Yannick Carissan and
Stéphane Humbel Recasting wave functions into valence
bond structures: a simple projection
method to describe excited states . . . 771--779
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Volume 37, Issue 9 . . . . . . . . . . . 784--785
Cláudio M. Lousada and
Pavel A. Korzhavyi Surface chemistry of oxygen on aluminum
--- Performance of the density
functionals: PBE, PBE0, M06, and M06-L 787--794
Min Li and
John Z. H. Zhang and
Fei Xia A new algorithm for construction of
coarse-grained sites of large
biomolecules . . . . . . . . . . . . . . 795--804
Alain C. Vaucher and
Moritz P. Haag and
Markus Reiher Real-time feedback from iterative
electronic structure calculations . . . 805--812
Xi Chen and
Fu-Quan Bai and
Yongan Tang and
Hong-Xing Zhang How the substituents in corannulene and
sumanene derivatives alter their
molecular assemblings and charge
transport properties? --- A theoretical
study with a dimer model . . . . . . . . 813--824
Bolong Huang $ 4 f $ fine-structure levels as the
dominant error in the electronic
structures of binary lanthanide oxides 825--835
Pin-Chih Su and
Michael E. Johnson Evaluating thermodynamic integration
performance of the new Amber molecular
dynamics package and assess potential
halogen bonds of enoyl-ACP reductase
(FabI) benzimidazole inhibitors . . . . 836--847
Maciej Dziubi\'nski and
Bogdan Lesyng Toward the identification of molecular
cogs . . . . . . . . . . . . . . . . . . 848--860
Davide Presti and
Frédéric Labat and
Alfonso Pedone and
Michael J. Frisch and
Hrant P. Hratchian and
Ilaria Ciofini and
Maria Cristina Menziani and
Carlo Adamo Modeling emission features of
salicylidene aniline molecular crystals:
a QM/QM' approach . . . . . . . . . . . 861--870
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Volume 37, Issue 10 . . . . . . . . . . 874--875
Hongbo Du and
Xianghong Qian The hydration properties of
carboxybetaine zwitterion brushes . . . 877--885
Y. Ohta Possible mechanism of BN fullerene
formation from a boron cluster:
Density-functional tight-binding
molecular dynamics simulations . . . . . 886--895
You Xu and
Kenno Vanommeslaeghe and
Alexey Aleksandrov and
Alexander D. MacKerell Jr. and
Lennart Nilsson Additive CHARMM force field for
naturally occurring modified
ribonucleotides . . . . . . . . . . . . 896--912
Roman Osman and
Mihaly Mezei and
Stanislav Engel The role of protein ``Stability
patches'' in molecular recognition: a
case study of the human growth
hormone-receptor complex . . . . . . . . 913--919
Leebyn Chong and
Fikret Aydin and
Meenakshi Dutt Implicit solvent coarse-grained model of
polyamidoamine dendrimers: Role of
generation and pH . . . . . . . . . . . 920--926
Evan J. Arthur and
Charles L. Brooks III Parallelization and improvements of the
generalized born model with a simple
switching function for modern graphics
processors . . . . . . . . . . . . . . . 927--939
Rodrigo Galindo-Murillo and
Luis Enrique Aguilar-Suárez and
Joaquín Barroso-Flores A mixed DFT-MD methodology for the \em
in silico development of drug releasing
macrocycles. Calix and
thia-calix[N]arenes as carriers for
Bosutinib and Sorafenib . . . . . . . . 940--946
Sergi Vela and
Maria Fumanal and
Jordi Ribas-Ariño and
Vincent Robert On the zeroth-order Hamiltonian for
CASPT2 calculations of spin crossover
compounds . . . . . . . . . . . . . . . 947--953
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37, Issue 11 . . . . . . . . . . . . . . 956--956
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Volume 37, Issue 11 . . . . . . . . . . 957--957
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Volume 37, Issue 11 . . . . . . . . . . 958--959
Artem B. Mamonov and
Mohammad Moghadasi and
Hanieh Mirzaei and
Shahrooz Zarbafian and
Laurie E. Grove and
Tanggis Bohnuud and
Pirooz Vakili and
Ioannis Ch. Paschalidis and
Sandor Vajda and
Dima Kozakov Focused grid-based resampling for
protein docking and mapping . . . . . . 961--970
Il Seung Youn and
Woo Jong Cho and
Kwang S. Kim Effects of an electric field on
interaction of aromatic systems . . . . 971--975
Yuedong Yang and
Yaoqi Zhou Effective protein conformational
sampling based on predicted torsion
angles . . . . . . . . . . . . . . . . . 976--980
Ingrid G. Prandi and
Lucas Viani and
Oliviero Andreussi and
Benedetta Mennucci Combining classical molecular dynamics
and quantum mechanical methods for the
description of electronic excitations:
the case of carotenoids . . . . . . . . 981--991
Bhaskar Sharma and
Y. Indra Neela and
G. Narahari Sastry Structures and energetics of
complexation of metal ions with ammonia,
water, and benzene: a computational
study . . . . . . . . . . . . . . . . . 992--1004
M. Witte and
U. Gerstmann and
A. Neuba and
G. Henkel and
W. G. Schmidt Density functional theory of the
Cu$_A$-like Cu$_2$S$_2$ diamond core in
Cu$_2$II(NGuaS)$_2$Cl$_2$ . . . . . . . 1005--1018
Eric G. Kratz and
Alice R. Walker and
Louis Lagard\`ere and
Filippo Lipparini and
Jean-Philip Piquemal and
G. Andrés Cisneros Software News and Updates: LICHEM: a
QM/MM program for simulations with
multipolar and polarizable force fields 1019--1029
Stefan Maintz and
Volker L. Deringer and
Andrei L. Tchougréeff and
Richard Dronskowski Software News and Updates: LOBSTER: a
tool to extract chemical bonding from
plane-wave based DFT . . . . . . . . . . 1030--1035
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Volume 37, Issue 12 . . . . . . . . . . 1039--1039
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Volume 37, Issue 12 . . . . . . . . . . 1040--1042
Jiaye Su and
Keda Yang Temperature dependence of the transport
of single-file water molecules through a
hydrophobic channel . . . . . . . . . . 1043--1047
Seydou Traoré and
Kyle E. Roberts and
David Allouche and
Bruce R. Donald and
Isabelle André and
Thomas Schiex and
Sophie Barbe Fast search algorithms for computational
protein design . . . . . . . . . . . . . 1048--1058
Jiri Brabec and
Chao Yang and
Evgeny Epifanovsky and
Anna I. Krylov and
Esmond Ng Reduced-cost sparsity-exploiting
algorithm for solving coupled-cluster
equations . . . . . . . . . . . . . . . 1059--1067
Daniela E. Ortega and
Quynh Nhu N. Nguyen and
Dean J. Tantillo and
Alejandro Toro-Labbé The catalytic effect of the NH$_3$ base
on the chemical events in the
caryolene-forming carbocation cascade 1068--1081
Emanuele Rossini and
Ernst-Walter Knapp Proton solvation in protic and aprotic
solvents . . . . . . . . . . . . . . . . 1082--1091
Johannes Heuser and
Sebastian Höfener Wave-function frozen-density embedding:
Approximate analytical nuclear
ground-state gradients . . . . . . . . . 1092--1101
Bachir Aoun Fullrmc, a rigid body reverse Monte
Carlo modeling package enabled with
machine learning and artificial
intelligence . . . . . . . . . . . . . . 1102--1111
Ronald D. Hills Jr. and
Nicholas McGlinchey Model parameters for simulation of
physiological lipids . . . . . . . . . . 1112--1118
Md Tamjidul Hoque and
Yuedong Yang and
Avdesh Mishra and
Yaoqi Zhou Software News and Updates: sDFIRE:
Sequence-specific statistical energy
function for protein structure
prediction by decoy selections . . . . . 1119--1124
Yu Takano and
Kazuto Nakata and
Yasushige Yonezawa and
Haruki Nakamura Software News and Updates: Development
of massive multilevel molecular dynamics
simulation program, PLATYpus (PLATform
for dYnamic protein unified simulation),
for the elucidation of protein functions 1125--1132
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Volume 37, Issue 13 . . . . . . . . . . 1136--1138
Yasushige Yonezawa A method for predicting protein
conformational pathways by using
molecular dynamics simulations guided by
difference distance matrices . . . . . . 1139--1146
Tiziana Ginex and
Jordi Muñoz-Muriedas and
Enric Herrero and
Enric Gibert and
Pietro Cozzini and
F. J. Luque Development and validation of
hydrophobic molecular fields derived
from the quantum mechanical IEF/PCM-MST
solvation models in $3$D-QSAR . . . . . 1147--1162
Xin Zhang and
Yuan Zhao and
Honggao Yan and
Zexing Cao and
Yirong Mo Combined QM(DFT)\slash MM molecular
dynamics simulations of the deamination
of cytosine by yeast cytosine deaminase
(yCD) . . . . . . . . . . . . . . . . . 1163--1174
Yuwei Zhou and
Jianming Wu and
Xin Xu Improving B3LYP heats of formation with
three-dimensional molecular descriptors 1175--1190
Svetlana Artemova and
Léonard Jaillet and
Stephane Redon Automatic molecular structure perception
for the universal force field . . . . . 1191--1205
Liudmyla K. Sviatenko and
Leonid Gorb and
Frances C. Hill and
Danuta Leszczynska and
Jerzy Leszczynski Structure and electrochemical properties
for complexes of nitrocompounds with
inorganic ions: a theoretical approach 1206--1213
Xiao Ru and
Ce Song and
Zijing Lin A genetic algorithm encoded with the
structural information of amino acids
and dipeptides for efficient
conformational searches of oligopeptides 1214--1222
Ghazaleh Taherzadeh and
Yuedong Yang and
Tuo Zhang and
Alan Wee-Chung Liew and
Yaoqi Zhou Sequence-based prediction of
protein--peptide binding sites using
support vector machine . . . . . . . . . 1223--1229
Jan \vRezá\vc Software News and Updates: Cuby: an
integrative framework for computational
chemistry . . . . . . . . . . . . . . . 1230--1237
Salvador Cardona-Serra and
Luis Escalera-Moreno and
José J. Baldoví and
Alejandro Gaita-Ariño and
Juan M. Clemente-Juan and
Eugenio Coronado Software News and Updates: SIMPRE1.2:
Considering the hyperfine and
quadrupolar couplings and the nuclear
spin bath decoherence . . . . . . . . . 1238--1244
Anonymous Cover Image, Volume 37, Issue 14 . . . . i--ii
Anonymous Issue Information --- Coming Soon:
Volume 37, Issue 14 . . . . . . . . . . 1245--1245
Anonymous Issue Information --- Copyright: Volume
37, Issue 14 . . . . . . . . . . . . . . 1246--1246
Anonymous Issue Information --- Editorial Board:
Volume 37, Issue 14 . . . . . . . . . . 1247--1247
Anonymous Issue Information --- Table of Contents:
Volume 37, Issue 14 . . . . . . . . . . 1248--1250
Hanzhong Liu and
Minghai Li and
Jue Fan and
Shuanghong Huo Inherent structure versus geometric
metric for state space discretization 1251--1258
Anna V. Pomogaeva and
Keiji Morokuma and
Alexey Y. Timoshkin Trimeric cluster of lithium amidoborane
--- the smallest unit for the modeling
of hydrogen release mechanism . . . . . 1259--1264
Israel Fernández and
Fernando P. Cossío Interplay between aromaticity and strain
in double group transfer reactions to
1,2-benzyne . . . . . . . . . . . . . . 1265--1273
David G. Tomlinson and
Andrey Asadchev and
Mark S. Gordon A new approach for second-order
perturbation theory . . . . . . . . . . 1274--1282
Kristopher Opron and
Kelin Xia and
Zach Burton and
Guo-Wei Wei Flexibility--rigidity index for
protein--nucleic acid flexibility and
fluctuation analysis . . . . . . . . . . 1283--1295
Hoora Shaghaghi and
Hossein Pasha Ebrahimi and
Fariba Fathi and
Niloufar Bahrami Panah and
Mehdi Jalali-Heravi and
Mohsen Tafazzoli A simple graphical approach to predict
local residue conformation using NMR
chemical shifts and density functional
theory . . . . . . . . . . . . . . . . . 1296--1305
Bun Chan and
Jong-Won Song and
Yukio Kawashima and
Kimihiko Hirao Performance of the OP correlation
functional in relation to its
formulation: Influence of the exchange
component and the effect of
incorporating same-spin correlations . . 1306--1312
Shulai Lei and
Beate Paulus and
Shujuan Li and
Burkhard Schmidt Curvature-dependent adsorption of water
inside and outside armchair carbon
nanotubes . . . . . . . . . . . . . . . 1313--1320
Lei Gao and
Yanli Zeng and
Xueying Zhang and
Lingpeng Meng Comparative studies on group III $
\sigma $-hole and $ \pi $-hole
interactions . . . . . . . . . . . . . . 1321--1327
Anonymous Cover Image, Volume 37, Issue 15 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 15 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 1329--1333
Charlotte Brückner and
Bernd Engels A theoretical description of charge
reorganization energies in molecular
organic P-type semiconductors . . . . . 1335--1344
Dumitru-Claudiu Sergentu and
Grégoire David and
Gilles Montavon and
Rémi Maurice and
Nicolas Galland Scrutinizing ``Invisible'' astatine: a
challenge for modern density functionals 1345--1354
Majid El-Hamdi and
Miquel Sol\`a and
Jordi Poater and
Alexey Y. Timoshkin Complexes of adamantane-based group 13
Lewis acids and superacids: Bonding
analysis and thermodynamics of hydrogen
splitting . . . . . . . . . . . . . . . 1355--1362
Wei-Wei Wang and
Jing-Shuang Dang and
Xiang Zhao and
Shigeru Nagase Regioselective multistep reconstructions
of half-saturated zigzag carbon
nanotubes . . . . . . . . . . . . . . . 1363--1366
Irina L. Rusakova and
Yury Yu. Rusakov and
Leonid B. Krivdin First example of the correlated
calculation of the one-bond
tellurium--carbon spin--spin coupling
constants: Relativistic effects,
vibrational corrections, and solvent
effects . . . . . . . . . . . . . . . . 1367--1372
Ignacy Cukrowski and
Paidamwoyo Mangondo Interacting quantum fragments-rooted
preorganized-interacting fragments
attributed relative molecular stability
of the Be$^{II}$ complexes of
nitrilotriacetic acid and
nitrilotri-$3$-propionic acid . . . . . 1373--1387
Muhammad A. Hagras and
Alexei A. Stuchebrukhov Electron tunneling in proteins program 1388--1395
Juan Pablo Martínez and
Miquel Sol\`a and
Alexander A. Voityuk Theoretical estimation of the rate of
photoinduced charge transfer reactions
in triphenylamine C$_{60}$
donor--acceptor conjugate . . . . . . . 1396--1405
Anonymous Cover Image, Volume 37, Issue 16 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1407--1412
Shalini Awasthi and
Venkat Kapil and
Nisanth N. Nair Sampling free energy surfaces as slices
by combining umbrella sampling and
metadynamics . . . . . . . . . . . . . . 1413--1424
Yixiang Cao and
Thomas Hughes and
Dave Giesen and
Mathew D. Halls and
Alexander Goldberg and
Tati Reddy Vadicherla and
Madhavi Sastry and
Bhargav Patel and
Woody Sherman and
Andrew L. Weisman and
Richard A. Friesner Highly efficient implementation of
pseudospectral time-dependent
density-functional theory for the
calculation of excitation energies of
large molecules . . . . . . . . . . . . 1425--1441
Vitaly V. Porsev and
Andrei V. Bandura and
Robert A. Evarestov Temperature dependence of strain energy
and thermodynamic properties of
V$_2$O$_5$-based single-walled
nanotubes: Zone-folding approach . . . . 1442--1450
Takao Tsuneda and
Raman K. Singh and
Ayako Nakata Relationship between orbital energy gaps
and excitation energies for long-chain
systems . . . . . . . . . . . . . . . . 1451--1462
Andrea Lombardi and
Fernando Pirani and
Antonio Lagan\`a and
Massimiliano Bartolomei Energy transfer dynamics and kinetics of
elementary processes (promoted) by
gas-phase CO$_2$--N$_2$ collisions:
Selectivity control by the anisotropy of
the interaction . . . . . . . . . . . . 1463--1475
Zhenlian Chen and
Jun Li A new method applicable to study solid
compounds with multiple polyhedral
structures . . . . . . . . . . . . . . . 1476--1483
Bitupon Borthakur and
Bernard Silvi and
Rian D. Dewhurst and
Ashwini K. Phukan Theoretical strategies toward
stabilization of singlet remote
N-heterocyclic carbenes . . . . . . . . 1484--1490
John Kendrick and
Andrew D. Burnett Software News and Updates: PDielec: the
calculation of infrared and terahertz
absorption for powdered crystals . . . . 1491--1504
Shilpa R. Nath and
Sudheer S. Kurup and
Kaustubh A. Joshi Software News and Updates: PyGlobal: a
toolkit for automated compilation of
DFT-based descriptors . . . . . . . . . 1505--1510
Gunter Hermann and
Vincent Pohl and
Jean Christophe Tremblay and
Beate Paulus and
Hans-Christian Hege and
Axel Schild Software News and Updates: ORBKIT: a
modular Python toolbox for
cross-platform postprocessing of quantum
chemical wavefunction data . . . . . . . 1511--1520
César Mogo and
João Brandão Software News and Updates:
$N$-dimensional switch function for
energy conservation in multiprocess
reaction dynamics . . . . . . . . . . . 1521--1524
Anonymous Cover Image, Volume 37, Issue 17 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1525--1530
N. L. Moreira and
B. G. A. Brito and
J. N. Teixeira Rabelo and
Ladir Cândido Quantum Monte Carlo study of the
energetics of small hydrogenated and
fluoride lithium clusters . . . . . . . 1531--1536
Andrey Alekseenko and
Olga Kononova and
Yaroslav Kholodov and
Kenneth A. Marx and
Valeri Barsegov SOP-GPU: influence of solvent-induced
hydrodynamic interactions on dynamic
structural transitions in protein
assemblies . . . . . . . . . . . . . . . 1537--1551
Natalia Zarycz and
Patricio F. Provasi and
Gabriel I. Pagola and
Marta B. Ferraro and
Stefano Pelloni and
Paolo Lazzeretti Computational study of basis set and
electron correlation effects on anapole
magnetizabilities of chiral molecules 1552--1558
Xianjin Xu and
Zhiwei Ma and
Hongmin Sun and
Xiaoqin Zou SM-TF: a structural database of small
molecule-transcription factor complexes 1559--1564
Changjun Chen and
Yanzhao Huang Walking freely in the energy and
temperature space by the modified
replica exchange molecular dynamics
method . . . . . . . . . . . . . . . . . 1565--1575
Indrajit Deb and
Rupak Pal and
Joanna Sarzynska and
Ansuman Lahiri Reparameterizations of the $ \chi $
torsion and Lennard-Jones $ \sigma $
parameters improve the conformational
characteristics of modified uridines . . 1576--1588
Martin A. Olsson and
Pär Söderhjelm and
Ulf Ryde Converging ligand-binding free energies
obtained with free-energy perturbations
at the quantum mechanical level . . . . 1589--1600
Daniel Bellinger and
Volker Settels and
Wenlan Liu and
Reinhold F. Fink and
Bernd Engels Influence of a polarizable surrounding
on the electronically excited states of
aggregated perylene materials . . . . . 1601--1610
Simona Tu\vsar and
Antonija Lesar Hydrogen bonding in the hydroxysulfinyl
radical-formic acid-water system: a
theoretical study . . . . . . . . . . . 1611--1625
Alexey V. Akimov Software News and Updates: Libra: an
open-source ``methodology discovery''
library for quantum and classical
dynamics simulations . . . . . . . . . . 1626--1649
Anonymous Cover Image, Volume 37, Issue 18 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1651--1656
Sudhir K. Sahoo and
Nisanth N. Nair CPMD/GULP QM/MM interface for modeling
periodic solids: Implementation and its
application in the study of Y-zeolite
supported Rh$_n$ clusters . . . . . . . 1657--1667
Donghai Yu and
Ruobing Du and
Ji-Chang Xiao pK a prediction for acidic
phosphorus-containing compounds using
multiple linear regression with
computational descriptors . . . . . . . 1668--1671
Francesco Zaccaria and
Lando P. Wolters and
Célia Fonseca Guerra and
Laura Orian Insights on selenium and tellurium
diaryldichalcogenides: a benchmark DFT
study . . . . . . . . . . . . . . . . . 1672--1680
Travis V. Harris and
Robert K. Szilagyi Protein environmental effects on
iron-sulfur clusters: a set of rules for
constructing computational models for
inner and outer coordination spheres . . 1681--1696
Leighton Jones and
Benjamin J. Whitaker Modeling a halogen dance reaction
mechanism: a density functional theory
study . . . . . . . . . . . . . . . . . 1697--1703
Sean T. Holmes and
Fahri Alkan and
Robbie J. Iuliucci and
Karl T. Mueller and
Cecil Dybowski Analysis of the bond-valence method for
calculating $^{29}$Si and $^{31}$P
magnetic shielding in covalent network
solids . . . . . . . . . . . . . . . . . 1704--1710
Maria M. Reif and
Martin Zacharias Rapid approximate calculation of water
binding free energies in the whole
hydration domain of (bio)macromolecules 1711--1724
Zhiguang Jia and
Jianhan Chen Necessity of high-resolution for
coarse-grained modeling of flexible
proteins . . . . . . . . . . . . . . . . 1725--1733
Yuedong Yang and
Jian Zhan and
Yaoqi Zhou Software News and Updates: SPOT-Ligand:
Fast and effective structure-based
virtual screening by binding homology
search according to ligand and receptor
similarity . . . . . . . . . . . . . . . 1734--1739
Israel Cabeza de Vaca and
Sandra Acebes and
Victor Guallar Software News and Updates: Ecoupling
server: a tool to compute and analyze
electronic couplings . . . . . . . . . . 1740--1745
Anonymous Cover Image, Volume 37, Issue 19 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1747--1747
Fernando José Holguín-Gallego and
Rodrigo Chávez-Calvillo and
Marco García-Revilla and
Evelio Francisco and
Ángel Martín Pendás and
Tomás Rocha-Rinza Electron correlation in the interacting
quantum atoms partition via
coupled-cluster Lagrangian densities . . 1753--1765
Tereza Zábojníková and
Radim Cajzl and
Jakob Kljun and
Zden\vek Chval and
Iztok Turel and
Jaroslav V. Burda Interactions of the ``piano-stool''
[ruthenium(II)($
\eta^6$-arene)(quinolone)Cl]$^+$
complexes with water; DFT computational
study . . . . . . . . . . . . . . . . . 1766--1780
David Mignon and
Thomas Simonson Comparing three stochastic search
algorithms for computational protein
design: Monte Carlo, replica exchange
Monte Carlo, and a multistart,
steepest-descent heuristic . . . . . . . 1781--1793
Stefan Vogt-Geisse and
Alejandro Toro-Labbé Chemical potential and reaction
electronic flux in symmetry controlled
reactions . . . . . . . . . . . . . . . 1794--1800
Tatiana Vasilevskaya and
Maria G. Khrenova and
Alexander V. Nemukhin and
Walter Thiel Methodological aspects of QM/MM
calculations: a case study on matrix
metalloproteinase-2 . . . . . . . . . . 1801--1809
Margareta R. A. Blomberg and
Per E. M. Siegbahn Improved free energy profile for
reduction of NO in cytochrome c
dependent nitric oxide reductase (cNOR) 1810--1818
Piero Procacci Reformulating the entropic contribution
in molecular docking scoring functions 1819--1827
Andreas Köster and
Thomas Spura and
Gábor Rutkai and
Jan Kessler and
Hendrik Wiebeler and
Jadran Vrabec and
Thomas D. Kühne Assessing the accuracy of improved
force-matched water models derived from
ab initio molecular dynamics simulations 1828--1838
Junpyo Kwon and
Myeongsang Lee and
Sungsoo Na Sodium chloride's effect on
self-assembly of diphenylalanine bilayer 1839--1846
Dmytro Kosenkov Software News and Updates: PyFREC:
Software for Förster electronic coupling
evaluation in molecular fragments . . . 1847--1854
Anonymous Cover Image, Volume 37, Issue 20 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1855--1855
Laura J. Kingsley and
Juan Esquivel-Rodríguez and
Ying Yang and
Daisuke Kihara and
Markus A. Lill Ranking protein--protein docking results
using steered molecular dynamics and
potential of mean force calculations . . 1861--1865
Anthony Scemama and
Thomas Applencourt and
Emmanuel Giner and
Michel Caffarel Quantum Monte Carlo with very large
multideterminant wavefunctions . . . . . 1866--1875
Emilia Makarewicz and
Jan Lundell and
Agnieszka J. Gordon and
Slawomir Berski On the nature of interactions in the
F$_2$OXe$^{\ldots }$NCCH$_3$ complex: Is
there the Xe(IV)\bond N bond? . . . . . 1876--1886
Morten S. Nòrby and
Jógvan Magnus Haugaard Olsen and
Jacob Kongsted and
Hans Jòrgen Aagard Jensen Multipole moments for embedding
potentials: Exploring different atomic
allocation algorithms . . . . . . . . . 1887--1896
Jan Huwald and
Stephan Richter and
Bashar Ibrahim and
Peter Dittrich Compressing molecular dynamics
trajectories: Breaking the
one-bit-per-sample barrier . . . . . . . 1897--1906
Li-Hua Gan and
Dan Lei and
Patrick W. Fowler Structural interconnections and the role
of heptagonal rings in endohedral
trimetallic nitride template fullerenes 1907--1913
Nils Herrmann and
Norah Heinz and
Michael Dolg and
Xiaoyan Cao Quantum chemical study of the
autoxidation of ascorbate . . . . . . . 1914--1923
Hiroo Nozaki and
Yosuke Fujii and
Kazuhide Ichikawa and
Taku Watanabe and
Yuichi Aihara and
Akitomo Tachibana Theoretical study of lithium ionic
conductors by electronic stress tensor
density and electronic kinetic energy
density . . . . . . . . . . . . . . . . 1924--1934
Amani Tahat and
Jordi Martí Multistate empirical valence bond study
of temperature and confinement effects
on proton transfer in water inside
hydrophobic nanochannels . . . . . . . . 1935--1946
Anonymous Cover Image, Volume 37, Issue 21 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 21 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 1947--1952
Ana M. Torres and
Steve Scheiner and
Ajit K. Roy and
Andrés M. Garay-Tapia and
John Bustamante and
Tapas Kar Segmentation and additive approach: a
reliable technique to study noncovalent
interactions of large molecules at the
surface of single-wall carbon nanotubes 1953--1961
Gabriel Aires Urquiza-Carvalho and
Wallace Duarte Fragoso and
Gerd Bruno Rocha Assessment of semiempirical enthalpy of
formation in solution as an effective
energy function to discriminate
native-like structures in protein decoy
sets . . . . . . . . . . . . . . . . . . 1962--1972
Tigran M. Abramyan and
James A. Snyder and
Aby A. Thyparambil and
Steven J. Stuart and
Robert A. Latour Cluster analysis of molecular simulation
trajectories for systems where both
conformation and orientation of the
sampled states are important . . . . . . 1973--1982
Hiroaki Nishizawa and
Yoshifumi Nishimura and
Masato Kobayashi and
Stephan Irle and
Hiromi Nakai Three pillars for achieving quantum
mechanical molecular dynamics
simulations of huge systems:
Divide-and-conquer, density-functional
tight-binding, and massively parallel
computation . . . . . . . . . . . . . . 1983--1992
Benjamin G. Janesko Topological analysis of the electron
delocalization range . . . . . . . . . . 1993--2005
A. Lamiable and
P. Thevenet and
P. Tufféry A critical assessment of hidden Markov
model sub-optimal sampling strategies
applied to the generation of peptide
$3$D models . . . . . . . . . . . . . . 2006--2016
Tetsuro Nagai and
George A. Pantelopulos and
Takuya Takahashi and
John E. Straub On the use of mass scaling for stable
and efficient simulated tempering with
molecular dynamics . . . . . . . . . . . 2017--2028
Steven Ramsey and
Crystal Nguyen and
Romelia Salomon-Ferrer and
Ross C. Walker and
Michael K. Gilson and
Tom Kurtzman Software News and Updates: Solvation
thermodynamic mapping of molecular
surfaces in AmberTools: GIST . . . . . . 2029--2037
Maarten G. Wolf and
Martin Hoefling and
Camilo Aponte-Santamaría and
Helmut Grubmüller and
Gerrit Groenhof Erratum: Corrigendum: \tt g\_membed:
Efficient insertion of a membrane
protein into an equilibrated lipid
bilayer with minimal perturbation . . . 2038--2038
Anonymous Cover Image, Volume 37, Issue 22 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2039--2043
