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ORCIDJournal of Computational Chemistry, Volume 23
Volume 23, Number 1, January 2002
- B. Jayaram
, K. McConnell, Surjit B. Dixit, A. Das, David L. Beveridge:
Free-energy component analysis of 40 protein-DNA complexes: A consensus view on the thermodynamics of binding at the molecular level. 1-14
- Shuanghong Huo, Irina Massova, Peter A. Kollman:
Computational alanine scanning of the 1: 1 human growth hormone-receptor complex. 15-27 - Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova:
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. 28-34 - Lalith E. Perera, Thomas A. Darden, Lee G. Pedersen:
Predicted solution structure of zymogen human coagulation FVII. 35-47 - Martin J. Field:
Simulating enzyme reactions: Challenges and perspectives. 48-58 - Maricel Torrent, Djamaladdin G. Musaev, Harold Basch, Keiji Morokuma:
Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase. 59-76 - Keith D. Ball, Burak Erman, Ken A. Dill:
The elastic net algorithm and protein structure prediction. 77-83 - Dean J. Tantillo, K. N. Houk:
Transition state docking: A probe for noncovalent catalysis in biological systems. Application to antibody-catalyzed ester hydrolysis. 84-95 - Ramkumar Rajamani, Jiali Gao:
Combined QM/MM study of the opsin shift in bacteriorhodopsin. 96-105 - Marek Orzechowski, Piotr Cieplak, Lucjan Piela:
Theoretical calculation of the coiled-coil stability in water in the context of its possible use as a molecular rack. 106-110 - Jaroslaw Meller, Michael Wagner, Ron Elber:
Maximum feasibility guideline in the design and analysis of protein folding potentials. 111-118 - Pemra Doruker, Robert L. Jernigan, Ivet Bahar:
Dynamics of large proteins through hierarchical levels of coarse-grained structures. 119-127 - Walter Rocchia, Sundaram Sridharan, Anthony Nicholls, Emil Alexov, Alessandro Chiabrera, Barry Honig:
Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects. 128-137 - Corey Hardin, Michael P. Eastwood, Michael C. Prentiss, Zaida Luthey-Schulten, Peter G. Wolynes:
Folding funnels: The key to robust protein structure prediction. 138-146 - Brian N. Dominy, Charles L. Brooks III:
Identifying native-like protein structures using physics-based potentials. 147-160 - D. K. Klimov, D. Thirumalai:
Is there a unique melting temperature for two-state proteins?. 161-165 - Hagai Meirovitch:
Polymer collapse, protein folding, and the percolation threshold. 166-171 - Ailan Cheng, David J. Diller, Steven L. Dixon, William J. Egan, George Lauri, Kenneth M. Merz Jr.:
Computation of the physio-chemical properties and data mining of large molecular collections. 172-183 - Sam Kalat, Geoffrey Mann, Jan Hermans:
Qmd-plot: A graphical utility for rapid preliminary analysis of time series of fluctuating data, developed in the context of molecular dynamics simulations. 184-188 - Marek Wojciechowski, Jeffrey Skolnick:
Docking of small ligands to low-resolution and theoretically predicted receptor structures. 189-197
Volume 23, Number 2, January 2002
- I-Jen Chen, Daxu Yin, Alexander D. MacKerell Jr.:
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. 199-213 - Olgun Guvench, Jörg Weiser, Peter S. Shenkin, István Kolossváry, W. Clark Still:
Application of the frozen atom approximation to the GB/SA continuum model for solvation free energy. 214-221 - Aline Thaís Bruni, Vitor B. P. Leite, Márcia M. C. Ferreira:
Conformational analysis: A new approach by means of chemometrics. 222-236 - Shuhua Li, Jing Ma, Yuansheng Jiang:
Linear scaling local correlation approach for solving the coupled cluster equations of large systems. 237-244 - John L. Klepeis, Christodoulos A. Floudas:
Ab initio prediction of helical segments in polypeptides. 245-266 - Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu, Kuo-Chen Chou:
Support vector machines for predicting HIV protease cleavage sites in protein. 267-274 - Andreas Klamt, Frank Eckert, Martin Hornig, Michael E. Beck, Thorsten Bürger:
Prediction of aqueous solubility of drugs and pesticides with COSMO-RS. 275-281 - Thomas Strassner, Markus Busold, Wolfgang A. Herrmann:
MM3 parametrization of four- and five-coordinated rhenium complexes by a genetic algorithm - Which factors influence the optimization performance? 282-290 - Patrizia Calaminici, Karl Jug, Andreas M. Köster, Cécile Arbez-Gindre, Constantinos G. Screttas:
Mechanism for large first hyperpolarizabilities of phosphonic acid stilbene derivatives. 291-297 - Raiker Witter, Wolfram Prie, Ulrich Sternberg:
Chemical shift driven geometry optimization. 298-305 - Reinhart Ahlrichs, Kakha Tsereteli:
Efficient linear algebra routines for symmetric matrices stored in packed form. 306-309 - Tsutomu Ikegami, Suehiro Iwata:
Spectral density calculation by using the Chebyshev expansion. 310-318
Volume 23, Number 3, February 2002
- Sheldon Dennis, Sandor Vajda:
Semiglobal simplex optimization and its application to determining the preferred solvation sites of proteins. 319-334 - Primo Pristovek, Heinz Rüterjans, Roman Jerala:
Semiautomatic sequence-specific assignment of proteins based on the tertiary structure - The program st2nmr. 335-340 - Caterina Benzi, Roberto Improta, Giovanni Scalmani, Vincenzo Barone:
Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution. 341-350 - Emma Sigfridsson, Ulf Ryde, Bruce L. Bush:
Restrained point-charge models for disaccharides. 351-364 - Jacco Van de Streek, Paul Verwer, Piet Bennema, Elias Vlieg:
On the irrelevance of electrostatics for the crystal structures and polymorphism of long even n-alkanes. 365-370 - Thomas Krüger, Alexander F. Sax:
Oligovalent link atoms in embedding calculations. 371-377 - Kazuhiro Ishida:
Accompanying coordinate expansion formulas derived with the solid harmonic gradient. 378-393 - Takao Otsuka, Seiji Koizumi, Kazunaka Endo, Hiroyuki Kawabe, Delano P. Chong:
Theoretical auger electron spectra of polymers by density functional theory calculations using model dimers. 394-401 - Shuzo Yoshioki:
Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein. 402-413 - Zheng-Wang Qu, Hui Zhu, Ze-Sheng Li, Qi-Yuan Zhang:
Theoretical study on the mechanism of the gas-phase reaction of diborane(3) anion with carbon disulfide. 414-419 - Alexander A. Auer, Trygve Helgaker, Wim Klopper:
Basis-set completeness profiles in two dimensions. 420-425
Volume 23, Number 4, March 2002
- Wensheng Cai, Xueguang Shao:
A fast annealing evolutionary algorithm for global optimization. 427-435 - Kangcheng Zheng, Juping Wang, Yong Shen, Wenlie Peng, Fengcun Yun:
Studies on 4, 7-di-substitution effects of one ligand in [Ru(Phen)3]2 with DFT method. 436-443 - H. Valdés, J. A. Sordo:
Ab initio and DFT studies on van der Waals trimers: The OCS·(CO2)2 complexes. 444-455 - Bouke P. van Eijck:
Crystal structure predictions using five space groups with two independent molecules. The case of small organic acids. 456-462 - Shugo Nakamura, Daisuke Kyono, Mitsunori Ikeguchi, Kentaro Shimizu:
New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates. 463-469 - Satoshi Ono, Masataka Kuroda, Junichi Higo, Nobuyuki Nakajima, Haruki Nakamura:
Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations. 470-476 - Gwon Hee Ko, William H. Fink:
Rapidly converging lattice sums for nonelectrostatic interactions. 477-483 - Khuloud Jaqaman, Peter J. Ortoleva:
New space warping method for the simulation of large-scale macromolecular conformational changes. 484-491 - Bing Wang, James F. Hinton, Peter Pulay:
Accurate prediction of proton chemical shifts. II. Peptide analogues. 492-497 - Matthew P. Repasky, Jayaraman Chandrasekhar, William L. Jorgensen:
Improved semiempirical heats of formation through the use of bond and group equivalents. 498-510 - Hideaki Nakamura:
Monte Carlo sampling algorithm for searching a scale-transformed energy space of polypeptides. 511-516
Volume 23, Number 5, April 2002
- Emilio Gallicchio, Linda Yu Zhang, Ronald M. Levy:
The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators. 517-529 - S. K. Mishra, P. C. Mishra:
An ab initio theoretical study of electronic structure and properties of 2-deoxyguanosine in gas phase and aqueous media. 530-540 - Philippe Marsal, Michel Roche:
Variational treatment of the vibrational Hamiltonian for NH3 and H2NO. 541-547 - Alessandra Villa, Alan E. Mark:
Calculation of the free energy of solvation for neutral analogs of amino acid side chains. 548-553 - Jordi Muñoz, Xavier Barril, Begoña Hernández, Modesto Orozco, F. Javier Luque:
Hydrophobic similarity between molecules: A MST-based hydrophobic similarity index. 554-563 - Wenjian Liu, Robert Franke:
Comprehensive relativistic ab initio and density functional theory studies on PtH, PtF, PtCl, and Pt(NH3)2Cl2. 564-575 - Michal Dallos, Hans Lischka, Elizete Ventura Do Monte, Michael Hirsch, Wolfgang Quapp:
Determination of energy minima and saddle points using multireference configuration interaction methods in combination with reduced gradient following: The S0 surface of H2CO and the T1 and T2 surfaces of acetylene. 576-583 - Chang Kon Kim, Hongok Won, Hoon Sik Kim, Yong Soo Kang, Hong Guang Li, Chan Kyung Kim:
Density functional theory studies on the dissociation energies of metallic salts: Relationship between lattice and dissociation energies. 584
Volume 23, Number 6, April 2002
- Roger A. Klein:
Ab initio conformational studies on diols and binary diol-water systems using DFT methods. Intramolecular hydrogen bonding and 1: 1 complex formation with water. 585-599 - Oleg V. Tsodikov, M. Thomas Record Jr., Yuri V. Sergeev:
Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature. 600-609 - Nicolas Ferré, Xavier Assfeld, Jean-Louis Rivail:
Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method. 610-624 - Jian-Jun Liu, Yi-Hong Ding, Yu-Guo Tao, Ji-Kang Feng, Chia-Chung Sun:
Theoretical study on the mechanism of the 1CHCl + NO reaction. 625-649 - Emma Langella, Nadia Rega, Roberto Improta, Orlando Crescenzi, Vincenzo Barone:
Conformational analysis of the tyrosine dipeptide analogue in the gas phase and in aqueous solution by a density functional/continuum solvent model. 650-661 - Jean-Luc Fattebert, François Gygi:
Density functional theory for efficient ab initio molecular dynamics simulations in solution. 662-666 - John E. Carpenter:
Computation of pressure components due to Class II force fields. 667-672 - Robert D. Skeel, Ismail Tezcan, David J. Hardy:
Multiple grid methods for classical molecular dynamics. 673-684
Volume 23, Number 7, May 2002
- Salvador León, David Zanuy, Carlos Alemán:
Influence of the presence of small gas molecules in the structure of comblike polyacrylates: A Monte Carlo study. 685-696 - Peter Comba, Rainer Remenyi:
A new molecular mechanics force field for the oxidized form of blue copper proteins. 697-705 - Paulo Fernando Bruno Gonçalves, Hubert Stassen:
New approach to free energy of solvation applying continuum models to molecular dynamics simulation. 706-714 - Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga:
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. 715-723 - Jérôme Golebiowski, Véronique Lamare, Manuel F. Ruiz-López:
Rb+/Cs+ selectivity of benzo and tribenzo derivatives of the 21C7 crown ether. A density functional study. 724-731 - Obis Castaño, Raúl Palmeiro, Luis Manuel Frutos, José Luisandrés:
Role of bifurcation in the bond shifting of cyclooctatetraene. 732-736 - Vladislav Vasilyev, Enrico O. Purisima:
A fast pairwise evaluation of molecular surface area. 737-745 - Patrick Bultinck, Stijn Augustynen, Hans W. Hilbers, Ed E. Moret, Jan P. Tollenaere:
Generate: A program for 3-D structure generation and conformational analysis of peptides and peptidomimetics. 746-754 - John E. Carpenter, Alan Christoffels, Yael Weinbach, Winston A. Hide:
Assessment of the parallelization approach of d2_cluster for high-performance sequence clustering. 755-757
Volume 23, Number 8, June 2002
- Lucas Visscher:
The Dirac equation in quantum chemistry: Strategies to overcome the current computational problems. 759-766 - Hermann Stoll, Bernhard Metz, Michael Dolg:
Relativistic energy-consistent pseudopotentials - Recent developments. 767-778 - Christoph Van Wüllen:
Spin densities in two-component relativistic density functional calculations: Noncollinear versus collinear approach. 779-785 - Kenneth G. Dyall:
A systematic sequence of relativistic approximations. 786-793 - Martin Kaupp, Roman Reviakine, Olga L. Malkina, Alexei Arbuznikov, Bernd Schimmelpfennig, Vladimir G. Malkin:
Calculation of electronic g-tensors for transition metal complexes using hybrid density functionals and atomic meanfield spin-orbit operators. 794-803 - Jochen Autschbach, S. Siekierski, M. Seth, Peter Schwerdtfeger, W. H. E. Schwarz:
Dependence of relativistic effects on electronic configuration in the neutral atoms of d- and f-block elements. 804-813 - Trond Saue, Trygve Helgaker:
Four-component relativistic Kohn-Sham theory. 814-823 - Martin Kleinschmidt, Jörg Tatchen, Christel M. Marian:
Spin-orbit coupling of DFT/MRCI wavefunctions: Method, test calculations, and application to thiophene. 824-833 - Maite García-Hernández, Christa Lauterbach, Sven Krüger, Alexei V. Matveev, Notker Rösch:
Comparative study of relativistic density functional methods applied to actinide species AcO22+ and AcF6 for Ac = U, Np. 834-846 - Takahito Nakajima, Takeshi Yanai, Kimihiko Hirao:
Relativistic electronic structure theory. 847-860
Volume 23, Number 9, July 2002
- Richard H. Henchman, James Andrew McCammon:
Extracting hydration sites around proteins from explicit water simulations. 861-869 - Andre Elvas Pereira Da Silva, Geraldo Magela e Silva:
Quantum bits with polyacetylene. 870-873 - Xiang-Yuan Li, Chun-Xiu Hu:
Theoretical investigation of electron transfer transition in tetracyanoethylene-contained organic complexes. 874-886 - Michael Hirsch, Wolfgang Quapp:
Improved RGF method to find saddle points. 887-894 - Johannes Neugebauer, Markus Reiher, Carsten Kind, Bernd A. Hess:
Quantum chemical calculation of vibrational spectra of large molecules - Raman and IR spectra for Buckminsterfullerene. 895-910 - Effendi Widjaja, Marc Garland:
Pure component spectral reconstruction from mixture data using SVD, global entropy minimization, and simulated annealing. Numerical investigations of admissible objective functions using a synthetic 7-species data set. 911-919 - Fan Wang, Lemin Li:
Analytical energy gradient evaluation in relativistic and nonrelativistic density functional calculations. 920-927 - Yoshiaki Amatatsu:
Ab initio study on the electronic structures of styrene in the Franck-Condon region. 928-937 - Katherine R. Greene, Kyle A. Beran:
Isomers of C20: An energy profile. 938-942
Volume 23, Number 10, July 2002
- Robert J. Buenker, J. L. Whitten, E. I. Izgorodina, Heinz-Peter Liebermann, Daria B. Kokh:
Use of exchange maximization to generate starting vectors for self-consistent field calculations on metal cluster/adsorbate systems. 943-949 - Yoshiaki Amatatsu:
Ab initio study on the photochemical behavior of styrene. 950-956 - Henryk A. Witek, Yoong-Kee Choe, James P. Finley, Kimihiko Hirao:
Intruder state avoidance multireference Møller-Plesset perturbation theory. 957-965 - Mustafa R. Helal, Yaser A. Yousef, Akef T. Afaneh:
Ab Initio calculations of the stabilization energies of the conformational and the structural isomers of C3H7X where X = F, Cl, and Br. 966-976 - Kalju Kahn, Thomas C. Bruice:
Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides. 977-996 - Hajime Torii:
Intensity-carrying modes important for vibrational polarizabilities and hyperpolarizabilities of molecules: Derivation from the algebraic properties of formulas and applications. 997-1006 - André Severo Pereira Gomes, Rogério Custodio:
Exact Gaussian expansions of Slater-type atomic orbitals. 1007-1012 - A.-L. Derepas, J.-M. Soudan, Valérie Brenner, Jean-Pierre Dognon, Ph. Millié:
Can we understand the different coordinations and structures of closed-shell metal cation-water clusters? 1013-1030
Volume 23, Number 11, August 2002
- Jian-Jun Liu, Yi-Hong Ding, Yu-Guo Tao, Ji-Kang Feng, Chia-Chung Sun:
Theoretical study on the mechanism of the 3CH2 + NO2 reaction. 1031-1044 - Daniel J. Price, Charles L. Brooks III:
Modern protein force fields behave comparably in molecular dynamics simulations. 1045-1057 - Ulf Ryde, Lars Olsen, Kristina Nilsson:
Quantum chemical geometry optimizations in proteins using crystallographic raw data. 1058-1070 - Tomonori Ida, Motohiro Mizuno, Kazunaka Endo:
Electronic state of small and large cavities for methane hydrate. 1071-1075 - Maciej Bobrowski, Adam Liwo, Stanislaw Oldziej, Danuta Jeziorek, Tadeusz Ossowski:
Ab initio study of the mechanism of singlet-dioxygen addition to hydroxyaromatic compounds: Negative evidence for the involvement of peroxa and endoperoxide intermediates. 1076-1089 - Buddhadeb Mallik, Artëm E. Masunov, Themis Lazaridis:
Distance and exposure dependent effective dielectric function. 1090-1099 - T. W. Whitfield, John E. Straub:
Gravitational smoothing as a global optimization strategy. 1100-1103 - A. S. Shalabi:
FA(I): Au+ and FA(II): Cu+ laser activity and photographic sensitization at the low coordinated surfaces of AgBr ab initio calculations. 1104-1120 - Ron L. Shepard, Isaiah Shavitt, Hans Lischka:
Reducing I/O costs for the eigenvalue procedure in large-scale configuration interaction calculations. 1121-1125
Volume 23, Number 12, September 2002
- Fatih Yaar, Handan Arkin, Tarik Çelik, Bernd A. Berg, Hagai Meirovitch:
Efficiency of the multicanonical simulation method as applied to peptides of increasing size: The heptapeptide deltorphin. 1127-1134 - Liliana Y. A. Dávila, Marília J. Caldas:
Applicability of MNDO techniques AM1 and PM3 to ring-structured polymers.