Journal of Computational Chemistry vol. 17 JCC 17(1) CONTENTS Potential Derived Charges Using a Geodesic Point Selection Scheme 1 Mark A. Spackman A Coupled Density Functional-Molecular Mechanics Monte Carlo 19 Simulation Method: The Water Molecule in Liquid Water I. Tu$"n, M. T. C. Martins-Costa, C. Millot, M. F. Ruiz-L"pez, and J. L. Rivail Superacidity of Neutral Brnsted Acids in Gas Phase 30 Peeter Burk, Ilmar A. Koppel, Ivar Koppel, Lev M. Yagupolskii, and Robert W. Taft Relative Stability of the 3A2, 1A2, and 1A1 States of Phenylnitrene: 42 A Difference-Dedicated Configuration Interaction Calculation O. Castell, V. M. Garc!a, C. Bo, and R. Caballol Using Redundant Internal Coordinates to Optimize Equilibrium 49 Geometries and Transition States Chunyang Peng, Philippe Y. Ayala, H. Bernhard Schlegel, and Michael J. Frisch Analytical First Derivatives of Molecular Surfaces with Respect to 57 Nuclear Coordinates Maurizio Cossi, Benedetta Mennucci, and Roberto Cammi Performance Analysis of the Double-Iterated Kalman Filter for Molecular 74 Structure Estimation D. Delfini, C. Nicolini, and E. A. Carrara Semiempirical Treatment of Electrostatic Potentials and Partial Charges 87 in Combined Quantum Mechanical and Molecular Mechanical Approaches Dirk Bakowies and Walter Thiel Toward High-Performance Computational Chemistry: I. Scalable Fock 109 Matrix Construction Algorithms Ian T. Foster, Jeffrey L. Tilson, Albert F. Wagner, Ron L. Shepard, Robert J. Harrison, Rick A. Kendall, and Rik J. Littlefield Toward High-Performance Computational Chemistry: II. A Scalable 124 Self-Consistent Field Program Robert J. Harrison, Martyn F. Guest, Rick A. Kendall, David E. Bernholdt, Adrian T. Wong, Mark Stave, James L. Anchell, Anthony C. Hess, Rik J. Littlefield, ===================================================================== JCC 17(2) CONTENTS Theoretical Investigations on 1,2-Ethanediol: The Problem of 133 Intramolecular Hydrogen Bonds S. Reiling, J. Brickmann, M. Schlenkrich, and P. A. Bopp Computation of Hydration Free Energies Using a Parametrized 148 Continuum Model: Study of Equilibrium Geometries and Reactive Processes in Water Solution I. Tu$"n, M. Ruiz-L"pez, D. Rinaldi, and J. Bertr n Pyrrolizidine Alkaloids Necine Bases: Ab Initio, Semiempirical, and 156 Molecular Mechanics Approaches to Molecular Properties M. Giordan, R. Custodio, and J. R. Trigo A Chemometric Analysis of Ab Initio Vibrational Frequencies and 167 Infrared Intensities of Methyl Fluoride A. L. M. S. de Azevedo, B. B. Neto, I. S. Scarminio, A. E. de Oliveira, and R. E. Bruns Direct CI Method in Restricted Configuration Spaces 178 A. I. Panin and O. V. Sizova Solvent Effects: 6. A Comparison between Gas Phase and Solution Acidities 185 K. B. Wiberg, H. Castejon, and T. A. Keith Molecular Dynamics Simulation of a Rhinovirus Capsid under 191 Rotational Symmetry Boundary Conditions S. Yoneda, M. Kitazawa, and H. Umeyama A Semiempirical Computational Study of Electron Transfer Reactivity of 204 One- vs. Two-Ring Model Systems for Anthracycline Pharmacophores. I. A Rationale for Mode of Action A. Sawyer, E. Sullivan, and Y. H. Mariam Inter Ca Atomic Potentials Derived from the Statistics of Average 226 Interresidue Distances in Proteins: Application to Bovine Pancreatic Trypsin Inhibitor T. Kikuchi A Metropolis Monte Carlo Method for Analyzing the Energetics 238 and Dynamics of Lipopolysaccharide Supramolecular Structure and Organization S. Jung, D. Min, and