Kyrylo Klimenko and
Victor Kuz'min and
Liudmila Ognichenko and
Leonid Gorb and
Manoj Shukla and
Natalia Vinas and
Edward Perkins and
Pavel Polishchuk and
Anatoly Artemenko and
Jerzy Leszczynski Novel enhanced applications of QSPR
models: Temperature dependence of
aqueous solubility . . . . . . . . . . . 2045--2051
Heiner Schröder and
Tobias Schwabe Efficient determination of accurate
atomic polarizabilities for polarizeable
embedding calculations . . . . . . . . . 2052--2059
Steven W. Rick A polarizable, charge transfer model of
water using the Drude oscillator . . . . 2060--2066
Dennis M. Elking Torque and atomic forces for Cartesian
tensor atomic multipoles with an
application to crystal unit cell
optimization . . . . . . . . . . . . . . 2067--2080
Szymon \'Smiga and
Fabio Della Sala and
Adam Buksztel and
Ireneusz Grabowski and
Eduardo Fabiano Accurate Kohn--Sham ionization
potentials from scaled-opposite-spin
second-order optimized effective
potential methods . . . . . . . . . . . 2081--2090
Iwona E. Weidlich and
Igor V. Filippov Software News and Updates: Using the
Gini coefficient to measure the chemical
diversity of small-molecule libraries 2091--2097
Michelle M. Kuttel and
Jonas Ståhle and
Göran Widmalm Software News and Updates: CarbBuilder:
Software for building molecular models
of complex oligo- and polysaccharide
structures . . . . . . . . . . . . . . . 2098--2105
Efthymios I. Ioannidis and
Terry Z. H. Gani and
Heather J. Kulik Software News and Updates: molSimplify:
a toolkit for automating discovery in
inorganic chemistry . . . . . . . . . . 2106--2117
Anonymous Cover Image, Volume 37, Issue 23 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 23 . . . . ii--ii
Anonymous Cover Image, Volume 37, Issue 23 . . . . iii--iii
Anonymous Issue Information . . . . . . . . . . . 2119--2123
Oleksandr Loboda and
Francesca Ingrosso and
Manuel F. Ruiz-López and
Heribert Reis and
Claude Millot Dipole and quadrupole polarizabilities
of the water molecule as a function of
geometry . . . . . . . . . . . . . . . . 2125--2132
Christian Tantardini and
Davide Ceresoli and
Enrico Benassi Source function and plane waves: Toward
complete Bader analysis . . . . . . . . 2133--2139
Yusuke Kanematsu and
Masanori Tachikawa and
Yu Takano Inverse Ubbelohde effect in the short
hydrogen bond of photosystem II:
Relation between H/D isotope effect and
symmetry in potential energy profile . . 2140--2145
Vera Stehr and
Reinhold F. Fink and
Carsten Deibel and
Bernd Engels Charge carrier mobilities in organic
semiconductor crystals based on the
spectral overlap . . . . . . . . . . . . 2146--2156
Xiping Gong and
Zhenhua Chen and
Wei Wu The application of Cholesky
decomposition in valence bond
calculation . . . . . . . . . . . . . . 2157--2162
Emanuele Rossini and
Ernst-Walter Knapp Erratum: Proton solvation in protic and
aprotic solvents [J. Comput. Chem. 2015,
37, 1082--1091] . . . . . . . . . . . . 2163--2164
Anonymous Cover Image, Volume 37, Issue 24 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 24 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 2165--2169
Evan J. Arthur and
Charles L. Brooks III Efficient implementation of constant pH
molecular dynamics on modern graphics
processors . . . . . . . . . . . . . . . 2171--2180
Matthias Witte and
Benjamin Grimm-Lebsanft and
Arne Goos and
Stephan Binder and
Michael Rübhausen and
Martin Bernard and
Adam Neuba and
Serge Gorelsky and
Uwe Gerstmann and
Gerald Henkel and
Wolf Gero Schmidt and
Sonja Herres-Pawlis Optical response of the Cu$_2$S$_2$
diamond core in Cu2II(NGuaS)$_2$Cl$_2$ 2181--2192
Sunghwan Choi and
Oh-Kyoung Kwon and
Jaewook Kim and
Woo Youn Kim Performance of heterogeneous computing
with graphics processing unit and many
integrated core for Hartree potential
calculations on a numerical grid . . . . 2193--2201
Manas Ghara and
Sudip Pan and
Anand Kumar and
Gabriel Merino and
Pratim K. Chattaraj Structure, stability, and nature of
bonding in carbon monoxide bound EX3+
complexes (E = group 14 element; X = H,
F, Cl, Br, I) . . . . . . . . . . . . . 2202--2211
Li-Hong Liu and
Dan Wu and
Shu-Hua Xia and
Ganglong Cui Theoretical study on photooxidation
mechanism of ruthenium complex
[Ru(II)-(bpy)$_2$ (TMBiimH$_2$)]$^{2+}$
with molecular oxygen . . . . . . . . . 2212--2219
Andreas Erlebach and
Timm Ott and
Christoph Otzen and
Stephanie Schubert and
Justyna Czaplewska and
Ulrich S. Schubert and
Marek Sierka Thermodynamic compatibility of actives
encapsulated into PEG-PLA nanoparticles:
In silico predictions and experimental
verification . . . . . . . . . . . . . . 2220--2227
Pingying Liu and
Qiufeng Chen and
Jing Ma Design of [2]rotaxane through image
threshold segmentation of electrostatic
potential image . . . . . . . . . . . . 2228--2241
Anonymous Cover Image, Volume 37, Issue 25 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 25 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 2243--2247
Praphasiri Dolbundalchok and
Daniel Peláez and
Emad F. Aziz and
Annika Bande Geometrical control of the interatomic
Coulombic decay process in quantum dots
for infrared photodetectors . . . . . . 2249--2259
Lynn Groß and
Carmen Herrmann Local electric dipole moments: a
generalized approach . . . . . . . . . . 2260--2265
Jingbai Li and
Giovana da Silva Ramos and
Andrey Yu Rogachev Stability of functionalized corannulene
cations [R-C$_{20}$H$_{10}$]$^+$: an
influence of the nature of R-Group . . . 2266--2278
Jorge I. Martínez-Araya A generalized operational formula based
on total electronic densities to obtain
$3$D pictures of the dual descriptor to
reveal nucleophilic and electrophilic
sites accurately on closed-shell
molecules . . . . . . . . . . . . . . . 2279--2303
Junji Seino and
Hiromi Nakai Informatics-Based Energy Fitting Scheme
for Correlation Energy at Complete Basis
Set Limit . . . . . . . . . . . . . . . 2304--2315
Xiaojun Li and
Zhijun Yan and
Shuna Li The nature of structure and bonding
between transition metal and mixed
Si\bond Ge tetramers: a $ 20$-electron
superatom system . . . . . . . . . . . . 2316--2323
Lynn Groß and
Carmen Herrmann Software News and Updates: GenLocDip: a
Generalized Program to Calculate and
Visualize Local Electric Dipole Moments 2324--2334
Anonymous Cover Image, Volume 37, Issue 26 . . . . i--i
Anonymous Cover Image, Volume 37, Issue 26 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 2335--2339
Kaori Ueno-Noto and
Keiko Takano Water molecules inside protein structure
affect binding of monosaccharides with
HIV-1 antibody 2G12 . . . . . . . . . . 2341--2348
Ruixing Wang and
Mikhail Ozhgibesov and
Hajime Hirao Partial Hessian fitting for determining
force constant parameters in molecular
mechanics . . . . . . . . . . . . . . . 2349--2359
D. Paschoal and
C. Fonseca Guerra and
M. A. L. de Oliveira and
T. C. Ramalho and
H. F. Dos Santos Predicting Pt-195 NMR chemical shift
using new relativistic all-electron
basis set . . . . . . . . . . . . . . . 2360--2373
A. Daniel Boese and
Joachim Sauer Accurate adsorption energies for small
molecules on oxide surfaces: CH$_4$
/MgO(001) and C$_2$H$_6$ /MgO(001) . . . 2374--2385
Jiahui Liu and
Yiying Zheng and
Ying Liu and
Haiyan Yuan and
Jingping Zhang Mechanistic insight on (E)-methyl
3-(2-aminophenyl)acrylate cyclization
reaction by multicatalysis of solvent
and substrate . . . . . . . . . . . . . 2386--2394
Jacek Koput Ab initio potential energy surface and
vibration-rotation energy levels of
silicon dicarbide, SiC$_2$ . . . . . . . 2395--2402
Anonymous Cover Image, Volume 37, Issue 27 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2403--2407
Stuart J. Davie and
Nicodemo Di Pasquale and
Paul L. A. Popelier Incorporation of local structure into
kriging models for the prediction of
atomistic properties in the water
decamer . . . . . . . . . . . . . . . . 2409--2422
Xingqing Xiao and
Michelle E. Hung and
Joshua N. Leonard and
Carol K. Hall Adding energy minimization strategy to
peptide-design algorithm enables better
search for RNA-binding peptides:
Redesigned $ \lambda N $ peptide binds
boxB RNA . . . . . . . . . . . . . . . . 2423--2435
Changhao Wang and
Peter H. Nguyen and
Kevin Pham and
Danielle Huynh and
Thanh-Binh Nancy Le and
Hongli Wang and
Pengyu Ren and
Ray Luo Calculating protein--ligand binding
affinities with MMPBSA: Method and error
analysis . . . . . . . . . . . . . . . . 2436--2446
Yu-ya Ohnishi and
Seiichiro Ten-no Explicitly correlated
frequency-independent second-order
Green's function for accurate ionization
energies . . . . . . . . . . . . . . . . 2447--2453
Maria Fumanal and
Chantal Daniel Description of excited states in
[Re(Imidazole)(CO)$_3$ (Phen)]$^+$
including solvent and spin-orbit
coupling effects: Density functional
theory versus multiconfigurational
wavefunction approach . . . . . . . . . 2454--2466
Wolfgang Quapp and
Josep Maria Bofill Reaction rates in a theory of
mechanochemical pathways . . . . . . . . 2467--2478
Anonymous Cover Image, Volume 37, Issue 28 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2479--2483
Václav Bazgier and
Karel Berka and
Michal Otyepka and
Pavel Baná\vs Exponential repulsion improves
structural predictability of molecular
docking . . . . . . . . . . . . . . . . 2485--2494
Arghya Chakavorty and
Lin Li and
Emil Alexov Electrostatic component of binding
energy: Interpreting predictions from
Poisson--Boltzmann equation and modeling
protocols . . . . . . . . . . . . . . . 2495--2507
D. Jiajun and
J. R. Maza and
Y. Xu and
T. Xu and
R. Momen and
S. R. Kirk and
S. Jenkins A stress tensor and QTAIM perspective on
the substituent effects of biphenyl
subjected to torsion . . . . . . . . . . 2508--2517
Roman \Lazarski and
Asbjörn Manfred Burow and
Luká\vs Grajciar and
Marek Sierka Density functional theory for molecular
and periodic systems using density
fitting and continuous fast multipole
method: Analytical gradients . . . . . . 2518--2526
Gennady L. Gutsev and
Kalayu G. Belay and
Lavrenty G. Gutsev and
Bala R. Ramachandran Structure and properties of iron oxide
clusters: From Fe$_6$ to Fe$_6$O$_{20}$
and from Fe$_7$ to Fe$_7$O$_{24}$ . . . 2527--2536
Benjamin P. Pritchard and
Edmond Chow Horizontal vectorization of electron
repulsion integrals . . . . . . . . . . 2537--2546
Anonymous Cover Image, Volume 37, Issue 29 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2547--2551
Steven C. Howell and
Xiangyun Qiu and
Joseph E. Curtis Monte Carlo simulation algorithm for
B-DNA . . . . . . . . . . . . . . . . . 2553--2563
Pierre O. Hubin and
Denis Jacquemin and
Laurence Leherte and
Daniel P. Vercauteren Parameterization of the ReaxFF reactive
force field for a proline-catalyzed
aldol reaction . . . . . . . . . . . . . 2564--2572
Velin Z. Spassov and
Lisa Yan A pH-dependent computational approach to
the effect of mutations on protein
stability . . . . . . . . . . . . . . . 2573--2587
Ming Xing Hu and
Tianlv Xu and
Roya Momen and
Guo Huan and
Steven R. Kirk and
Samantha Jenkins and
Michael Filatov A QTAIM and stress tensor investigation
of the torsion path of a light-driven
fluorene molecular rotary motor . . . . 2588--2596
Michael M. H. Graf and
Manuela Maurer and
Chris Oostenbrink Free-energy calculations of residue
mutations in a tripeptide using various
methods to overcome inefficient sampling 2597--2605
Nicodemo Di Pasquale and
Michael Bane and
Stuart J. Davie and
Paul L. A. Popelier Software News and Updates: FEREBUS:
Highly parallelized engine for kriging
training . . . . . . . . . . . . . . . . 2606--2616
Anonymous Cover Image, Volume 37, Issue 30 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2617--2621
Michio Katouda and
Akira Naruse and
Yukihiko Hirano and
Takahito Nakajima Massively parallel algorithm and
implementation of RI-MP2 energy
calculation for peta-scale many-core
supercomputers . . . . . . . . . . . . . 2623--2633
Hong Liu and
You-Liang Zhu and
Zhong-Yuan Lu and
Florian Müller-Plathe A kinetic chain growth algorithm in
coarse-grained simulations . . . . . . . 2634--2646
Carlos Silva Lopez and
Olalla Nieto Faza and
Frank De Proft and
Antonios Kolocouris Assessing the attractive/repulsive force
balance in axial cyclohexane C--H$_{ax}$
\dottedbondY$_{ax}$ contacts: a combined
computational analysis in
monosubstituted cyclohexanes . . . . . . 2647--2658
Matteo Signorile and
Alessandro Damin and
Francesca Bonino and
Valentina Crocell\`a and
Carlo Lamberti and
Silvia Bordiga The role of dispersive forces
determining the energetics of adsorption
in Ti zeolites . . . . . . . . . . . . . 2659--2666
Patrick V. Holec and
Benjamin J. Hackel Software News and Updates: PyMOL360:
Multi-user gamepad control of molecular
visualization software . . . . . . . . . 2667--2669
Anonymous Cover Image, Volume 37, Issue 31 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2671--2671
Sergei F. Vyboishchikov Correlation energy, correlated electron
density, and exchange-correlation
potential in some spherically confined
atoms . . . . . . . . . . . . . . . . . 2677--2686
Shinji Iida and
Tadaaki Mashimo and
Takashi Kurosawa and
Hironobu Hojo and
Hiroya Muta and
Yuji Goto and
Yoshifumi Fukunishi and
Haruki Nakamura and
Junichi Higo Variation of free-energy landscape of
the p53 C-terminal domain induced by
acetylation: Enhanced conformational
sampling . . . . . . . . . . . . . . . . 2687--2700
Hiroaki Nishizawa and
Hisashi Okumura Rapid QM/MM approach for biomolecular
systems under periodic boundary
conditions: Combination of the
density-functional tight-binding theory
and particle mesh Ewald method . . . . . 2701--2711
Tianlv Xu and
James Farrell and
Yuning Xu and
Roya Momen and
Steven R. Kirk and
Samantha Jenkins and
David J. Wales QTAIM and stress tensor interpretation
of the (H$_2$O)$_5$ potential energy
surface . . . . . . . . . . . . . . . . 2712--2721
Huan Guo and
Alejandro Morales-Bayuelo and
Tianlv Xu and
Roya Momen and
Lingling Wang and
Ping Yang and
Steven R. Kirk and
Samantha Jenkins Distinguishing and quantifying the
torquoselectivity in competitive
ring-opening reactions using the stress
tensor and QTAIM . . . . . . . . . . . . 2722--2733
Son Tung Ngo and
Huynh Minh Hung and
Minh Tho Nguyen Fast and accurate determination of the
relative binding affinities of small
compounds to HIV-1 protease using
non-equilibrium work . . . . . . . . . . 2734--2742
Anonymous Cover Image, Volume 37, Issue 32 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2743--2747
Noor Asidah Mohamed and
Richard T. Bradshaw and
Jonathan W. Essex Evaluation of solvation free energies
for small molecules with the AMOEBA
polarizable force field . . . . . . . . 2749--2758
Shintaro Maekawa and
Krzysztof Moorthi and
Yasuteru Shigeta Refractive indices of organo-metallic
and -metalloid compounds: a long-range
corrected DFT study . . . . . . . . . . 2759--2769
Nohad Gresh and
David Perahia and
Benoit de Courcy and
Johanna Foret and
Céline Roux and
Lea El-Khoury and
Jean-Philip Piquemal and
Laurent Salmon Complexes of a Zn-metalloenzyme binding
site with hydroxamate-containing
ligands. A case for detailed
benchmarkings of polarizable molecular
mechanics/dynamics potentials when the
experimental binding structure is
unknown . . . . . . . . . . . . . . . . 2770--2782
Ignacy Cukrowski and
Filip Sagan and
Mariusz Pawe\l Mitoraj On the Stability of Cis- and
Trans-2-Butene Isomers. An Insight Based
on the FAMSEC, IQA, and ETS-NOCV Schemes 2783--2798
Sadegh Salehzadeh and
Farahnaz Maleki New equation for calculating total
interaction energy in one noncyclic ABC
triad and new insights into
cooperativity of noncovalent bonds . . . 2799--2807
Youhan Lee and
Roberta Poloni and
Jihan Kim Probing gas adsorption in MOFs using an
efficient ab initio Widom insertion
Monte Carlo method . . . . . . . . . . . 2808--2815
Dan Fraenkel Erratum: Corrigendum: Ion strength limit
of computed excess functions based on
the linearized Poisson--Boltzmann
equation . . . . . . . . . . . . . . . . 2816--2816
Anonymous Cover Image, Volume 38, Issue 1 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1--5
Hiromi Nakai and
Takeshi Yoshikawa and
Yutaro Nonaka Efficient pole-search algorithm for
dynamic polarizability: Toward
alternative excited-state calculation
for large systems . . . . . . . . . . . 7--14
Axel Wuttke and
Ricardo A. Mata Visualizing dispersion interactions
through the use of local orbital spaces 15--23
Duc D. Nguyen and
Guo-Wei Wei The impact of surface area, volume,
curvature, and Lennard-Jones potential
to solvation modeling . . . . . . . . . 24--36
Jacek Koput Ab initio potential energy surface and
vibration-rotation energy levels of
beryllium monohydroxide . . . . . . . . 37--43
Alvaro Muñoz-Castro and
R. Bruce King Evaluation of bonding, electron
affinity, and optical properties of
M@C$_{28}$ (M = Zr, Hf, Th, and U): Role
of $d$- and $f$-orbitals in endohedral
fullerenes from relativistic DFT
calculations . . . . . . . . . . . . . . 44--50
Sebastian Dohm and
Eckhard Spohr and
Martin Korth Software News and Updates: Developing
adaptive QM/MM computer simulations for
electrochemistry . . . . . . . . . . . . 51--58
Anonymous Cover Image, Volume 38, Issue 2 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 59--63
Ity Sharma and
George A. Kaminski Using polarizable POSSIM force field and
fuzzy-border continuum solvent model to
calculate pK$_a$ shifts of protein
residues . . . . . . . . . . . . . . . . 65--80
James S. M. Anderson and
Juan I. Rodríguez and
Paul W. Ayers and
Andreas W. Götz Relativistic (SR-ZORA) quantum theory of
atoms in molecules properties . . . . . 81--86
Enrico Benassi Benchmarking of density functionals for
a soft but accurate prediction and
assignment of $^1$H and $^{13}$C NMR
chemical shifts in organic and
biological molecules . . . . . . . . . . 87--92
Charles C. Kirkpatrick and
John N. Truong and
Bruce A. Kowert $d$-electron count, ion-pairing and
diagonal twist angles in
metallo-bis(dithiolene) complexes . . . 93--100
Yosuke Sumiya and
Tetsuya Taketsugu and
Satoshi Maeda Full rate constant matrix contraction
method for obtaining branching ratio of
unimolecular decomposition . . . . . . . 101--109
Peter L. Walters and
Thomas C. Allen and
Nancy Makri Direct determination of discrete
harmonic bath parameters from molecular
dynamics simulations . . . . . . . . . . 110--115
Christopher Ehlert and
Tillmann Klamroth The quest for best suited references for
configuration interaction singles
calculations of core excited states . . 116--126
Anonymous Cover Image, Volume 38, Issue 3 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 127--131
Bastien Belzunces and
Sophie Hoyau and
Magali Benoit and
Nathalie Tarrat and
Fabienne Bessac Theoretical study of the atrazine
pesticide interaction with pyrophyllite
and Ca$^{2+}$-montmorillonite clay
surfaces . . . . . . . . . . . . . . . . 133--143
Li-Hua Gan and
Rui Wu and
Jian-Lei Tian and
Joseph Clarke and
Christopher Gibson and
Patrick W. Fowler From C$_{58}$ to C$_{62}$ and back:
Stability, structural similarity, and
ring current . . . . . . . . . . . . . . 144--151
Song Liu and
Lizhe Zhu and
Fu Kit Sheong and
Wei Wang and
Xuhui Huang Adaptive partitioning by local
density-peaks: an efficient
density-based clustering algorithm for
analyzing molecular dynamics
trajectories . . . . . . . . . . . . . . 152--160
John P. Cvitkovic and
George A. Kaminski Developing multisite empirical force
field models for Pt(II) and cisplatin 161--168
Cheng Wang and
Yingkai Zhang Improving scoring-docking-screening
powers of protein--ligand scoring
functions using random forest . . . . . 169--177
Valter H. Carvalho-Silva and
Vincenzo Aquilanti and
Heibbe C. B. de Oliveira and
Kleber C. Mundim Deformed transition-state theory:
Deviation from Arrhenius behavior and
application to bimolecular hydrogen
transfer reaction rates in the tunneling
regime . . . . . . . . . . . . . . . . . 178--188
Anonymous Cover Image, Volume 38, Issue 4 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 189--193
Fahimeh Ghasemi and
Afshin Fassihi and
Horacio Pérez-Sánchez and
Alireza Mehri Dehnavi The role of different sampling methods
in improving biological activity
prediction using deep belief network . . 195--203
Julien Pilmé Electron localization function from
density components . . . . . . . . . . . 204--210
Yuta Kajiwara and
Satoshi Yasuda and
Yuuki Takamuku and
Takeshi Murata and
Masahiro Kinoshita Identification of thermostabilizing
mutations for a membrane protein whose
three-dimensional structure is unknown 211--223
Salvador Cardona-Serra and
Stefano Sanvito Influence of the dipolar interactions on
the relative stability in spin crossover
systems . . . . . . . . . . . . . . . . 224--227
Dmytro Bykov and
Thomas Kjaergaard The GPU-enabled
divide-expand-consolidate RI-MP2 method
(DEC-RI-MP2) . . . . . . . . . . . . . . 228--237
Danny Schlüns and
Mirko Franchini and
Andreas W. Götz and
Johannes Neugebauer and
Christoph R. Jacob and
Lucas Visscher Software News and Updates: Analytical
gradients for subsystem density
functional theory within the
Slater-function-based Amsterdam density
functional program . . . . . . . . . . . 238--249
Anonymous Cover Image, Volume 38, Issue 5 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 251--255
Alessandro Erba and
Dominique Caglioti and
Claudio Marcelo Zicovich-Wilson and
Roberto Dovesi Nuclear-relaxed elastic and
piezoelectric constants of materials:
Computational aspects of two
quantum-mechanical approaches . . . . . 257--264
Peter P. Passler and
Thomas S. Hofer Conserving the linear momentum in
stochastic dynamics: Dissipative
particle dynamics as a general strategy
to achieve local thermostatization in
molecular dynamics simulations . . . . . 265--275
Jason W. Labonte and
Jared Adolf-Bryfogle and
William R. Schief and
Jeffrey J. Gray Residue-centric modeling and design of
saccharide and glycoconjugate structures 276--287
Marek Szczepaniak and
Jerzy Moc Anomerization reaction of bare and
microhydrated $d$-erythrose via
explicitly correlated coupled cluster
approach. Two water molecules are
optimal . . . . . . . . . . . . . . . . 288--303
Xiaoling Zhan and
Hu Shi and
Hongguang Liu and
Jin Yong Lee Applying strong external electric field
to thiophene-based oligomers: a
promising approach to upgrade
semiconducting performance . . . . . . . 304--311
Anonymous Cover Image, Volume 38, Issue 6 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 313--317
Marco Pagliai and
Giordano Mancini and
Ivan Carnimeo and
Nicola De Mitri and
Vincenzo Barone Electronic absorption spectra of
pyridine and nicotine in aqueous
solution with a combined molecular
dynamics and polarizable QM/MM approach 319--335
Timothy L. Fletcher and
Paul L. A. Popelier Toward amino acid typing for proteins in
FFLUX . . . . . . . . . . . . . . . . . 336--345
Miguel Jorge and
Nuno M. Garrido and
Carlos J. V. Simões and
Cândida G. Silva and
Rui M. M. Brito Predicting hydrophobic solvation by
molecular simulation: 1. Testing
united-atom alkane models . . . . . . . 346--358
Miguel Jorge Predicting hydrophobic solvation by
molecular simulation: 2. New united-atom
model for alkanes, alkenes, and alkynes 359--369
Amir Karton How reliable is DFT in predicting
relative energies of polycyclic aromatic
hydrocarbon isomers? Comparison of
functionals from different rungs of
Jacob's ladder . . . . . . . . . . . . . 370--382
Katharina Krause and
Wim Klopper Software News and Updates:
Implementation of the Bethe--Salpeter
equation in the TURBOMOLE program . . . 383--388
Ingo Heimbach and
Florian Rhiem and
Fabian Beule and
David Knodt and
Josef Heinen and
Robert O. Jones Software News and Updates: pyMolDyn:
Identification, structure, and
properties of cavities/vacancies in
condensed matter and molecules . . . . . 389--394
Anonymous Cover Image, Volume 38, Issue 7 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 395--399
Elena I. Davydova and
Anna S. Lisovenko and
Alexey Y. Timoshkin Complex beryllium amidoboranes:
Structures, stability, and evaluation of
their potential as hydrogen storage
materials . . . . . . . . . . . . . . . 401--405
Yoshio Nishimoto and
Dmitri G. Fedorov Three-body expansion of the fragment
molecular orbital method combined with
density-functional tight-binding . . . . 406--418
Antoni Oliver and
Christopher A. Hunter and
Rafel Prohens and
Josep L. Rosselló A surface site interaction point
methodology for macromolecules and huge
molecular databases . . . . . . . . . . 419--426
Martina Rube\vsová and
Veronika Jurásková and
Petr Slaví\vcek Efficient modeling of liquid phase
photoemission spectra and reorganization
energies: Difficult case of multiply
charged anions . . . . . . . . . . . . . 427--437
Haiyan Yuan and
Jingping Zhang Mechanistic insights on DBU catalyzed $
\beta $-amination of NBS to chalcone
driving by water: Multiple roles of
water . . . . . . . . . . . . . . . . . 438--445
Beibei Liu and
Bao Wang and
Rundong Zhao and
Yiying Tong and
Guo-Wei Wei Software News and Updates: ESES:
Software for Eulerian solvent excluded
surface . . . . . . . . . . . . . . . . 446--466
Braulio Valdebenito-Maturana and
Jose Antonio Reyes-Suarez and
Jaime Henriquez and
David S. Holmes and
Raquel Quatrini and
Ehmke Pohl and
Mauricio Arenas-Salinas Software News and Updates: Mutantelec:
An In Silico mutation simulation
platform for comparative electrostatic
potential profiling of proteins . . . . 467--474
Anonymous Cover Image, Volume 38, Issue 8 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 475--479
Ricardo Pino-Rios and
Osvaldo Yañez and
Diego Inostroza and
Lina Ruiz and
Carlos Cardenas and
Patricio Fuentealba and
William Tiznado Proposal of a simple and effective local
reactivity descriptor through a
topological analysis of an
orbital-weighted Fukui function . . . . 481--488
Michio Katouda and
Takahito Nakajima MPI/OpenMP hybrid parallel algorithm for
resolution of identity second-order
Mòller--Plesset perturbation calculation
of analytical energy gradient for
massively parallel multicore
supercomputers . . . . . . . . . . . . . 489--507
Koen M. Visscher and
C. Ruben Vosmeer and
Rosa A. Luirink and
Daan P. Geerke A systematic approach to calibrate a
transferable polarizable force field
parameter set for primary alcohols . . . 508--517
No\`elia Pueyo Bellafont and
Francesc Viñes and
Wolfgang Hieringer and
Francesc Illas Predicting core level binding energies
shifts: Suitability of the projector
augmented wave approach as implemented
in VASP . . . . . . . . . . . . . . . . 518--522
Francesc Viñes and
Francesc Illas Electronic structure of stoichiometric
and reduced ZnO from periodic
relativistic all electron hybrid density
functional calculations using numeric
atom-centered orbitals . . . . . . . . . 523--529
