JCC 16(1) CONTENTS An Application of the Miertus-Scrocco-Tomasi Solvation Model in 1 Molecular Mechanics and Dynamics Simulations A. A. Varnek, G. Wipff, A. S. Glebov, and D. Feil On the Evaluation of the Solvent Polarization Apparent Charges in 20 the Polarizable Continuum Model: A New Formulation Elena L. Coiti$o, Jacopo Tomasi, and Roberto Cammi Propella[34]Prismane and Its Congeners: A MO-Theoretical Study 31 Rolf Gleiter, Karl-Heinz Pfeifer, and Wolfram Koch Implementation of Reaction Field Methods in Quantum Chemistry 37 Computer Codes A. H. de Vries, P. Th. van Duijnen, A. H. Juffer, J. A. C. Rullmann, J. P. Dijkman, H. Merenga, and B. T. Thole Force Field Parameters for Sulfates and Sulfamates Based on Ab Initio 56 Calculations: Extensions of AMBER and CHARMm Fields Cornelis J. M. Huige and Cornelis Altona Geometric Molecular Similarity from Volume-Based Distance Minimization: 80 Application to Saxitoxin and Tetrodotoxin Michel Petitjean Implementation of a Parallel Direct SCF Algorithm on Distributed 91 Memory Computers Thomas R. Furlani and Harry F. King Path Integral Molecular Dynamics Methods: Application to Neon 105 Juan J. Morales and Mar!a J. Nuevo An Examination of a Density Functional/Molecular Mechanical 113 Coupled Potential Robert V. Stanton, David S. Hartsough, and Kenneth M. Merz Jr. Announcement 129 Errata 130 Diskette Submission Instructions I ========================================================== JCC 16(2) CONTENTS Atomic Radii Scales and Electron Properties Deduced from the Charge Density 133 L. Fern ndez Pacios Ab Initio SCF Calculations on Low-Energy Conformers of Cyclohexaglycine 146 Hans-Joachim Bhm and Stefan Brode Geometry-Dependent Atomic Charges: Methodology and Application to 154 Alkanes, Aldehydes, Ketones, and Amides U. Dinur and A. T. Hagler Poling: Promoting Conformational Variation 171 Andrew Smellie, Steven L. Teig, and Peter Towbin A Vibrational Molecular Force Field of Model Compounds with 188 Biological Interest. IV. Parameters for the Different Glycosidic Linkages of Oligosaccharides Manuel Dauchez, Philippe Derreumaux, Philippe Lagant, and Grard Vergoten Solving the Finite-Difference, Nonlinear, Poisson-Boltzmann Equation 200 under a Linear Approach Xiang Zhexin, Shi Yunyu, and Xu Yinwu Is the Stereomutation of Methane Possible? 207 Melanie J. M. Pepper, Isaiah Shavitt, Paul von Ragu Schleyer, Mikhail N. Glukhovtsev, Rudolf Janoschek, and Martin Quack Parallel Implementation of a Mesh-Based Density Functional Electronic 226 Structure Code Y. S. Li, M. C. Wrinn, J. M. Newsam, and M. P. Sears (Continued) Monte Carlo Study of Lipid Membranes: Simulation of Diparmitoyl- 235 phosphatidylcholine Bilayers in Gel and Liquid-Crystalline Phases Tooru Taga and Kazuhumi Masuda A Molecular Mechanical Model That Reproduces the Relative Energies 243 for Chair and Twist-Boat Conformations of 1,3-Dioxanes Allison E. Howard, Piotr Cieplak, and Peter A. Kollman Diskette Submission Instructions I ===================================================== JCC 16(3) ONTENTS The Geometry of Pyrazole: A Test for Ab Initio Calculations 263 Antonio L. Llamas-Saiz, Concepci"n Foces-Foces, Otilia M", Manuel Y $ez, Eric Elguero, and Jos Elguero The Double Cubic Lattice Method: Efficient Approaches to Numerical 273 Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies Frank Eisenhaber, Philip Lijnzaad, Patrick Argos, Chris Sander, and Michael Scharf Evaluation of Moment Statistics for Molecular Modeling 285 Kenny B. Lipkowitz and Michael A. Peterson Conformational Analysis and Flexibility of Carbohydrates Using 296 the CICADA Approach with MM3 Jaroslav Koca, Serge Prez, and Anne Imberty Generalized Alteration of Structure and Parameters: A New Method 311 for Free-Energy Perturbations in Systems Containing Flexible Degrees of Freedom Daniel L. Severance, Jonathan W. Essex, and William L. Jorgensen Small-Amplitude Protein Conformational Dynamics: Second-Order 328 