This monograph presents the molecular theory and necessary tools for the study of solvent-induced interactions and forces. After introducing the reader to the basic definitions of solvent-induced interactions, the author provides a brief analysis of the statistical thermodynamics. The book thoroughly overviews the connection of those interactions with thermodynamics and consequently focuses on specifically discussing the hydrophobic-hydrophilic interactions and forces. The importance of the implementation of hydrophilic interactions and forces in various biochemical processes is thoroughly analyzed, while evidence based on theory, experiments, and simulated calculations supporting that hydrophilic interactions and forces are far more important than the corresponding hydrophobic effects in many biochemical processes such as protein folding, self-assembly of proteins, molecular recognitions, are described in detail. This title is of great interest to students and researchers working in the fields of chemistry, physics, biochemistry, and molecular biology.
Author(s): Arieh Ben-Naim
Series: Physical Chemistry in Action
Publisher: Springer
Year: 2023
Language: English
Pages: 184
City: Cham
Preface
References
Acknowledgments
Contents
Abbreviations
1 Introduction, Definitions and Motivations for Studying Solvent-Induced Interactions
1.1 Definitions; Direct and Indirect Interactions
1.2 The Connection Between the Work for the Process ( inftyto R ) and Solvation Gibbs or Helmholtz Energies
1.3 The Protein Folding Problem (PFP)
1.4 Some Historical Landmarks in the Study SII in Attempting to Understand the PFP
1.4.1 The Early Dominance of Hydrogen Bonds, and Its Unfortunate Fall
1.4.2 The Rise of the HϕO Effect
1.4.3 The Cracks, and the Eventual Fall of the HϕO Effects in Protein Folding
1.4.4 The Rise and Possible Dominance of the HϕI Effects
1.5 Some Concluding Remarks
References
2 A Brief Introduction to Statistical Thermodynamics
2.1 Statistical Thermodynamics and Thermodynamics
2.2 The Two Postulates of Statistical Thermodynamics
2.3 The Boltzmann Definition of Entropy
2.4 Ensembles, and the Fundamental Thermodynamic Quantities
2.4.1 The Isolated System; The E, V, N Ensemble
2.4.2 The Isothermal-Isochoric System; The T, V, N Ensemble
2.4.3 The Isothermal-Isobaric System; The T, P, N Ensemble
2.5 The “Classical” of Statistical Thermodynamics
2.6 Some Results for an Ideal Gas
2.7 Molecular Distribution Functions
2.7.1 The Singlet Distribution Function in the Canonical Ensemble
2.7.2 The Pair Distribution Function in the Canonical Ensemble
2.8 The Pair Correlation Function
References
3 Solvent-Induced Interactions and Forces, Definitions and Connections with Thermodynamics
3.1 Definition of the Potential of Mean Force Between Two Simple Particles in a Solvent
3.2 The Potential of Mean Force
3.3 Direct and Indirect Interactions
3.4 Direct and Indirect Forces
3.5 Generalization of the Statistical Mechanical Expression for the Indirect Solvent-Induced Force
3.5.1 Increasing the Direct Force on A
3.5.2 Longer Range Forces Between Two Hydrophilic Surfaces
3.6 Concluding Remarks
References
4 Hydrophobic Interactions and Forces
4.1 Early Evidence for HφO Interactions
4.2 Some Theoretical Results About the HφO Interactions
4.3 Temperature Dependence of the HφO Interactions
4.4 Simulated Results on HφO Interactions and Forces
4.5 Conditional Solvation and Conditional HφO Interactions
4.6 Hydrophobic Interactions Among Many Non-polar Molecules
References
5 Hydrophilic Interactions and Forces
5.1 Theoretical Evidence on HφI Effects
5.1.1 Direct Formation of HB
5.1.2 Interaction Through a Water-Bridge
5.2 Evidence for HφI Effect Based on Experimental Data
5.3 Simulated Results on HφI Interactions and Forces
5.4 Temperature Dependence of HφI Interactions and Forces
5.5 Concluding Remarks
References
6 Implementation of the HφI Interactions and Forces in Some Biochemical Processes
6.1 The Problem of Stability of the 3D Structures of Proteins
6.2 The “Speed” of the Folding Process
6.3 Self-assembly of Proteins
6.4 Solvent-Induced Effect in Molecular Recognition
6.5 Solvation and Solubility of Globular Proteins
6.6 Cold Denaturation of Proteins
6.7 Concluding Remarks
References
Appendix A The BN3D Model of Water and the Corresponding Pair Potential
References
Appendix B Solvation Thermodynamics of Water in Liquid Water
B.1 Experimental Values of ΔGw2*
B.2 The Contribution of the Hydrogen-Bonding to the Solvation Gibbs Energy of Water in Water
B.3 Theoretical Estimate of ΔGw2*
References
References and Suggested Reading
Index
