Stop the war!Остановите войну!
for scientists:
default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDJournal of Computational Chemistry, Volume 26
Volume 26, Number 1, January 2005
- Kaori Fukuzawa
, Kazuo Kitaura, Masami Uebayasi, Kotoko Nakata, Tsuguchika Kaminuma, Tatsuya Nakano:
Ab initio quantum mechanical study of the binding energies of human estrogen receptor with its ligands: An application of fragment molecular orbital method. 1-10
- Maria Kontoyianni, Glenn S. Sokol, Laura M. McCellan:
Evaluation of library ranking efficacy in virtual screening. 11-22 - Steven L. Dixon, Kenneth M. Merz Jr., Giorgio Lauri, James C. Ianni:
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method. 23-34 - Zhong-Zhi Yang, Li-Dong Gong, Dong-Xia Zhao, Ming-Bo Zhang:
Method and algorithm of obtaining the molecular intrinsic characteristic contours (MICCs) of organic molecules. 35-47 - Art E. Cho, John A. Wendel, Nagarajan Vaidehi, Peter M. Kekenes-Huskey, Wely B. Floriano, Prabal K. Maiti, William A. Goddard III:
The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals. 48-71 - Malek O. Khan, Gareth Kennedy, Derek Y. C. Chan:
A scalable parallel Monte Carlo method for free energy simulations of molecular systems. 72-77 - Kyoungrim Lee, Cezary Czaplewski, Seung-Yeon Kim, Jooyoung Lee:
An efficient molecular docking using conformational space annealing. 78-87 - Bing Suo, Gaohong Zhai, Yubin Wang, Zhenyi Wen, Xiangqian Hu, Lemin Li:
Parallelization of MRCI based on hole-particle symmetry. 88-96 - F. Martin, Hendrik Zipse:
Charge distribution in the water molecule - A comparison of methods. 97-105 - Wenli Zou, Wenjian Liu:
Extensive theoretical studies on the low-lying electronic states of indium monochloride cation, InCl+. 106-113
- Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case:
Junmei Wang, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, and David A. Case, "Development and testing of a general amber force field" Journal of Computational Chemistry(2004) 25(9) 1157-1174. 114-
Volume 26, Number 2, January 2005
- Serena Donnini, Alan E. Mark, André H. Juffer, Alessandra Villa:
Incorporating the effect of ionic strength in free energy calculations using explicit ions. 115-122 - Robert J. Deeth, Natalie Fey, Benjamin Williams-Hubbard:
DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment. 123-130 - David de Sancho, Lidia Prieto, Ana M. Rubio, Antonio Rey:
Evolutionary method for the assembly of rigid protein fragments. 131-141 - Daniela Bertolini Depizzol, Marcia Helena Moreira Paiva, Thiago Oliveira Dos Santos, Anderson Coser Gaudio:
MoCalc: A new graphical user interface for molecular calculations. 142-144 - Zuzana Benkova, Andrzej J. Sadlej, Roma E. Oakes, Steven E. J. Bell:
Reduced-size polarized basis sets for calculations of molecular electric properties. I. The basis set generation. 145-153 - Roma E. Oakes, Steven E. J. Bell, Zuzana Benkova, Andrzej J. Sadlej:
Reduced-size polarized basis sets for calculations of molecular electric properties. II. Simulation of the Raman spectra. 154-159 - Mitsuhito Wada, Minoru Sakurai:
A quantum chemical method for rapid optimization of protein structures. 160-168 - H. Sun, Paul W.-C. Kung:
Urea: An ab initio and force field study of the gas and solid phases. 169-174 - Sandro Chiodo, Nino Russo, Emilia Sicilia:
Newly developed basis sets for density functional calculations. 175-184 - Li Wang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study and rate constant calculation for the reactions of SH (SD) with Cl2, Br2, and BrCl. 184-193 - W. Dean Harman, Carl Trindle:
Charge donation to and dearomatization of benzene attending complexation: DFT estimates of binding energies of TpMXO(L) with benzene, for Tp = hydridotris(pyrazolyl) borate, MXO = MoNO, ReCO, and WNO, and L = ammonia, N-methylimidazole, pyridine, phosphine, methyl isocyanide, and carbon monoxide. 194-200