Analytic Relation between Cartesian Coordinates and Dihedral Angles Shinji Sunada and Nobuhiro Go Numerical Solution of the Nonlinear Poisson-Boltzmann 337 Equation: Developing More Robust and Efficient Methods Michael J. Holst and Faisal Saied (Continued) Symplectic Integrators and the Conservation of Angular Momentum 365 Mei-Qing Zhang and Robert D. Skeel An Efficient Simulation Technique for Electrostatic Free Energies 370 with Applications to Azurin Bo Svensson and Bo Jnsson An Application of the Reaction Field Theory to Hydrated Metal 378 Cations in the Framework of the MNDO, AM1, and PM3 Methods Takao Furuki, Minoru Sakurai, and Yoshio Inoue Ab Initio Calculation of Molar Volumes: Comparison with Experiment 385 and Use in Solvation Models Ming Wah Wong, Kenneth B. Wiberg, and Michael J. Frisch Diskette Submission Instructions I ============================================= JCC 16(4) CONTENTS Parallel Computation of the MP2 Energy on Distributed Memory Computers 395 Antonio M. M rquez and Michel Dupuis SINDO1 Study of the Photoreaction of Tetramethylene Sulfone 405 Heiko Gerwens and Karl Jug Fast, Fuzzy C-Means Clustering of Data Sets with Many Features 414 Bjorn K. Alsberg Improved Methods for Semiempirical Solvation Models 422 Daniel A. Liotard, Gregory D. Hawkins, Gillian C. Lynch, Christopher J. Cramer, and Donald G. Truhlar The Extended Law of Corresponding States and the Intermolecular 441 Potentials for He_He and Ne_Ne H. Behnejad, A. Maghari, and M. Najafi Calculation of Binding Energy Differences for Receptor-Ligand 445 Systems Using the Poisson-Boltzmann Method Jian Shen and Florante A. Quiocho Prediction of LUMO Energy and Rate Constant by Comparative Molecular 449 Field Analysis (CoMFA) Sung-Eun Yoo and Ok Ja Cha A Molecular Mechanics/Grid Method for Evaluation of Ligand-Receptor 454 Interactions Brock A. Luty, Zelda R. Wasserman, Pieter F. W. Stouten, C. Nicholas Hodge, Martin Zacharias, and J. Andrew McCammon Theoretical Investigation of the Relative Stabilities of XSSX and X2SS 465 Isomers (X = F, C1, H, and CH3) F. Matthias Bickelhaupt, Miquel Sol, and Paul von Ragu Schleyer Determination of C-Terminal Structure of Human C_Ha_Ras 478 Oncogenic Protein Jeong Hyeok Yoon, Jae Kwang Shin, and Mu Shik Jhon Intervals and the Deduction of Drug Binding Site Models 486 Gordon M. Crippen Parameterization and Evaluation of a Flexible Water Model 501 David M. Ferguson Calculating the Electric Potential of Macromolecules: A Simple 512 Method for Molecular Surface Triangulation Xiang Zhexin, Shi Yunyu, and Xu Yingwu Analytical Approach to Very Large Benzenoid Polymers 517 T. Zivkovic, M. Randic, D. J. Klein, H.-Y. Zhu, and N. Trinajstic Diskette Submission Instructions I =============================================================== JCC 16(5) Force and Virial of Torsional-Angle-Dependent Potentials 527 H. Bekker, H. J. C. Berendsen, and W. F. van Gunsteren The Exponents Method for Calculating Equilibrium Concentrations of Eomplex Species in Solution 534 Frederico F. Campos and John S. Rollett Uncoupled Hartree-Fock Calculations of the Polarizability and Hyperpolarizabilities of Nitrophenols 545 R. Bursi, M. Lankhorst, and D. Feil IDevelopment of Optimized MST/SCRF Methods for Semiempirical Calculations: The MNDO and PM3 Hamiltonians 563 Modesto Orozco, M. Bachs, and F. J. Luque On the Accuracy of Density Functionals and Their Basis Set Dependence: An Extensive Study on the Main Group Homonuclear Diatomic Molecules 576 Li2 to Br2 Roland H. Hertwig and Wolfram Koch INDO Parameters for the Elements of the I and II Transition Rows 586 O. V. Sizova and V. I. Baranovski An Empirical Force Field. I. Alkanes 595 Jan L. M. Dillen An Empirical Force Field. II. Crystalline Alkanes 610 Jan L. M. Dillen Unusual Conformational-Determining Interactions in Oxymethyl- pyridines: An Ab Initio Study and an Improved Method for Refining Molecular Mechanics Parameters 620 Per-Ola Norrby, Kenneth