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ORCIDJournal of Computational Chemistry, Volume 30
Volume 30, Number 1, 15 January 2009
- Gernot Frenking, Charles L. Brooks III, Shigeyoshi Sakaki:
Editors' note. 1 - Vincenzo Barone, Mirco Zerbetto, Antonino Polimeno:
Hydrodynamic modeling of diffusion tensor properties of flexible molecules. 2-13 - Olga Yuzlenko, Katarzyna Kiec-Kononowicz
:
Molecular modeling of A1 and A2A adenosine receptors: Comparison of rhodopsin- and beta2-adrenergic-based homology models through the docking studies. 14-32 - Bing Niu, Lin Lu, Liang Liu, Tian Hong Gu, Kai-Yan Feng, Wen-Cong Lu, Yu-Dong Cai:
HIV-1 protease cleavage site prediction based on amino acid property. 33-39 - Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano:
Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation. 40-50 - Bryan M. Wong:
Noncovalent interactions in supramolecular complexes: A study on corannulene and the double concave buckycatcher. 51-56 - Matthew A. Addicoat, Gregory F. Metha:
Kick: Constraining a stochastic search procedure with molecular fragments. 57-64 - Lukás Bucinský, Stanislav Biskupic, Michal Ilcin, Vladimír Lukes, Viliam Laurinc:
On relativistic effects in ground state potential curves of Zn2, Cd2, and Hg2 dimers. A CCSD(T) study. 65-74 - Daniel Escudero, Antonio Frontera, David Quiñonero, Pere M. Deyà:
Interplay between anion-pi and hydrogen bonding interactions. 75-82 - Wissam Helal, Stefano Evangelisti, Thierry Leininger, Daniel Maynau:
Ab-initio multireference study of an organic mixed-valence Spiro molecular system. 83-92 - Weiyang Chen, Bo Liao, Wen Zhu, Hao Liu, Qingguang Zeng:
An ant colony pairwise alignment based on the dot plots. 93-97 - Ángel Martín Pendás, M. A. Blanco, Evelio Francisco:
Steric repulsions, rotation barriers, and stereoelectronic effects: A real space perspective. 98-109 - Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa:
Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. 110-118 - A. S. Zyubin, A. M. Mebel, Michitoshi Hayashi, Huan-Cheng Chang, S. H. Lin:
Quantum chemical modeling of photoadsorption properties of the nitrogen-vacancy point defect in diamond. 119-131 - Michael D. Altman, Jaydeep P. Bardhan, Jacob K. White, Bruce Tidor:
Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements. 132-153 - Nikolaj Otte, Marco Bocola, Walter Thiel:
Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases. 154-162 - Ke Chen, Yingfu Jiang, Li Du, Lukasz A. Kurgan:
Prediction of integral membrane protein type by collocated hydrophobic amino acid pairs. 163-172
Volume 30, Number 2, 30 January 2009
- Juan Manuel Ramírez-Anguita, Àngels González-Lafont, José M. Lluch:
Formation pathways of DMSO from DMS-OH in the presence of O2 and NOx: A theoretical study. 173-182 - Wen Lai Huang, Qingshan Zhu:
DFT calculations on the electronic structures of BiOX (X = F, Cl, Br, I) photocatalysts with and without semicore Bi 5d states. 183-190 - Dmitri V. Sakharov, Carmay Lim:
Force fields including charge transfer and local polarization effects: Application to proteins containing multi/heavy metal ions. 191-202 - Artur Galstyan, Ernst-Walter Knapp:
Accurate redox potentials of mononuclear iron, manganese, and nickel model complexes. 203-211 - Chris Oostenbrink:
Efficient free energy calculations on small molecule host-guest systems - A combined linear interaction energy/one-step perturbation approach. 212-221 - Anmin Zheng, Shang-Bin Liu, Feng Deng:
13C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models. 222-235 - Hui Zhang, Guiling Zhang, Jing-Yao Liu, Miao Sun, Bo Liu, Ze-Sheng Li:
Theoretical study on the reaction of SiH(CH3)3 with SiH3 radical. 236-242 - Alexey Aleksandrov, Thomas Simonson:
Molecular mechanics models for tetracycline analogs. 243-255 - Xiaolei Zhu, Luhua Lai:
A novel method for enzyme design. 256-267 - Edgar Luttmann, Daniel L. Ensign, Vaidyanathan Vishal, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark S. Friedrichs, Vijay S. Pande:
Accelerating molecular dynamic simulation on the cell processor and Playstation 3. 268-274 - Albert Poater, Ana Gallegos Saliner, Ramon Carbó-Dorca, Jordi Poater, Miquel Solà, Luigi Cavallo, Andrew P. Worth:
Modeling the structure-property relationships of nanoneedles: A journey toward nanomedicine. 275-284 - Chao Deng, Xiao-Peng Wu, Xiao-Ming Sun, Yi Ren, Ying-Hong Sheng:
Neutral hydrolyses of carbon disulfide: An ab initio study of water catalysis. 285-294 - Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Zong-Wen Pang, Li-Qin Du, Kuo-Chen Chou:
Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design. 295-304
- Li-Ping Ju, Ke-Li Han, John Z. H. Zhang:
Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions. 305-316 - Jon Baker, Krzysztof Wolinski, Massimo Malagoli, Don Kinghorn, Pawel Wolinski, Gábor Magyarfalvi, Svein Saebo, Tomasz Janowski, Peter Pulay:
Quantum chemistry in parallel with PQS. 317-335
Volume 30, Number 3, February 2009
- Edmond P. F. Lee, Daniel K. W. Mok, Foo-Tim Chau, John M. Dyke:
A combined ab initio and Franck-Condon factor simulation study on the photodetachment spectrum of ScO2-. 337-345 - Ján Busa, Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Ming-Chya Wu:
Enveloping triangulation method for detecting internal cavities in proteins and algorithm for computing their surface areas and volumes. 346-357 - Yi Ren, Hiroshi Yamataka:
Does alpha-effect exist in E2 reactions? A G2(+) investigation. 358-365 - Ivo Cacelli, Carlo Federico Lami, Giacomo Prampolini:
Force-field modeling through quantum mechanical calculations: Molecular dynamics simulations of a nematogenic molecule in its condensed phases. 366-378 - António J. C. Varandas:
Møller-Plesset perturbation energies and distances for HeC20 extrapolated to the complete basis set limit. 379-388 - Al Mokhtar Lamsabhi, Otilia Mó, Soledad Gutiérrez-Oliva, Patricia Pérez, Alejandro Toro-Labbé, Manuel Yáñez:
The mechanism of double proton transfer in dimers of uracil and 2-thiouracil - The reaction force perspective. 389-398 - Lingchun Song, Jinshuai Song, Yirong Mo, Wei Wu:
An efficient algorithm for energy gradients and orbital optimization in valence bond theory. 399-406 - Wan-Chun Cheng, Soonmin Jang, Chen-Chang Wu, Ren-Jie Lin, Hsiu-Feng Lu, Feng-Yin Li:
Site specificity of the alphaC-H bond dissociation energy for a naturally occurring beta-hairpin peptide - An ab initio study. 407-414 - C. Mediavilla, José Tortajada, V. G. Baonza:
Modeling high pressure reactivity in unsaturated systems: Application to dimethylacetylene. 415-422 - Yinglong Miao, Peter J. Ortoleva:
Molecular dynamics/order parameter extrapolation for bionanosystem simulations. 423-437 - Li-Qin Xue, Xian-Yong Pang, Gui-Chang Wang:
Selective oxidation of styrene on an oxygen-adsorbed Au(111): A density functional theory study. 438-446 - Maik Goette, Helmut Grubmüller:
Accuracy and convergence of free energy differences calculated from nonequilibrium switching processes. 447-456 - Loukas Petridis, Jeremy C. Smith:
A molecular mechanics force field for lignin. 457-467 - Cristopher Camacho, Henryk A. Witek, Shigeyoshi Yamamoto:
Intruder states in multireference perturbation theory: The ground state of manganese dimer. 468-478 - Stephan Frickenhaus, Srinivasaraghavan Kannan, Martin Zacharias:
Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping. 479-492 - Hao Zhang, Yun-Hong Zhang, Feng Wang:
Theoretical understanding on the v1-SO42- band perturbed by the formation of magnesium sulfate ion pairs. 493-503
Volume 30, Number 4, March 2009
- Rong Wang, Jian-Sheng Wang, Gui-Rong Liu, Jongyoon Han, Yuzong Chen:
Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse-grained hybrid molecular dynamics approach. 505-513 - Daan P. Geerke, Sandra Luber, Koni H. Marti, Wilfred F. van Gunsteren:
On the direct calculation of the free energy of quantization for molecular systems in the condensed phase. 514-523 - Wenli Zou, Wenjian Liu:
Comprehensive ab initio calculation and simulation on the low-lying electronic states of TlX (X = F, Cl, Br, I, and At). 524-539 - Katalin E. Kövér, Tamás Beke, András Lipták, András Perczel:
Combined NMR three-bond scalar coupling measurements and QM calculations to calculate OH-rotamer equilibrium of polyalcohols. 540-550 - Inmaculada García Cuesta, Alfredo M. J. Sánchez De Merás, Stefano Pelloni, Paolo Lazzeretti:
Understanding the ring current effects on magnetic shielding of hydrogen and carbon nuclei in naphthalene and anthracene. 551-564 - Lei Yang, Jing-Yao Liu, Su-Qin Wan, Ze-Sheng Li:
Theoretical studies of the reactions of CF3CHCLOCHF2/CF3CHFOCHF2 with OH radical and Cl atom and their product radicals with OH. 565-580 - Darren J. Simpson, Thomas Bredow, Andrea R. Gerson:
MSINDO study of acid promoted dissolution of planar MgO and NiO surfaces. 581-588 - Wenbo Yu, Lei Liang, Zijing Lin, Sanliang Ling, Maciej Haranczyk, Maciej Gutowski:
Comparison of some representative density functional theory and wave function theory methods for the studies of amino acids. 589-600 - Keith T. Butler, F. Javier Luque, Xavier Barril:
Toward accurate relative energy predictions of the bioactive conformation of drugs. 601-610 - Li Wang, Jing-Yao Liu, Hong Gao, Su-Qin Wan, Ze-Sheng Li:
Dual-level direct dynamics studies for the reactions of OH radical with bromine-substituted ethanes. 611-620 - Oliver J. Clarke, Martin J. Parker:
Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model. 621-630 - Zunnan Huang, Chung F. Wong:
Conformational selection of protein kinase A revealed by flexible-ligand flexible-protein docking. 631-644 - Zanxia Cao, Zhixiong Lin, Jun Wang, Haiyan Liu:
Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field. 645-660
- V. Ganesh:
MeTA studio: A cross platform, programmable IDE for computational chemist. 661-672
Volume 30, Number 5, 15 April 2009
- Andreas Vitalis, Rohit V. Pappu:
ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions. 673-699 - Pei-Kun Yang, Carmay Lim:
Strategies to model the near-solute solvent molecular density/polarization. 700-709 - Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Marcel Swart, Joost N. P. Van Stralen, Friedrich Matthias Bickelhaupt, Maria João Ramos:
Role of the variable active site residues in the function of thioredoxin family oxidoreductases. 710-724 - Yun-Xiang Lu, Jian-Wei Zou, Ji-Cai Fan, Wen-Na Zhao, Yong-Jun Jiang, Qing-Sen Yu:
Ab initio calculations on halogen-bonded complexes and comparison with density functional methods. 725-732 - Jeffrey S. Tan, Stephan X. M. Boerrigter, Raymond P. Scaringe, Kenneth R. Morris:
Application of error-ranked singular value decomposition for the determination of potential-derived atomic-centered point charges. 733-742 - Lonnie D. Crosby, Shawn M. Kathmann, Theresa L. Windus:
Implementation of dynamical nucleation theory with quantum potentials. 743-749 - Pär Söderhjelm, Ulf Ryde:
Conformational dependence of charges in protein simulations. 750-760 - Volker Hähnke, Bettina Hofmann, Tomislav Grgat, Ewgenij Proschak, Dieter Steinhilber, Gisbert Schneider:
PhAST: Pharmacophore alignment search tool. 761-771 - Yingfu Jiang, Paul Iglinski, Lukasz A. Kurgan:
Prediction of protein folding rates from primary sequences using hybrid sequence representation. 772-783 - Victor M. Anisimov, Vladislav L. Bugaenko:
QM/QM docking method based on the variational finite localized molecular orbital approximation. 784-798 - Frank Eckert, Ivo Leito, Ivari Kaljurand, Agnes Kütt, Andreas Klamt, Michael Diedenhofen:
Prediction of acidity in acetonitrile solution with COSMO-RS. 799-810 - Grzegorz Mazur, Radoslaw Wlodarczyk:
Application of the dressed time-dependent density functional theory for the excited states of linear polyenes. 811-817 - Loriano Storchi, Giuseppe Vitillaro, Francesco Tarantelli:
Implementation and use of a direct, partially integral-driven non-Dyson propagator method for molecular ionization. 818-825 - Hiroaki Umeda, Yuichi Inadomi, Hiroaki Honda, Umpei Nagashima:
Parallel Fock matrix construction program for molecular orbital calculation - Specific computer with a hierarchical network. 826-831 - Sandro Chiodo, Nino Russo:
One-electron spin-orbit contribution by effective nuclear charges. 832-839
Volume 30, Number 6, 30 April 2009
- Hua Zhu, Daiqian Xie:
N2O in small para-hydrogen clusters: Structures and energetics. 841-846 - Hua-Qing Yang, Song Qin, Chang-Wei Hu:
Theoretical study on the gas-phase reaction mechanism between nickel monoxide and methane for syngas production. 847-863 - Mark S. Friedrichs, Peter K. Eastman, Vaidyanathan Vishal, Mike Houston, Scott LeGrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande:
Accelerating molecular dynamic simulation on graphics processing units. 864-872 - Gwonchan Yoon, Hyeong-Jin Park, Sungsoo Na, Kilho Eom:
Mesoscopic model for mechanical characterization of biological protein materials. 873-880 - Jason Martin, Jon Baker, Peter Pulay:
Comments on the molecular geometry of ferrocene: The dangers of using quantum chemistry programs as black boxes. 881-883 - Jorge A. Vila, Héctor A. Baldoni, Harold A. Scheraga:
Performance of density functional models to reproduce observed 13Calpha chemical shifts of proteins in solution. 884-892 - T. R. Walsh, T. Liang:
A multipole-based water potential with implicit polarization for biomolecular simulations. 893-899 - Shuyan Li, Lili Xi, Chengqi Wang, Jiazhong Li, Beilei Lei, Huanxiang Liu, Xiaojun Yao:
A novel method for protein-ligand binding affinity prediction and the related descriptors exploration. 900-909 - Amanda M. Salisburg, Ashley L. Deline, Katrina W. Lexa, George C. Shields, Karl N. Kirschner:
Ramachandran-type plots for glycosidic linkages: Examples from molecular dynamic simulations using the Glycam06 force field. 910-921 - Nitin S. Sapre, Swagata Gupta, Nilanjana Pancholi, Neelima Sapre:
A group center overlap based approach for "3D QSAR" studies on TIBO derivatives. 922-933 - Vincenzo Barone, Maurizio Casarin, Daniel Forrer, Michele Pavone, Mauro Sambi, Andrea Vittadini:
Role and effective treatment of dispersive forces in materials: Polyethylene and graphite crystals as test cases. 934-939 - Peng Zhou, Feifei Tian, Zhicai Shang:
2D depiction of nonbonding interactions for protein complexes. 940-951 - Yi Luo, Satoshi Maeda, Koichi Ohno:
Automated exploration of stable isomers of H+(H2O)n (n = 5-7) via ab initio calculations: An application of the anharmonic downward distortion following algorithm. 952-961 - Hajime Okamoto, Tetsuo Yamada, Shuichiro Kihara, Kazumasa Takechi, Hiroyuki Takagi, Kyozaburo Takeda:
Conformational transitions of cyclic D, L-peptides. 962-973 - Emanuel H. Rubensson, Elias Rudberg, Pawel Salek:
Truncation of small matrix elements based on the Euclidean norm for blocked data structures. 974-977 - Guohua Gao, Xiang Xu, Hong Seok Kang:
A theoretical study on fullerene-dizincocene hybrids. 978-982 - Jakub Kaminský, Jirí Sebek, Petr Bour:
Molecular dynamics with restrictions derived from optical spectra. 983-991 - Sarah Remmert, Carol A. Parish:
Energetic analyses of chair and boat conformations of maleimide substituted cyclohexane derivatives. 992-998 - Ilya V. Loksha, James R. Maiolo III, Cheng W. Hong, Albert H. Ng, Christopher D. Snow:
SHARPEN - Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network. 999-1005
Volume 30, Number 7, May 2009
- Cun-Xi Liu, Ze-Rong Li, Chong-Wen Zhou, Xiang-Yuan Li:
Accurate prediction of thermodynamic properties of alkyl peroxides by combining density functional theory calculation with least-square calibration. 1007-1015 - James S. Wright, Hooman Shadnia, Leonid L. Chepelev:
Stability of carbon-centered radicals: Effect of functional groups on the energetics of addition of molecular oxygen. 1016-1026 - Erika Ivonne López-Martínez, Luz María Rodríguez-Valdez, Norma Flores-Holguín, Alfredo Márquez-Lucero, Daniel Glossman-Mitnik:
Theoretical study of electronic properties of organic photovoltaic materials. 1027-1037 - Shunzhou Wan, Peter V. Coveney:
A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes. 1038-1050 - Lixin Zhan, Jeff Z. Y. Chen, Wing-Ki Liu:
Comparison of predicted native structures of Met-enkephalin based on various accessible-surface-area solvent models. 1051-1058 - Xavier Periole, Lucy R. Allen, Kamil Tamiola, Alan E. Mark, Emanuele Paci:
Probing the free energy landscape of the FBP28WW domain using multiple techniques. 1059-1068 - Stanislav Böhm, Otto Exner:
Interaction of two functional groups through the benzene ring: Theory and experiment. 1069-1074 - Miguel Angelo Fonseca de Souza, Elizete Ventura, Regiane C. M. U. Araújo, Mozart N. Ramos, Silmar Andrade do Monte:
CASSCF and multireference CI with singles and doubles study of low-lying valence and Rydberg states of 2H-tetrazole. 1075-1081 - Juan I. Rodríguez, Andreas M. Köster, Paul W. Ayers, Ana Santos-Valle, Alberto Vela, Gabriel Merino:
An efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfaces. 1082-1092 - Heiko Jacobsen:
Chemical bonding in view of electron charge density and kinetic energy density descriptors. 1093-1102 - Jin Wang, Jin Huai Liu:
Novel bi-transition metallic encapsulated naphthalene-like Si20 prismatic cage: A DFT investigation. 1103-1110 - Laura R. Hofto, Caroline E. Lee, Mauricio Cafiero:
The importance of aromatic-type interactions in serotonin synthesis: Protein-ligand interactions in tryptophan hydroxylase and aromatic amino acid decarboxylase. 1111-1115 - Young Kee Kang, Nam Sook Kang:
Conformational preferences of N-methoxycarbonyl proline dipeptide. 1116-1127 - Hong-Liang Xu, Fang-Fang Wang, Zhi-Ru Li, Bing-Qiang Wang, Di Wu, Wei Chen, Guang-Tao Yu, Feng Long Gu, Yuriko Aoki:
The nitrogen edge-doped effect on the static first hyperpolarizability of the supershort single-walled carbon nanotube. 1128-1134 - Ji-Lai Li, Cai-Yun Geng, Yuxiang Bu, Xu-Ri Huang, Chia-Chung Sun:
Conformational transition pathway in the allosteric process of calcium-induced recoverin: Molecular dynamics simulations. 1135-1145 - Ramon Carbó-Dorca, Ana Gallegos, Ángel J. Sánchez:
Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution. 1146-1159