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
• 
  Hannes Kopitz, Daniel A. Cashman, Stefania Pfeiffer-Marek, Holger Gohlke:
  Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance-dependent dielectric model. 1004-1013

Volume 33, Number 10, April 2012

Full Papers

• 
  Valentina Cantatore, Giovanni Granucci, Maurizio Persico:
  Stochastic model for photoinduced anisotropy. 1015-1022
• 
  K. V. Turcheniuk, Alexander B. Rozhenko:
  (σ³, λ⁵)-phosphoranes versus (σ³_, λ³)-thiaphosphiranes: Quantum chemical investigation of products of phosphaalkene sulfurization. 1023-1028
• 
  Antonio Ricci, 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, Jing Wang, Zhao-Shuo Tian, Zai-Feng Xie, Fu-Quan Bai:
  Theoretical investigation on the photophysical properties of N-heterocyclic carbene iridium (III) complexes (fpmb)_xIr(bptz)_3-x (x = 1-2). 1038-1046
• 
  Sambath Baskaran, Masilamani Tamizmani, Thanigachalam Mahalakshmi, Chinnappan Sivasankar:
  A [Fe(CB₆)] platform for binding of small molecules: Insights from DFT calculations. 1047-1054
• 
  Ivo Cacelli, Antonella Cimoli, Paolo Roberto Livotto, Giacomo Prampolini:
  An automated approach for the parameterization of accurate intermolecular force-fields: Pyridine as a case study. 1055-1067
• 
  Emmanuel N. Koukaras, Aristides D. Zdetsis, Panaghiotis Karamanis, Claude Pouchan, Aggelos Avramopoulos, Manthos G. Papadopoulos:
  Structural and static electric response properties of highly symmetric lithiated silicon cages: Theoretical predictions. 1068-1079
• 
  Martin Dracínský, Petr Bour:
  Vibrational averaging of the chemical shift in crystalline α-glycine. 1080-1089

Volume 33, Number 11, April 2012

Full Papers

• 
  Angelo Domenico Quartarolo, Sandro Giuseppe Chiodo, Nino Russo:
  A TDDFT investigation of bay substituted perylenediimides: Absorption and intersystem crossing. 1091-1100
• 
  Riguang Zhang, Luzhi Song, Baojun Wang, Zhong Li:
  A density functional theory investigation on the mechanism and kinetics of dimethyl carbonate formation on Cu₂O catalyst. 1101-1110
• 
  Milan Randic, Damir Vukicevic, Alexandru T. Balaban, Marjan Vracko, Dejan Plavsic:
  Conjugated circuits currents in hexabenzocoronene and its derivatives formed by joining proximal carbons. 1111-1122
• 
  Robert A. Evarestov, Andrei V. Bandura:
  First-principles calculations on the four phases of BaTiO₃. 1123-1130
• 
  Asit K. Chandra, Thérèse Zeegers-Huyskens:
  A theoretical investigation of the interaction between substituted carbonyl derivatives and water: Open or cyclic complexes? 1131-1141
• 
  Timothy H. Click, Sergei Y. Ponomarev, George A. Kaminski:
  Importance of electrostatic polarizability in calculating cysteine acidity constants and copper(I) binding energy of Bacillus subtilis CopZ. 1142-1151
• 
  Alexander H. Boschitsch, Pavel V. Danilov:
  Formulation of a new and simple nonuniform size-modified poisson-boltzmann description. 1152-1164

Volume 33, Number 12, May 2012

Original Articles

• 
  Supriya Saha, Sougata Pal, Pranab Sarkar, A. L. Rosa, Thomas 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, Samuel Genheden, Karin Wichmann, Ulf Ryde:
  A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections. 1179-1189
• 
  Patrick Laflamme, Alexandre Beaudoin, Thomas Chapaton, Claude Spino, Armand Soldera:
  Simulated infrared spectra of triflic acid during proton dissociation. 1190-1196
• 
  Tibor András Rokob, Lubomír Rulísek:
  Curvature correction for microiterative optimizations with QM/MM electronic embedding. 1197-1206

