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Tables of Contents for Physical Chemistry
Chapter/Section Title
Page #
Page Count
Preface
xvii
About the Authors
xix
Introduction
The Human Genome and Beyond
4
2
Transcription and Translation
6
4
Ion Channels
10
1
References
11
1
Suggested Reading
12
1
Problem
12
3
The First Law: Energy Is Conserved
Concepts
15
1
Applications
16
1
Energy Conversion and Conservation
16
13
Systems and Surroundings
17
1
Energy Exchanges
18
10
First Law of Thermodynamics
28
1
Describing the State of a System
29
16
Variables of State
29
2
Equations of State
31
2
Paths Connecting Different States
33
3
Dependence of the Energy and Enthalpy of a Pure Substance on P, V, and T
36
8
Relations Between Heat Exchanges and DE and DH
44
1
Phase Changes
45
2
Chemical Reactions
47
9
Heat Effects of Chemical Reactions
47
3
Temperature Dependence of ΔH
50
1
The Energy Change ΔE for a Reaction
51
1
Standard Enthalpies (or Heats) of Formation
51
2
Bond Energies
53
3
Molecular Interpretations of Energy and Enthalpy
56
1
Summary
57
3
State Variables
57
1
Unit Conversions
57
1
General Equations
57
1
Pressure-Volume Work Only
58
1
Solids and Liquids
58
1
Gases
59
1
Phase Changes
59
1
Chemical Reactions
60
1
Mathematics Needed for Chapter 2
60
1
References
61
1
Suggested Reading
61
1
Problems
61
8
The Second Law: The Entropy of the Universe Increases
Concepts
69
1
Applications
69
1
Historical Development of the Second Law: The Carnot Cycle
69
4
A New State Function, Entropy
73
2
The Second Law of Thermodynamics: Entropy Is Not Conserved
75
2
Molecular Interpretation of Entropy
77
4
Fluctuations
79
2
Measurement of Entropy
81
1
Chemical Reactions
81
1
Third Law of Thermodynamics
82
5
Temperature Dependence of Entropy
82
1
Temperature Dependence of the Entropy Change for a Chemical Reaction
83
1
Entropy Change for a Phase Transition
84
1
Pressure Dependence of Entropy
85
2
Spontaneous Chemical Reactions
87
1
Gibbs Free Energy
87
10
ΔG and a System's Capacity to Do Nonexpansion Work
87
1
Spontaneous Reactions at Constant T and P
88
1
Calculation of Gibbs Free Energy
89
2
Temperature Dependence of Gibbs Free Energy
91
3
Pressure Dependence of Gibbs Free Energy
94
3
Phase Changes
97
1
Helmholtz Free Energy
97
1
Noncovalent Reactions
97
9
Hydrophobic Interactions
100
1
Proteins and Nucleic Acids
101
5
Use of Partial Derivatives in Thermodynamics
106
5
Relations Among Partial Derivatives
107
4
Summary
111
2
State Variables
111
1
Unit Conversions
111
1
General Equations
111
1
ΔG and a System's Capacity to Do Nonexpansion Work
111
1
Spontaneous Reactions at Constant T and P
111
1
Changes in Entropy and Gibbs Free Energy
112
1
References
113
1
Suggested Reading
113
1
Problems
113
8
Free Energy and Chemical Equilibria
Concepts
121
1
Applications
122
1
Chemical Potential (Partial Molar Gibbs Free Energy)
122
3
Gibbs Free Energy and the Chemical Potential
122
1
The Sum Rule for Partial Molar Quantities
123
1
Chemical Potential and Directionality of Chemical Reaction
123
2
Reactions of Gases: The Ideal Gas Approximation
125
5
Dependence of Chemical Potential on Partial Pressures
125
2
Equilibrium Constant
127
3
Nonideal Systems
130
11
Activity
130
1
Standard States
131
8
Activity Coefficients of Ions
139
2
The Equilibrium Constant and the Standard Gibbs Free Energies of the Reactants and Products
141
12
Calculation of Equilibrium Concentrations: Ideal Solutions
144
6
Temperature Dependence of the Equilibrium Constant
150
3
Galvanic Cells
153
6
Standard Electrode Potentials
156
2
Concentration Dependence of
158
1
Biochemical Applications of Thermodynamics
159
11
Thermodynamics of Metabolism
165
5
Biological Redox Reactions
170
6
NADH-Q Reductase
171
1
Cytochrome Reductase
172
1
Cytochrome c Oxidase
172
1
Double Strand Formation in Nucleic Acids
172
3
Ionic Effect on Protein-Nucleic Acid Interactions
