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ORCIDJournal of Computational Chemistry, Volume 24
Volume 24, Number 1, 15 January 2003
- Stephen C. Harvey, Chunlin Wang, Stephane Teletchea
, Richard Lavery:
Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking. 1-9
- Andrew Smellie, Robert V. Stanton, Randy Henne, Steven L. Teig:
Conformational analysis by intersection: CONAN. 10-20 - Asim Okur, Bentley Strockbine, Viktor Hornak, Carlos Simmerling:
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. 21-31 - Carles Curutchet, Albert Salichs, Xavier Barril, Modesto Orozco, Francisco Javier Luque:
Transferability of fragmental contributions to the octanol/water partition coefficient: An NDDO-based MST study. 32-45 - Giuliano Alagona, Caterina Ghio, Peter A. Kollman:
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): A QM/FE approach. 46-56 - Edward C. Sherer, Darrin M. York, Christopher J. Cramer:
Fast approximate methods for calculating nucleic acid base pair interaction energies. 57-67 - Scott Brown, Teresa Head-Gordon:
Cool walking: A new Markov chain Monte Carlo sampling method. 68-76 - Danny Barash, Linjing Yang, Xiaoliang Qian, Tamar Schlick:
Inherent speedup limitations in multiple time step/particle mesh Ewald algorithms. 77-88 - Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill:
MOPED: Method for optimizing physical energy parameters using decoys. 89-97 - Gregori Ujaque, Dean J. Tantillo, Yunfeng Hu, K. N. Houk, Kinya Hotta, Donald Hilvert:
Catalysis on the coastline: Theozyme, molecular dynamics, and free energy perturbation analysis of antibody 21D8 catalysis of the decarboxylation of 5-nitro-3-carboxybenzisoxazole. 98-110 - Karl Nicholas Kirschner, Anita H. Lewin, J. Phillip Bowen:
Molecular mechanics force-field development for amino acid zwitterions. 111-128
Volume 24, Number 2, 30 January 2003
- Matteo Ceccarelli, Piero Procacci, Massimo Marchi:
An ab initio force field for the cofactors of bacterial photosynthesis. 129-142 - Francesca Massi, John E. Straub:
Structural and dynamical analysis of the hydration of the Alzheimer's beta-amyloid peptide. 143-153 - Alexander V. Mitin, Jon Baker, Krzysztof Wolinski, Peter Pulay:
Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression. 154-160 - Jose Manuel Hermida-Ramón, Steve Brdarski, Gunnar Karlström, Ulf Berg:
Inter- and intramolecular potential for the N-formylglycinamide-water system. A comparison between theoretical modeling and empirical force fields. 161-176 - Mireia Garcia-Viloca, Cristóbal Alhambra, Donald G. Truhlar, Jiali Gao:
Hydride transfer catalyzed by xylose isomerase: Mechanism and quantum effects. 177-190 - John L. Klepeis, Christodoulos A. Floudas:
Prediction of beta-sheet topology and disulfide bridges in polypeptides. 191-208 - Takumi Hori, Hideaki Takahashi, Tomoshige Nitta:
Hybrid QM/MM molecular dynamics simulations for an ionic SN2 reaction in the supercritical water: OH- + CH3Cl -> CH3OH + Cl-. 209-221 - Robert J. Petrella, Ioan Andricioaei, Bernard R. Brooks, Martin Karplus:
An improved method for nonbonded list generation: Rapid determination of near-neighbor pairs. 222-231 - D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce:
Exact rotamer optimization for protein design. 232-243 - Satoshi Okumoto, Shinichi Yamabe:
Computational study of epoxy-amine reactions. 244-253
- Vsevolod Katritch, Maxim Totrov, Ruben Abagyan:
ICFF: A new method to incorporate implicit flexibility into an internal coordinate force field. 254-265
Volume 24, Number 3, February 2003
- George A. Kaminski, Richard A. Friesner, Ruhong Zhou:
A computationally inexpensive modification of the point dipole electrostatic polarization model for molecular simulations. 267-276 - Genyuan Li, Herschel A. Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos:
