Journal of Computational Chemistry, Volume 33

Volume 33, Number 1, January 2012

• 
  A. Laref:
  Tight-binding molecular dynamics simulation of ZnSe liquid within the local environment dependence. 1-10
• 
  Chengqi Wang, Lili Xi, Shuyan Li, Huanxiang Liu, Xiaojun Yao:
  A sequence-based computational model for the prediction of the solvent accessible surface area for α-helix and β-barrel transmembrane residues. 11-17
• 
  Xiang Po Du, Veng Cheong Lo, Yuan Xu Wang:
  The effect of structure and phase transformation on the mechanical properties of Re₂N and the stability of Mn₂N. 18-24
• 
  Floris P. Buelens, Helmut Grubmüller:
  Linear-scaling soft-core scheme for alchemical free energy calculations. 25-33
• 
  Hongjiang Zhang, Jean-Paul Malrieu, Haibo Ma, Jing Ma:
  Implementation of renormalized excitonic method at ab initio level. 34-43
• 
  Uppula Purushotham, Dolly Vijay, G. Narahari Sastry:
  A computational investigation and the conformational analysis of dimers, anions, cations, and zwitterions of L-phenylalanine. 44-59
• 
  Yusuke Ootani, Tetsuya Taketsugu:
  Ab initio molecular dynamics approach to tunneling splitting in polyatomic molecules. 60-65
• 
  Li Wang, Yanjie Li, Hong-Qing He, Jinglai Zhang:
  Hydrogen abstraction reactions of OH radicals with CH₃CH₂CH₂Cl and CH₃CHClCH₃: 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, Shuhui Lv, Yijia Bai, Yanjie Xia, Xiaojuan Liu, Jian Meng:
  First-principle investigation of magnetic coupling mechanism in hypothesized A-site-ordered perovskite YMn₃Sc₄O₁₂. 82-87
• 
  Yu Li Yan, Yuan Xu Wang:
  Electronic structure and low temperature thermoelectric properties of In₂₄ M₈ O₄₈ (M = Ge⁴⁺, Sn⁴⁺, Ti⁴⁺, and Zr⁴⁺). 88-92
• 
  Xu-Geng Guo, Jing-Lai Zhang, 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, Ming-Der Su:
  Theoretical investigations of the reactivities of four-membered N-heterocyclic carbene analogues of the group 13 elements. 103-111
• 
  Andreas Orthaber, Alexander F. Sax, Kevin A. Francesconi:
  Oxygen versus sulfur: Structure and reactivity of substituted arsine oxides and arsine sulfides. 112-117

Volume 33, Number 2, January 2012

• 
  Kiumars Shahrokh, Anita M. Orendt, Garold S. Yost, Thomas E. Cheatham III:
  Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle. 119-133
• 
  Benjamin Helmich, Marek Sierka:
  Similarity recognition of molecular structures by optimal atomic matching and rotational superposition. 134-140
• 
  Timothy R. Lucas, Brad A. Bauer, Joseph E. Davis, Sandeep Patel:
  Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields. 141-152
• 
  Qishi Du, Si-Yu Long, Jian-Zong Meng, Ri-Bo Huang:
  Empirical formulation and parameterization of cation-π interactions for protein modeling. 153-162
• 
  Lingli Tang, Linwei Sai, Jijun Zhao, Ruifeng Qiu:
  A Topological method for global optimization of clusters: Application to (TiO₂)_n (n = 1-6). 163-169
• 
  Nitin Wadnerkar, Vijayanand Kalamse, Shyi-Long Lee, Ajay Chaudhari:
  Verification of DFT-predicted hydrogen storage capacity of VC₃H₃ complex using molecular dynamics simulations. 170-174
• 
  Sermsiri Chaiwongwattana, Mayuree Phonyiem, Viwat Vchirawongkwin, Supakit Prueksaaroon, Kritsana Sagarik:
  Dynamics and mechanism of structural diffusion in linear hydrogen bond. 175-188
• 
  Joseph D. Yesselman, Daniel J. Price, Jennifer L. Knight, Charles L. Brooks III:
  MATCH: An atom-typing toolset for molecular mechanics force fields. 189-202
• 
  Hui Zhang, Liu Yang, Jing-Yao Liu, Ze-Sheng Li:
  Theoretical study on the reaction CX₃ + SiH(CH₃)₃ (X = H, F). 203-210
• 
  Nana Ma, Chunguang Liu, Yong-Qing Qiu, Shiling Sun, Zhongmin Su:
  Theoretical investigation on redox-switchable second-order nonlinear optical responses of push-pull Cp*CoEt₂C₂B₄H₃-expanded (metallo)porphyrins. 211-219
• 
  Jie Ying Gao, Cheng Hua Zhang, Mei Ming Luo, Chan Kyung Kim, Wei Chu, Ying Xue:
  Mechanism for the reaction of 2-naphthol with N-methyl-N-phenyl-hydrazine suggested by the density functional theory investigations. 220-230
• 
  Jianan Wang, Hong-Liang Xu, Shiling Sun, Ting Gao, Hong-Zhi Li, Hui Li, Zhongmin Su:
  An effective method for accurate prediction of the first hyperpolarizability of alkalides. 231-236