Isabel Lage-Estebanez and
Lourdes del Olmo and
Rafael López and
José Manuel García de la Vega The role of errors related to DFT
methods in calculations involving ion
pairs of ionic liquids . . . . . . . . . 530--540
Yang Xie and
Jinyong Ying and
Dexuan Xie Software News and Updates: SMPBS: Web
server for computing biomolecular
electrostatics using finite element
solvers of size modified
Poisson--Boltzmann equation . . . . . . 541--552
Adam K. Sieradzan and
Rafa\l Jakubowski Software News and Updates: Introduction
of steered molecular dynamics into UNRES
coarse-grained simulations package . . . 553--562
Anonymous Cover Image, Volume 38, Issue 9 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 563--567
Zhubin Hu and
Bin Zhou and
Zhenrong Sun and
Haitao Sun Prediction of excited-state properties
of oligoacene crystals using polarizable
continuum model-tuned range-separated
hybrid functional approach . . . . . . . 569--575
Guido F. von Rudorff and
Tobias Watermann and
Xiang-Yang Guo and
Daniel Sebastiani Conformational Space of a Polyphilic
Molecule with a Fluorophilic Side Chain
Integrated in a DPPC Bilayer . . . . . . 576--583
Lin Li and
Arghya Chakravorty and
Emil Alexov DelPhiForce, a tool for electrostatic
force calculations: Applications to
macromolecular binding . . . . . . . . . 584--593
Chao Wang and
Yizhong Yuan and
Xiaohui Tian Assessment of range-separated exchange
functionals and nonempirical functional
tuning for calculating the static second
hyperpolarizabilities of streptocyanines 594--600
Sarah Witzke and
Nanna Holmgaard List and
Jógvan Magnus Haugaard Olsen and
Casper Steinmann and
Michael Petersen and
Maarten T. P. Beerepoot and
Jacob Kongsted An averaged polarizable potential for
multiscale modeling in phospholipid
membranes . . . . . . . . . . . . . . . 601--611
Jingyuan Gao and
Wenliang Li and
Jingping Zhang Theoretical simulation of CO$_2$ capture
in organic cage impregnated with
polyoxometalates . . . . . . . . . . . . 612--619
Marc Esser and
Stefan Maintz and
Richard Dronskowski Automated first-principles mapping for
phase-change materials . . . . . . . . . 620--628
Volker Lesch and
Diddo Diddens and
Carlos E. S. Bernardes and
Benjamin Golub and
Alain Dequidt and
Veronika Zeindlhofer and
Marcello Sega and
Christian Schröder Software News and Updates: ForConX: a
forcefield conversion tool based on XML 629--638
Anonymous Cover Image, Volume 38, Issue 10 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 639--644
Mina Jafari and
Paul M. Zimmerman Reliable and efficient reaction path and
transition state finding for surface
reactions with the growing string method 645--658
Marilia T. C. Martins-Costa and
Manuel F. Ruiz-López Reaching multi-nanosecond timescales in
combined QM/MM molecular dynamics
simulations through parallel horsetail
sampling . . . . . . . . . . . . . . . . 659--668
Koichi Ohno and
Naoki Kishimoto and
Takeaki Iwamoto and
Hiroko Satoh Global exploration of isomers and
isomerization channels on the quantum
chemical potential energy surface of
H$_3$CNO$_3$ . . . . . . . . . . . . . . 669--687
Vijay Madhav Miriyala and
Jan \vRezá\vc Description of non-covalent interactions
in SCC-DFTB methods . . . . . . . . . . 688--697
Pouya Partovi-Azar and
Payam Kaghazchi Time-dependent density functional theory
study on direction-dependent electron
and hole transfer processes in molecular
systems . . . . . . . . . . . . . . . . 698--703
Yoshimichi Andoh and
Noriyuki Yoshii and
Atsushi Yamada and
Susumu Okazaki Evaluation of atomic pressure in the
multiple time-step integration algorithm 704--713
Christian Margreitter and
Maria M. Reif and
Chris Oostenbrink Update on phosphate and charged
post-translationally modified amino acid
parameters in the GROMOS force field . . 714--720
Xiaojuan Yu and
Hua Hou and
Baoshan Wang Prediction on dielectric strength and
boiling point of gaseous molecules for
replacement of SF$_6$ . . . . . . . . . 721--729
Kun Yuan and
Rui-Sheng Zhao and
Jia-Jia Zheng and
Hong Zheng and
Shigeru Nagase and
Sheng-Dun Zhao and
Yan-Zhi Liu and
Xiang Zhao Van der Waals heterogeneous layer-layer
carbon nanostructures involving $ \pi
\cdots $H-C-C-H$ \cdots \pi \cdots
$H-C-C-H stacking based on graphene and
graphane sheets . . . . . . . . . . . . 730--739
Baofeng Zhang and
Denise Kilburg and
Peter Eastman and
Vijay S. Pande and
Emilio Gallicchio Efficient Gaussian density formulation
of volume and surface areas of
macromolecules on graphical processing
units . . . . . . . . . . . . . . . . . 740--752
Carlos E. S. Bernardes Software News and Updates: AGGREGATES:
Finding structures in simulation results
of solutions . . . . . . . . . . . . . . 753--765
Anonymous Cover Image, Volume 38, Issue 11 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 767--771
Sirous Yourdkhani and
Miros\law Jab\lo\'nski Revealing the physical nature and the
strength of charge-inverted hydrogen
bonds by SAPT(DFT), MP2, SCS-MP2, MP2C,
and CCSD(T) methods . . . . . . . . . . 773--780
Francesc Viñes and
Oriol Lamiel-García and
Kyoung Chul Ko and
Jin Yong Lee and
Francesc Illas Systematic study of the effect of HSE
functional internal parameters on the
electronic structure and band gap of a
representative set of metal oxides . . . 781--789
Ryuhei Harada and
Yu Takano and
Yasuteru Shigeta Common folding processes of
mini-proteins: Partial formations of
secondary structures initiate the
immediate protein folding . . . . . . . 790--797
Xiaojun Zhou and
Fan Wang Barrier heights of hydrogen-transfer
reactions with diffusion quantum Monte
Carlo method . . . . . . . . . . . . . . 798--806
Álvaro Vega-Vega and
Carmen Barrientos and
Antonio Largo Metallic monoboronyl compounds:
Prediction of their structure and
comparison with the cyanide analogues 807--815
Evelio Francisco and
Daniel Menéndez Crespo and
Aurora Costales and
Ángel Martín Pendás A multipolar approach to the interatomic
covalent interaction energy . . . . . . 816--829
Ellie L. Fought and
Vaibhav Sundriyal and
Masha Sosonkina and
Theresa L. Windus Saving time and energy with
oversubscription and semi-direct
Mòller--Plesset second order perturbation
methods . . . . . . . . . . . . . . . . 830--841
Ilya A. Kaliman and
Anna I. Krylov Software News and Updates: New algorithm
for tensor contractions on multi-core
CPUs, GPUs, and accelerators enables
CCSD and EOM-CCSD calculations with over
1000 basis functions on a single compute
node . . . . . . . . . . . . . . . . . . 842--853
Anonymous Cover Image, Volume 38, Issue 12 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 855--859
Lynn Groß and
Marc Philipp Bahlke and
Torben Steenbock and
Christian Klinke and
Carmen Herrmann Modeling adsorbate-induced property
changes of carbon nanotubes . . . . . . 861--868
Saswata Dasgupta and
John M. Herbert Standard grids for high-precision
integration of modern density
functionals: SG-2 and SG-3 . . . . . . . 869--882
Renato Pereira Orenha and
Régis Tadeu Santiago and
Roberto Luiz Andrade Haiduke and
Sérgio Emanuel Galembeck How computational methods and
relativistic effects influence the study
of chemical reactions involving Ru--NO
complexes? . . . . . . . . . . . . . . . 883--891
Jacek Koput Ab initio potential energy surface and
vibration-rotation energy levels of
sulfur dioxide . . . . . . . . . . . . . 892--900
Yaowarat Surakhot and
Viktor Laszlo and
Chirawat Chitpakdee and
Vinich Promarak and
Taweesak Sudyoadsuk and
Nawee Kungwan and
Tim Kowalczyk and
Stephan Irle and
Siriporn Jungsuttiwong Theoretical rationalization for reduced
charge recombination in bulky
carbazole-based sensitizers in solar
cells . . . . . . . . . . . . . . . . . 901--909
Rei Matsuzaki and
Satoshi Yabushita Optimization of complex Slater-type
functions with analytic derivative
methods for describing photoionization
differential cross sections . . . . . . 910--925
Anton Raskovalov Software News and Updates: a new
extension of classical molecular
dynamics: an electron transfer algorithm 926--932
Simon W. L. Hogan and
Tanja van Mourik Erratum: Corrigendum: Competition
between Hydrogen and Halogen Bonding in
Halogenated 1-Methyluracil:Water Systems 933--933
Anonymous Cover Image, Volume 38, Issue 13 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 935--939
Duc D. Nguyen and
Bao Wang and
Guo-Wei Wei Accurate, robust, and reliable
calculations of Poisson--Boltzmann
binding energies . . . . . . . . . . . . 941--948
Sean T. Holmes and
Shi Bai and
Robbie J. Iuliucci and
Karl T. Mueller and
Cecil Dybowski Calculations of solid-state $^{43}$Ca
NMR parameters: a comparison of periodic
and cluster approaches and an evaluation
of DFT functionals . . . . . . . . . . . 949--956
Jesús Jara-Cortés and
José Manuel Guevara-Vela and
Ángel Martín Pendás and
Jesús Hernández-Trujillo Chemical bonding in excited states:
Energy transfer and charge
redistribution from a real space
perspective . . . . . . . . . . . . . . 957--970
Hujun Shen and
Mingsen Deng and
Yachao Zhang Extension of CAVS coarse-grained model
to phospholipid membranes: the
importance of electrostatics . . . . . . 971--980
Jurgens Hendrik de Lange and
Ignacy Cukrowski Toward deformation densities for
intramolecular interactions without
radical reference states using the
fragment, atom, localized, delocalized,
and interatomic (FALDI) charge density
decomposition scheme . . . . . . . . . . 981--997
Stefania Di Tommaso and
Diane Bousquet and
Delphine Moulin and
Frédéric Baltenneck and
Priscilla Riva and
Hervé David and
Aziz Fadli and
Jérôme Gomar and
Ilaria Ciofini and
Carlo Adamo Theoretical approaches for predicting
the color of rigid dyes in solution . . 998--1004
Timothy L. Fletcher and
Paul L. A. Popelier FFLUX: Transferability of polarizable
machine-learned electrostatics in
peptide chains . . . . . . . . . . . . . 1005--1014
Anonymous Erratum . . . . . . . . . . . . . . . . 1015--1015
Anonymous Cover Image, Volume 38, Issue 14 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1017--1021
Florian Krausbeck and
Jan-Grimo Sobez and
Markus Reiher Stabilization of activated fragments by
shell-wise construction of an embedding
environment . . . . . . . . . . . . . . 1023--1038
Riccardo Volpi and
Mathieu Linares Study of the cold charge transfer state
separation at the TQ1/PC$_{71}$ BM
interface . . . . . . . . . . . . . . . 1039--1048
Jih\`ene Jerbi and
Michael Springborg Computational study of the reactivity of
cytosine derivatives . . . . . . . . . . 1049--1056
Changhao Wang and
Li Xiao and
Ray Luo Numerical interpretation of molecular
surface field in dielectric modeling of
solvation . . . . . . . . . . . . . . . 1057--1070
Gaëtan Rubez and
Jean-Matthieu Etancelin and
Xavier Vigouroux and
Michael Krajecki and
Jean-Charles Boisson and
Eric Hénon GPU accelerated implementation of NCI
calculations using promolecular density 1071--1083
Marika Savarese and
Umberto Raucci and
Ryoichi Fukuda and
Carlo Adamo and
Masahiro Ehara and
Nadia Rega and
Ilaria Ciofini Comparing the performance of TD-DFT and
SAC-CI methods in the description of
excited states potential energy
surfaces: an excited state proton
transfer reaction as case study . . . . 1084--1092
Uyen Q. Ly and
My-Phuong Pham and
Maurice J. Marks and
Thanh N. Truong Density functional theory study of
mechanism of epoxy-carboxylic acid
curing reaction . . . . . . . . . . . . 1093--1102
Anonymous Cover Image, Volume 38, Issue 15 . . . . i--i
Anonymous Cover Image, Volume 38, Issue 15 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 1103--1110
Jonathan Hirst and
Wonpil Im and
Joan-Emma Shea Introduction: Simulating Biomolecules:
Festschrift to commemorate the 60th
birthday of Charles L. Brooks III . . . 1111--1113
Sunhwan Jo and
Xi Cheng and
Jumin Lee and
Seonghoon Kim and
Sang-Jun Park and
Dhilon S. Patel and
Andrew H. Beaven and
Kyu Il Lee and
Huan Rui and
Soohyung Park and
Hui Sun Lee and
Beno\^\it Roux and
Alexander D. MacKerell, Jr. and
Jeffrey B. Klauda and
Yifei Qi and
Wonpil Im Review: CHARMM--GUI 10 years for
biomolecular modeling and simulation . . 1114--1124
Ester Sesmero and
Jodian A. Brown and
Ian F. Thorpe Molecular simulations to delineate
functional conformational transitions in
the HCV polymerase . . . . . . . . . . . 1125--1137
Alex Dickson and
Christopher T. Bailey and
John Karanicolas Optimal allosteric stabilization sites
using contact stabilization analysis . . 1138--1146
You Xu and
Alessandra Villa and
Lennart Nilsson The free energy of locking a ring:
Changing a deoxyribonucleoside to a
locked nucleic acid . . . . . . . . . . 1147--1157
Hossein Mohammadiarani and
Harish Vashisth Insulin mimetic peptide S371 folds into
a helical structure . . . . . . . . . . 1158--1166
Yoshiharu Mori and
Yuko Okamoto Conformational changes of ubiquitin
under high pressure conditions: a
pressure simulated tempering molecular
dynamics study . . . . . . . . . . . . . 1167--1173
Qi Huang and
Jocelyn M. Rodgers and
Russell J. Hemley and
Toshiko Ichiye Extreme biophysics: Enzymes under
pressure . . . . . . . . . . . . . . . . 1174--1182
Zhe Jia and
Christine Ackroyd and
Tingting Han and
Vibhor Agrawal and
Yinling Liu and
Kenneth Christensen and
Brian Dominy Effects from metal ion in tumor
endothelial marker 8 and anthrax
protective antigen: BioLayer
Interferometry experiment and molecular
dynamics simulation study . . . . . . . 1183--1190
Christopher G. Myers and
B. Montgomery Pettitt Phage-like packing structures with mean
field sequence dependence . . . . . . . 1191--1197
Robert C. Harris and
Nanjie Deng and
Ronald M. Levy and
Ryosuke Ishizuka and
Nobuyuki Matubayasi Computing conformational free energy
differences in explicit solvent: an
efficient thermodynamic cycle using an
auxiliary potential and a free energy
functional constructed from the end
points . . . . . . . . . . . . . . . . . 1198--1208
Leon A. Sakkal and
Kyle Z. Rajkowski and
Roger S. Armen Prediction of consensus binding mode
geometries for related chemical series
of positive allosteric modulators of
adenosine and muscarinic acetylcholine
receptors . . . . . . . . . . . . . . . 1209--1228
Cen Gao and
Jeremy Desaphy and
Michal Vieth Are induced fit protein conformational
changes caused by ligand-binding
predictable? A molecular dynamics
investigation . . . . . . . . . . . . . 1229--1237
E. Prabhu Raman and
Sirish Kaushik Lakkaraju and
Rajiah Aldrin Denny and
Alexander D. MacKerell Jr Estimation of relative free energies of
binding using pre-computed ensembles
based on the single-step free energy
perturbation and the site-identification
by ligand competitive saturation
approaches . . . . . . . . . . . . . . . 1238--1251
Sam Tonddast-Navaei and
Bharath Srinivasan and
Jeffrey Skolnick On the importance of composite protein
multiple ligand interactions in protein
pockets . . . . . . . . . . . . . . . . 1252--1259
Christopher R. Ellis and
Cheng-Chieh Tsai and
Fang-Yu Lin and
Jana Shen Conformational dynamics of cathepsin D
and binding to a small-molecule BACE1
inhibitor . . . . . . . . . . . . . . . 1260--1269
Shuai Wei and
Charles L. Brooks III and
Aaron T. Frank A rapid solvent accessible surface area
estimator for coarse grained molecular
simulations . . . . . . . . . . . . . . 1270--1274
Lisa E. Felberg and
David H. Brookes and
Eng-Hui Yap and
Elizabeth Jurrus and
Nathan A. Baker and
Teresa Head-Gordon PB-AM: an open-source, fully analytical
linear Poisson--Boltzmann solver . . . . 1275--1282
Anonymous Cover Image, Volume 38, Issue 16 . . . . i--i
Anonymous Cover Image, Volume 38, Issue 16 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 1283--1290
Garrett B. Goh and
Nathan O. Hodas and
Abhinav Vishnu Review: Deep learning for computational
chemistry . . . . . . . . . . . . . . . 1291--1307
Bercem Dutagaci and
Maryam Sayadi and
Michael Feig Heterogeneous dielectric generalized
Born model with a van der Waals term
provides improved association energetics
of membrane-embedded transmembrane
helices . . . . . . . . . . . . . . . . 1308--1320
Andrea Bazzoli and
John Karanicolas ``Solvent hydrogen-bond occlusion'': a
new model of polar desolvation for
biomolecular energetics . . . . . . . . 1321--1331
Kuo Hao Lee and
Jianhan Chen Optimization of the GBMV2 implicit
solvent force field for accurate
simulation of protein conformational
equilibria . . . . . . . . . . . . . . . 1332--1341
Mark A. Olson and
Michael S. Lee and
In-Chul Yeh Membrane insertion of fusion peptides
from Ebola and Marburg viruses studied
by replica-exchange molecular dynamics
simulations . . . . . . . . . . . . . . 1342--1352
Bin Song and
Nathaniel Charest and
Herbert Alexander Morriss-Andrews and
Valeria Molinero and
Joan-Emma Shea Systematic derivation of implicit
solvent models for the study of polymer
collapse . . . . . . . . . . . . . . . . 1353--1361
Fouad S. Husseini and
David Robinson and
Neil T. Hunt and
Anthony W. Parker and
Jonathan D. Hirst Computing infrared spectra of proteins
using the exciton model . . . . . . . . 1362--1375
Fiona L. Kearns and
Phillip S. Hudson and
Henry L. Woodcock and
Stefan Boresch Computing converged free energy
differences between levels of theory via
nonequilibrium work methods: Challenges
and opportunities . . . . . . . . . . . 1376--1388
Sudipta Kumar Sinha and
Mohit Mehta and
Sandeep Patel A charge equilibration formalism for
treating charge transfer effects in MD
simulations: Application to water
clusters . . . . . . . . . . . . . . . . 1389--1409
Jaewoon Jung and
Yuji Sugita Multiple program/multiple data molecular
dynamics method with multiple time step
integrator for large biological systems 1410--1418
Travis Johnston and
Boyu Zhang and
Adam Liwo and
Silvia Crivelli and
Michela Taufer In situ data analytics and indexing of
protein trajectories . . . . . . . . . . 1419--1430
Catherine A. Hurd and
Nicholas A. Besley and
David Robinson A QM/MM study of the nature of the
entatic state in plastocyanin . . . . . 1431--1437
Cathy Ng and
Padmavathy Nandha Premnath and
Olgun Guvench Rigidity and flexibility in the
tetrasaccharide linker of proteoglycans
from atomic-resolution molecular
simulation . . . . . . . . . . . . . . . 1438--1446
Osamu Miyashita and
Chigusa Kobayashi and
Takaharu Mori and
Yuji Sugita and
Florence Tama Flexible fitting to cryo-EM density map
using ensemble molecular dynamics
simulations . . . . . . . . . . . . . . 1447--1461
Michael D. Ward and
Shivangi Nangia and
Eric R. May Evaluation of the hybrid resolution PACE
model for the study of folding,
insertion, and pore formation of
membrane associated peptides . . . . . . 1462--1471
Greg Starek and
J. Alfredo Freites and
Simon Bern\`eche and
Douglas J. Tobias Gating energetics of a voltage-dependent
K$^+$ channel pore domain . . . . . . . 1472--1478
Asanga Bandara and
Afra Panahi and
George A. Pantelopulos and
John E. Straub Exploring the structure and stability of
cholesterol dimer formation in
multicomponent lipid bilayers . . . . . 1479--1488
Anonymous Cover Image, Volume 38, Issue 17 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1489--1494
Christian J. Suess and
Jonathan D. Hirst and
Nicholas A. Besley Quantum chemical calculations of
tryptophan heme electron and excitation
energy transfer rates in myoglobin . . . 1495--1502
Hiroto Tachikawa Effects of zero point vibration on the
reaction dynamics of water dimer cations
following ionization . . . . . . . . . . 1503--1508
Juan Carlos Sancho-García and
Ángel José Pérez-Jiménez and
Marika Savarese and
Éric Brémond and
Carlo Adamo Determining the role of the underlying
orbital-dependence of PBE0-DH and
PBE-QIDH double-hybrid density
functionals . . . . . . . . . . . . . . 1509--1514
Vincent Pohl and
Gunter Hermann and
Jean Christophe Tremblay An open-source framework for analyzing
$N$-electron dynamics. I.
Multideterminantal wave functions . . . 1515--1527
Chong Yang and
Andreas Dreuw Evaluation of the restricted virtual
space approximation in the
algebraic-diagrammatic construction
scheme for the polarization propagator
to speed-up excited-state calculations 1528--1537
Sjoerd J. de Vries and
Martin Zacharias Fast and accurate grid representations
for atom-based docking with partner
flexibility . . . . . . . . . . . . . . 1538--1546
George Opletal and
Timothy C. Petersen and
Amanda S. Barnard and
Salvy P. Russo On reverse Monte Carlo constraints and
model reproduction . . . . . . . . . . . 1547--1551
Johannes M. Dieterich and
William C. Witt and
Emily A. Carter Software News and Updates: libKEDF: an
accelerated library of kinetic energy
density functionals . . . . . . . . . . 1552--1559
Anonymous Cover Image, Volume 38, Issue 18 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1561--1565
Kenji Hirano and
Hiroshi Nakano and
Yoshihide Nakao and
Hirofumi Sato and
Shigeyoshi Sakaki Photo absorption of $p$-coumaric acid in
aqueous solution: RISM--SCF--SEDD theory
approach . . . . . . . . . . . . . . . . 1567--1573
Zhifeng Lin and
Tian Lu and
Xun-Lei Ding A theoretical investigation on doping
superalkali for triggering considerable
nonlinear optical properties of
Si$_{12}$ C$_{12}$ nanostructure . . . . 1574--1582
Andrew L. Ferguson BayesWHAM: a Bayesian approach for free
energy estimation, reweighting, and
uncertainty quantification in the
weighted histogram analysis method . . . 1583--1605
Anand Kumar and
Miquel Duran and
Miquel Sol\`a Is coronene better described by Clar's
aromatic $ \pi $-sextet model or by the
AdNDP representation? . . . . . . . . . 1606--1611
Natacha Gillet and
Bernard Lévy and
Vicent Moliner and
Isabelle Demachy and
Aurélien de la Lande Theoretical estimation of redox
potential of biological quinone
cofactors . . . . . . . . . . . . . . . 1612--1621
Swapnil Mahajan and
Yves-Henri Sanejouand Jumping between protein conformers using
normal modes . . . . . . . . . . . . . . 1622--1630
Teerapong Pirojsirikul and
Andreas W. Götz and
John Weare and
Ross C. Walker and
Karol Kowalski and
Marat Valiev Combined quantum-mechanical molecular
mechanics calculations with NWChem and
AMBER: Excited state properties of green
fluorescent protein chromophore analogue
in aqueous solution . . . . . . . . . . 1631--1639
Dariusz W. Szczepanik and
Miquel Sol\`a and
Marcin Andrzejak and
Barbara Pawe\lek and
Justyna Dominikowska and
Mercedes Kuku\lka and
Karol Dyduch and
Tadeusz M. Krygowski and
Halina Szatylowicz The role of the long-range exchange
corrections in the description of
electron delocalization in aromatic
species . . . . . . . . . . . . . . . . 1640--1654
Anonymous Cover Image, Volume 38, Issue 19 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1655--1659
Alvaro Muñoz-Castro and
R. Bruce King On the formation of smaller $p$-block
endohedral fullerenes: Bonding analysis
in the E@C$_{20}$ (E = Si, Ge, Sn, Pb)
series from relativistic DFT
calculations . . . . . . . . . . . . . . 1661--1667
Osvaldo Yañez and
Alejandro Vásquez-Espinal and
Diego Inostroza and
Lina Ruiz and
Ricardo Pino-Rios and
William Tiznado A Fukui function-guided genetic
algorithm. Assessment on structural
prediction of Si$_n$ ($ n = 12$--$ 20$)
clusters . . . . . . . . . . . . . . . . 1668--1677
Kuan-Yu Liu and
Jie Liu and
John M. Herbert Accuracy of finite-difference harmonic
frequencies in density functional theory 1678--1684
Daijiro Nozaki and
Wolf Gero Schmidt Current density analysis of electron
transport through molecular wires in
open quantum systems . . . . . . . . . . 1685--1692
Nils Schieschke and
Roberto Di Remigio and
Luca Frediani and
Johannes Heuser and
Sebastian Höfener Combining frozen-density embedding with
the conductor-like screening model using
Lagrangian techniques for response
properties . . . . . . . . . . . . . . . 1693--1703
Premaja R. Remya and
Cherumuttathu H. Suresh Theoretical evidence for bond stretch
isomerism in Grubbs olefin metathesis 1704--1711
Tamara Papp and
László Kollár and
Tamás Kégl Theoretical insights into the nature of
Pt--Sn bond: Reevaluating the
bonding/back-bonding properties of
trichlorostannate with comparison to the
cyano ligand . . . . . . . . . . . . . . 1712--1726
Jindal K. Shah and
Eliseo Marin-Rimoldi and
Ryan Gotchy Mullen and
Brian P. Keene and
Sandip Khan and
Andrew S. Paluch and
Neeraj Rai and
Lucienne L. Romanielo and
Thomas W. Rosch and
Brian Yoo and
Edward J. Maginn Software News and Updates: Cassandra: an
open source Monte Carlo package for
molecular simulation . . . . . . . . . . 1727--1739
Anonymous Cover Image, Volume 38, Issue 20 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1741--1745
José A. Gámez and
Markus Hölscher and
Walter Leitner On the applicability of density
functional theory to manganese-based
complexes with catalytic activity toward
water oxidation . . . . . . . . . . . . 1747--1751
Matthias Witte and
Martin Rohrmüller and
Uwe Gerstmann and
Gerald Henkel and
Wolf Gero Schmidt and
Sonja Herres-Pawlis [Cu$_6$ (NGuaS)$_6$]$^{2+}$ and its
oxidized and reduced derivatives:
Confining electrons on a torus . . . . . 1752--1761
Dóra Papp and
Petra Rovó and
Imre Jákli and
Attila G. Császár and
András Perczel Four faces of the interaction between
ions and aromatic rings . . . . . . . . 1762--1773
Paul G. Mezey and
Zoltan Antal An alternative to the ``Star Path''
enhancement of the ADMA linear scaling
method for protein modeling . . . . . . 1774--1779
Athanassios C. Tsipis Exploring possible reaction pathways for
the o-atom transfer reactions to
unsaturated substrates catalyzed by a
[Ni-NO$_2$] [Ni-NO] redox couple using
DFT methods . . . . . . . . . . . . . . 1780--1788
Ian L. Rogers and
Kevin J. Naidoo Producing DFT/MM enzyme reaction
trajectories from SCC-DFTB/MM driving
forces to probe the underlying
electronics of a glycosyltransferase
reaction . . . . . . . . . . . . . . . . 1789--1798
Borys Szefczyk and
Dawid Grabarek and
El\.zbieta Walczak and
Tadeusz Andruniów Excited-state minima and emission
energies of retinal chromophore
analogues: Performance of CASSCF and CC2
methods as compared with CASPT2 . . . . 1799--1810
Jeroen A. Rombouts and
Andreas W. Ehlers and
Koop Lammertsma A quantitative analysis of light-driven
charge transfer processes using Voronoi
partitioning of time dependent
DFT-derived electron densities . . . . . 1811--1818
Anonymous Cover Image, Volume 38, Issue 21 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1819--1823
Shigeru Yamaguchi and
Takahiro Nishimura and
Yuta Hibe and
Masaki Nagai and
Hirofumi Sato and
Ian Johnston Regularized regression analysis of
digitized molecular structures in
organic reactions for quantification of
steric effects . . . . . . . . . . . . . 1825--1833
Matteo Masetti and
Francesco Musiani and
Mattia Bernetti and
Federico Falchi and
Andrea Cavalli and
Stefano Ciurli and
Maurizio Recanatini Development of a multisite model for
Ni(II) ion in solution from
