Evidence map›Paper›PMID 19402609›Full record

ArticleThe journal of physical chemistry. B2009

Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects.

Nidhi Singh, Arieh Warshel

Abstract read
In one paragraph

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.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Exploring the Drug Resistance of HCV Protease.The journal of physical chemistry. B · 2017
    Article
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  5. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Nidhi SinghDepartment of Chemistry, 418 SGM Building, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089-1062, USA.
Arieh Warshel

Funding

THEORETICAL STUDIES OF ENZYMATIC REACTIONSR01GM024492 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI WARSHEL, ARIEH · 1985 to 2017
$5.0M
COMPUTER SIMULATION OF ELECTRON TRANSFER REACTIONSR01GM040283 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI WARSHEL, ARIEH · 1988 to 2016
$4.2M
NIGMS NIH HHS R01 GM024492NIGMS NIH HHS R01 GM040283NIGMS NIH HHS R01 GM40283
6 · The paper itself

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.

Indexed as

EntropyMicroscopySensitivity and SpecificitySodiumSolventsTime FactorsVibrationSodiumSolvents

Identifiers

PMID19402609
PMCPMC2738853

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.