Letters to the editor

• 
  Wolf-Dietrich Ihlenfeldt:
  Comment on the paper "indexing molecules with chemical graph Identifiers" by Elisabeth Gregori-Puigjané, Rut Garriga-Sust, and Jordi Mestres. 237

Letters to the Editor

• 
  Elisabet Gregori-Puigjané, Rut Garriga-Sust, Jordi Mestres:
  Response to the comment by Wolf Ihlenfeldt on the paper "Indexing molecules with chemical graph identifiers". 238

Volume 33, Number 3, January 2012

Original Articles

• 
  Hirofumi Fujimoto, Mariko Higuchi, Manabu Koike, Hirotaka Ode, Miroslav Pinak, Juraj Kotulic Bunta, Toshiyuki Nemoto, Takashi Sakudoh, Naoko Honda, Hideaki Maekawa, Kimiaki Saito, Kozo Tsuchida:
  A possible overestimation of the effect of acetylation on lysine residues in KQ mutant analysis. 239-246
• 
  Jean Marie Ducéré, Anne Hemeryck, Alain Estève, Mehdi Djafari Rouhani, Georges Landa, Philippe Ménini, Cyril Tropis, André Maisonnat, Pierre Fau, Bruno Chaudret:
  A computational chemist approach to gas sensors: Modeling the response of SnO₂ to CO, O₂, and H₂O Gases. 247-258
• 
  Eshel Faraggi, Tuo Zhang, Yuedong Yang, Lukasz A. Kurgan, 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, 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, Kumar Vanka:
  A new approximate method for the stochastic simulation of chemical systems: The representative reaction approach. 276-285
• 
  Takaharu Mori, Fumiko Ogushi, Yuji Sugita:
  Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods. 286-293
• 
  Vicente Ruiz de Angulo, Juan Cortés, Josep M. Porta:
  Rigid-CLL: Avoiding constant-distance computations in cell linked-lists algorithms. 294-300
• 
  Xue Li, Zheng Fu, Kenneth M. Merz Jr.:
  QM/MM refinement and analysis of protein bound retinoic acid. 301-310
• 
  Xiao-Jing Liu, Ian P. Hamilton, Robert P. Krawczyk, Peter Schwerdtfeger:
  The stability of small helical gold nanorods: A relativistic density functional study. 311-318
• 
  Yulia N. Kalugina, Victor N. Cherepanov, Mikhail A. Buldakov, Natalia Zvereva-Loëte, Vincent Boudon:
  Theoretical investigation of the ethylene dimer: Interaction energy and dipole moment. 319-330

