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ORCIDJournal of Computational Chemistry, Volume 22
Volume 22, Number 1, 15 January 2001
- Donald E. Williams:
Improved intermolecular force field for crystalline oxohydrocarbons including OHO hydrogen bonding. 1-20
- István Kolossváry, György M. Keserü
:
Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3. 21-30 - Masao Masamura:
Ab initio molecular orbital study of OH-(H2O)n in the gas phase. 31-37 - Michael G. Razumov, Vladimir L. Melnikov, Igor V. Pletnev:
Molecular mechanics calculations of -diketonate, aqua, and aqua-diketonate complexes of lanthanide ions using Gillespie-Kepert model. 38-50 - Mikko Linnolahti, Pipsa Hirva, Tapani A. Pakkanen:
Geometry prediction of bridged zirconocene dichlorides by quantum chemical methods. 51-64 - Alfred D. French, Anne-Marie Kelterer, Glenn P. Johnson, Michael K. Dowd, Christopher J. Cramer:
HF/6-31G* energy surfaces for disaccharide analogs. 65-78 - Marcel Swart, Piet Th. van Duijnen, Jaap G. Snijders:
A charge analysis derived from an atomic multipole expansion. 79-88 - Thomas Bredow, Gerald Geudtner, Karl Jug:
Development of the cyclic cluster approach for ionic systems. 89-101 - Kazunaka Endo, Seiji Koizumi, Takao Otsuka, M. Suhara, T. Morohasi, E. Z. Kurmaev, Delano P. Chong:
Analysis of XPS and XES of diamond and graphite by DFT calculations using model molecules. 102-108 - Michael Meyer, Thomas Steinke, Maria Brandl, Jürgen Sühnel:
Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. 109-124 - Masao Masamura:
Ab initio molecular orbital study on the structures and energetics of CH3OH(H2O)n and CH3SH(H2O)n in the gas phase. 125-131 - Matthias Prall:
Software news and commentsVMD: a graphical tool for the modern chemists. 132-134
Volume 22, Number 2, 30 January 2001
- Luis Carballeira, Ignacio Pérez-Juste:
Role of the anomeric effect in methanediamines in the gas phase and aqueous solutions. 135-150 - Thomas Krüger, Alexander F. Sax:
Distorted silicon hydrides - a comparative study with various density functionals. 151-161 - Salvador León, Carlos Alemán, Francesc Escalé, Manuel Laso:
MCDP: an advanced tool to simulate comb-like polymers. 162-171 - Daniel Beuve-Mery, Mehdi Rahman, Philippe Ducarme, Robert Brasseur:
Practical aspects of computational chemistry calculations through PC networks: the RAMSES-Beowulf implementation. 172-177 - Sergey Vyazovkin:
Modification of the integral isoconversional method to account for variation in the activation energy. 178-183 - Zhong-Hui Duan, Robert Krasny:
An adaptive treecode for computing nonbonded potential energy in classical molecular systems. 184-195 - Béla Paizs, Pedro Salvador, Attila G. Császár, Miquel Duran, Sándor Suhai:
Intermolecular bond lengths: extrapolation to the basis set limit on uncorrected and BSSE-corrected potential energy hypersurfaces. 196-207 - Don Steiger, Rainer Glaser:
Lattice sum calculations for 1/rp interactions via multipole expansions and Euler summation. 208-215 - Elfi Kraka, Dieter Cremer:
The para-didehydropyridine, para-didehydropyridinium, and related biradicals - a contribution to the chemistry of enediyne antitumor drugs. 216-229 - Didier Bégué, Claude Pouchan:
Density functional finite cluster method for polarizability of large BeN three-dimensional systems. 230-240 - Sándor Kristyán, Gábor I. Csonka:
Fitting atomic correlation parameters for RECEP (rapid estimation of correlation energy from partial charges) method to estimate molecular correlation energies within chemical accuracy. 241-254 - Xavier Gironés, David Robert, Ramon Carbó-Dorca:
TGSA: A molecular superposition program based on topo-geometrical considerations. 255-263
Volume 22, Number 3, February 2001
- Hiroyuki Ito, Hiroshi Nakatsuji:
Roles of proteins in the electron transfer in the photosynthetic reaction center of Rhodopseudomonas viridis: bacteriopheophytin to ubiquinone. 265-272 - René de Gelder, Ron Wehrens, Jos A. Hageman:
A generalized expression for the similarity of spectra: application to powder diffraction pattern classification. 273-289 - Siegfried Höfinger, Thomas Simonson:
Dielectric relaxation in proteins: a continuum electrostatics model incorporating dielectric heterogeneity of the protein and time-dependent charges. 290-305 - Padeleimon Karafiloglou:
A method to calculate the weights of nbo electronic structures from Moffitt's theorem. 306-315 - Satoshi Okumoto, Shinichi Yamabe:
A computational study of base-catalyzed reactions between isocyanates and epoxides affording 2-oxazolidones and isocyanurates. 316-326 - Yong Zhang, Xiao-Zeng You:
Charge redistribution effect on the properties of charge transfer complexes HnRXY and HnRX2 (X, Y = F, Cl, Br, I; R = O, S, N, P). 327-338 - Marcos R. Betancourt, Jeffrey Skolnick:
Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. 339-353 - Andrzej J. Gorczko:
Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds. 354-365 - Nathaniel R. Luman, Michael P. King, Joseph D. Augspurger:
Predicting 15N amide chemical shifts in proteins. I. An additive model for the backbone contribution. 366-372
Volume 22, Number 4, March 2001
- Dmitrii N. Rassokhin, Victor S. Lobanov, Dimitris K. Agrafiotis:
Nonlinear mapping of massive data sets by fuzzy clustering and neural networks. 373-386 - Josep Maria Anglada, Emili Besalú, Josep Maria Bofill, Ramon Crehuet:
On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states. 387-406 - Ingolf Sommer, Richard Brimacombe:
Methods for refining interactively established models of ribosomal RNA towards a physico-chemically plausible structure. 407-417 - Ingo Muegge:
Effect of ligand volume correction on PMF scoring. 418-425 - Petr Bou:
Computations of the Raman optical activity via the sum-over-states expansions. 426-435 - Pei Tang, Igor Zubryzcki, Yan Xu:
Ab Initio Calculation of structures and properties of halogenated general anesthetics: halothane and sevoflurane. 436-444 - Kevin J. Naidoo, Michelle Kuttel:
Water structure about the dimer and hexamer repeat units of amylose from molecular dynamics computer simulations. 445-456 - Alexey K. Mazur:
Molecular dynamics of minimal B-DNA. 457-467 - Michael J. Holst, Nathan A. Baker, Feng Wang:
ErratumAdaptive multilevel finite element solution of the Poisson-Boltzmann equation I. Algorithms and examples. 475
Volume 22, Number 5, 15 April 2001
- Francisco Torrens, José Sánchez-Marín, Ignacio Nebot-Gil:
New dimension indices for the characterization of the solvent-accessible surface. 477-487 - Dimitris K. Agrafiotis, Dmitrii N. Rassokhin, Victor S. Lobanov:
Multidimensional scaling and visualization of large molecular similarity tables. 488-500 - Vincent Kräutler, Wilfred F. van Gunsteren, Philippe H. Hünenberger:
A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. 501-508 - Kerstin Möhle, Hans-Jörg Hofmann, Walter Thiel:
Description of peptide and protein secondary structures employing semiempirical methods. 509-520 - Yuhki Ohtsuka, Kazufumi Ohkawa, Hiroshi Nakatsuji:
