Cover
Pearson Advanced Chemistry Series
Physical Chemistry: Principles and Applications in Biological Sciences
Copyright
Brief Contents
Contents
Preface
New to This Edition
About the Authors
1. Introduction
Neuroscience
The Human Genome and Beyond
Transcription and Translation
Ion Channels
Single-molecule Methods
Reference
Suggested Reading
Problems
2. The First Law: Energy Is Conserved
Concepts
Applications
Energy Conversion and Conservation
Systems and Surroundings
Energy Exchanges
Work
Heat
Internal Energy
Constant Volume Heat Capacity
Constant Volume Heat Capacity of Diatomic Gases
Constant Volume Heat Capacity of Monatomic Solids
Heat Capacity of Molecular Solids and Liquids
State and Path Variables
Reversible Paths and Reversible Processes
Equations of State
The Enthalpy
The Constant Pressure Heat Capacity of an Ideal Gas
Dependence of the Energy and Enthalpy of a Pure Substance on p, V, and T
Liquids or Solids
Gases
Phase Changes
Chemical Reactions
Heat Effects of Chemical Reactions
Temperature Dependence of Δ[Sub(r)]H
Standard Enthalpies of Formation
The Energy Change ΔE for a Reaction
Computing Reaction Energies from First Principles
Quantum Chemical Calculations
Bond Energies
Molecular Interpretations of Energy and Enthalpy
Summary
References
Suggested Reading
Problems
3. The Second Law: The Entropy of the Universe Increases
Concepts
Applications
Toward the Second Law: The Carnot Cycle
A New State Function, Entropy
The Second Law of Thermodynamics
Molecular Interpretation of Entropy
Fluctuations
Measurement of Entropy
Chemical Reactions
Third Law of Thermodynamics
Temperature Dependence of Entropy
Temperature Dependence of the Entropy Change for a Chemical Reaction
Entropy Change for a Phase Transition
Pressure Dependence of Entropy
Spontaneous Chemical Reactions
Gibbs Free Energy
ΔG and a System’s Capacity to Do Nonexpansion Work
Spontaneous Processes at Constant T and p
Calculation of Gibbs Free Energy
Temperature Dependence of Gibbs Free Energy
Pressure Dependence of Gibbs Free Energy
Phase Changes
Helmholtz Free Energy
Noncovalent Reactions
Hydrophobic Interactions
Proteins and Nucleic Acids
Use of Partial Derivatives in Thermodynamics
Relations Among Partial Derivatives
The Thermodynamic Square
The Gibbs-Helmholtz Equation
Summary
References
Suggested Reading
Problems
4. Free Energy and Chemical Equilibria
Concepts
Applications
Partial Molar Gibbs Energy
Chemical Potential
The Sum Rule for Partial Molar Quantities
Directionality of Chemical Reaction
Reactions of Ideal Gases
Dependence of Chemical Potential on Partial Pressures
Equilibrium Constant
Nonideal Systems
Activity
Standard States
Activity Coefficients of Ions
Equilibrium and the Standard Gibbs Free Energy
Calculation of Equilibrium Concentrations: Ideal Solutions
Temperature Dependence of the Equilibrium Constant
Biochemical Applications of Thermodynamics
Thermodynamics of Metabolism
Isothermal Titration Calorimetry
Double Strand Formation in Nucleic Acids
Ionic Effect on Protein–Nucleic Acid Interactions
Summary
References
Suggested Reading
Problems
5. The Statistical Foundations of Biophysical Chemistry
Concepts
Applications
Maxwell Boltzmann Statistics
The Boltzmann Distribution
The Maxwell-Boltzmann Distribution
The Maxwell-Boltzmann Distribution and the Speed
Statistical Thermodynamics
Statistical Mechanical Internal Energy
Work
Heat
Most Probable (Boltzmann) Distribution
Statistical Mechanical Entropy
Examples of Entropy and Probability
Partition Function: Applications
The Random Walk
Calculation of Some Mean Values for the Random-Walk Problem
Diffusion
Average Dimension of a Linear Polymer
Helix–Coil Transitions
Helix–Coil Transition in a Polypeptide
Helix–Coil Transition in a Double-Stranded Nucleic Acid
Binding of Small Molecules by a Polymer
Identical-and-Independent-Sites Model
Langmuir Adsorption Isotherm
Nearest-Neighbor Interactions and Statistical Weights
Cooperative Binding, Anticooperative Binding, and Excluded-Site Binding