Wrnmark, Bjrn kermark, and Christina Moberg The Relaxation of Molecular Crystal Structures Using a Distributed Multipole Electrostatic Model D. J. Willock, S. L. Price, M. Leslie, and c. R. A. Catlow Conformational Memories and a Simulated Anneling Program That Learns: Application to LTB4 648 Frank Guarnieri and Stephen R. Wilson Nonlocal Density Functional Calculation of Gas Phase Heats of Formation 654 Dariush Habibollahzandeh, M. Edward Grice, Monica C. Concha, Jane S. Murry, and Peter Politzer Diskette Submission Instructions I =============================================== JCC 16(6) CONTENTS Theoretical Study of the Gas-Phase Addition of HF and HCl to Ethylene: Analysis of the Catalytic Action of Dimeric Halides M. I. Menndez, D. Su rez, J. A. Sordo, and T. L. Sordo 659 Efficient Conformational Space Sampling for Nucleosides Using Internal Coordinate Monte Carlo Simulations and a Modified Furanose Description H. A. Gabb, R. Lavery, and C. Prvost 667 A Simple Yet Accurate Boundary Element Method for Continuum Dielectric Calculations Enrico O. Purisima and Shahul H. Nilar 681 Potential Energy Function for Cation-Peptide Interactions: An Ab Initio Study Benot Roux and Martin Karplus 690 The Role of the Carboxylate Ion in Models of Acyl-Chymotrypsin Weida Tong and Valerian T. D'Souza 705 Dynamic Load Balancing Algorithms for Replicated Data Molecular Dynamics William S. Young and Charles L. Brooks III 715 The True Diatomic Potential as a Perturbed Morse Function Mounzer Dagher, Mounif Kobersi, and Hafez Kobeissi 723 Genetic Algorithms: A Robust Scheme for Geometry Optimizations and Global Minimum Structure Problems 729 Jordi Mestres and Gustavo E. Scuseria An Analytical Algorithm for the Rapid Determination of the Solvent Accessibility of Points in a Three-Dimensional Lattice around a Solute Molecule Tony You and Donald Bashford 743 The Electronic Structure of Weakly Bound Systems. I. Rare-Gas Bimolecular Cations Gustavo E. L"pez 758 The Electronic Structure of Weakly Bound Systems. II. NeX+ and ArX+ (X=H2O, HCl, and HF) Bimolecular Cations Gustavo E. L"pez 768 Comparison of Potential-Derived Charge and Atomic Multipole Models in Calculating Electrostatic Potentials and Energies of Some Nucleic Acid Bases and Pairs James P. Ritchie and Ann S. Copenhaver 777 Diskette Submission Instructions I ============================================================= JCC 16(7) Accurate Modeling of the Intramolecular Electrostatic Energy of Proteins 791 Michael J. Dudek and Jay W. Ponder An Improved Algorithm for the Analytical Computation of Solvent- 817 Excluded Volume. The Treatment of Singularities in Solvent-Accessible Surface Area and Volume Functions Valentin Gogonea and Eiji Osawa Mono- and Poly-Ligated Complexes of Zn2+: An Ab Initio Analysis of the 843 Metal-Ligand Interaction Energy Nohad Gresh, Walter J. Stevens, and Morris Krauss Energetics of Zn2+ Binding to a Series of Biologically Relevant Ligands: 856 A Molecular Mechanics Investigation Grounded on Ab Initio Self- Consistent Field Supermolecular Computations Nohad Gresh Force Field Studies of Cholesterol and Cholesteryl Acetate Crystals and 883 Cholesterol-Cholesterol Intermolecular Interactions Congxin Liang, Liqun Yan, Jrg-R. Hill, Carl S. Ewig, Terry R. Stouch, and Arnold T. Hagler The Fast Multipole Boundary Element Method for Molecular 898 Electrostatics: An Optimal Approach for Large Systems Ranganathan Bharadwaj, Andreas Windemuth, S. Sridharan, Barry Honig, and Anthony Nicholls An Improved Molecular Modeling Method for the Prediction of 914 Enantioselectivity J. Aerts Diskette Submission Instructions I ================================================================ JCC 16(8) A New Optimization Technique for Artificial Neural Networks Applied to 923 Prediction of Force Constants of Large Molecules Thomas H. Fischer, Wesley P. Petersen, and Hans Peter Lthi An Improved Description of the Molecular Charge Density