R. I. Hollingsworth A Comparison between Two Massively Parallel Algorithms for 250 Monte Carlo Computer Simulation: An Investigation in the Grand Canonical Ensemble G. S. Heffelfinger and M. E. Lewitt ===================================================================== JCC 17(3) CONTENTS An Improvement of Davidson's Iteration Method: Applications to 267 MRCI and MRCEPA Calculations H. J. J. van Dam, J. H. van Lenthe, G. L. G. Sleijpen, and H. A. van Der Vorst Comparative Study of Free Energies of Solvation of Phenylimidazole 273 Inhibitors of Cytochrome P450cam by Free Energy Simulation, AMSOL, and Poisson Boltzmann Methods Dan Harris and Gilda Loew Theoretical and Practical Aspects of the Convergence Properties 289 of the Dynamically Defined Reaction Path Method Gy. Dmtr, M. I. B n, and L. L. Stach" An Ab Initio Study of Heterodienophiles Addition to 298 2,3-Diaza-1,3-Butadiene: An Example of Endo-Lone-Pair Effect on the Reaction Energy Barrier Branko S. Jursic and Zoran Zdravkovski Simulation of the Infrared Spectra of Amorphous Silicon Alloys 306 B. W. Clare, P. J. Jennings, J. C. L. Cornish, G. T. Hefter, and D. J. Santjojo Computational Developments in Generalized Valence Bond Calculations 313 Youliang Wang and Raymond A. Poirier A New Parallel Method for Molecular Dynamics Simulation of 326 Macromolecular Systems Steve Plimpton and Bruce Hendrickson The 1 : 1 Glycine Zwitterion-Water Complex: An Ab Initio Electronic 338 Structure Study Yanbo Ding and Karsten Krogh-Jespersen Electrostatic Binding Energy Calculation Using the Finite Difference 350 Solution to the Linearized Poisson-Boltzmann Equation: Assessment of Its Accuracy Jian Shen and John Wendoloski Registration, Orientation, and Similarity of Molecular Electrostatic 358 Potentials through Multipole Matching Daniel E. Platt and B. David Silverman Charges Fit to Electrostatic Potentials. II. Can Atomic Charges be 367 Unambiguously Fit to Electrostatic Potentials? Michelle Miller Francl, Christina Carey, Lisa Emily Chirlian, and David M. Gange ===================================================================== JCC 17(4) SPECIAL ISSUE ON MOLECULAR MECHANICS PART I CONTENTS Editorial 385 N. L. Allinger and P. von R. Schleyer Optimization of the Lennard-Jones Parameters for a Combined Ab Initio 386 Quantum Mechanical and Molecular Mechanical Potential Using the 3-21G Basis Set M. Freindorf and J. Gao Molecular Mechanics Calculations of Conjugated Amides and an 396 Ab Initio Investigation of Acrylamide and Its b-Amino Derivative: Conformational Analysis and Rotational Barriers U. Berg and N. Bladh Determination of the Stereochemistry of Natural Products from Nuclear 409 Magnetic Resonance Data by Constrained Molecular Dynamics M. Falk, P. F. Spierenburg, and J. A. Walter Peptide Docking Using Dynamic Programming 418 K. Gulukota, S. Vajda, and C. Delisi A Comparison of Conformational Energies Calculated by Several 429 Molecular Mechanics Methods K. Gundertofte, T. Liljefors, P.-O. Norrby, and I. Pettersson Force Field Parameters for Carbohydrates 450 S. Reiling, M. Schlenkrich, and J. Brickmann Molecular Dynamics for Proteins: Performance Evaluation on Massively 469 Parallel Computers Based on Mesh Networks Using a Space Decomposition Approach P. Ballestrero, P. Baglietto, and C. Ruggiero New Implementation of and the Modeling by the Extended Simulated 476 Annealing Process to Structures of T4 Lysozyme Mutants at the 86th Residue S. Endo, J. Higo, K. Nagayama, and H. Wako