Water in Biology : a Molecular View.

Intro
Contents
Prologue
Acknowledgments
Chapter 1
Introduction
Chapter 2
Background
The Basics of Thermodynamics
Energy and the First Law of Thermodynamics
Entropy and the Second Law of Thermodynamics
Third Law
Summary on the Review of Thermodynamics
The Rudiments of Quantum Mechanics
Some Brief Comments on Quantum Mechanics, and Their Relevance to Computations on Biological Systems, Especially with Regard to the Water in These Systems
Vibrations and Rotations
Normal Modes
More Approximations
Quantum Effects
Tunneling
Zero Point Energy
Vibrations and the Infrared (IR) Spectrum
Examples
Spin: Protons, Neutrons, and Electrons Have Spin Angular Momentum
Electrons-Spin
Protons and Other Nuclei
The Consequences of Quantum Effects in Computations
Difficulties with Quantum Calculations
Thermodynamics of Irreversible Processes, and the Onsager Reciprocal Relations
Jarzynski Equality
Summary on ORR
Non-Linearity, Chaos: Far from Equilibrium Phenomena
Summary, Overall
References
Chapter 3
Phases: 3 Dimensional and 2 Dimensional Phases and Phase Changes
Ice 1h, the Bernal-Fowler Rules, and Bjerrum Defects
The Basic Thermodynamics of Phase Change
Solubility and Phase Separation of Liquids-Liquid-Liquid Phase Diagrams
Colligative Properties
Phase Equilibria in Biology
Metastability
Other Phase Changes in Biological Systems
Second Order Phase Transitions
Two Dimensional Phases
Summary of Phase Transitions so Far
More Phases, and Complications
Amorphous Phases, and the Fragile to Strong Transition
Gel-Sol Transitions
Emulsions and Microemulsions
Coacervates
Ionic Liquids
Summary
References
Chapter 4.

Solvation by Water: Ions, Other Hydrophilic Species, and Larger Molecules, Especially Amino Acids, and on to Proteins
Solvation of Metal Ions
Hydration of Small Ions, Mainly Monovalent
Dilute Solutions
Debye-Hückel Theory
Summary, Part 1
Hydrolysis of Al3+ and Fe3+
Part 2
Summary Part 2
Part 3: Amino Acids, and Related Ions
Hydration of Biologically Interesting Molecules
Sugars More Generally
Amino Acid Hydration
Amino Acids with Lipid
Summary Part 3
Summary, Overall
References
Chapter 5
Nucleic Acid Hydration: Effects on Structure, Thermodynamics, and Dynamics
Some General Considerations, Principally Concerning Thermodynamics and Structure, on DNA Hydration, with Some Consideration of RNA as Well
Transcription with Hydration
Transcription
RNA, and the Effect of the 2'OH Group That RNA Has On Its Sugar Moiety
Fragile to Strong Crossover
Summary
References
Chapter 6
Ionic Conduction and Diffusion
Random Walks
Hydrogen and Hydroxide Ions
Proton Wires
More on Conductivity
Conductance of Solutions of Dilute Salt
Simulations of Concentrated Solutions
Electrorheology
Summary
References
Chapter 7
Acids and Bases with Particular Reference to Amino Acids
Definitions
Production of Hydronium and Related Ions
Measurement of pH
Hydrolysis
Correction for Activity Coefficient
Buffers
Amino Acids
Summary
References
Chapter 8
Surfaces: Colloids, Small Particles, Surfactants, and Macroscopic Liquid Surfaces
The Motion of Colloid Particles in an Electric Field
The Double Layer
Hydrophobicity
Myelin
The Marangoni Effect
More on Surfactants
Proteins
A Partial Review, and Where Some New Techniques Fit in
Summary
References
Chapter 9
Hydrogen Bonds and Proton Paths.

Hydrogen Bond Strength as a Function of Distance
Hydrogen Bonds in Confined Spaces
What Accounts for the Difference in Hydrogen Bonds?
Hydrogen Bond Properties
Non-Electrostatic Properties of Hydrogen Bonds
Proton Delocalization
The Proton Wavelength
Charge Delocalization
Cooperativity
Proton Paths
Tunneling
Summary
References
Chapter 10
Confined Spaces and Water Clusters
Inorganic Confined Water
Vibrations
Dielectric Relaxation
Effects on Protein Structure with Confined Water
Ion Pairs and Larger Ion-Containing Clusters
Summarizing Our Discussion of Clusters
Capillary Condensation
Summary
Appendix on Dielectric Constant
References
Chapter 11
Channels and Transporters
Classes of Channels and Transporters
Summary
References
Chapter 12
Three Special Topics
Radiation
Summary
Vibrations of Water with Proteins
Summary
Conclusion
Anhydrobiosis and Desiccation
Summary
References
Chapter 13
Simulations, Quantum Calculations, and Other Calculations
Ensembles
Quantum Calculations
Summary
References
Chapter 14
Conclusion
Chapter 15
Epilogue
Appendix: Boltzmann Distribution and Some Uses
Boltzmann Distribution
Phase Space, and Getting to β = 1/kbT
Other Thermodynamic Quantities
Degrees of Freedom
Normal Modes
Summary
Index
About the Authors
Blank Page.