A new diversity index.

We introduce here a new index of diversity based on consideration of reasonable propositions that such an index should have in order to represent diversity. The behaviour of the index is compared with that of the Gini-Simpson diversity index, and is found to predict more realistic values of diversity for small communities, in particular when each species is equally represented and for small communities. The index correctly provides a measure of true diversity that is equal to the species richness across all values of species and organism numbers when all species are equally represented, as well as Hill's more stringent 'doubling' criterion when they are not. In addition, a new graphical interpretation is introduced that permits a straightforward visual comparison of pairs of indices across a wide range within a parameter space based on species and organism numbers.

A Kirkwood-Buff analysis of local properties of solutions.

For decades, the properties of liquid mixtures have been analyzed in terms of excess thermodynamic functions. These functions convey global or macroscopic information on the system. In this work, a complementary view, based on the local properties of the same system is suggested. These properties are richer and more informative regarding the local densities, composition and solvation effect. A few examples ranging from Lennard-Jones particles, to inert gas mixtures, to aqueous solutions are presented, stressing the local information that cannot be obtained directly from global properties.

A critique of some recent suggestions to correct the Kirkwood-Buff integrals.

This article is a thorough critique of some recent publications by Matteoli, Lepori, Ruckenstein and others who suggested a correction to the Kirkwood-Buff integrals to obtain "better" information on the molecular interactions. It is shown that the suggested "corrected" Kirkwood-Buff integrals are, in fact, less informative than the original integrals. A detailed and critical examination of the arguments that led to the suggested correction reveals some serious flaws. Therefore, it is argued that the corrected Kirkwood-Buff integrals should be "recorrected" to restore their original definition and meaning.

Molecular recognition--viewed through the eyes of the solvent.

The binding of a ligand L to a specific site on an adsorbent molecule P is usually studied within the lock-and-key model. In this article we argue that the presence of an aqueous solvent may change dramatically the means by which a ligand recognizes its binding site. The main factor, originating from the specific property of water, is the ability of a water molecule to form a hydrogen-bond-bridge between a functional group on L and a functional group on P. This factor will change the criterion for selecting the best binding site.

A possible involvement of solvent-induced interactions in drug design.

We propose to study a new factor in designing new drugs. Most approaches to the drug design problem focus on the direct interactions between the drug and the corresponding target. We propose to study specific solvent-induced effects that can contribute to the binding Gibbs energy between the drug and its target. We estimate that these indirect effects will contribute significantly to the binding affinity and hopefully improve the clinical efficiency of the drugs.

Solvent effect on binding thermodynamics of biopolymers.

The indirect solvent-induced effect on the free energy of binding of biopolymers is examined within the framework of classical statistical mechanics. We focus specifically on the role of the solute-solvent hydrogen bonding. In particular, we have estimated the first order solvent effect on the indirect interaction between two biopolymers. We find that the solvent-induced interactions between two hydrophilic groups through water-bridged hydrogen bonds could significantly enhance the binding free energy. Some preliminary estimates indicate that this effect is significant and perhaps could be crucial in molecular recognition processes. Furthermore, we have calculated, from crystal structure data, the distance distribution between all the oxygens and nitrogens on the surface of some proteins that do not belong to the binding domain. In most cases we found an enhanced peak in the range of 4-5 A, which is where we expect to find strong solvent-induced interactions.

Solvent effects on protein association and protein folding.

Solvent effects on the thermodynamics of two processes--folding of proteins and association between proteins--are examined in detail. A complete inventory of the multitude of solvent effects may be obtained by employing the concept of conditional solvation free energy. This theoretical tool allows for the isolation of specific side-chain effects from the entire protein and for the study of its contribution to the overall free energy change in small model compounds. Some numerical examples are presented, and ways of estimating other cases, for which no relevant experimental data are available, are suggested. Our findings lead to the conclusion that the currently used hydrophobicity scales, based on partition coefficients between water and an organic solvent, are inadequate measures of the contribution of side chains being transferred from water to the interior of the protein. We have also tentatively concluded that correlation between hydrophilic functional groups might be more important than correlations between hydrophobic side chains.

Solvation thermodynamics of biopolymers. I. Separation of the volume and surface interactions with estimates for proteins.

The present paper is a systematic first approach to the problem of solvation thermodynamics of biomolecules. Most previous approaches have been only crude estimates of solvent contributions, and have simply assessed solvation free energy as proportional to surface areas. Here we estimate the various contributions and divide them into (a) hard-core interactions dependent upon the entire volume of solute and (b) the remainder of interactions manifested through surfaces, such as van der Waals, charge-charge, or hydrogen bonds. We have estimated the work to create a cavity with scaled-particle theory (SPT), the van der Waals interactions on the surface, and hydrogen bonds between the surface and the solvent. The conclusion here is that this latter term is the largest component of the solvation free energy of proteins. From estimates on nine diverse proteins, it is clear that the larger the protein, the more dominant is the hydrogen-bond term. In the next paper, we indicate that correlations between hydrogen-bonding groups on the surfaces could increase the magnitude of the hydrogen-bond contribution.

Solvation thermodynamics of biopolymers. II. Correlations between functional groups.

The extent of correlations between functional groups that can form hydrogen bonds with solvent molecules has been estimated. From the observed distance distribution of functional groups on the surfaces of several proteins, and from the extent of correlation between pairs of such functional groups, we conclude that the assumption of independence of functional groups made in part I is probably a good approximation. The reason is that even when correlations exist there is, on average, cancellation of the positive and negative correlations. The relevance of hydrogen bonding with the solvent to the relative stability of different conformers of biopolymers is also indicated.

Theory of preferential solvation of nonelectrolytes.

The concepts of local compositions around a solute and preferential solvation of a solute are defined in terms of the Kirkwood-Buff integrals. The difference between the local and the bulk composition is a measure of the preferential solvation of a solute with respect to the various components of the solvent. A statistical mechanical theory is developed that leads to simple relationships between local compositions and experimentally measurable quantities. Some preliminary results on preferential solvation of methane in mixtures of water-ethanol and water-p-dioxane are presented.