Physical Chemistry for the Biological Sciences

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.

Auteur

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.

Texte du rabat
A new edition with complete, up-to-date and expanded material for a working knowledge of physical chemistry for the biological sciences The second edition of Physical Chemistry for the Biological Sciences builds on the success of the first edition with important updates and new material to provide a state-of-the-art introduction to physical chemistry for both professionals and students. The topics discussed include thermodynamics, kinetics, quantum mechanics, spectroscopy, statistical mechanics, and hydrodynamics. As in the first edition, most of the subjects can be understood without advanced mathematics. However, because modern day students often have a strong background in mathematics, more advanced treatments are also presented. Some of the additions are: Multivariable calculus, which students can have the option of utilizing if desired. Maxwell relationships, formulation of equilibria in terms of the chemical potential, and extensive discussion of activity coefficients. Extended treatment of quantum mechanics, including molecular vibrations and tunneling. Electronic structure of molecules utilizing molecular orbitals as well as Hartree-Fock and density functional theory. Statistical mechanics, including the Boltzmann distribution, partition functions, and statistical ensembles, with applications to biology. Computer simulations utilizing molecular dynamics and Monte Carlo methods, as well as hybrid quantum/classical approaches, and applications to enzyme reactions. Carefully designed illustrations (some in color) and problems and examples from the biological sciences reinforce the concepts presented. Suitable for both two semester and one semester undergraduate and graduate courses in physical chemistry, this monograph can be used as a textbook, reference volume and supplementary guide for teachers, students and science professionals in all fields of chemistry and biology.

Contenu

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 -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-Rays by a Crystal 206

9.3 Structure Determination 208

9.4 Neutron Diffraction 212

9.5 Nucleic Acid Structure 213

9.6 Protein Structure 216

9.7 Enzyme Catalysis 219

References 222

Problems 223

10. Electronic Spectra 225

10.1 Introduction 225

10.2 Absorption Spectra 226

10.3 Ultraviolet Spectra of Proteins 228

10.4 Nucleic Acid Spectra 230

10.5 Prosthetic Groups 231

10.6 Difference Spectroscopy 233

10.7 X-Ray Absorption Spectroscopy 236

10.8 Fluorescence and Phosphorescence 236

10.9 RecBCD: Helicase Activity Monitored by Fluorescence 240

10.10 Fluorescence Energy Transfer: A Molecular Ruler 241

10.11 Application of Energy Transfer to Biological Systems 243

10.12 Dihydrofolate Reductase 245

References 247

Problems 248

11. Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization 253

11.1 Introduction 253

11.2 Optical Rotary Dispersion 254

11.3 Circular Dichroism 256

11.4 Optical Rotary Dispersion and Circular Dichroism of Proteins 257

11.5 Optical Rotation and Circular Dichroism of Nucleic Acids 259

11.6 Small Molecule Binding to DNA 260

11.7 Protein Folding 263

11.8 Interaction of DNA with Zinc Finger Proteins 266

11.9 Fluorescence Polarization 267

11.10 Integration of HIV Genome Into Host Genome 269

11.11 -Ketoglutarate Dehydrogenase 270

References 272

Problems 273

12. Vibrations in Macromolecules 277

12.1 Introduction 277

12.2 Infrared Spectroscopy 278

12.3 Raman Sp…