Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems

PREFACE xvii

ACKNOWLEDGMENTS xxi

SYMBOLS USED IN THIS BOOK xxiii

1. Introduction 1

Part I. BASIC TOPICS 5

2. Fundamental Principles 7

3. Ab initio Methods 19

4. Semiempirical Methods 32

5. Density Functional Theory 42

6. Molecular Mechanics 49

7. Molecular Dynamics and Monte Carlo Simulations 60

8. Predicting Molecular Geometry 67

9. Constructing a Z-Matrix 73

10. Using Existing Basis Sets 78

11. Molecular Vibrations 92

12. Population Analysis 99

13. Other Chemical Properties 107

14. The Importance of Symmetry 125

15. Efficient Use of Computer Resources 128

16. How to Conduct a Computational Research Project 135

Part II. ADVANCED TOPICS 145

17. Finding Transition Structures 147

18. Reaction Coordinates 159

19. Reaction Rates 164

20. Potential Energy Surfaces 173

21. Conformation Searching 179

22. Fixing Self-Consistent Field Convergence Problems 193

23. QM/MM 198

24. Solvation 206

25. Electronic Excited States 216

26. Size Consistency 223

27. Spin Contamination 227

28. Basis Set Customization 231

29. Force Field Customization 239

30. Structure-Property Relationships 243

31. Computing NMR Chemical Shifts 252

32. Nonlinear Optical Properties 256

33. Relativistic Effects 261

34. Band Structures 266

35. Mesoscale Methods 273

36. Synthesis Route Prediction 277

Part III. APPLICATIONS 281

37. The Computational Chemist's View of the Periodic Table 283

38. Biomolecules 296

39. Simulating Liquids 302

40. Polymers 307

41. Solids and Surfaces 318

Appendix. Software Packages 322

GLOSSARY 360

Bibliography 370

INDEX 371