Electron transfer in the c-type cytochrome subunit of the photosynthetic reaction center of Rhodopseudomonas viridis: ab initio theoretical study. 521-527 - Shuhei Fukawa, Masahiko Hada, Ryoichi Fukuda, Shinji Tanaka, Hiroshi Nakatsuji:
Relativistic effects and the halogen dependencies in the 13C chemical shifts of CH4-nIn, CH4-nBrn, CCl4-nIn, and CBr4-nIn (n=0-4). 528-536 - Wolfgang Quapp:
Comment On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states [by J. M. Anglada, E. Besalú, J. M. Bofill, and R. Crehuet, J Comput Chem 2001, 22, 4, 387-406]. 537-540 - Josep Maria Bofill:
Reply on the comment On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states [by J. M. Anglada, E. Besalú, J. M. Bofill, and R. Crehuet, J Comput Chem 2001, 22, 4, 387-406]. 541-544
Volume 22, Number 6, 30 April 2001
- Xiang-Yuan Li:
Electron transfer between tryptophan and tyrosine: Theoretical calculation of electron transfer matrix element for intramolecular hole transfer. 565-579 - Jean-Loup Faulon:
Stochastic generator of chemical structure. 4. Building polymeric systems with specified properties. 580-590 - Linda Yu Zhang, Emilio Gallicchio, Richard A. Friesner, Ronald M. Levy:
Solvent models for protein-ligand binding: Comparison of implicit solvent poisson and surface generalized born models with explicit solvent simulations. 591-607 - J. Andrew Grant, Barry T. Pickup, Anthony Nicholls:
A smooth permittivity function for Poisson-Boltzmann solvation methods. 608-640 - Oleg Borodin, Grant D. Smith, Richard L. Jaffe:
Ab initio quantum chemistry and molecular dynamics simulations studies of LiPF6/poly(ethylene oxide) interactions. 641-654 - Fredrik Blomgren, Sven Larsson, Stephen F. Nelsen:
Electron transfer in bis(hydrazines), a critical test for application of the Marcus model. 655-664 - Fokke Dijkstra, Joop H. van Lenthe:
Software news and updates. 665-672
Volume 22, Number 7, May 2001
- Irene Nobeli, John B. O. Mitchell, Alexander Alex, Janet M. Thornton:
Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes. 673-688 - Laurent Emmanuel Dardenne, Araken dos Santos Werneck, Març de Oliveira Neto, Paulo Mascarello Bisch:
Reassociation of fragments using multicentered multipolar expansions: peptide junction treatments to investigate electrostatic properties of proteins. 689-701 - Luis Fernández Pacios, Pedro C. Gómez:
Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycine. 702-716 - Bilha Sandak:
Multiscale fast summation of long-range charge and dipolar interactions. 717-731 - Péter Hudáky, Imre Jákli, Attila G. Császár, András Perczel:
Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N-formyl-L-valinamide and N-formyl-L-phenylalaninamide. 732-751 - Andrei M. Tokmachev, Andreì L. Tchougréeff:
Semiempirical implementation of strictly localized geminals for analysis of molecular electronic structure. 752-764 - Pedro Salvador, Béla Paizs, Miquel Duran, Sándor Suhai:
On the effect of the BSSE on intermolecular potential energy surfaces. Comparison of a priori and a posteriori BSSE correction schemes. 765-786 - Zorka Smedarchina, Antonio Fernández-Ramos, Willem Siebrand:
DOIT: a program to calculate thermal rate constants and mode-specific tunneling splittings directly from quantum-chemical calculations. 787-801 - Pei Tang, Igor Zubryzcki, Yan Xu:
Ab initio calculation of structures and properties of halogenated general anesthetics: halothane and sevoflurane. 802 - Josep Maria Anglada, Emili Besalú, Josep Maria Bofill, Ramon Crehuet:
On the quadratic reaction path evaluated in a reduced potential energy surface model and the problem to locate transition states. 803