thermodynamic and kinetic data . . . . . 1834--1843
Talapunur Vikramaditya and
Shiang-Tai Lin Assessing the role of Hartree--Fock
exchange, correlation energy and long
range corrections in evaluating
ionization potential, and electron
affinity in density functional theory 1844--1852
Martin Krupi\vcka and
Kantharuban Sivalingam and
Lee Huntington and
Alexander A. Auer and
Frank Neese A toolchain for the automatic generation
of computer codes for correlated
wavefunction calculations . . . . . . . 1853--1868
Joaquín Calbo and
Juan C. Sancho-García and
Enrique Ortí and
Juan Aragó DLPNO-CCSD(T) scaled methods for the
accurate treatment of large
supramolecular complexes . . . . . . . . 1869--1878
Seonghoon Kim and
Jumin Lee and
Sunhwan Jo and
Charles L. Brooks III and
Hui Sun Lee and
Wonpil Im Software News and Updates: CHARMM-GUI
ligand reader and modeler for CHARMM
force field generation of small
molecules . . . . . . . . . . . . . . . 1879--1886
Jean-Baptiste Chéron and
Martin Zacharias and
Serge Antonczak and
Sébastien Fiorucci Software News and Updates: Update of the
ATTRACT force field for the prediction
of protein--protein binding affinity . . 1887--1890
Anonymous Cover Image, Volume 38, Issue 22 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1891--1895
Léa El Khoury and
Sehr Naseem-Khan and
Karolina Kwapien and
Zeina Hobaika and
Richard G. Maroun and
Jean-Philip Piquemal and
Nohad Gresh Importance of explicit smeared
lone-pairs in anisotropic polarizable
molecular mechanics. Torture track
angular tests for exchange-repulsion and
charge transfer contributions . . . . . 1897--1920
Ryuhei Harada and
Yasuteru Shigeta Structural dissimilarity sampling with
dynamically self-guiding selection . . . 1921--1929
Hernán R. Sánchez Revisiting the thermochemistry of
chlorine fluorides . . . . . . . . . . . 1930--1940
Nicolas Chéron and
Eugene I. Shakhnovich Effect of sampling on BACE-1 ligands
binding free energy predictions via
MM--PBSA calculations . . . . . . . . . 1941--1951
Anis Ghazouani and
Jalel M'halla Simple computing of the viscosity of
water--dioxane mixtures, according to a
fluctuating SPC/E-I$_h$ interstitial
model . . . . . . . . . . . . . . . . . 1952--1965
Andrés G. Algarra Computational insights into the S$_3$
transfer reaction: a special case of
double group transfer reaction featuring
bicyclically delocalized aromatic
transition state geometries . . . . . . 1966--1973
Zhe Jia and
Lin Li and
Arghya Chakravorty and
Emil Alexov Software News and Updates: Treating ion
distribution with Gaussian-based smooth
dielectric function in DelPhi . . . . . 1974--1979
Anonymous Cover Image, Volume 38, Issue 23 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1981--1986
Inaki Morao and
Dmitri G. Fedorov and
Roger Robinson and
Michelle Southey and
Andrea Townsend-Nicholson and
Mike J. Bodkin and
Alexander Heifetz Rapid and accurate assessment of
GPCR--ligand interactions using the
fragment molecular orbital-based
density-functional tight-binding method 1987--1990
Lei Sun and
Li Yang and
Ya-Dong Zhang and
Qi Shi and
Rui-Feng Lu and
Wei-Qiao Deng Accurate van der Waals force field for
gas adsorption in porous materials . . . 1991--1999
Nguyen-Quoc-Khanh Le and
Quang-Thai Ho and
Yu-Yen Ou Incorporating deep learning with
convolutional neural networks and
position specific scoring matrices for
identifying electron transport proteins 2000--2006
Ming Huang and
Wenjun Huang and
Fei Wen and
Ronald G. Larson Efficient estimation of binding free
energies between peptides and an MHC
class II molecule using coarse-grained
molecular dynamics simulations with a
weighted histogram analysis method . . . 2007--2019
Takao Tsuneda and
Raman K. Singh and
Ayako Nakata On low-lying excited states of extended
nanographenes . . . . . . . . . . . . . 2020--2029
Rei Matsuzaki and
Satoshi Yabushita Calculation of photoionization
differential cross sections using
complex Gauss-type orbitals . . . . . . 2030--2040
I-Hsiang Lin and
Yu-Huan Lu and
Hsin-Tsung Chen Nitrogen-doped C$_{60}$ as a robust
catalyst for CO oxidation . . . . . . . 2041--2046
Matthew Harger and
Daniel Li and
Zhi Wang and
Kevin Dalby and
Louis Lagard\`ere and
Jean-Philip Piquemal and
Jay Ponder and
Pengyu Ren Tinker--OpenMM: Absolute and relative
alchemical free energies using AMOEBA on
GPUs . . . . . . . . . . . . . . . . . . 2047--2055
Anonymous Cover Image, Volume 38, Issue 24 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2057--2061
Amir Karton and
Nitai Sylvetsky and
Jan M. L. Martin W4-17: a diverse and high-confidence
dataset of atomization energies for
benchmarking high-level electronic
structure methods . . . . . . . . . . . 2063--2075
Silvia Díaz and
Mateusz Z. Brela and
Soledad Gutiérrez-Oliva and
Alejandro Toro-Labbé and
Artur Michalak ETS-NOCV Decomposition of the Reaction
Force: The HCN/CNH Isomerization
Reaction Assisted by Water . . . . . . . 2076--2087
Robert A. Evarestov and
Andrei V. Bandura and
Vitaly V. Porsev and
Alexey V. Kovalenko First-principles modeling of
hafnia-based nanotubes . . . . . . . . . 2088--2099
Yujia Pang and
Wenliang Li and
Jingping Zhang Gas adsorption in Mg-porphyrin-based
porous organic frameworks: a
computational simulation by
first-principles derived force field . . 2100--2107
Dalibor Hr\vsak and
Jógvan Magnus Haugaard Olsen and
Jacob Kongsted Optimization and transferability of
non-electrostatic repulsion in the
polarizable density embedding model . . 2108--2117
Jaime Rodríguez-Guerra Pedregal and
Giuseppe Sciortino and
Jordi Guasp and
Martí Municoy and
Jean-Didier Maréchal Software News and Updates: GaudiMM: a
modular multi-objective platform for
molecular modeling . . . . . . . . . . . 2118--2126
Stephan N. Steinmann and
Paul Fleurat-Lessard and
Andreas W. Götz and
Carine Michel and
Rodrigo Ferreira de Morais and
Philippe Sautet Letters to the Editor: Molecular
mechanics models for the image charge, a
comment on ``Including image charge
effects in the molecular dynamics
simulations of molecules on metal
surfaces'' . . . . . . . . . . . . . . . 2127--2129
Stefano Corni Letters to the Editor: Reply to
``Molecular mechanics models for the
image charge'' . . . . . . . . . . . . . 2130--2133
Anonymous Cover Image, Volume 38, Issue 25 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2135--2139
Fabian Weber and
Emad F. Aziz and
Annika Bande Interdependence of ICD rates in paired
quantum dots on geometry . . . . . . . . 2141--2150
Marco Campetella and
Federica Maschietto and
Mike J. Frisch and
Giovanni Scalmani and
Ilaria Ciofini and
Carlo Adamo Charge transfer excitations in TDDFT: a
ghost-hunter index . . . . . . . . . . . 2151--2156
Per E. M. Siegbahn and
Xichen Li Cluster size convergence for the
energetics of the oxygen evolving
complex in PSII . . . . . . . . . . . . 2157--2160
Sadanandam Namsani and
Bhasker Gahtori and
Sushil Auluck and
Jayant K. Singh An interaction potential to study the
thermal structure evolution of a
thermoelectric material: $ \beta
$-Cu$_2$Se . . . . . . . . . . . . . . . 2161--2170
Maja Gruden and
Ljubica Andjeklovi\'c and
Akkarapattiakal Kuriappan Jissy and
Stepan Stepanovi\'c and
Matija Zlatar and
Qiang Cui and
Marcus Elstner Benchmarking density functional tight
binding models for barrier heights and
reaction energetics of organic molecules 2171--2185
Lakshmanan Sandhiya and
Hendrik Zipse O--O bond homolysis in hydrogen peroxide 2186--2192
Chigusa Kobayashi and
Jaewoon Jung and
Yasuhiro Matsunaga and
Takaharu Mori and
Tadashi Ando and
Koichi Tamura and
Motoshi Kamiya and
Yuji Sugita Software News and Updates: GENESIS 1.1:
a hybrid-parallel molecular dynamics
simulator with enhanced sampling
algorithms on multiple computational
platforms . . . . . . . . . . . . . . . 2193--2206
Anonymous Cover Image, Volume 38, Issue 26 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2207--2211
Kimichi Suzuki and
Keiji Morokuma and
Satoshi Maeda Multistructural microiteration technique
for geometry optimization and reaction
path calculation in large systems . . . 2213--2221
Shi Deng and
Qiantao Wang and
Pengyu Ren Estimating and modeling charge transfer
from the SAPT induction energy . . . . . 2222--2231
Ramachandran Rakhi and
Cherumuttathu H. Suresh A DFT study on
1,4-dihydro-1,4-azaborinine annulated
linear polyacenes: Absorption spectra,
singlet-triplet energy gap, aromaticity,
and HOMO--LUMO energy modulation . . . . 2232--2240
Jing-Shuang Dang and
Wei-Wei Wang and
Jia-Jia Zheng and
Shigeru Nagase and
Xiang Zhao Formation of Stone--Wales edge:
Multistep reconstruction and growth
mechanisms of zigzag nanographene . . . 2241--2247
Samik Bose and
Debashree Ghosh An interaction energy driven biased
sampling technique: a faster route to
ionization spectra in condensed phase 2248--2257
Manash Protim Borpuzari and
Rahul Kar A new nonempirical tuning scheme with
single self-consistent field
calculation: Comparison with global and
IP-tuned range-separated functional . . 2258--2267
Shanshan Cao and
Haiyan Yuan and
Yang Yang and
Mang Wang and
Xiaoying Zhang and
Jingping Zhang Mechanistic investigation inspired ``on
water'' reaction for hydrobromic
acid-catalyzed Friedel--Crafts-type
reaction of $ \beta $-naphthol and
formaldehyde . . . . . . . . . . . . . . 2268--2275
Andreas Lücke and
Uwe Gerstmann and
Thomas D. Kühne and
Wolf G. Schmidt Efficient PAW-based bond strength
analysis for understanding the
In/Si(111)($ 8 \times 2$)--($ 4 \times
1$) phase transition . . . . . . . . . . 2276--2282
Anonymous Cover Image, Volume 38, Issue 27 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2283--2287
Haiyan Yuan and
Pin Xiao and
Yiying Zheng and
Jingping Zhang DFT studies on the mechanism of
Ag$_2$CO$_3$-catalyzed hydroazidation of
unactivated terminal alkynes with
TMS-N$_3$: an insight into the silver(I)
activation mode . . . . . . . . . . . . 2289--2297
Changjun Chen Constructing a multidimensional free
energy surface like a spider weaving a
web . . . . . . . . . . . . . . . . . . 2298--2306
Bun Chan and
Yukio Kawashima and
Kimihiko Hirao Correlation functional in
screened-exchange density functional
theory procedures . . . . . . . . . . . 2307--2315
Johannes Heuser and
Sebastian Höfener Analytical nuclear excited-state
gradients for the Tamm--Dancoff
approximation using uncoupled
frozen-density embedding . . . . . . . . 2316--2325
Jun Chen and
Neil Qiang Su and
Xin Xu and
Dong H. Zhang Accurate potential energy surfaces for
hydrogen abstraction reactions: a
benchmark study on the XYG3 doubly
hybrid density functional . . . . . . . 2326--2334
Titus Adrian Beu and
Alexandra Farca\cs CHARMM force field and molecular
dynamics simulations of protonated
polyethylenimine . . . . . . . . . . . . 2335--2348
Carolin Hühn and
Andreas Erlebach and
Dorothea Mey and
Lothar Wondraczek and
Marek Sierka Ab Initio energetics of SiO bond
cleavage . . . . . . . . . . . . . . . . 2349--2353
Pin-Chia Hsu and
Bart M. H. Bruininks and
Damien Jefferies and
Paulo Cesar Telles de Souza and
Jumin Lee and
Dhilon S. Patel and
Siewert J. Marrink and
Yifei Qi and
Syma Khalid and
Wonpil Im Software News and Updates: CHARMM-GUI
Martini Maker for modeling and
simulation of complex bacterial
membranes with lipopolysaccharides . . . 2354--2363
Anonymous Cover Image, Volume 38, Issue 28 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2365--2369
Vitor H. Menezes da Silva and
Ana Paula de Lima Batista and
Oscar Navarro and
Ataualpa A. C. Braga Theoretical study on selectivity trends
in ($N$-heterocyclic carbene)-Pd
catalyzed Mizoroki--Heck reactions:
Exploring density functionals methods
and molecular models . . . . . . . . . . 2371--2377
Gunter Hermann and
Vincent Pohl and
Jean Christophe Tremblay An open-source framework for analyzing
$N$-electron dynamics. II. Hybrid
density functional theory/configuration
interaction methodology . . . . . . . . 2378--2387
Xiang-Yang Liu and
Pin Xiao and
Wei-Hai Fang and
Ganglong Cui Theoretical studies of spin
state-specific $ [2 + 2] $ and $ [5 + 2]
$ photocycloaddition reactions of
$n$-(1-penten-5-yl)maleimide . . . . . . 2388--2395
Francesco Villa and
David Mignon and
Savvas Polydorides and
Thomas Simonson Comparing pairwise-additive and
many-body generalized Born models for
acid/base calculations and protein
design . . . . . . . . . . . . . . . . . 2396--2410
Yuichi Tanaka and
Yukio Kawashima and
Norio Yoshida and
Haruyuki Nakano Solvatochromism and preferential
solvation of Brooker's merocyanine in
water--methanol mixtures . . . . . . . . 2411--2419
Mateusz Snamina and
Grzegorz Mazur and
Piotr Petelenz Partial atomic multipoles for internally
consistent microelectrostatic
calculations . . . . . . . . . . . . . . 2420--2429
Guangchao Liang and
Nathan J. DeYonker and
Xuan Zhao and
Charles Edwin Webster Prediction of the reduction potential in
transition-metal containing complexes:
How expensive? For what accuracy? . . . 2430--2438
Anders Lervik and
Enrico Riccardi and
Titus S. van Erp Software News and Updates: PyRETIS: a
well-done, medium-sized Python library
for rare events . . . . . . . . . . . . 2439--2451
Anonymous Cover Image, Volume 38, Issue 29 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2453--2457
Peter I. Maxwell and
Paul L. A. Popelier Unfavorable regions in the Ramachandran
plot: Is it really steric hindrance? The
interacting quantum atoms perspective 2459--2474
Ismail A. M. Ibrahim Electronic structure, magnetic
properties, and mixed valence character
of Ce$_2$Ni$_3$Si$_5$ from first
principles calculations . . . . . . . . 2475--2480
Chao Huang and
Wenjian Liu and
Yunlong Xiao and
Mark R. Hoffmann iVI: an iterative vector interaction
method for large eigenvalue problems . . 2481--2499
Oinam Romesh Meitei and
Andreas Heßelmann Intramolecular interactions in
sterically crowded hydrocarbon molecules 2500--2508
Eleni Michael and
Savvas Polydorides and
Thomas Simonson and
Georgios Archontis Simple models for nonpolar solvation:
Parameterization and testing . . . . . . 2509--2519
Masahiko Nakano and
Takeshi Yoshikawa and
So Hirata and
Junji Seino and
Hiromi Nakai Computerized implementation of
higher-order electron-correlation
methods and their linear-scaling
divide-and-conquer extensions . . . . . 2520--2527
Rahul Chakraborty and
Samik Bose and
Debashree Ghosh Effect of solvation on the ionization of
guanine nucleotide: a hybrid QM/EFP
study . . . . . . . . . . . . . . . . . 2528--2537
Matthew J. L. Mills and
Kenneth L. Sale and
Blake A. Simmons and
Paul L. A. Popelier Software News and Updates: Rhorix: an
interface between quantum chemical
topology and the $3$D graphics program
blender . . . . . . . . . . . . . . . . 2538--2552
Anonymous Cover Image, Volume 38, Issue 30 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2553--2557
Ryosuke Ishizuka and
Nobuyuki Matubayasi Effective charges of ionic liquid
determined self-consistently through
combination of molecular dynamics
simulation and density-functional theory 2559--2569
Sean McConnell and
Johannes Kästner Instanton rate constant calculations
close to and above the crossover
temperature . . . . . . . . . . . . . . 2570--2580
Robert A. Evarestov and
Andrei V. Bandura and
Vitaly V. Porsev and
Alexey V. Kovalenko Phonon spectra, electronic, and
thermodynamic properties of WS$_2$
nanotubes . . . . . . . . . . . . . . . 2581--2593
Nickolas D. Charistos and
Anastasios G. Papadopoulos and
Thomas A. Nikopoulos and
Alvaro Muñoz-Castro and
Michael P. Sigalas Canonical orbital contributions to the
magnetic fields induced by global and
local diatropic and paratropic ring
currents . . . . . . . . . . . . . . . . 2594--2604
Jayangika N. Dahanayake and
Chandana Kasireddy and
Jonathan M. Ellis and
Derek Hildebrandt and
Olivia A. Hull and
Joseph P. Karnes and
Dylan Morlan and
Katie R. Mitchell-Koch Evaluating electronic structure methods
for accurate calculation of $^{19}$F
chemical shifts in fluorinated amino
acids . . . . . . . . . . . . . . . . . 2605--2617
Philipp Pracht and
Christoph Alexander Bauer and
Stefan Grimme Automated and efficient quantum chemical
determination and energetic ranking of
molecular protonation sites . . . . . . 2618--2631
Kuo Hao Lee and
Jianhan Chen Efficacy of independence sampling in
replica exchange simulations of ordered
and disordered proteins . . . . . . . . 2632--2640
William J. Allen and
Brian C. Fochtman and
Trent E. Balius and
Robert C. Rizzo Customizable de novo design strategies
for DOCK: Application to HIVgp41 and
other therapeutic targets . . . . . . . 2641--2663
Anonymous Cover Image, Volume 38, Issue 31 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2665--2670
Ryuhei Harada and
Yasuteru Shigeta Temperature-shuffled parallel cascade
selection molecular dynamics accelerates
the structural transitions of proteins 2671--2674
Gabriel R. Schleder and
Adalberto Fazzio and
Jeverson T. Arantes Dynamic covalent bond from first
principles: Diarylbibenzofuranone
structural, electronic, and oxidation
studies . . . . . . . . . . . . . . . . 2675--2679
Filip \vSebesta and
Mateusz Z. Brela and
Silvia Diaz and
Sebastian Miranda and
Jane S. Murray and
Soledad Gutiérrez-Oliva and
Alejandro Toro-Labbé and
Artur Michalak and
Jaroslav V. Burda The influence of the metal cations and
microhydration on the reaction
trajectory of the N$_3$O$_2$ thymine
proton transfer: Quantum mechanical
study . . . . . . . . . . . . . . . . . 2680--2692
Andreas J. Achazi and
Dirk Andrae and
Hans-Ulrich Reissig and
Beate Paulus A computational study of samarium
diiodide-induced cyclizations of
$N$-oxoalkyl-substituted methyl
indole-$3$-carboxylates --- a rationale
of the diastereoselectivity . . . . . . 2693--2700
Jeremy P. Coe and
Nuno M. S. Almeida and
Martin J. Paterson Investigation of challenging spin
systems using Monte Carlo configuration
interaction and the density matrix
renormalization group . . . . . . . . . 2701--2712
Dario Ghersi and
Abhishek Parakh and
Mihaly Mezei Comparison of a quantum random number
generator with pseudorandom number
generators for their use in molecular
Monte Carlo simulations . . . . . . . . 2713--2720
Neda Khanjari and
Hossein Eslami and
Florian Müller-Plathe Adaptive-numerical-bias metadynamics . . 2721--2729
Agnieszka S. Karczy\'nska and
Cezary Czaplewski and
Pawe\l Krupa and
Magdalena A. Mozolewska and
Keehyoung Joo and
Jooyoung Lee and
Adam Liwo Ergodicity and model quality in
template-restrained canonical and
temperature/Hamiltonian replica exchange
coarse-grained molecular dynamics
simulations of proteins . . . . . . . . 2730--2746
Anonymous Cover Image, Volume 38, Issue 32 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 2747--2751
Mohamed Amaouch and
Dumitru-Claudiu Sergentu and
David Steinmetz and
Rémi Maurice and
Nicolas Galland and
Julien Pilmé The bonding picture in hypervalent
XF$_3$ (X = Cl, Br, I, At) fluorides
revisited with quantum chemical topology 2753--2762
Olaseni Sode and
Jasmine N. Cherry Development of a Flexible-Monomer
Two-Body Carbon Dioxide Potential and
Its Application to Clusters up to
(CO$_2$)$_{13}$ . . . . . . . . . . . . 2763--2774
Matteo Piccardo and
Alessandro Soncini A full-pivoting algorithm for the
Cholesky decomposition of two-electron
repulsion and spin-orbit coupling
integrals . . . . . . . . . . . . . . . 2775--2783
Lizé-Mari Ferreira and
Alan Eaby and
Jan Dillen The topology of the Coulomb potential
density. A comparison with the electron
density, the virial energy density, and
the Ehrenfest force density . . . . . . 2784--2790
Debarati DasGupta and
Varun Mandalaparthy and
Bhyravabhotla Jayaram A component analysis of the free
energies of folding of 35 proteins: a
consensus view on the thermodynamics of
folding at the molecular level . . . . . 2791--2801
Arpita Varadwaj and
Pradeep R. Varadwaj and
Koichi Yamashita Hybrid organic--inorganic CH$_3$ NH$_3$
PbI$_3$ perovskite building blocks:
Revealing ultra-strong hydrogen bonding
and Mulliken inner complexes and their
implications in materials design . . . . 2802--2818
Miquel Torrent-Sucarrat and
Sara Navarro and
Fernando P. Cossío and
Josep M. Anglada and
Josep M. Luis Relevance of the DFT method to study
expanded porphyrins with different
topologies . . . . . . . . . . . . . . . 2819--2828
Anonymous Cover Image, Volume 39, Issue 1 . . . . i--i
Anonymous Cover Image, Volume 39, Issue 1 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 1--5
Suliman Adam and
Michaela Knapp-Mohammady and
Jun Yi and
Ana-Nicoleta Bondar Revised CHARMM force field parameters
for iron-containing cofactors of
photosystem II . . . . . . . . . . . . . 7--20
Stefano Pelloni and
Paolo Lazzeretti Polygonal current models for polycyclic
aromatic hydrocarbons and graphene
sheets of various shapes . . . . . . . . 21--34
John Hamilton and
Evangelia Kotsikorou Parameterization of the GPR119 Receptor
Agonist AR231453 . . . . . . . . . . . . 35--41
Giuseppe Sciortino and
Jaime Rodríguez-Guerra Pedregal and
Agustí Lledós and
Eugenio Garribba and
Jean-Didier Maréchal Prediction of the interaction of
metallic moieties with proteins: an
update for protein-ligand docking
techniques . . . . . . . . . . . . . . . 42--51
Luis Alvarez-Thon and
Liliana Mammino Information on Gas-Phase Diatomic
Molecules from Magnetically Induced
Current Densities . . . . . . . . . . . 52--60
Masakazu Matsumoto and
Takuma Yagasaki and
Hideki Tanaka Software News and Updates: GenIce:
Hydrogen-Disordered Ice Generator . . . 61--64
Anonymous Cover Image, Volume 39, Issue 2 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 65--69
Ma del Refugio Cuevas-Flores and
Marco Antonio Garcia-Revilla and
Massimiliano Bartolomei Noncovalent interactions between
cisplatin and graphene prototypes . . . 71--80
Torben Steenbock and
Carmen Herrmann Toward an automated analysis of exchange
pathways in spin-coupled systems . . . . 81--92
Enrique M. Cabaleiro-Lago and
Berta Fernández and
Jesús Rodríguez-Otero Dissecting the concave--convex $ \pi
$--$ \pi $ interaction in corannulene
and sumanene dimers: SAPT(DFT) analysis
and performance of DFT
dispersion-corrected methods . . . . . . 93--104
Yoshifumi Nishimura and
Hiromi Nakai Parallel implementation of efficient
charge--charge interaction evaluation
scheme in periodic divide-and-conquer
density-functional tight-binding
calculations . . . . . . . . . . . . . . 105--116
Xiaofang Cao and
Chunying Rong and
Aiguo Zhong and
Tian Lu and
Shubin Liu Molecular acidity: an accurate
description with information-theoretic
approach in density functional
reactivity theory . . . . . . . . . . . 117--129
Adrian Calborean and
Cristian Morari and
Pascale Maldivi Combined molecular and periodic DFT
analysis of the adsorption of Co
macrocycles on graphene . . . . . . . . 130--138
Anonymous Cover Image, Volume 39, Issue 3 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 139--142
Yasuhiro Imada and
Haruki Nakamura and
Yu Takano Density functional study of porphyrin
distortion effects on redox potential of
heme . . . . . . . . . . . . . . . . . . 143--150
Debdutta Chakraborty and
Pratim Kumar Chattaraj Confinement induced thermodynamic and
kinetic facilitation of some
Diels--Alder reactions inside a CB[7]
cavitand . . . . . . . . . . . . . . . . 151--160
Debdutta Chakraborty and
Pratim Kumar Chattaraj Host--guest interactions between octa
acid and cations/nucleobases . . . . . . 161--175
Anna Bronova and
Thomas Bredow and
Robert Glaum and
Mark J. Riley and
Werner Urland Software News and Updates: BonnMag:
Computer program for ligand-field
analysis of $ f^n $ systems within the
angular overlap model . . . . . . . . . 176--186
Anonymous Cover Image, Volume 39, Issue 4 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 187--190
Al'ona Furmanchuk and
James E. Saal and
Jeff W. Doak and
Gregory B. Olson and
Alok Choudhary and
Ankit Agrawal Prediction of Seebeck coefficient for
compounds without restriction to fixed
stoichiometry: a machine learning
approach . . . . . . . . . . . . . . . . 191--202
Tomonari Sumi and
Yutaka Maruyama and
Ayori Mitsutake and
Kenji Mochizuki and
Kenichiro Koga Application of reference-modified
density functional theory: Temperature
and pressure dependences of solvation
free energy . . . . . . . . . . . . . . 202--217
Bao Wang and
Chengzhang Wang and
Kedi Wu and
Guo-Wei Wei Breaking the polar-nonpolar division in
solvation free energy prediction . . . . 217--233
Satoshi Maeda and
Yu Harabuchi and
Makito Takagi and
Kenichiro Saita and
Kimichi Suzuki and
Tomoya Ichino and
Yosuke Sumiya and
Kanami Sugiyama and
Yuriko Ono Software News and Updates:
Implementation and performance of the
artificial force induced reaction method
in the GRRM17 program . . . . . . . . . 233--251
Anonymous Cover Image, Volume 39, Issue 5 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 251--254
François Godey and
Alexandre Fleury and
Aziz Ghoufi and
Armand Soldera The extent of the glass transition from
molecular simulation revealing an
overcrank effect . . . . . . . . . . . . 255--261
Sam Azadi and
Ranber Singh and
Thomas D. Kühne Nuclear quantum effects induce
metallization of dense solid molecular
hydrogen . . . . . . . . . . . . . . . . 262--268
Mohsen Abbaspour and
Hamed Akbarzadeh and
Sirous Salemi and
Khodanazar Pirfalak Molecular dynamics simulation of liquid
water and ice nanoclusters using a new
effective HFD-like model . . . . . . . . 269--278
Sandro Jurinovich and
Lorenzo Cupellini and
Ciro A. Guido and
Benedetta Mennucci Software News and Updates: EXAT:
EXcitonic Analysis Tool . . . . . . . . 279--286
Anonymous Cover Image, Volume 39, Issue 6 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 287--291
Yunwen Tao and
Wenli Zou and
Dieter Cremer and
Elfi Kraka Correlating the vibrational spectra of
structurally related molecules: a
spectroscopic measure of similarity . . 293--306
Ruixing Wang and
Mikhail Ozhgibesov and
Hajime Hirao Analytical Hessian fitting schemes for
efficient determination of
force-constant parameters in molecular
mechanics . . . . . . . . . . . . . . . 307--318
Paul Murphy and
Jeremy P. Coe and
Martin J. Paterson Development of spin-orbit coupling for
stochastic configuration interaction
techniques . . . . . . . . . . . . . . . 319--327
Simone Calvello and
Matteo Piccardo and
Shashank Vittal Rao and
Alessandro Soncini CERES: an ab initio code dedicated to
the calculation of the electronic
structure and magnetic properties of
lanthanide complexes . . . . . . . . . . 328--337
Chao Huang and
Wenjian Liu and
Yunlong Xiao and
Mark R. Hoffmann Erratum: ``iVI: an iterative vector
interaction method for large eigenvalue
problems'' [J. Comput. Chem. \bf 38,
2481 (2017)] . . . . . . . . . . . . . . 338--338
Anonymous Cover Image, Volume 39, Issue 7 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 339--342
