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Journal of Computational Chemistry, Volume 25
Volume 25, Number 1, 15 January 2004
- Sandeep Patel
, Charles L. Brooks III:
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. 1-16 - Stewart A. Adcock:
Peptide backbone reconstruction using dead-end elimination and a knowledge-based forcefield. 16-27 - Nandou Lu, David A. Kofke, Thomas B. Woolf:
Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods. 28-40 - Luc Claes, Jean-Pierre François, Michael S. Deleuze
:
Theoretical study of the internal conversion of sulfoxide precursors of poly-isothianaphthene and related polymers. 40-50 - Haruhiko Fukaya
, Taizo Ono:
DFT-GIAO calculations of 19F NMR chemical shifts for perfluoro compounds. 51-60 - Michael J. McQuaid, Huai Sun, David Rigby:
Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains. 61-71 - Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun:
Ab initio direct dynamics studies on the reaction of H atom with CH3CH2Cl. 72-82 - Manuel Piacenza
, Stefan Grimme:
Systematic quantum chemical study of DNA-base tautomers. 83-99 - Ricard Casadesús, Miquel Moreno
, Àngels González-Lafont
, José M. Lluch
, Matthew P. Repasky:
Testing electronic structure methods for describing intermolecular H · · · H interactions in supramolecular chemistry. 99-105 - Takao Motoki, Akinobu Shiga:
New reaction simulator LUMMOX and its application for prediction of catalytic activities. 106-111 - Martin Preuss, Wolf G. Schmidt, Kaori Seino
, Jürgen Furthmüller
, Friedhelm Bechstedt:
Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials. 112-122 - Juha Linnanto
, Jouko E. Korppi-Tommola:
Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: Comparison of semiempirical, ab initio, and density functional results. 123-138 - Ivan Tubert-Brohman, Cristiano Ruch Werneck Guimarães
, Matthew P. Repasky, William L. Jorgensen:
Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens. 138-150 - Bülent Balta, Viktorya Aviyente
:
Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer - Erratum. 151
Volume 25, Number 2, 30 January 2004
- Xavier Gironés, Ramon Carbó-Dorca
:
TGSA-Flex: Extending the capabilities of the Topo-Geometrical superposition algorithm to handle flexible molecules. 153-159 - Nohad Gresh, Gen-Bin Shi:
Conformation-dependent intermolecular interaction energies of the triphosphate anion with divalent metal cations. Application to the ATP-binding site of a binuclear bacterial enzyme. A parallel quantum chemical and polarizable molecular mechanics investigation. 160-168 - Ho-Jin Lee
, Jong Hyun Kim, Hee Jung Jung, Kun-Young Kim, Eun-Jung Kim, Young-Sang Choi, Chang-Ju Yoon:
Computational study of conformational preferences of thioamide-containing azaglycine peptides. 169-178 - Ayako Nakata, T. Baba, H. Takahashi, Hiromi Nakai
:
Theoretical study on the excited states of psoralen compounds bonded to a thymine residue. 179-188 - Célia Fonseca Guerra
, Jan-Willem Handgraaf
, Evert Jan Baerends, Friedrich Matthias Bickelhaupt
:
Voronoi deformation density (VDD) charges: Assessment of the Mulliken, Bader, Hirshfeld, Weinhold, and VDD methods for charge analysis. 189-210 - Thomas S. Hofer
, Hung T. Tran, Christian F. Schwenk, Bernd M. Rode:
Characterization of dynamics and reactivities of solvated ions by ab initio simulations. 211-217 - Yue Zhang, Shaowen Zhang, Qian Shu Li:
A dual-level ab initio and hybrid density functional theory dynamics study on the unimolecular decomposition reaction C2H5O CH2O + CH3. 218-226 - Susana Pereira
, Pedro Alexandrino Fernandes, Maria João Ramos
