Journal of Computational Chemistry, Volume 34

Volume 34, Number 1, January 2013

Editorials

• 
  Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, Peter R. Schreiner:
  New paint and a new engine. 1

Full Papers

• 
  Mark Pinsky, Amir Zait, Maayan Bonjack, David Avnir:
  Continuous symmetry analyses: C_nv and D_n measures of molecules, complexes, and proteins. 2-9
• 
  Susanne Pape, Franziska Hoffgaard, Mirjam Dür, Kay Hamacher:
  Distance dependency and minimum amino acid alphabets for decoy scoring potentials. 10-20
• 
  Toru Matsui, Yasutaka Kitagawa, Mitsutaka Okumura, Yasuteru Shigeta, Shigeyoshi Sakaki:
  Consistent scheme for computing standard hydrogen electrode and redox potentials. 21-26
• 
  Andriy Samsonyuk, Christoph Scheurer:
  Configuration space partitioning and matrix buildup scaling for the vibrational configuration interaction method. 27-37
• 
  Jinshuai Song, Zhenhua Chen, Sason Shaik, Wei Wu:
  An efficient algorithm for complete active space valence bond self-consistent field calculation. 38-48
• 
  J. Drujon, Yannick Carissan:
  Pseudopotentials for hybridized carbon atoms. 49-59
• 
  Jin Yang, Paul J. Dauenhauer, Ashwin Ramasubramaniam:
  The role of water in the adsorption of oxygenated aromatics on Pt and Pd. 60-66
• 
  Yu Liu, Lei Zhao, Wentao Li, Dongyu Zhao, Miao Song, Yongliang Yang:
  FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm. 67-75

Volume 34, Number 2, January 2013

Full Papers

• 
  Milan Randic:
  Very efficient search for nucleotide alignments. 77-82
• 
  Yutaka Uejima, Ryo Maezono:
  GPGPU for orbital function evaluation with a new updating scheme. 83-94
• 
  Yutong Zhao, Fu Kit Sheong, Jian Sun, Pedro Sander, Xuhui Huang:
  A fast parallel clustering algorithm for molecular simulation trajectories. 95-104
• 
  Paul Mach, Patrice Koehl:
  An analytical method for computing atomic contact areas in biomolecules. 105-120
• 
  Yuan Liu, Jijun Zhao, Fengyu Li, Zhongfang Chen:
  Appropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methods. 121-131
• 
  Yannick G. Spill, Guillaume Bouvier, Michael Nilges:
  A convective replica-exchange method for sampling new energy basins. 132-140
• 
  Eric A. C. Bushnell, 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, Nobuaki Koga:
  Variationally determined electronic states for the theoretical analysis of intramolecular interaction. II. Qualitative nature of the P‒O bond in phosphine oxides. 149-161

Volume 34, Number 3, January 2013

Full Papers

• 
  Yang Zhong, Sandeep Patel:
  Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field. 163-174
• 
  Robert A. Evarestov, Andrei V. Bandura, Dmitrii D. Kuruch:
  BaTiO₃-based nanolayers and nanotubes: First-principles calculations. 175-186
• 
  Joakim P. M. Jämbeck, Francesca Mocci, Alexander Lyubartsev, Aatto Laaksonen:
  Partial atomic charges and their impact on the free energy of solvation. 187-197
• 
  Hiroshi C. Watanabe, Marcus Elstner, 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, Sebastian Radestock, Elena Schmidt, Holger Gohlke:
  Global and local indices for characterizing biomolecular flexibility and rigidity. 220-233
• 
  Josep M. Porta, Leonard Jaillet:
  Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation. 234-244
• 
  Elijah Roberts, John E. Stone, Zaida Luthey-Schulten:
  Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. 245-255

