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ORCIDJournal of Computational Chemistry, Volume 15
Volume 15, Number 1, January 1994
- Josep Maria Bofill
:
Updated Hessian Matrix and the Restricted Step Method for Locating Transition Structures. 1-11 - Cristóbal Alhambra, Francisco Javier Luque, Modesto Orozco:
Comparison of NDDO and Quasi-Ab Initio Approaches to Compute Semiempirical Molecular Electrostatic Potentials. 12-22 - Carl W. David:
Hydrating Peptides Using a Sprouting Technique. 23-28 - Jiro Shimada, Hiroki Kaneko, Toshikazu Takada:
Performance of Fast Multipole Methods for Calculating Electrostatic Interactions in Biomacromolecular Simulations. 29-43 - William S. Young, Charles L. Brooks III:
Implementation of a Data Parallel, Logical Domain Decomposition Method for Interparticle Interactions in Molecular Dynamics of Structured Molecular Fluids. 44-53 - Zhenghong Zhang, Pawel M. Kozlowski, Ludwik Adamowicz:
Newton-Raphson Optimization of the Explicitly Correlated Gaussian Functions for Calculations of the Ground State of the Helium Atom. 54-60 - Darrin M. York, Lee J. Bartolotti, Thomas A. Darden, Lee G. Pedersen, M. W. Anderson:
Simulations of the Solution Structure of HIV-1 Protease in the Presence and Absence of Bound Zinc. 61-71 - Daniel I. Okunbor, Robert D. Skeel:
Canonical Numerical Methods for Molecular Dynamics Simulations. 72-79 - Charles D. Schwieters, Herschel Rabitz:
Display of the Flow of Energy in Molecules. 80-89 - Takao Furuki, Akihiro Umeda, Minoru Sakurai, Yoshio Inoue, Riiciro Chujo, Kazuaki Harata:
General Parameterization of a Reaction Field Theory Combined with the Boundary Element Method. 90-104 - David A. Pearlman:
Free Energy Derivatives: A New Method for Probing the Convergence Problem in Free Energy Calculations. 105-123
Volume 15, Number 2, February 1994
- Ricard Gelabert, Miquel Moreno, José M. Lluch:
Applicability of the WKB Method in Asymmetric Double Wells with Degenerate and Nondegenerate Minima. 125-131 - Rudolf Janoschek, Walter M. F. Fabian, Gert Kollenz, C. Oliver Kappe:
Conformation and Reactivity of a-Oxo-Ketenes: Ab Initio and Semiempirical /AM1, PM3) Calculations. 132-143 - Joaquim José Soares Neto:
Parallel Algorithm for Calculating Ro-Vibrational States of Diatomic Molecules. 144-148 - Ching-Lung Lin, Robert H. Wood:
Free Energy of Solvation of a Small Lennard-Jones Particle. 149-154 - Mark J. Forster, Barbara Mulloy:
Rationalizing Nuclear Overhauser Efect Data for Compounds Adopting Multiple-Solution Conformations. 155-161 - J. R. Maple, Ming-Jing Hwang, Thomas P. Stockfisch, Uri Dinur, Marvin Waldman, Carl S. Ewig, Arnold T. Hagler:
Derication of Class II Force Fields. I. Methology and Quantum Force Field for the Alkyl Functional Group and Alkane Molecules. 162-182 - Jesús Rodríguez:
Semiempirical Study of Compounds with Intramolecular O-H--O Hydrogen Bonds. II. Further Verification of a Modified MNDO Method. 183-189 - Arun Mlhotra, Robert K.-Z. Tan, Stephen C. Harvey:
Utilization of Shape Data in Molecular Mechanics Using a Potential Based on Sherical Harmonic Surfaces. 190-199 - Bingze Wang, George P. Ford:
Atomic Charges Derived from a Fast and Accurate Method for Electrostatic Potentials Based on Modified AM1 Calculations. 200-207 - Barry J. Hardy, Richard W. Pastor:
Conformational Sampling of Hydrocarbon and Lipid Chains in an Orienting Potential. 208-226 - William Kile Glunt, Thomas L. Hayden, Marcos Raydan:
Preconditioners for Distance Matrix Algorithms. 227-232 - Andrew R. Leach, Richard A. Lewis:
A Ring-Bracing Approach to Computer-Assisted Ligand Design. 233-240 - Lawrence M. Pratt, C. C. Chu:
Computational Study of the Hydrolysis of Degradable Polysaccharide Biomaterials: Subtituent Effects on the Hydrolytic Mechanism. 241-248
Volume 15, Number 3, March 1994
- Norman L. Allinger, Yi Fan:
Force Field Calculations (MM3) on Glyoxal, Quinones, and Related Compounds. 251-268 - Vincent Théry, Daniel Rinaldi, Jean-Louis Rivail, Bernard Maigret, György G. Ferenczy:
Quantum Mechanical Computations on Very Large Molecular Systems: The Local Self-Consistent Field Method. 269-282 - Ruifeng Liu, Norman L. Allinger:
Molecular Mechanics (MM3) Calculations on Alkyl Radicals. 283-299 - Ljubomir J. Buturovic, Temple F. Smith, Sandor Vajda:
Finite-State and Reduced-Parameter Representations of Protein Backbone Conformations. 300-312 - Anibal Sierraalta, Fernando Ruette:
A Comarative Study of Effective Core Potential and Full-Electron Calculations in Mo Compounds. I. An ANalysis of Topological Properties of Bond Charge Distribution. 313-321 - Andrea Dorigo, Paul von Ragué Schleyer, Pavel Hobza:
The Structures of LiNC, NaNC, and KNC: Potential Energy Surface for the Orbiting Motion of the Metal Cation around the CN Group. 322-332 - Xiannong Chen, Libero Bartolotti, Khalid Ishaq, Alexander Tropsha:
Molecular Simulation of Alkyl Boronic Acids: Molecular Mechanics and Solvation Free Energy Calculations. 333-345 - Z.-L. Cai:
Ab Initio Study of Low-Lying Electronic States of the PF2 Radical. 345-350 - Stephen E. DeBolt, David A. Pearlman, Peter A. Kollman:
Free Energy Peturbation Calculations on Parallel Computers: Demonstrations of Scalable Linear Speedup. 351-374
Volume 15, Number 4, April 1994
- José Ramón Alvarez-Collado:
Normal Coordinates-Finite Elements Calculation of 3D Vibrational Energy Levels: Hanon-Heiles and Eckart Potentials, H3+ Molecule. 377-384 - Gábor I. Csonka, Pal Hencsei:
Ab Initio Molecular Orbital Study of 1-Fluorosilatrane. 385-394 - Vincenzo Barone, Carlo Adamo:
Modulation of Intramolecular Proton Transfer by Electronic Excitation and Environment: 2-Pyridone as a Case Study. 395-404 - Francisco Javier Ramírez, Víctor Hernández, Juan Teodomiro López Navarrete:
Transferable Semiempirical Quadratic Force Fields: The Case of Polythiophene and Shorter Oligomers. 405-423 - Stefan Grimme:
MRD-CI Studies of Vertical Excitation Energies of Unsaturated Hydrocarbon Molecules. 424-432 - Mahmoud Ghomi, Jean-Marc Victor, Charles Henriet:
Monte Carlo Simulations on Short Single-Stranded Oligonucleotides. I. Application to RNA Trimers. 433-445 - Margarida Bachs, F. Javier Luque, Modesto Orozco:
Optimization of Solute Cavities and van der Waals Parameters in Ab Initio MST-SCRF Calculations of Neutral Molecules. 446-454 - Berta Fernández, Miguel A. Ríos:
Parametrization of a Force Field for Studying Some Beta Lactams. 455-465 - Lorenzo Pisani, Enrico Clementi:
Relativistic Dirac-Fock Calculations for Closed-Shell Molecules. 466-474
Volume 15, Number 5, May 1994
- Xavier Assfeld, Manuel F. Ruiz-López, J. Gonzalez, Ramón López, José A. Sordo, Tomás L. Sordo Gonzalo:
Theoretical Analysis of the Role of the Solvent on the Reaction on the Reaction Mechanismus: One-Step versus Two-Step Ketene-Imine Cycloaddition. 479-487 - Ruben Abagyan, Maxim Totrov, Dmitry Kuznetsov:
ICM - A New Method for Protein Modeling and Design: Applications to Docking and Strucutre Prediction from the Distorted Native Conformation. 488-506 - Michel Petitjean:
On the Analytical Calculation o van der Waals Surfaces and Volumes: Some Numerical Aspects. 507-523 - Ulrich Sternberg, Fran-Thomas Koch, Margit Möllhoff:
New Approach to the Semiempirical Calcualtion of Atomic Charges for Polypeptides and Large Molecular Systems. 524-531 - Philippe Derreumaux, Guihua Zhang, Tamar Schlick, Bernard R. Brooks:
A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. 532-552 - Jan Florián, Steve Scheiner:
Variation of Atomic Charges during Proton Transfer in Hydrogen Bonds. 553-560 - Alfred D. French, Michael K. Dowd:
Analysis of the Ring-Form Tautomers of Psicose with MM3(92). 561-570
Volume 15, Number 6, June 1994
- Olav Vahtras, Hans Jorgen Aagard Jensen:
Direct One-Index Transformations in Multiconfiguration Response Calculations. 573-579 - P. Battersby, J. R. Dean, S. M. Hitchen, W. R. Tomlinson, P. M. Myers:
Interaction between Carbon Dioxide and Naphthalene: A Molecular Modeling Approach. 580-587 - Tilman Brodmeier, Ernö Pretsch:
Application of Genetic Algorithms in Molecular Modeling. 588-595 - Ahmed M. El-Nahas, Paul von Ragué Schleyer:
Structures and Stabilization Energies of Methyl Anions with Main Group Stubstituens from the First Five Periods. 596-627 - Juan C. Meza, Mónica L. Martinez:
Direct Search for the Molecular Conformation Problem. 627-632 - Gustavo A. Arteca:
Shape Analysis of Hydrogen-Bonded Networks in Solvation Clusters. 633-643 - Brian W. Clare, G. Talukder, Philip J. Jennings, John C. L. Cornish, Glenn T. Hefter:
Effect of Charge on Bond Strength in Hydrogenated Amorphous Silicon. 644-652 - Hebert F. M. da Costa, David A. Micha:
Atomic Orbital Basis Sets for Molecular Interactions. 653-661 - Carl W. David:
X-PLORing Extrarisomal Peptide Folding during Synthesis. 662-665
Volume 15, Number 7, July 1994
- Peter J. Steinbach, Bernard R. Brooks:
New Spherical-Cutoff Methods for Long-Range Forces in Macromolecular Simulation. 667-683 - Shuzo Yoshioki:
Internal Dynamics of a Global Protein under External Force Field. 684-703 - Peter L. Cummins, Jill E. Gready:
Thermodynamic Integration Calculations on the Relative Free Energies of Complex Ions in Aqueous Solution: Application to Ligands of Dihydrofolate Reductace. 704-718 - Donald E. Williams:
Failure of Net Atomic Charge Models to Represent the van der Waals Envelope Electric Potential of n-Alkanes. 719-732 - Steven L. Dixon, Peter C. Jurs:
Fast Geometry Optimization Using a Modifed Extended Hückel Method: Results for Molecules Containing H, C, N, O, and F. 733-746 - Alexander V. Mitin:
Iterative Methods for the Calculation of a Few of the Lowest Eigenvalues and Corresponding Eigenvectors of the AX = Lamda BX Equation with Real Symmetric Matrices of Large Dimension. 747-751 - H. Sun:
Force Field for Computation of Conformational Energies, Structures, and Vibrational Frequencies of Aromatic Polyesters. 752-768 - Fanbing Li, Weili Cui, Norman L. Allinger:
Expanding Molecular Dynamics Simulations to the NMR Time Scale. I. Studies of Conformational Interconversions of 1, 1-Difluoro-4.4-Dimethylcycloheptane Using MM3-MD. 769-781 - Jesús R. Flores, P. Redondo:
High-Precision Atomic Computations from Finite Element Techniques: Second-Order Correlation Energeis for Be, Ca, Sr, Cd, Yb, and Hg. 782-790
Volume 15, Number 8, August 1994
- Wolf-Dietrich Ihlenfeldt, Johann Gasteiger:
Hash Codes for the Indentification and Classification of Molecular Structure Elements. 793-813 - Ian J. Palmer, Janos Ladik:
New Implementation of a Program to Calculate Correlated Band Structures of Polymers: An Application to the Band Strucutre of Polyparaphenylene (PPP). 814-819 - Jean-François Gibrat, Jean Garnier, Nobuhiro Go:
Normal Mode Analysis of Oligomeric Proteins: Reduction of the Memory Requirement by Consideration of Rigid Geomertry and Molecular Symmetry. 820-837 - Michele E. Clamp, P. G. Baker, C. J. Stirling, Andy Brass:
Hybrid Monte Carlo: An Efficient Algorithm for Condensed Matter Simulation. 838-846 - F. Javier Luque, Margarida Bachs, Modesto Orozco:
An Optimized AM1/MST Method for the MST-SCRF Representation of Solvated Systems. 847-857 - Taihin Zhou, Aimin Liu:
Study of Localized Molecular Orbitals Using Group Theory Methods and Its Approach to the Many-Electron Correlation Problem. IV. The Symmetry-Adaptation of Many-Center Integrals and Hamiltonian Matrix Elements in MCSCF Calculations. 858-865 - Guyan Liang, J. Phillip Bowen, James A. Bentley:
Molecular Mechanics (MM3) Parameterization of Hydroxylamine and Methyl Derivatives. 866-874 - Ann M. Schmiedekamp, Igor A. Topol, Stanley K. Burt, Holy Razafinjanahary, Henry Chemette, Timothy Pfalzgraff, Christopher J. Michejda:
Triazene Proton Affinities: A Comparison between Density Functional, Hartree-Fock, and Post-Hartree-Fock Methods. 875-892 - Zhenghong Zhang, Ludwik Adamowicz:
Explicitly Correlated Gaussian Functions with r2n, 12 Factors for Calculations of the Ground State of the Helium Atom. 893-898 - Peter S. Shenkin, D. Quentin McDonald:
Cluster Analysis of Molecular Conformations. 899-916
Volume 15, Number 9, September 1994
- Uri Dinur, Arnold T. Hagler:
On the FUnctional Representation of Bond Energy Functions. 919-924 - Gábor I. Csonka, Miklóklos Erdösy, József Réffy:
Structure of Disiloxane: A Semiempirical and Post-Hartree-Fock Study. 925-936 - Ludek Matyska, Jaroslav Koca:
D-CICADA : A Software for Confromational PES Elucidation on Network of Workstations. 937-946 - Roberta Susnow, Clarence Schutt, Herschel Rabitz, Shankar Subramaniam:
Conformational Study of Dipeptides: A Sensitivity Analysis Approach. 947-962 - Roberta Susnow, Clarence Schutt, Herschel Rabitz:
Principal Component Analysis of Dipeptides. 963-980 - R. Santamaria, A. Vázquez:
Structural and Electronic Property Changes of the Nucleic Acid Bases upon Base Pair Formation. 981-996 - Niels Grønbech-Jensen, Sebastian Doniach:
Long Time Overdamped Langevin Dynamics of Molecular Chains. 997-1012 - Yasuyuki Kurita, Chiyozo Takayama, Shizuya Tanaka:
Decomposition Analysis of the Intermolecular Interaction Energies in Thw pi-pi Stacking Complexes: Quinhydrone and N, N, N, N-Tetramethyl-p-Diaminobenzene-Chloranil Complex. 1013-1018 - Timothy M. Glennon, Yajun Zheng, Scott M. Le Grand, Brad A. Shutzberg, Kenneth M. Merz Jr.:
A Force Field for Monosaccharides and (1->4) Linked Polysaccharides. 1019-1040 - Gilles Klopman, Dan Fercu:
Application of the Multple Computer Automated Structure Evaluation Methodology to a Qantitative Structure-Activity Relationship Study of Acidity. 1041-1050
Volume 15, Number 10, October 1994
- W. Biemolt, A. P. J. Jansen:
Potential Energy Surfaces for Rh-CO from DFT Calculations. 1053-1063 - Bernd Beck, Guntram Rauhut, Timothy Clark:
The Natural Atomic Orbital Point Charge Model for PM3: Multipole Moments and Molecular Electrostatic Potentials. 1064-1073 - Roberta Susnow, Nancie Senko, Timothy Ocain:
Conformational Sensitivity Analysis of FKBP-FK506/ Rapamycin Complexes. 1074-1090 - Jean M. J. Tronchet, István Komáromi:
Conformation Energy around the N(sp3) - O Single Bond. 1091-1104 - Maxim Totrov, Ruben Abagyan:
Efficient Parallelization of the Energy, Surface, and Dericative Calculations for Internal Coordinate Mechanics. 1105-1112 - Jordi Mestres, Miquel Solà, Miquel Duran, Ramon Carbó:
On the Calculation of Ab Initio Quantum Molecular Similarities for Large Systems: Fitting the Electron Density. 1113-1120 - Alexander J. Pertsin, Jutta Hahn, Hans P. Grossmann:
Incorporation of Bond-Length Constraints in Monte Carlo Simulations of Cyclic and Linear Molecules: Conformational Sampling for Cyclic Alkanes as Test Systems. 1121-1126 - Juan-Luis Pascual-Ahuir, Estanislao Silla, Iñaki Tuñón:
GEPOL: An Improved Description of Molecular Surfaces. III. A New Algorithm for the Computation of a Silvent- Excluding Surface. 1127-1139 - Alain-Dominique Gorse, Michel Pesquer:
The Use of Fraga's Potential with AMI Atomic Point Charges in the Evaluation of Spectral Shifts: Application to TICT Molecules. 1139-1150 - Uwe Versteeg, Wolfram Koch:
The Valence Isomers of (CH)8 and (SiH)8: An Ab Inition MO Study. 1151-1162 - Brian K. Schmitz, William B. Euler:
A Computaional Study of Azine, Azoethene, and Diimine Linkages. 1163-1175 - Brian T. Luke:
Stable Conformations of CH3CH2OCH2CH2OH: A Comparison of Theoretical Methods. 1176-1185
Volume 15, Number 11, November 1994
- Richard J. Wheatley, John B. O. Mitchell:
Gaussian Multipoles in Practice: Electrostatic Energeis for Intermolecular Potentials. 1187-1198 - Frank Jensen:
Transition Structure Modeling by Intersecting Potetntial Energy Surfaces. 1199-1216 - Kim K. Baldridge, R. Fine, Arnold T. Hagler:
The Effects of Solvent Screening in Quantum Mechanical Calculations in Protein Systems. 1217-1227 - Peter I. Nagy, Joseph E. Bitar, Douglas A. Smith:
Comparison of the Molecular Mechanics+Generalized Born/Surface Area and the Ab Initio+Monte Carlo Simulation Methods in Estimating Conformational Equilibria in Aqueous Solution. 1228-1240 - B. G. Rao, M. A. Murcko:
Recersed Stereochemical Preference in Binding of Ro31-8959 to HIV-1 Proteinase: A Free Energy Perturbation Analysis. 1241-1253 - Mangalya Kar, Terry G. Lenz, John D. Vaughan:
Thermodynamic Molecular Mechanics Force Field: Modified QCFF Program. 1254-1265 - Raúl E. Valdés-Pérez:
Algorithm to Infer the Strucutres of Molecular Formulas within a Reaction Pathway. 1266-1278 - Junichi Higo, Mariko Yamaki, Michiru Hogyoku, Takuya Takahashi, Shigeru Endo, Kuniaki Nagayama:
Stability of Two-Dimensional Crystalline Aggregates of a PRotein Studied by Molecular Dynamics. 1278-1290 - Fransiska S. Ganda-Kesuma, Kenneth J. Miller:
Linear Dependency in the Refinement of Force Constants with the Jacobian Method. 1291-1301 - Frank Guarnieri, W. Clark Still:
A Rapidly Convergent Simulation Method: Mixed Monte Carlo/Stochastic Dynamics. 1302-1310 - Haiyan Liu, Yunyu Shi:
Combined Molecular Mechanical and Quantum Mechanical Potential Study of a Nucleophilic Addition Reaction in Solution. 1311-1318
Volume 15, Number 12, December 1994
- Norman L. Allinger, Liqun Yan, Kuo-Hsiang Chen:
Molecular Mechanics Calculations (MM2 and MM3) on Enamines and Aniline Derivatives. 1321-1330 - Andrew E. Torda, Wilfred F. van Gunsteren:
Algorithms for Clustering Molecular Dynamics Confogurations. 1331-1340 - R. Arnaud:
Ab Inition Study of Some CH3OCXYCH2 Radicals: The Influence of Anomeric Effects on Their Strucutre and Their Stability. 1341-1356 - Nathaniel O. J. Malcolm, Joseph J. W. McDouall:
A Variational Biothogonal Valence Bond Method. 1357-1364 - Nathaniel O. J. Malcolm, Joseph J. W. McDouall:
A Variational Biothogonal Valence Bond Descriptions of 1, 3-Dipoles. 1357-1364 - Junichi Higo, Shigeru Endo, Kuniaki Nagayama, Tomoyoshi Ito, Toshiyuki Fukushige, Toshikazu Ebisuzaki, Daiichiro Sugimoto, Hiroo Miyagawa, Kunihiro Kitamura, Junichiro Makino:
Application of a High-Performance, Special-Purpose Computer, GRAPE-2A, to Molecular Dynamics. 1372-1376 - Antony J. Stone, Chong Sze Tong:
Anisotropy of Atom-Atom Repulsions. 1377-1392 - Alexander A. Cohen, Shimon E. Schatzmiller:
Implementation of Artificial Intelligence for Automatic Drug Design. I. Stepwise Computation of the Interactive Drug-Design Sequence. 1393-1402 - Kenneth D. Gibson, Harold A. Scheraga:
A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization. 1403-1413 - Kenneth D. Gibson, Harold A. Scheraga:
An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization. 1414-1428 - Marcel L. Verdonk, R. W. Tjerkstra, I. S. Ridder, Jan A. Kanters, Jan Kroon, W. J. M. van der Kemp:
ToBaD: A MEthod for the Estimation of Torsion Barriers from Crystal Structure Data; Conformational Analysis of N, N-Dimethylaniline and Derivatives. 1429-1436 - Lawrence R. Schmitz, Yi Ren Chen:
Heats of Formation of Organic Molecules Calculated from AB Initio Theory and a Group Equivalent Scheme: Alkenes. 1437-1445 - Yi Fan, Norman L. Allinger:
Molecular Mechanics (MM3) Calculations on Azoxy Compounds. 1446-1462
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