in Force 937 Fields with Atomic Multipole Moments Uwe Koch and Ernst Egert The Molecular Structures and the Absorption Maxima of the 945 H-Chromophores of the Indigoid Dyes P. C. Chen An Empirical Boundary Potential for Water Droplet Simulations 951 Jonathan W. Essex and William L. Jorgensen Conformational Analysis of Jet-Cooled Tryptophan Analogs and Histamine 973 Using the MM3(94) Force Field: Comparison with Experiment Mark Sulkes A Comprehensive Study of the Rotational Energy Profiles of 984 Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide Torsional Parameters David S. Maxwell, Julian Tirado-Rives, and William L. Jorgensen Determination of Net Atomic Charges Using a Modified Partial Equalization 1011 of Orbital Electronegativity Method. IV. Application to Hypervalent Sulfur- and Phosphorus-Containing Molecules Je Myung Park, Oh Young Kwon, Kyoung Tai No, Mu Shik Jhon, and Harold A. Scheraga Electrostatic Bonding Models: A Test on Group 1 and 2 Metal Complexes 1027 with H2O, NH3, H2S, PH3, and Related Ligands Eric Magnusson A Rapid Method for Calculating Derivatives of Solvent Accessible 1038 Surface Areas of Molecules S. Sridharan, Anthony Nicholls, and Kim A. Sharp Ab Initio Molecular Orbital Studies of Nonidentity Allyl Transfer 1045 Reactions Ikchoon Lee, Chang Kon Kim, and Bon-Su Lee Diskette Submission Instructions I =================================================================== JCC 16(9) CONTENTS On the Existence of SH3, SeH3, and TeH3: Discrepancies between 1055 All-Electron and Pseudopotential Calculations Bruce A. Smart and Carl H. Schiesser A Density Functional Treatment of Organolithium Compounds: 1067 Comparison to Ab Initio, Semiempirical, and Experimental Results Lawrence M. Pratt and Ishrat M. Khan Molecular Dynamics Simulation with a Continuum Electrostatic Model 1081 of the Solvent Michael K. Gilson, J. Andrew McCammon, and Jeffry D. Madura Internal Motions of Carbohydrates as Probed by Comparative Molecular 1096 Modeling and Nuclear Magnetic Resonance of Ethyl b-Lactoside Soren B. Engelsen, Serge Prez, Isabelle Braccini, and Catherine Herv Du Penhoat Error Evaluation in the Design of a Special-Purpose Processor That 1120 Calculates Nonbonded Forces in Molecular Dynamics Simulations Takashi Amisaki, Takaji Fujiwara, Akihiro Kusumi, Hiroo Miyagawa, and Kunihiro Kitamura PVM-AMBER: A Parallel Implementation of the AMBER Molecular 1131 Mechanics Package for Workstation Clusters Eric Swanson and Terry P. Lybrand Evaluating Polarizable Potentials on Distributed Memory Parallel 1141 Computers: Program Development and Applications Dan N. Bernardo, Yanbo Ding, Karsten Krogh-Jespersen, and Ronald M. Levy Implementation of the ECEPP Algorithm, the Monte Carlo Minimization 1153 Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer D. R. Ripoll, M. S. Pottle, K. D. Gibson, H. A. Scheraga, and A. Liwo Hydrophobic Solvation of Methane and Nonbond Parameters of the 1164 TIP3P Water Model Yaxiong Sun and Peter A. Kollman IMOMM: A New Integrated Ab Initio + Molecular Mechanics Geometry 1170 Optimization Scheme of Equilibrium Structures and Transition States Feliu Maseras and Keiji Morokuma Diskette Submission Instructions =================================================================== JCC 16(10) CONTENTS Discrete, Dynamic Polymer Modeling: A Pseudo-Diatomic Model 1181 of Lignin Marc R. Roussel and Carmay Lim Algorithms for Constrained Molecular Dynamics 1192 Eric Barth, Krzysztof Kuczera, Benedict Leimkuhler, and Robert D. Skeel Flexible Ligand Docking without Parameter Adjustment across Four 1210 Ligand-Receptor Complexes Kevin P. Clark and Ajay A Comparative Quantum Mechanical Study of Bond Separation 1227 Energies as a Measure of Cyclic Conjugation D. B. Chesnut Toward Similarity Measures for Macromolecular Bodies: MEDLA 1238 Test Calculations for Substituted Benzene Systems P. Duane Walker and Paul G. Mezey Ab Initio and Molecular Mechanics (MM2 and