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ORCIDJournal of Computational Chemistry, Volume 16
Volume 16, Number 1, January 1995
- Alexandre Varnek, Georges Wipff, A. S. Glebov, D. Feil:
An Application of the Miertus-Scrocco-Tomasi Solvation Model in Molecular Mechanics and Dynamics Simulations. 1-19 - Elena Laura Coitiño
, Jacopo Tomasi, Roberto Cammi:
On the Evaluation of the Solvent Polarization Apparent Charges in the Polarizable Contnuum Model: A New Formulation. 20-30 - Rolf Gleiter, Karl-Heinz Pfeifer, Wolfram Koch:
Propella[34] Prismane and Its Congeners: A MO-Theoretical Study. 31-36 - A. H. de Vries, Piet Th. van Duijnen, A. H. Juffer, J. A. C. Rullmann, J. P. Dijkmann, H. Merenga, B. Theo Thole:
Implementation of Reaction Field Methods in Quantum Chemistry Computer Codes. 37-55 - Cornelis J. M. Huige, Cornelis Altona:
Force Field Parameters for Sulfates and Sulfamates Based on Ab Initio Calculations: Extensions of AMBER and CHARMm Fields. 56-79 - Michel Petitjean:
Geometric Molecular Similarity from Volume-Based Distance Minimization Application to Saxitoxin and Tetrodotoxin. 80-90 - Thomas R. Furlani, Harry F. King:
Implemenation of a Parallel Direct SCF Algorithm on Distributed Memory Computers. 91-104 - Juan J. Morales, María J. Nuevo:
Path Integral Molecular Dynamics Methods: Application to Neon. 105-112 - Robert V. Stanton, David S. Hartsough, Kenneth M. Merz Jr.:
An Examination of a Density Functional/Molecular Mechanical Coupled Potential. 113-128
Volume 16, Number 2 , February 1995
- Luis Fernández Pacios:
Atomic Radii Scales and Electron Properties Deduced from the Charge Density. 133-145 - Hans-Joachim Böhm, Stefan Brode:
Ab Initio SCF Calculations on Low-Energy Conformers of Cyclohexaglycine. 146-153 - U. Dinur, Arnold T. Hagler:
Geomerty-Dependent Atomic Charges: Methodology and Application to Alkanes, Aldehydes, Ketones, and Amides. 154-170 - Andrew Smellie, Steven L. Teig, Peter Towbin:
Poling: Promoting Conformational Variation. 171-187 - Manuel Dauchez, Philippe Derreumaux, Philippe Lagenat, Gérard Vergoten:
A Vibrational Molecular Force Field of Model Compounds with Biological Interest. IV. Parameters for the Different Glycosidic Linkages of Oligoaccharides. 188-199 - Xiang Zhexin, Shi Yunyu, Xu Yinwu:
Solving the Finite-Difference, Nonlinear, Poisson-Boltzmann Equation under a Linear Approach. 200-206 - Melanie J. M. Pepper, Isaiah Shavitt, Paul von Ragué Schleyer, Mikhail N. Glukhovtsev, Rudolf Janoschek, Martin Quack:
Is the Stereomutation of Methane Possible? 207-225 - Y. S. Li, M. C. Wrinn, John M. Newsam, Mark P. Sears:
Parallel Implementation of a Mesh-Based Density Functional Electronic Structure Code. 226-234 - Tooru Taga, Kazuhumi Masuda:
Monte Carlo Study of Lipid Membranes: Simulation of Diparmitoyl-phosphatidylcholine Bilayers in Gel and Liquid-Crystalline Phases. 235-242 - Allison E. Howard, Piotr Cieplak, Peter A. Kollman:
A Molecular Mechanical Model That Reproduces the Relative Energies for Chair and Twist-Boat Conformations of 1, 3-Dioxanes. 243-262
Volume 16, Number 3, March 1995
- Antonio L. Llamas-Saiz, Concepción Foces-Foces, Otilia Mó, Manuel Yáñez, Eric Elguero, José Elguero:
Geometry of Pyrazole: A Test for Ab Initio Calculations. 163-272 - Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, Michael Scharf:
The Double Cubic Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies. 273-284 - Kenny B. Lipkowitz, Michael A. Peterson:
Evaluation of Moment Statistics for Molecular Modeling. 285-295 - Jaroslav Koca, Serge Pérez, Anne Imberty:
Conformational Analysis and Flexibility of Carbohydrates Using the CICADA Approach with MM3. 296-310 - Daniel L. Severance, Jonathan W. Essex, William L. Jorgensen:
Generalized Alteration of Structure and Parameters: A New Method for Free- Energy Perturbations in Systems Containing Flexible Degrees of Freedom. 311-327 - Shinji Sunada, Nobuhiro Go:
Small-Amplitude Protein Conformational Dynamics: Second Order Analytic Relation between Cartesian Coordinates and Dijedral Angles. 328-336 - Michael J. Holst, Faisal Saied:
Numerical Solution of t he Nonlinear Poisson-Blotzmann Equation: Developing More Robust and Efficient Methods. 337-364 - Mei-Qing Zhang, Robert D. Skeel:
Symplectic Integrators and the Conservation of Angular Momentum. 365-369 - Bo Svensson, Bo Jönsson:
An Efficient Simulation Technique for Electrostatic Free Energies with Applications to Azurin. 370-377 - Takao Furuki, Minoru Sakurai, Yoshio Inoue:
An Application of the Reaction Field Theory to Hydrated Metal Cations in the Framework of the MNDO, AM1, and OM3 Methods. 378-384 - Ming Wah Wong, Kenneth B. Wiberg, Michael J. Frisch:
Ab Initio Calculation of Molar Volumes: Compariso with Experiment and Use in Solvation Models. 365-394
Volume 16, Number 4, April 1995
- Antonio M. Márquez, Michel Dupuis:
Parallel Computation of the MP2 Energy on Distributed Memory Computers. 395-404 - Heiko Gerwens, Karl Jug:
SINDO1 Study of the Photoreaction of Tetramethylene Sulfone. 405-413 - Bjørn K. Alsberg:
Fast, Fuzzy C-Means Clustering of Data Sets with Many Features. 414-421 - Daniel A. Liotard, Gregory D. Hawkins, Gillian C. Lynch, Christopher J. Cramer, Donald G. Truhlar:
Improved Methods for Semiempirical Solvation Models. 422-440 - H. Behnejad, A. Maghari, M. Najafi:
The Extended Law of Corresponding States and the Intermolecular Potentials for Je-He and Ne-Ne. 441-444 - Jian Shen, Florante A. Quiocho:
Calculation of Binding Energy Differences for Receptor-Ligand Systems Using the Poisson-Boltzmann Method. 445-448 - Sung-Eun Yoo, Ok Ja Cha:
Prediction of LUMO Energy and Rate Constant by Comparative Molecular Field Analysis(CoMFA). 449-453 - Brock A. Luty, Zelda R. Wasserman, Pieter F. W. Stouten, C. Nicholas Hodge, Martin Zacharias, James Andrew McCammon:
A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor Interactions. 454-464 - Friedrich Matthias Bickelhaupt, Miquel Solà, Paul von Ragué Schleyer:
Theoretical Investigation of the Relative Stabilites of XSSX and X2SS Isomers (X=F, C1, H, and CH3. 465-477 - Jeong Hyeok Yoon, Jae Kwang Shin, Mu Shik Jhon:
Determination of C- Terminal Structure of Human C-Ha-Ras Oncogenic Protein. 478-485 - Gordon M. Crippen:
Intervals and the Deduction of Drug Binding Site Models. 486-500 - David M. Ferguson:
Parameterization and Evaluation of a Flexible Water Model. 501-511 - Xiang Zhexin, Shi Yunyu, Xu Yingwu:
Calculating the Electric Potential of Macromolecules: A Simple Method for Molecular Surface Triangulation. 512-516 - Tomislav P. Zivkovic, Milan Randic, Douglas J. Klein, Hongyao Zhu, Nenad Trinajstic:
Analytical Approach to Very Large Benzenoid Polymers. 517-526
Volume 16, Number 5, May 1995
- Henk Bekker, H. J. C. Berendesen, Wilfred F. van Gunsteren:
Force and Cirial of Torsional-Angle-Dependent Potentials. 527-533 - Frederico F. Campos, John S. Rollett:
The Exponents Method for Calculating Equilibrium Concentrations of Complex Species in Solution. 534-544 - R. Bursi, M. Lankhorst, D. Feil:
Uncoupled Hartree-Fock Calculations of the Polarizability and Hyperpolarizabilities of Nitrophenols. 545-562 - Modesto Orozco, Margarida Bachs, F. Javier Luque:
Development of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamilitonians. 563-575 - Roland H. Hertwig, Wolfram Koch:
On the Accuracy of Density Functionals and Theiro Basis Set Dependence: An Extensive Study on the Main Group Homonuclear Diatomic Molecules Li2 to Br2. 576-585 - O. V. Sizova, Victor Ivanovich Baranovski:
INDO Parameters for the Elements of the I and II Transition Rows. 586-594 - Jan L. M. Dillen:
An Empirical Force Field I. Alkanes. 595-609 - Jan L. M. Dillen:
An Empirical Force Field II. Crystalline Alkanes. 610-619 - Per-Ola Norrby, Kenneth Wärnmark, Björn Âkermark, Christina Moberg:
Unusual Conformational-Determining Interactions in Oxymethylpyridines: An Ab Initio Study and an Improved Method for Refining Molecular Mechanics Parameters. 620-627 - David J. Willock, Sally L. Price, Maurice Leslie, C. Richard A. Catlow:
The Relaxation of Molecular Crystal Structures Using a Distributed Multipole Electrostatic Model. 628-647 - Frank Guarnieri, Stephen R. Wilson:
Conformational Memories and a Simulated Annealing Program That Learns: Application to LTB4. 648-653 - Dariush Habibollahzadeh, M. Edward Grice, Monica C. Concha, Jane S. Murray, Peter Politzer:
Nonlocal Density Functional Calculation of Gas Phase Heats of Formation. 654-658
Volume 16, Number 6, June 1995
- María Isabel Menéndez Rodríguez, Dimas Suárez, José A. Sordo, Tomás Luis Sordo:
Theoretical Study of the Gas-Phase Addition of HF and HCI to Ethylene: Analysis of the Catalytic Action of Dimeric Halides. 659-666 - Henry A. Gabb, Richard Lavery, Chantal Prévost:
Efficient Conformational Space Samling for Nucleosides Using Internal Coordinat Monte Carlo Simulations and a Modified Furanose Description. 667-680 - Enrico O. Purisima, Shahul H. Nilar:
A Samle Yet Accurate Boundary Element Method for Contituum Dielectric Calculations. 681-689 - Benoît Roux, Martin Karplus:
Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study. 690-704 - Weida Tong, Valerian T. D'Souza:
The Role of the Carboxylate Ion in Models of Acyl-Chymotrypsin. 705-714 - William S. Young, Charles L. Brooks III:
Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics. 715-722 - Mounzer Dagher, Mounif Kobersi, Hafez Kobeissi:
The True Diatomic Potential as a Perturbed Morse Function. 723-728 - Jordi Mestres, Gustavo E. Scuseria:
Genetic Algorithms: A Robust Scheme for Geometry Optimizations and Global Minimum Structure Problems. 729-742 - Tony You, Donald Bashford:
An Analytical Algorithm for the Rapid Determination of the Solvent Accessibility of Points in a Three-Dimensional Lattice around a Solute Molecule. 743-757 - Gustaveo E. Lopéz:
The Electronic Strucure of Weakley Bound Systems. I. Rare-Gas Bimolecular Cations. 758-767 - Gustaveo E. Lopéz:
The Electronic Strucure of Weakley Bound Systems. II. NeX+ and ArX+ (X=H2O, HCI, and HF) Bimolecular Cations. 768-776 - James P. Ritchie, Ann S. Compenhaver:
Comparison of Potential-Derived Charge and Atomic Multipole Models in Calculating Electrostatic Potentials and Energies of Some Muleic Acid Bases and Pairs. 777-790
Volume 16, Number 7, July 1995
- Michael J. Dudek, Jay W. Ponder:
Accurate Modeling of the Intramolecular Electrostaric Energy of Proteins. 791-816 - Valentin Gogonea, Eihi Osawa:
An Improved Algorithm for the Analystical Computation of Solvent-Excluded Volume. The Treatment of Singulatities in Solvent-Accessible Surface Area and Volume Functions. 817-842 - Nohad Gresh, Walter J. Stewens, Morris Krauss:
Mono- and Poly- Ligated Complexes of Zn2+: An Ab Initio Analysis of the Metal-Ligand Interaction Energy. 843-855 - Nohad Gresh:
Energetics of Zn2+ Binding to a Series of Biologically Relecant Ligands: A Molecular Mechanics Investigation Grounded on Ab Initio Self-Consistent Field Supermolecular Computations. 856-882 - Congxin Liang, Liqun Yan, Jörg-Rüdiger Hill, Carl S. Ewig, Terry R. Stouch, Arnold T. Hagler:
Force Field Studies of Cholesterol and Chelesteryl Acetate Crystals and Cholesterol-Cholesterol Intermolecular Interactions. 883-897 - Ranganathan Bharadwaj, Andreas Windemuth, S. Sriharan, Barry Honig, Antony Nocholls:
A Fast Multipole Boundary Element Method for Molecular Electrostatics: An Optimal Approach for Large Systems. 898-913 - Joep Aerts:
An Improved Molecular Modeling Method for the Prediction of Enantioselectivity. 914-922
Volume 16, Number 8, August 1995
- Thomas H. Fischer, Wesley P. Petersen, Hans Peter Lüthi:
A New Optimization Technique for Artificial Neural Networks Applied to Prediction of Force Constants of Large Molecules. 923-936 - Uwe Koch, Ernst Egent:
An Improbed Description of the Molecular Charge Density in Force Fields with Atomic Multipole Moments. 937-944 - P. C. Chen:
The Molecular Structures and the Absorption Maxima of the H-Chromophores of t he Indigoid Dyes. 945-950 - Jonathan W. Essex, William L. Jorgensen:
An Empirical Boundary Potential for Water Droplet Simulations. 951-972 - Mark Sulkes:
Conformational Analysis of Jet-Cooled Tryptohan Analogs and Histamine Using the MM3(94) Force Field: Comparison with Experiment. 973-983 - David S. Maxwell, Julian Tirado-Rives, William L. Jorgensen:
A Comprehensive Study of the Rotational Energy Profiles of Orgenic Systems by Ab Initio MO Theory, Forming a Base for Pepetide Torsional Parameters. 984-1010 - Je Myung Park, Oh Young Kwon, Kyoung Tai No, Mu Shik Jhon, Harold A. Scheraga:
Determination of Net Atomics Charges Using a Modified Partial Equalization or Orbital Electronegativity Method. IC. Application to Hypervalent Sulfur and Phosphorus-Containing Molecules. 1011-1027 - Eric Magnusson:
Electrostatic Bonding Models: A Test on Group 1 and 2 Complexes with H2, NH3, H2S, Ph3, and Related Liquids. 1027-1038 - S. Sridharan, Antony Nicholls, Kim A. Sharp:
A Rapid Method for Calculating Derivatives of Solvent Accessible Surface Areas of Molecules. 1038-1044 - Ikchoon Lee, Chang Kon Kim, Bon-Su Lee:
Ab Initio Orbital Studies of Nonidentity Allyl Transfer Reactions. 1045-1054
