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ORCIDJournal 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 - Nisanth N. Nair, Thomas Bredow, Karl Jug:
Molecular dynamics implementation in MSINDO: Study of silicon clusters. 1255-1263 - K. Fiaty, C. Charcosset, B. Perrin, R. Couturier, B. Maïsterrena:
ATP-dependent active transport simulations based on a phosphatase-channel-kinase membrane structure. 1264-1276 - Wolfgang Quapp:
Reaction pathways and projection operators: Application to string methods. 1277-1285 - Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos:
Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine. 1286-1294 - Robert M. Dirks, Niles A. Pierce:
An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. 1295-1304 - Gordon M. Crippen:
Cluster distance geometry of polypeptide chains. 1305-1312
Volume 25, Number 11, August 2004
- Yuri A. Kosinsky, Pavel E. Volynsky, Philippe Lagant, Gérard Vergoten, Ei-Ichiro Suzuki, Alexander S. Arseniev, Roman G. Efremov:
Development of the force field parameters for phosphoimidazole and phosphohistidine. 1313-1321 - Marina Udier-Blagovi, Patricia Morales De Tirado, Shoshannah A. Pearlman, William L. Jorgensen:
Accuracy of free energies of hydration using CM1 and CM3 atomic charges. 1322-1332 - Roberto Improta, Vincenzo Barone:
Assessing the reliability of density functional methods in the conformational study of polypeptides: The treatment of intraresidue nonbonding interactions. 1333-1341 - Kenneth B. Wiberg:
Basis set effects on calculated geometries: 6-311++G** vs. aug-cc-pVDZ. 1342-1346 - Jaime Fernández Rico, Rafael López, Ignacio Ema, Guillermo Ramírez:
Electrostatic potentials and fields from density expansions of deformed atoms in molecules. 1347-1354 - Jaime Fernández Rico, Rafael López, Guillermo Ramírez, Ignacio Ema, E. V. Ludeña:
Analytical method for the representation of atoms-in-molecules densities. 1355-1363 - Bo Liao, Tian-Ming Wang:
New 2D graphical representation of DNA sequences. 1364-1368 - Gennady N. Chuev, Maxim V. Fedorov:
Wavelet algorithm for solving integral equations of molecular liquids. A test for the reference interaction site model. 1369-1377 - Aisha El-Sherbiny, Raymond A. Poirier:
An evaluation of the radial part of numerical integration commonly used in DFT. 1378-1384 - Dawoon Jung, Jie Floyd, Tamara M. Gund:
A comparative molecular field analysis (CoMFA) study using semiempirical, density functional, ab initio methods and pharmacophore derivation using DISCOtech on sigma 1 ligands. 1385-1399 - Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III:
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. 1400-1415 - Peter A. Sims, Chung F. Wong, James Andrew McCammon:
Charge optimization of the interface between protein kinases and their ligands. 1416-1429
Volume 25, Number 12, September 2004
- Yun Xiang, Da W. Zhang, John Z. H. Zhang:
Fully quantum mechanical energy optimization for protein-ligand structure. 1431-1437 - Jörg-Rüdiger Hill, Johann Plank:
Retardation of setting of plaster of Paris by organic acids: Understanding the mechanism through molecular modeling. 1438-1448 - Hui Li, Jan H. Jensen:
Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: New energy gradients and molecular surface tessellation. 1449-1462 - Stefan Grimme:
Accurate description of van der Waals complexes by density functional theory including empirical corrections. 1463-1473 - Tim N. Heinz, Philippe H. Hünenberger:
A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions. 1474-1486 - Daiqian Xie, Jun Zeng:
Hydrogen bonding and solvatochromatic shift of the lowest 1(n, *) excitation of s-tetrazine in its hydrated clusters and dilute solutions. 1487-1495 - Bahram Hemmateenejad, Mohammad A. Safarpour, Ramin Miri, Fariba Taghavi:
Application of ab initio theory to QSAR study of 1, 4-dihydropyridine-based calcium channel blockers using GA-MLR and PC-GA-ANN procedures. 1495-1503 - Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III:
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. 1504-1514 - Leslaw K. Bieniasz:
A fourth-order accurate, Numerov-type, three-point finite-difference discretization of electrochemical reaction-diffusion equations on nonuniform (exponentially expanding) spatial grids in one-dimensional space geometry. 1515-1521 - Ilona Hudáky, Péter Hudáky, András Perczel:
Solvation model induced structural changes in peptides. A quantum chemical study on Ramachandran surfaces and conformers of alanine diamide using the polarizable continuum model. 1522-1531 - Christian Silvio Pomelli:
A tessellationless integration grid for the polarizable continuum model reaction field. 1532-1541 - Xavier López, Jorge A. Fernández, Susanna Romo, Jean François Paul, Leonid Kazansky, Josep M. Poblet:
Are the solvent effects critical in the modeling of polyoxoanions? 1542-1549
Volume 25, Number 13, October 2004
- Karl Jug, Thomas Bredow:
Models for the treatment of crystalline solids and surfaces. 1551-1567 - Holger Merlitz, Thomas Herges, Wolfgang Wenzel:
Fluctuation analysis and accuracy of a large-scale in silico screen. 1568-1575 - Chinapong Kritayakornupong, Kristof Plankensteiner, Bernd M. Rode:
Structure and dynamics of the Cr(III) ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation. 1576-1583 - Alexander D. MacKerell Jr.:
Empirical force fields for biological macromolecules: Overview and issues. 1584-1604 - Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang, Gregory S. Couch, Daniel M. Greenblatt, Elaine C. Meng, Thomas E. Ferrin:
UCSF Chimera - A visualization system for exploratory research and analysis. 1605-1612 - Felix Autenrieth, Emad Tajkhorshid, Jérôme Baudry, Zaida Luthey-Schulten:
Classical force field parameters for the heme prosthetic group of cytochrome c. 1613-1622 - Jason Wagoner, Nathan A. Baker:
Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. 1623-1629 - Richard E. Gillilan, Ryan H. Lilien:
Optimization and dynamics of protein-protein complexes using B-splines. 1630-1646 - Maria Del Carmen Michelini, Nino Russo, Mohammad Esmaïl Alikhani, Bernard Silvi:
Energetic and topological analysis of the reaction of Mo and Mo2 with NH3, C2H2, and C2H4 molecules. 1647-1655 - Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren:
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. 1656-1676
Volume 25, Number 14, November 2004
- Publisher's Note: "Software News and Updates" section of the Journal of Computational Chemistry. i
- Edward N. Brothers, Dimas Suárez, David W. Deerfield II, Kenneth M. Merz Jr.:
PM3-compatible zinc parameters optimized for metalloenzyme active sites. 1677-1692 - Xueguang Shao, Longjiu Cheng, Wensheng Cai:
A dynamic lattice searching method for fast optimization of Lennard-Jones clusters. 1693-1698 - Zhi-Xiang Wang, Yong Duan:
Solvation effects on alanine dipeptide: A MP2/cc-pVTZ//MP2/6-31G** study of (Φ, Ψ) energy maps and conformers in the gas phase, ether, and water. 1699-1716 - Joseph P. Kenny, Steven Benson, Yuri Alexeev, Jason Sarich, Curtis L. Janssen, Lois Curfman McInnes, Manojkumar Krishnan, Jarek Nieplocha, Elizabeth Jurrus, Carl Fahlstrom, Theresa L. Windus:
Component-based integration of chemistry and optimization software. 1717-1725 - Qi Shen, Jian-Hui Jiang, Chen-Xu Jiao, Wei-Qi Lin, Guo-Li Shen, Ru-Qin Yu:
Hybridized particle swarm algorithm for adaptive structure training of multilayer feed-forward neural network: QSAR studies of bioactivity of organic compounds. 1726-1735 - Cristina P. Gonçalves, José R. Mohallem:
A new algorithm to handle finite nuclear mass effects in electronic calculations: The ISOTOPE program. 1736-1739 - Oh-Seuk Lee, Kiyull Yang, Keum Duck Kang, In Sun Koo, Chan-Kyung Kim, Ikchoon Lee:
Ab initio and DFT studies on hydrolyses of phosphorus halides. 1740-1748 - F. Marty Ytreberg, Daniel M. Zuckerman:
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. 1749-1759 - Julien Michel, Richard D. Taylor, Jonathan W. Essex:
The parameterization and validation of generalized born models using the pairwise descreening approximation. 1760-1770 - Masao Masamura:
The effect of basis set superposition error on the convergence of intermolecular interaction energies for deprotonated complexes. 1771-1778 - Pawel Szabelski, Julian Talbot:
Kinetics and equilibrium of multicomponent adsorption on chiraly templated surfaces. 1779-1786 - Ernesto Estrada, Eduardo J. Delgado, Joel B. Alderete, Gonzalo A. Jaña:
Quantum-connectivity descriptors in modeling solubility of environmentally important organic compounds. 1787-1796 - Premal S. Shah, Geoffrey K. Hom, Stephen L. Mayo:
Preprocessing of rotamers for protein design calculations. 1797-1800
- Jason Wagoner, Nathan A. Baker:
Jason Wagoner and Nathan A. Baker, "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models, "Journal of Computational Chemistry(2004) 25(13) 1623-1629. 1801
Volume 25, Number 15, November 2004
- Shunzhou Wan, Peter V. Coveney, Darren R. Flower:
Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: Can the α3 and β2m domains be neglected? 1803-1813 - Michael P. Belmares, Mario Blanco, William A. Goddard III, Richard B. Ross, Gregg A. Caldwell, Shih-Hung Chou, J. Pham, Peter M. Olofson, Cristina Thomas:
Hildebrand and Hansen solubility parameters from Molecular Dynamics with applications to electronic nose polymer sensors. 1814-1826 - Jian Wan, Li Zhang, Guangfu Yang:
Quantitative structure-activity relationships for phenyl triazolinones of protoporphyrinogen oxidase inhibitors: A density functional theory study. 1827-1832 - Weizhong Yan, Ying Xue, Hua Zhu, Jun Zeng, Daiqian Xie:
A theoretical study of solvent effects on tautomerism and electronic absorption spectra of 3-hydroxy-2-mercaptopyridine and 2, 3-dihydroxypyridine. 1833-1839 - Robert J. Deeth, Natalie Fey:
The performance of nonhybrid density functionals for calculating the structures and spin states of Fe(II) and Fe(III) complexes. 1840-1848 - Evangelos A. Coutsias, Chaok Seok, Ken A. Dill:
Using quaternions to calculate RMSD. 1849-1857 - Henryk A. Witek, Keiji Morokuma:
Systematic study of vibrational frequencies calculated with the self-consistent charge density functional tight-binding method. 1858-1864 - Bernd Kuhn, Peter A. Kollman, Martin Stahl:
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. 1865-1872 - Claudio Marcelo Zicovich-Wilson, Fabien Pascale, C. Roetti, V. R. Saunders, Roberto Orlando, Roberto Dovesi:
Calculation of the vibration frequencies of α-quartz: The effect of Hamiltonian and basis set. 1873-1881 - Yoshiumi Kawamura, Hiromi Nakai:
A hybrid approach combining energy density analysis with the interaction energy decomposition method. 1882-1887 - Jia-Xu Zhang, Jing-Yao Liu, Ze-Sheng Li, Chia-Chung Sun:
Theoretical study on reaction mechanism of the fluoromethylene radical with nitrogen dioxide. 1888-1894 - Eric Martineau, Pierre-Jean L'Heureux, John R. Gunn:
Biased fragment distribution in MC simulation of protein folding. 1895-1903 - Roberto L. A. Haiduke, Luiz G. M. de Macedo, Rugles C. Barbosa, Albérico B. F. da Silva:
A polynomial version of the generator coordinate Dirac-Fock method. 1904-1909 - Yasuhito Ohta, Koji Ohta:
Interconversion behavior of the CH bond in the CH radical cation: Ab initio molecular dynamics study. 1910-1919 - Philippe Soler, Franck Fuster, Hilaire Chevreau:
Fast topological analysis of 2D and 3D grids of data: Application to the atoms in molecule (AIM) and the electron localization function (ELF). 1920-1925 - Heather Netzloff, Mark S. Gordon:
Fast fragments: The development of a parallel effective fragment potential method. 1926-1936
Volume 25, Number 16, December 2004
- Francesc Corcho, Josep Cantó, Juan Jesús Pérez:
Comparative analysis of the conformational profile of substance P using simulated annealing and molecular dynamics. 1937-1952 - Joseph M. Hayes, James C. Greer, David A. Morton-Blake:
A force-field description of short-range repulsions for high density alkane molecular dynamics simulations. 1953-1966 - Michael S. Lee, Freddie R. Salsbury Jr., Mark A. Olson:
An efficient hybrid explicit/implicit solvent method for biomolecular simulations†. 1967-1978 - Otto Exner, Stanislav Böhm:
Enthalpies of formation of monoderivatives of hydrocarbons: Interaction of polar groups with an alkyl group. 1979-1986 - Jaime Fernández Rico, Rafael López, Ignacio Ema, Guillermo Ramírez:
Efficiency of the algorithms for the calculation of Slater molecular integrals in polyatomic molecules. 1987-1994 - Rie Tatsumi, Yoshifumi Fukunishi, Haruki Nakamura:
A hybrid method of molecular dynamics and harmonic dynamics for docking of flexible ligand to flexible receptor. 1995-2005 - Ramkumar V. Vadali, Yan Shi, Sameer Kumar, Laxmikant V. Kalé, Mark E. Tuckerman, Glenn J. Martyna:
Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers. 2006-2022 - Xingfa Gao, Hui Yuan, Zhenling Chen, Yuliang Zhao:
Theoretical studies of structures and stabilities of a new odd-numbered fullerene dimer: C141. 2023-2030 - Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif A. Eriksson, Maria João Ramos:
Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme. 2031-2037 - John Mongan, David A. Case, James Andrew McCammon:
Constant pH molecular dynamics in generalized Born implicit solvent. 2038-2048 - Ninad V. Prabhu, Peijuan Zhu, Kim A. Sharp:
Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. 2049-2064 - Joris van Droogenbroeck, Ben Swerts, Lothar Schäfer, Christian Van Alsenoy:
Solids modeled by ab initio crystal field methods, part 22: The Fock matrix transformed supermolecule model and the structure determination of D-erythronic acid-3, 4-carbonate. 2065-2072 - Chan Kyung Kim, Kyung A. Lee, Kwan Hoon Hyun, Heung Jin Park, In Young Kwack, Chang Kon Kim, Hai Whang Lee, Bon-Su Lee:
Prediction of physicochemical properties of organic molecules using van der Waals surface electrostatic potentials. 2073-2079
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