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ORCIDJournal of Computational Chemistry, Volume 17
Volume 17, Number 1, 15 January 1996
- Mark A. Spackman:
Potential derived charges using a geodesic point selection scheme. 1-18 - Iñaki Tuñón, Marilia T. C. Martins-Costa, Claude Millot, Manuel F. Ruiz-López, Jean-Louis Rivail:
A coupled density functional-molecular mechanics Monte Carlo simulation method: The water molecule in liquid water. 19-29 - Peeter Burk, Ilmar A. Koppel, Ivar Koppel, Lev M. Yagupolskii, Robert W. Taft:
Superacidity of neutral Brfnsted acids in gas phase. 30-41 - O. Castell, V. M. García, C. Bo, Rosa Caballol:
Relative stability of the 3A2, 1A2, and 1A1 states of phenylnitrene: A difference-dedicated configuration interaction calculation. 42-48 - Chunyang Peng, Philippe Y. Ayala, H. Bernhard Schlegel, Michael J. Frisch:
Using redundant internal coordinates to optimize equilibrium geometries and transition states. 49-56 - Maurizio Cossi, Benedetta Mennucci, Roberto Cammi:
Analytical first derivatives of molecular surfaces with respect to nuclear coordinates. 57-73 - D. Delfini, Claudio Nicolini, Enrico A. Carrara:
Performance analysis of the double-iterated Kalman filter for molecular structure estimation. 74-86 - Dirk Bakowies, Walter Thiel
:
Semiempirical treatment of electrostatic potentials and partial charges in combined quantum mechanical and molecular mechanical approaches. 87-108 - Ian T. Foster, Jeffrey L. Tilson, Albert F. Wagner, Ron L. Shepard, Robert J. Harrison, Ricky A. Kendall, Rik J. Littlefield:
Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms. 109-123 - Robert J. Harrison, Martyn F. Guest, Ricky A. Kendall, David E. Bernholdt, Adrian T. Wong, Mark Stave, James L. Anchell, Anthony C. Hess, Rik J. Littlefield, George L. Fann, Jarek Nieplocha, Greg S. Thomas, David Elwood, Jeffrey L. Tilson, Ron L. Shepard, Albert F. Wagner, Ian T. Foster, Ewing L. Lusk, Rick Stevens:
Toward high-performance computational chemistry: II. A scalable self-consistent field program. 124-132
Volume 17, Number 2, 30 January 1996
- Stephan Reiling, Jürgen Brickmann, Michael Schlenkrich, Philippe A. Bopp:
Theoretical investigations on 1, 2-ethanediol: The problem of intramolecular hydrogen bonds. 133-147 - Iñaki Tuñón, Manuel F. Ruiz-López, Daniel Rinaldi, Juan Bertrán:
Computation of hydration free energies using a parameterized continuum model: Study of equilibrium geometries and reactive processes in water solution. 148-155 - Marcelo Giordan, Rogério Custodio, José Roberto Trigo:
Pyrrolizidine alkaloids necine bases: Ab initio, semiempirical, and molecular mechanics approaches to molecular properties. 156-166 - Ana Luiza M. S. de Azevedo, Benício B. Neto, Ieda S. Scarminio, Anselmo E. de Oliveira, Roy E. Bruns:
A chemometric analysis of ab initio vibrational frequencies and infrared intensities of methyl fluoride. 167-177 - A. I. Panin, O. V. Sizova:
Direct CI method in restricted configuration spaces. 178-184 - Kenneth B. Wiberg, Henry Castejon, Todd A. Keith:
Solvent effects: 6. A comparison between gas phase and solution acidities. 185-190 - Shigetaka Yoneda, Masako Kitazawa, Hideaki Umeyama:
Molecular dynamics simulation of a rhinovirus capsid under rotational symmetry boundary conditions. 191-203 - Alesia Sawyer, Erica Sullivan, Yitbarek H. Mariam:
A semiempirical computational study of electron transfer reactivity of one- vs. two-ring model systems for anthracycline pharmacophores. I. A rationale for mode of action. 204-225 - Takeshi Kikuchi:
Inter-C atomic potentials derived from the statistics of average interresidue distances in proteins: Application to bovine pancreatic trypsin inhibitor. 226-237 - Seunho Jung, Dugki Min, Rawle I. Hollingsworth:
A metropolis Monte Carlo method for analyzing the energetics and dynamics of lipopolysaccharide supramolecular structure and organization. 238-249 - Grant Heffelfinger, Martin E. Lewitt:
A comparison between two massively parallel algorithms for Monte Carlo computer simulation: An investigation in the grand canonical ensemble. 250-265
Volume 17, Number 3, February 1996
- Huub J. J. Van Dam, J. H. Van Lenthe, Gerard L. G. Sleijpen, Henk A. van der Vorst:
An improvement of Davidson's iteration method: Applications to MRCI and MRCEPA calculations. 267-272 - Dan Harris, Gilda Loew:
Comparative study of free energies of solvation of phenylimidazole inhibitors of cytochrome P450cam by free energy simulation, AMSOL, and Poisson Boltzmann methods. 273-288 - Gyula Dömötör, Miklós I. Bán, László L. Stachó:
Theoretical and practical aspects of the convergence properties of the dynamically defined reaction path method. 289-297 - Branko S. Jursic, Zoran Zdravkovski:
An ab initio study of heterodienophiles addition to 2, 3-diaza-1, 3-butadiene: An example of endo-lone-pair effect on the reaction energy barrier. 298-305 - Brian W. Clare, Philip J. Jennings, John C. L. Cornish, Glenn T. Hefter, D. J. Santjojo:
Simulation of the infrared spectra of amorphous silicon alloys. 306-312 - Youliang Wang, Raymond A. Poirier:
Computational developments in generalized valence bond calculations. 313-325 - Steve Plimpton, Bruce Hendrickson:
A new parallel method for molecular dynamics simulation of macromolecular systems. 326-337 - Yanbo Ding, Karsten Krogh-Jespersen:
The 1: 1 glycine zwitterion-water complex: An ab initio electronic structure study. 338-349 - Jian Shen, John J. Wendoloski:
Electrostatic binding energy calculation using the finite difference solution to the linearized Poisson-Boltzmann equation: Assessment of its accuracy. 350-357 - Daniel E. Platt, B. David Silverman:
Registration, orientation, and similarity of molecular electrostatic potentials through multipole matching. 358-366 - Michelle Miller Francl, Christina Carey, Lisa Emily Chirlian, David M. Gange:
Charges fit to electrostatic potentials. II. Can atomic charges be unambiguously fit to electrostatic potentials? 367-383
Volume 17, Number 4, March 1996
- Marek Freindorf, Jiali Gao:
Optimization of the Lennard-Jones parameters for a combined ab initio quantum mechanical and molecular mechanical potential using the 3-21G basis set. 386-395 - Ulf Berg, Nina Bladh:
Molecular mechanics calculations of conjugated amides and an ab initio investigation of acrylamide and its -amino derivative: Conformational analysis and rotational barriers. 396-408 - Michael Falk, Peter F. Spierenburg, John A. Walter:
Determination of the stereochemistry of natural products from nuclear magnetic resonance data by constrained molecular dynamics. 409-417 - Kamalakar Gulukota, Sandor Vajda, Charles DeLisi:
Peptide docking using dynamic programming. 418-428 - Klaus Gundertofte, Tommy Liljefors, Per-Ola Norrby, Ingrid Pettersson:
A comparison of conformational energies calculated by several molecular mechanics methods. 429-449 - Stephan Reiling, Michael Schlenkrich, Jürgen Brickmann:
Force field parameters for carbohydrates. 450-468 - P. Ballestrero, Pierpaolo Baglietto, C. Ruggiero:
Molecular dynamics for proteins: Performance evaluation on massively parallel computers based on mesh networks using a space decomposition approach. 469-475 - Shigeru Endo, Junichi Higo, Kuniaki Nagayama, Hiroshi Wako:
New implementation of and the modeling by the extended simulated annealing process to structures of T4 lysozyme mutants at the 86th residue. 476-488
Volume 17, Numbers 5-6, 1996
- Thomas A. Halgren:
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. 490-519 - Thomas A. Halgren:
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular. interactions. 520-552 - Thomas A. Halgren:
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94. 553-586 - Thomas A. Halgren, Robert B. Nachbar:
Merck molecular force field. IV. conformational energies and geometries for MMFF94. 587-615 - Thomas A. Halgren:
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules. 616-641 - Norman L. Allinger, Kuo-Hsiang Chen, Jenn-Huei Lii:
An improved force field (MM4) for saturated hydrocarbons. 642-668 - Neysa Nevins, Kuo-Hsiang Chen, Norman L. Allinger:
Molecular mechanics (MM4) calculations on alkenes. 669-694 - Neysa Nevins, Jenn-Huei Lii, Norman L. Allinger:
Molecular mechanics (MM4) calculations on conjugated hydrocarbons. 695-729 - Neysa Nevins, Norman L. Allinger:
Molecular mechanics (MM4) vibrational frequency calculations for alkenes and conjugated hydrocarbons. 730-746 - Norman L. Allinger, Kuo-Hsiang Chen, John A. Katzenellenbogen, Scott R. Wilson, Gregory M. Anstead:
Hyperconjugative effects on carbon - Carbon bond lengths in molecular mechanics (MM4). 747-755
Volume 17, Number 7, May 1996