Software News and Updates

• 
  René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C. Smith, K. Anton Feenstra:
  Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module. 1207-1214
• 
  Markus Wagener, Jacob de Vlieg, Sander B. Nabuurs:
  Flexible protein-ligand docking using the Fleksy protocol. 1215-1217
• 
  Alla P. Toropova, Andrey A. Toropov, Anna Lombardo, Alessandra Roncaglioni, Emilio Benfenati, Giuseppina C. Gini:
  Coral: QSAR models for acute toxicity in fathead minnow (Pimephales promelas). 1218-1223

Volume 33, Number 13, May 2012

Original Articles

• 
  You Lu, Zhenggang Lan, Walter Thiel:
  Monomeric adenine decay dynamics influenced by the DNA environment. 1225-1235
• 
  Marta González, Roi Álvarez Rodríguez, Maria Magdalena Cid, 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, Marcos Mandado:
  Chemical reactivity in the framework of pair density functional theories. 1240-1251
• 
  Deok-Soo Kim, Joonghyun Ryu, Hayong Shin, Youngsong Cho:
  Beta-decomposition for the volume and area of the union of three-dimensional balls and their offsets. 1252-1273

Full Papers

• 
  Jyh Shing Lin, Shao-Yu Lu, Po-Jung Tseng, Wen-Chi Chou:
  Temperature dependence of vibrational modes of CH3‒C≡C(ads) and I(ads) coadsorbed on Ag(111): Ab initio molecular dynamics approach. 1274-1283

Volume 33, Number 14, May 2012

Full Papers

• 
  Uttam Sinha Mahapatra, Sudip Chattopadhyay:
  Diagnosis of the performance of the state-specific multireference coupled-cluster method with different truncation schemes. 1285-1303
• 
  Peter Deglmann, Stephan Schenk:
  Thermodynamics of chemical reactions with COSMO-RS: The extreme case of charge separation or recombination. 1304-1320
• 
  Yanli Zeng, Min Zhu, Xiaoyan Li, Shijun Zheng, 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, Yihong Ding, Haiping Fang:
  Unexpectedly strong anion-π interactions on the graphene flakes. 1328-1337

Software News and Updates

• 
  Thiago C. F. Gomes, Munir S. Skaf:
  Cellulose-Builder: A toolkit for building crystalline structures of cellulose. 1338-1346

Volume 33, Number 15, June 2012

Full Papers

• 
  Feng Yu:
  Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center. 1347-1352
• 
  Shanshan Tang, 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, Alfred Uhlherr, Alan Dorin, David G. Green:
  Molecular dynamics extended for fluctuating networks: Application to water. 1364-1373
• 
  Ye Mei, Yong L. Li, Juan Zeng, 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

Software News and Updates

• 
  William B. Sherman:
  HolT Hunter: Software for identifying and characterizing low-strain DNA holliday triangles. 1393-1405

Volume 33, Number 16, June 2012

Original Articles

• 
  Jhon Zapata-Rivera, Rosa Caballol, Carmen Jiménez Calzado:
  The role of macrocyclic ligands in the peroxo/superoxo nature of Ni-O2 biomimetic complexes. 1407-1415
• 
  Chang G. Ji, John Z. H. Zhang:
  Effect of interprotein polarization on protein-protein binding energy. 1416-1420
• 
  Anan Wu, 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

Full Papers

• 
  Shuhui Lv, Xiaojuan Liu, Hongping Li, Lin Han, Zhongchang Wang, Jian Meng:
  Insulator-metal transition driven by pressure and B-site disorder in double perovskite La2CoMnO6. 1433-1439

Original Articles

• 
  Christopher J. R. Illingworth, Sree V. Chintapalli, Stefano A. Serapian, Andrew D. Miller, Vaclav Veverka, Mark D. Carr, Christopher A. Reynolds:
  The statistical significance of selected sense-antisense peptide interactions. 1440-1447