Arpita Varadwaj and
Pradeep R. Varadwaj and
Koichi Yamashita Do surfaces of positive electrostatic
potential on different halogen
derivatives in molecules attract? Like
attracting like! . . . . . . . . . . . . 343--350
U\ugur Bozkaya Analytic energy gradients for
orbital-optimized MP3 and MP2.5 with the
density-fitting approximation: an
efficient implementation . . . . . . . . 351--360
Majda Misini Ignjatovi\'c and
Paulius Mikulskis and
Pär Söderhjelm and
Ulf Ryde Can MM/GBSA calculations be sped up by
system truncation? . . . . . . . . . . . 361--372
Michael Trumm On the isotropy of induced multipole
moments in heavy ion complexes . . . . . 373--379
Anonymous Cover Image, Volume 39, Issue 8 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 381--385
Nikoleta Ivanova and
Anela Ivanova Testing the limits of model membrane
simulations --- bilayer composition and
pressure scaling . . . . . . . . . . . . 387--396
Himanshu Goel and
Zachary W. Windom and
Amber A. Jackson and
Neeraj Rai Performance of density functionals for
modeling vapor liquid equilibria of
CO$_2$ and SO$_2$ . . . . . . . . . . . 397--406
Ivantha Guruge and
Ghazaleh Taherzadeh and
Jian Zhan and
Yaoqi Zhou and
Yuedong Yang B-factor profile prediction for RNA
flexibility using support vector
machines . . . . . . . . . . . . . . . . 407--411
Krishna Kant Singh and
Stephane Redon Single-pass incremental force updates
for adaptively restrained molecular
dynamics . . . . . . . . . . . . . . . . 412--423
Roland Tóbiás and
Attila G. Császár and
László Gyevi-Nagy and
Gyula Tasi Definitive thermochemistry and kinetics
of the interconversions among conformers
of $n$-butane and $n$-pentane . . . . . 424--437
Yana Kholod and
Michael DeFilippo and
Brittany Reed and
Danielle Valdez and
Grant Gillan and
Dmytro Kosenkov Software News and Updates: Excitation
energy transfer pathways in
light-harvesting proteins: Modeling with
PyFREC . . . . . . . . . . . . . . . . . 438--449
Anonymous Cover Image, Volume 39, Issue 9 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 451--455
Shridhar R. Gadre and
C. H. Suresh Preface . . . . . . . . . . . . . . . . 457--457
Antonio Bauzá and
Saikat Kumar Seth and
Antonio Frontera Molecular electrostatic potential and
``atoms-in-molecules'' analyses of the
interplay between $ \pi $-hole and lone
pair$ \cdots \pi $ /X--H$ \cdots \pi $
/metal$ \cdots \pi $ interactions . . . 458--463
Peter Politzer and
Jane S. Murray $ \sigma $-holes and $ \pi $-holes:
Similarities and differences . . . . . . 464--471
S\lawomir J. Grabowski Two faces of triel bonds in boron
trihalide complexes . . . . . . . . . . 472--480
Changwei Wang and
Yuzhuang Fu and
Lina Zhang and
David Danovich and
Sason Shaik and
Yirong Mo Hydrogen- and Halogen-Bonds between Ions
of like Charges: Are They
Anti-Electrostatic in Nature? . . . . . 481--487
Padinjare Veetil Bijina and
Cherumuttathu H. Suresh and
Shridhar R. Gadre Electrostatics for probing lone pairs
and their interactions . . . . . . . . . 488--499
Steve Scheiner Comparison of Various Means of
Evaluating Molecular Electrostatic
Potentials for Noncovalent Interactions 500--510
Guillaume Acke and
Sofie Van Damme and
Remco W. A. Havenith and
Patrick Bultinck Interpreting the behavior of the NICSzz
by resolving in orbitals, sign, and
positions . . . . . . . . . . . . . . . 511--519
Anonymous Cover Image, Volume 39, Issue 10 . . . . i--i
Anonymous Cover Image, Volume 39, Issue 10 . . . . ii--ii
Anonymous Issue Information . . . . . . . . . . . 521--525
Boris Galabov and
Valia Nikolova and
Diana Cheshmedzhieva and
Boriana Hadjieva and
Henry F. Schaefer III Hyperconjugative effects in $ \pi
$-hydrogen bonding: Theory and
experiment . . . . . . . . . . . . . . . 527--534
Debdutta Chakraborty and
Pratim Kumar Chattaraj Reactions involving some gas molecules
through sequestration on Al$_{12}$ Be
cluster: an electron density based study 535--545
Ibon Alkorta and
Joseph C. R. Thacker and
Paul L. A. Popelier An interacting quantum atom study of
model S$_N$2 reactions (X$^-$ $ \cdot $$
\cdot$$ \cdot $CH$_3$ X, X = F, Cl, Br,
and I) . . . . . . . . . . . . . . . . . 546--556
Freija De Vleeschouwer and
Mats Denayer and
Balazs Pinter and
Paul Geerlings and
Frank De Proft Characterization of chalcogen bonding
interactions via an in-depth conceptual
quantum chemical analysis . . . . . . . 557--572
Ekaterina Bartashevich and
Vladimir Tsirelson A comparative view on the potential
acting on an electron in a molecule and
the electrostatic potential through the
typical halogen bonds . . . . . . . . . 573--580
Piero Macchi and
Fabio Ragaini and
Nicola Casati and
Anna Krawczuk and
Angelo Sironi Experimental and theoretical electron
density of intermediates in
palladium-phenanthroline catalyzed
carbonylation of amines and reductive
carbonylation of nitroarenes . . . . . . 581--586
Giovanni Macetti and
Leonardo Lo Presti and
Carlo Gatti Spin density accuracy and distribution
in azido Cu(II) complexes: a source
function analysis . . . . . . . . . . . 587--603
Paul L. A. Popelier A fully analytical integration of
properties over the $3$D volume of the $
\beta $ sphere in topological atoms . . 604--613
Anonymous Cover Image, Volume 39, Issue 11 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 615--619
Trung Hai Nguyen and
Huan-Xiang Zhou and
David D. L. Minh Using the Fast Fourier Transform in
binding free energy calculations . . . . 621--636
Chiara Ricca and
Frédéric Labat and
Claudia Zavala and
Nino Russo and
Carlo Adamo and
Gabriel Merino and
Emilia Sicilia B,N-Codoped graphene as catalyst for the
oxygen reduction reaction: Insights from
periodic and cluster DFT calculations 637--647
Jakub Krajniak and
Zidan Zhang and
Sudharsan Pandiyan and
Eric Nies and
Giovanni Samaey Reverse mapping method for complex
polymer systems . . . . . . . . . . . . 648--664
Minh Khoa Nguyen and
Léonard Jaillet and
Stéphane Redon ART-RRT: As-Rigid-As-Possible
exploration of ligand unbinding pathways 665--678
Mohammadreza Eidi and
Mohsen Vafaee and
Mitra Rooein Complementary version of fermion coupled
coherent states method and Gram--Schmidt
algorithm: Theory and applications for
electronic states of H$_2$ and H$_2^+$ 679--684
Ximena Zarate and
Mario Saavedra-Torres and
Angela Rodriguez-Serrano and
Tatiana Gomez and
Eduardo Schott Exploring the relevance of thiophene
rings as bridge unit in
acceptor-bridge-donor dyes on
self-aggregation and performance in
DSSCs . . . . . . . . . . . . . . . . . 685--698
Anonymous Cover Image, Volume 39, Issue 12 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 699--703
Jonathan Higham and
Richard H. Henchman Overcoming the limitations of cutoffs
for defining atomic coordination in
multicomponent systems . . . . . . . . . 705--710
Rasmus Fonseca and
Dominik Budday and
Henry van den Bedem Collision-free Poisson motion planning
in ultra high-dimensional molecular
conformation spaces . . . . . . . . . . 711--720
Karteek K. Bejagam and
Samrendra Singh and
Sanket A. Deshmukh Development of non-bonded interaction
parameters between graphene and water
using particle swarm optimization . . . 721--734
Federica Maschietto and
Marco Campetella and
Michael J. Frisch and
Giovanni Scalmani and
Carlo Adamo and
Ilaria Ciofini How are the charge transfer descriptors
affected by the quality of the
underpinning electronic density? . . . . 735--742
Per E. M. Siegbahn Is there computational support for an
unprotonated carbon in the E$_4$ state
of nitrogenase? . . . . . . . . . . . . 743--747
Nivedita Rajendiran and
Jacob D. Durrant Pyrite: a \tt blender plugin for
visualizing molecular dynamics
simulations using industry-standard
rendering techniques . . . . . . . . . . 748--755
Anonymous Cover Image, Volume 39, Issue 13 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 757--761
Torsten Sachse and
Todd J. Martínez and
Benjamin Dietzek and
Martin Presselt A program for automatically predicting
supramolecular aggregates and its
application to urea and porphin . . . . 763--772
Beibei An and
Keke Wen and
Songyan Feng and
Xiao Pan and
Wenpeng Wu and
Xugeng Guo and
Jinglai Zhang Theoretical insights into the 1D-charge
transport properties in a series of
hexaazatrinaphthylene-based discotic
molecules . . . . . . . . . . . . . . . 773--779
Suranjan Shil and
Carmen Herrmann Performance of range-separated hybrid
exchange-correlation functionals for the
calculation of magnetic exchange
coupling constants of organic diradicals 780--787
Jan P. Unsleber and
Thomas Dresselhaus and
Kevin Klahr and
David Schnieders and
Michael Böckers and
Dennis Barton and
Johannes Neugebauer Serenity: a subsystem quantum chemistry
program . . . . . . . . . . . . . . . . 788--798
Min Zheng and
Mark P. Waller Yoink: an interaction-based partitioning
API . . . . . . . . . . . . . . . . . . 799--806
Alexey V. Odinokov and
Nikita O. Dubinets and
Alexander A. Bagaturyants pyEFP: Automatic decomposition of the
complex molecular systems into rigid
polarizable fragments . . . . . . . . . 807--814
Anonymous Cover Image, Volume 39, Issue 14 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 815--819
Mikhail S. Bukharov and
Valery G. Shtyrlin and
Edward M. Gilyazetdinov and
Nikita Yu. Serov and
Timur I. Madzhidov Hydration of copper(II) amino acids
complexes . . . . . . . . . . . . . . . 821--826
Sankar Ghorai and
Pinaki Chaudhury Predicting stability limits for pure and
doped dicationic noble gas clusters
undergoing Coulomb explosion: a parallel
tempering based study . . . . . . . . . 827--838
Sarah N. Johnson and
Gregory S. Tschumper Hydrogen bonding in the mixed HF/HCl
dimer: Is it better to give or receive? 839--843
Jaita Banerjee and
Stefan Behnle and
Martin C. E. Galbraith and
Volker Settels and
Bernd Engels and
Ralf Tonner and
Reinhold F. Fink Comparison of the periodic slab approach
with the finite cluster description of
metal-organic interfaces at the example
of PTCDA on Ag(110) . . . . . . . . . . 844--852
Lukasz Szeleszczuk and
Dariusz Maciej Pisklak and
Monika Zieli\'nska-Pisklak Does the choice of the crystal structure
influence the results of the periodic
DFT calculations? A case of glycine
alpha polymorph GIPAW NMR parameters
computations . . . . . . . . . . . . . . 853--861
Luis Alvarez-Thon and
Natalia Inostroza-Pino Spin-orbit effects on magnetically
induced current densities in the $ M^-_5
$ clusters ($M$ = N, P, As, Sb, Bi, Mc) 862--868
Anonymous Cover Image, Volume 39, Issue 15 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 869--873
Enhua Xu and
Seiichiro L. Ten-no Partially linearized external models to
active-space coupled-cluster through
connected hextuple excitations . . . . . 875--880
Bai Amutha Anjali and
Cherumuttathu H. Suresh Predicting reduction potentials of
1,3,6-triphenyl fulvenes using molecular
electrostatic potential analysis of
substituent effects . . . . . . . . . . 881--888
Chuancai Sun and
Lijuan Zhu and
Chao Zhang and
Ce Song and
Cuihong Wang and
Meiling Zhang and
Yaoming Xie and
Henry F. Schaefer III Conformers, properties, and docking
mechanism of the anticancer drug
docetaxel: DFT and molecular dynamics
studies . . . . . . . . . . . . . . . . 889--900
Cherumuttathu H. Suresh and
Neetha Mohan and
Therese Davis Della A Noncovalent Binding Strategy to
Capture Noble Gases, Hydrogen and
Nitrogen . . . . . . . . . . . . . . . . 901--908
Masato Kobayashi and
Toshikazu Fujimori and
Tetsuya Taketsugu Automated error control in
divide-and-conquer self-consistent field
calculations . . . . . . . . . . . . . . 909--916
João Paulo Ataide Martins and
Marco Antônio Rougeth de Oliveira and
Mário Sérgio Oliveira de Queiroz Web-4D-QSAR: a web-based application to
generate 4D-QSAR descriptors . . . . . . 917--924
Anonymous Cover Image, Volume 39, Issue 16 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 925--929
Takafumi Shiraogawa and
Masahiro Ehara and
Sandro Jurinovich and
Lorenzo Cupellini and
Benedetta Mennucci Frenkel-exciton decomposition analysis
of circular dichroism and circularly
polarized luminescence for
multichromophoric systems . . . . . . . 931--935
Harsh Bhatia and
Attila G. Gyulassy and
Vincenzo Lordi and
John E. Pask and
Valerio Pascucci and
Peer-Timo Bremer Topo MS: Comprehensive topological
exploration for molecular and
condensed-matter systems . . . . . . . . 936--952
Petar Zuvela and
Jonathan David and
Ming Wah Wong Interpretation of ANN-based QSAR models
for prediction of antioxidant activity
of flavonoids . . . . . . . . . . . . . 953--963
Yusuke Kondo and
Masato Kobayashi and
Tomoko Akama and
Takeshi Noro and
Tetsuya Taketsugu All-electron relativistic computations
on the low-lying electronic states, bond
length, and vibrational frequency of CeF
diatomic molecule with spin-orbit
coupling effects . . . . . . . . . . . . 964--972
Jurgens H. de Lange and
Daniel M. E. van Niekerk and
Ignacy Cukrowski FALDI-based decomposition of an atomic
interaction line leads to $3$D
representation of the multicenter nature
of interactions . . . . . . . . . . . . 973--985
Karel Mena-Ulecia and
Fabian Gonzalez-Norambuena and
Ariela Vergara-Jaque and
Horacio Poblete and
William Tiznado and
Julio Caballero Study of the affinity between the
protein kinase PKA and
homoarginine-containing peptides derived
from kemptide: Free energy perturbation
(FEP) calculations . . . . . . . . . . . 986--992
Rakesh Parida and
Santanab Giri Negative influence of p K$_a$ on
activation energy barrier: a case study
for double proton transfer reaction in
inorganic acid dimers . . . . . . . . . 993--998
Louis Vanduyfhuys and
Steven Vandenbrande and
Jelle Wieme and
Michel Waroquier and
Toon Verstraelen and
Veronique Van Speybroeck Extension of the QuickFF force field
protocol for an improved accuracy of
structural, vibrational, mechanical and
thermal properties of metal-organic
frameworks . . . . . . . . . . . . . . . 999--1011
Anonymous Cover Image, Volume 39, Issue 17 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1013--1017
Chérif F. Matta Quantum crystallography: From the
intersection to the union of
crystallography and quantum mechanics 1019--1020
Lou Massa and
Chérif F. Matta Quantum crystallography: a perspective 1021--1028
Vladimir Tsirelson Early days of quantum crystallography: a
personal account . . . . . . . . . . . . 1029--1037
Walter Polkosnik and
Lou Massa Single determinant $N$-representability
and the kernel energy method applied to
water clusters . . . . . . . . . . . . . 1038--1043
Stijn Fias and
Farnaz Heidar-Zadeh and
James S. M. Anderson and
Paul W. Ayers and
Robert G. Parr A reference-free stockholder
partitioning method based on the force
on electrons . . . . . . . . . . . . . . 1044--1050
James S. M. Anderson and
Paul W. Ayers The general setting for the zero-flux
condition: the Lagrangian and zero-flux
conditions that give the Heisenberg
equation of motion . . . . . . . . . . . 1051--1058
Leon Cohen The eigenvalue problem in phase space 1059--1067
Carol Frishberg and
Leon Cohen Contracted Schrödinger equation in
quantum phase-space . . . . . . . . . . 1068--1075
Anonymous Cover Image, Volume 39, Issue 18 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1077--1081
Viraht Sahni Generalization of the Schrödinger Theory
of Electrons . . . . . . . . . . . . . . 1083--1089
Tymofii Yu. Nikolaienko and
Eugene S. Kryachko and
Grygoriy A. Dolgonos On the Existence of He--He Bond in the
Endohedral Fullerene He$_2$ @C$_{60}$ 1090--1102
Jesús Jara-Cortés and
Jesús Hernández-Trujillo Energetic Analysis of Conjugated
Hydrocarbons Using the Interacting
Quantum Atoms Method . . . . . . . . . . 1103--1111
Carlo Gatti and
Giovanni Macetti and
Russell J. Boyd and
Chérif F. Matta An Electron Density Source-Function
Study of DNA Base Pairs in Their Neutral
and Ionized Ground States$^+$ . . . . . 1112--1128
Christopher Farley and
Amit Aggarwal and
Sunaina Singh and
Aaron Dolor and
Philip To and
Alexander Falber and
Maxwell Crossley and
Charles Michael Drain A Structural Model of Nitro-Porphyrin
Dyes Based on Spectroscopy and Density
Functional Theory . . . . . . . . . . . 1129--1142
Francesco Caruso and
Sarah Paumier and
Miriam Rossi X-Ray Crystal Structure of Embelin and
Its DFT Scavenging of Superoxide Radical 1143--1148
Marco Farren-Dai and
Stanley Cameron and
Michel B. Johnson and
Khashayar Ghandi Crystal Structure and Properties of
Imidazo-Pyridine Ionic Liquids . . . . . 1149--1157
Mohamed F. Shibl and
Salvador Moncho and
Edward N. Brothers What Happens Without Nickel? Cyclization
Reactions of Ethylene with Ethanedithial
and Related Molecules . . . . . . . . . 1158--1167
Anonymous Cover Image, Volume 39, Issue 19 . . . . i--i
Anonymous Issue Information . . . . . . . . . . . 1169--1176
Miroslaw Jablo\'nski Hydride-Triel Bonds . . . . . . . . . . 1177--1191
Noriyuki Yoshii and
Yoshimichi Andoh and
Susumu Okazaki Pressure tensor for electrostatic
interaction calculated by fast multipole
method with periodic boundary condition 1192--1199
David D. L. Minh Power transformations improve
interpolation of grids for molecular
mechanics interaction energies . . . . . 1200--1207
Julia Schacht and
Johannes Horst Budau and
Nicola Gaston and
Beate Paulus Aluminum oxo-fluoride clusters: a first
principle investigation of stability,
synthetic considerations, and the
interaction with water . . . . . . . . . 1208--1214
Andrés M. Escorcia and
Jeaphianne P. M. van Rijn and
Gui-Juan Cheng and
Patrick Schrepfer and
Thomas B. Brück and
Walter Thiel Molecular dynamics study of taxadiene
synthase catalysis . . . . . . . . . . . 1215--1225
Bikramjit Sharma and
Amalendu Chandra Nature of hydration shells of a
polyoxy-anion with a large cationic
centre: the case of iodate ion in water 1226--1235
Ashley L. Shoaf and
Craig A. Bayse Trigger bond analysis of nitroaromatic
energetic materials using Wiberg bond
indices . . . . . . . . . . . . . . . . 1236--1248
Alvaro J. Lopez and
Leandro Martínez Parametric models to compute tryptophan
fluorescence wavelengths from classical
protein simulations . . . . . . . . . . 1249--1258
Lisa A. Fredin and
Thomas C. Allison Semiempirical configuration interaction
calculations for ru-centered dyes* . . . 1259--1266
Hamed Akbarzadeh and
Mohsen Abbaspour and
Esmat Mehrjouei and
Samira Ramezanzadeh Pt-Co nanocluster in hollow carbon
nanospheres . . . . . . . . . . . . . . 1267--1274
Ruslan Shupanov and
Alexander Chertovich and
Pavel Kos Micellar polymerization: Computer
simulations by dissipative particle
dynamics . . . . . . . . . . . . . . . . 1275--1284
Joachim Laun and
Daniel Vilela Oliveira and
Thomas Bredow Consistent Gaussian basis sets of
double- and triple-zeta valence with
polarization quality of the fifth period
for solid-state calculations . . . . . . 1285--1290
Tomonori Hayami and
Kota Kasahara and
Haruki Nakamura and
Junichi Higo Molecular dynamics coupled with a
virtual system for effective
conformational sampling . . . . . . . . 1291--1299
Lukasz Szeleszczuk and
Dariusz Maciej Pisklak and
Monika Zieli\'nska-Pisklak Can we predict the structure and
stability of molecular crystals under
increased pressure? First-principles
study of glycine phase transitions . . . 1300--1306
Chung F. Wong Steered molecular dynamics simulations
for uncovering the molecular mechanisms
of drug dissociation and for drug
screening: a test on the focal adhesion
kinase . . . . . . . . . . . . . . . . . 1307--1318
Toshiyuki Takayanagi and
Taiki Nakatomi Automated reaction path searches for
spin-forbidden reactions . . . . . . . . 1319--1326
Jacek Koput Ab initio potential energy surface and
vibration-rotation energy levels of
germanium dicarbide, GeC$_2$ . . . . . . 1327--1334
Hannes Konrad Buchholz and
Matthias Stein Accurate lattice energies of organic
molecular crystals from periodic
Turbomole calculations . . . . . . . . . 1335--1343
Henrique S. Fernandes and
Maria J. Ramos and
Nuno M. F. S. A. Cerqueira molUP: a VMD plugin to handle QM and
ONIOM calculations using the Gaussian
software . . . . . . . . . . . . . . . . 1344--1353
Daniel J. Mermelstein and
Charles Lin and
Gard Nelson and
Rachael Kretsch and
J. Andrew McCammon and
Ross C. Walker Fast and flexible GPU accelerated
binding free energy calculations within
the amber molecular dynamics package . . 1354--1358
Anonymous Cover Image, Volume 39, Issue 20 . . . . 1--1
Anonymous Cover Image, Volume 39, Issue 20 . . . . 1--1
Anonymous Issue Information . . . . . . . . . . . 1359--1366
Eduardo M. Sproviero Intramolecular Natural Energy
Decomposition Analysis: Applications to
the Rational Design of Foldamers . . . . 1367--1386
Chih-Kai Lin Theoretical study of nitrogen-doped
graphene nanoflakes: Stability and
spectroscopy depending on dopant types
and flake sizes . . . . . . . . . . . . 1387--1397
Peiwen Zhao and
Yuxiang Bu Azobenzene-bridged diradical Janus
nucleobases with photo-converted
magnetic properties between
antiferromagnetic and ferromagnetic
couplings . . . . . . . . . . . . . . . 1398--1405
Domenico Ninno and
Giovanni Cantele and
Fabio Trani Real-space grid representation of
momentum and kinetic energy operators
for electronic structure calculations 1406--1412
Rebekka Haack and
Stephan Schulz and
Georg Jansen Dispersion interactions between
neighboring Bi atoms in (BiH$_3$)$_2$
and Te(BiR$_2$)$_2$ . . . . . . . . . . 1413--1423
E. F. V. de Carvalho and
O. Roberto-Neto Effects of multidimensional tunneling in
the kinetics of hydrogen abstraction
reactions of O($^3$P) with CH$_3$OCHO 1424--1432
Tim Raeker and
Björn Jansen and
Dominik Behrens and
Bernd Hartke Simulations of optically switchable
molecular machines for particle
transport . . . . . . . . . . . . . . . 1433--1443
Kedi Wu and
Zhixiong Zhao and
Renxiao Wang and
Guo-Wei Wei Top P--S: Persistent homology-based
multi-task deep neural networks for
simultaneous predictions of partition
coefficient and aqueous solubility . . . 1444--1454
Semeho Prince A. Edorh and
Stéphane Redon Incremental update of electrostatic
interactions in adaptively restrained
particle simulations . . . . . . . . . . 1455--1469
Lukasz Wola\'nski and
Dawid Grabarek and
Tadeusz Andruniów Is the choice of a standard zeroth-order
Hamiltonian in CASPT2 ansatz optimal in
calculations of excitation energies in
protonated and unprotonated Schiff bases
of retinal? . . . . . . . . . . . . . . 1470--1480
Hongyu Zhou and
Zheng Dong and
Peng Tao Recognition of protein allosteric states
and residues: Machine learning
approaches . . . . . . . . . . . . . . . 1481--1490
Kento Kasahara and
Hirofumi Sato Time-dependent pair distribution
functions based on Smoluchowski equation
and application to an electrolyte
solution . . . . . . . . . . . . . . . . 1491--1497
Koichi Ohno and
Yoshitomo Kodaya and
Hideo Yamakado Quantum chemical exploration of
formaldehyde clusters (H$_2$CO)$_n$ ($n$
= 2--4) . . . . . . . . . . . . . . . . 1498--1507
Mojtaba Alipour Dipole moments of molecules with
multi-reference character from optimally
tuned range-separated density functional
theory . . . . . . . . . . . . . . . . . 1508--1516
Jurgens H. de Lange and
Ignacy Cukrowski Exact and exclusive electron
localization indices within QTAIM atomic
basins . . . . . . . . . . . . . . . . . 1517--1530
Marco Heinen Calculating particle pair potentials
from fluid-state pair correlations:
Iterative Ornstein--Zernike inversion 1531--1543
Ken Sakata Force constant decomposition for
penta-coordinated $X$H$_3$Cl$_2^-$ ($X$
= C, Si, Ge) structures . . . . . . . . 1544--1550
Shun Sakuraba and
Ikuo Fukuda Performance evaluation of the
zero-multipole summation method in
modern molecular dynamics software . . . 1551--1560
F. N. N. Pansini and
F. A. L. de Souza and
C. T. Campos Molecules under external electric field:
On the changes in the electronic
structure and validity limits of the
theoretical predictions . . . . . . . . 1561--1567
Quentin R. Johnson and
Richard J. Lindsay and
Tongye Shen CAMERRA: an analysis tool for the
computation of conformational dynamics
by evaluating residue-residue
associations . . . . . . . . . . . . . . 1568--1578
Anonymous Cover Image, Volume 39, Issue 21 . . . . C1
Anonymous Cover Image, Volume 39, Issue 21 . . . . C2
Anonymous Issue Information . . . . . . . . . . . 1579--1584
Laura Lutz-Kappelman and
Yuemei Zhang and
Gordon J. Miller Magnetic ordering and metal-atom site
preference in tetragonal CrMnAs:
Electronic correlation effects . . . . . 1585--1593
Stanislav M. Avdoshenko Fullerene Faraday cage keeps magnetic
properties of inner cluster pristine . . 1594--1598
Maxim I. Kozlov and
Vladimir V. Poddubnyy and
Ilya O. Glebov Calculation of the excited states
properties of LH1 complex of
\bionameThermochromatium tepidum . . . . 1599--1606
Anna Romanova and
Konstantin Lyssenko and
Ivan Ananyev Estimations of energy of noncovalent
bonding from integrals over interatomic
zero-flux surfaces: Correlation trends
and beyond . . . . . . . . . . . . . . . 1607--1616
Yaqian Wang and
Jinfeng Liu and
Jinjin Li and
Xiao He Fragment-based quantum mechanical
calculation of protein-protein binding
affinities . . . . . . . . . . . . . . . 1617--1628
Kumari Soniya and
Amalendu Chandra Free energy landscapes of prototropic
tautomerism in pyridoxal 5'-phosphate
Schiff bases at the active site of an
enzyme in aqueous medium . . . . . . . . 1629--1638
Yang Li and
Junsheng Chen and
Tian-Shu Chu Fluoride anion sensing mechanism of a
BODIPY-linked hydrogen-bonding probe . . 1639--1647
Andreas Klamt and
Michael Diedenhofen A refined cavity construction algorithm
for the conductor-like screening model 1648--1655
Peter L. Cummins and
Babu Kannappan and
Jill E. Gready Revised mechanism of carboxylation of
ribulose-1,5-biphosphate by Rubisco from
large scale quantum chemical
calculations . . . . . . . . . . . . . . 1656--1665
Maximilian J. Dombrowsky and
Sven Jager and
Benjamin Schiller and
Benjamin E. Mayer and
Sebastian Stammler and
Kay Hamacher StreaMD: Advanced analysis of molecular
dynamics using R . . . . . . . . . . . . 1666--1674
Leandro Zanotto and
Gabriel Heerdt and
Paulo C. T. Souza and
Guido Araujo and
Munir S. Skaf High performance collision cross section
calculation --- HPCCS . . . . . . . . . 1675--1681
Jing Huang and
Justin A. Lemkul and
Peter K. Eastman and
Alexander D. MacKerell Jr. Molecular dynamics simulations using the
drude polarizable force field on GPUs
with OpenMM: Implementation, validation,
and benchmarks . . . . . . . . . . . . . 1682--1689
Anonymous Cover Image, Volume 39, Issue 22 . . . . C1
Anonymous Cover Image, Volume 39, Issue 22 . . . . C2
Anonymous Issue Information . . . . . . . . . . . 1691--1696
Wenli Zou and
Ziyu Cai and
Jiankang Wang and
Kunyu Xin An open library of relativistic core
electron density function for the QTAIM