Software News and Updates

• 
  Kyu Il Lee, Sunhwan Jo, Huan Rui, Bernhard Egwolf, Benoît Roux, Richard W. Pastor, Wonpil Im:
  Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores. 331-339
• 
  Anna-Pitschna E. Kunz, Jane R. Allison, Daan P. Geerke, Bruno A. C. Horta, Philippe H. Hünenberger, Sereina Riniker, Nathan Schmid, Wilfred F. van Gunsteren:
  New functionalities in the GROMOS biomolecular simulation software. 340-353

Erratum

• 
  Laban Bondesson, Elias Rudberg, Yi Luo, Pawel Salek:
  Erratum: Basis set dependence of solute-solvent interaction energy of benzene in water: A HF/DFT study. 354

Volume 33, Number 4, February 2012

• 
  Michael Honigmann, Robert J. Buenker, Heinz-Peter Liebermann:
  Complex configuration interaction calculations of the cross section for the dissociative electron attachment process e^- + F₂ → F. 355-362
• 
  Katharina Meier, Walter Thiel, 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, Dong-Xia Zhao, 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, Ziyou Li, 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_N2 reaction of F^- with NH₂F: Nonstatistical central barrier recrossing dynamics. 401-405
• 
  Marcus Lundberg:
  Understanding cross-boundary events in ONIOM QM: QM' calculations. 406-415
• 
  Gennady L. Gutsev, Charles A. Weatherford, Lewis E. Johnson, Purusottam Jena:
  Structure and properties of the aluminum borates Al(BO₂)_n and Al(BO₂)_n^-, (n = 1-4). 416-424
• 
  Sudip Pan, Santanab Giri, Pratim Kumar Chattaraj:
  A computational study on the hydrogen adsorption capacity of various lithium - Doped boron hydrides. 425-434
• 
  Alexandra Vardi-Kilshtain, Asaf Azuri, Dan Thomas Major:
  Path-integral calculations of heavy atom kinetic isotope effects in condensed phase reactions using higher-order trotter factorizations. 435-441
• 
  Jorge M. C. Marques, A. A. C. C. Pais, 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, 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

Software News and Updates

• 
  Francois Berenger, Rojan Shrestha, Yong Zhou, David Simoncini, Kam Y. J. Zhang:
  Durandal: Fast exact clustering of protein decoys. 471-474

Volume 33, Number 5, February 2012

Original Articles

• 
  Francesco Rao, Martin Spichty:
  Thermodynamics and kinetics of large-time-step molecular dynamics. 475-483
• 
  Bu-Tong Li, Lu-Lin Li, Hai-Shun Wu:
  Theoretical calculation about the valence and rydberg excited states of hydrogen cyanide. 484-489
• 
  Wenming Sun, Yuxiang Bu, Yixuan Wang:
  Interaction and protection mechanism between li@C₆₀ and nucleic acid bases (NABs): Performance of PM6-DH2 on noncovalent interaction of NABs-Li@C60. 490-501
• 
  Fabrice Avaltroni, Clémence Corminboeuf:
  Identifying clusters as low-lying mimina - efficiency of stochastic and genetic algorithms using inexpensive electronic structure levels. 502-508
• 
  Israel Fernández, Friedrich 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, Huanxiang Liu, Xiaojun Yao:
  Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: A molecular modeling perspective. 527-536
• 
  Hua Dong, Bo-Zhen Chen, Ming-Bao Huang, Roland Lindh:
  The bergman cyclizations of the enediyne and its N-substituted analogs using multiconfigurational second-order perturbation theory. 537-549
• 
  Shuntaro Chiba, Yuichi Harano, Roland Roth, Masahiro Kinoshita, Minoru Sakurai:
  Evaluation of protein-ligand binding free energy focused on its entropic components. 550-560
• 
  Stefano Costanzi, Santiago Vilar:
  In Silico screening for agonists and blockers of the β₂ adrenergic receptor: Implications of inactive and activated state structures. 561-572
• 
  Tim Geppert, Felix Reisen, Max Pillong, Volker Hähnke, Yusuf Tanrikulu, Christian P. Koch, Anna Maria Perna, Tatiana Batista Perez, Petra Schneider, Gisbert Schneider:
  Virtual screening for compounds that mimic protein-protein interface epitopes. 573-579

