This page intentionally left blank Physical Chemistry for the Life Sciences Library of Congress Number: 2010940703 © 2006, 2011 by P.W. Atkins and J. de Paula All rights reserved. Printed in Italy by L.E.G.O. S.p.A First printing Published in the United States and Canada by W. H. Freeman and Company 41 Madison Avenue New York, NY 10010 www.whfreeman.com ISBN-13: 978-1-4292-3114-5 ISBN-10: 1-4292-3114-9 Published in the rest of the world by Oxford University Press Great Clarendon Street Oxford OX2 6DP United Kingdom www.oup.com ISBN: 978-0-19-956428-6 Physical Chemistry for the Life Sciences Second edition Peter Atkins Professor of Chemistry, Oxford University Julio de Paula Professor of Chemistry, Lewis & Clark College W. H. Freeman and Company New York This page intentionally left blank Contents in brief Prolog xxi Fundamentals 1 PART 1 Biochemical thermodynamics 21 1 The First Law 23 2 The Second Law 69 3 Phase equilibria 94 4 Chemical equilibrium 135 5 Thermodynamics of ion and electron transport 181 PART 2 The kinetics of life processes 217 6 The rates of reactions 219 7 Accounting for the rate laws 243 8 Complex biochemical processes 273 PART 3 Biomolecular structure 311 9 Microscopic systems and quantization 313 10 The chemical bond 364 11 Macromolecules and self-assembly 407 PART 4 Biochemical spectroscopy 461 12 Optical spectroscopy and photobiology 463 13 Magnetic resonance 514 Resource section 1 Atlas of structures 546 2 Units 558 3 Data 560 Answers to odd-numbered exercises 573 Index of Tables 577 Index 579 This page intentionally left blank Full contents 1.4 The measurement of heat 32 Prolog xxi (a) Heat capacity 33 The structure of physical chemistry xxi (b) The molecular interpretation of heat capacity 34 (a) The organization of science xxi Internal energy and enthalpy 34 (b) The organization of our presentation xxii 1.5 The internal energy 35 Applications of physical chemistry to biology and medicine xxii (a) Changes in internal energy 35 (a) Techniques for the study of biological systems xxii (b) Protein folding xxiii Example 1.1 Calculating the change in internal energy 36 (c) Rational drug design xxv (b) The internal energy as a state function 37 (d) Biological energy conversion xxv (c) The First Law of thermodynamics 38 1.6 The enthalpy 38 Fundamentals 1 (a) The definition of enthalpy 39 F.1 Atoms, ions, and molecules 1 (b) Changes in enthalpy 39 (a) Bonding and nonbonding interactions 1 (c) The temperature dependence of the enthalpy 41 (b) Structural and functional units 2 In the laboratory 1.1 Calorimetry 42 (c) Levels of structure 3 (a) Bomb calorimeters 42 F.2 Bulk matter 4 (a) States of matter 4 Example 1.2 Calibrating a calorimeter and measuring (b) Physical state 5 the energy content of a nutrient 43 (c) Equations of state 8 (b) Isobaric calorimeters 44 F.3 Energy 10 (c) Differential scanning calorimeters 44 (a) Varieties of energy 11 Physical and chemical change 46 (b) The Boltzmann distribution 13 1.7 Enthalpy changes accompanying physical processes 46 Checklist of key concepts 17 (a) Phase transitions 46 Checklist of key equations 17 (b) Enthalpies of vaporization, fusion, and sublimation 47 Discussion questions 18 1.8 Bond enthalpy 49 Exercises 18 Example 1.3 Using mean bond enthalpies 51 Projects 19 1.9 Thermochemical properties of fuels 52 PART 1 Biochemical thermodynamics 21 Case study 1.2 Biological fuels 55 1.10 The combination of reaction enthalpies 57 1 The First Law 23 Example 1.4 Using Hess’s law 58 The conservation of energy 23 1.11 Standard enthalpies of formation 58 1.1 Systems and surroundings 24 Example 1.5 Using standard enthalpies of formation 59 1.2 Work and heat 25 (a) Exothermic and endothermic processes 25 1.12 Enthalpies of formation and computational chemistry 61 (b) The molecular interpretation of work and heat 26 1.13 The variation of reaction enthalpy with temperature 62 (c) The molecular interpretation of temperature 26 Example 1.6 Using Kirchhoff’s law 63 Case study 1.1 Energy conversion in organisms 27 Checklist of key concepts 64 1.3 The measurement of work 29 