N Identical Sites in a Linear Array with Nearest-Neighbor Interactions
Identical Sites in Nonlinear Arrays with Nearest-Neighbor Interactions
Summary
References
Suggested Reading
Problems
6. Physical Equilibria
Concepts
Applications
Membranes and Transport
Ligand Binding
Colligative Properties
Phase Equilibria
One component systems
Solutions of Two or More Components
Membranes
Lipid Molecules
Lipid Bilayers
Phase Transitions in Lipids, Bilayers, and Membranes
Surface Tension
Surface Free Energy
Vapor Pressure and Surface Tension
Biological Membranes
Colligative Properties
Boiling-point elevation and freezing-point depression
Osmotic Pressure
Molecular-Weight Determination
Summary
References
Suggested Reading
Problems
7. Electrochemistry
Concepts
Applications
Basic Electricity
Capacitance and Electrical Neutrality
Ground and the Reference Potential
The Electrochemical Cell
Reversibility in the Electrochemical Cell
Electrical Work, Electrochemical Potential, and Free Energy
Standard Electrochemical Potentials
Concentration Dependence of ε
Transmembrane Equilibria
Donnan Effect and Donnan Potential
Plasma Membrane Potentials and the Na[Sup(+)], K[Sup(+)] ATPase
Biological Redox Reactions and Membranes
Oxidative Phosphorylation
NADH-Q Reductase (Complex I)
Succinate Dehydrogenase (Complex II)
Coenzyme Q – Cytochrome c Oxidoreductase (Complex III)
Cytochrome c Oxidase (Complex IV)
Mitochondrial Oxidation of NAD[Sup(+)]
ATP Synthase
Summary
References
Suggested Reading
Problems
8. The Motions of Biological Molecules
Concepts
Applications
Molecular Motion and Molecular Collisions
The Collision Tube
Random Walks in a Gas
Diffusion
The Diffusion Coefficient and Fick’s First Law
Fick’s Second Law
The Einstein-Smoluchowski Relation
Determination of the Diffusion Coefficient
Values of the Diffusion and Self-Diffusion Coefficient
The Frictional Coefficient
f and D
Shape Factor
Diffusion Coefficients of Random Coils
Sedimentation
Analytical Centrifugation
Sedimentation Equilibrium
Molecular Weights from Sedimentation and Diffusion
Density-Gradient Centrifugation
Viscosity
Measurement of Viscosity
Viscosities of Solutions
Electrophoresis
Gel Electrophoresis
Conformations of Nucleic Acids
Pulsed-Field Gel Electrophoresis
Protein Molecular Weights
Protein Charge
Macromolecular Interactions
Size and Shape of Macromolecules
Summary
References
Suggested Reading
Problems
9. Kinetics: Rates of Chemical Reactions
Concepts
Applications
Kinetics
Rate Law
Order of a Reaction
Experimental Rate Data
Zero-Order Reactions
First-Order Reactions
Second-Order Reactions
Renaturation of DNA as an Example of a Second-Order Reaction
Reactions of Other Orders
Determining the Order and Rate Coefficient of a Reaction
Reaction Mechanisms and Rate Laws
Parallel Reactions
Series Reactions (First Order)
Equilibrium and Kinetics
Complex Reactions
Deducing a Mechanism from Kinetic Data
Temperature Dependence
Transition-State Theory
Electron Transfer Reactions: Marcus Theory
Ionic Reactions and Salt Effects
Isotopes and Stereochemical Properties
Very Fast Reactions
Relaxation Methods
Relaxation Kinetics
Diffusion-Controlled Reactions
Single-Molecule Kinetics
Photochemistry and Photobiology
Vision
Photosynthesis
Summary
References
Suggested Reading
Problems
10. Enzyme Kinetics
Concepts
Applications
Catalytic Antibodies and RNA Enzymes—Ribozymes
Enzyme Kinetics
Michaelis–Menten Kinetics
Kinetic Data Analysis
Two Intermediate Complexes
Competition and Inhibition
Competition
Competitive Inhibition
Noncompetitive Inhibition
Allosteric Effects
Single-Molecule Kinetics
Summary
References
Suggested Reading
Problems
11. Molecular Structures and Interactions: Theory
Concepts
Application to Vision
Origins of Quantum Theory
Origins: Blackbody Radiation
Origins: Hydrogen Emission
Origins: Photoelectric Effect
Origins: Electrons as Waves
Origins: Heisenberg Uncertainty Principle
Origins: Classical Waves and Quantization
Quantum Mechanical Calculations
Wave Mechanics and Wavefunctions
The Schrödinger Equation
Solving Wave Mechanical Problems