analysis with pseudopotentials . . . . . 1697--1706
Alexey Aleksandrov and
Fang-Yu Lin and
Beno\^\it Roux and
Alexander D. MacKerell Jr. Combining the polarizable Drude force
field with a continuum electrostatic
Poisson--Boltzmann implicit solvation
model . . . . . . . . . . . . . . . . . 1707--1719
Dawid Grabarek and
Tadeusz Andruniów Initial excited-state relaxation of
locked retinal protonated Schiff base
chromophore. An insight from coupled
cluster and multireference perturbation
theory calculations . . . . . . . . . . 1720--1727
A. Lara and
M. Riquelme and
E. Vöhringer-Martinez Partition coefficients of methylated DNA
bases obtained from free energy
calculations with molecular electron
density derived atomic charges . . . . . 1728--1737
Hiroshi Takeuchi Size-guided multi-seed heuristic method
for geometry optimization of clusters:
Application to benzene clusters . . . . 1738--1746
Sara Del Galdo and
Giordano Mancini and
Isabella Daidone and
Laura Zanetti Polzi and
Andrea Amadei and
Vincenzo Barone Tyrosine absorption spectroscopy:
Backbone protonation effects on the side
chain electronic properties . . . . . . 1747--1756
Ghazaleh Taherzadeh and
Yuedong Yang and
Haodong Xu and
Yu Xue and
Alan Wee-Chung Liew and
Yaoqi Zhou Predicting lysine-malonylation sites of
proteins using sequence and predicted
structural features . . . . . . . . . . 1757--1763
Jakub Krajniak and
Zidan Zhang and
Sudharsan Pandiyan and
Eric Nies and
Giovanni Samaey Coarse-grained molecular dynamics
simulations of polymerization with
forward and backward reactions . . . . . 1764--1778
Tobias Kramer and
Matthias Noack and
Alexander Reinefeld and
Mirta Rodríguez and
Yaroslav Zelinskyy Efficient calculation of open quantum
system dynamics and time-resolved
spectroscopy with distributed memory
HEOM (DM--HEOM) . . . . . . . . . . . . 1779--1794
Moein Goodarzi and
Fariba Nazari and
Francesc Illas Electronic and structural properties of
Li$_n$ @Be$_2$ B$_8$ ( n = 1-14) and
Li$_n$ @Be$_2$ B$_{36}$ ( n = 1-21)
nanoflakes shed light on possible anode
materials for Li-based batteries . . . . 1795--1805
Murat Keçeli and
Fabiano Corsetti and
Carmen Campos and
Jose E. Roman and
Hong Zhang and
Álvaro Vázquez-Mayagoitia and
Peter Zapol and
Albert F. Wagner SIESTA--SIPs: Massively parallel
spectrum-slicing eigensolver for an ab
initio molecular dynamics package . . . 1806--1814
Juan M. Clemente-Juan and
Andrew Palii and
Boris Tsukerblat and
Eugenio Coronado VIBPACK: a package to treat
multidimensional electron-vibrational
molecular problems with application to
magnetic and optical properties . . . . 1815--1827
Anonymous Cover Image, Volume 39, Issue 23 . . . . C1
Anonymous Cover Image, Volume 39, Issue 23 . . . . C2
Anonymous Issue Information . . . . . . . . . . . 1829--1834
Toshiyuki Takayanagi and
Taiki Nakatomi and
Yoshiteru Yonetani On the ion-pair dissociation mechanisms
in the small NaCl$ \cdot $ (H$_2$O)$_6$
cluster: a perspective from reaction
path search calculations . . . . . . . . 1835--1842
Mohammad H. Kowsari and
Leila Tohidifar Systematic evaluation and refinement of
existing all-atom force fields for the
simulation of liquid acetonitrile . . . 1843--1853
Karol Dyduch and
Monika Srebro-Hooper and
Bun Yeoul Lee and
Artur Michalak Exploring the conformational space of
cobalt(III)-salen catalyst for CO$_2$
/epoxide copolymerization: Effect of
quaternary ammonium salts on preference
of alternative isomers . . . . . . . . . 1854--1867
Milena Petkovi\'c and
Dura Nakarada and
Mihajlo Etinski When hydroquinone meets methoxy radical:
Hydrogen abstraction reaction from the
viewpoint of interacting quantum atoms 1868--1877
Raman K. Singh and
Takeshi Iwasa and
Tetsuya Taketsugu Insights into geometries, stabilities,
electronic structures, reactivity
descriptors, and magnetic properties of
bimetallic Ni$_m$ Cu$_{n - m}$ ($ m = 1,
2$; $ n = 3$--$ 13$) clusters:
Comparison with pure copper clusters . . 1878--1889
Duncan W. Stuart and
Nicholas J. Mosey Direct inversion of the iterative
subspace with contracted planewave basis
functions . . . . . . . . . . . . . . . 1890--1901
Pradeep R. Varadwaj and
Arpita Varadwaj and
Helder M. Marques and
Koichi Yamashita Halogen in materials design:
Chloroammonium lead triiodide perovskite
(ClNH$_3$PbI$_3$) a dynamical bandgap
semiconductor in $3$D for photovoltaics 1902--1912
Yuki Mitsuta and
Shusuke Yamanaka and
Takashi Kawakami and
Mitsutaka Okumura Automated Search of Minimum Free-Energy
Path by Umbrella Integration . . . . . . 1913--1921
Aurelio Rodríguez and
Roberto Rodríguez-Fernández and
Saulo A. Vázquez and
George L. Barnes and
James J. P. Stewart and
Emilio Martínez-Núñez tsscds2018: a code for automated
discovery of chemical reaction
mechanisms and solving the kinetics . . 1922--1930
Lukas Turcani and
Enrico Berardo and
Kim E. Jelfs stk: a Python toolkit for supramolecular
assembly . . . . . . . . . . . . . . . . 1931--1942
Anonymous Cover Image, Volume 39, Issue 24 . . . . C1
Ignacio Lizana and
Eduardo J. Delgado Theoretical insights on the inhibition
mechanism of a class A serine hydrolase
by avibactam . . . . . . . . . . . . . . 1943--1948
László von Szentpály Eliminating symmetry problems in
electronegativity equalization and
correcting self-interaction errors in
conceptual DFT . . . . . . . . . . . . . 1949--1969
Takeshi Ishikawa and
Kota Sakakura and
Yuji Mochizuki RI-MP3 calculations of biomolecules
based on the fragment molecular orbital
method . . . . . . . . . . . . . . . . . 1970--1978
Wenlan Liu and
Sofia Canola and
Andreas Köhn and
Bernd Engels and
Fabrizia Negri and
Reinhold F. Fink A model Hamiltonian tuned toward high
level ab initio calculations to describe
the character of excitonic states in
perylenebisimide aggregates . . . . . . 1979--1989
Thao P. Nguyen and
Ji Hoon Shim Hybrid density functional study on the
electronic structures and properties of
P3HT-PbS and P3HT-CdS hybrid interface
for photovoltaic applications . . . . . 1990--1999
Helen Nathalia Thompson and
Claudia Elizabeth Thompson and
Rafael Andrade Caceres and
Laurent Emmanuel Dardenne and
Paulo Augusto Netz and
Hubert Stassen Prion protein conversion triggered by
acidic condition: a molecular dynamics
study through different force fields . . 2000--2011
Taras Dauzhenka and
Petras J. Kundrotas and
Ilya A. Vakser Computational Feasibility of an
Exhaustive Search of Side-Chain
Conformations in Protein-Protein Docking 2012--2021
Gabriel A. Urquiza-Carvalho and
Gerd B. Rocha and
Rafael López Efficient algorithm for expanding
theoretical electron densities in
Canterakis--Zernike functions . . . . . 2022--2032
Anonymous Cover Image, Volume 39, Issue 25 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2033--2038
Hiroya Nakata and
Dmitri G. Fedorov Analytic second derivatives for the
efficient electrostatic embedding in the
fragment molecular orbital method . . . 2039--2050
James Dix and
Leo Lue and
Paola Carbone Why different water models predict
different structures under 2D
confinement . . . . . . . . . . . . . . 2051--2059
Yutaro Sugiura and
Kento Suzuki and
Toshiyuki Takayanagi and
Yukiumi Kita and
Masanori Tachikawa Reduction of OH vibrational frequencies
in amino acids by positron attachment 2060--2066
V. S. Sandeep Inakollu and
Haibo Yu A systematic benchmarking of
computational vibrational spectroscopy
with DFTB3: Normal mode analysis and
Fast Fourier Transform dipole
autocorrelation function . . . . . . . . 2067--2078
Wei Chen and
Andrew L. Ferguson Molecular enhanced sampling with
autoencoders: On-the-fly collective
variable discovery and accelerated free
energy landscape exploration . . . . . . 2079--2102
Van Tan Tran and
Quoc Tri Tran Spin State Energetics of VGe$_n^{-
\slash 0}$ ($n$ = 5--7) Clusters and New
Assignments of the Anion Photoelectron
Spectra . . . . . . . . . . . . . . . . 2103--2109
Daniel R. Roe and
Thomas E. Cheatham III Parallelization of CPPTRAJ enables large
scale analysis of molecular dynamics
trajectory data . . . . . . . . . . . . 2110--2117
Marcello Sega and
György Hantal and
Balázs Fábián and
Pál Jedlovszky Pytim: a Python package for the
interfacial analysis of molecular
simulations . . . . . . . . . . . . . . 2118--2125
M. Nava Implementing dimer metadynamics using
gromacs . . . . . . . . . . . . . . . . 2126--2132
Manfred Speldrich and
Jan van Leusen and
Paul Kögerler CONDON 3.0: An Updated Software Package
for Magnetochemical Analysis --- All the
Way to Polynuclear Actinide Complexes 2133--2145
Anonymous Cover Image, Volume 39, Issue 26 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2147--2151
M. W. Li and
P. M. Zimmerman Stepwise basis set selection . . . . . . 2153--2162
Robert A. Evarestov and
Andrei V. Bandura Infrared and Raman active vibrational
modes in MoS$_2$-based nanotubes:
Symmetry analysis and first-principles
calculations . . . . . . . . . . . . . . 2163--2172
Adrian F. Morrison and
Evgeny Epifanovsky and
John M. Herbert Double-buffered, heterogeneous CPU + GPU
integral digestion algorithm for
single-excitation calculations involving
a large number of excited states . . . . 2173--2182
Miroslaw Jablo\'nski Bond paths between distant atoms do not
necessarily indicate dominant
interactions . . . . . . . . . . . . . . 2183--2195
Ulrich Kuenzer and
Martin Klotz and
Thomas S. Hofer Probing vibrational coupling via a
grid-based quantum approach --- an
efficient strategy for accurate
calculations of localized normal modes
in solid-state systems . . . . . . . . . 2196--2209
Rhys Heffernan and
Kuldip Paliwal and
James Lyons and
Jaswinder Singh and
Yuedong Yang and
Yaoqi Zhou Single-sequence-based prediction of
protein secondary structures and solvent
accessibility by deep whole-sequence
learning . . . . . . . . . . . . . . . . 2210--2216
Marisa E. Smith and
N. J. B. Green and
S. M. Pimblott Methods for the Simulation of the
Slowing of Low-Energy Electrons in Water 2217--2225
Manuela Maurer and
Niels Hansen and
Chris Oostenbrink Comparison of free-energy methods using
a tripeptide-water model system . . . . 2226--2242
Roberto Cammi and
Bo Chen and
Martin Rahm Analytical calculation of pressure for
confined atomic and molecular systems
using the eXtreme-Pressure Polarizable
Continuum Model . . . . . . . . . . . . 2243--2250
Adrien Stoliaroff and
Stéphane Jobic and
Camille Latouche PyDEF 2.0: An Easy to Use Post-treatment
Software for Publishable Charts
Featuring a Graphical User Interface . . 2251--2261
Anonymous Cover Image, Volume 39, Issue 27 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2263--2267
Xue Wu and
Si Zhou and
Xiaoming Huang and
Maodu Chen and
R. Bruce King and
Jijun Zhao Revisit of large-gap Si$_{16}$ clusters
encapsulating group-IV metal atoms (Ti,
Zr, Hf) . . . . . . . . . . . . . . . . 2268--2272
Dirkie Myburgh and
Stuart von Berg and
Jan Dillen A comparison of energetic criteria to
probe the stabilizing interaction
resulting from a bond path between
congested atoms . . . . . . . . . . . . 2273--2282
Jurgens H. de Lange and
Daniël M. E. van Niekerk and
Ignacy Cukrowski FALDI-based criterion for and the origin
of an electron density bridge with an
associated (3,-1) critical point on
Bader's molecular graph . . . . . . . . 2283--2299
Irina Silanteva and
Andrei V. Komolkin Representation of DNA environment:
Spiral staircase distribution function 2300--2306
Xian Chen and
Jian Song and
Zhe-Ning Chen and
Tan Jin and
Fengqin Long and
Hua Xie and
Yisong Zheng and
Wei Zhuang and
Lu Zhang Rational designing of
$8$-hydroxyquinolin-imidazolinone-based
fluorescent protein mutants with
dramatically red shifted emission: a
computational study . . . . . . . . . . 2307--2315
Haiyan Yuan and
Lihan Zhu and
Wenliang Li and
Jingping Zhang Mechanistic insight on water and
substrate catalyzed the synthesis of
3-(1
H-indol-$3$-yl)-$2$-(4-methoxybenzyl)isoindolin-$1$-one: Driving by noncovalent interactions 2316--2323
Min Qian and
Bowen Qin and
Haiyan Yuan and
Wenliang Li and
Jingping Zhang Mechanistic insights into
N-Bromosuccinimide-promoted synthesis of
imidazo[1,2-a]pyridine in water:
Reactivity mediated by substrates and
solvent . . . . . . . . . . . . . . . . 2324--2332
Masao Hayami and
Junji Seino and
Yuya Nakajima and
Masahiko Nakano and
Yasuhiro Ikabata and
Takeshi Yoshikawa and
Takuro Oyama and
Kenta Hiraga and
So Hirata and
Hiromi Nakai RAQET: Large-scale two-component
relativistic quantum chemistry program
package . . . . . . . . . . . . . . . . 2333--2344
Anonymous Cover Image, Volume 39, Issue 28 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2345--2349
Lihua Xu and
Anshuman Kumar and
Bryan M. Wong Linear polarizabilities and second
hyperpolarizabilities of
streptocyanines: Results from
broken-symmetry DFT and new CCSD(T)
benchmarks . . . . . . . . . . . . . . . 2350--2359
Adam K. Sieradzan and
Artur Gieldo\'n and
Yanping Yin and
Yi He and
Harold A. Scheraga and
Adam Liwo A new protein nucleic-acid
coarse-grained force field based on the
UNRES and NARES-2P force fields . . . . 2360--2370
Antoni Oliver and
Christopher A. Hunter and
Rafel Prohens and
Josep Lluis Rosselló An improved methodology to compute
surface site interaction points using
high density molecular electrostatic
potential surfaces . . . . . . . . . . . 2371--2377
Talapunur Vikramaditya and
Jeng-Da Chai and
Shiang-Tai Lin Impact of non-empirically tuning the
range-separation parameter of long-range
corrected hybrid functionals on
ionization potentials, electron
affinities, and fundamental gaps . . . . 2378--2384
Jingbai Li and
Divya Tadakamalla and
Andrey Yu. Rogachev Modulating stability of functionalized
fullerene cations [R-C$_60$]$^+$ with
the nature of R-group . . . . . . . . . 2385--2396
Dan Hu and
Xiaoqing Guan and
Yukun Wang Weighted least square analysis method
for free energy calculations . . . . . . 2397--2404
Keisuke Takahashi and
Itsuki Miyazato Rapid estimation of activation energy in
heterogeneous catalytic reactions via
machine learning . . . . . . . . . . . . 2405--2408
Xianjin Xu and
Chengfei Yan and
Xiaoqin Zou MDockPeP: an ab-initio protein-peptide
docking server . . . . . . . . . . . . . 2409--2413
Anonymous Cover Image, Volume 39, Issue 29 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2415--2419
Xiaowang W. Zhou and
Michael E. Foster and
Ryan B. Sills An Fe-Ni-Cr embedded atom method
potential for austenitic and ferritic
systems . . . . . . . . . . . . . . . . 2420--2431
Jian-Biao Liu and
Xin Chen and
Jun-Bo Lu and
Hong-Qiang Cui and
Jun Li Polarizable force field parameterization
and theoretical simulations of ThCl$_4$
-LiCl molten salts . . . . . . . . . . . 2432--2438
Christine E. Schulz and
Achintya Kumar Dutta and
Róbert Izsák and
Dimitrios A. Pantazis Systematic High-Accuracy Prediction of
Electron Affinities for Biological
Quinones . . . . . . . . . . . . . . . . 2439--2451
Izaac Mitchell and
Bálint Aradi and
Alister J. Page Density functional tight binding-based
free energy simulations in the DFTB+
program . . . . . . . . . . . . . . . . 2452--2458
Elena Yu. Tupikina and
Alexandra A. Efimova and
Gleb S. Denisov and
Peter M. Tolstoy Outer electronic shell visualization by
NMR chemical shift Laplacian of a helium
probe . . . . . . . . . . . . . . . . . 2459--2462
Sebastian Schwalbe and
Torsten Hahn and
Simon Liebing and
Kai Trepte and
Jens Kortus Fermi--Löwdin orbital self-interaction
corrected density functional theory:
Ionization potentials and enthalpies of
formation . . . . . . . . . . . . . . . 2463--2471
German P. Barletta and
Marcia Anahi Hasenahuer and
Maria Silvina Fornasari and
Gustavo Parisi and
Sebastian Fernandez-Alberti Dynamics fingerprints of active
conformers of epidermal growth factor
receptor kinase . . . . . . . . . . . . 2472--2480
Thiago Castilho Elias and
Humberto César Brandão de Oliveira and
Nelson José Freitas da Silveira MB-Isoster: a software for bioisosterism
simulation . . . . . . . . . . . . . . . 2481--2487
Anonymous Cover Image, Volume 39, Issue 30 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2489--2493
Mark A. Hallen and
Jeffrey W. Martin and
Adegoke Ojewole and
Jonathan D. Jou and
Anna U. Lowegard and
Marcel S. Frenkel and
Pablo Gainza and
Hunter M. Nisonoff and
Aditya Mukund and
Siyu Wang and
Graham T. Holt and
David Zhou and
Elizabeth Dowd and
Bruce R. Donald OSPREY 3.0: Open-source protein redesign
for you, with powerful new features . . 2494--2507
Nayara D. Coutinho and
Flavio O. Sanches-Neto and
Valter H. Carvalho-Silva and
Heibbe C. B. de Oliveira and
Luiz A. Ribeiro and
Vincenzo Aquilanti Kinetics of the OH + HCl $ \to $ H$_2$O
+ Cl reaction: Rate determining roles of
stereodynamics and roaming and of
quantum tunneling . . . . . . . . . . . 2508--2516
Manuel Utecht and
Tina Gaebel and
Tillmann Klamroth Desorption induced by low energy charge
carriers on Si(111)-$ 7 \times 7 $:
First principles molecular dynamics for
benzene derivates . . . . . . . . . . . 2517--2525
Deyan Raychev and
Gotthard Seifert and
Jens-Uwe Sommer and
Olga Guskova A comparative analysis of symmetric
diketopyrrolopyrrole-cored small
conjugated molecules with aromatic
flanks: From geometry to charge
transport . . . . . . . . . . . . . . . 2526--2538
Sehee Na and
Thomas Steinbrecher and
Thorsten Koslowski Thermodynamic integration network
approach to ion transport through
protein channels: Perspectives and
limits . . . . . . . . . . . . . . . . . 2539--2550
Jérôme Eberhardt and
Roland H. Stote and
Annick Dejaegere Unrolr: Structural analysis of protein
conformations using stochastic proximity
embedding . . . . . . . . . . . . . . . 2551--2557
Anonymous Cover Image, Volume 39, Issue 31 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2559--2563
Titus Adrian Beu and
Andrada-Elena Ailenei and
Alexandra Farcas CHARMM force field for protonated
polyethyleneimine . . . . . . . . . . . 2564--2575
Tomoaki Yagi and
Hirofumi Sato A simple model of planar membrane: an
integral equation investigation . . . . 2576--2581
Jahanzeb Khan and
Yunpeng Liu and
Tianqi Zhao and
Hua Geng and
Wei Xu and
Zhigang Shuai High performance thermoelectric
materials based on metal organic
coordination polymers through
first-principles band engineering . . . 2582--2588
Gabriel I. Pagola and
Martin A. B. Larsen and
Marta Ferraro and
Stephan P. A. Sauer The influence of relativistic effects on
nuclear magnetic resonance spin-spin
coupling constant polarizabilities of
H$_2$ O$_2$, H$_2$ S$_2$, H$_2$ Se$_2$,
and H$_2$ Te$_2$ . . . . . . . . . . . . 2589--2600
Songyan Feng and
Keke Wen and
Yubing Si and
Xugeng Guo and
Jinglai Zhang Theoretical studies on thermally
activated delayed fluorescence mechanism
of a series of organic light-emitting
diodes emitters comprising
2,7-diphenylamino-9,9-dimethylacridine
as electron donor . . . . . . . . . . . 2601--2606
Andrea Salvadori and
Marco Fus\`e and
Giordano Mancini and
Sergio Rampino and
Vincenzo Barone Diving into chemical bonding: an
immersive analysis of the electron
charge rearrangement through virtual
reality . . . . . . . . . . . . . . . . 2607--2617
Anonymous Cover Image, Volume 39, Issue 32 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2619--2623
Justin A. Lemkul and
Alexander D. MacKerell Jr. Polarizable force field for RNA based on
the classical Drude oscillator . . . . . 2624--2646
Anna Kristina Schnack-Petersen and
Pi A. B. Haase and
Rasmus Faber and
Patricio F. Provasi and
Stephan P. A. Sauer RPA(D) and HRPA(D): Two new models for
calculations of NMR indirect nuclear
spin-spin coupling constants . . . . . . 2647--2666
Naveen K. Dandu and
Olajumoke Adeyiga and
Dipak Panthi and
Shaina A. Bird and
Samuel O. Odoh Performance of density functional theory
for describing hetero-metallic
active-site motifs for
methane-to-methanol conversion in
metal-exchanged zeolites . . . . . . . . 2667--2678
Mitsugu Araki and
Hiroaki Iwata and
Biao Ma and
Atsuto Fujita and
Kei Terayama and
Yukari Sagae and
Fumie Ono and
Koji Tsuda and
Narutoshi Kamiya and
Yasushi Okuno Improving the Accuracy of Protein-Ligand
Binding Mode Prediction Using a
Molecular Dynamics-Based Pocket
Generation Approach . . . . . . . . . . 2679--2689
Ayush K. Narsaria and
Jordi Poater and
Célia Fonseca Guerra and
Andreas W. Ehlers and
Koop Lammertsma and
F. Matthias Bickelhaupt Rational design of near-infrared
absorbing organic dyes: Controlling the
HOMO--LUMO gap using quantitative
molecular orbital theory . . . . . . . . 2690--2696
Michael Böhme and
Winfried Plass rhOver: Determination of magnetic
anisotropy and related properties for
dysprosium(III) single-ion magnets by
semiempirical approaches utilizing
Hartree--Fock wave functions . . . . . . 2697--2712
Anonymous Cover Image, Volume 40, Issue 1 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1--10
Keiji Morokuma Foreword . . . . . . . . . . . . . . . . 11--13
Koichi Ohno and
Hiroko Satoh and
Takeaki Iwamoto and
Hiroaki Tokoyama and
Hideo Yamakado Exploration of Carbon Allotropes with
Four-membered Ring Structures on Quantum
Chemical Potential Energy Surfaces . . . 14--28
Bun Chan and
Yukio Kawashima and
Kimihiko Hirao The reHISS Three-Range Exchange
Functional with an Optimal Variation of
Hartree--Fock and Its Use in the
reHISSB-D Density Functional Theory
Method . . . . . . . . . . . . . . . . . 29--38
Michel Dupuis and
Meghana Nallapu Maximal orbital analysis of molecular
wavefunctions . . . . . . . . . . . . . 39--50
Vindi M. Jayasinghe-Arachchige and
Qiaoyu Hu and
Gaurav Sharma and
Thomas J. Paul and
Marcus Lundberg and
David Quinonero and
Tatjana N. Parac-Vogt and
Rajeev Prabhakar Hydrolysis of chemically distinct sites
of human serum albumin by
polyoxometalate: a hybrid QM\slash MM
(ONIOM) study . . . . . . . . . . . . . 51--61
AbdelRahman A. Dahy and
Nobuaki Koga Imine hydrosilylation using an iron
complex catalyst: a computational study 62--71
Maria Fumanal and
Yu Harabuchi and
Etienne Gindensperger and
Satoshi Maeda and
Chantal Daniel Excited-State Reactivity of
[Mn(im)(CO)$_3$ (phen)]$^+$: a
Structural Exploration . . . . . . . . . 72--81
Bun Chan and
Leo Radom An ONIOM investigation of the effect of
conformation on bond dissociation
energies in peptides . . . . . . . . . . 82--88
Masayoshi Nakano and
Takanori Nagami and
Takayoshi Tonami and
Kenji Okada and
Soichi Ito and
Ryohei Kishi and
Yasutaka Kitagawa and
Takashi Kubo Quantum Master Equation Approach to
Singlet Fission Dynamics in Pentacene
Linear Aggregate Models: Size
Dependences of Excitonic Coupling
Effects . . . . . . . . . . . . . . . . 89--104
Jong-Won Song and
Kimihiko Hirao Accelerated long-range corrected
exchange functional using a two-Gaussian
operator combined with one-parameter
progressive correlation functional
[LC-BOP(2Gau)] . . . . . . . . . . . . . 105--112
Kyohei Kawashima and
Takehiro Sato and
Masamichi Ogasawara and
Ken Kamikawa and
Seiji Mori Theoretical investigations of
Rh-catalyzed asymmetric 1,4-addition to
enones using planar-chiral
phosphine-olefin ligands . . . . . . . . 113--118
David A. Hrovat and
Xue-Bin Wang and
Weston Thatcher Borden Calculations on 1,8-naphthoquinone
predict that the ground state of this
diradical is a singlet . . . . . . . . . 119--126
Takafumi Shiraogawa and
Gaelle Candel and
Ryoichi Fukuda and
Ilaria Ciofini and
Carlo Adamo and
Akimitsu Okamoto and
Masahiro Ehara Photophysical properties of fluorescent
imaging biological probes of nucleic
acids: SAC-CI and TD-DFT study . . . . . 127--134
Lara A. Patel and
James T. Kindt Simulations of NaCl Aggregation from
Solution: Solvent Determines Topography
of Free Energy Landscape . . . . . . . . 135--147
Rei Matsuzaki and
Kazuo Takatsuka Electronic and nuclear flux analysis on
nonadiabatic electron transfer reaction:
a view from single-configuration
adiabatic Born--Huang representation . . 148--163
Chisa Higuchi and
Hiromasa Tanaka and
Kazunari Yoshizawa Molecular understanding of the adhesive
interactions between silica surface and
epoxy resin: Effects of interfacial
water . . . . . . . . . . . . . . . . . 164--171
Yukio Kawashima and
Keisuke Sawada and
Takahito Nakajima and
Masanori Tachikawa A path integral molecular dynamics study
on intermolecular hydrogen bond of
acetic acid-arsenic acid anion and
acetic acid-phosphoric acid anion
clusters . . . . . . . . . . . . . . . . 172--180
Nozomi Takagi and
Masayuki Nakagaki and
Kazuya Ishimura and
Ryoichi Fukuda and
Masahiro Ehara and
Shigeyoshi Sakaki Electronic processes in NO dimerization
on Ag and Cu clusters: DFT and MRMP2
studies . . . . . . . . . . . . . . . . 181--190
Evgeniy G. Gordeev and
Valentine P. Ananikov Switching the nature of catalytic
centers in Pd\slash NHC systems by
solvent effect driven non-classical
R-NHC Coupling . . . . . . . . . . . . . 191--199
Xuetao Shi and
H. Bernhard Schlegel Controlling the strong field
fragmentation of ClCHO$^+$ using two
laser pulses --- an ab initio molecular
dynamics simulation . . . . . . . . . . 200--205
Takao Tsuneda Theoretical investigations on
geometrical and electronic structures of
silver clusters . . . . . . . . . . . . 206--211
Alexey L. Kaledin and
Craig L. Hill and
Tianquan Lian and
Djamaladdin G. Musaev A bulk adjusted linear combination of
atomic orbitals (BA-LCAO) approach for
nanoparticles . . . . . . . . . . . . . 212--221
Yoshinori Ato and
Akihide Hayashi and
Hiroaki Koga and
Kohei Tada and
Takashi Kawakami and
Shusuke Yamanaka and
Mitsutaka Okumura Theoretical study of correlations
between the coordination structures and
catalytic activities in
polymer-stabilized au nanocluster
catalysts . . . . . . . . . . . . . . . 222--228
Katelyn M. Dreux and
Gregory S. Tschumper Examination of the structures,
energetics, and vibrational frequencies
of small sulfur-containing prototypical
dimers, (H$_2$ S)$_2$ and H$_2$ O\slash
H$_2$ S . . . . . . . . . . . . . . . . 229--236
Chikashi Shinagawa and
Yusuke Morikawa and
Shin-ichi Nishimura and
Hiroshi Ushiyama and
Atsuo Yamada and
Koichi Yamashita A Theoretical study on the charge and
discharge states of Na-ion battery
cathode material, Na$_1 + x$FePO$_4$F 237--246
Paul Jerabek and
Peter Schwerdtfeger and
Gernot Frenking Dative and electron-sharing bonding in
transition metal compounds . . . . . . . 247--264
Takashi Tsuchimochi and
Seiichiro L. Ten-no Extending spin-symmetry projected
coupled-cluster to large model spaces
using an iterative null-space projection
technique . . . . . . . . . . . . . . . 265--278
Tatsuya Iioka and
Satoshi Takahashi and
Yuichiro Yoshida and
Yoshihiro Matsumura and
Shuichi Hiraoka and
Hirofumi Sato A kinetics study of ligand substitution
reaction on dinuclear platinum
complexes: Stochastic versus
deterministic approach . . . . . . . . . 279--285
Anonymous Cover Image, Volume 40, Issue 2 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 288--296