:
Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2-azido-2-deoxyribonucleoside 5-diphosphates. 227-237 - Holger Gohlke, David A. Case:
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. 238-250 - Qian-Shu Li, Chao Yang Wang:
Direct dynamic study on the hydrogen abstraction reaction CH3CN + OH CH2CN + H2O. 251-257 - Zheng-Wang Qu, Hui Zhu
, Ze-Sheng Li, Xing-Kang Zhang, Qi-Yuan Zhang:
Density functional investigation of reaction of borohydride cation BH2+ with propylene. 258-264 - Michael Feig, Alexey Onufriev
, Michael S. Lee, Wonpil Im, David A. Case, Charles L. Brooks III:
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. 265-284 - Tamás Beke
, Imre G. Csizmadia, András Perczel:
On the flexibility of -peptides. 285-307 - Jean-Philip Piquemal
, Benjamin Williams-Hubbard, Natalie Fey
, Robert J. Deeth
, Nohad Gresh, Claude Giessner-Prettre:
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA-LF. 308 - Yi-Gui Wang, Chérif F. Matta
, Nick Henry Werstiuk:
Comparison of localization and delocalization indices obtained with Hartree-Fock and conventional correlated methods: Effect of Coulomb correlation. 309-459
Volume 25, Number 3, February 2004
- Vladimir Pelmenschikov
, Kyung-Bin Cho
, Per E. M. Siegbahn:
Class I ribonucleotide reductase revisited: The effect of removing a proton on Glu441. 311-321 - Jennifer I. Chavez, Maira M. Carrillo, Kyle A. Beran:
Isomers of C20: An energy profile III. 322-327 - Robert J. Harrison
:
Krylov subspace accelerated inexact Newton method for linear and nonlinear equations. 328-334 - Jií Kolafa
:
Time-reversible always stable predictor-corrector method for molecular dynamics of polarizable molecules. 335-342 - Vinzenz Bachler:
A simple computational scheme for obtaining localized bonding schemes and their weights from a CASSCF wave function. 343-367 - A. N. Artemyev, Eduardo V. Ludeña
, Valentin V. Karasiev
, Antonio J. Hernández:
A finite B-spline basis set for accurate diatomic molecule calculations. 368-374 - Luca Frediani, Roberto Cammi
, Christian Silvio Pomelli
, Jacopo Tomasi, Kenneth Ruud
:
New developments in the symmetry-adapted algorithm of the Polarizable Continuum Model. 375-385 - Ivan Infante
, Lucas Visscher
:
QM/MM study of aqueous solvation of the uranyl fluoride [UO2F42-] complex. 386-392 - Serena Donnini, André H. Juffer
:
Calculation of affinities of peptides for proteins. 393-411 - Marco Cecchini
, Peter Kolb
, Nicolas Majeux, Amedeo Caflisch:
Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. 412-422 - Li Sheng, Ze-Sheng Li, Jing-Yao Liu, Jing-Fa Xiao, Chia-Chung Sun:
Theoretical study on the rate constants for the C2H5 + HBr C2H6 + Br reaction. 423-428 - Rachel Crespo-Otero
, Luis A. Montero
, Giselle Rosquete, J. Alexander Padrón-García, Raúl H. González-Jonte:
Theoretical model of internal rotation in monosubstituted derivatives of furfural. 429-438 - Xavier Fradera, Miquel Solà
:
Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory. 439-446 - Shingo Urata, Seiji Tsuzuki, Akira Takada, Masuhiro Mikami, Tadafumi Uchimaru, Akira Sekiya:
Analysis of the intermolecular interactions between CH3OCH3, CF3OCH3, CF3OCF3, and CH2F2, CHF3. 447-459 - Ayako Nakata, T. Baba, H. Takahashi, Hiromi Nakai
:
Theoretical study on the excited states of psoralen compounds bonded to a thymine residue. 309
Volume 25, Number 4, March 2004
- Yi Ren, San-Yan Chu:
Modified Gaussian-2 level investigation of the identity ion-pair SN2 reactions of lithium halide and methyl halide with inversion and retention mechanisms. 461-471 - Lingchun Song, Wei Wu, Qianer Zhang, Sason Shaik:
A practical valence bond method: A configuration interaction method approach with perturbation theoretic facility. 472-478 - Emilio Gallicchio
, Ronald M. Levy:
AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. 479-499 - Xiang-Yuan Li, Ke-Xiang Fu:
Continuous medium theory for nonequilibrium solvation: I. How to correctly evaluate solvation free energy of nonequilibrium. 500-509 - Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson
, Ken A. Dill:
A kinematic view of loop closure. 510-528 - Mitsunori Ikeguchi:
Partial rigid-body dynamics in NPT, NPAT and NPT ensembles for proteins and membranes. 529-541 - Michael J. Liddell, Davor Margetic, Anthony S. Mitchell, Ronald N. Warrener:
An AM1 semiempirical study of host-guest complexation in hemicarcerand complexes. 542-557 - Li Wang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Direct ab initio dynamics studies on the hydrogen-abstraction reactions of OH radicals with HOX (X = F, Cl, and Br). 558-564 - S. Banu Ozkan, Hagai Meirovitch:
Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphin. 565-572 - Francisco Corzana, Mohammed S. Motawia
, Catherine Hervé du Penhoat, Serge Pérez, Sarah M. Tschampel, Robert J. Woods
, Søren Balling Engelsen
:
A hydration study of (1->4) and (1->6) linked alpha-glucans by comparative 10 ns molecular dynamics simulations and 500-MHz NMR. 573-586 - Johannes Neugebauer
, Markus Reiher
:
Vibrational center-ligand couplings in transition metal complexes. 587-597 - Shinichi Yamabe, Noriko Tsuchida:
A computational study of the role of hydrogen bonds in SN1 and E1 reactions. 598-608 - Maxim Totrov
:
Accurate and efficient generalized born model based on solvent accessibility: Derivation and application for LogP octanol/water prediction and flexible peptide docking. 609-619
Volume 25, Number 5, 15 April 2004
- Martin R. Saunders:
Stochastic search for isomers on a quantum mechanical surface. 621-626 - Richard I. Maurer, Christopher A. Reynolds
:
A multilayered approach to approximating solute polarization. 627-631 - Zheng Yuan, John S. Mattick
, Rohan D. Teasdale
:
SVMtm: Support vector machines to predict transmembrane segments. 632-636 - John Cullen:
Performance of the Harris functional for extended basis sets at the Hartree-Fock and density functional levels. 637-648 - Siân T. Howard
, Colin D. Abernethy:
Intramolecular CHCcarbene hydrogen bonds and competing interactions in monoprotonated tripodal carbenes. 649-659 - Ali Khalaf Al-Matar
, David A. Rockstraw:
A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters. 660-668 - Fan Wang, Lemin Li:
Numerical examination of performance of some exchange-correlation functionals for molecules containing heavy elements. 669-677 - Michael Patra, Mikko Karttunen
:
Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties. 678-689 - Bülent Balta
, Viktorya Aviyente
:
Solvent effects on glycine II. Water-assisted tautomerization. 690-703 - Piotr Zarzycki
, Robert Charmas, Pawel Szabelski:
Study of proton adsorption at heterogeneous oxide/electrolyte interface. Prediction of the surface potential using Monte Carlo simulations and 1-pK approach. 704-711 - Eran Eyal, Rafael Najmanovich
, Brendan J. McConkey, Marvin Edelman, Vladimir Sobolev:
Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. 712-724 - Paul Winget
, Timothy Clark
:
Enthalpies of formation from B3LYP calculations. 725-733 - D. B. Chesnut, L. D. Quin:
Nature of bonding in the sulfuryl group. 734-738 - Kazuhiro Ishida:
Accurate and fast algorithm of the molecular incomplete gamma function with a complex argument. 739-748 - Harry A. Stern:
Simple algorithm for isothermal-isobaric molecular dynamics. 749-761 - M. Michael Gromiha, Shandar Ahmad
, Makiko Suwa
:
Neural network-based prediction of transmembrane -strand segments in outer membrane proteins. 762-767 - M. K. Shukla, Jerzy Leszczynski:
TDDFT investigation on nucleic acid bases: Comparison with experiments and standard approach. 768-778
Volume 25, Number 6, 30 April 2004
- Matthias Keil, Thomas E. Exner
, Jürgen Brickmann:
Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network. 779-789 - David Curcó, Carlos Alemán
:
Performance of SuSi: A method for generating atomistic models of amorphous polymers based on a random search of energy minima. 790-798 - Rochus Schmid
:
Car-Parrinello simulations with a real space method. 799-812 - Jun Zeng
, Daiqian Xie:
Hydrogen bonding and solvent effects on the lowest 1(n, *) excitations of triazines in water. 813-822 - Nohad Gresh, Sherif A. Kafafi, Jean-François Truchon, Dennis R. Salahub:
Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study. 823-834 - Xiang-Yuan Li, Ke-Xiang Fu, Quan Zhu, Min-Hua Shan:
Continuous medium theory for nonequilibrium solvation: II. Interaction energy between solute charge and reaction field and single-sphere model for spectral shift. 835-842 - Jinn-Moon Yang
:
Development and evaluation of a generic evolutionary method for protein-ligand docking. 843-857 - Ricardo L. Mancera
, Per Källblad, Nikolay P. Todorov:
Ligand-protein docking using a quantum stochastic tunneling optimization method. 858-864 - Yang Zhang
, Jeffrey Skolnick:
SPICKER: A clustering approach to identify near-native protein folds. 865-871 - Dmitri G. Fedorov, Ryan M. Olson, Kazuo Kitaura, Mark S. Gordon, Shiro Koseki:
A new hierarchical parallelization scheme: Generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO). 872-880 - Feng Yang, Zhen-Dong Wang, Yun-Ping Huang:
Modification of the Wiener index 4. 881-887 - Fabien Pascale
, Claudio Marcelo Zicovich-Wilson
, F. López Gejo, Bartolomeo Civalleri
, Roberto Orlando, Roberto Dovesi:
The calculation of the vibrational frequencies of crystalline compounds and its implementation in the CRYSTAL code. 888-897
Volume 25, Number 7, May 2004
- Harold Basch, Mark A. Ratner:
Reduced basis set for the gold atom in cluster complexes. 899-906 - Yi Zhao, Wenguo Xu, Qian-Shu Li, Yaoming Xie, Henry F. Schaefer III:
The arsenic clusters Asn (n = 1-5) and their anions: Structures, thermochemistry, and electron affinities. 907-920 - Anatoliy Volkov, Philip Coppens:
Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning. 921-934 - Alexander H. Boschitsch, Marcia O. Fenley:
Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation. 935-955 - Juan Cortés, Thierry Siméon
, Magali Remaud-Siméon, Vinh Tran:
Geometric algorithms for the conformational analysis of long protein loops. 956-967 - Xiaoping Han, Yue Zhang, Huibin Xu:
First-principles pair potentials across the metal-ceramic interface. 968-973 - Massimiliano Aschi
, Costantino Zazza
, Riccardo Spezia
, Cecilia Bossa
, Alfredo Di Nola, Maurizio Paci, Andrea Amadei
:
Conformational fluctuations and electronic properties in myoglobin. 974-984 - Arnaud Blondel:
Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal Alchemical path, and practical solutions. 985-993 - Mihai V. Putz
, Nino Russo
, Emilia Sicilia:
On the applicability of the HSAB principle through the use of improved computational schemes for chemical hardness evaluation. 994-1003
Volume 25, Number 8, June 2004