Outline of Wave Mechanical Procedures
Particle in a Box
Example of a Particle-in-a-Box Calculation
Tunneling
Simple Harmonic Oscillator
Rigid Rotator
Hydrogen Atom
Electron Distribution
Electron Distribution in a Hydrogen Atom
Many-Electron Atoms
Hybridization
Origins: Postulates
Summary
References
Suggested Reading
Problems
12. Molecular Structures and Interactions: Biomolecules
Concepts
Molecular Orbitals
Delocalized Orbitals
Molecular Structure and Molecular Orbitals
Geometry and Stereochemistry
Transition Metal Ligation
Charge Distributions and Dipole Moments
Intermolecular and Intramolecular Forces
Bond Stretching and Bond Angle Bending
Rotation Around Bonds
Noncovalent Interactions
Electrostatic Energy and Coulomb’s Law
Net Atomic Charges and Dipole Moments
Dipole–Dipole Interactions
London Attraction
van der Waals Repulsion
London–van der Waals Interaction
The Lowest-Energy Conformation
Hydrogen Bonds
Hydrophobic and Hydrophilic Environments
Molecular Dynamics Simulation
Monte Carlo Method
Molecular Dynamics Method
Outlook
Summary
References
Suggested Reading
Problems
13. Optical Spectroscopy
Concepts
Applications
Electromagnetic Spectrum
Color and Refractive Index
Absorption and Emission of Radiation
Radiation-Induced Transitions
Classical Oscillators
Quantum Mechanical Description
Lifetimes and Line Width
Role of Environment in Electronic Absorption Spectra
Beer–Lambert Law
Proteins and Nucleic Acids: Ultraviolet Absorption Spectra
Amino Acid Spectra
Polypeptide Spectra
Secondary Structure
Nucleic Acids
Rhodopsin: A Chromophoric Protein
Fluorescence
Simple Theory
Excited-State Properties
Fluorescence Quenching
Excitation Transfer
Molecular Rulers
Fluorescence Polarization
Phosphorescence
Single-Molecule Fluorescence Spectroscopy
Optical Rotatory Dispersion and Circular Dichroism
Polarized Light
Optical Rotation
Circular Dichroism
Circular Dichroism of Nucleic Acids and Proteins
Vibrational Spectroscopy
Infrared Absorption
Raman Scattering
Summary
References
Suggested Reading
Problems
14. Magnetic Resonance
Concepts
Applications
Nuclear Magnetic Resonance
Nuclear Spin Energy Levels
The Spectrum
A Pulse in the Rotating Frame
Interactions in Nuclear Magnetic Resonance
Chemical Shifts
Spin–Spin Coupling, Scalar Coupling, or J-Coupling
Relaxation Mechanisms
Nuclear Overhauser Effect
Multidimensional NMR Spectroscopy
Determining Macromolecular Structure by NMR
Electron Paramagnetic Resonance
Magnetic Field Gradients, Diffusion and Microscopy
Magnetic Resonance Imaging
NMR Hardware Overview
Summary
References
Suggested Reading
Problems
15. Macromolecular Structure and X-Ray Diffraction
Concepts
Applications
Lattices
Symmetry
Symmetry in Three Dimensions
Images
X-Rays
Emission of X-Rays
Image Formation
Scattering of X-Rays
Diffraction of X-Rays by a Crystal
Measuring the Diffraction Pattern
Bragg Reflection of X-Rays
Intensity of Diffraction
Unit Cell
Determination of Molecular Structure
Calculation of Diffracted Intensities from Atomic Coordinates: The Structure Factor
Calculation of Atomic Coordinates from Diffracted Intensities
The Phase Problem
Direct Methods
Isomorphous Replacement
Multiwavelength Anomalous Diffraction
Determination of a Crystal Structure
Accessing Crystal Structures
Scattering of X-Rays by Noncrystalline Materials
Absorption of X-Rays
Extended Fine Structure of Edge Absorption (EXAFS)
X-Rays from Synchrotron Radiation and Free-Electron Lasers
Electron Diffraction
Neutron Diffraction
Electron Microscopy
Resolution, Contrast, and Radiation Damage
Transmission and Scanning Electron Microscopes
Image Enhancement and Reconstruction
Scanning Tunneling and Atomic Force Microscopy
Summary
References
Suggested Reading
Problems
Appendix Mathematics
Derivatives
Integration
Improper Integrals
Exponents and Logarithms
Series and Approximations
Mathematics for Quantum Mechanics: Hilbert Space
References
Appendix. Tables
Selected Answers to End of Chapter Problems
Index
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Z