175
1
Summary
176
3
Chemical Potential (Partial Molar Gibbs Free Energy)
176
1
Standard States and Activities
177
1
Gibbs Free-Energy Change and Equilibrium Constant for a Chemical Reaction
178
1
Galvanic Cells
178
1
Mathematics Needed for Chapter 4
179
1
References
179
1
Suggested Reading
179
1
Problems
179
8
Free Energy and Physical Equilibria
Concepts
187
1
Applications
187
1
Membranes and Transport
187
1
Ligand Binding
188
1
Colligative Properties
188
1
Phase Equilibria
188
25
One-Component Systems
189
1
Boiling Point and Freezing Point
189
4
Solutions of Two or More Components
193
4
Equilibrium Dialysis
197
1
The Scatchard Equation
198
4
Cooperative Binding and Anticooperative Binding
202
4
Free Energy of Transfer Between Phases
206
4
Donnan Effect and Donnan Potential
210
3
Membranes
213
14
Lipid Molecules
213
1
Lipid Bilayers
214
2
Phase Transitions in Lipids, Bilayers, and Membranes
216
2
Surface Tension
218
4
Surface Free Energy
222
2
Vapor Pressure and Surface Tension
224
1
Biological Membranes
225
2
Active and Passive Transport
227
4
Colligative Properties
231
8
Molecular-Weight Determination
239
2
Vapor-Pressure Lowering
240
1
Summary
241
3
Phase Equilibrium
241
1
Solutions
242
2
References
244
1
Suggested Reading
245
1
Internet
245
1
Problems
245
8
Molecular Motion and Transport Properties
Concepts
253
1
Applications
254
1
Kinetic Theory
255
10
Brownian Motion and Random Molecular Motion
255
1
Velocities of Molecules, Translational Kinetic Energy, and Temperature
256
5
Maxwell-Boltzmann Distribution of Velocities
261
4
Molecular Collisions
265
1
Mean Free Path
266
1
Diffusion
267
12
The Random Walk and Diffusion in a Gas
267
2
Diffusion Coefficient and Fick's First Law
269
2
Fick's Second Law
271
1
Determination of the Diffusion Coefficient
272
1
Relationship Between the Diffusion Coefficient and the Mean-Square Displacement
273
1
Determination of the Diffusion Coefficient by Laser Light Scattering
274
1
Diffusion Coefficient and Molecular Parameters
275
1
Solvation
276
1
Shape Factor
277
2
Diffusion Coefficients of Random Coils
279
1
Sedimentation
279
6
Determination of the Sedimentations Coefficient
281
2
Standard Sedimentation Coefficient
283
2
Determination of Molecular Weights from Sedimentation and Diffusion
285
4
Determination of Molecular Weights from Sedimentation Equilibrium
285
3
Density-Gradient Centrifugation
288
1
Viscosity
289
2
Measurement of Viscosity
290
1
Viscosities of Solutions
291
1
Electrophoresis
291
10
Gel Electrophoresis
292
1
DNA Sequencing
293
1
Double-Stranded DNA
294
1
DNA Fingerprinting
294
2
Conformations of Nucleic Acids
296
1
Pulsed-Field Gel Electrophoresis
297
2
Protein Molecular Weights
299
1
Protein Charge
300
1
Macromolecular Interactions
301
1
Size and Shape of Macromolecules
301
1
Summary
302
5
Kinetic Theory
302
2
Diffusion
304
1
Sedimentation
304
1
Frictional Coefficient and Molecular Parameters
305
1
Combination of Diffusion and Sedimentation
305
1
Viscosity
305
1
Electrophoresis
306
1
Gel Electrophoresis
306
1
References
307
1
Suggested Reading
307
1
Problems
307
8
Kinetics: Rates of Chemical Reactions
Concepts
315
1
Applications
316
1
Kinetics
316
25
Rate Law
318
1
Order of a Reaction
318
2
Experimental Rate Data
320
1
Zero-Order Reactions
321
1
First-Order Reactions
322
7
Second-Order Reactions
329
5
Renaturation of DNA as an Example of a Second-Order Reaction
334
4
Reactions of Other Orders
338
1
Determining the Order and Rate Constant of a Reaction
338
3
Reaction Mechanisms and Rate Laws
341
13
Parallel Reactions
343
2
Series Reactions (First Order)
345
4
Equilibrium and Kinetics
349
2
Complex Reactions
351
1
Deducing a Mechanism from Kinetic Data
352
2
Temperature Dependence
354
3
Transition-State Theory
357
3
Electron Transfer Reactions: Marcus Theory
360
2
Ionic Reactions and Salt Effects
362
1