Erratum

• 
  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 [J. Comp. Chem. 33, 1440-1447]. 256
• 
  Paola Antoniotti, Elena Bottizzo, Stefano Borocci, Maria Giordani, Felice Grandinetti:
  Gas-phase reactions of SiH_n⁺ (n = 1, 2) with NF₃: A computational investigation on the detailed mechanistic aspects [J. Comp. Chem. 33, 1918-1926]. 257

Volume 34, Number 4, February 2013

Full Papers

• 
  Stephen J. Barigye, Yovani Marrero-Ponce, Yoan Martínez López, Francisco Torrens, Luis Manuel Artiles-Martínez, Ricardo W. Pino-Urias, Oscar Martínez Santiago:
  Relations frequency hypermatrices in mutual, conditional and joint entropy-based information indices. 259-274
• 
  Angelika Baranowska-Laczkowska, Berta Fernández, Robert Zalesny:
  New basis sets for the evaluation of interaction-induced electric properties in hydrogen-bonded complexes. 275-283
• 
  Li Yang, Alauddin Ahmed, Stanley I. Sandler:
  Comparison of two simulation methods to compute solvation free energies and partition coefficients. 284-293
• 
  Lukasz Piekos, Mariusz Pawel Mitoraj:
  Theoretical description of dihydrogen/hydride and trihydride molybdocene complexes: An insight from static and molecular dynamics simulations. 294-304
• 
  Hongguang Liu, Jin Yong Lee:
  Electric field assisted oxygen removal from the basal plane of the graphitic material. 305-310
• 
  Sheng-You Huang, Xiaoqin Zou:
  A nonredundant structure dataset for benchmarking protein-RNA computational docking. 311-318

Software News and Updates

• 
  Alexander V. Popov, Yury N. Vorobjev, Dmitry O. Zharkov:
  MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface. 319-325
• 
  Xuchang Ouyang, Shuo Zhou, Chinh Tran To Su, Zemei Ge, Runtao Li, Chee Keong Kwoh:
  CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints. 326-336

Volume 34, Number 5, February 2013

Full Papers

• 
  Pawel Malyszek, Jacek Koput:
  Accurate Ab initio potential energy surface and vibration-rotation energy levels of hydrogen peroxide. 337-345
• 
  Alessandro Erba, Matteo Ferrabone, Roberto Orlando, Roberto Dovesi:
  Accurate dynamical structure factors from ab initio lattice dynamics: The case of crystalline silicon. 346-354
• 
  Gonzalo Astray, Juan F. Gálvez, Juan C. Mejuto, Oscar A. Moldes, Iago Montoya:
  Esters flash point prediction using artificial neural networks. 355-359
• 
  Hongmei Liu, Hongbo Wang, Jianwei Zhao, Manabu Kiguchi:
  Molecular rectification in triangularly shaped graphene nanoribbons. 360-365
• 
  Jirí Kessler, Martin Dracínský, Petr Bour:
  Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties. 366-371
• 
  Binju Wang, Zexing Cao:
  How water molecules modulate the hydration of CO₂ in water solution: Insight from the cluster-continuum model calculations. 372-378
• 
  Raman K. Singh, Takao Tsuneda:
  Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions. 379-386
• 
  Zhixiong Lin, 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, Kumar Vanka:
  Solving the problem of negative populations in approximate accelerated stochastic simulations using the representative reaction approach. 394-404
• 
  Danny E. P. Vanpoucke, Patrick Bultinck, Isabel Van Driessche:
  Extending Hirshfeld-I to bulk and periodic materials. 405-417

Letters to the Editor

• 
  Thomas A. Manz:
  Comment on "Extending hirshfeld-i to bulk and periodic materials". 418-421
• 
  Danny E. P. Vanpoucke, Isabel Van Driessche, Patrick Bultinck:
  Reply to 'comment on "extending hirshfeld-I to bulk and periodic materials"'. 422-427

