Literature DB >> 28186751

Relationship between Solvation Thermodynamics from IST and DFT Perspectives.

Ronald M Levy1, Di Cui1, Bin W Zhang1, Nobuyuki Matubayasi2.   

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.

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Year:  2017        PMID: 28186751      PMCID: PMC5869707          DOI: 10.1021/acs.jpcb.6b12889

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  47 in total

1.  Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm.

Authors:  Chia-En Chang; Michael K Gilson
Journal:  J Am Chem Soc       Date:  2004-10-13       Impact factor: 15.419

2.  Temperature weighted histogram analysis method, replica exchange, and transition paths.

Authors:  Emilio Gallicchio; Michael Andrec; Anthony K Felts; Ronald M Levy
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

3.  Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

Authors:  Robert Abel; Tom Young; Ramy Farid; Bruce J Berne; Richard A Friesner
Journal:  J Am Chem Soc       Date:  2008-02-12       Impact factor: 15.419

4.  High-energy water sites determine peptide binding affinity and specificity of PDZ domains.

Authors:  Thijs Beuming; Ramy Farid; Woody Sherman
Journal:  Protein Sci       Date:  2009-08       Impact factor: 6.725

5.  Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Authors:  Crystal N Nguyen; Tom Kurtzman Young; Michael K Gilson
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

6.  Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

Authors:  Robert C Harris; Nanjie Deng; Ronald M Levy; Ryosuke Ishizuka; Nobuyuki Matubayasi
Journal:  J Comput Chem       Date:  2016-12-23       Impact factor: 3.376

7.  Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

Authors:  K Vanommeslaeghe; E Prabhu Raman; A D MacKerell
Journal:  J Chem Inf Model       Date:  2012-11-28       Impact factor: 4.956

8.  A Stochastic Solution to the Unbinned WHAM Equations.

Authors:  Bin W Zhang; Junchao Xia; Zhiqiang Tan; Ronald M Levy
Journal:  J Phys Chem Lett       Date:  2015-09-14       Impact factor: 6.475

9.  Thermodynamics of buried water clusters at a protein-ligand binding interface.

Authors:  Zheng Li; Themis Lazaridis
Journal:  J Phys Chem B       Date:  2006-01-26       Impact factor: 2.991

10.  Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.

Authors:  Crystal N Nguyen; Tom Kurtzman; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2015-12-04       Impact factor: 6.006

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  4 in total

1.  Solvation Thermodynamics from the Perspective of Endpoints DFT.

Authors:  Ronald M Levy; Nobuyuki Matubayasi; Bin W Zhang
Journal:  J Phys Chem B       Date:  2020-12-11       Impact factor: 2.991

2.  The Role of Interfacial Water in Protein-Ligand Binding: Insights from the Indirect Solvent Mediated Potential of Mean Force.

Authors:  Di Cui; Bin W Zhang; Nobuyuki Matubayasi; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2018-01-12       Impact factor: 6.006

3.  Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.

Authors:  Yoshiki Ishii; Naoki Yamamoto; Nobuyuki Matubayasi; Bin W Zhang; Di Cui; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2019-04-16       Impact factor: 6.006

4.  The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations.

Authors:  Bin W Zhang; Di Cui; Nobuyuki Matubayasi; Ronald M Levy
Journal:  J Phys Chem B       Date:  2018-04-23       Impact factor: 2.991

  4 in total

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