Volume 26, Number 3, February 2005
- K. Fiaty, C. Charcosset, B. Perrin, R. Couturier, B. Maïsterrena:
Simulations of the active transport of a neutral solute based on a kinase-channel-phosphatase topology. 201-213 - Robert J. Gdanitz, Gary D. Black, Carina Lansing, Bruce J. Palmer, Karen Schuchardt:
Registering the Amica electronic structure code in the Extensible Computational Chemistry Environment. 214-225 - Yuhui Qu, Xiufang Bian:
Electronic structure and stability of AlnPn (n = 2-4) clusters. 226-234 - Joanna Makowska, Mariusz Makowski, Adam Liwo, Lech Chmurzynski:
Theoretical calculations of homoconjugation equilibrium constants in systems modeling acid-base interactions in side chains of biomolecules using the potential of mean force. 235-242 - Charles F. F. Karney, Jason E. Ferrara, Stephan Brunner:
Method for computing protein binding affinity. 243-251 - Matthew A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher J. Fennell, J. Daniel Gezelter:
OOPSE: An object-oriented parallel simulation engine for molecular dynamics. 252-271 - Minoru Saito, Isao Okazaki, Masayuki Oda, Ikuo Fujii:
A free energy calculation study of the effect of HF substitution on binding affinity in ligand-antibody interactions. 272-282 - F. Wennmohs, M. Schindler:
Development of a multipoint model for sulfur in proteins: A new parametrization scheme to reproduce high-level ab initio interaction energies. 283-293 - Josef Seda, Jaroslav V. Burda, Jerzy Leszczynski:
Study of electronic spectra of free-base porphin and Mg-porphin: Comprehensive comparison of variety of ab initio, DFT, and semiempirical methods. 294-303 - Panagiotis G. Karamertzanis, Constantinos C. Pantelides:
Ab initio crystal structure prediction - I. Rigid molecules. 304-324
Volume 26, Number 4, March 2005
- Yasuyo Hatano, Shigeyoshi Yamamoto, Hiroshi Tatewaki:
Characterization of molecular orbitals by counting nodal regions. 325-333 - Shura Hayryan, Chin-Kun Hu, Jaroslav Skrivánek, Edik Hayryan, Imrich Pokorný:
A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients. 334-343 - Ángel Martín Pendás, Evelio Francisco, M. A. Blanco:
Two-electron integrations in the Quantum Theory of Atoms in Molecules with correlated wave functions. 344-351 - Michael Meyer, Alexandre Hocquet, Jürgen Sühnel:
Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. 352-364 - Pablo Campomanes, María Isabel Menéndez Rodríguez, Ramón López, Tomás Luis Sordo:
Stereodynamics of bond rotation in tertiary 1-naphthoic acid amides: A computational study. 365-373 - Eckart Bindewald, Jeffrey Skolnick:
A scoring function for docking ligands to low-resolution protein structures. 374-383 - Philippe Carbonniere, Tecla Lucca, Claude Pouchan, Nadia Rega, Vincenzo Barone:
Vibrational computations beyond the harmonic approximation: Performances of the B3LYP density functional for semirigid molecules. 384-388 - Mehdi Mobli, Raymond J. Abraham:
Quantum vs. classical models of the nitro group for proton chemical shift calculations and conformational analysis. 389-398 - Quan Zhu, Ke-Xiang Fu, Xiang-Yuan Li, Zhen Gong, Jian-Yi Ma:
Continuous medium theory for nonequilibrium solvation: III. Solvation shift by monopole approximation and multipole expansion in spherical cavity. 399-409
Volume 26, Number 5, April 2005
- Veronika Kasalová, Henry F. Schaefer III:
Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn-(n = 1-8). 411-435 - Mari Tamaoki, Yusuke Yamauchi, Hiromi Nakai:
Short-time Fourier transform analysis of ab initio molecular dynamics simulation: Collision reaction between CN and C4H6. 436-442 - Rajeev Prabhakar, Keiji Morokuma, Djamaladdin G. Musaev:
A comparative study of various computational approaches in calculating the structure of pyridoxal 5r-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment. 443-446 - Robert Ponec, Gleb Yuzhakov, Markku R. Sundberg:
Chemical structures from the analysis of domain-averaged fermi holes. Nature of the Mn-Mn bond in bis(pentacarbonylmanganese). 447-454 - Ana Gallegos, Ramon Carbó-Dorca, François Lodier, Eric Cancès, Andreas Savin:
Maximal probability domains in linear molecules. 455-460 - Qishi Du, Paul G. Mezey, Kuo-Chen Chou:
Heuristic molecular lipophilicity potential (HMLP): A 2D-QSAR study to LADH of molecular family pyrazole and derivatives. 461-470 - Carlos A. Stortz:
Comparative performance of MM3(92) and two TINKERTM MM3 versions for the modeling of carbohydrates. 471-483 - Bing Liu, Jiaju Zhou:
SARS-CoV protease inhibitors design using virtual screening method from natural products libraries. 484-490 - Andrei M. Tokmachev, Andreì L. Tchougréeff:
Transferability of parameters of strictly local geminals' wave function and possibility of sequential derivation of molecular mechanics. 491-505 - Pierre Tufféry, Frédéric Guyon, Philippe Derreumaux:
Improved greedy algorithm for protein structure reconstruction. 506-513
- Lingchun Song, Yirong Mo, Qianer Zhang, Wei Wu:
XMVB: A program for ab initio nonorthogonal valence bond computations. 514-521
Volume 26, Number 6, April 2005
- Raúl A. Bustos Marún, Eduardo A. Coronado, Juan C. Ferrero:
Fitting complex potential energy surfaces to simple model potentials: Application of the simplex-annealing method. 523-531 - Vinzenz Bachler:
The behavior of transition metal nitrido bonds towards protonation rationalized by means of localized bonding schemes and their weights. 532-551 - Ping Li, Yuxiang Bu:
Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase. 552-560 - Peter L. Cummins, Jill E. Gready:
Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation. 561-568 - Núria González-García, Àngels González-Lafont, José M. Lluch:
Electronic structure study of the initiation routes of the dimethyl sulfide oxidation by OH. 569-583 - Qingyu Kong, Li Zhao, Wenning Wang, Chen Wang, Can Xu, Wingham Zhang, Lei Liu, Kangnian Fan, Yufen Li, Jun Zhuang:
Magic number silicon dioxide-based clusters: Laser ablation-mass spectrometric and density functional theory studies. 584-598 - Peter Pulay, Svein Saebo, Massimo Malagoli, Jon Baker:
Accuracy and efficiency of atomic basis set methods versus plane wave calculations with ultrasoft pseudopotentials for DNA base molecules. 599-605 - T. K. Manojkumar, Chunzhi Cui, Kwang S. Kim:
Theoretical insights into the mechanism of acetylcholinesterase-catalyzed acylation of acetylcholine. 606-611 - Pedro L. Muiño:
The OH. + CH3SH reaction: Support for an addition-elimination mechanism from ab initio calculations. 612-618 - Manfred Rudolph:
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. I. Presentation of the basic concept and application to a pure diffusion system. 619-632 - Manfred Rudolph:
Attaining exponential convergence for the flux error with second- and fourth-order accurate finite-difference equations. II. Application to systems comprising first-order chemical reactions. 633-641 - Hong-Qing He, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study for the reaction of CH3OCl with Cl atom. 642-650
Volume 26, Number 7, May 2005
- Eva Darian, Vladimir Hnizdo, Adam Fedorowicz, Harshinder Singh, Eugene Demchuk:
Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations. 651-660 - Marcus Lundberg, Per E. M. Siegbahn:
Agreement between experiment and hybrid DFT calculations for OH bond dissociation enthalpies in manganese complexes. 661-667 - Peter A. Sims, Chung F. Wong, Danka Vuga, James Andrew McCammon, Bartholomew M. Sefton:
Relative contributions of desolvation, inter- and intramolecular interactions to binding affinity in protein kinase systems. 668-681 - Eric J. Sorin, Vijay S. Pande:
Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. 682-690 - Min-Yi Shen, Karl F. Freed:
A simple method for faster nonbonded force evaluations. 691-698 - L. Renee Olano, Steven W. Rick:
Fluctuating charge normal modes: An algorithm for implementing molecular dynamics simulations with polarizable potentials. 699-707 - Alán Aspuru-Guzik, Romelia Salomón-Ferrer, Brian Austin, William A. Lester Jr.:
A sparse algorithm for the evaluation of the local energy in quantum Monte Carlo. 708-715 - Anti Liivat, Alvo Aabloo, John O. Thomas:
Development of a force field for Li2SiF6. 716-724 - Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren:
An improved nucleic acid parameter set for the GROMOS force field. 725-737 - Fredrik Blomgren, Sven Larsson:
Exploring the potential energy surface of retinal, a comparison of the performance of different methods. 738-742 - Neil Gohaud, Didier Bégué, Clovis Darrigan, Claude Pouchan:
New parallel software (P_Anhar) for anharmonic vibrational calculations: Application to (CH3Li)2. 743-754
Volume 26, Number 8, June 2005
- Robert J. Petrella, Martin Karplus:
Electrostatic energies and forces computed without explicit interparticle interactions: A linear time complexity formulation. 755-787 - Hirofumi Fujimoto, Miroslav Pinak, Toshiyuki Nemoto, Peter O'Neill, Etsuo Kume, Kimiaki Saito, Hideaki Maekawa:
Molecular dynamics simulation of clustered DNA damage sites containing 8-oxoguanine and abasic site. 788-798 - Si-Dian Li, Chang-Qing Miao, Jin-Chang Guo, Guang-Ming Ren:
Carbon boronyls: Species with higher viable possibility than boron carbonyls at the density functional theory. 799-802 - Frank J. Owens:
Stability of (C60)2 and epoxide dimers, (C60)2ON, and their anions. 803-806 - Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study on the reaction mechanism of the methyl radical with nitrogen oxides. 807-817 - Akifumi Oda, Noriyuki Yamaotsu, Shuichi Hirono:
New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models. 818-826 - Alessandro Genoni, Arianna Fornili, Maurizio Sironi:
Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals. 827-835 - Theodore S. Dibble:
Computations on the A-X transition of isoprene-OH-O2 peroxy radicals. 836-845 - Jaime Fernández Rico, Ramón López, Ignacio Ema, Guillermo Ramírez:
Translation of STO charge distributions. 846-855
- Alán Aspuru-Guzik, Romelia Salomón-Ferrer, Brian Austin, Raul Perusquía-Flores, Mary A. Griffin, Ricardo A. Oliva, David Skinner, Dominik Domin, William A. Lester Jr.:
Zori 1.0: A parallel quantum Monte Carlo electronic structure package. 856-862
- Jason Wagoner, Nathan A. Baker:
Erratum to "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, " by Jason Wagoner and Nathan A. Baker. 863-
Volume 26, Number 9, July 2005
- Ia. I. Dobrogorskaia-Méreau, Alexander V. Nemukhin:
Quantum chemical modeling of the reduction of cis-diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anion. 865-870 - Gui-Chang Wang, Jun Li, Xiu-Fang Xu, Rui-Fang Li, Junji Nakamura:
The relationship between adsorption energies of methyl on metals and the metallic electronic properties: A first-principles DFT study. 871-878 - Andreas Schreiber, Michael Humbert, Alexander Benz, Ursula Dietrich:
3D-Epitope-Explorer (3DEX): Localization of conformational epitopes within three-dimensional structures of proteins. 879-887 - Per E. M. Siegbahn, Alexander F. Shestakov:
Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase. 888-898 - Wayne J. Pullan:
An unbiased population-based search for the geometry optimization of Lennard-Jones clusters: 2 leq N leq 372. 899-906 - Jaroslav V. Burda, Michal Zeizinger, Jerzy Leszczynski:
Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters. 907-914 - Art E. Cho, Victor Guallar, Bruce J. Berne, Richard A. Friesner:
Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach. 915-931 - Roberto L. A. Haiduke, Luiz G. M. de Macedo, Albérico B. F. da Silva:
An accurate relativistic universal Gaussian basis set for hydrogen through Nobelium without variational prolapse and to be used with both uniform sphere and Gaussian nucleus models. 932-940 - Illia Horenko, Sönke Lorenz, Christof Schütte, Wilhelm Huisinga:
Adaptive approach for nonlinear sensitivity analysis of reaction kinetics. 941-948 - Thomas S. Hofer, Bernhard R. Randolf, Bernd M. Rode:
Structure-breaking effects of solvated Rb(I) in dilute aqueous solution - An ab initio QM/MM MD approach. 949-956 - Sanjay Banerjee, John A. Board Jr.:
Efficient charge assignment and back interpolation in multigrid methods for molecular dynamics. 957-967
Volume 26, Number 10, July 2005
- Li Yang, Ji-Kang Feng, Ai-Min Ren:
Theoretical studies on the electronic and optical properties of two new alternating fluorene/carbazole copolymers. 969-979 - Chang-Guo Zhan, Shi-Xian Deng, Jaime G. Skiba, Beth A. Hayes, Sarah M. Tschampel, George C. Shields, Donald W. Landry:
First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine. 980-986 - Toru Inaba, Saisei Tahara, Nobutaka Nisikawa, Hiroshi Kashiwagi, Fumitoshi Sato:
All-electron density functional calculation on insulin with quasi-canonical localized orbitals. 987-993 - Ying Xue, Chan Kyung Kim, Yong Guo, Daiqian Xie, Guosen Yan:
DFT study and Monte Carlo simulation on proton transfers of 2-amino-2-oxazoline, 2-amino-2-thiazoline, and 2-amino-2-imidazoline in the gas phase and in water. 994-1005 - G. Theodoor De Jong, Daan P. Geerke, Axel Diefenbach, Miquel Solà, Friedrich Matthias Bickelhaupt:
Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study. 1006-1020 - Michael S. Crocker, Scott S. Hampton, Thierry Matthey, Jesús A. Izaguirre:
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms. 1021-1031 - Hsien-Da Huang, Tzong-Yi Lee, Shih-Wei Tzeng, Li-Cheng Wu, Jorng-Tzong Horng, Ann-Ping Tsou, Kuan-Tsae Huang:
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites. 1032-1041 - Stefano Borini, Daniel Maynau, Stefano Evangelisti:
A combined freeze-and-cut strategy for the description of large molecular systems using a localized orbitals approach. 1042-1051 - Jean-Philip Piquemal, Antonio Marquez, Olivier Parisel, Claude Giessner-Prettre:
A CSOV study of the difference between HF and DFT intermolecular interaction energy values: The importance of the charge transfer contribution. 1052-1062 - Jerod Parsons, J. Bradley Holmes, J. Maurice Rojas, Jerry Tsai, Charlie E. M. Strauss:
Practical conversion from torsion space to Cartesian space for in silico protein synthesis. 1063-1068 - Lesley D. Lloyd, Roy L. Johnston, Saïd Salhi:
Strategies for increasing the efficiency of a genetic algorithm for the structural optimization of nanoalloy clusters. 1069-1078 - Piotr Zarzycki, Pawel Szabelski, Robert Charmas:
Role of the surface heterogeneity in adsorption of hydrogen ions on metal oxides: Theory and simulations. 1079-1088
Volume 26, Number 11, August 2005
- Anatoly M. Ruvinsky, A. V. Kozintsev:
New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. 1089-1095 - Caterina Benzi, Maurizio Cossi, Roberto Improta, Vincenzo Barone:
Building cavities in a fluid of spherical or rod-like particles: A contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model. 1096-1105 - Michael S. Schuurman, Wesley D. Allen, Henry F. Schaefer III:
The ab initio limit quartic force field of BH3. 1106-1112 - Nohad Gresh, Jean-Philip Piquemal, Morris Krauss:
Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations. 1113-1130 - Jens Antony, Jean-Philip Piq