Program

GORDON RESEARCH CONFERENCE

on

Computational Chemistry

Donald B. Boyd and Peter Kollman, Co-chairmen
Boyd Hall, Plymouth State College, Plymouth, New Hampshire
July 4-8, 1988

July 4, 1988, Monday Morning, 9:00 a.m. - 12:20 p.m.

Donald B. Boyd (Eli Lilly and Company)
Peter Kollman (University of California, San Francisco)
Introductory Remarks.

John J. Wendeloski (DuPont)
Session Chairman and Discussion Leader
Macromolecular Simulations.

Axel T. Brunger, Yale University
Computational Tools for Structural Biology.

Terry R. Stouch (Naval Research Laboratory)
Molecular Dynamics Simulations of Simple Lipid Systems.

Wilfred F. van Gunsteren (University of Groningen)
On Comparing Computer Simulations of Macromolecules withExperimental Data.

Monday Evening Poster Session, 7:30 p.m. - 9:30 p.m.

Jeffry D. Madura (University of Houston), B. Montgomery Pettitt, and J. Andrew McCammon
Determination of Transition State Geometries and Relative Free Energies of Activation in Condensed Phase.

James R. Damewood, Jr. (University of Delaware) and Wolfgang C. F. Muehlbauer
Calculation of Intermolecular Potential Energy Surfaces Using Modified Molecular Mechanics Techniques.

Lee F. Kuyper (Burroughs Wellcome Company), Kenneth M. Merz, Jr. (University of California, San Francisco), and Peter A. Kollman
Relative Solvation Free Energies of Benzene, Anisole, and 1,2,3-Trimethoxybenzene: Theoretical and Experimental Analysis.

Salvatore Profeta, Jr. (Glaxo Inc., Research Triangle Park) and V. N. Balaji (Allergan)
Conformational Energy Mapping Using MM2: Utility and Validity of Variable Energy Convergence Criteria With Applications to 2-D Energy Maps for Peptides and Drug Molecules.

Jerry A. Boatz (North Dakota State University) and Mark S. Gordon
Decomposition of Normal Coordinate Vibrational Frequencies.

Mark S. Gordon (North Dakota State University), Kiet Nguyen, Larry P. Davis (Air Force Office of Scientific Research), Larry W. Burggraf, and Krishnan Raghavachari (AT&T Bell Laboratories)
Theoretical Analysis of the Reaction Si+ + SiH3CH3.

Kim K. Baldridge (North Dakota State University) and Mark S. Gordon
Illustration of Electronic Structure-Dynamics Interface.

Krzysztof Kuczera (Harvard University), John Kuriyan, and Martin Karplus
Molecular Dynamics of Myoglobin.

J. Phillip Bowen (University of North Carolina at Chapel Hill), Vikram Reddy (Center for Disease Control), Donald G. Patterson, Jr., and Norman L. Allinger (University of Georgia)
Molecular Mechanics Treatment of Halogenated Dibenzo-p-dioxins and Dibenzofurans: MM2 Parameters for Aromatic Halides, Divinyl Ethers, and Related Compounds.

Kerwin D. Dobbs (University of Texas at Austin), James E. Boggs, and Alan H. Cowley
New, Unsaturated Three- and Four-Membered Rings: Formal Addition of CH2, SiH2, GeH2, or SnH2 to Phoshaalkyne Triple Bonds.

Donald B. Boyd (Eli Lilly and Company), David W. Smith, James J. P. Stewart (United States Air Force Academy), and Erich Wimmer (Cray Research)
Importance of Criteria for Self-Consistent Field Convergence and Geometry Optimization in AM1, MNDO, and MINDO/3 Molecular Orbital Calculations.

William J. Welsh (University of Missouri, St. Louis), Eric Towler, and Mary Dudley
Computational Chemistry Studies of Antifolate Drugs for Treatment of Pneumocystis Carinii Pneumonia (PCP) in AIDS Patients: Trimetrexate and Analogues.

John T. Blair (Rutgers University), Karsten Krogh-Jespersen, and Ronald M. Levy
Solute-Solvent Interactions in Ground and Excited Electronic States.

George Chang (Columbia University), Wayne C. Guida (Ciba-Geigy), and W. C. Still (Columbia University)
Examination of Monte Carlo Approaches for Analysis of Conformational Space.

Donald Bashford (Harvard University), C. Chothia (MRC Laboratory of Molecular Biology, Cambridge), and A. M. Lesk
The Use of Sequence Templates to Investigate the Determinants of Protein Folds.

Kyoko Watanabe (University of Pennsylvania) and Michael L. Klein
Molecular Dynamics Study of a Sodium Octanoate Micelle in Aqueous Solution.

Robert E. Bruccoleri (Massachusetts General Hospital), Jiri Novotny, and Edgar Haber
Prediction of Polypeptide Segments Using Conformational Search.

Michael McKee (Auburn University)
Ab Initio Calculations on the Boron Hydrides through B9H15.

Michelle M. Francl (Bryn Mawr College) and Yuh-Min Chook
Cis-Trans Isomerization of Alkenyl Aluminum Complexes.

