Literature DB >> 16851760

Density functional theory of solvation and its relation to implicit solvent models.

Rosa Ramirez1, Daniel Borgis.   

Abstract

We describe a density functional theory approach to solvation in molecular solvents. The solvation free energy of a complex solute can be obtained by direct minimization of a density functional, instead of the thermodynamic integration scheme necessary when using atomistic simulations. In the homogeneous reference fluid approximation, the expression of the free-energy functional relies on the knowledge of the direct correlation function of the pure solvent. After discussing general molecular solvents, we present a generic density functional describing a dipolar solvent and we show how it can be reduced to the conventional implicit solvent models when the solvent microscopic structure is neglected. With respect to those models, the functional includes additional effects such as the microscopic structure of the solvent, the dipolar saturation effect, and the nonlocal character of the dielectric constant. We also show how this functional can be minimized numerically on a three-dimensional grid around a solute of complex shape to provide, in a single shot, both the average solvent structure and the absolute solvation free energy.

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Year:  2005        PMID: 16851760     DOI: 10.1021/jp045453v

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


  11 in total

1.  Incorporating dipolar solvents with variable density in Poisson-Boltzmann electrostatics.

Authors:  Cyril Azuara; Henri Orland; Michael Bon; Patrice Koehl; Marc Delarue
Journal:  Biophys J       Date:  2008-09-26       Impact factor: 4.033

2.  Variational implicit-solvent predictions of the dry-wet transition pathways for ligand-receptor binding and unbinding kinetics.

Authors:  Shenggao Zhou; R Gregor Weiß; Li-Tien Cheng; Joachim Dzubiella; J Andrew McCammon; Bo Li
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-03       Impact factor: 11.205

Review 3.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

4.  Polar-solvation classical density-functional theory for electrolyte aqueous solutions near a wall.

Authors:  Vadim Warshavsky; Marcelo Marucho
Journal:  Phys Rev E       Date:  2016-04-18       Impact factor: 2.529

5.  New theoretical method for rapid prediction of solvation free energy in water.

Authors:  Shuangliang Zhao; Zhehui Jin; Jianzhong Wu
Journal:  J Phys Chem B       Date:  2011-05-10       Impact factor: 2.991

6.  Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities.

Authors:  Jaydeep P Bardhan
Journal:  J Mech Behav Mater       Date:  2013-12

Review 7.  Implicit Solvation Methods for Catalysis at Electrified Interfaces.

Authors:  Stefan Ringe; Nicolas G Hörmann; Harald Oberhofer; Karsten Reuter
Journal:  Chem Rev       Date:  2021-12-20       Impact factor: 72.087

8.  Continuum Electrostatic Behavior of a 3D-RISM Theory.

Authors:  Benoît Roux
Journal:  J Phys Chem B       Date:  2020-08-17       Impact factor: 2.991

9.  Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments.

Authors:  Zaven Ovanesyan; Bharat Medasani; Marcia O Fenley; Guillermo Iván Guerrero-García; Mónica Olvera de la Cruz; Marcelo Marucho
Journal:  J Chem Phys       Date:  2014-12-14       Impact factor: 3.488

Review 10.  Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly.

Authors:  Clarisse Gravina Ricci; Bo Li; Li-Tien Cheng; Joachim Dzubiella; J Andrew McCammon
Journal:  Front Mol Biosci       Date:  2018-02-12
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