Solvation Thermodynamics and Its Applications.

In this article, we start by describing a few "definitions" of the solvation processes, which were used in the literature until about 1980. Then, we choose one of these definitions and show that it has a simple molecular interpretation. This fact led to a of the and the corresponding thermodynamic quantities.

Is Time's Asymmetry Related to Irreversible Processes and the Second Law?

In this article, we start by describing one of the most characteristic properties of time: "". From this property, numerous authors have concluded that irreversible processes, that proceed in one direction, must be related to time's arrow. It is shown that while time's decrease can never occur, irreversible processes can be reversed, although with extremely low probability.

Solvation free energy arithmetic for small organic molecules.

Solvent-mediated interactions contribute to ligand binding affinities in computational drug design and provide a challenge for theoretical predictions. In this study, we analyze the solvation free energy of benzene derivatives in water to guide the development of predictive models for solvation free energies and solvent-mediated interactions. We use a spatially resolved analysis of local solvation free energy contributions and define solvation free energy arithmetic, which enable us to construct additive models to describe the solvation of complex compounds.

Information, Entropy, Life, and the Universe.

In (2015), I wrote a book with the same title as this article. The book's subtitle is: "" On the book's dedication page, I wrote []: In the first part of this article, I will present the definitions of two central concepts: the "Shannon measure of information" (SMI), in Information Theory, and "Entropy", in Thermodynamics. Following these definitions, I will discuss the In the second part of the article, I will examine the question of whether and the are, or are not within the of the concepts of SMI and Entropy.

Temperature Dependence of Hydrophobic and Hydrophilic Forces and Interactions.

Molecular dynamics simulations are used to compare the forces and Gibbs free energies associated with bringing small hydrophobic and hydrophilic solutes together in an aqueous solution at different temperatures between 280 and 360 °K. For the hydrophilic solutes, different relative orientations are used to distinguish between direct, intersolute hydrogen bonds (Hbond) and solutes simultaneously hydrogen bonding to a solvent water bridge. Interestingly, the temperature dependence of the hydrophobic and directly hydrogen bonding solutes turns out to be opposite to that of the bridged hydrophilic solutes, with the Δ becoming more negative for the former and less negative for the latter with increasing temperature.

Entropy and Time.

The idea that entropy is associated with the "arrow of time" has its roots in Clausius's statement on the Second Law: "." However, the explicit association of the entropy with time's arrow arises from Eddington. In this article, we start with a brief review of the idea that the "increase in entropy" is somehow associated with the direction in which time increases.

An Informational Theoretical Approach to the Entropy of Liquids and Solutions.

It is well known that the statistical mechanical theory of liquids has been lagging far behind the theory of either gases or solids, See for examples: Ben-Naim (2006), Fisher (1964), Guggenheim (1952) Hansen and McDonald (1976), Hill (1956), Temperley, Rowlinson and Rushbrooke (1968), O'Connell (1971). Information theory was recently used to derive and interpret the entropy of an ideal gas of simple particles (i.e.

Hydrophobic-hydrophilic forces in protein folding.

The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as well as from interactions with the solvent (solvent-induced forces). We present a statistical-mechanical formalism that describes both these direct and indirect, solvent-induced thermodynamic forces on groups of the protein.

Myths and verities in protein folding theories: from Frank and Evans iceberg-conjecture to explanation of the hydrophobic effect.

Starting from the seminal article by Frank and Evans where the "iceberg formation" idea was first expressed, we follow the evolution of this idea to the explanation of the hydrophobic effect. We show that the idea of iceberg formation can provide an explanation to the entropy, and enthalpy of solvation of non-polar solutes in water, provided one first explains why a simple non-polar solute would form icebergs in the first place. Having done that, the questions regarding the outstanding large hydrophobic solvation Gibbs energy remains unexplained.

Theoretical aspects of self-assembly of proteins: a Kirkwood-Buff-theory approach.

A new approach to the problem of self-assembly of proteins induced by temperature, pressure, or changes in solute concentration is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. In this article we focus on the pressure and solute effects on the association-dissociation equilibrium.

Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach.

A new approach to the problem of pressure-denaturation (PD) and solute-denaturation (SD) of proteins is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. It is found that both problems have one factor in common; the excluded volumes of the folded and the unfolded forms with respect to the solvent molecules.

Levinthal's question revisited, and answered.