Janet Cicariello (Rutgers University) and Wilma K. Olson
Theoretical Analysis of the Long-Range Electrostatic Potential of Supercoiled DNA.

Mark A. Murcko (Merck Sharp and Dohme, West Point)
Using Ab Initio Calculations to Develop Molecular Mechanics Parameters for Use In Biological Simulations.

Mark Froimowitz (McLean Hospital) and Ahammadunny P. A.
Conformational Free Energies of Cyclic Enkephalin Analogs.

Donna A. Bassolino (Rutgers University), Douglas B. Kitchen, Dorothea Kominos, Arthur Pardi, and Ronald M. Levy
New Methods for the Refinement of Protein Structures Generated from Solution NMR Data: Application to Rabbit Neutrophil Polypeptide (NP-5).

Byungkook Lee (National Institutes of Health)
Thermodynamics of Solvent Reorganization Upon Dissolution of Hydrocarbon Solutes in Aqueous and Hydrocarbon Solvents.

Daniel A. Kleier (DuPont)
The Role of Electronic Structure Calculations in Optimizing the Activity of a New Class of Photosystem I Herbicides.

Peter D. J. Grootenhuis (Organon) and Peter A. Kollman (University of California, San Francisco)
Free Energy Calculations on Molecular Host-Guest Complexes.

Marcus E. Brewster (Pharmatec), James J. Kaminski (University of Florida, College of Pharmacy), and Nicholas Bodor
Hydride Transfer Between 1-Methyl-1,4-dihydronicotinamide and the 1-Methylnicotinamide Cation, A Theoretical Study.

T. J. O'Donnell (National Center for Supercomputing Applications) and John S. Garavelli (University of Illinois at Chicago)
A Proposal for a Standard Format for Molecular Description Files.

James J. P. Stewart (United States Air Force Academy)
Re-Optimization of Parameters for MNDO.

John McKelvey (Eastman Kodak, Rochester)
Quick-Pi: A Generalized Omega Method.

July 5, 1988, Tuesday Morning, 9:00 a.m. - 12:05 p.m.

Norman L. Allinger (University of Georgia)
Session Chairman and Discussion Leader
Molecular Mechanics.

Tommy Liljefors (University of Lund)
Molecular Mechanics in Structure-Activity Studies.

W. Clark Still (Columbia University)
Modeling of Molecular Complexes.

Thomas A. Halgren (Merck Sharp and Dohme, Rahway)
On the Representation of Angle Bending Potentials in Empirical Force Fields.

Tuesday Evening, 7:30 p.m. - 9:20 p.m.

Yoshikazu Oka (Takeda Chemical Industries)
Session Chairman and Discussion Leader
Molecular Modeling in the Chemical and Pharmaceutical Industries of Japan.

Klaus Mueller (Hoffmann-LaRoche, Basel)
Combined Use of Computer Modeling and Structural Databases in Chemical Research.

Robert S. Pearlman (University of Texas, College of Pharmacy)
Rapid Generation of High Quality Approximate 3D Molecular Structures.

July 6, 1988, Wednesday Morning, 9:00 a.m. - 12:05 p.m.

William L. Jorgensen (Purdue University)
Session Chairman and Discussion Leader
Macromolecular Simulations.

Nobuhiro Go (Kyoto University)
Simulation of Conformational Dynamics of Proteins: Harmonic and Anharmonic Aspects.

Shoshana J. Wodak (Universite Libre de Bruxelles)
Contributions from Electronic Polarizability to Electrostatic Interactions in Proteins.

Stephen H. Bryant (Brookhaven National Laboratory)
Energy Functions from the Database of Known Protein Structures?

Wednesday Evening Poster Session, 7:30 p.m. - 9:30 p.m.

Volker Buss (Universitat Duisburg) and Peter Faupel
Evidence for, and Proposed Structure of, a New Folded Conformation of Methotrexate.

Keerthi Jayasuriya (Picatinny Arsenal) and Sury Iyer
A Computational Analysis of Ortho-lithiation Reaction Mechanism.

Gerhard Barnickel (E. Merck, Darmstadt)
Conversion Tools for Connection between Different Force-Field Programs Using CPECM.

Francesc Manaut (Institut Municipal d'Investigacio Medica, Barcelona), J. Jose, and F. Sanz
Automatic Search of Maximum Similarity between Molecular Electrostatic Potential Distributions.

Nick C. Perry (Chemical Design Ltd., Oxford)
A Multivariate QSAR Study on Histamine H2 Antagonist Activity Using Structural Parameters Determined by Molecular Modelling.

Scott G. Wierschke (Wright-Patterson Air Force Base)
A Computational Study of the Tensile and Compressive Properties of Ordered Polymers via the Austin Model 1 (AM1) Semiempirical Molecular Orbital Method.

Jorge A. Medrano (Buenos Aires University), Roberto C. Bochicchio, and Hector F. Reale
On the Extension of the Quantum Theory of Valence and Bonding to Periodic Systems.