Vladimir Mironov and
Yuri Alexeev and
Vikram Khipple Mulligan and
Dmitri G. Fedorov A systematic study of minima in alanine
dipeptide . . . . . . . . . . . . . . . 297--309
Nuwan De Silva and
Matthew A. Adreance and
Mark S. Gordon Application of a semi-empirical
dispersion correction for modeling water
clusters . . . . . . . . . . . . . . . . 310--315
Akitomo Tachibana New aspects of quantum electrodynamics
on electronic structure and dynamics . . 316--327
Apurba Nandi and
Chen Qu and
Joel M. Bowman Diffusion Monte Carlo Calculations of
Zero-Point Energies of Methanol and
Deuterated Methanol . . . . . . . . . . 328--332
Takashi Kawakami and
Koichi Miyagawa and
Sandeep Sharma and
Toru Saito and
Mitsuo Shoji and
Satoru Yamada and
Shusuke Yamanaka and
Mitsutaka Okumura and
Takahito Nakajima and
Kizashi Yamaguchi UNO DMRG CAS CI calculations of
binuclear manganese complex
Mn(IV)$_2$O$_2$ (NHCHCO$_2$)$_4$: Scope
and applicability of Heisenberg model 333--341
Varinia Bernales and
Robert D. Froese Rhodium catalyzed hydroformylation of
olefins . . . . . . . . . . . . . . . . 342--348
Kohei Shimamura and
Fuyuki Shimojo and
Aiichiro Nakano and
Shigenori Tanaka Ab initio molecular dynamics study of
prebiotic production processes of
organic compounds at meteorite impacts
on ocean . . . . . . . . . . . . . . . . 349--359
Tomoo Miyahara and
Hiroshi Nakatsuji Photoelectron spectrum of NO$_2^-$:
SAC-CI gradient study of
vibrational--rotational structures . . . 360--374
Ryuto Kimura and
Yuh Hijikata and
Clothilde A. Eveleens and
Alister J. Page and
Stephan Irle Chiral-selective etching effects on
carbon nanotube growth at edge carbon
atoms . . . . . . . . . . . . . . . . . 375--380
Jaime Rodríguez-Guerra Pedregal and
Ignacio Funes-Ardoiz and
Giuseppe Sciortino and
José-Emilio Sánchez-Aparicio and
Gregori Ujaque and
Agustí Lledós and
Jean-Didie Maréchal and
Feliu Maseras GARLEEK: Adding an extra flavor to ONIOM 381--386
Anna S. Savchenkova and
Alexander S. Semenikhin and
Ivan V. Chechet and
Sergey G. Matveev and
Alexander A. Konnov and
Alexander M. Mebel Mechanism and rate constants of the
CH$_2$ + CH$_2$ CO reactions in triplet
and singlet states: a theoretical study 387--399
Milena Vujovi\'c and
Mioy Huynh and
Sebastian Steiner and
Pablo Garcia-Fernandez and
Marcus Elstner and
Qiang Cui and
Maja Gruden Exploring the applicability of density
functional tight binding to transition
metal ions. Parameterization for nickel
with the spin-polarized DFTB3 model . . 400--413
Naoki Nakatani and
Masahiko Hada Can large active-space CASSCF
calculation make sense to the reaction
analysis of iron complex? A benchmark
study of methane oxidation reaction by
FeO$^+$ . . . . . . . . . . . . . . . . 414--420
Kentaro Matsumoto and
Masayoshi Takayanagi and
Yuichi Suzuki and
Nobuaki Koga and
Masataka Nagaoka Atomistic chemical computation of olefin
polymerization reaction catalyzed by
(pyridylamido)hafnium(IV) complex:
Application of Red Moon simulation . . . 421--429
Leonid A. Kaledin and
Alexey L. Kaledin and
Michael C. Heaven The electronic structure of thorium
monoxide: Ligand field assignment of
states in the range 0--5 eV . . . . . . 430--446
Ya-Ting Wang and
Xiang-Yang Liu and
Wei-Hai Fang Mechanism of the O$_2$ ($^1 \Delta_g$)
generation from the Cl$_2$ /H$_2$O$_2$
basic aqueous solution explored by the
combined ab initio calculation and
nonadiabatic dynamics simulation . . . . 447--455
Muneaki Kamiya and
Tetsuya Taketsugu Ab initio surface hopping excited-state
molecular dynamics approach on the basis
of spin-orbit coupled states: an
application to the A-band
photodissociation of CH$_3$I . . . . . . 456--463
Pham N. Khanh and
Cam-Tu D. Phan and
Dai Q. Ho and
Quan Van Vo and
Vu T. Ngan and
Minh Tho Nguyen and
Nguyen T. Trung Insights into the cooperativity between
multiple interactions of dimethyl
sulfoxide with carbon dioxide and water 464--474
Yoshitake Sakae and
John E. Straub and
Yuko Okamoto Enhanced sampling method in molecular
simulations using genetic algorithm for
biomolecular systems . . . . . . . . . . 475--481
Tatsuhiko Kashimura and
Tomoya Ikezaki and
Yusuke Ohta and
Satoshi Yabushita Potential energy surfaces and
nonadiabatic transitions in the
asymptotic regions of ICN
photodissociation to study the
interference effects in the F$_1$ and
F$_2$ spin-rotation levels of the CN
products . . . . . . . . . . . . . . . . 482--499
Miho Hatanaka and
Tomonari Wakabayashi Theoretical study of lanthanide-based in
vivo luminescent probes for detecting
hydrogen peroxide . . . . . . . . . . . 500--506
Iori Harada and
Akira Nakayama and
Jun-ya Hasegawa Constraint structure optimization to a
specific minimum using ionization energy 507--514
Rebecca Hanscam and
Eric M. Shepard and
Joan B. Broderick and
Valérie Copié and
Robert K. Szilagyi Secondary structure analysis of peptides
with relevance to iron-sulfur cluster
nesting . . . . . . . . . . . . . . . . 515--526
Thom Vreven and
Stephen C. Miller Computational investigation into the
fluorescence of luciferin analogues . . 527--531
Tao Yu and
Florence Fabunmi and
Jingsong Huang and
Bobby G. Sumpter and
Jacek Jakowski A fast scheme to calculate electronic
couplings between P3HT polymer units
using diabatic orbitals for charge
transfer dynamics simulations . . . . . 532--542
Henrik Quanz and
Peter R. Schreiner TUNNEX: an easy-to-use
Wentzel--Kramers--Brillouin (WKB)
implementation to compute tunneling
half-lives . . . . . . . . . . . . . . . 543--547
Anonymous Cover Image, Volume 40, Issue 3 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 549--553
Simon W. L. Hogan and
Tanja van Mourik Halogen bonding in mono- and dihydrated
halobenzene . . . . . . . . . . . . . . 554--561
G. L. Gutsev and
K. V. Bozhenko and
L. G. Gutsev and
A. N. Utenyshev and
S. M. Aldoshin Hydrogenation of $3$ d-metal oxide
clusters: Effects on the structure and
magnetic properties . . . . . . . . . . 562--571
Hannu T. Vuori and
J. Mikko Rautiainen and
Erkki T. Kolehmainen and
Heikki M. Tuononen Benson group additivity values of
phosphines and phosphine oxides: Fast
and accurate computational
thermochemistry of organophosphorus
species . . . . . . . . . . . . . . . . 572--580
Taiji Nakamura and
Takako Kudo The planarity of heteroatom analogues of
benzene: Energy component analysis and
the planarization of hexasilabenzene . . 581--590
Maria Johanna Ungerer and
Cornelia Gertina Catharina Elizabeth van Sittert and
Derik Johannes van der Westhuizen and
Henning Manfred Krieg Density functional theory study with and
without COSMO of H$_2$ SO$_4$ reactions
in an aqueous environment for metal
extraction . . . . . . . . . . . . . . . 591--606
Subhamoy Mahajan and
Tian Tang Martini coarse-grained model for
polyethylenimine . . . . . . . . . . . . 607--618
Jalal Z. A. Laloo and
Nandini Savoo and
Nassirah Laloo and
Lydia Rhyman and
Ponnadurai Ramasami ExcelAutomat 1.3: Fragment analysis
based on the
distortion/interaction-activation strain
model . . . . . . . . . . . . . . . . . 619--624
Anonymous Cover Image, Volume 40, Issue 4 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 625--629
Asja A. Kroeger and
Amir Karton A computational foray into the mechanism
and catalysis of the adduct formation
reaction of guanine with crotonaldehyde 630--637
Xin Wu and
Pavlo O. Dral and
Axel Koslowski and
Walter Thiel Big data analysis of ab Initio molecular
integrals in the neglect of diatomic
differential overlap approximation . . . 638--649
Federica Maschietto and
Juan Sanz García and
Marco Campetella and
Ilaria Ciofini Using density based indexes to
characterize excited states evolution 650--656
Cheng-Xing Cui and
Dongdong Xu and
Bo-Wen Ding and
Ling-Bo Qu and
Yu-Ping Zhang and
Yu Lan Benchmark study of popular density
functionals for calculating binding
energies of three-center two-electron
bonds . . . . . . . . . . . . . . . . . 657--670
Piotr Durlak and
Zdzislaw Latajka Investigations of the hydrogen bond in
the crystals of tropolone and
thiotropolone via Car--Parrinello and
path integral molecular dynamics . . . . 671--687
Mehrnoosh Arrar and
Fernando Martín Boubeta and
Maria Eugenia Szretter and
Mariela Sued and
Leonardo Boechi and
Daniela Rodriguez On the accurate estimation of free
energies using the Jarzynski equality 688--696
Jonathan Campeggio and
Antonino Polimeno and
Mirco Zerbetto DiTe2: Calculating the diffusion tensor
for flexible molecules . . . . . . . . . 697--705
Anonymous Cover Image, Volume 40, Issue 5 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 707--711
Patrick Müller and
Kristof Karhan and
Matthias Krack and
Uwe Gerstmann and
Wolf Gero Schmidt and
Matthias Bauer and
Thomas D. Kühne Impact of finite-temperature and
condensed-phase effects on theoretical
X-ray absorption spectra of transition
metal complexes . . . . . . . . . . . . 712--716
Walid Lamine and
Salima Boughdiri and
Lorraine Christ and
Christophe Morell and
Henry Chermette Coordination chemistry of Zn$^{2+}$ with
Sal(ph)en ligands: Tetrahedral
coordination or penta-coordination? A
DFT analysis . . . . . . . . . . . . . . 717--725
Shweta Bhagat and
Minhajul Arfeen and
Gourav Das and
Neha Patel and
Prasad V. Bharatam Electronic and ligating properties of
carbocyclic carbenes: a theoretical
investigation . . . . . . . . . . . . . 726--733
Dzmitry V. Shakhno and
Aleh V. Shakhno and
Eugene Paulechka Efficient implementation of periodic
boundary conditions in Monte Carlo
simulation . . . . . . . . . . . . . . . 734--739
Athinthra Sethurajan and
Sergey Krachkovskiy and
Gillian Goward and
Bartosz Protas Bayesian uncertainty quantification in
inverse modeling of electrochemical
systems . . . . . . . . . . . . . . . . 740--752
Milan Randi\'c Benzenoid rings resonance energies and
local aromaticity of benzenoid
hydrocarbons . . . . . . . . . . . . . . 753--762
Anonymous Cover Image, Volume 40, Issue 6 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 763--767
Detlev Conrad Mielczarek and
Chourouk Nait Saidi and
Patrice Paricaud and
Laurent Catoire Generalized Prediction of Enthalpies of
Formation Using DLPNO-CCSD(T) Ab Initio
Calculations for Molecules Containing
the Elements H, C, N, O, F, S, Cl, Br 768--793
Christopher Robertson and
Jesús González-Vázquez and
Ines Corral and
Sergio Díaz-Tendero and
Cristina Díaz Nonadiabatic scattering of NO off Au$_3$
clusters: a simple and robust diabatic
state manifold generation method for
multiconfigurational wavefunctions . . . 794--810
Lukasz Szeleszczuk and
Dariusz M. Pisklak and
Monika Zieli\'nska-Pisklak How does the NMR thermometer work?
Application of combined quantum
molecular dynamics and GIPAW
calculations into the study of lead
nitrate . . . . . . . . . . . . . . . . 811--819
Kai Trepte and
Sebastian Schwalbe and
Torsten Hahn and
Jens Kortus and
Der-You Kao and
Yoh Yamamoto and
Tunna Baruah and
Rajendra R. Zope and
Kushantha P. K. Withanage and
Juan E. Peralta and
Koblar A. Jackson Analytic atomic gradients in the
Fermi--Löwdin orbital self-interaction
correction . . . . . . . . . . . . . . . 820--825
Gaoqi He and
Yiping Song and
Wenhao Wei and
Xia Wang and
Xingjian Lu and
Honglin Li eSHAFTS: Integrated and graphical drug
design software based on $3$D molecular
similarity . . . . . . . . . . . . . . . 826--838
Pierpaolo Morgante and
Roberto Peverati ACCDB: a collection of chemistry
databases for broad computational
purposes . . . . . . . . . . . . . . . . 839--848
Anonymous Cover Image, Volume 40, Issue 7 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 849--853
Bodo Alexander Voigt and
Torben Steenbock and
Carmen Herrmann Structural diradical character . . . . . 854--865
Sean R. McConnell and
Johannes Kästner Instanton rate constant calculations
using interpolated potential energy
surfaces in nonredundant, rotationally
and translationally invariant
coordinates . . . . . . . . . . . . . . 866--874
Sergei F. Vyboishchikov and
Alexander A. Voityuk Iterative Atomic Charge Partitioning of
Valence Electron Density . . . . . . . . 875--884
Mohammed AlQuraishi Parallelized Natural Extension Reference
Frame: Parallelized Conversion from
Internal to Cartesian Coordinates . . . 885--892
Yifei Qi and
Jumin Lee and
Jeffery B. Klauda and
Wonpil Im CHARMM-GUI Nanodisc Builder for modeling
and simulation of various nanodisc
systems . . . . . . . . . . . . . . . . 893--899
Vivek Gavane and
Shruti Koulgi and
Vinod Jani and
Mallikarjunachari V. N. Uppuladinne and
Uddhavesh Sonavane and
Rajendra Joshi TANGO: a high through-put conformation
generation and semiempirical
method-based optimization tool for
ligand molecules . . . . . . . . . . . . 900--909
Anonymous Cover Image, Volume 40, Issue 8 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 911--915
Steven M. Maley and
Robert C. Mawhinney Isothiirane: a Molecular Structure
Dilemma Resolved . . . . . . . . . . . . 916--924
Masato Takenaka and
Yoshikazu Hashimoto and
Takeshi Iwasa and
Tetsuya Taketsugu and
Gediminas Seniutinas and
Armandas Balcytis and
Saulius Juodkazis and
Yoshiaki Nishijima First Principles Calculations Toward
Understanding SERS of 2,2'-Bipyridyl
Adsorbed on Au, Ag, and Au-Ag Nanoalloy 925--932
Shreyas Malpathak and
Xinyou Ma and
William L. Hase Addressing an instability in
unrestricted density functional theory
direct dynamics simulations . . . . . . 933--936
Christian Tantardini When does a hydrogen bond become a van
der Waals interaction? a topological
answer . . . . . . . . . . . . . . . . . 937--943
Diego Cesario and
Mariagrazia Fortino and
Tiziana Marino and
Francesca Nunzi and
Nino Russo and
Emilia Sicilia The role of the halogen bond in
iodothyronine deiodinase: Dependence on
chalcogen substitution in naphthyl-based
mimetics . . . . . . . . . . . . . . . . 944--951
Michael R. Mananghaya and
Gil N. Santos and
Dennis Yu Solubility of aminotriethylene glycol
functionalized single wall carbon
nanotubes: a density functional based
tight binding molecular dynamics study 952--958
Anonymous Cover Image, Volume 40, Issue 9 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 959--964
Yirong Mo and
Wei Wu and
Zexing Cao Editorial . . . . . . . . . . . . . . . 965--965
Miao Yan and
Hai-Ru Li and
Xiao-Yun Zhao and
Xiao-Qin Lu and
Yue-Wen Mu and
Hai-Gang Lu and
Si-Dian Li Fluxional Bonds in Planar B$_{19}^-$,
Tubular Ta@B$_{20}^-$, and Cage-Like
B$_{39}^-$ . . . . . . . . . . . . . . . 966--970
Yan Ying Liang and
Bo Li and
Xuan Xu and
Feng Long Gu and
Chaoyuan Zhu A Density Functional Theory Study on
Nonlinear Optical Properties of Double
Cage Excess Electron Compounds:
Theoretically Design $M$
[Cu(Ag)@(NH$_3$)$_n$] ($M$ = Be, Mg and
Ca; $n$ = 1--3) . . . . . . . . . . . . 971--979
Cen-Feng Fu and
Ruiqi Zhang and
Qiquan Luo and
Xingxing Li and
Jinlong Yang Construction of direct Z-Scheme
photocatalysts for overall water
splitting using two-dimensional van der
Waals heterojunctions of metal
dichalcogenides . . . . . . . . . . . . 980--987
Xiufang Song and
Fengying Zhang and
Yuxiang Bu Dynamic relaying properties of a $ \beta
$-turn peptide in long-range electron
transfer . . . . . . . . . . . . . . . . 988--996
ZhiYe Zhu and
Yi Zhao and
WanZhen Liang Singlet\slash triplet exciton
dissociation and charge recombination in
donor-acceptor ThQs-C$_{60}$ /PDIxCN$_2$
complexes . . . . . . . . . . . . . . . 997--1004
Yang Xu and
Peng Bao and
Kai Song and
Qiang Shi Theoretical study of proton coupled
electron transfer reaction in the light
state of the AppA BLUF photoreceptor . . 1005--1014
Changwei Wang and
David Danovich and
Sason Shaik and
Wei Wu and
Yirong Mo Attraction between electrophilic caps: a
counterintuitive case of noncovalent
interactions . . . . . . . . . . . . . . 1015--1022
Chao Huang and
Wenjian Liu iVI-TD-DFT: an iterative vector
interaction method for exterior/interior
roots of TD-DFT . . . . . . . . . . . . 1023--1037
Yong-Heng Wang and
An-An Wu and
Kai Tan and
Xin Lu Metal-catalyzed alkyne oxidation/C--H
functionalization: Effects of oxidant,
temperature, and metal catalyst on
chemoselectivity . . . . . . . . . . . . 1038--1044
Dading Huang and
Yifei Qi and
Jianing Song and
John Z. H. Zhang Calculation of hot spots for
protein-protein interaction in
p53/PMI-MDM2\slash MDMX complexes . . . 1045--1056
Yuanyuan Li and
Yanzhen Gan and
Zexing Cao Computational insight into excited
states of the ring-opening radicals from
the pyrolysis of furan biofuels . . . . 1057--1065
Anonymous Cover Image, Volume 40, Issue 10 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1067--1072
Chui-Peng Kong and
Xin Gao and
Ran Jia and
Hong-Xing Zhang Investigating detailed mechanism of
hydrogen molecules adsorbing on
single-wall carbon nanotubes using
fitted force field parameters containing
carbon-carbon interactions . . . . . . . 1073--1083
Dongzheng Yang and
Xixi Hu and
Daiqian Xie Quantum dynamics of vibration-vibration
energy transfer for vibrationally
excited HF colliding with H$_2$ . . . . 1084--1090
Cheng Shang and
Si-Da Huang and
Zhi-Pan Liu Massively parallelization strategy for
material simulation using
high-dimensional neural network
potential . . . . . . . . . . . . . . . 1091--1096
Yu-Chen Wang and
Yi Zhao Effect of an underdamped vibration with
both diagonal and off-diagonal
exciton-phonon interactions on
excitation energy transfer . . . . . . . 1097--1104
Xin Chen and
Ya-Fan Zhao and
Yang-Yang Zhang and
Jun Li TGMin: an efficient global minimum
searching program for free and
surface-supported clusters . . . . . . . 1105--1112
Igor Ying Zhang and
Jianming Wu and
Xin Xu Accurate heats of formation of
polycyclic saturated hydrocarbons
predicted by using the XYG3 type of
doubly hybrid functionals . . . . . . . 1113--1122
Huaiyu Zhang and
Chen Zhou and
Yirong Mo and
Wei Wu Performance of the VBSCF method for
pericyclic and $ \pi $ bond shift
reactions . . . . . . . . . . . . . . . 1123--1129
Zhigang Ni and
Wei Li and
Shuhua Li Fully optimized implementation of the
cluster-in-molecule local correlation
approach for electron correlation
calculations of large systems . . . . . 1130--1140
Hui Li and
Di Wang and
Xin Zhao and
Li-Nan Lu and
Cui Liu and
Li-Dong Gong and
Dong-Xia Zhao and
Zhong-Zhi Yang Reaction mechanism of NO with
hydrolysates of NAMI-A: an MD simulation
by combining the QM\slash MM(ABEEM) with
the MD-FEP method . . . . . . . . . . . 1141--1150
Xin Xu and
Jun Chen and
Shu Liu and
Dong H. Zhang An ab initio-based global potential
energy surface for the SH$_3$ system and
full-dimensional state-to-state quantum
dynamics study for the H$_2$ + HS $ \to
$ H$_2$ S + H reaction . . . . . . . . . 1151--1160
Yun-An Yan and
Jian Liu and
Jiushu Shao A semiclassical initial-value
representation for quantum propagator
and Boltzmann operator . . . . . . . . . 1161--1171
FuKit Sheong and
Jing-Xuan Zhang and
Zhenyang Lin Revitalizing Spin Natural Orbital
Analysis: Electronic Structures of
Mixed-Valence Compounds, Singlet
Biradicals, and Antiferromagnetically
Coupled Systems . . . . . . . . . . . . 1172--1184
Anonymous Cover Image, Volume 40, Issue 11 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1185--1189
Stefan Mattsson and
Beate Paulus Density Functional Theory Calculations
of Structural, Electronic, and Magnetic
Properties of the $3$ d Metal
Trifluorides $M$F$_3$ ($M$ = Ti--Ni) in
the Solid State . . . . . . . . . . . . 1190--1197
Laura J. S. Lopes and
Tony Leli\`evre Analysis of the adaptive multilevel
splitting method on the isomerization of
alanine dipeptide . . . . . . . . . . . 1198--1208
Florent Réal and
Valérie Vallet and
Michel Masella Improving the description of solvent
pairwise interactions using local
solute/solvent three-body functions. The
case of halides and carboxylates in
aqueous environment . . . . . . . . . . 1209--1218
Mengyu Liu and
Yanli Zeng and
Zheng Sun and
Lingpeng Meng Predicting the halogen- n ( n = 3-6)
synthons to form the ``windmill''
pattern bonding based on the
halogen-bonded interactions . . . . . . 1219--1226
Miao Yan and
Hai-Ru Li and
Xin-Xin Tian and
Yue-Wen Mu and
Hai-Gang Lu and
Si-Dian Li Fluxional bonds in quasi-planar
B$^{2-}_{18}$ and half-sandwich
$M$B$^-_{18}$ ($M$ = K, Rb, and Cs) . . 1227--1232
Sandra Romero-Molina and
Yasser B. Ruiz-Blanco and
Mirja Harms and
Jan Münch and
Elsa Sanchez-Garcia PPI-Detect: a support vector machine
model for sequence-based prediction of
protein-protein interactions . . . . . . 1233--1242
Anonymous Cover Image, Volume 40, Issue 12 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1243--1247
Kelly N. Tran and
Shuqiang Niu and
Toshiko Ichiye Reduction potential calculations of the
Fe-S clusters in Thermus thermophilus
respiratory complex I . . . . . . . . . 1248--1256
Haixin Wei and
Ray Luo and
Ruxi Qi An efficient second-order
Poisson--Boltzmann method . . . . . . . 1257--1269
Xiaohui Wang and
Xingzhao Tu and
Boming Deng and
John Z. H. Zhang and
Zhaoxi Sun BAR-based optimum adaptive steered MD
for configurational sampling . . . . . . 1270--1289
Arghya Chakravorty and
Emilio Gallicchio and
Emil Alexov A grid-based algorithm in conjunction
with a Gaussian-based model of atoms for
describing molecular geometry . . . . . 1290--1304
Andrew S. Rosen and
Justin M. Notestein and
Randall Q. Snurr Identifying promising metal-organic
frameworks for heterogeneous catalysis
via high-throughput periodic density
functional theory . . . . . . . . . . . 1305--1318
Michal Lesiuk Efficient singular-value decomposition
of the coupled-cluster triple excitation
amplitudes . . . . . . . . . . . . . . . 1319--1332
Anonymous Cover Image, Volume 40, Issue 13 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1333--1337
Changyan Zhu and
Xingxing Zhang and
Min Zhang and
Yun Geng and
Xingman Liu and
Zhongmin Su Insight into spin-orbital interaction
using MCSCF method: a special analysis
of the $^1 \Sigma_g^+$ electronic state
in C$_2$ and the linear polyacetylenic
C$_4$ and C$_6$ . . . . . . . . . . . . 1338--1343
Isuru R. Ariyarathna and
Evangelos Miliordos Electronic and geometric structure
analysis of neutral and anionic alkali
metal complexes of the C$X$ series ($X$
= O, S, Se, Te, Po): the case of $M$
(CX)$_n = 1 - 4$ ($M$ = Li, Na) and
their dimers . . . . . . . . . . . . . . 1344--1351
Zhifang Yang and
Yanping Zheng and
Wenliang Li and
Jingping Zhang Investigation of two-dimensional
HF-based MXenes as the anode materials
for Li/Na-ion batteries: a DFT study . . 1352--1359
Hieu Thanh Nguyen and
Tam Van-Thanh Mai and
Lam Kim Huynh $m$HDFS--HoF: a generalized multilevel
homodesmotic fragment-separation
reaction based program for
heat-of-formation calculation for
acyclic hydrocarbons . . . . . . . . . . 1360--1373
Wenhong Yang and
Zhifeng Ma and
Jun Yi and
Sadia Ahmed and
Wen-Hua Sun Catalytic performance of
bis(imino)pyridine Fe\slash Co complexes
toward ethylene polymerization by
2D-\slash 3D-QSPR modeling . . . . . . . 1374--1386
Nguyen Tien Trung and
Pham Ngoc Khanh and
Alfredo J. Palace Carvalho and
Minh Tho Nguyen Remarkable shifts of C$_{sp2}$-H and O-H
stretching frequencies and stability of
complexes of formic acid with
formaldehydes and thioformaldehydes . . 1387--1400
Oscar A. Douglas-Gallardo and
David Adrian Saez and
Stefan Vogt-Geisse and
Esteban Vöhringer-Martinez Electronic structure benchmark
calculations of inorganic and
biochemical carboxylation reactions . . 1401--1413
Anonymous Cover Image, Volume 40, Issue 14 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1415--1419
Juan Sanz García and
Martial Boggio-Pasqua and
Ilaria Ciofini and
Marco Campetella Excited state tracking during the
relaxation of coordination compounds . . 1420--1428
Sergey A. Samsonov and
Martin Zacharias and
Isaure Chauvot de Beauchene Modeling large protein-glycosaminoglycan
complexes using a fragment-based
approach . . . . . . . . . . . . . . . . 1429--1439
Dongdong Wang and
Jingwei Weng and
Wenning Wang An unconventional ligand-binding
mechanism of substrate-binding proteins:
MD simulation and Markov state model
analysis of BtuF . . . . . . . . . . . . 1440--1448
Bastien Belzunces and
Sophie Hoyau and
Fabienne Bessac Interaction of Metamitron and Fenhexamid
with Ca$^{2+}$-Montmorillonite Clay
Surfaces: a Density Functional Theory
Molecular Dynamics Study . . . . . . . . 1449--1462
Christian Kollmar and
Kantharuban Sivalingam and
Benjamin Helmich-Paris and
Celestino Angeli and
Frank Neese A perturbation-based super-CI approach
for the orbital optimization of a CASSCF
wave function . . . . . . . . . . . . . 1463--1470
Markus Höhnerbach and
Paolo Bientinesi Accelerating AIREBO: Navigating the
Journey from Legacy to High-Performance
Code . . . . . . . . . . . . . . . . . . 1471--1482
Anonymous Cover Image, Volume 40, Issue 15 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1483--1487
Rameswar Bhattacharjee and
Tirthick Majumder and
Ayan Datta Analysis of pseudo Jahn--Teller
distortion based on natural bond orbital
theory: Case study for silicene . . . . 1488--1495
Evangelos A. Coutsias and
Michael J. Wester RMSD and Symmetry . . . . . . . . . . . 1496--1508
Katerina Kyriakidou and
Padeleimon Karafiloglou and
Eric Glendening and
Frank Weinhold To Be or Not to Be: Demystifying the
2nd-Quantized Picture of Complex
Electronic Configuration Patterns in
Chemistry with Natural Poly-Electron
Population Analysis . . . . . . . . . . 1509--1520
Semmy Wellem Taju and
Yu-Yen Ou DeepIon: Deep learning approach for
classifying ion transporters and ion
channels from membrane proteins . . . . 1521--1529
Ryuhei Harada and
Ryunosuke Yoshino and
Hiroaki Nishizawa and
Yasuteru Shigeta Temperature-pressure shuffling outlier
flooding method enhances the
conformational sampling of proteins . . 1530--1537
Yoshifumi Nishimura and
Hiromi Nakai D cdftbmd: Divide-and-Conquer Density
Functional Tight-Binding Program for
Huge-System Quantum Mechanical Molecular
Dynamics Simulations . . . . . . . . . . 1538--1549
Anonymous Cover Image, Volume 40, Issue 16 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1551--1555
Dhivya Manogaran Making and breaking of small water
clusters: a combined quantum chemical
and molecular dynamics approach . . . . 1556--1569
Soohyung Park and
Kerney J. Glover and
Wonpil Im U-shaped caveolin-1 conformations are
tightly regulated by hydrogen bonds with
lipids . . . . . . . . . . . . . . . . . 1570--1577
Qiuling Zhu and
Xugeng Guo and
Jinglai Zhang Theoretical study on photophysical
properties of a series of functional
pyrimidine-based organic light-emitting
diodes emitters presenting thermally
activated delayed fluorescence . . . . . 1578--1585
Yanze Wu and
Huai Sun and
Liang Wu and
Joshua D. Deetz Extracting the mechanisms and kinetic
models of complex reactions from
atomistic simulation data . . . . . . . 1586--1592
Tiago Leyser da Costa Gouveia and