Full Papers

• 
  Hao Tang, Zhuo Li, Yu-Hong Yang, Ying Zhao, Su-Qin Wan, Hui-Ling Liu, Xu-Ri Huang:
  Comparison of the FeO2+ and FeS2+ complexes in the cyanide and isocyanide ligand environment for methane hydroxylation. 1448-1457
• 
  Pradip K. Biswas, Nadeem A. Vellore, Jeremy A. Yancey, Tugba G. Kucukkal, Galen Collier, Bernard R. Brooks, Steven J. Stuart, Robert A. Latour:
  Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. 1458-1466

Volume 33, Number 17, June 2012

Full Papers

• 
  Denise Steiner, Chris Oostenbrink, Wilfred F. van Gunsteren:
  Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. 1467-1477
• 
  Sergey Gusarov, Bhalchandra S. Pujari, Andriy Kovalenko:
  Efficient treatment of solvation shells in 3D 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, Thanisorn Yakhanthip, Yaowarat Surakhot, Janeeya Khunchalee, Taweesak Sudyoadsuk, Vinich Promarak, Nawee Kungwan, 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

Volume 33, Number 18, July 2012

Full Papers

• 
  David Gfeller, Olivier Michielin, Vincent Zoete:
  Expanding molecular modeling and design tools to non-natural sidechains. 1525-1535
• 
  Daniel J. Sindhikara, Norio Yoshida, 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, Wenlan Liu, Jens Pflaum, Reinhold F. Fink, Bernd Engels:
  Comparison of the electronic structure of different perylene-based dye-aggregates. 1544-1553
• 
  Andrei V. Bandura, Robert A. Evarestov:
  First-principles calculations on thermodynamic properties of BaTiO3 rhombohedral phase. 1554-1563
• 
  Keda Yang, Jiaye Su, Hongxia Guo:
  GPU accelerated numerical simulations of viscoelastic phase separation model. 1564-1571

Software News and Updates

• 
  Jussi Lehtola, Mikko Hakala, Arto Sakko, Keijo Hämäläinen:
  ERKALE - A flexible program package for X-ray properties of atoms and molecules. 1572-1585

Volume 33, Number 19, July 2012

Full Papers

• 
  Jing Wang, Jiande Gu, Jerzy Leszczynski:
  The electronic spectra and the H-bonding pattern of the sulfur and selenium substituted guanines. 1587-1593
• 
  Robert J. Buenker, Heinz-Peter Liebermann:
  Ab initio study of the positronation of the CaO and SrO molecules including calculation of annihilation rates. 1594-1602
• 
  Tomasz Berezniak, Andres Jäschke, Jeremy C. Smith, Petra Imhof:
  Stereoselection in the diels-alderase ribozyme: A molecular dynamics study. 1603-1614
• 
  John Kendrick, Frank J. J. Leusen, Marcus A. Neumann:
  Empirical van der Waals corrections to solid-state density functional theory: Iodine and phosphorous containing molecular crystals. 1615-1622
• 
  Chiara Panosetti, Werner A. Hofer:
  Adsorption of metadiiodobenzene on Cu(110): A theoretical study. 1623-1631

Software News and Updates

• 
  Semen O. Yesylevskyy:
  Pteros: Fast and easy to use open-source C++ library for molecular analysis. 1632-1636
• 
  R. Jeffrey Largent, William F. Polik, J. R. Schmidt:
  Symmetrizer: Algorithmic determination of point groups in nearly symmetric molecules. 1637-1642

Software News and Updates: Commentary

• 
  Benjamin P. Roberts, Gustavo de M. Seabra, Adrian E. Roitberg, Kenneth M. Merz Jr., Erik Deumens, Juan Torras, Samuel B. Trickey:
  Comment on "a minimal implementation of the AMBER-GAUSSIAN interface for Ab Initio QM/MM-MD simulation". 1643-1644