Correlation method for variance reduction of Monte Carlo integration in RS-HDMR. 277-283 - Carles Curutchet, Christopher J. Cramer, Donald G. Truhlar, Manuel F. Ruiz-López, Daniel Rinaldi, Modesto Orozco, F. Javier Luque:
Electrostatic component of solvation: Comparison of SCRF continuum models. 284-297 - Christopher S. Page, Massimo Olivucci:
Ground and excited state CASPT2 geometry optimizations of small organic molecules. 298-309 - Kazuyoshi Ikeda, Oxana V. Galzitskaya, Haruki Nakamura, Junichi Higo:
beta-Hairpins, alpha-helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal beta-hairpin of SH3 domain. 310-318 - Takashi Yoshida, Kazuhisa Sakakibara, Masatoshi Asami, Kuo-Hsiang Chen, Jenn-Huei Lii, Norman L. Allinger:
Molecular mechanics (MM3) calculations on lithium amide compounds. 319-327 - Alicia C. Lorenzo, Pedro Geraldo Pascutti, Paulo Mascarello Bisch:
Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations. 328-339 - Zheng-Wang Qu, Hui Zhu, Xing-Kang Zhang, Qi-Yuan Zhang:
Density functional investigation on electron-transfer catalysis of cycloreversion of cyclobutane: Radical anion mechanism. 340-344 - Jinshan Li, Feng Zhao, Fuqian Jing:
An ab initio study of intermolecular interactions of nitromethane dimer and nitromethane trimer. 345-352 - Andrew J. Bordner, G. A. Huber:
Boundary element solution of the linear Poisson-Boltzmann equation and a multipole method for the rapid calculation of forces on macromolecules in solution. 353-367 - Jaroslav Koca, Chang-Guo Zhan, Robert C. Rittenhouse, Rick L. Ornstein:
Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. 368-378 - Yi-Gui Wang, Nick Henry Werstiuk:
A practical and efficient method to calculate AIM localization and delocalization indices at post-HF levels of theory. 379-385 - Christofer S. Tautermann, Andreas F. Voegele, Thomas Loerting, Peter Kaps, Klaus R. Liedl:
Extended method for adiabatic mode reordering. 386-395 - Asit K. Chandra, Tadafumi Uchimaru, Masaaki Sugie, Akira Sekiya:
Ab initio study on the structures of fluorinated formates and hydrogen abstraction reaction with OH radical. 396-407
Volume 24, Number 4, March 2003
- Shridhar R. Gadre:
Foreword. 408 - Christophe Chipot:
Rational determination of charge distributions for free energy calculations. 409-415 - Ibon Alkorta, Jose Elguero, Enrique Espinosa, Ignasi Mata, Elies Molins:
Comparison of electron density properties in frozen and relaxed electronic distributions. 416-421 - Carlo Gatti, Fausto Cargnoni, Luca Bertini:
Chemical information from the source function. 422-436 - Nathaniel O. J. Malcolm, Paul L. A. Popelier:
An improved algorithm to locate critical points in a 3D scalar field as implemented in the program MORPHY. 437-442 - George Maroulis:
Ab initio determination of the electric multipole moments and static (hyper)polarizability of HCCX, X = F, Cl, Br, and I. 443-452 - Chérif F. Matta:
Application of the quantum theory of atoms in molecules to selected physico-chemical and biophysical problems: Focus on correlation with experiment. 453-463 - Frank De Proft, Ricardo Vivas-Reyes, Anik Peeters, Christian Van Alsenoy, Paul Geerlings:
Hirshfeld partitioning of the electron density: Atomic dipoles and their relation with functional group properties. 463-470 - Daniel J. Grimwood, Ian Bytheway, Dylan Jayatilaka:
Wave functions derived from experiment. V. Investigation of electron densities, electrostatic potentials, and electron localization functions for noncentrosymmetric crystals. 470-483 - K. Babu, Shridhar R. Gadre:
Ab initio quality one-electron properties of large molecules: Development and testing of molecular tailoring approach. 484-495 - Eduardo Chamorro, Patricio Fuentealba, Andreas Savin:
Electron probability distribution in AIM and ELF basins. 496-504 - Peter Politzer, Jane S. Murray, Pat Lane:
Electrostatic potentials and covalent radii. 505-511 - Christopher E. Whitehead, Curt M. Breneman, Nagamani Sukumar, M. Dominic Ryan:
Transferable atom equivalent multicentered multipole expansion method. 512-529
Volume 24, Number 5, 15 April 2003
- Marcin Król:
Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. 531-546 - Paola Facchini, Felice Grandinetti:
Concerning the reaction between singlet nitrenium ions and water: A computational investigation on competitive reaction paths. 547-564 - Marcus Elstner, Qiang Cui, Petra Munih, Efthimios Kaxiras, Thomas Frauenheim, Martin Karplus:
Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis. 565-581 - Takashi Amisaki, Shinjiro Toyoda, Hiroh Miyagawa, Kunihiro Kitamura:
Development of hardware accelerator for molecular dynamics simulations: A computation board that calculates nonbonded interactions in cooperation with fast multipole method. 582-592 - Jia-Yan Wu, Jing-Yao Liu, Ze-Sheng Li, Xu-Ri Huang, Chia-Chung Sun:
Dual-level direct dynamics studies for the reactions of dimethyl ether with hydrogen atom and methyl radical. 593-600 - Gabriela L. Borosky:
Theoretical study concerning the reactivity of imine derivatives of polycyclic aromatic hydrocarbons. 601-608 - José-Vicente Pitarch Ruiz, José Sánchez-Marín, Daniel Maynau:
Vertical spectrum of the C2H2+ system. An open shell (SC)2-CAS-SDCI study. 609-617 - Chandra Saravanan, Yihan Shao, Roi Baer, Philip N. Ross, Martin Head-Gordon:
Sparse matrix multiplications for linear scaling electronic structure calculations in an atom-centered basis set using multiatom blocks. 618-622 - Meng-Sheng Liao, Yun Lu, Steve Scheiner:
Performance assessment of density-functional methods for study of charge-transfer complexes. 623-631 - Andrea C. Vaiana, Andreas Schulz, Jürgen Wolfrum, Markus Sauer, Jeremy C. Smith:
Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching. 632-639 - C. F. Cloud III, Martin Schwartz:
Systematic errors in DFT calculations of haloalkane heats of formation. 640-646 - Genyuan Li, Maxim Artamonov, Herschel A. Rabitz, Sheng-Wei Wang, Panos G. Georgopoulos, Metin Demiralp:
High-dimensional model representations generated from low order terms - lp-RS-HDMR. 647-656
- Tomasz Róg, Krzysztof Murzyn, Konrad Hinsen, Gerald R. Kneller:
nMoldyn: A program package for a neutron scattering oriented analysis of molecular dynamics simulations. 657-667
Volume 24, Number 6, 30 April 2003
- Maurizio Cossi, Nadia Rega, Giovanni Scalmani, Vincenzo Barone:
Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. 669-681 - David Bosch, Mercedes Campillo, Leonardo Pardo:
Binding of proteins to the minor groove of DNA: What are the structural and energetic determinants for kinking a basepair step?. 682-691 - A. S. Zyubin, A. M. Mebel:
Performance of time-dependent density functional and Green functions methods for calculations of excitation energies in radicals and for Rydberg electronic states. 692-700 - Laura Masgrau, Àngels González-Lafont, José M. Lluch:
Dependence of the rate constants on the treatment of internal rotation modes: The reaction OH + CH3SH CH3S + H2O as an example. 701-706 - Luis Lorenzo, Ricardo A. Mosquera:
A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations. 707-713 - Axel Koslowski, Michael E. Beck, Walter Thiel:
Implementation of a general multireference configuration interaction procedure with analytic gradients in a semiempirical context using the graphical unitary group approach. 714-726 - Yu-Dong Cai, Xiao-Jun Liu, Kuo-Chen Chou:
Prediction of protein secondary structure content by artificial neural network. 727-731 - Peter M. W. Gill, Siu-Hung Chien:
Radial quadrature for multiexponential integrands. 732-740 - Tanja Schulz-Gasch, Martin Stahl:
Mechanistic insights into oxidosqualene cyclizations through homology modeling. 741-753 - Markus Pernpointner, Lucas Visscher:
Parallelization of four-component calculations. II. Symmetry-driven parallelization of the 4-Spinor CCSD algorithm. 754-759 - Thom Vreven, Keiji Morokuma, Ödön Farkas, H. Bernhard Schlegel, Michael J. Frisch:
Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. 760-769 - David Zanuy, Carlos Alemán, Manuel Laso, Sebastián Muñoz-Guerra:
Thermally induced phase transition in helical comblike poly(-peptide)s: An atomistic simulation. 770-778 - Matteo Pappalardo, Danilo Milardi, Domenico M. Grasso, Carmelo La Rosa:
Free energy perturbation and molecular dynamics calculations of copper binding to azurin. 779-785 - Mark Pinsky, Dina Yogev-Einot, David Avnir:
Statistical analysis of the estimation of distance measures. 786-796
Volume 24, Number 7, May 2003
- Philippe Arnaud, Krystyna Zakrzewska, Bernard Meunier:
Theoretical study of the interaction between a high-valent manganese porphyrin oxyl-(hydroxo)-Mn(IV)-TMPyP and double-stranded DNA. 797-805 - Majda Sekkal-Rahal, Nezha Sekkal, Dirk C. Kleb, Paul Bleckmann:
Structures and energies of D-galactose and galabiose conformers as calculated by ab initio and semiempirical methods. 806-818 - José Mario Martínez, Leandro Martínez:
Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking. 819-825 - Kenshu Kamiya, Yoko Sugawara, Hideaki Umeyama:
Algorithm for normal mode analysis with general internal coordinates. 826-841 - Yu-Ren Jiang, Jing-Ya Liu, Yue-Hua Hu, Toyohisa Fujita:
Novel topological index for research on structure-property relationships of complex organic compounds. 842-849 - Valentina Vetere, Pascale Maldivi, Carlo Adamo:
Comparative studies of quasi-relativistic density functional methods for the description of lanthanide and actinide complexes. 850-858 - Ignacio Ema, J. M. García de la Vega, Guillermo Ramírez, Rafael López, Jaime Fernández Rico, H. Meissner, J. Paldus:
Polarized basis sets of Slater-type orbitals: H to Ne atoms. 859-868 - Carlos Renato Zacharias, Maurício Ruv Lemes, Arnaldo Dal Pino Júnior, David Santo Orcero:
Predicting structural models for silicon clusters. 869-875 - Mark Bathe, Gregory C. Rutledge:
Inverse Monte Carlo procedure for conformation determination of macromolecules. 876-890 - Joseph V. Turner, David J. Cutler, Ian Spence, Desmond J. Maddalena:
Selective descriptor pruning for QSAR/QSPR studies using artificial neural networks. 891-897 - Miroslav Pinak:
8-oxoguanine lesioned B-DNA molecule complexed with repair enzyme hOGG1: A molecular dynamics study. 898-907
Volume 24, Number 8, June 2003
- Fillmore Freeman, Elika Derek:
A computational study of conformational interconversions in 1, 4-dithiacyclohexane (1, 4-dithiane). 909-919 - Wataru Shinoda, Masuhiro Mikami:
Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency. 920-930 - Yong Wu, Daiqian Xie, Ying Xue:
Ab initio studies for the photodissociation mechanism of hydroxyacetone. 931-938 - Shinichi Yamabe, Noriko Tsuchida:
A computational study of interactions between acetic acid and water molecules. 939-947 - Zhongfang Chen, Haijun Jiao, Gotthard Seifert, Anselm H. C. Horn, Dengke Yu, Timothy Clark, Walter Thiel, Paul von Ragué Schleyer:
The structure and stability of Si60 and Ge60 cages: A computational study. 948-953 - Kathryn N. Rankin, Traian Sulea, Enrico O. Purisima:
On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations. 954-962 - Ying Xue, Chun Ho Kang, Chan Kyung Kim, Ikchoon Lee:
Theoretical studies on the gas-phase pyrolysis of 2-phenoxycarboxylic acids: An ONIOM approach. 963-972 - Marcelo Zaldini Hernandes, João Bosco P. Da Silva, Ricardo L. Longo:
Chemometric study of liquid water simulations. I. The parameters of the TIP4P model potential. 973-981 - Eliseo Ruiz, Antonio Rodríguez-Fortea, Joan Cano, Santiago Alvarez, Pere Alemany:
About the calculation of exchange coupling constants in polynuclear transition metal complexes. 982-989 - Dominic R. Alfonso, Kenneth D. Jordan:
A flexible nudged elastic band program for optimization of minimum energy pathways using ab initio electronic structure methods. 990-996
- János G. Ángyán, Christophe Chipot, François Dehez, Christof Hättig, Georg Jansen, Claude Millot:
OPEP: A tool for the optimal partitioning of electric properties. 997-1008
Volume 24, Number 9, 15 July 2003
- Christopher C. Lovallo, Mariusz Klobukowski:
Development of new pseudopotential methods: Improved model core potentials for the first-row transition metals. 1009-1015 - Kristin L. Meagher, Luke T. Redman, Heather A. Carlson:
Development of polyphosphate parameters for use with the AMBER force field. 1016-1025 - András Perczel, Ödön Farkas, Imre Jákli, Igor A. Topol, Imre G. Csizmadia:
Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF, MP2, DFT, and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory. 1026-1042 - Jos A. Hageman, Ron Wehrens, René de Gelder, Lutgarde M. C. Buydens:
Powder pattern indexing using the weighted crosscorrelation and genetic algorithms. 1043-1051 - David C. Chatfield, Alberto Augsten, Cassian D'Cunha, Sergio E. Wong:
Methyl dynamics in crystalline amino acids: MD and NMR. 1052-1058 - Shenghua Shi, Lisa Yan, Yang Yang, Jodi Fisher-Shaulsky, Tom Thacher:
An extensible and systematic force field, ESFF, for molecular modeling of organic, inorganic, and organometallic systems. 1059-1076 - Toshimasa Ishida, George C. Schatz:
A local interpolation scheme using no derivatives in potential sampling: Application to O(1D) + H2 system. 1077-1086 - Alice Glättli, Xavier Daura, Wilfred F. van Gunsteren:
A novel approach for designing simple point charge models for liquid water with three interaction sites. 1087-1096 - Lionello Pogliani:
Complete graph conjecture for inner-core electrons: Homogeneous index case. 1097-1109 - Suzanne W. Sirois, Emil I. Proynov, Jean-François Truchon, Christos M. Tsoukas, Dennis R. Salahub:
A density functional study of the hydrogen-bond network within the HIV-1 protease catalytic site cleft. 1110-1119 - Roger A. Klein:
Hydrogen bonding in diols and binary diol-water systems investigated using DFT methods. II. Calculated infrared OH-stretch frequencies, force constants, and NMR chemical shifts correlate with hydrogen bond geometry and electron density topology. A reevaluation of geometrical criteria for hydrogen bonding. 1120-1131 - Nikolay A. Anikin, Vladislav L. Bugaenko, M. V. Frash, Leonid Gorb, Jerzy Leszczynski:
Localized basis orbitals: Minimization of 2-electron integrals array and orthonormality of basis set. 1132-1141 - Erik Van Lenthe, Evert Jan Baerends:
Optimized Slater-type basis sets for the elements 1-118. 1142-1156
Volume 24, Number 10, 30 July 2003
- András Perczel, Anna K. Füzéry, Attila G. Császár:
Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide, a model for polar side-chain containing peptides. 1157-1171 - Vladimir Hnizdo, Adam Fedorowicz, Harshinder Singh, Eugene Demchuk:
Statistical thermodynamics of internal rotation in a hindering potential of mean force obtained from computer simulations. 1172-1183 - Jon Baker, Peter Pulay:
Assessment of the OLYP and O3LYP density functionals for first-row transition metals. 1184-1191