Modern thermodynamics for chemists and biochemists

Cover......Page 1
Foreword......Page 6
Preface......Page 10
Contents......Page 12
Index of symbols......Page 22
Index of units-of-measure......Page 28
List of Tables......Page 29
PART 1  Fundamentals......Page 32
  1.1 Some very familiar concepts …......Page 34
  1.2 The macroscopic viewpoint......Page 35
  1.4 State functions......Page 36
  1.5 Extensive and intensive state functions......Page 37
  1.6 The mole number n......Page 38
  1.8 Equilibrium......Page 39
  1.9 Changes in state......Page 41
  1.11 Pressure......Page 44
  1.12 The ideal gas......Page 47
  1.13 Pressure – a molecular interpretation......Page 48
  EXERCISES......Page 49
  2.1 Work – an initial definition......Page 51
  2.2 The work done by an expanding gas......Page 52
  2.3 Path functions......Page 54
  2.4 An important sign convention......Page 57
  2.5 Useful work …......Page 58
  2.7 Quasistatic paths......Page 59
  2.9 P,V diagrams......Page 62
  2.10 Changes at constant pressure......Page 65
  2.11 Thermodynamic cycles......Page 66
  EXERCISES......Page 71
  3.1 Temperature......Page 74
  3.2 The ideal gas law......Page 77
  3.4 Dalton's law of partial pressures......Page 79
  3.6 Heat......Page 81
  3.7 Some more definitions......Page 87
  3.8 How to get work from heat......Page 89
  3.9 Temperature – a deeper look......Page 98
  EXERCISES......Page 105
  4.1 What this chapter is about......Page 107
  4.2 Functions of more than one variable......Page 108
  4.3 Partial derivatives......Page 109
  4.4 Systems of constant mass......Page 111
  4.5 Partial derivatives and state functions......Page 113
  4.6 A look ahead …......Page 115
  EXERCISES......Page 119
PART 2  The Three Laws......Page 122
  Summary......Page 124
  5.1 The First Law......Page 125
  5.2 A molecular interpretation of internal energy......Page 126
  5.4 Internal energy and temperature......Page 127
  5.5 The First Law, state functions, and path functions......Page 130
  5.6 The First Law and cycles......Page 132
  5.7 The mathematics of U......Page 133
  5.8 The First Law in open, closed and isolated systems......Page 135
  5.9 The First Law in an isolated system......Page 136
  5.11 The First Law in a closed system – the isochoric change, dV =0......Page 137
  5.12 The heat capacity at constant volume, CV......Page 138
  5.14 The First Law in a closed system – the isobaric change, dP= 0......Page 145
  5.15 Reversible and irreversible paths......Page 148
  5.16 Mixing......Page 157
  5.17 Friction......Page 159
  5.18 Friction and irreversible paths......Page 165
  5.19 Real paths......Page 171
  EXERCISES......Page 175
  Summary......Page 177
  6.1 Man's most important technology......Page 178
  6.2 Enthalpy......Page 179
  6.3 The mathematics of H......Page 182
  6.4 Endothermic and exothermic reactions......Page 184
  6.5 Enthalpy, directionality and spontaneity......Page 187
  6.6 The difference ΔH - ΔU......Page 189
  6.7 Phase changes......Page 192
  6.8 Measuring enthalpy changes – calorimetry......Page 194
  6.9 Calculating enthalpy changes – Hess's law......Page 196
  6.10 Chemical standards......Page 199
  6.11 Standard enthalpies of formation......Page 209
  6.12 Ionic enthalpies......Page 215
  6.13 Bond energies......Page 216
  6.14 The variation of ΔH with temperature......Page 221
  6.15 The variation of ΔrH⊖  with temperature......Page 229
  6.16 Flames and explosions......Page 231
  EXERCISES......Page 237
  7.1 What this chapter is about......Page 239
  7.2 Ideal gases......Page 240
  7.4 CV and CP for ideal gases......Page 241
  7.6 The isochoric path, dV=0......Page 249
  7.7 The isobaric path, dP = 0......Page 250
  7.8 The isothermal path, dT = 0......Page 251
  7.9 The adiabatic path, đq = 0......Page 252
  7.10 The key ideal gas equations......Page 260
  7.11 Case Study: The Carnot cycle......Page 261
  7.12 Case Study: The thermodynamic pendulum......Page 267
  EXERCISES......Page 285
  8.1 A familiar picture......Page 289
  8.2 Spontaneity, unidirectionality and irreversibility......Page 291
  8.3 Some more examples of spontaneous, unidirectional, and irreversible changes......Page 292
  8.4 Spontaneity and causality......Page 294
  EXERCISE......Page 297
  Summary......Page 298
  9.1 The Second Law......Page 299
  9.2 Entropy – a new state function......Page 300
  9.3 The Clausius inequality......Page 303