Volume 33, Number 20, July 2012

Full Papers

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

Volume 33, Number 21, August 2012

• 
  Pieter Chys, Pablo Chacón:
  Spinor product computations for protein conformations. 1717-1729
• 
  Jens Antony, Stefan Grimme:
  Fully ab initio protein-ligand interaction energies with dispersion corrected density functional theory. 1730-1739
• 
  Nikhil Taxak, Prashant V. Desai, Bhargav Patel, Michael Mohutsky, Valentine J. Klimkowski, Vijay Gombar, 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, Xavier López, Coen de Graaf, Nathalie Guihéry, Nicolas Suaud, Nadia Benamor:
  Rationalization of the behavior of M2(CH3CS2)4I (M = Ni, Pt) chains at room temperature from periodic density functional theory and ab initio cluster calculations. 1748-1761
• 
  D. Koley, E. Arunan, S. Ramakrishnan:
  Computational investigations on covalent dimerization/oligomerization of polyacenes: Is it relevant to soot formation? 1762-1772
• 
  Hongfang Yang, Qisheng Song, Xinyu Song, Yuxiang Bu:
  Multi-zinc-expanded graphene patches: Tetraradical versus diradical character. 1773-1780

Volume 33, Number 22, August 2012

Full Paper

• 
  Weihua Zhu, Qingli Yan, Jinshan Li, Bibo Cheng, Yuling Shao, Xuelan Xia, 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

Original Articles

• 
  Hui Liu, Fang Wang, Gui-Xiang Wang, Xuedong Gong:
  Theoretical investigations on structure, density, detonation properties, and sensitivity of the derivatives of PYX. 1790-1796
• 
  Andreas Dreuw, Matthias A. Polkehn, Robert Binder, Alexander Heckel, Stefan Knippenberg:
  Computational design of improved two-photon active caging compounds based on nitrodibenzofuran. 1797-1805
• 
  Massimiliano Bartolomei, Fernando Pirani, Antonio Laganà, Andrea Lombardi:
  A full dimensional grid empowered simulation of the CO2 + CO2 processes. 1806-1819

Original Article

• 
  Fang Wang, Hong-Chen Du, Hui Liu, Xuedong Gong:
  Density functional theory study of high-pressure effect on crystalline 4, 4′, 6, 6′-tetra(azido)hydrazo-1, 3, 5-triazine. 1820-1830

Original Articles

• 
  Luis Fernández Pacios, Cristina Gómez-Casado, Leticia Tordesillas, Arantxa Palacín, Rosa Sánchez-Monge, Araceli Díaz-Perales:
  Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes. 1831-1844

Volume 33, Number 23, September 2012

Full Papers

• 
  Hanna Kjær, Monia R. Nielsen, Gabriel I. Pagola, Marta B. Ferraro, Paolo Lazzeretti, Stephan P. A. Sauer:
  Nuclear magnetic resonance J coupling constant polarizabilities of hydrogen peroxide: A basis set and correlation study. 1845-1853
• 
  Guangfen Wu, Mingli Yang, Xingyu Guo, Jinlan Wang:
  Comparative DFT study of N2 and no adsorption on vanadium clusters Vn (n = 2-13). 1854-1861
• 
  Qunyan Wu, Chunmei Deng, Qian Peng, Yingli Niu, Zhigang Shuai:
  Quantum chemical insights into the aggregation induced emission phenomena: A QM/MM study for pyrazine derivatives. 1862-1869
• 
  Yulei Guan, Bolun Yang:
  Kinetics for the hydrogen-abstraction of CH4 with NO2. 1870-1879
• 
  Theresa J. Foster, Alexander D. MacKerell Jr., Olgun Guvench:
  Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. 1880-1891
• 
  Malin Uppsten, Bo Durbeej:
  Quantum chemical comparison of vertical, adiabatic, and 0-0 excitation energies: The PYP and GFP chromophores. 1892-1901

Software News and Updates

• 
  Andrey A. Toropov, Alla P. Toropova, Bakhtiyor F. Rasulev, Emilio Benfenati, Giuseppina C. Gini, Danuta Leszczynska, Jerzy Leszczynski:
  Coral: QSPR modeling of rate constants of reactions between organic aromatic pollutants and hydroxyl radical. 1902-1906

