Physical Chemistry for the Biological Sciences

Gordon G. Hammes, PhD, is the Distinguished Service Professor of Biochemistry Emeritus at Duke University. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences, and has received several national awards, including the American Chemical Society Award in Biological Chemistry and the American Society for Biochemistry and Molecular Biology William C. Rose Award. Dr. Hammes was Editor of the journal Biochemistry from 1992-2003.
 
Sharon Hammes-Schiffer, PhD, is the Swanlund Professor of Chemistry at the University of Illinois at Urbana-Champaign. She is a fellow of the American Physical Society, the American Chemical Society, the Biophysical Society, and the American Association for the Advancement of Science. She is a member of the American Academy of Arts and Sciences, the National Academy of Sciences, and the International Academy of Quantum Molecular Science. Dr. Hammes-Schiffer has served as the Deputy Editor of The Journal of Physical Chemistry B and is currently the Editor-in-Chief of Chemical Reviews.

This book provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required. This book can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences.

Preface to First Edition xv
 
Preface to Second Edition xvii
 
THERMODYNAMICS 1
 
1. Heat, Work, and Energy 3
 
1.1 Introduction 3
 
1.2 Temperature 4
 
1.3 Heat 5
 
1.4 Work 6
 
1.5 Definition of Energy 9
 
1.6 Enthalpy 11
 
1.7 Standard States 12
 
1.8 Calorimetry 13
 
1.9 Reaction Enthalpies 16
 
1.10 Temperature Dependence of the Reaction Enthalpy 18
 
References 19
 
Problems 20
 
2. Entropy and Gibbs Energy 23
 
2.1 Introduction 23
 
2.2 Statement of the Second Law 24
 
2.3 Calculation of the Entropy 26
 
2.4 Third Law of Thermodynamics 28
 
2.5 Molecular Interpretation of Entropy 29
 
2.6 Gibbs Energy 30
 
2.7 Chemical Equilibria 32
 
2.8 Pressure and Temperature Dependence of the Gibbs Energy 35
 
2.9 Phase Changes 36
 
2.10 Additions to the Gibbs Energy 39
 
Problems 40
 
3. Applications of Thermodynamics to Biological Systems 43
 
3.1 Biochemical Reactions 43
 
3.2 Metabolic Cycles 45
 
3.3 Direct Synthesis of ATP 49
 
3.4 Establishment of Membrane Ion Gradients by Chemical Reactions 51
 
3.5 Protein Structure 52
 
3.6 Protein Folding 60
 
3.7 Nucleic Acid Structures 63
 
3.8 DNA Melting 67
 
3.9 RNA 71
 
References 72
 
Problems 73
 
4. Thermodynamics Revisited 77
 
4.1 Introduction 77
 
4.2 Mathematical Tools 77
 
4.3 Maxwell Relations 78
 
4.4 Chemical Potential 80
 
4.5 Partial Molar Quantities 83
 
4.6 Osmotic Pressure 85
 
4.7 Chemical Equilibria 87
 
4.8 Ionic Solutions 89
 
References 93
 
Problems 93
 
CHEMICAL KINETICS 95
 
5. Principles of Chemical Kinetics 97
 
5.1 Introduction 97
 
5.2 Reaction Rates 99
 
5.3 Determination of Rate Laws 101
 
5.4 Radioactive Decay 104
 
5.5 Reaction Mechanisms 105
 
5.6 Temperature Dependence of Rate Constants 108
 
5.7 Relationship Between Thermodynamics and Kinetics 112
 
5.8 Reaction Rates Near Equilibrium 114
 
5.9 Single Molecule Kinetics 116
 
References 118
 
Problems 118
 
6. Applications of Kinetics to Biological Systems 121
 
6.1 Introduction 121
 
6.2 Enzyme Catalysis: The Michaelis-Menten Mechanism 121
 
6.3 alpha-Chymotrypsin 126
 
6.4 Protein Tyrosine Phosphatase 133
 
6.5 Ribozymes 137
 
6.6 DNA Melting and Renaturation 142
 
References 148
 
Problems 149
 
QUANTUM MECHANICS 153
 
7. Fundamentals of Quantum Mechanics 155
 
7.1 Introduction 155
 
7.2 Schrödinger Equation 158
 
7.3 Particle in a Box 159
 
7.4 Vibrational Motions 162
 
7.5 Tunneling 165
 
7.6 Rotational Motions 167
 
7.7 Basics of Spectroscopy 169
 
References 173
 
Problems 174
 
8. Electronic Structure of Atoms and Molecules 177
 
8.1 Introduction 177
 
8.2 Hydrogenic Atoms 177
 
8.3 Many-Electron Atoms 181
 
8.4 Born-Oppenheimer Approximation 184
 
8.5 Molecular Orbital Theory 186
 
8.6 Hartree-Fock Theory and Beyond 190
 
8.7 Density Functional Theory 193
 
8.8 Quantum Chemistry of Biological Systems 194
 
References 200
 
Problems 201
 
SPECTROSCOPY 203
 
9. X-ray Crystallography 205
 
9.1 Introduction 205
 
9.2 Scattering of X-Ray