- John R. Kneisler, Norman L. Allinger:
Ab initio and density functional theory study of structures and energies for dimethoxymethane as a model for the anomeric effect. 757-766 - Gábor I. Csonka, Pal Hencsei:
The structure of 1-chlorosilatrane: An ab initio molecular orbital and a density functional theory study. 767-780 - Ralf Stegmann, Gernot Frenking:
Silaacetylene: A possible target for experimental studies. 781-789 - Hideo Nakajima, Ohgi Takahashi, Osamu Kikuchi:
Rapid evaluation of molecular electrostatic potential maps for amino acids, peptides, and proteins by empirical functions. 790-805 - F. Javier Luque, Margarida Bachs, Carlos Alemán, Modesto Orozco:
Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CCl4. 806-820 - András Perczel, Ödön Farkas, Imre G. Csizmadia:
Peptide models XVI. The identification of selected HCO - L - SER - NH2 conformers via a systematic grid search using ab initio potential energy surfaces. 821-834 - Branko S. Jursic:
Density functional Gaussian-type orbital approach in theoretical study of S2F2 isomerization. 835-840 - Jirí Sponer, Jerzy Leszczynski, Pavel Hobza:
Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. 841-850 - Xiaoping Cao, Muzhen Liao, Xuejun Chen, Bo Li:
Molecular symmetry and ab initio calculations. II. Symmetry-Matrix and symmetry-Supermatrix in the Dirac-Fock method. 851-863 - Randy J. Zauhar, Alexandre Varnek:
A fast and Space-Efficient boundary element method for computing electrostatic and hydration effects in large molecules. 864-877 - Shuzo Yoshioki:
Internal dynamics of a globular protein in water. 878-887 - Jon Baker, Fora Chan:
The location of transition states: A comparison of Cartesian, Z-matrix, and natural internal coordinates. 888-904 - Ramón López, José A. Sordo, Tomás Luis Sordo, Paul von Ragué Schleyer:
Ab initio study of the formation of C3H3+ from the reaction of CH3+ with acetylene. 905-909 - Masaki Tomimoto, Nobuhiro Go, Hiroshi Wako:
Conformational analysis of nucleic acid molecules with flexible furanose rings in dihedral angle space. 910-917
Volume 17, Number 8, June 1996
- Alexei A. Buchachenko, Alexei Yu. Baisogolov, Nikolai F. Stepanov:
Decoupling approximations for quantum vibrational predissociation dynamics: The tests on the low-level golden rule approaches for some rare gas - Cl2, ICl complexes. 919-930 - Delbert R. Black, Craig G. Parker, S. Scott Zimmerman, Milton L. Lee:
Enantioselective binding of -pinene and of some cyclohexanetriol derivatives by cyclodextrin hosts: A molecular modeling study. 931-939 - Guyan Liang, Peter C. Fox, J. Phillip Bowen:
Parameter analysis and refinement toolkit system and its application in MM3 parameterization for phosphine and its derivatives. 940-953 - Wendell Forst:
Sum and density of states of polyatomic systems with hindered rotors. 954-961 - Andrey A. Bliznyuk, Jill E. Gready:
Numerical calculation of molecular surface area. I.Assessment of Errors. 962-969 - Andrey A. Bliznyuk, Jill E. Gready:
Numerical calculation of molecular surface area. II. Speed of calculation. 970-975 - Marcia O. Fenley, Wilma K. Olson, Kiat Chua, Alexander H. Boschitsch:
Fast adaptive multipole method for computation of electrostatic energy in simulations of polyelectrolyte DNA. 976-991 - Lawrence A. Covick, Kenneth M. Sando:
Portable, parallel transformation: Distributed-Memory approach. 992-1001 - Louis Carlacci, S. Walter Englander:
Loop problem in proteins: Developments on Monte Carlo simulated annealing approach. 1002-1012 - Shusen Li, Ching-Hsien Huang:
Molecular mechanics simulation studies of dienoic hydrocarbons: From alkenes to 1-Palmitoyl-2-linoleoyl-phosphatidylcholines. 1013-1024 - Boris A. Reva, Michel F. Sanner, Arthur J. Olson, Alexei V. Finkelstein:
Lattice modeling: Accuracy of energy calculations. 1025-1032 - Rohit V. Pappu, William J. Schneller, David L. Weaver:
Electrostatic multipole representation of a polypeptide chain: An algorithm for simulation of polypeptide properties. 1033-1055 - Hiroshi Tatewaki, Shinichi Katsuki, Yoshiko Sakai, Eisaku Miyoshi:
Applications of spectral-Representation model as a potential method for Cu clusters. 1056-1067 - Karl-Heinz Ott, Bernd Meyer:
Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations. 1068-1084
Volume 17, Number 9, 15 July 1996