Isotopes and Stereochemical Properties
363
2
Very Fast Reactions
365
7
Relaxation Methods
365
1
Relaxation Kinetics
366
6
Diffusion-Controlled Reactions
372
2
Photochemistry and Photobiology
374
4
Vision
377
1
Photosynthesis
378
3
Summary
381
6
Zero-Order Reactions
381
1
First-Order Reactions
381
1
Second-Order Reactions
382
1
Temperature Dependence
383
2
Electron Transfer Reactions: Marcus Theory
385
1
Relaxation Kinetics
385
1
Diffusion-Controlled Reactions
386
1
Absorption of Light
386
1
Photochemistry
386
1
Mathematics Needed for Chapter 7
387
1
References
387
1
Suggested Reading
388
1
Problems
388
13
Enzyme Kinetics
Concepts
401
1
Applications
401
2
Catalytic Antibodies and RNA Enzymes-Ribozymes
401
2
Enzyme Kinetics
403
3
Michaelis-Menten Kinetics
406
9
Kinetic Data Analysis
409
4
Two Intermediate Complexes
413
2
Competition and Inhibition
415
8
Competion
415
1
Competitive Inhibition
416
2
Noncompetitive Inhibition
418
1
Allosteric Effects
419
3
Single-Molecule Kinetics
422
1
Summary
423
2
Typical Enzyme Kinetics
423
1
Michaelis--Menten Mechanism
424
1
Monod-Wyman-Changeux Mechanism
425
1
Mathematics Needed for Chapter 8
425
1
References
426
1
Suggested Reading
426
1
Problems
427
10
Molecular Structures and Interactions: Theory
Concepts
437
1
Applications
437
1
The Process of Vision
438
3
Origins of Quantum Theory
441
5
Blackbody Radiation
442
2
Photoelectric Effect
444
1
Electrons as Waves
444
1
Heisenberg Uncertainty Principle
445
1
Quantum Mechanical Calculations
446
3
Wave Mechanics and Wavefunctions
446
3
Schrodinger's Equation
449
6
Solving Wave Mechanical Problems
451
1
Outline of wave Mechanical Procedures
452
3
Particle in a Box
455
8
Tunneling
463
2
Simple Harmonic Oscillator
465
3
Rigid Rotator
468
1
Hydrogen Atom
469
1
Electron Distribution
470
19
Electron Distribution in a Hydrogen Atom
471
5
Many-Electron Atoms
476
3
Molecular Orbitals
479
5
Hybridization
484
2
Delocalized Orbitals
486
3
Molecular Structure and Molecular Orbitals
489
4
Geometry and Stereochemistry
489
2
Transition Metal Ligation
491
2
Charge Distributions and Dipole Moments
493
1
Intermolecular and Intramolecular Forces
493
4
Bond Stretching and Bond Angle Bending
494
1
Rotation Around Bonds
495
2
Noncovalent Interactions
497
17
Electrostatic Energy and Coulomb's Law
497
3
Net Atomic Charges and Dipole Moments
500
3
Dipole-Dipole Interactions
503
2
London Attraction
505
1
van der Waals Repulsion
506
1
London-van der Waals Interaction
507
1
The Lowest-Energy Conformation
508
2
Hydrogen Bonds
510
2
Hydrophobic and Hydrophilic Environments
512
2
Molecular Dynamics Simulation
514
2
Monte Carlo Method
514
1
Molecular Dynamics Method
515
1
Outlook
516
1
Summary
517
1
Photoelectric Effect
517
1
Wave-Particle Duality
517
1
Heisenberg Uncertainty Principle
517
1
Schrodinger's Equation
518
1
Some Useful Operators
518
5
Systems Whose Schrodinger Equation Can Be Solved Exactly
519
2
Coulomb's Law
521
1
Dipoles and Their Interaction Energy
521
1
Intramolecular (Within) and Intermolecular (Between) Interactions
521
2
Mathematics Needed for Chapter 9
References
523
1
Suggested Reading
523
1
Problems
524
7
Molecular Structures and Interactions: Spectroscopy
Concepts
531
1
Applications
532
1
Electromagnetic Spectrum
532
1
Color and Refractive Index
533
2
Absorption and Emission of Radiation
535
13
Radiation-Induced Transitions
536
2
Classical Oscillators
538
1
Quantum Mechanical Description
538
2
Lifetimes and Line Width
540
1
Role of Environment in Electronic Absorption Spectra
541
2
Beer-Lambert Law
543
5
Proteins and Nucleic Acids: Ultraviolet Absorption Spectra
548
6
Amino Acid Spectra
549
1
Polypeptide Spectra
549
2
Secondary Structure
551
1
Origin of Spectroscopic Changes
551
1
Nucleic Acids
552
1
Rhodopsin: A Chromorphic Protein
553
1
Fluorescence
554
13
Simple Theory
555
1
Excited-State Properties
556
4