  9.4 Real changes......Page 304
  9.5 Two examples......Page 306
  9.6 The First and Second Laws combined......Page 311
  9.7 The mathematics of entropy......Page 313
  9.8 Entropy changes for an ideal gas......Page 316
  9.9 Entropy changes at constant pressure......Page 321
  9.10 Phase changes......Page 322
  9.11 The Third Law of Thermodynamics......Page 327
  9.12 T,S diagrams......Page 328
  EXERCISES......Page 330
  Summary......Page 334
  10.1 The Clausius statement of the Second Law......Page 335
  10.2 The Kelvin–Planck statement of the Second Law......Page 340
  10.3 Heat engines and heat pumps......Page 344
  10.4 Irreversibility......Page 346
  10.5 A graphical interpretation......Page 348
  10.6 The Carathéodory statement......Page 352
  10.7 Carnot engines and Carnot pumps......Page 354
  10.8 Real engines......Page 359
  EXERCISE......Page 362
  11.1 What this chapter is about......Page 363
  11.3 Order and disorder......Page 364
  11.4 Macrostates and microstates......Page 365
  11.6 Measuring disorder......Page 368
  11.7 What happens when a gas expands into a vacuum......Page 371
  11.8 The Boltzmann equation......Page 372
  11.9 Maxwell's demon......Page 375
  11.11 Thermoeconomics......Page 378
  11.12 Organodynamics......Page 379
  EXERCISES......Page 381
  12.1 The Third Law......Page 382
  12.2 Absolute entropies......Page 383
  12.3 Approaching absolute zero......Page 388
  EXERCISES......Page 393
PART 3  Free energy, spontaneity, and equilibrium......Page 394
  Summary......Page 396
  13.1 Changes in closed systems......Page 398
  13.2 Spontaneous changes in closed systems......Page 400
  13.3 Gibbs free energy......Page 405
  13.4 The significance of the non-conservative function......Page 406
  13.5 Enthalpy- and entropy-driven reactions......Page 408
  13.6 The mathematics of G......Page 409
  13.7 Helmholtz free energy......Page 416
  13.9 Maximum available work......Page 417
  13.10 How to make non-spontaneous changes happen......Page 421
  13.11 Coupled systems …......Page 422
  13.12 … an explanation of frictional heat, and tidying a room …......Page 424
  13.14 Climate change and global warming – the `big picture'......Page 426
  13.15 Standard Gibbs free energies......Page 428
  13.16 Gibbs free energies at non-standard pressures......Page 430
  13.17 The Gibbs free energy of mixtures......Page 432
  13.18 The `Fourth Law' of Thermodynamics......Page 439
  EXERCISES......Page 442
  Summary......Page 444
  14.1 Chemical reactions......Page 446
  14.2 How  Gsys(τ) varies over time......Page 448
  14.3 Chemical equilibrium......Page 454
  14.4 The pressure thermodynamic equilibrium constant Kp.........Page 459
  14.5 ... and the meaning of ΔrGp⊖......Page 461
  14.6 Non-equilibrium systems......Page 463
  14.7 Another equilibrium constant, Kx .........Page 467
  14.8 ... and a third equilibrium constant, Kc......Page 468
  14.9 Two worked examples – methane and ammonia......Page 470
  14.10 How the equilibrium constant varies with temperature......Page 475
  14.11 Le Chatelier's principle......Page 479
  14.12 Thermodynamics meets kinetics......Page 480
  14.13 The Arrhenius equation......Page 486
  14.14 The overall effect of temperature on chemical reactions......Page 490
  14.15 A final thought......Page 491
  EXERCISES......Page 492
PART 4  Chemical applications......Page 496
  15.1 Vapour pressure......Page 498
  15.2 Vapour pressure and external pressure......Page 501
  15.3 The Gibbs free energy of phase changes......Page 502
  15.4 Melting and boiling......Page 503
  15.5 Changing the external pressure Pex......Page 509
  15.6 The Clapeyron and Clausius–Clapeyron equations......Page 512
  15.7 Phase changes, ideal gases and real gases......Page 516
  15.8 The mathematics of Gs,  Gl and  Gg......Page 528
  EXERCISES......Page 531
  Summary......Page 533
  16.1 The ideal solution......Page 534
  16.2 The Gibbs free energy of an ideal solution......Page 542
  16.3 Equilibria of reactions in solution......Page 548
  16.4 Dilute solutions, molalities and molar concentrations......Page 551
  16.5 Multi-state equilibria and chemical activity......Page 553
  16.6 Coupled reactions in solution......Page 557
  EXERCISES......Page 561
  Summary......Page 565
  17.1 Dissociation......Page 566
  17.2 The ionisation of pure water, pH and pOH......Page 567
  17.3 Acids......Page 569
  17.4 Bases......Page 576
