Literature DB >> 30990682

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

Yoshiki Ishii1, Naoki Yamamoto1, Nobuyuki Matubayasi1,2, Bin W Zhang3, Di Cui3, Ronald M Levy3.   

Abstract

A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously established in the one-dimensional, energy representation and formulating a new expression in a mixed four-dimensional representation (three dimensions for position and one dimension for energy). The space was further divided into a set of discrete regions with respect to the relative position of a solvent molecule from the solute, and the spatially decomposed energetics of solvation were analyzed for small molecules with a methyl, amine, or hydroxyl group and alanine dipeptide in solvent water. It was observed that the density of the solvation free energy is weakly dependent on the solute site in the excluded-volume region and is distinctively favorable in the first shells of the solute atoms that can readily form hydrogen bonds with water. The solvent-reorganization term reduces faster with the separation from the solute than the direct interaction between the solute and solvent, and the latter governs the energetics in the second shell and outer regions. The sum of the contributions to the free energy from the excluded volume and first shell was found to deviate significantly from the total sum over all the regions, implying that the solvation free energy is not spatially localized near the solute in a quantitative sense. Still, a local description was shown to be valid as confirmed by the correlation of the total value of free energy with the corresponding value obtained by integrating the free-energy density to the second shell. The theoretical framework developed in the present work to spatially decompose the solvation free energy can thus be useful to identify stabilizing or destabilizing regions of solvent proximate to a solute and to analyze the role that the displacement of interfacial water plays in the thermodynamics of molecular association.

Entities:  

Year:  2019        PMID: 30990682      PMCID: PMC6570404          DOI: 10.1021/acs.jctc.8b01309

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  49 in total

1.  Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.

Authors:  Hisashi Okumura
Journal:  Phys Chem Chem Phys       Date:  2010-10-29       Impact factor: 3.676

2.  Dissecting the THz spectrum of liquid water from first principles via correlations in time and space.

Authors:  Matthias Heyden; Jian Sun; Stefan Funkner; Gerald Mathias; Harald Forbert; Martina Havenith; Dominik Marx
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-21       Impact factor: 11.205

3.  Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding.

Authors:  Tom Young; Robert Abel; Byungchan Kim; Bruce J Berne; Richard A Friesner
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-04       Impact factor: 11.205

4.  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

5.  Communication: Free-energy analysis of hydration effect on protein with explicit solvent: equilibrium fluctuation of cytochrome c.

Authors:  Yasuhito Karino; Nobuyuki Matubayasi
Journal:  J Chem Phys       Date:  2011-01-28       Impact factor: 3.488

Review 6.  Water at biomolecular binding interfaces.

Authors:  Zheng Li; Themis Lazaridis
Journal:  Phys Chem Chem Phys       Date:  2006-11-24       Impact factor: 3.676

7.  New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap.

Authors:  Robert A Pearlstein; Qi-Ying Hu; Jing Zhou; David Yowe; Julian Levell; Bethany Dale; Virendar K Kaushik; Doug Daniels; Susan Hanrahan; Woody Sherman; Robert Abel
Journal:  Proteins       Date:  2010-09

8.  The effect of water displacement on binding thermodynamics: concanavalin A.

Authors:  Zheng Li; Themis Lazaridis
Journal:  J Phys Chem B       Date:  2005-01-13       Impact factor: 2.991

9.  Free-energy analysis of solubilization in micelle.

Authors:  Nobuyuki Matubayasi; Kuo Kan Liang; Masaru Nakahara
Journal:  J Chem Phys       Date:  2006-04-21       Impact factor: 3.488

10.  Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation.

Authors:  Nobuyuki Matubayasi; Wataru Shinoda; Masaru Nakahara
Journal:  J Chem Phys       Date:  2008-05-21       Impact factor: 3.488

View more
  5 in total

1.  Short solvent model for ion correlations and hydrophobic association.

Authors:  Ang Gao; Richard C Remsing; John D Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-07       Impact factor: 11.205

2.  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

3.  Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.

Authors:  Peng He; Sheila Sarkar; Emilio Gallicchio; Tom Kurtzman; Lauren Wickstrom
Journal:  J Phys Chem B       Date:  2019-10-01       Impact factor: 2.991

4.  Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.

Authors:  Lieyang Chen; Anthony Cruz; Daniel R Roe; Andrew C Simmonett; Lauren Wickstrom; Nanjie Deng; Tom Kurtzman
Journal:  J Chem Theory Comput       Date:  2021-04-08       Impact factor: 6.006

5.  Anion-cation contrast of small molecule solvation in salt solutions.

Authors:  Stefan Hervø-Hansen; Jan Heyda; Mikael Lund; Nobuyuki Matubayasi
Journal:  Phys Chem Chem Phys       Date:  2022-02-02       Impact factor: 3.676

  5 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.