ArticleThe journal of physical chemistry. B2009
Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Exploring the Drug Resistance of HCV Protease.The journal of physical chemistry. B · 2017Article
- Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions.The journal of physical chemistry. B · 2017Article
- Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization.Proteins · 2015Article
- Article
- Examining the case for the effect of barrier compression on tunneling, vibrationally enhanced catalysis, catalytic entropy and related issues.FEBS letters · 2010Review
- Absolute binding free energy calculations: on the accuracy of computational scoring of protein-ligand interactions.Proteins · 2010Article
- A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes.Proteins · 2010Article
- At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?Proteins · 2010Review
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2 authors.
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Abstract
The evaluation of the solvation entropies is a major conceptual and practical challenge. On the one hand, it is interesting to quantify the factors that are responsible for the solvation entropies in solutions, whereas on the other, it is essential to be able to assess the contributions of the solvation entropies to the binding free energies and related properties. In fact, the solvation entropies are neglected in almost all of the studies of the binding entropies. The main problem is that widely used approaches, such as the quasiharmonic (QH) approximation, do not provide reliable results particularly in cases of shallow potential and multidimensional surfaces while brute force evaluations of the entropic effects by simulating temperature dependence of the free energy converges very slowly. This paper addresses the above issue by starting with an analysis of the factors that are responsible for the negative solvation entropy of ions, showing that it is not due to the change in the solvent vibration modes or to the solvent force constant but to the changes in the solvent configurational space upon change in the solute charges. We begin by clarifying that when one deals with aqueous solutions, it is easy to evaluate the corresponding entropic effect by the Langevin dipole (LD) treatment. However, in this work we are interested in developing a general microscopic tool that can be used to study similar effects in the proteins. To this end, we explore the ability of our restraint release (RR) approach to evaluate the solvation entropy. We start this analysis by reviewing the foundation of this approach and in particular, the requirements of minimizing the enthalpy contribution to the RR free energy. We then establish that our approach is not a specialized harmonic treatment but a rather powerful general approach. Moving to the main topic of this work, we demonstrate that the RR approach provides quantitative results for the solvation entropies of monovalent and divalent ions and effectively captures the physics of these entropic effects. The success of the current approach indicates that it should be applicable to the studies of the solvation entropies in the proteins and also, in examining hydrophobic effects. Thus, we believe that the RR approach provides a powerful tool for evaluating the corresponding contributions to the binding entropies and, eventually, to the binding free energies. This holds promise for extending the information theory modeling to proteins and protein-ligand complexes in aqueous solutions and consequently, facilitating computer-aided drug design.
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