Checklist of key equations 65 (a) Sign conventions 29 Discussion questions 65 (b) Expansion work 30 Exercises 65 (c) Maximum work 31 Projects 68 viii FULL CONTENTS (a) The chemical potential of a gas 112 2 The Second Law 69 (b) The chemical potential of a solvent 112 Entropy 70 (c) The chemical potential of a solute 114 2.1 The direction of spontaneous change 70 Example 3.2 Determining whether a natural water can 2.2 Entropy and the Second Law 71 support aquatic life 116 (a) The definition of entropy 71 (b) The entropy change accompanying heating 73 Case study 3.2 Gas solubility and breathing 117 (c) The entropy change accompanying a phase transition 75 (d) Real solutions: activities 118 (d) Entropy changes in the surroundings 77 Case study 3.3 The Donnan equilibrium 119 2.3 Absolute entropies and the Third Law of thermodynamics 77 Example 3.3 Analyzing a Donnan equilibrium 121 In the laboratory 2.1 The measurement of entropies 78 (e) The thermodynamics of dissolving 121 2.4 The molecular interpretation of the Second and Third Laws 80 Colligative properties 122 (a) The Boltzmann formula 80 3.9 The modification of boiling and freezing points 123 (b) The relation between thermodynamic and statistical entropy 81 3.10 Osmosis 125 (c) The residual entropy 82 In the laboratory 3.1 Osmometry 127 2.5 Entropy changes accompanying chemical reactions 82 Example 3.4 Determining the molar mass of an enzyme from (a) Standard reaction entropies 82 measurements of the osmotic pressure 127 (b) The spontaneity of chemical reactions 83 Checklist of key concepts 128 The Gibbs energy 84 Checklist of key equations 129 2.6 Focusing on the system 84 Further information 3.1 The phase rule 129 (a) The definition of the Gibbs energy 84 Further information 3.2 Measures of concentration 130 (b) Spontaneity and the Gibbs energy 85 Example 3.5 Relating mole fraction and molality 131 Case study 2.1 Life and the Second Law 85 Discussion questions 132 2.7 The hydrophobic interaction 86 Exercises 132 2.8 Work and the Gibbs energy change 88 Projects 134 Example 2.1 Estimating a change in Gibbs energy for 4 Chemical equilibrium 135 a metabolic process 89 Thermodynamic background 135 Case study 2.2 The action of adenosine triphosphate 90 4.1 The reaction Gibbs energy 135 Checklist of key concepts 90 4.2 The variation of ΔG with composition 137 r Checklist of key equations 91 (a) The reaction quotient 137 Discussion questions 91 Exercises 91 Example 4.1 Formulating a reaction quotient 138 Projects 92 (b) Biological standard states 139 Example 4.2 Converting between thermodynamic and 3 Phase equilibria 94 biological standard states 140 The thermodynamics of transition 94 4.3 Reactions at equilibrium 140 3.1 The condition of stability 94 (a) The significance of the equilibrium constant 142 3.2 The variation of Gibbs energy with pressure 95 (b) The composition at equilibrium 143 3.3 The variation of Gibbs energy with temperature 98 Example 4.3 Calculating an equilibrium composition 143 3.4 Phase diagrams 99 (c) The molecular origin of chemical equilibrium 144 (a) Phase boundaries 100 (b) The location of phase boundaries 101 Case study 4.1 Binding of oxygen to myoglobin and (c) Characteristic points 103 hemoglobin 144 (d) The phase diagram of water 105 4.4 The standard reaction Gibbs energy 146 Phase transitions in biopolymers and aggregates 106 Example 4.4 Calculating the standard reaction Gibbs energy 3.5 The stability of nucleic acids and proteins 106 of an enzyme-catalyzed reaction 146 Example 3.1 Predicting the melting temperature of DNA 107 (a) Standard Gibbs energies of formation 147 (b) Stability and instability 149 3.6 Phase transitions of biological membranes 108 The response of equilibria to the conditions 149 Case study 3.1 The use of phase diagrams in the study of proteins 109 4.5 The presence of a catalyst 150 4.6 The effect of temperature 150 The thermodynamic description of mixtures 110 Coupled reactions in bioenergetics 151 3.7 The chemical potential 110 3.8 Ideal and ideal–dilute solutions 111 Case study 4.2 ATP and the biosynthesis of proteins 152