  17.5 The Henderson-Hasselbalch approximation......Page 579
  17.6 Buffer solutions......Page 580
  17.7 Why buffer solutions maintain constant pH......Page 583
  17.8 How approximate is the Henderson-Hasselbalch approximation?......Page 584
  17.9 Buffer capacity......Page 585
  17.10 Other reactions involving hydrogen ions......Page 592
  17.11 The mass action effect......Page 597
  17.12 Water as a reagent......Page 598
  EXERCISES......Page 600
  18.1 Non-volatile solutes......Page 602
  18.2 Elevation of the boiling point......Page 603
  18.3 Depression of the freezing point......Page 606
  EXERCISE......Page 610
  19.1 Mixing......Page 611
  19.2 Osmosis......Page 613
  19.3 Osmotic pressure......Page 614
  19.5 A note on hydrostatic pressure......Page 619
  EXERCISES......Page 621
  Summary......Page 622
  20.1 Work and electricity......Page 623
  20.2 Electrical work and Gibbs free energy......Page 625
  20.3 Half-cells......Page 627
  20.4 The electrochemical cell......Page 630
  20.5 Anodes and cathodes .........Page 631
  20.6 …and the flow of ions and electrons......Page 632
  20.7 The chemistry of the Daniell Cell......Page 633
  20.8 Currents, voltages and electrode potentials......Page 634
  20.9 A different type of Daniell cell......Page 635
  20.10 Different types of electrode......Page 636
  20.11 Different types of electrochemical cell......Page 638
  20.12 The electromotive force......Page 643
  20.13 Oxidising agents and reducing agents......Page 650
  20.14 The thermodynamics of electrochemical cells......Page 652
  20.15 The Nernst equation......Page 655
  20.16 Redox reactions......Page 659
  EXERCISES......Page 662
  Summary......Page 664
  21.1 The fundamental functions......Page 665
  21.2 Pure substances......Page 666
  21.3 Heat capacities......Page 667
  21.4 The Maxwell relations......Page 668
  21.5 The chain rule......Page 671
  21.6 The thermodynamic equations-of-state......Page 672
  21.7 The difference CP- CV......Page 676
  21.8 The Joule–Thomson coefficient......Page 679
  21.9 The compressibility factor......Page 683
  EXERCISES......Page 685
  Summary......Page 686
  22.1 Real gases and fugacity......Page 687
  22.2 Real solutions and activity......Page 690
  EXERCISES......Page 699
PART 5  Biochemical applications......Page 702
  Summary......Page 704
  23.1 Thermodynamics and biochemistry......Page 705
  23.2 A note on standards......Page 706
  23.3 The biochemical standard state......Page 707
  23.4 Why this is important......Page 709
  23.5 The implications of the biochemical standard state......Page 710
  23.6 Transformed equations......Page 712
  23.7  G(H+) and G′(H+), and ΔfG⊖(H+) and ΔfG⊖′(H+)......Page 714
  23.8 E⊖(H+, H2) and E⊖′(H+, H2)......Page 717
  23.9 ΔfG⊖′(H2)......Page 720
  23.10 Transformed standard molar Gibbs free energies of formation ΔfG⊖′......Page 722
  23.11 ΔrG⊖ and ΔrG⊖′......Page 725
  23.12 Kr and Kr′......Page 727
  23.13 Gsys and Gsys for an unbuffered reaction......Page 728
  23.14 Gsys and Gsys for a buffered reaction......Page 735
  23.15 Water as a biochemical reagent......Page 738
  EXERCISES......Page 739
  24.1 Creating order without breaking the Second Law: open systems......Page 742
  24.3 Life's primary `energy currency' – ATP......Page 743
  24.4 NADH is an energy currency too......Page 746
  24.5 Glycolysis – substrate-level phosphorylation of ADP......Page 747
  24.6 The metabolism of pyruvate......Page 750
  24.7 The TCA cycle......Page 751
  24.8 Oxidative phosphorylation, and the chemi-osmotic potential......Page 754
  24.9 The efficiency of glucose metabolism......Page 766
  24.10 Photosynthesis......Page 768
  EXERCISES......Page 776
  25.1 Protein structure......Page 778
  25.2 The thermodynamics of protein folding......Page 779
  25.3 Protein-ligand interactions......Page 794
  25.4 Protein folding kinetics......Page 800
  EXERCISES......Page 810
  26.1 Self-assembly of large complexes......Page 811
  26.2 Non-ideal gases and the formation of liquids......Page 812
  26.3 Kinetics of nucleated molecular polymerisation......Page 813
  26.4 Molecular mechanisms in protein aggregation......Page 817
  26.6 The thermodynamics of self-assembly for systems with defined final structures......Page 818
  26.7 Towards the design of self-assembling systems......Page 822
Glossary......Page 826
Bibliography......Page 875
Index......Page 878