Fluorescence Quenching
560
1
Excitation Transfer
561
2
Molecular Rulers
563
1
Fluorescence Polarization
564
1
Phosphorescence
565
1
Single-Molecule Fluorescence Spectroscopy
565
2
Optical Rotatory Dispersion and Circular Dichroism
567
6
Polarized Light
568
3
Optical Rotation
571
2
Circular Dichroism
573
1
Circular Dichroism of Nucleic Acids and Proteins
573
3
Vibrational Spectra, Infrared Absorption, and Raman Scattering
576
3
Infrared Absorption
576
1
Raman Scattering
577
2
Nuclear Magnetic Resonance
579
4
The Spectrum
581
2
Interactions in Nuclear Magnetic Resonance
583
15
Chemical Shifts
583
2
Spin-Spin Coupling, Scalar Coupling, or J-Coupling
585
3
Relaxation Mechanisms
588
2
Nuclear Overhauser Effect
590
1
Multidimensional NMR Spectroscopy
590
4
Determination of Macromolecular Structure by Nuclear Magnetic Resonance
594
2
Electron Paramagnetic Resonance
596
1
Magnetic Resonance Imaging
597
1
Summary
598
3
Absorption and Emission
598
2
Excitation Transfer
600
1
Optical Rotatory Dispersion and Circular Dichroism
600
1
Nuclear Magnetic Resonance
600
1
References
601
1
Suggested Reading
601
2
Problems
603
12
Molecular Distributions and Statistical Thermodynamics
Concepts
615
1
Applications
615
1
Binding of Small Molecules by a Polymer
616
12
Identical-and-Independent-Sites Model
617
2
Langmuir Adsorption Isotherm
619
1
Nearest-Neighbor Interactions and Statistical Weights
620
2
Cooperative Binding, Anticooperative Binding, and Excluded-Site Binding
622
3
N Identical Sites in a Linear Array with Nearest-Neighbor Interactions
625
1
Identical Sites in Nonlinear Arrays with Nearest-Neighbor Interactions
626
2
The Random Walk
628
8
Calculation of Some Mean Values for the Random-Walk Problem
630
4
Diffusion
634
1
Average Dimension of a Linear Polymer
634
2
Helix-Coil Transitions
636
9
Helix-Coil Transition in a Polypeptide
636
5
Helix-Coil Transition in a Double-Stranded Nucleic Acid
641
4
Statistical Thermodynamics
645
14
Statistical Mechanic Internal Energy
646
1
Work
647
1
Heat
648
1
Most Probable (Boltzmann) Distribution
649
4
Quantum Mechanical Distributions
653
1
Statistical Mechanical Entropy
653
1
Examples of Entropy and Probability
654
4
Partition Function: Applications
658
1
Summary
659
3
Binding of Small Molecules by a Polymer
659
1
Random-Walk and Related Topics
660
1
Helix-Coil Transitions
660
1
Statistical Thermodynamics
661
1
Mathematics Needed for Chapter 11
662
1
References
662
1
Suggested Reading
663
1
Problems
663
4
Macromolecular Structure and X-Ray Diffraction
Concepts
667
1
Applications
667
1
Visible Images
668
1
X Rays
668
16
Emission of X Rays
669
1
Image Formation
669
1
Scattering of X Rays
670
5
Diffraction of X Rays by a Crystal
675
3
Measuring the Diffraction Pattern
678
1
Bragg Reflection of X Rays
679
2
Intensity of Diffraction
681
2
Unit Cell
683
1
Determination of Molecular Structure
684
14
Calculation of Diffracted Intensities from Atomic Coordinates: The Structure Factor
684
2
Calculation of Atomic Coordinates from Diffracted Intensities
686
2
The Phase Problem
688
1
Direct Methods
688
1
Isomorphous Replacement
688
2
Multiwavelength Anomalous Diffraction
690
1
Determination of a Crystal Structure
691
3
Scattering of X Rays by Noncrystalline Materials
694
1
Absorption of X Rays
695
1
Extended Fine Structure of Edge Absorption
696
1
X Rays from Synchrotron Radiation
697
1
Electron Diffraction
698
1
Neutron Diffraction
699
1
Electron Microscopy
700
4
Resolution, Contrast, and Radiation Damage
700
1
Transmission and Scanning Electron Microscopes
701
1
Image Enhancement and Reconstruction
701
1
Scanning Tunneling and Atomic Force Microscopy
702
2
Summary
704
3
X-ray Diffraction
704
3
Neutron Diffraction
707
1
Electron Microscopy
707
1
Mathematics Needed for Chapter 12
707
1
References
708
1
Suggested Reading
708
1
Problems
709
3
Appendix
712
13
Answers
725
3
Index
728