Volume 22, Number 8, June 2001
- Bouke P. van Eijck, Wijnand T. M. Mooij, Jan Kroon:
Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part II. Accurate energy minimization. 805-815 - Bouke P. van Eijck:
Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part III. Effect of lattice vibrations. 816-826 - Chang Kon Kim, Jongok 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. 827-834 - Mayumi Kamishima, Masaaki Kojima, Yuzo Yoshikawa:
Calculation of stacking geometries by a modified MM2 method. 835-845 - Hannes H. Loeffler, Christoph A. Sotriffer, Rudolf H. Winger, Klaus R. Liedl, Bernd M. Rode:
Calculation of sequence-dependent free energies of hydration of dipeptides formed by alanine and glycine. 846-860 - Thomas Bredow, Gerald Geudtner, Karl Jug:
MSINDO parameterization for third-row transition metals. 861-887 - Chong Hak Chae, Dong Gweon Oh, Whanchul Shin:
Flexible molecular superposition: development of a combined similarity index and application of the constrained optimization technique. 888-900
Volume 22, Number 9, 15 July 2001
- Rafa Wysokiski, Danuta Michalska:
The performance of different density functional methods in the calculation of molecular structures and vibrational spectra of platinum(II) antitumor drugs: cisplatin and carboplatin. 901-912 - Luke Fisher, Thomas Holme:
MM3 parameterization for the BN dative bond. 913-922 - Sundaram Arulmozhiraja, Tadatake Sato, Akira Yabe:
Benzdiynes revisited: ab initio and density functional theory. 923-930 - G. te Velde, Friedrich Matthias Bickelhaupt, Evert Jan Baerends, Célia Fonseca Guerra, Stan J. A. van Gisbergen, Jaap G. Snijders, Tom Ziegler:
Chemistry with ADF. 931-967 - Alessandro Toniolo, M. Persico:
Efficient calculation of Franck-Condon factors and vibronic couplings in polyatomics. 968-975 - Vitaly A. Rassolov, Mark A. Ratner, John A. Pople, Paul C. Redfern, Larry A. Curtiss:
6-31G* basis set for third-row atoms. 976-984 - J. J. Borrás-Almenar, Juan M. Clemente-Juan, Eugenio Coronado, Boris S. Tsukerblat:
MAGPACK1 A package to calculate the energy levels, bulk magnetic properties, and inelastic neutron scattering spectra of high nuclearity spin clusters. 985-991
Volume 22, Number 10, 30 July 2001
- Paul D. Kirchhoff, Rob Brown, Scott Kahn, Marvin Waldman, C. M. Venkatachalam:
Application of structure-based focusing to the estrogen receptor. 993-1003 - Kyu-Kwang Han, Ki Hae Kim, Byung Jin Mhin, Hyeon S. Son:
Application of the multiensemble sampling to the hydration free energy. 1004-1009 - Tran Trung Tran, Herbert R. Treutlein, Antony W. Burgess:
Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force field. 1010-1025 - Tran Trung Tran, Herbert R. Treutlein, Antony W. Burgess:
Conformational analysis of thiopeptides: (, ) maps of thio-substituted dipeptides. 1026-1037 - Gilles Tiraboschi, Marie-Claude Fournié-Zaluski, Bernard-Pierre Roques, Nohad Gresh:
Intramolecular chelation of Zn2+ by - and -mercaptocarboxamides. A parallel ab initio and polarizable molecular mechanics investigation. Assessment of the role of multipole transferability. 1038-1047 - Piotr Cieplak, James W. Caldwell, Peter A. Kollman:
Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. 1048-1057 - Vladimir A. Bushenkov, J. P. Prates Ramalho, Georgi V. Smirnov:
Adsorption integral equation via complex approximation with constraints: kernel of general form. 1058-1066 - Xiang-Yuan Li, Ji-Feng Liu:
A theoretical study of solvent effect and reaction mechanism of electron transfer reaction between indole side chain and phenol side chain of peptide involving tryptophan and tyrosine. 1067-1081 - Pawel Kdzierski, W. Andrzej Sokalski:
Analysis of the transferability of atomic multipoles for amino acids in modeling macromolecular charge distribution from fragments. 1082-1097 - Narutoshi Kamiya, Junichi Higo:
Repeated-annealing sampling combined with multicanonical algorithm for conformational sampling of bio-molecules. 1098-1106 - Shoji Morita, Shogo Sakai:
IMiCMO: a new integrated ab initio multicenter molecular orbitals method for molecular dynamics calculations in solvent cluster systems. 1107-1112 - Christopher J. Van Zele, Mark A. Cunningham, Marvin W. Makinen:
Validation of nitroxyl spin-label force-field parameters through molecular dynamics simulations. 1113-1123
Volume 22, Number 11, August 2001
- Maral Basma, S. Sundara, Dilek Çalgan, Tereza Vernali, Robert J. Woods:
Solvated ensemble averaging in the calculation of partial atomic charges. 1125-1137 - Annia Galano, J. Raúl Alvarez-Idaboy, Luis A. Montero, Annik Vivier Bunge:
OH hydrogen abstraction reactions from alanine and glycine: A quantum mechanical approach. 1138-1153 - Donald E. Williams:
Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals. 1154-1166 - Edward C. Sherer, Christopher J. Cramer:
Quantum chemical characterization of the cytosine: 2-Aminopurine base pair. 1167-1179 - Carles Curutchet, Modesto Orozco, F. Javier Luque:
Solvation in octanol: parametrization of the continuum MST model. 1180-1193 - Christopher J. Cramer, Anne-Marie Kelterer, Alfred D. French:
When anomeric effects collide. 1194-1204 - Lukas D. Schuler, Xavier Daura, Wilfred F. van Gunsteren:
An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. 1205-1218
Volume 22, Number 12, September 2001
- Junmei Wang, Peter A. Kollman:
Automatic parameterization of force field by systematic search and genetic algorithms. 1219-1228 - Tommi Hassinen, Mikael Peräkylä:
New energy terms for reduced protein models implemented in an off-lattice force field. 1229-1242 - Hiroaki Umeda, Shiro Koseki, Umpei Nagashima, Michael W. Schmidt:
Parallelization of multireference perturbation calculations with GAMESS. 1243-1251 - Hideaki Takahashi, Takumi Hori, Hideaki Hashimoto, Tomoshige Nitta:
A hybrid QM/MM method employing real space grids for QM water in the TIP4P water solvents. 1252-1261 - Christian Silvio Pomelli, Jacopo Tomasi, Roberto Cammi:
A Symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution. 1262-1272 - Gerhard Bringmann, Jörg Mühlbacher, Charlotte Repges, Jörg Fleischhauer:
MD-based CD calculations for the assignment of the absolute axial configuration of the naphthylisoquinoline alkaloid dioncophylline A. 1273-1278 - Jerzy Cioslowski, Agnieszka Szarecka:
First-principles conformational analysis of the C36H36 spheriphane, a prototype hydrocarbon host cage. 1279-1286 - Shura Hayryan, Chin-Kun Hu, Shun-Yun Hu, Rung-Ji Shang:
Multicanonical parallel simulations of proteins with continuous potentials. 1287-1296
Volume 22, Number 13, October 2001
- Gernot Frenking, Norman L. Allinger:
Editors' preface. 7-8 - Paul von Ragué Schleyer:
An appreciation. 9-11 - Glênisson de Oliveira, Jan M. L. Martin, Indira K. C. Silwal, Joel F. Liebman:
Definitive heat of formation of methylenimine, CH2NH, and of methylenimmonium ion, CH2NH2+, by means of W2 theory . 1297-1305 - Wim Klopper, Claire C. M. Samson, György Tarczay, Attila G. Császár:
Equilibrium inversion barrier of NH3 from extrapolated coupled-cluster pair energies. 1306-1314