- Evgeny B. Krissinel, Noam Agmon:
Spherical symmetric diffusion problem. 1085-1098 - Per E. M. Siegbahn:
Models for the description of the H3O+ and OH- ions in water. 1099-1107 - Xiang-Yuan Li, An-Min Tian, Fu-Cheng He, Guo-Sen Yan:
Electron transfer integral between two zero-overlap states. 1108-1111 - Christophe Chipot, Peter A. Kollman, David A. Pearlman:
Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions. 1112-1131 - Arnaud Blondel, Martin Karplus:
New formulation for derivatives of torsion angles and improper torsion angles in molecular mechanics: Elimination of singularities. 1132-1141 - Juan C. Meza, Richard S. Judson, T. R. Faulkner, Adi M. Treasurywala:
A comparison of a direct search method and a genetic algorithm for conformational searching. 1142-1151 - Bernard Delley:
High order integration schemes on the unit sphere. 1152-1155 - Bo R. Svensson, Clifford E. Woodward:
Constant-NT simulations: Free energy difference method for excess adsorption. 1156-1162 - Takako Kudo, Fujiko Hashimoto, Mark S. Gordon:
Ab initio study of cyclic siloxanes (H2SiO)n: n = 3, 4, 5. 1163-1170 - Adi M. Treasurywala, Edward P. Jaeger, Melissa L. Peterson:
Conformational searching methods for small molecules. III. Study of stochastic methods available in SYBYL and MACROMODEL. 1171-1182
Volume 17, Number 10, 30 July 1996
- Paulo J. A. Ribeiro-Claro, Ana Margarida Amado, J. J. C. Teixeira-Dias:
Structures and vibrational frequencies of vanadium (V) oligomers: An ab initio study using effective core potentials. 1183-1196 - Bjørn K. Alsberg, Vidar R. Jensen, Knut J. Børve:
Use of multivariate methods in the analysis of calculated reaction pathways. 1197-1216 - John R. Gunn, Richard A. Friesner:
Parallel implementation of a protein structure refinement algorithm. 1217-1228 - Paul Beroza, Donald R. Fredkin:
Calculation of amino acid pKaS in a protein from a continuum electrostatic model: Method and sensitivity analysis. 1229-1244 - Guang Wu, Sven Jacobs, M. G. Verbruggen, Albert T. H. Lenstra, Christian Van Alsenoy, Herman J. Geise, Luc van Meervelt:
Phenylene vinylene oligomers studied by theoretical methods: Joint analysis of computational and x-ray results of the configurational isomers of 1, 4-bis[2-(3, 4, 5-trimethoxyphenyl)ethenyl]benzene. 1245-1257 - Qishi Du, Gustavo A. Arteca:
Derivation of fused-sphere molecular surfaces from properties of the electrostatic potential distribution. 1258-1268 - Shankar Kumar, Philip W. Payne, Maximiliano Vásquez:
Method for free-energy calculations using iterative techniques. 1269-1275 - T. Komatsu, T. Noro, F. Sasaki, H. Tatewaki:
Quality of correlating functions generated from commonly used basis sets. 1276-1286
Volume 17, Number 11, August 1996
- Marc F. Lensink, Janez Mavri, Herman J. C. Berendsen:
Simultaneous integration of mixed quantum-classical systems by density matrix evolution equations using interaction representation and adaptive time step integrator. 1287-1295 - Romano T. Kroemer, Peter Hecht, Klaus R. Liedl:
Different electrostatic descriptors in comparative molecular field analysis: A comparison of molecular electrostatic and coulomb potentials. 1296-1308 - Oscar N. Ventura, Martina Kieninger, Elena Laura Coitiño:
Density functional study of isomerization of fluoro- and chloroformaldehyde radical cations. 1309-1317 - Serguei Patchkovskii, Walter Thiel:
Analytical second derivatives of the energy in MNDO methods. 1318-1327 - N. Swamy Kandadai, M. Rami Reddy:
Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques. 1328-1338 - Sean A. C. McDowell:
Dipole moment derivatives and integrated intensities for the vibrational transitions of N2 HF. 1339-1343 - Zhongxiang Zhou, Philip Payne, Max Vasquez, Nat Kuhn, Michael Levitt:
Finite-difference solution of the Poisson-Boltzmann equation: Complete elimination of self-energy. 1344-1351 - Jerzy Cioslowski, Boris B. Stefanov, Pere Constans:
Efficient algorithm for quantitative assessment of similarities among atoms in molecules. 1352-1358 - Marc Couty, Michael B. Hall:
Basis sets for transition metals: Optimized outer p functions. 1359-1370 - Jorge Llano, Luis A. Montero:
Bonding contribution to restricted internal rotations in saccharides. 1371-1384 - Julian Tirado-Rives, William L. Jorgensen:
Viability of molecular modeling with pentium-based PCs. 1385-1386