Chemistry by Computer An Overview of the Applications of Computers in Chemistry
Chemistry by Computer An Overview of the Applications of Computers in Chemistry Stephen Wilson Theoretical Chemistry Department University of Oxford Oxford, England PLENUM PRESS NEW YORK AND LONDON
Wilson, S. (Stephen), 1950- Chemistry by computer. Library of Congress Cataloging in Publication Data Includes bibliographies and index. 1. Chemistry-Data processing. I. Title. QD39.3.E46W55 1986 542'.8 ISBN-13: 978-1-4612-9262-3 e-isbn-13: 978-1-4613-2137-8 DOl: 10.t007/978-1-4613-2137-8 86-18746 First Printing-October 1986 Second Printing-November 1987 1986 Plenum Press, New York Softcover reprint of the hardcover 1st edition 1986 A Division of Plenum Publishing Corporation 233 Spring Street, New York, N.Y. 10013 All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher
To Kati and Jonathan
Preface Computers have been applied to problems in chemistry and the chemical sciences since the dawn of the computer age; however, it is only in the past ten or fifteen years that we have seen the emergence of computational chemistry as a field of research in its own right. Its practitioners, computational chemists, are neither chemists who dabble in computing nor programmers who have an interest in chemistry, but computational scientists whose aim is to solve a wide range of chemical problems using modern computing machines. This book gives a broad overview of the methods and techniques employed by the computational chemist and of the wide range of problems to which he is applying them. It is divided into three parts. The first part records the basics of chemistry and of computational science that are essential to an understanding of the methods of computational chemistry. These methods are described in the second part of the book. In the third part, a survey is given of some areas in which the techniques of computational chemistry are being applied. As a result of the limited space available in a single volume, the areas covered are necessarily selective. Nevertheless, a sufficiently wide range of applications are described to provide the reader with a balanced overview of the many problems being attacked by computational studies in chemistry. vii
viii Preface It is intended that this book should prove useful to a wide variety of scientists. Undergraduate chemists will use it as an introduction to computational chemistry. Experimental research chemists should use this book to gain an understanding of the ways in which the techniques of computational chemistry can aid their research programs. These techniques have potential applications in fields as diverse as radioastronomy and astrochemistry, solid-state and nuclear physics, organic synthetic chemistry, catalysis, molecular biology, pharmacology, and molecular electronics. Although the present volume does not provide a detailed survey of any of these fields, it does present a broad overview of many of them. A bibliography is given at the end of each chapter to enable the interested reader to investigate a particular method or application in more detail. Finstock, Oxford Stephen Wilson
Contents PART I. BASICS 1. Introduction... 2. Chemistry by Computer 2.1. Computational Chemistry 2.2. Isolated Atoms and Molecules 2.3. Bulk Properties of Atoms and Molecules Bibliography.......... 3. Computers and Computation... 3.1. Computers, Computer Science, and the Computational Sciences 3.2. Hardware....... 3.3. Software....... 3.3.1. High-Level Languages 3.3.2. Software Engineering. 3.4. Future Directions Bibliography...... 3 7 7 9 14 17 19 19 21 24 24 28 34 36 PART II. METHODS 4. Quantum Chemistry 4.1. Quantum Chemistry 41 41 ix
x Contents 4.2. The Schrodinger Equation.... 4.3. The Electronic Schrodinger Equation. 4.4. Self-Consistent-Field Calculations 4.5. Electron Correlation.... 4.6. Theoretical Model ChemIstry 4.7. The Nuclear Schrodinger Equation Bibliography........ 5. Molecular Mechanics 5.1. Ball-and-Stick Models. 5.2. The Force Field... 5.3. Minimization of the Energy 5.3.l. Conjugate-Direction Methods 5.3.2. Newton Methods 5.4. An Example: n-butane. 5.5. Molecular Mechanics Bibliography... 6. Chemical Reactions 6.l. Reactions.... 6.2. Molecular Collisions 6.3. Chemical Kinetics 6.4. Organic Synthetic Routes Bibliography.... 7. Simulation of Liquids and Solids 7.1. The Condensed Phases of Matter 7.2. Liquid Simulation..... 7.3. The Monte Carlo Method 7.4. The Molecular-Dynamics Method 7.5. Simulation of Solids. Bibliography.... 42 44 57 65 71 73 83 85 85 87 98 99 102 105 109 110 III III 112 121 125 133 135 135 135 138 153 160 163 PART III. APPLICATIONS 8. Interstellar Molecules and Interstellar Chemistry 8.1. Background 167 167
Contents xi 8.2. Molecules in Space.......... 168 8.3. Computational Studies of Interstellar Radicals and Ions........... 174 8.3.1. Protonated Nitrogen Molecule. 177 8.3.2. Cyanoethynyl Radical... 179 8.3.3. Butadiynyl Radical..... 180 8.3.4. Metastable Organic Radicals.. 182 8.3.5. Radicals and Ions Containing Second-Row Atoms... 183 8.3.6. Rare-Gas Ions 183 8.4. Interstellar Chemistry Bibliography... 185 188 9. Computational Pharmacology. 9.1. Background..... 9.2. Theoretical Pharmacology 9.3. Molecular Graphics Bibliography... 10. Molecular Biology 10.1. Background 10.2. Proteins.... 10.3. Computational Studies of Proteins Bibliography....... 11. New Horizons 11.1. Preamble 11.2. Molecular Electronics 11.3. Molecular Rectifiers. 11.4. Molecular Computers Author Index. Subject Index 189 189 191 194 199 201 201 202 207 213 215 215 217 218 223 225 227