Renan Borsoi Campos and
Ronny Rocha Ribeiro and
Fábio Souza Nunes DFT analysis of the linkage isomerism in
penta(ammine)ruthenium(II/III) complexes
of benzotriazole: Natural bond orbital
method approach and a comprehensive
energy decomposition analysis . . . . . 1593--1598
Qing Wang and
Mingxing Fu and
Xiaojun Li and
Runfeng Huang and
Rainer E. Glaser and
Lili Zhao Aluminum alkoxy-catalyzed biomass
conversion of glucose to
$5$-hydroxymethylfurfural: Mechanistic
study of the cooperative bifunctional
catalysis . . . . . . . . . . . . . . . 1599--1608
Anonymous Cover Image, Volume 40, Issue 17 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1609--1613
Nadia Ben Amor and
Marie-Catherine Heitz RASPT2 study of the valence excited
states of an iron-porphyrin-carbonyl
model complex . . . . . . . . . . . . . 1614--1621
Hui Sun Lee and
Wonpil Im Stalis: a Computational Method for
Template-Based Ab Initio Ligand Design 1622--1632
Jan Rezác Description of halogen bonding in
semiempirical quantum-mechanical and
self-consistent charge
density-functional tight-binding methods 1633--1642
He Su and
Hui Wang and
Hongyan Wang and
Yunxiang Lu and
Zhengdan Zhu Description of noncovalent interactions
involving $ \pi $-system with high
precision: an assessment of RPA, MP2,
and DFT-D methods . . . . . . . . . . . 1643--1651
Dhananjay C. Joshi and
Jung-Hsin Lin Delineating Protein--Protein Curvilinear
Dissociation Pathways and Energetics
with Na\"\ive Multiple-Walker Umbrella
Sampling Simulations . . . . . . . . . . 1652--1663
Graham D. Fletcher and
Colleen Bertoni and
Murat Keçeli and
Michael D'Mello Valence: A Massively Parallel
Implementation of the Variational
Subspace Valence Bond Method . . . . . . 1664--1673
Anonymous Cover Image, Volume 40, Issue 18 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1675--1679
Christopher D. Cooper A Boundary-Integral Approach for the
Poisson--Boltzmann Equation with
Polarizable Force Fields . . . . . . . . 1680--1692
Xin Sun and
Xin Li and
Jiong Yang and
Jinyang Xi and
Ryky Nelson and
Christina Ertural and
Richard Dronskowski and
Weishu Liu and
Gerald J. Snyder and
David J. Singh and
Wenqing Zhang Achieving band convergence by tuning the
bonding ionicity in $n$-type
Mg$_3$Sb$_2$ . . . . . . . . . . . . . . 1693--1700
Huan Zhang and
Lili Qiu and
Dan Hu Finite-Temperature Dimer Method for
Finding Saddle Points on Free Energy
Surfaces . . . . . . . . . . . . . . . . 1701--1706
Awatef Hattab and
Zoubeida Dhaouadi and
Alhadji Malloum and
Jean Jules Fifen and
Souad Lahmar and
Nino Russo and
Emilia Sicilia Structures, binding energies,
temperature effects, infrared
spectroscopy of [Mg(NH$_3$)$_{n = 1 - -
10}$]$^+$ clusters from DFT and MP2
investigations . . . . . . . . . . . . . 1707--1717
John P. Cvitkovic and
Connor D. Pauplis and
George A. Kaminski PKA17 --- a Coarse-Grain Grid-Based
Methodology and Web-Based Software for
Predicting Protein $ p K_a $ Shifts . . 1718--1726
Fotis A. Baltoumas and
Stavros J. Hamodrakas and
Vassiliki A. Iconomidou The gram-negative outer membrane
modeler: Automated building of
lipopolysaccharide-rich bacterial outer
membranes in four force fields . . . . . 1727--1734
Anonymous Cover Image, Volume 40, Issue 19 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1735--1735
Isuru R. Ariyarathna and
Evangelos Miliordos Electronic and geometric structure
analysis of neutral and anionic metal
nitric chalcogens: the case of MNX
series (M = Li, Na, Be and X=O, S, Se,
Te) . . . . . . . . . . . . . . . . . . 1740--1751
Andrew Mahler and
Kassidy Panno and
Benjamin G. Janesko and
Salvador Moncho and
Edward N. Brothers Tunable model promoters in DFT
simulations of catalysts . . . . . . . . 1752--1757
Martin Manak Voronoi-based detection of pockets in
proteins defined by large and small
probes . . . . . . . . . . . . . . . . . 1758--1771
Ming-Xia Zhang and
Hong-Liang Xu A greener catalyst for hydroboration of
imines-external electric field modify
the reaction mechanism . . . . . . . . . 1772--1779
Zhifeng Ma and
Kasumi Ukaji and
Naoki Nakatani and
Hiroshi Fujii and
Masahiko Hada Substitution effects on olefin
epoxidation catalyzed by Oxoiron(IV)
porphyrin $ \pi $-cation radical
complexes: a DFT study . . . . . . . . . 1780--1788
Mickael G. Delcey and
Lasse Kragh Sòrensen and
Morgane Vacher and
Rafael C. Couto and
Marcus Lundberg Efficient calculations of a large number
of highly excited states for
multiconfigurational wavefunctions . . . 1789--1799
Anonymous Cover Image, Volume 40, Issue 20 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1801--1805
Haomiao Zhang and
Qiankun Gong and
Haozhe Zhang and
Changjun Chen Combining the biased and unbiased
sampling strategy into one convenient
free energy calculation method . . . . . 1806--1815
Miquel Garcia-Ratés and
Frank Neese Efficient implementation of the
analytical second derivatives of
Hartree--Fock and hybrid DFT energies
within the framework of the
conductor-like polarizable continuum
model . . . . . . . . . . . . . . . . . 1816--1828
Shi Jun Ang and
Cher Tian Ser and
Ming Wah Wong Modeling halogen bonding with planewave
density functional theory: Accuracy and
challenges . . . . . . . . . . . . . . . 1829--1835
Arpita Varadwaj and
Helder M. Marques and
Pradeep R. Varadwaj Nature of halogen-centered
intermolecular interactions in crystal
growth and design: Fluorine-centered
interactions in dimers in crystalline
hexafluoropropylene as a prototype . . . 1836--1860
Iliya V. Getmanskii and
Vitaliy V. Koval and
Alexander I. Boldyrev and
Ruslan M. Minyaev and
Vladimir I. Minkin Molecular dynamics study of a new
metastable allotropic crystalline form
of gallium-supertetrahedral gallium . . 1861--1865
Atsushi Ishikawa and
Yoshitaka Tateyama Reaction energy benchmarks of
hydrocarbon combustion by Gaussian basis
and plane wave basis approaches . . . . 1866--1873
Anonymous Cover Image, Volume 40, Issue 21 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1875--1879
Ramon Carbó-Dorca Book Review: \booktitle``Solved and
unsolved problems of structural
chemistry'' by Milan Randi\'c, Marjana
Novic, and Dejan Plavsi\'c, CRC Press,
Boca Raton, 2016, xx + 472 pp. ISBN
13-978-1-4987-1151-7 . . . . . . . . . . 1880--1880
Tianlv Xu and
Roya Momen and
Alireza Azizi and
Tanja van Mourik and
Herbert Früchtl and
Steven R. Kirk and
Samantha Jenkins The destabilization of hydrogen bonds in
an external E-field for improved switch
performance . . . . . . . . . . . . . . 1881--1891
Majid El-Hamdi and
Alexey Y. Timoshkin Hydrogen splitting by pyramidalized
13--15 donor--acceptor cryptands: a
computational study . . . . . . . . . . 1892--1901
Jeaphianne P. M. van Rijn and
Andrés M. Escorcia and
Walter Thiel QM/MM study of the taxadiene synthase
mechanism . . . . . . . . . . . . . . . 1902--1910
Jacek Koput Ab initio structure and
vibration-rotation dynamics of
germylene, GeH$_2$ . . . . . . . . . . . 1911--1918
Jaewoon Jung and
Wataru Nishima and
Marcus Daniels and
Gavin Bascom and
Chigusa Kobayashi and
Adetokunbo Adedoyin and
Michael Wall and
Anna Lappala and
Dominic Phillips and
William Fischer and
Chang-Shung Tung and
Tamar Schlick and
Yuji Sugita and
Karissa Y. Sanbonmatsu Scaling molecular dynamics beyond
100,000 processor cores for large-scale
biophysical simulations . . . . . . . . 1919--1930
Anonymous Cover Image, Volume 40, Issue 22 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1931--1935
Mahendra Thapa and
Eric Johnson and
Mark Rance Effect of monovalent ion binding on
molecular dynamics of the S100-family
calcium-binding protein calbindin
D$_{9k}$ . . . . . . . . . . . . . . . . 1936--1945
Laura J. Weiser and
Erik E. Santiso A CGenFF-based force field for
simulations of peptoids with both cis
and trans peptide bonds . . . . . . . . 1946--1956
Srijita Paul and
Sandip Paul Molecular dynamics simulation study on
the inhibitory effects of
choline-O-sulfate on hIAPP
protofibrilation . . . . . . . . . . . . 1957--1968
Walker M. Jones and
Aaron G. Davis and
R. Hunter Wilson and
Katherine L. Elliott and
Isaiah Sumner A conserved asparagine in a
ubiquitin-conjugating enzyme positions
the substrate for nucleophilic attack 1969--1977
Antonia Freibert and
Johannnes M. Dieterich and
Bernd Hartke Exploring self-organization of molecular
tether molecules on a gold surface by
global structure optimization . . . . . 1978--1989
Pham Vu Nhat and
Nguyen Thanh Si and
Minh Tho Nguyen Comment on ``Theoretical Investigations
on Geometrical and Electronic Structures
of Silver Clusters'' . . . . . . . . . . 1990--1993
Anonymous Cover Image, Volume 40, Issue 23 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 1995--1999
Hiroya Nakata and
Shandan Bai Development of a new parameter
optimization scheme for a reactive force
field based on a machine learning
approach . . . . . . . . . . . . . . . . 2000--2012
François Rousse and
Stéphane Redon Incremental solver for orbital-free
density functional theory . . . . . . . 2013--2027
Eric D. Glendening and
Stephen J. Wright and
Frank Weinhold Efficient optimization of natural
resonance theory weightings and bond
orders by gram-based convex programming 2028--2035
Taku Hayashi and
Ka Hung Lee and
Hiroki Iida and
Eiji Yashima and
Stephan Irle and
Yuh Hijikata The helix-inversion mechanism in
double-stranded helical oligomers
bridged by rotary cyclic boronate esters 2036--2042
Hiroko X. Kondo and
Ayumi Kusaka and
Colin K. Kitakawa and
Jinta Onari and
Shusuke Yamanaka and
Haruki Nakamura and
Yu Takano Hydrogen bond donors and acceptors are
generally depolarized in $ \alpha
$-helices as revealed by a molecular
tailoring approach . . . . . . . . . . . 2043--2052
Panagiotis D. Kolokathis and
Oleg M. Braun KoBra: a rate constant method for
prediction of the diffusion of sorbates
inside nanoporous materials at different
loadings . . . . . . . . . . . . . . . . 2053--2066
Anonymous Cover Image, Volume 40, Issue 24 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2067--2067
Kentaro Kido A noniterative mean-field QM/MM-type
approach with a linear response
approximation toward an efficient
free-energy evaluation . . . . . . . . . 2072--2085
Deepak Ojha and
Amalendu Chandra Vibrational echo spectroscopy of aqueous
sodium bromide solutions from first
principles simulations . . . . . . . . . 2086--2095
Ryosuke Hirano and
Tsubasa Yabuchi and
Minoru Sakurai and
Tadaomi Furuta Development of an ATP force field for
coarse-grained simulation of ATPases and
its application to the maltose
transporter . . . . . . . . . . . . . . 2096--2102
Mirzam Carreon-Gonzalez and
Annik Vivier-Bunge and
Juan Raul Alvarez-Idaboy Thiophenols, Promising Scavengers of
Peroxyl Radicals: Mechanisms and
kinetics . . . . . . . . . . . . . . . . 2103--2110
Emma L. Cates and
Tanja van Mourik Halogen bonding with the halogenabenzene
bird structure, halobenzene, and
halocyclopentadiene . . . . . . . . . . 2111--2118
Vijay Singh and
Shigeyoshi Sakaki and
Milind M. Deshmukh Theoretical prediction of Ni(I)-catalyst
for hydrosilylation of pyridine and
quinoline . . . . . . . . . . . . . . . 2119--2130
Taichi Inagaki and
Masataka Nagaoka Electrode polarization effects on
interfacial kinetics of ionic liquid at
graphite surface: an extended
Lagrangian-based constant potential
molecular dynamics simulation study . . 2131--2145
Ellie L. Fought and
Vaibhav Sundriyal and
Masha Sosonkina and
Theresa L. Windus Improving efficiency of semi-direct
Mòller--Plesset second-order perturbation
methods through oversubscription on
multiple nodes . . . . . . . . . . . . . 2146--2157
Anonymous Cover Image, Volume 40, Issue 25 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2159--2163
Emilia A. Lubecka and
Adam Liwo Introduction of a bounded penalty
function in contact-assisted simulations
of protein structures to omit false
restraints . . . . . . . . . . . . . . . 2164--2178
Mohsen Abbaspour and
Majid Namayandeh Jorabchi and
Hamed Akbarzadeh and
Sirous Salemi and
Reyhaneh Ebrahimi Molecular dynamics simulation of
anticancer drug delivery from carbon
nanotube using metal nanowires . . . . . 2179--2190
Julien Eng and
Beth A. Laidlaw and
Thomas J. Penfold On the geometry dependence of
tuned-range separated hybrid functionals 2191--2199
Álvaro Valdés and
Rita Prosmiti Quantum effects on the stability of the
He$_5$I$_2$ van der Waals conformers . . 2200--2206
Tejender Singh and
Prasad V. Bharatam Donor$ \to $ acceptor coordination
interactions in 1,3-bis(NHC)triazenyl
Cations: an electronic structure
analysis . . . . . . . . . . . . . . . . 2207--2215
Christopher J. Stein and
Markus Reiher autoCAS: A Program for Fully Automated
Multiconfigurational Calculations . . . 2216--2226
Xiaobo Sun and
Thomas M. Soini and
Jordi Poater and
Trevor A. Hamlin and
F. Matthias Bickelhaupt PyFrag 2019-Automating the exploration
and analysis of reaction mechanisms . . 2227--2233
Eric D. Glendening and
Clark R. Landis and
Frank Weinhold NBO 7.0: New vistas in localized and
delocalized chemical bonding theory . . 2234--2241
Anonymous Cover Image, Volume 40, Issue 26 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2243--2247
Juan Andrés and
Paul W. Ayers and
Roberto A. Boto and
Ramon Carbó-Dorca and
Henry Chermette and
Jerzy Cioslowski and
Julia Contreras-García and
David L. Cooper and
Gernot Frenking and
Carlo Gatti and
Farnaz Heidar-Zadeh and
Laurent Joubert and
Ángel Martín Pendás and
Eduard Matito and
István Mayer and
Alston J. Misquitta and
Yirong Mo and
Julien Pilmé and
Paul L. A. Popelier and
Martin Rahm and
Eloy Ramos-Cordoba and
Pedro Salvador and
W. H. Eugen Schwarz and
Shant Shahbazian and
Bernard Silvi and
Miquel Sol\`a and
Krzysztof Szalewicz and
Vincent Tognetti and
Frank Weinhold and
Émilie-Laure Zins Nine questions on energy decomposition
analysis . . . . . . . . . . . . . . . . 2248--2283
Alyona A. Starikova and
Maxim G. Chegerev and
Andrey G. Starikov and
Vladimir I. Minkin Rational Design of Electronically Labile
Dinuclear Fe and Co complexes with
1,10-Phenanthroline-5,6-Diimine: a DFT
study . . . . . . . . . . . . . . . . . 2284--2292
Andrey V. Kulsha and
Dmitry I. Sharapa Superhalogen and Superacid . . . . . . . 2293--2300
Javaria Batool and
Torsten Hahn and
Mark R. Pederson Magnetic Signatures of Hydroxyl- and
Water-Terminated Neutral and
Tetra-Anionic Mn$_12$-Acetate . . . . . 2301--2308
Roberto Cammi The Role of Computational Chemistry in
the Experimental Determination of the
Dipole Moment of Molecules in Solution 2309--2317
Stefano Borocci and
Felice Grandinetti and
Nico Sanna and
Paola Antoniotti and
Francesca Nunzi Noncovalent Complexes of the Noble-Gas
Atoms: Analyzing the Transition from
Physical to Chemical Interactions . . . 2318--2328
Giorgia Beata and
Gianpaolo Perego and
Bartolomeo Civalleri CRYSPLOT: a new tool to visualize
physical and chemical properties of
molecules, polymers, surfaces, and
crystalline solids . . . . . . . . . . . 2329--2338
Pavlo O. Dral MLatom: a program package for quantum
chemical research assisted by machine
learning . . . . . . . . . . . . . . . . 2339--2347
Asanga Bandara and
Afra Panahi and
George A. Pantelopulos and
John E. Straub Exploring the Structure and Stability of
Cholesterol Dimer Formation in
Multicomponent Lipid Bilayers . . . . . 2348--2348
Anonymous Cover Image, Volume 40, Issue 27 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2349--2353
VineetKumar Choudhary and
ArvindKumar Bhatt and
Dibyajit Dash and
Neeraj Sharma DFT calculations on molecular
structures, HOMO--LUMO study, reactivity
descriptors and spectral analyses of
newly synthesized diorganotin(IV)
$2$-chloridophenylacetohydroxamate
complexes . . . . . . . . . . . . . . . 2354--2363
Daniel Vilela Oliveira and
Joachim Laun and
Michael F. Peintinger and
Thomas Bredow BSSE-correction scheme for consistent
Gaussian basis sets of double- and
triple-zeta valence with polarization
quality for solid-state calculations . . 2364--2376
Aymerick Batlogg and
Maria Fumanal Computational Assessment of MLCT versus
MC Stabilities in First-to-Third-Row $
d^6 $ Pseudo-Octahedral Transition Metal
Complexes . . . . . . . . . . . . . . . 2377--2390
Petr Popov and
Sergei Grudinin and
Andrii Kurdiuk and
Pavel Buslaev and
Stephane Redon Controlled-advancement rigid-body
optimization of nanosystems . . . . . . 2391--2399
Olena Lenchuk and
Philipp Adelhelm and
Doreen Mollenhauer Comparative study of density functionals
for the description of lithium-graphite
intercalation compounds . . . . . . . . 2400--2412
Taeyong Park and
Minkyung Baek and
Hasup Lee and
Chaok Seok GalaxyTongDock: Symmetric and asymmetric
ab initio protein-protein docking web
server with improved energy parameters 2413--2417
Carsten Kutzner and
Szilárd Páll and
Martin Fechner and
Ansgar Esztermann and
Bert L. de Groot and
Helmut Grubmüller More bang for your buck: Improved use of
GPU nodes for GROMACS 2018 . . . . . . . 2418--2431
Ke Li and
Shanlong Li and
Wei Huang and
Chunyang Yu and
Yongfeng Zhou MembrFactory: a Force Field and
composition Double Independent Universal
Tool for Constructing Polyamide Reverse
Osmosis Membranes . . . . . . . . . . . 2432--2438
Anonymous Cover Image, Volume 40, Issue 28 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2439--2443
Taniya Manzoor and
Altaf Hussain Pandith Enhancing the photoresponse by
CdSe-Dye-TiO$_2$-based multijunction
systems for efficient dye-sensitized
solar cells: a theoretical outlook . . . 2444--2452
Tomonori Hayami and
Junichi Higo and
Haruki Nakamura and
Kota Kasahara Multidimensional virtual-system coupled
canonical molecular dynamics to compute
free-energy landscapes of peptide
multimer assembly . . . . . . . . . . . 2453--2463
Alexei Nikitin and
Gianluca Del Frate Development of Nonbonded Models for
Metal Cations Using the Electronic
Continuum Correction . . . . . . . . . . 2464--2472
Qingqing Jia and
Hai-Bei Li and
Mo Luo and
Jingjing Wang Effects of Electronic Structure of
Adjacent Carbon on the Strength of
C-F\dottedbond H-F Organofluorine
Hydrogen Bonds . . . . . . . . . . . . . 2473--2481
Natieli Alves da Silva and
Roberto Luiz Andrade Haiduke Infrared intensity analysis of hydroxyl
stretching modes in carboxylic acid
dimers by means of the charge--charge
flux--dipole flux model . . . . . . . . 2482--2490
Lisa Warczinski and
Robert Franke and
Volker Staemmler ESCAPE: a novel approach for a fast
estimation of dynamic correlation
energies: Application to large organic
molecules . . . . . . . . . . . . . . . 2491--2501
Chuan Li and
Zhe Jia and
Arghya Chakravorty and
Swagata Pahari and
Yunhui Peng and
Sankar Basu and
Mahesh Koirala and
Shailesh Kumar Panday and
Marharyta Petukh and
Lin Li and
Emil Alexov DelPhi Suite: New Developments and
Review of Functionalities . . . . . . . 2502--2508
Dennis Svatunek and
Kendall N. Houk autoDIAS: a python tool for an automated
distortion/interaction activation strain
analysis . . . . . . . . . . . . . . . . 2509--2515
Anonymous Cover Image, Volume 40, Issue 29 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2517--2521
Jacek Koput Ab Initio Ground-State Potential Energy
Function and Vibration--Rotation Energy
Levels of Aluminum Monohydride . . . . . 2522--2529
Syrine Daoudi and
Abderrahmane Semmeq and
Michael Badawi and
Xavier Assfeld and
Youssef Arfaoui and
Mariachiara Pastore Electronic structure and optical
properties of isolated and
TiO$_2$-grafted free base porphyrins for
water oxidation: a challenging test case
for DFT and TD-DFT . . . . . . . . . . . 2530--2538
Han-Wen Pei and
Aatto Laaksonen Feature vector clustering molecular
pairs in computer simulations . . . . . 2539--2549
Athanassios C. Tsipis Trans-philicity
(trans-influence/trans-effect) ladders
for square planar platinum(II) complexes
constructed by $^{35}$Cl NMR probe . . . 2550--2562
Martin Becker and
Marek Sierka Density functional theory for molecular
and periodic systems using density
fitting and continuous fast multipole
method: Stress tensor . . . . . . . . . 2563--2570
Kazushi Fujimoto and
Rajadeep Singh Payal and
Tomonori Hattori and
Wataru Shinoda and
Masayuki Nakagaki and
Shigeyoshi Sakaki and
Susumu Okazaki Development of dissociative force field
for all-atomistic molecular dynamics
calculation of fracture of polymers . . 2571--2576
Shuntaro Chiba and
Yasushi Okuno and
Teruki Honma and
Mitsunori Ikeguchi Force-field parametrization based on
radial and energy distribution functions 2577--2585
Antonio Suma and
Erik Poppleton and
Michael Matthies and
Petr Sulc and
Flavio Romano and
Ard A. Louis and
Jonathan P. K. Doye and
Cristian Micheletti and
Lorenzo Rovigatti TacoxDNA: a user-friendly web server for
simulations of complex DNA structures,
from single strands to origami . . . . . 2586--2595
Anonymous Cover Image, Volume 40, Issue 30 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2597--2601
José E. Barquera-Lozada Vorticity: Simplifying the analysis of
the current density . . . . . . . . . . 2602--2610
Ping Liu and
Lixia Ling and
Hao Lin and
Baojun Wang Understanding the Role of Surface Oxygen
in Hg Removal on Un-Doped and
Mn/Fe-Doped CeO$_2$ (111) . . . . . . . 2611--2621
Yuuichi Orimoto and
Satoru Shirane and
Yuriko Aoki Extent of structural change during the
reaction and its relationship to
isoselectivity in polypropylene
polymerization with
ansa-zirconocene/borate catalyst: a
computational study . . . . . . . . . . 2622--2635
Arindam Sannyal and
Joonkyung Jang and
Md. Shajahan and
Joyanta K. Saha Thermal Effect on Positive Patterned
Self-Assembled Monolayer Grown from a
Droplet of Alkanethiol . . . . . . . . . 2636--2642
Sirous Yourdkhani and
Miros\law Jab\lo'nski Physical nature of silane\dottedbond
carbene dimers revealed by
state-of-the-art ab initio calculations 2643--2652
Ramon Carbó-Dorca and
Tanmoy Chakraborty Divagations about the periodic table:
Boolean hypercube and quantum similarity
connections . . . . . . . . . . . . . . 2653--2663
Franziska Hess Efficient Implementation of Cluster
Expansion Models in Surface Kinetic
Monte Carlo Simulations with Lateral
Interactions: Subtraction Schemes,
Supersites, and the Supercluster
Contraction . . . . . . . . . . . . . . 2664--2676
Burkhard Schmidt and
Rupert Klein and
Leonardo Cancissu Araujo WavePacket: a Matlab package for
numerical quantum dynamics. III.
Quantum-classical simulations and
surface hopping trajectories . . . . . . 2677--2688
Anonymous Cover Image, Volume 40, Issue 31 . . . . C1--C1
Anonymous Issue Information . . . . . . . . . . . 2689--2693
Masataka Yamauchi and
Hisashi Okumura Replica sub-permutation method for
molecular dynamics and Monte Carlo
simulations . . . . . . . . . . . . . . 2694--2711
Christian Dreßler and
Arne Scherrer and
Paul Ahlert and
Daniel Sebastiani Efficient representation of the linear
density-density response function . . . 2712--2721
Kosuke Takeda and
Kazushi Fujimoto and
Noriyuki Yoshii and
Susumu Okazaki Molecular dynamics study of
solubilization of cyclohexane, benzene,
and phenol into mixed micelles composed
of sodium dodecyl sulfate and
octaethylene glycol monododecyl ether 2722--2729
Yao-Xiao Zhao and
Meng-Yang Li and
Yi-Ming Xiong and
Shirin Rahmani and
Kun Yuan and
Rui-Sheng Zhao and
Masahiro Ehara and
Shigeru Nagase and
Xiang Zhao Pivotal Role of Nonmetal Atoms in the
Stabilities, Geometries, Electronic
Structures, and Isoelectronic Chemistry
of Sc$_3$X@C$_{80}$ (X = C, N, and O) 2730--2738
Jinsol Yang and
Minkyung Baek and
Chaok Seok GalaxyDock3: Protein--ligand docking
that considers the full ligand
conformational flexibility . . . . . . . 2739--2748
Yue Wu and
Shengfu Zhang and
Shuangshuang Cai and
Xiong Xiao and
Cheng Yin and
Jian Xu and
Shuxing Qiu and
Wenzhou Yu and
Meilong Hu and
Liangying Wen Transformation of organic sulfur and its
functional groups in Nantong and Laigang
coal under microwave irradiation . . . . 2749--2760
Yi-Gui Wang and
Ericka C. Barnes and
Savas Kaya and
Vinit Sharma The Reactivity of Ambident Nucleophiles:
Marcus Theory or Hard and Soft Acids and
Bases Principle? . . . . . . . . . . . . 2761--2777
Takeshi Yoshikawa and
Nana Komoto and
Yoshifumi Nishimura and
Hiromi Nakai GPU-Accelerated Large-Scale
Excited-State Simulation Based on
Divide-and-Conquer Time-Dependent
Density-Functional Tight-Binding . . . . 2778--2786
Anonymous Cover Image, Volume 40, Issue 32 . . . . C1
Anonymous Issue Information . . . . . . . . . . . 2787--2792
Mark A. Vincent and
Arnaldo F. Silva and
Paul L. A. Popelier Atomic Partitioning of the MPn $ (n = 2,
3, 4) $ Dynamic Electron Correlation
Energy by the Interacting Quantum Atoms
Method: a Fast and Accurate
Electrostatic Potential Integral
Approach . . . . . . . . . . . . . . . . 2793--2800
Xiangyu Jia Solvation Free Energy Calculations: The
Combination between the Implicitly
Polarized Fixed-charge Model and the
Reference Potential Strategy . . . . . . 2801--2809
Talapunur Vikramaditya and
Shiang-Tai Lin Limitations of Global Hybrids in
Predicting the Geometries and Torsional
Energy Barriers of Dimeric Systems and
the Role of Hartree Fock and DFT
Exchange . . . . . . . . . . . . . . . . 2810--2818
Sombat Ketrat and
Thana Maihom and
Piti Treesukul and
Bundet Boekfa and
Jumras Limtrakul Theoretical study of methane adsorption
and C-H bond activation over Fe-embedded
graphene: Effect of external electric
field . . . . . . . . . . . . . . . . . 2819--2826
Shuaifei Guo and
Cuihong Sun and
Lingpeng Meng and
Yanli Zeng The mechanism of ring-opening
polymerization of L-lactide by ICl$_3$
catalysts: Halogen bond catalysis or
participating in reactions? . . . . . . 2827--2833
Alexey Aleksandrov A Molecular Mechanics Model for Flavins 2834--2842
Sebastian Schwalbe and
Kai Trepte and
Lenz Fiedler and
Alex I. Johnson and
Jakob Kraus and
Torsten Hahn and
Juan E. Peralta and
Koblar A. Jackson and
Jens Kortus Interpretation and Automatic Generation
of Fermi-Orbital Descriptors . . . . . . 2843--2857
Elena Yu. Tupikina and
Gleb S. Denisov and
Peter M. Tolstoy Anticooperativity of FH$ \cdots $Cl$^-$
hydrogen bonds in [FH$_n$ Cl]$^-$
clusters $ (n = 1 \ldots {} 6)$ . . . . 2858--2867
Saeedreza Emamian and
Tian Lu and
Holger Kruse and
Hamidreza Emamian Exploring Nature and Predicting Strength
of Hydrogen Bonds: a Correlation
Analysis Between Atoms-in-Molecules
Descriptors, Binding Energies, and
Energy Components of Symmetry-Adapted
Perturbation Theory . . . . . . . . . . 2868--2881
Yuqi Zhang and
Stefano Forli and
Anna Omelchenko and
Michel F. Sanner AutoGridFR: Improvements on AutoDock
Affinity Maps and Associated Software
Tools . . . . . . . . . . . . . . . . . 2882--2886
Subhamoy Mahajan and
Tian Tang Erratum: ``Martini Coarse-Grained Model
for Polyethylenimine'' [J. Comput. Chem.
2019, \bf 40, 607--618, DOI:
10.1002/jcc.25747] . . . . . . . . . . . 1730--1734