Evidence map›Paper›PMID 28186751›Full record

ReviewThe journal of physical chemistry. B2017

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

Ronald M Levy, Di Cui, Bin W Zhang, Nobuyuki Matubayasi

Abstract readReview
In one paragraph

Review in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
1.2field-weighted citation impact, top 25% of its field
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

9 citing papers in PubMed, 23 citations in OpenAlex.

  1. Article
  2. Temperature Dependence of Hydrotropy.The journal of physical chemistry. B · 2024
    Article
  3. Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024
    Article
  4. Cooperativity in Sorption Isotherms.Langmuir : the ACS journal of surfaces and colloids · 2023
    Article
  5. Solvation Thermodynamics from the Perspective of Endpoints DFT.The journal of physical chemistry. B · 2020
    Review
  6. Article
  7. Article
  8. Article
  9. Article
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

4 authors at 2 institutions in 2 countries.

Ronald M LevyCenter for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States.ORCID 0000-0001-8696-5177
Di CuiCenter for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States.
Bin W ZhangCenter for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States.
Nobuyuki MatubayasiDivision of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan and Elements Strategy Initiative for Catalysts and Batteries, Kyoto University , Katsura, Kyoto 615-8520, Japan.
Temple University · USKyoto University · JP

Funding

DYNAMICS OF PEPTIDES AND PROTEINSR01GM030580 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI LEVY, RONALD · 1985 to 2018
$6.1M
Computer Cluster for Computational Biology and BiophysicsS10OD020095 · OD · TEMPLE UNIV OF THE COMMONWEALTH · PI LEVY, RONALD · 2015 to 2015
$442k
NIGMS NIH HHS R01 GM030580NIH HHS S10 OD020095
6 · The paper itself

Abstract

Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.

Indexed as

Quantum TheoryThermodynamicsSolubilitySolutionsSolventsSolutionsSolvents

Identifiers

PMID28186751
PMCPMC5869707
OpenAlexW2586662873

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

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.