- Olgun Guvench, Charles L. Brooks III:
Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. 1005-1014 - Nathalie Basdevant
, Daniel Borgis, Tâp Ha-Duong
:
A semi-implicit solvent model for the simulation of peptides and proteins. 1015-1029 - Delano P. Chong, Erik Van Lenthe, Stan J. A. van Gisbergen, Evert Jan Baerends:
Even-tempered slater-type orbitals revisited: From hydrogen to krypton. 1030-1036 - Henk Bekker, Jur P. van den Berg, Tsjerk A. Wassenaar
:
A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints. 1037-1046 - Anil Kumar, Michaela Knapp-Mohammady, P. C. Mishra, Sándor Suhai:
A theoretical study of structures and electron affinities of radical anions of guanine-cytosine, adenine-thymine, and hypoxanthine-cytosine base pairs. 1047-1059 - Arturo Robertazzi, James A. Platts:
Hydrogen bonding, solvation, and hydrolysis of cisplatin: A theoretical study. 1060-1067 - Abdallah Sayyed-Ahmad
, Kagan Tuncay
, Peter J. Ortoleva:
Efficient solution technique for solving the Poisson-Boltzmann equation. 1068-1074 - Leslaw K. Bieniasz
:
Improving the accuracy of the spatial discretization in finite-difference electrochemical kinetic simulations, by means of the extended Numerov method. 1075-1083 - András Perczel, Péter Hudáky, Anna K. Füzéry, Imre G. Csizmadia:
Stability issues of covalently and noncovalently bonded peptide subunits. 1084-1100 - Zlatko Vasilkoski, David L. Weaver:
Diffusion-collision model algorithms for protein folding kinetics. 1101-1107
Volume 25, Number 9, 15 July 2004
- Publisher's note: Sir John A. Pople, 1925-2004. 1108
- J. Ulises Reveles, Andreas M. Köster:
Geometry optimization in density functional methods. 1109-1116 - Andy Becue
, Nathalie Meurice:
Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density. 1117-1126 - Kenneth B. Wiberg, Yi-Gui Wang:
Conformational energies for 2-substituted butanes. 1127-1132 - Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe:
Sampling protein conformations and pathways. 1133-1148 - Genyuan Li, Jacqueline Schoendorf, Tak-San Ho, Herschel A. Rabitz
:
Multicut-HDMR with an application to an ionospheric model. 1149-1156 - Junmei Wang
, Romain M. Wolf, James W. Caldwell, Peter A. Kollman, David A. Case:
Development and testing of a general amber force field. 1157-1174 - Hiroaki Umeda, Shiro Koseki, Umpei Nagashima:
Improvement of parallelization performance of GAMESS: Global sum and (semi-)direct integral calculation in multireference perturbation calculation. 1175-1183 - Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study on the mechanism of the 1CHCl + NO2 reactions. 1184-1190 - Sergio Aragon:
A precise boundary element method for macromolecular transport properties. 1191-1205 - Christopher C. Lovallo
, Mariusz Klobukowski:
Improved model core potentials for the second- and third-row transition metals. 1206-1213
Volume 25, Number 10, 30 July 2004
- Delia Soto-Castro, Patricia Guadarrama:
Macrocyclic vs. dendrimeric effect. A DFT study. 1215-1226 - Ignacio Fdez. Galván
, M. Elena Martín, Manuel A. Aguilar
:
A new method to locate saddle points for reactions in solution by using the free-energy gradient method and the mean field approximation. 1227-1233 - David Muñoz
, Coen de Graaf, Francesc Illas
:
Putting error bars on the Ab Initio theoretical estimates of the magnetic coupling constants: The parent compounds of superconducting cuprates as a case study. 1234-1241 - Martin Almlöf, Bjørn Olav Brandsdal
, Johan Åqvist:
Binding affinity prediction with different force fields: Examination of the linear interaction energy method. 1242-1254