Volume 34, Number 6, March 2013

Full Papers

• 
  Louis P. Lee, Daniel J. Cole, Mike C. Payne, Chris-Kriton Skylaris:
  Natural bond orbital analysis in the ONETEP code: Applications to large protein systems. 429-444
• 
  Mohsen Chitsaz, Stephen L. Mayo:
  GRID: A high-resolution protein structure refinement algorithm. 445-450
• 
  Michael F. Peintinger, Daniel Vilela Oliveira, Thomas Bredow:
  Consistent gaussian basis sets of Triple-Zeta valence with polarization quality for solid-State Calculations. 451-459
• 
  János Pipek, Szilvia Nagy:
  An economic prediction of refinement coefficients in wavelet-based adaptive methods for electron structure calculations. 460-465
• 
  Jack Yang, Mark P. Waller:
  Revealing noncovalent interactions in quantum crystallography: Taurine revisited. 466-470
• 
  Soumya Ganguly Neogi, 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, Sergei Grudinin, Stephane Redon:
  Block-adaptive quantum mechanics: An adaptive divide-and-conquer approach to interactive quantum chemistry. 492-504
• 
  Jorge M. C. Marques, Francisco Baptista Pereira:
  A detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy. 505-517

Software News and Updates

• 
  David D. Jenkins, Jason B. Harris, Elizabeth E. Howell, Robert J. Hinde, Jérôme Baudry:
  STAAR: Statistical analysis of aromatic rings. 518-522

Volume 34, Number 7, March 2013

Full Papers

• 
  Ananth P. Kaushik, Paulette Clancy:
  Solvent-driven symmetry of self-assembled nanocrystal superlattices - A computational study. 523-532
• 
  Vladimir V. Rybkin, Anton O. Simakov, Vebjørn Bakken, Simen Reine, Thomas Kjærgaard, Trygve Helgaker, 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, Daniel K. W. Mok, Edmond P. F. Lee, John M. Dyke:
  Rate coefficients of the CF₃CHFCF₃ + H → CF₃CFCF₃ + H₂ reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths. 545-557
• 
  Shelley A. Smith, Karen E. Hand, Melissa L. Love, Glake Hill, David H. Magers:
  Conventional strain energies of azetidine and phosphetane: Can density functional theory yield reliable results? 558-565
• 
  Jianan Wang, Jun-Ling Jin, Yun Geng, Shiling Sun, Hong-Liang Xu, Ying-Hua Lu, Zhongmin Su:
  An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes. 566-575
• 
  Bradley Scott Perrin Jr., Shuqiang Niu, Toshiko Ichiye:
  Calculating standard reduction potentials of [4Fe-4S] proteins. 576-582
• 
  Mingyue Zheng, Yanlian Li, Bing Xiong, Hualiang Jiang, Jingkang Shen:
  Water PMF for predicting the properties of water molecules in protein binding site. 583-592
• 
  Jihyun Shim, Xiao Zhu, Robert B. Best, Alexander D. MacKerell Jr.:
  (Ala)₄-X-(Ala)₄ as a model system for the optimization of the χ₁ and χ₂ amino acid side-chain dihedral empirical force field parameters. 593-603

Software News and Updates

• 
  Yuye He, Chin Yee Liew, Nitin Sharma, Sze Kwang Woo, Yi Ting Chau, Chun Wei Yap:
  PaDEL-DDPredictor: Open-source software for PD-PK-T prediction. 604-610

Volume 34, Number 8, March 2013

Full Papers

• 
  Marcus V. P. dos Santos, Eduardo C. Aguiar, João Bosco P. Da Silva, Ricardo L. Longo:
  PICVib: An accurate, fast, and simple procedure to investigate selected vibrational modes at high theoretical levels. 611-621
• 
  Satoru G. Itoh, Hisashi Okumura:
  Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules. 622-639

Full Paper

• 
  Ning Ma, Ying-Hua Chung, Arjan van der Vaart:
  Free energy simulation of helical transitions. 640-645

