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ORCIDJournal 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 Cn- (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
- Wolf-Dietrich Ihlenfeldt:
Comment on the paper "indexing molecules with chemical graph Identifiers" by Elisabeth Gregori-Puigjané, Rut Garriga-Sust, and Jordi Mestres. 237
- 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
- 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
- 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
- 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, Z. Y. 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 SN2 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
- 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
- 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, Clemence Corminboeuf:
Identifying clusters as low-lying mimina - efficiency of stochastic and genetic algorithms using inexpensive electronic structure levels. 502-508 - Israel Fernández, F. Matthias Bickelhaupt:
Alder-ene reaction: Aromaticity and activation-strain analysis. 509-516 - Shuming Zhang:
A reliable and efficient first principles-based method for predicting pKa values. III. Adding explicit water molecules: Can the theoretical slope be reproduced and pKa 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
- Tian Lu, Feiwu Chen:
Multiwfn: A multifunctional wavefunction analyzer. 580-592
- 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
- Jun-Xi Liang, Zhi-Yuan Geng, Yong-Cheng Wang:
Density functional study of SN2 substitution reactions for CH3Cl + CX1X2•- (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
- 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
- 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
- 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 LinSi0/+, n = 1-8: New insights on their stability. 800-809
- 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
- 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
- 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
- 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
- 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