Volume 33, Number 24, September 2012

Full Papers

• 
  Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren, 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, Elena Bottizzo, Stefano Borocci, Maria Giordani, Felice Grandinetti:
  Gas-phase reactions of SiHn+ (n = 1, 2) with NF3: A computational investigation on the detailed mechanistic aspects. 1918-1926
• 
  Tae-Rae Kim, Sangho Oh, Joshua SungWoo Yang, Sanghyuk Lee, Seokmin Shin, 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, Silvia Ferrer, Vicent Moliner, Iñaki Tuñón, Juan Bertrán:
  Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution. 1948-1959

Software News and Updates

• 
  Chuan Li, Lin Li, Jie Zhang, Emil Alexov:
  Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. 1960-1966

Letters to the Editor

• 
  Kameron R. Jorgensen, Angela K. Wilson:
  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

Volume 33, Number 25, September 2012

Full Papers

• 
  Lu Zhang, Daniel-Adriano Silva, YiJing Yan, Xuhui Huang:
  Force field development for cofactors in the photosystem II. 1969-1980
• 
  Nail A. Gumerov, Konstantin Berlin, David Fushman, Ramani Duraiswami:
  A hierarchical algorithm for fast debye summation with applications to small angle scattering. 1981-1996
• 
  Vishal Maingi, Vaibhav Jain, Prasad V. Bharatam, Prabal K. Maiti:
  Dendrimer building toolkit: Model building and characterization of various dendrimer architectures. 1997-2011

Full Paper

• 
  Janus Juul Eriksen, Stephan P. A. Sauer, Kurt V. Mikkelsen, Hans Jorgen Aagard Jensen, Jacob Kongsted:
  On the importance of excited state dynamic response electron correlation in polarizable embedding methods. 2012-2022

Full Papers

• 
  Werner Reckien, Florian Janetzko, Michael F. Peintinger, Thomas Bredow:
  Implementation of empirical dispersion corrections to density functional theory for periodic systems. 2023-2031
• 
  Brent R. Wilson, Nathan J. DeYonker, Angela K. Wilson:
  Prediction of hydrocarbon enthalpies of formation by various thermochemical schemes. 2032-2042

Software News and Updates

• 
  Konrad Hinsen, Eric Pellegrini, Slawomir Stachura, Gerald R. Kneller:
  nMoldyn 3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations. 2043-2048

Volume 33, Number 26, October 2012

Full Papers

• 
  Otello Maria Roscioni, Edmond P. F. Lee, John M. Dyke:
  Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes. 2049-2057
• 
  Vitaly N. Glushkov, Xavier 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, Arpita Varadwaj, Gilles H. Peslherbe:
  An electronic structure theory investigation of the physical chemistry of the intermolecular complexes of cyclopropenylidene with hydrogen halides. 2073-2082
• 
  Franck Rabilloud:
  Structure and stability of coinage metal fluoride and chloride clusters (M_nF_n and M_nCl_n, M = Cu, Ag, or Au; n = 1-6). 2083-2091
• 
  Zdenek Futera, James A. Platts, Jaroslav V. Burda:
  Binding of piano-stool Ru(II) complexes to DNA; QM/MM study. 2092-2101
• 
  Claudia Wessel, Christoph Reimann, Alexander Müller, Dominik Weber, Martin Lerch, Thorsten Ressler, Thomas Bredow, Richard Dronskowski:
  Electronic structure and thermodynamics of V2O3 polymorphs. 2102-2107
• 
  Katharina Meier, Nathan Schmid, Wilfred F. van Gunsteren:
  Interfacing the GROMOS (bio)molecular simulation software to quantum-chemical program packages. 2108-2117
• 
  Luís Pinto Da Silva, Joaquim C. G. Esteves da Silva:
  Density functional theory study of 1, 2-dioxetanone decomposition in condensed phase. 2118-2123

Letters to the Editor

• 
  Daniel Roca-Sanjuán, Marcus Lundberg, David A. Mazziotti, Roland Lindh:
  Comment on "Density functional theory study of 1, 2-dioxetanone decomposition in condensed phase". 2124-2126
• 
  Luís Pinto Da Silva, Joaquim C. G. Esteves da Silva:
  Response to "comment on density functional theory study of 1, 2-dioxetanone decomposition in condensed phase". 2127-2130

