Water in biology : a molecular view / Michael E. Green and Alisher M. Kariev.

Format:

Book

Author/Creator:

Green, Michael E., author.

Series:

Biochemistry Research Trends Series

Language:

English

Subjects (All):

Water--Analysis.

Water.

Molecular biology.

Biological interfaces.

Physical Description:

1 online resource (262 pages)

Edition:

1st ed.

Place of Publication:

New York : Nova Science Publishers, Inc., [2023]

Summary:

"Water is well known to be an essential component of all biological systems. Thousands of papers describe a role for water interacting with ions, proteins, nucleic acids, and lipids. In this book, the authors discuss the background chemistry and physics, including a very brief review of thermodynamics and quantum mechanics, to the limited extent needed for the remainder of the book. The various behaviors of water at surfaces, in solutions, in hydrating ions, proton transport, as well as the phase changes that involve water, are introduced. Hydrogen bonds, their networks, and the way they are associated with proteins are discussed, along with proton transport, which is important in a number of biological systems. The authors then proceed to discuss water in confined spaces, and in channels and transporters, which are topics particularly important in biology. Some special topics are interesting, like anhydrobiosis, and those are touched upon briefly. The authors have made no attempt to make this book comprehensive; the thousands of papers that have been published that are relevant provide far too much material for a single volume. Enough material is presented so that the reader sees what is now known, or at least is thought to be known. As with any science, sometimes we are pretty sure of something, only to find ground shifting under us as new experimental results show that what we thought we knew, we didn't. However, a snapshot of the authors' present state of knowledge is useful. Knowledge is progressing so rapidly that at least some will need updating as this is being written, but this is a good time to summarize what is currently known, and provide background information that will help understand what is coming"-- Provided by publisher.

Contents:

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

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

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

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

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

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

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

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

Appendix on Dielectric Constant

Chapter 11

Channels and Transporters

Classes of Channels and Transporters

Chapter 12

Three Special Topics

Radiation

Vibrations of Water with Proteins

Conclusion

Anhydrobiosis and Desiccation

Chapter 13

Simulations, Quantum Calculations, and Other Calculations

Ensembles

Quantum Calculations

Chapter 14

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

Index

About the Authors

Blank Page.

Notes:

Description based on print version record.

Includes bibliographical references and index.

Other Format:

Print version: Green, Michael E. Water in Biology: a Molecular View

ISBN:

9798886977547

OCLC:

1376934523