Chemistry by Computer. An Overview of the Applications of Computers in Chemistry

Transcription

1 Chemistry by Computer An Overview of the Applications of Computers in Chemistry

2 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

3 Wilson, S. (Stephen), Chemistry by computer. Library of Congress Cataloging in Publication Data Includes bibliographies and index. 1. Chemistry-Data processing. I. Title. QD39.3.E46W '.8 ISBN-13: e-isbn-13: DOl: 10.t007/ First Printing-October 1986 Second Printing-November 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 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

4 To Kati and Jonathan

5 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

6 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

7 Contents PART I. BASICS 1. Introduction Chemistry by Computer 2.1. Computational Chemistry 2.2. Isolated Atoms and Molecules 2.3. Bulk Properties of Atoms and Molecules Bibliography Computers and Computation Computers, Computer Science, and the Computational Sciences 3.2. Hardware Software High-Level Languages Software Engineering Future Directions Bibliography PART II. METHODS 4. Quantum Chemistry 4.1. Quantum Chemistry ix

8 x Contents 4.2. The Schrodinger Equation The Electronic Schrodinger Equation Self-Consistent-Field Calculations 4.5. Electron Correlation Theoretical Model ChemIstry 4.7. The Nuclear Schrodinger Equation Bibliography Molecular Mechanics 5.1. Ball-and-Stick Models The Force Field Minimization of the Energy 5.3.l. Conjugate-Direction Methods Newton Methods 5.4. An Example: n-butane Molecular Mechanics Bibliography Chemical Reactions 6.l. Reactions Molecular Collisions 6.3. Chemical Kinetics 6.4. Organic Synthetic Routes Bibliography Simulation of Liquids and Solids 7.1. The Condensed Phases of Matter 7.2. Liquid Simulation The Monte Carlo Method 7.4. The Molecular-Dynamics Method 7.5. Simulation of Solids. Bibliography III III PART III. APPLICATIONS 8. Interstellar Molecules and Interstellar Chemistry 8.1. Background

9 Contents xi 8.2. Molecules in Space Computational Studies of Interstellar Radicals and Ions Protonated Nitrogen Molecule Cyanoethynyl Radical Butadiynyl Radical Metastable Organic Radicals Radicals and Ions Containing Second-Row Atoms Rare-Gas Ions Interstellar Chemistry Bibliography Computational Pharmacology Background Theoretical Pharmacology 9.3. Molecular Graphics Bibliography Molecular Biology Background Proteins Computational Studies of Proteins Bibliography New Horizons Preamble Molecular Electronics Molecular Rectifiers Molecular Computers Author Index. Subject Index