Volume 33, Number 27, October 2012

Full Papers

• 
  Patrick C. Marais, Julian Kenwood, Keegan Carruthers Smith, Michelle Kuttel, James E. Gain:
  Efficient compression of molecular dynamics trajectory files. 2131-2141
• 
  Wenping Guo, Anan Wu, Igor Ying Zhang, Xin Xu:
  XO: An extended ONIOM method for accurate and efficient modeling of large systems. 2142-2160
• 
  Ruairidh S. Hunter, 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

Software News and Updates

• 
  Mario Ulises Delgado-Jaime, Serena DeBeer:
  Expedited analysis of DFT outputs: Introducing moanalyzer. 2180-2185
• 
  Thomas Weymuth, Moritz P. Haag, Karin Kiewisch, Sandra Luber, Stephan Schenk, Christoph R. Jacob, Carmen Herrmann, Johannes Neugebauer, Markus Reiher:
  MOVIPAC: Vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations. 2186-2198
• 
  Janez Konc, Matjaz Depolli, Roman Trobec, Kati Rozman, Dusanka Janezic:
  Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites. 2199-2203
• 
  Giovanni Garberoglio:
  OBGMX: A web-based generator of GROMACS topologies for molecular and periodic systems using the universal force field. 2204-2208

Errata

• 
  Edyta Malolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard N. Fejer, Joanne M. Carr, David J. Wales:
  Erratum: Symmetrization of the AMBER and CHARMM force fields [J. Comp. Chem. 31, 1402]. 2209
• 
  Shuntaro Chiba, Yuichi Harano, Roland Roth, Masahiro Kinoshita, Minoru Sakurai:
  Evaluation of protein-ligand binding free energy focused on its entropic components [J. Comp. Chem. 33, 550-560]. 2210

Volume 33, Number 28, October 2012

Full Papers

• 
  Chanda-Malis Ouk, Natalia Zvereva-Loëte, Yohann Scribano, Béatrice Bussery-Honvault:
  Transition state theory thermal rate constants and RRKM-based branching ratios for the N(2D) + CH4 reaction based on multi-sState and multi-reference Ab Initio calculations of interest for the titan's chemistry. 2211-2224
• 
  Maarten G. Wolf, 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, Claudio Greco, Roland Mitric, Vlasta Bonacic-Koutecký, Peter Saalfrank:
  BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study. 2233-2242
• 
  Jian Wang, Yu Wang, Jesus M. Ugalde:
  Electron-pair density decomposition for core-valence separable systems. 2243-2249
• 
  An Ghysels, Benjamin T. Miller, Frank C. Pickard IV, Bernard R. Brooks:
  Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. 2250-2275

Software News and Updates

• 
  Roberto Orlando, Massimo Delle Piane, Ian J. Bush, Piero Ugliengo, Matteo Ferrabone, Roberto Dovesi:
  A new massively parallel version of CRYSTAL for large systems on high performance computing architectures. 2276-2284

Volume 33, Number 29, November 2012

Full Papers

• 
  Orsolya Gereben, 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, Bruna L. Marcial, Juliana Fedoce Lopes, Wagner B. De Almeida, 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
• 
  Mikhail V. Vener, A. N. Egorova, Andrei V. Churakov, Vladimir G. Tsirelson:
  Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions. 2303-2309
• 
  Jirí Kessler, Milan Jakubek, Bohumil Dolenský, Petr Bour:
  Binding energies of five molecular pincers calculated by explicit and implicit solvent models. 2310-2317
• 
  Athanassios C. Tsipis, 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, Leonardo Guidoni:
  Quantum monte carlo study of the retinal minimal model C5H6NH2+. 2332-2339
• 
  Sushil Kumar Mishra, Johan Sund, Johan Åqvist, Jaroslav Koca:
  Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. 2340-2350
• 
  Siegfried Höfinger, Angela Acocella, Sergiu C. Pop, Tetsu Narumi, Kenji Yasuoka, Titus Beu, Francesco Zerbetto:
  GPU-accelerated computation of electron transfer. 2351-2356