Attempts to answer the Levinthal question "How proteins fold to give such a unique structure" are discussed. In the first part of this article, we focus on a few reasons as to why the solution to the protein-folding problem (PFP) has been elusive for a very long time. One is a result of the misinterpretation of Anfinsen's Thermodynamic hypothesis which led to the conclusion that the native structure of a protein must be at a global minimum of the Gibbs energy.

Some aspects of the protein folding problem examined in one-dimensional systems.

Some concepts, such as energy landscape, Gibbs energy landscape, and cooperativity, frequently used in the theory of protein folding, are examined exactly in one-dimensional systems. It is shown that much of the confusion that exists regarding these, and other concepts arise from the misinterpretation of Anfinsen's thermodynamic hypothesis.

One dimensional model for water and aqueous solutions. Part V. Monte Carlo simulation of dilute solutions of hard rod in waterlike particles.

We have carried out Monte Carlo simulation on the primitive one dimensional model for water described earlier [A. Ben-Naim, J. Chem.

Local and global properties of mixtures in one-dimensional systems. II. Exact results for the Kirkwood-Buff integrals.

The Kirkwood-Buff integrals for two-component mixtures in one-dimensional systems are calculated directly. The results are applied to square-well particles and found to agree with those obtained by the inversion of the Kirkwood-Buff theory of solutions.

One-dimensional model for water and aqueous solutions. IV. A study of "hydrophobic interactions".

The solute-solute pair correlation function and the potential of mean force (PMF) between two hard-rod solutes in two solvents are studied in one-dimensional systems. One solvent consists of particles interacting via square well (SW) potential. The second consists of particles interacting via "hydrogen-bond-like" (HB) pair potential.

Pair correlation functions of simple solutes in a Lennard-Jones solvent.

We have calculated the pair correlation functions for several binary mixtures composed of simple solutes in a Lennard-Jones solvent. In particular, we have studied the solute-solute pair correlation functions and their dependence on the total density, the solvent Lennard-Jones parameters, and on the solute-solute energy parameter. All the results were obtained from solving the Percus-Yevick equations, as well as from Monte Carlo simulations.

The Kirkwood-Buff integrals for one-component liquids.

The Kirkwood-Buff integrals (KBIs) for one-component systems are calculated from either the pair correlation functions or from experimental macroscopic quantities. As in the case of mixtures, the KBIs provide important information on the local densities around a molecule. In the low density limit (rho-->0) one can extract from the KBI some information on the strength of the intermolecular forces.

Pair correlation functions in mixtures of Lennard-Jones particles.

The pair correlation functions for a mixture of two Lennard-Jones particles were computed by both the Percus-Yevick equations and by molecular dynamics. The changes in the pair correlation function resulting from changes in the composition of the mixtures are quite unexpected. Essentially, identical changes are obtained from the Percus-Yevick equations and from molecular dynamics simulations.

One-dimensional model for water and aqueous solutions. III. Solvation of hard rods in aqueous mixtures.

A simple one-dimensional model for aqueous solution is applied to study the solvation thermodynamics of a simple solute (here, a hard-rod particle) in mixtures of waterlike particles and a cosolvent. Two kinds of cosolvents are considered, one that stabilizes and one that destabilizes the "structure of water." The results obtained for the Gibbs energy, entropy, enthalpy, and heat capacity of solvation are in qualitative agreement with experimental data on the solvation of argon and methane in mixtures of water and ethanol and of water and p-dioxane.

Local and global properties of mixtures in one-dimensional systems. Part I. Mixtures of two simple components.

Two sets of quantities are calculated for two-component mixtures in one dimension. One consists of the traditional excess thermodynamic quantities which provide global information on the mixtures. The second, referred to as local properties, consists of the Kirkwood-Buff integrals, local composition, solvation, and preferential solvation quantities.

One-dimensional model for water and aqueous solutions. II. Solvation of inert solutes in water.

The two one-dimensional models introduced in Part I are used to study the thermodynamics of solvation of inert solutes in water. It is shown that the anomalously large Gibbs energy of solvation of inert solutes in water, on one hand, and the large negative entropy of solvation, on the other hand, arise from different molecular sources. While the primitive model can give rise to a large positive solvation Gibbs energy, it fails to show large negative entropy and enthalpy of solvation.

One-dimensional model for water and aqueous solutions. I. Pure liquid water.

Two simplified one-dimensional models for waterlike particles are studied. One is referred to as the primitive model which is a simplified version of a model introduced by Ben-Naim in 1992 [Statistical Thermodynamics for Chemists and Biochemists (Plenum, New York, 1992)]. The second, referred to as the primitive cluster model, is a simplified version of the model used by Lovett and Ben-Naim in 1969 [J.