Software News and Updates

• 
  Tian Lu, Feiwu Chen:
  Multiwfn: A multifunctional wavefunction analyzer. 580-592

Erratum

• 
  D. Heringer, T. A. Niehaus, Marius Wanko, Thomas Frauenheim:
  Analytical excited state forces for the time-dependent density-functional tight-binding method [Journal of Computational Chemistry 28, 2589]. 593

Volume 33, Number 6, March 2012

Full Papers

• 
  Jun-Xi Liang, Zhi-Yuan Geng, Yong-Cheng Wang:
  Density functional study of S_N2 substitution reactions for CH₃Cl + CX¹X^2•- (X¹X² = HH, HF, HCl, HBr, HI, FF, ClCl, BrBr, and II). 595-606
• 
  Florent Barbault, 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, Shigeyoshi Sakaki:
  Two-step evaluation of binding energy and potential energy surface of van der Waals complexes. 617-628
• 
  Soumya Ganguly Neogi, Pinaki Chaudhury:
  Structure and spectroscopy of water-fluoride microclusters: A combined genetic algorithm and DFT-based study. 629-639
• 
  Niels Hansen, Jozica Dolenc, Matthias Knecht, Sereina Riniker, 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, A. Gulans, P. Havu, Esko I. 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, J. Martin Herold, Dmitri B. Kireev:
  Assessment of free energy predictors for ligand binding to a methyllysine histone code reader. 659-665
• 
  Jinliang Li, Zhenzhen Zhao, Cui Yu, Hongbo Wang, Jianwei Zhao:
  Theoretical investigation on the transportation behavior of molecular wires with redox reaction. 666-672
• 
  A. Laref, S. Laref, S. Bin-Omran:
  Electronic structure, X-ray absorption, and optical spectroscopy of LaCoO₃ in the ground-state and excited-states. 673-684
• 
  Hui Zhang, Yang Liu, Jing-Yao Liu, Ze-Sheng Li:
  Theoretical study and rate constants calculation for the reactions X + CF₃CH₂OCF₃ (X = F, Cl, Br). 685-690
• 
  Jan Rezác, Kevin E. Riley, Pavel Hobza:
  Evaluation of the performance of post-Hartree-Fock methods in terms of intermolecular distance in noncovalent complexes. 691-694
• 
  Katrin Tonigold, Axel Groß:
  Dispersive interactions in water bilayers at metallic surfaces: A comparison of the PBE and RPBE functional including semiempirical dispersion corrections. 695-701
• 
  Milan Randic:
  Very efficient search for protein alignment - VESPA. 702-707

Software News and Updates

• 
  Sergio Rampino, Noelia Faginas Lago, Antonio Laganà, Fermín Huarte-Larrañaga:
  An extension of the grid empowered molecular simulator to quantum reactive scattering. 708-714

Volume 33, Number 7, March 2012

Reviews

• 
  Wenjing Zhang, Yanyan Zhu, Donghui Wei, Mingsheng Tang:
  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

