Table of Contents

Preface xix

Acknowledgments xxi

PART 1 BASIC PRINCIPLES 1

1. Thermodynamics 3

2. Four Basic Quantum Mechanical Models of Nuclear and Electronic Motion: A Synopsis 35

3. Molecular Structure and Interactions 51

4. Water and the Hydrophobic Effect 77

PART 2 STATISTICAL MECHANICS: THE MOLECULAR BASIS OF THERMODYNAMICS 91

5. The Molecular Partition Function 93

6. System Ensembles and Partition Functions 111

7. Sampling Molecular Systems with Simulations 137

PART 3 BINDING TO MACROMOLECULES 161

8. Binding Equilibria 163

9. Thermodynamics of Molecular Interactions 185

10. Elements of Statistical Mechanics of Liquids and Solutions 197

11. Analysis of Binding Equilibria in Terms of Partition Functions 213

12. Coupled Equilibria 223

13. Allosteric Function 239

14. Charged Groups: Binding of Hydrogen Ions, Solvation, and Charge–Charge Interactions 255

PART 4 CONFORMATIONAL STABILITY AND CONFORMATION CHANGE 277

15. Some Elements of Polymer Physics 279

16. Helix-Coil Equilibria 291

17. Protein Unfolding Equilibria 311

18. Elasticity of Biological Materials 347

PART 5 KINETICS AND IRREVERSIBLE PROCESSES 357

19. Kinetics 359

20. Kinetics of Protein Folding 389

21. Irreversible and Stochastic Processes 415

APPENDICES 437

Index 491

About the Author

JAN HERMANS, PhD, is Emeritus Professor in the Departmentof Biochemistry and Biophysics at the University of North Carolinaat Chapel Hill. He is the author of over 130 papers in the field ofprotein and macromolecular biophysics. BARRY LENTZ, PhD, is Professor in the Department ofBiochemistry and Biophysics at the University of North Carolina atChapel Hill and Director of the UNC Molecular & CellularBiophysics Program. He has authored roughly 130 original researchpublications in the field of biophysics, focusing on biomembranemicrostructure and cell function.