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ORCIDJournal of Computational Chemistry, Volume 34
Volume 34, Number 1, January 2013
- Charles L. Brooks III, Masahiro Ehara
, Gernot Frenking, Peter R. Schreiner:
New paint and a new engine. 1
- Mark Pinsky, Amir Zait, Maayan Bonjack, David Avnir:
Continuous symmetry analyses: Cnv and Dn 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
- 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 V. 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
- 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
- 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 SiHn+ (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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Ning Ma, Ying-Hua Chung, Arjan van der Vaart:
Free energy simulation of helical transitions. 640-645
- 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, Guowei Wei, Nathan A. Baker:
Parameterization of a geometric flow implicit solvation model. 687-695 - Halina Szatylowicz, Tadeusz Marek Krygowski, Célia Fonseca Guerra, Friedrich 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
- 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
- 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
- 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 Ernesto 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
- 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
- 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
- Kunal Roy, Pratim Chakraborty, Indrani Mitra, Probir Kumar Ojha, Supratik Kar, Rudra Narayan Das:
Some case studies on application of "rm2" metrics for judging quality of quantitative structure-activity relationship predictions: Emphasis on scaling of response data. 1071-1082
Volume 34, Number 13, May 2013
- 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