Full Papers

• 
  Michael E. Lasinski, Nichols A. Romero, Shawn T. Brown, Jean-Philippe Blaudeau:
  Recent performance improvements to the DFT and TDDFT in GAMESS. 723-731
• 
  Abolghasem Beheshti, Siavash Riahi, Mohammad Reza Ganjali, Parviz Norouzi:
  Highlighting and trying to overcome a serious drawback with qspr studies; data collection in different experimental conditions (mixed-QSPR). 732-747
• 
  Juan Andrés, Slawomir Berski, Luis R. Domingo, Patricio 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, Attila Farkas, Ari P. Seitsonen, Herbert Over:
  "First-Principles" kinetic monte carlo simulations revisited: CO oxidation over RuO₂(110). 757-766
• 
  Vladimír Sládek, Vladimír Lukes, Michal Ilcin, Stanislav Biskupic:
  Ab initio calculation of structure and transport properties of He...X (X = Zn, Cd, Hg) van der Waals complexes. 767-778
• 
  Maël Bosson, Caroline Richard, Antoine Plet, Sergei Grudinin, Stephane Redon:
  Interactive quantum chemistry: A divide-and-conquer ASED-MO method. 779-790
• 
  Sampath Koppole, Michael Schaefer:
  A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias. 791-799
• 
  Truong Ba Tai, Minh Tho Nguyen:
  Electronic structure and thermochemical properties of silicon-doped lithium clusters Li_nSi^0/+, n = 1-8: New insights on their stability. 800-809

Software News and Updates

• 
  Philipp Plessow, Florian Weigend:
  Seminumerical calculation of the Hartree-Fock exchange matrix: Application to two-component procedures and efficient evaluation of local hybrid density functionals. 810-816

Volume 33, Number 8, March 2012

Full Papers

• 
  Jiande Gu, Jing Wang, Yaoming Xie, Jerzy Leszczynski, 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, 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, Amalendu Chandra:
  Voids and necks in liquid ammonia and their roles in diffusion of ions of varying size. 843-852
• 
  Barbara Logan Mooney, L. René Corrales, Aurora E. Clark:
  MoleculaRnetworks: An integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation. 853-860
• 
  Cai-Hua Zhou, Xiang Zhao:
  Chemically modified fullerene derivatives as photosensitizers in photodynamic therapy: A first-principles study. 861-867

Software News and Updates

• 
  Ying Zhao, Antonio De Nicola, Toshihiro Kawakatsu, Giuseppe Milano:
  Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks. 868-880
• 
  Arnim Hellweg, Michael Diedenhofen, Uwe Huniar:
  thermocalc - A poor man's approach to computational thermochemistry. 881-886
• 
  R. Thomas Ullmann, G. Matthias Ullmann:
  GMCT : A Monte Carlo simulation package for macromolecular receptors. 887-900
• 
  André A. S. T. Ribeiro, Ricardo B. de Alencastro:
  Mixed monte carlo/molecular dynamics simulations in explicit solvent. 901-905
• 
  Ilya A. Balabin, Xiangqian Hu, David N. Beratan:
  Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD. 906-910

Letters to the Editor

• 
  Joop H. van Lenthe, H. B. Broer-Braam, Zahid Rashid:
  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, Yirong Mo:
  Reply to comment on the paper "An efficient Algorithm for Energy Gradients and Orbital Optimization in Valence Bond Theory". 914-915

Volume 33, Number 9, April 2012

Full Papers

• 
  Gleb Y. Solomentsev, Niall J. English, 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, Alexander Lukyanov, Kurt Kremer, Christine Peter:
  Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models. 937-949
• 
  Jeffrey S. Tan, Stephan X. M. Boerrigter, Raymond P. Scaringe, Kenneth R. Morris:
  Core-shell potential-derived point charges. 950-957
• 
  Gustavo L. C. Moura, Alfredo Mayall Simas:
  Quantum molecular mechanics - a noniterative procedure for the fast Ab Initio calculation of closed shell systems. 958-969
• 
  P. Nuno Palma, Maria João Bonifácio, Ana Isabel Loureiro, Patrício Soares-da-Silva:
  Computation of the binding affinities of catechol-O-methyltransferase inhibitors: Multisubstate relative free energy calculations. 970-986
• 
  Ch. Bheema Lingam, K. Ramesh Babu, Surya P. Tewari, G. Vaitheeswaran:
  Density functional study of electronic, bonding, and vibrational properties of Ca (NH₂BH₃)₂. 987-997
• 
  Shi-Bao Wang, Arvin Huang-Te Li, Sheng D. Chao:
  Liquid properties of dimethyl ether from molecular dynamics simulations using Ab Initio force fields. 998-1003
•