Ingrid Pettersson (Royal Danish School of Pharmacy), Tommy Liljefors (University of Lund), and Klaus Bogeso (Lundbeck A/S, Denmark)
Conformational Analysis of Some D-1 Dopamine Receptor Agonists and Antagonists.

Flemming Steen Jorgensen (Royal Danish School of Pharmacy)
Muscarinic Agonists - Towards a Common Pharmacophore Model for Enantiomers with Very Different Biological Potency.

Carol A. Venanzi (New Jersey Institute of Technology) and Krishnan Namboodiri (Naval Research Laboratory)
Structure-Function Relationships in Artificial Enzymes.

Thomas J. Venanzi (College of New Rochelle) and Carol A. Venanzi (New Jersey Institute of Technology)
Electrostatic Potential Patterns of Amiloride Analogs.

M. Katharine Holloway (Merck Sharp and Dohme, West Point), Kenneth M. Merz (University of California, San Francisco), and Charles H. Reynolds (Rohm and Haas)
A Theoretical Study of the Azophenine Potential Surface.

Sandor Vajda (Mount Sinai School of Medicine), Istvan P. Sugar, and C. DeLisi
Combinatorial Optimization Methods for Predicting the Backbone Structure in Polypeptides.

Robin J. Breckenridge (Sandoz, Basel) and Hans-Peter Weber
Tertiary Conformation of Marine Snail alpha-Conotoxin: Strategy for Conformational Searching Using Molecular Dynamics.

Stephen R. Wilson (New York University), Jules W. Moskowitz, Kevin E. Schmidt, and Weili Cui
Applications of Simulated Annealing to the Conformational Analysis of Flexible Molecules.

Renee L. DesJarlais (University of California, San Francisco), Brian Shoichet, Dale Bodian, George L. Seibel, and Irwin D. Kuntz, Jr.
A Second Generation Computer-Assisted Inhibitor Design Method.

Martin Head-Gordon (Carnegie-Mellon University) and John A. Pople
A New Method For Two Electron Integral Evaluation.

Kevin E. Gilbert (Indiana University, Bloomington), J. J. Gajewski, and T. W. Kreek
Molecular Mechanics and Transition Metal Complexes.

Alan H. Katz (Wyeth-Ayerst)
An On-Line System to Guide the Chemist in Using Computational Chemistry Software.

DeLos F. DeTar (Florida State University)
Toward Standards for Force Field Representation.

Paul Weiner (Alliant), Roberto Gomberts, and Nick Camp
Parallel Processing in Computational Chemistry.

Regine Snay Bohacek (Ciba-Geigy) and Robert Jernigan (National Institutes of Health)
Configurational Statistics of Methyl Vinyl Ether-Maleic Anhydride Copolymer.

Frank H. Clarke (Ciba-Geigy)
Partition Coefficients of Ions: Determination of Distribution Profiles.

M. Rami Reddy (University of North Carolina at Chapel Hill) and Max Berkowitz
Hydration Forces between Parallel DNA Double Helices: Computer Simulations.

T. A. Halgren (Merck Sharp and Dohme, Rahway) and B. L. Bush
The Use of Enzyme Site Maps in Designing Enzyme Inhibitors.

Richard D. Cramer III (Tripos Associates), David E. Patterson, and Jeffrey D. Bunce
Comparative Molecular Field Analysis (CoMFA).

July 7, 1988, Thursday Morning, 9:00 a.m. - 12:05 p.m.

Werner Braun (Eidgenossische Technische Hochschule, Zurich)
Session Chairman and Discussion Leader
Distance Geometry.

Irwin D. Kuntz, Jr. (University of California, San Francisco)
Use of Distance Geometry for Structural Analysis.

Jeffrey M. Blaney (DuPont)
Distance Geometry Approach to Ligand-Macromolecule Docking.

J. Scott Dixon (Smith Kline and French)
Ligand Design Methodology.

Thursday Dinner: New England Buffet
Thursday Evening, 7:30 p.m. - 9:20 p.m.

Kendall N. Houk (National Science Foundation)
Session Chairman and Discussion Leader
Transition Structures of Pericyclic Reactions.

Michael J. S. Dewar (University of Texas)
Use of Quantum Mechanical Models for Studies of Reaction Mechanisms.

John A. Pople (Carnegie-Mellon University)
General Theory of Molecular Energies.

July 8, 1988, Friday Morning, 8:50 a.m. - 11:45 a.m.

Stelian Grigoras (Dow Corning)
Session Chairman and Discussion Leader
Polymer Conformation in Liquid and Solid State.

Michael C. Zerner (University of Florida)
Quantum Chemical Studies on the Structure and Spectroscopy of Large Transition Metal Systems.

Joseph W. Lauher (State University of New York, Stony Brook)
Molecular Modeling in Organometallic Chemistry.

Jeremy K. Burdett (University of Chicago)
Theoretical Studies of Solids.


The program listed here is a facsimile of the original one prepared for the conference. The program does not have last minute additions, withdrawals, or substitutions. For the poster presentations, affiliations and first names are listed for the presenter(s); such information for coauthors are listed if it was supplied with the original poster abstract.

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