MM3) Calculations of 1250 Nonconjugated Positively Charged Nitrogen-Containing Compounds Georgia B. McGaughey, Eugene L. Stewart, and J. Phillip Bowen Ab Initio Calculations of the Ultraviolet Resonance Raman Spectra of Uracil 1261 ==================================================================== JCC 16(11) CONTENTS Density Functional Theory and Moleculer Clusters 1315 Pavel Hobza, Jir! Sponer, and Tom s Reschel Analysis of the Updated Hessian Matrices for Locating Transition Structures 1326 Josep Maria Bofill and M"nica Comajuan Multidimensional Free-Energy Calculations Using the Weighted Histogram 1339 Analysis Method Shankar Kumar, John M. Rosenberg, Djamal Bouzida, Robert H. Swendsen, and Peter A. Kollman Gradient SHAKE: An Improved Method for Constrained Energy 1351 Minimization in Macromolecular Simulations Yong Duan, Shankar Kumar, John M. Rosenberg, and Peter A. Kollman Application of the Multimolecule and Multiconformational RESP 1357 Methodology to Biopolymers: Charge Derivation for DNA, RNA, and Proteins Piotr Cieplak, Wendy D. Cornell, Christopher Bayly, and Peter A. Kollman A Molecular Dynamics Study of the Inhibition of Chicken Dihydrofolate 1378 Reductase by a Phenyl Triazine Andrew R. Leach and Teri E. Klein An Efficient Approach to Calculation of Zero-Flux Atomic Surfaces and 1394 Generation of Atomic Integration Data Boris B. Stefanov and Jerzy Cioslowski Docking Flexible Molecules: A Case Study of Three Proteins 1405 R. S. Judson, Y. T. Tan, E. Mori, C. Melius, E. P. Jaeger, A. M. Treasurywala, and A. Mathiowetz A Highly Portable Parallel Implementation of AMBER4 Using the Message 1420 Passing Interface Standard James J. Vincent and Kenneth M. Merz, Jr. Effects of the Cutoff Center on the Mean Potential and Pair 1428 Distribution Functions in Liquid Water Razif R. Gabdoulline and Chong Zheng Energy Minimization of Peptide Analogues Using Genetic Algorithms 1434 Frank Herrmann and S ndor Suhai Erratum 1445 Announcement 1447 Diskette Submission Instructions I ================================================================== JCC 16(12) Remarks on the Use of the Apparent Surface Charges (ASC) Methods 1449 in Solvation Problems: Iterative versus Matrix-Inversion Procedures and the Renormalization of the Apparent Charges R. Cammi and J. Tomasi Localization and Quantitative Evaluation of Potent Local Binding Sites 1459 on the Accessible Lennard-Jones Surface Alexander A. Cohen and Shimon E. Shatzmiller Incorporating the Protein-Dipole Langevin-Dipole Model into 1468 Tanford-Kirkwood Theory Xiang Zhexin, Huang Fuhua, Shi Yunyu, and Xu Yinwu Application of the Shape Group Method to Conformational Processes: 1474 Shape and Conjugation Changes in the Conformers of 2-Phenyl Pyrimidine P. Duane Walker, Paul G. Mezey, Gerald M. Maggiora, Mark A. Johnson, and James D. Petke Calculation of Molecular Geometries, Relative Conformational Energies, 1483 Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Functional Theory Alain St.-Amant, Wendy D. Cornell, Peter A. Kollman, and Thomas A. Halgren Numerical Evaluation of Three- and Four-Center Bielectronic Integrals 1507 Using Exponential-Type Atomic Orbitals J. C. Cesco, C. C. Denner, A. E. Rosso, J. E. Perez, F. S. Ortiz, R. H. Contreras, C. G. Giribet, and M. C. Ruiz de Az#a Calculation of Relative Free Energy Differences for the Covalent Hydration 1513 of Organic Compounds: A Combined Quantum Mechanical and Free Energy Perturbation Study Mark D. Erion and M. Rami Reddy Harmonic Analysis of Large Systems. I. Methodology 1522 Bernard R. Brooks, Dusanka Janezic, and Martin Karplus Harmonic Analysis of Large Systems. II. Comparison of Different 1543 Protein Models Dusanka Janezic and Bernard R. Brooks Harmonic Analysis of Large Systems. III. Comparison with 1554 Molecular Dynamics Dusanka Janezic, Richard M. Venable, and Bernard R. Brooks Author Index 1569 Subject Index 1577 Volume Contents I Diskette Submission Instructions XV