Young D.C. 2001 Computational chemistry a practical guide for applying techniques to real-world problems

Computational Chemistry: A Practical Guide for Applying Techniques to Real-World Problems. David C. Young Copyright ( 2001 John Wiley & Sons, Inc.

ISBNs: 0-471-33368-9 (Hardback); 0-471-22065-5 (Electronic)

COMPUTATIONAL

CHEMISTRY

Designations used by companies to distinguish their products are often claimed as trademarks. In all instances where John Wiley & Sons, Inc., is aware of a claim, the product names appear in initial capital or all capital letters. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration.

Copyright ( 2001 by John Wiley & Sons, Inc. All rights reserved.

No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic or mechanical, including uploading, downloading, printing, decompiling, recording or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without the prior written permission of the Publisher. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-6011, fax (212) 850-6008, E-Mail: PERMREQ @ WILEY.COM.

This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold with the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional person should be sought.

ISBN 0-471-22065-5

This title is also available in print as ISBN 0-471-33368-9.

For more information about Wiley products, visit our web site at www.Wiley.com.

To Natalie, Gregory, Ariel, and little Isaac

viii CONTENTS

4.1HuÈckel 33

4.2Extended HuÈckel 33

4.3PPP 33

4.4CNDO 34

4.5MINDO 34

4.6MNDO 34

4.7INDO 35

4.8ZINDO 35

4.9SINDO1 35

4.10PRDDO 36

4.11AM1 36

4.12PM3 37

4.13PM3/TM 37

4.14Fenske±Hall Method 37

4.15TNDO 37

4.16SAM1 38

4.17Gaussian Theory 38

4.18Recommendations 39 Bibliography 39

5.1Basic Theory 42

5.2 Linear Scaling Techniques 43

5.3Practical Considerations 45

5.4Recommendations 46 Bibliography 46

6.1Basic Theory 49

6.2 Existing Force Fields 53

6.3Practical Considerations 56

6.4Recommendations 57 Bibliography 58

7.1Molecular Dynamics 60

7.2Monte Carlo Simulations 62

7.5Practical Considerations 64 Bibliography 65

CONTENTS ix

8.1 Specifying Molecular Geometry 67

8.2Building the Geometry 67

8.3 Coordinate Space for Optimization 68

8.4Optimization Algorithm 70

9.3Linear Molecules 74

9.4Ring Systems 75 Bibliography 77

10.1Contraction Schemes 78

10.2Notation 81

10.3 Treating Core Electrons 84

10.4Common Basis Sets 85

10.5 Studies Comparing Results 89

Bibliography 90

11.1 Harmonic Oscillator Approximation 92

11.2Anharmonic Frequencies 94

11.3Peak Intensities 95

11.4Zero-point Energies and Thermodynamic Corrections 96

11.5Recommendations 96 Bibliography 96

12.1 Mulliken Population Analysis 99

12.2 LoÈwdin Population Analysis 100

12.3 Natural Bond-Order Analysis 100

12.4Atoms in Molecules 101

12.5Electrostatic Charges 102

12.6 Charges from Structure Only 102

12.7Recommendations 103 Bibliography 105

xCONTENTS

13.1 Methods for Computing Properties 107

13.2Multipole Moments 110

13.3Fermi Contact Density 110

13.4Electronic Spatial Extent and Molecular Volume 111

13.5 Electron A½nity and Ionization Potential 111

13.6Hyper®ne Coupling 112

13.7Dielectric Constant 112

13.8Optical Activity 113

13.9Biological Activity 113

13.10 Boiling Point and Melting Point 114

13.11Surface Tension 114

13.12Vapor Pressure 115

13.13Solubility 115

13.14Di¨usivity 115

13.15Visualization 115

13.16Conclusions 121 Bibliography 121

14.1Wave Function Symmetry 127

14.2Transition Structures 127 Bibliography 127

15.1Time Complexity 128

15.2Labor Cost 132

15.3Parallel Computers 132 Bibliography 133

16.1What Do You Want to Know? How Accurately? Why? 135

16.2How Accurate Do You Predict the Answer Will Be? 135

16.3How Long Do You Predict the Research Will Take? 136

16.4What Approximations Are Being Made? Which Are Signi®cant? 136

Bibliography 142

17.1Introduction 147

17.2 Molecular Mechanics Prediction 148

17.3 Level of Theory 149

17.4Use of Symmetry 151

17.5Optimization Algorithms 151

17.8Relaxation Methods 155

17.9 Potential Surface Scans 155

17.10Solvent E¨ects 155

17.11Verifying That the Correct Geometry Was Obtained 155

17.12Checklist of Methods for Finding Transition Structures 156

Bibliography 157

18.1Minimum Energy Path 159

18.2 Level of Theory 160

18.3 Least Motion Path 161

18.4Relaxation Methods 161

18.5Reaction Dynamics 162

18.6 Which Algorithm to Use 162 Bibliography 162

19.1Arrhenius Equation 164

19.2Relative Rates 165

19.3 Hard-sphere Collision Theory 165

19.4 Transition State Theory 166

19.5 Variational Transition State Theory 166

19.6Trajectory Calculations 167

19.7Statistical Calculations 168

19.8Electronic-state Crossings 169

19.9Recommendations 169 Bibliography 170

23.3Energy Subtraction 200

23.4 Self Consistent Method 201

23.5 Truncation of the QM Region 202

23.6Region Partitioning 203

23.7Optimization 203

23.8 Incorporating QM Terms in Force Fields 203

23.9Recommendations 204 Bibliography 204

24.3Analytic Equations 207

24.4Group Additivity Methods 208