Full Papers

• 
  Goran Kovacevic, Aleksandar Sabljic:
  Theoretical study on the mechanism and kinetics of addition of hydroxyl radicals to fluorobenzene. 646-655
• 
  Drahomír Hnyk, Elambalassery G. Jayasree:
  Cationic Closo-carboranes 2. Do computed ¹¹B and ¹³C NMR chemical shifts support their experimental availability? 656-661
• 
  Soumen Saha, Rituparna Bhattacharjee, Ram Kinkar Roy:
  Hardness potential derivatives and their relation to fukui indices. 662-672
• 
  Jian-Dong Zhang, Shu-Jin Li, 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, Jaehun Chun, Zhan Chen, Guo-Wei Wei, Nathan A. Baker:
  Parameterization of a geometric flow implicit solvation model. 687-695
• 
  Halina Szatylowicz, Tadeusz Marek Krygowski, Célia Fonseca Guerra, F. Matthias Bickelhaupt:
  Complexes of 4-substituted phenolates with HF and HCN: Energy decomposition and electronic structure analyses of hydrogen bonding. 696-705

Volume 34, Number 9, April 2013

Full Papers

• 
  Florent Réal, Michael Trumm, Bernd Schimmelpfennig, Michel Masella, 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, Themis Lazaridis:
  Membrane protein native state discrimination by implicit membrane models. 731-738
• 
  Jin Yu Xiang, 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, Marcin Hoffmann, Aneta Kuron, Malgorzata Korycka-Machala, Jaroslaw Dziadek:
  The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics. 750-756
• 
  Jia-Lin Chang, Cyong-Huei Huang, Sue-Chang Chen, Tsung-Hao Yin, 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, Slawomir Berski, Sergio Martí, Juan Andrés:
  New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis. 780-789
• 
  Nikola Minovski, Andrej Perdih, Marjana Novic, Tomaz Solmajer:
  Cluster-based molecular docking study for in silico identification of novel 6-fluoroquinolones as potential inhibitors against mycobacterium tuberculosis. 790-801

Volume 34, Number 10, April 2013

Full Papers

• 
  Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva:
  Acceleration of coarse grain molecular dynamics on GPU architectures. 803-818
• 
  Angelika Baranowska-Laczkowska, Wojciech Bartkowiak, Robert W. Góra, Filip Pawlowski, Robert Zalesny:
  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 π-conjugated molecules. 819-826
• 
  Ole Schütt, Daniel Sebastiani:
  Spectroscopic fingerprints of toroidal nuclear quantum delocalization via Ab Initio path integral simulations. 827-835
• 
  Thomas Simonson, Priyadarshi Satpati:
  Simulating GTP: Mg and GDP: Mg with a simple force field: A structural and thermodynamic analysis. 836-846
• 
  Juan Zeng, LiLi Duan, John Z. H. Zhang, 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, Evert Jan Baerends:
  Assessment of density functional methods for reaction energetics: Iridium-catalyzed water oxidation as case study. 870-878
• 
  Yoonjoo Choi, Karl E. Griswold, Chris Bailey-Kellogg:
  Structure-based redesign of proteins for minimal T-cell epitope content. 879-891

Volume 34, Number 11, April 2013

Full Papers

• 
  Jennifer L. Knight, Joseph D. Yesselman, Charles L. Brooks III:
  Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. 893-903
• 
  Jeffrey R. Wagner, Gouthaman S. Balaraman, Michiel J. M. Niesen, Adrien B. Larsen, Abhinandan Jain, Nagarajan Vaidehi:
  Advanced techniques for constrained internal coordinate molecular dynamics. 904-914
• 
  Xiaohua Zhang, Sergio E. Wong, 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, Heinz-Peter Liebermann, Yu Zhang, Yong Wu, Lingling Yan, Chunhua Liu, Yizhi Qu, Jianguo Wang:
  Adjustment of born-oppenheimer electronic wave functions to simplify close coupling calculations. 928-937
• 
  Anthony Scemama, Michel Caffarel, Emmanuel Oseret, William Jalby:
  Quantum monte carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond. 938-951
• 
  Heng-Qing Wu, Rong-Lin Zhong, Yu-He Kan, Shiling Sun, Min Zhang, Hong-Liang Xu, Zhongmin Su:
  After the electronic field: Structure, bonding, and the first hyperpolarizability of HArF. 952-957
• 
  Rahul Kar, Jong-Won Song, Kimihiko Hirao:
  Long-range corrected functionals satisfy Koopmans' theorem: Calculation of correlation and relaxation energies. 958-964