Software News and Updates

• 
  Damien Farrell, Jens Erik Nielsen:
  DataPipeline: Automated importing and fitting of large amounts of biophysical data. 2357-2362

Volume 33, Number 30, November 2012

Feature Articles

• 
  Frank Weinhold:
  Natural bond orbital analysis: A critical overview of relationships to alternative bonding perspectives. 2363-2379

Full Papers

• 
  Marie L. Laury, Matthew J. Carlson, Angela K. Wilson:
  Vibrational frequency scale factors for density functional theory and the polarization consistent basis sets. 2380-2387
• 
  Ity Sharma, George A. Kaminski:
  Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order fuzzy-border continuum solvation model. 2388-2399
• 
  Patricio González-Navarrete, Luis R. Domingo, Juan Andrés, Slawomir Berski, 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, Alexander V. Yakubovich, Pavel V. Nikolaev, Ilya Volkovets, Andrey V. Solov'yov:
  MesoBioNano explorer - A universal program for multiscale computer simulations of complex molecular structure and dynamics. 2412-2439

Software News and Updates

• 
  Frank Weinhold:
  Natural bond critical point analysis: Quantitative relationships between natural bond orbital-based and QTAIM-based topological descriptors of chemical bonding. 2440-2449

Volume 33, Number 31, December 2012

Full Papers

• 
  Wenbo Yu, Xibing He, Kenno Vanommeslaeghe, 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, Kenneth Jung, David Baker:
  Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. 2483-2491
• 
  Abu Md. Asaduzzaman, Guy A. G. Chappellaz, Georg Schreckenbach:
  Relationship between dye-iodine binding and cell voltage in dye-sensitized solar cells: A quantum-mechanical look. 2492-2497
• 
  Bu-Tong Li, Zi-Zhang Wei, Hai-Shun Wu:
  The valence and Rydberg excited states of CH₂: A theoretical exploration. 2498-2503
• 
  Johannes Flick, Frank Tristram, Wolfgang Wenzel:
  Modeling loop backbone flexibility in receptor-ligand docking simulations. 2504-2515
• 
  Yunqing Han, Tianxiang Li, Kozo Saito:
  Comprehensive method based on model free method and IKP method for evaluating kinetic parameters of solid state reactions. 2516-2525

Software News and Updates

• 
  David Vega, Yosslen Aray, Jesús Rodríguez:
  C library for topological study of the electronic charge density. 2526-2531

Volume 33, Number 32, December 2012

Full Papers

• 
  David Ferro-Costas, Nicolás Otero, Ana M. Graña, Ricardo A. Mosquera:
  A QTAIM-based energy partitioning for understanding the physical origin of conformational preferences: Application to the Z effect in O=C-X-R and related units. 2533-2543
• 
  Yulia N. Kalugina, Mikhail A. Buldakov, Victor N. Cherepanov:
  Static hyperpolarizability of the van der Waals complex CH₄‒N₂. 2544-2553

Original Article

• 
  Lennart Heinzerling, Robert Klein, Matthias Rarey:
  Fast force field-based optimization of protein-ligand complexes with graphics processor. 2554-2565

Full Papers

• 
  Daniel P. Oehme, Robert T. C. Brownlee, 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, Ani Anciaux-Sedrakian, Xavier Rozanska, Diego Klahr, Thomas Guignon, Paul Fleurat-Lessard:
  Accelerating VASP electronic structure calculations using graphic processing units. 2581-2589
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  Amanda G. Riojas, Joshua R. John, T. Gavin Williams, Angela K. Wilson:
  Proton affinities of deoxyribonucleosides via the ONIOM-ccCA methodology. 2590-2601

Software News and Updates

• 
  Timo Strunk, Moritz Wolf, Martin Brieg, Konstantin V. Klenin, A. Biewer, Frank Tristram, Matthias Ernst, P. J. Kleine, N. Heilmann, Ivan Kondov, Wolfgang Wenzel:
  SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems. 2602-2613