Computational Chemistry

DAVID YOUNG, PhD, is a scientist with Cytoclonal Pharmaceutics in Dallas, Texas. Prior to joining the team at Cytoclonal, Dr. Young worked as a super-computer analyst for Nichols Research Corporation and Computer Sciences Corporation, and as an affiliate professor of chemistry at Auburn University.

• PREFACE xviiACKNOWLEDGMENTS xxiSYMBOLS USED IN THIS BOOK xxiii1. Introduction 1Part I. BASIC TOPICS 52. Fundamental Principles 73. Ab initio Methods 194. Semiempirical Methods 325. Density Functional Theory 426. Molecular Mechanics 497. Molecular Dynamics and Monte Carlo Simulations 608. Predicting Molecular Geometry 679. Constructing a Z-Matrix 7310. Using Existing Basis Sets 7811. Molecular Vibrations 9212. Population Analysis 9913. Other Chemical Properties 10714. The Importance of Symmetry 12515. Efficient Use of Computer Resources 12816. How to Conduct a Computational Research Project 135Part II. ADVANCED TOPICS 14517. Finding Transition Structures 14718. Reaction Coordinates 15919. Reaction Rates 16420. Potential Energy Surfaces 17321. Conformation Searching 17922. Fixing Self-Consistent Field Convergence Problems 19323. QM/MM 19824. Solvation 20625. Electronic Excited States 21626. Size Consistency 22327. Spin Contamination 22728. Basis Set Customization 23129. Force Field Customization 23930. Structure-Property Relationships 24331. Computing NMR Chemical Shifts 25232. Nonlinear Optical Properties 25633. Relativistic Effects 26134. Band Structures 26635. Mesoscale Methods 27336. Synthesis Route Prediction 277Part III. APPLICATIONS 28137. The Computational Chemist's View of the Periodic Table 28338. Biomolecules 29639. Simulating Liquids 30240. Polymers 30741. Solids and Surfaces 318Appendix. Software Packages 322GLOSSARY 360Bibliography 370INDEX 371