Software News and Updates

• 
  Nadine Homeyer, Holger Gohlke:
  FEW: A workflow tool for free energy calculations of ligand binding. 965-973
• 
  Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhenmin Tang, Jing-Yu Yang:
  TargetATPsite: A template-free method for ATP-binding sites prediction with residue evolution image sparse representation and classifier ensemble. 974-985

Volume 34, Number 12, May 2013

Full Papers

• 
  Karina Kornobis, Neeraj Kumar, Piotr Lodowski, Maria Jaworska, Piotr Piecuch, Jesse J. Lutz, Bryan M. Wong, Pawel M. Kozlowski:
  Electronic structure of the S₁ state in methylcobalamin: Insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations. 987-1004
• 
  Yanliang Ren, Bo Chi, Osama Melhem, Ke Wei, Lingling Feng, Yongjian Li, Xinya Han, Ding Li, Ying Zhang, Jian Wan, Xin Xu, 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, 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, Stefan Boresch, Chris Oostenbrink:
  Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies. 1024-1034
• 
  Martin Rohrmüller, Sonja Herres-Pawlis, Matthias Witte, Wolf Gero Schmidt:
  Bis-μ-oxo and μ-η²: η²-peroxo dicopper complexes studied within (time-dependent) density-functional and many-body perturbation theory. 1035-1045
• 
  Zhanghui Chen, Xiangwei Jiang, Jingbo Li, Shu-Shen Li, Linwang Wang:
  PDECO: Parallel differential evolution for clusters optimization. 1046-1059
• 
  Debashree Ghosh, Dmytro Kosenkov, Vitalii Vanovschi, Joanna Flick, Ilya Kaliman, Yihan Shao, Andrew T. B. Gilbert, Anna I. Krylov, Lyudmila V. Slipchenko:
  Effective fragment potential method in Q-CHEM: A guide for users and developers. 1060-1070

Software News and Updates

• 
  Kunal Roy, Pratim Chakraborty, Indrani Mitra, Probir Kumar Ojha, Supratik Kar, Rudra Narayan Das:
  Some case studies on application of "r_m²" metrics for judging quality of quantitative structure-activity relationship predictions: Emphasis on scaling of response data. 1071-1082

Volume 34, Number 13, May 2013

Full Papers

• 
  Jeremy P. Coe, Daniel J. Taylor, Martin J. Paterson:
  Monte carlo configuration interaction applied to multipole moments, ionisation energies and electron affinities. 1083-1093
• 
  Liudmyla K. Sviatenko, Leonid Gorb, Frances Hill, Jerzy Leszczynski:
  Theoretical study of ionization and one-electron oxidation potentials of N-heterocyclic compounds. 1094-1100
• 
  Rui Yang, Alistair P. Rendell:
  First principles study of gallium cleaning for hydrogen-contaminated α-Al₂O₃(0001) surfaces. 1101-1111
• 
  Michel Masella, Daniel Borgis, Philippe Cuniasse:
  A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics. 1112-1124
• 
  Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard G. Maroun, 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, Chang G. Ji, Dai Q. Xie, John Z. H. Zhang:
  Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. 1136-1142
• 
  Eldhose Iype, Markus Hütter, A. P. J. Jansen, Silvia V. Nedea, C. C. M. Rindt:
  Parameterization of a reactive force field using a monte carlo algorithm. 1143-1154

Software news and updates

• 
  Torsten Kerber,