Volume 16, Number 9, September 1995
- Bruce A. Smart, Carl H. Schiesser:
On the Existence of SH3, and TeH3: Discrepanticies between All-Electron and Pseudopotential Calculations. 1055-1066 - Lawrence M. Pratt, Ishrat M. Khan:
A Density Functional Treatment of Organolithium Compounds: Comparison to Ab Initio, Semiempirical, and Epreimental Results. 1067-1080 - Micahel K. Golson, James Andrew McCammon, Jeffrey D. Madura:
Molecular Dynamics Simulation with a Comtinuum Electrostatic Model of the Solvent. 1081-1095 - Søren Balling Engelsen, Serge Pérez, Isabelle Braccini, Catherine Hervé du Penhoat:
Internal Motions of Carbohydrates as PRobed by Comparative Molecular Modeling and Nuclear Magnetic Resonance of Ethyl beta-Lactoside. 1096-1119 - Takashi Amisaki, Takaji Fujiwara, Akihiro Kusumi, Hiroo Miyagawa, Kunihiro Kitamura:
Error Evaluation in the Disign of a Special-Purpose Processor That Calculates Nonbonded Forces in Molecular Dynamics Simulations. 1120-1130 - Eric Swanson, Terry P. Lybrand:
PVM-AMBER: A Parallel Implementation of the AMBER Molecular Mechanics Package for Workstation Clusters. 1131-1140 - Dan N. Bernardo, Yanbo Ding, Karsten Krogh-Jespersen, Ronald M. Levy:
Evaluating Polarizable Potentials on Distributed Memory Parallel Computers: Program Development and Applications. 1141-1152 - Daniel R. Ripoll, Marcia S. Pottle, Kenneth D. Gibson, Harold A. Scheraga, Adam Liwo:
Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer. 1153-1163 - Yaxiong Sun, Peter A. Kollman:
Hydrophobic Solvation of Methane and Nonbond Parameters of the TIP3P Water Model. 1164-1169 - Feliu Maseras, Keiji Morokuma:
IMOMM: A New Integrated Ab Initio + Molecular Mechanics Geometry Optimization Scheme of Equilibrium Structures and Transition States. 1170-1179
Volume 16, Number 10, October 1995
- Marc R. Roussel, Carmay Lim:
Discrete, Dynamic Polymer Modelin: A Pseudo-Diatomic Model of Lignin. 1181-1191 - Eric Barth, Krzysztof Kuczera, Benedict J. Leimkuhler, Robert D. Skeel:
Algorithms for Constrained Molecular Dynamics. 1192-1209 - Kevin P. Clark:
Flexible Ligand Docking without Parameter Adjustment across Four Ligand-Receptor Complexes. 1210-1226 - D. B. Chesnut:
A Comparative Quatnum Mechanical Study of Bond Separation Energies as a Measure of Cyclic Conjugation. 1227-1237 - P. Duane Walker, Paul G. Mezey:
Toward Similarity Measures for Macromolecular Bodies: MEDLA Test Calculations for Substituted Benzene Systems. 1238-1249 - Georgia B. McGaughey, Eugene L. Stewart, J. Phillip Bowen:
Ab Initio and Molecular Mechanics /MM2 and MM3) Calculations of Nonconjugated Positively Charged Nitrogen-Containg Compounds. 1250-1260 - Warner L. Peticolas, Thomas Rush III:
Ab Initio Calculations of the Ultraviolet Resonance Raman Spectra of Uracil. 1261-1270 - James Turner, Paul Weiner, Barry Robson, Ravi Venugopal, Harry Schubele III, Ramen Singh:
Reduced Variable Molecular Dynamics. 1271-1290 - Adrian T. Wong, Robert J. Harrison:
Approaches to Large-Scale Parallel Self-Consisten Field Calculations. 1291-1300 - Ida M. B. Nielsen, Edward T. Seidl:
Parallel Direct Implementations of Second-Order Perturbation Theories. 1301-1314
Volume 16, Number 11, January 1995
- Pavel Hobza, Jirí Sponer, Tomas Reschel:
Density Functional Theory and Moleculer Clusters. 1315-1325 - Josep Maria Bofill, Mónica Comajuan:
Analysis of the Updated Hessian Matrices for Locating Transition Strucutres. 1326-1338 - Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, Peter A. Kollman:
Multidimensional Free-Energy Calculations Using the Weighted Histogram Analysis Method. 1339-1350 - Piotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman:
Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and Proteins. 1357-1376 - Andrew R. Leach, Teri E. Klein:
A Molecualr Dynamics Study of the Inhibition of Chicken Dihydrofolate Reductase by a Phenyl Triazine. 1378-1393 - Boris R. Stefanov, Jerzy Cieslowski:
Ann Efficient Approach to Calculation of Zero-Flux Atimic Surfaces and Generation of Atimic Intergration Data. 1394-1404 - Richard S. Judson, Y. T. Tan, E. Mori, C. Melius, Edward P. Jaeger, Adi M. Treasurywala, Alan M. Mathiowetz:
Docking Flexible Molecules: A Case Study of Three Proteins. 1405-1419 - James J. Vincent, Kenneth M. Merz Jr.:
A Highly Portable Parallel Implementation of AMBER4 Using the Message Passing Interface Standart. 1420-1427 - Razif R. Gabdoulline, Chong Zheng:
Effects of the Cutoff Center on the MEan Potential and Pair Distribution Functions in Liquid Water. 1428-1433 - Frank Herrmann, Sándor Suhai:
Energy Minimization of Peptide Ananlogues Using Genetic Algorithms. 1434-1445
Volume 16, Number 12, December 1995
- Roberto Cammi, Jacopo Tomasi:
Remarks on the Use of the Apparent Surface Charges /ASC) Methods in Solvation Problems: Iterative versus Matrix-Inversion Procedures and the Renormalization of the Apparent Charges. 1449-1458 - Alexander A. Cohen, Shimon E. Schatzmiller:
Localization and Quantitative Evaluation of Potent Local Binding Sites on the Accessible Lennard-Jones Surface. 1459-1467 - Xiang Zhexin, Huang Fuhua, Shi Yunyu, Xu Yinwu:
Incorporating the Protein-Dipole Langevin-Dipole Model into Tanford-Kirkwood Theory. 1468-1473 - P. Duane Walker, Paul G. Mezey, Gerald M. Maggiora, Mark A. Johnson, James D. Petke:
Application of the Shape Group Method to Conformation Processes: Shape and Conjugation Changes in the Conformers of 2-Phenyl Pyrimidine. 1474-1482 - Alain St.-Amant, Wendy D. Cornell, Peter A. Kollman, Thomas A. Halgren:
Calculation of Molecular Geometries, Relative Conformational Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Function Theory. 1483-1506 - Juan C. Cesco, Claudia C. Denner, Ana E. Rosso, Jorge E. Pérez, F. S. Ortiz, Rubén H. Contreras, C. G. Giribet, M. C. Ruiz de Azúa:
Numerical Evaluation of Three- and Four- Center Bielectronic Integrals Using Exponential- Type Atomic Orbitals. 1507-1512 - Mark D. Erion, M. Rami Reddy:
Calculation of Relative Free Energy Differrences for the Covalent Hydration of Organic Compounds: A Combined Quantum Mechanical and Free Energy Perturbation Study. 1513-1521 - Bernard R. Brooks, Dusanka Janezic, Martin Karplus:
Harmonic Analysis of Large Systems. I. Methodology. 1522-1542 - Dusanka Janezic, Martin Karplus:
Harmonic Analysis of Large Systems. II. Comaprison of Different Protein Models. 1543-1553 - Dusanka Janezic, Richard M. Venable, Martin Karplus:
Harmonic Analysis of Large Systems. III. Comparison with Molecular Dynamics. 1554-1568
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