Literature DB >> 23212974

Parameterization of a geometric flow implicit solvation model.

Dennis G Thomas1, Jaehun Chun, Zhan Chen, Guowei Wei, Nathan A Baker.   

Abstract

Implicit solvent models are popular for their high computational efficiency and simplicity over explicit solvent models and are extensively used for computing molecular solvation properties. The accuracy of implicit solvent models depends on the geometric description of the solute-solvent interface and the solvent dielectric profile that is defined near the surface of the solute molecule. Typically, it is assumed that the dielectric profile is spatially homogeneous in the bulk solvent medium and varies sharply across the solute-solvent interface. However, the specific form of this profile is often described by ad hoc geometric models rather than physical solute-solvent interactions. Hence, it is of significant interest to improve the accuracy of these implicit solvent models by more realistically defining the solute-solvent boundary within a continuum setting. Recently, a differential geometry-based geometric flow solvation model was developed, in which the polar and nonpolar free energies are coupled through a characteristic function that describes a smooth dielectric interface profile across the solvent-solute boundary in a thermodynamically self-consistent fashion. The main parameters of the model are the solute/solvent dielectric coefficients, solvent pressure on the solute, microscopic surface tension, solvent density, and molecular force-field parameters. In this work, we investigate how changes in the pressure, surface tension, solute dielectric coefficient, and choice of different force-field charge and radii parameters affect the prediction accuracy for hydration free energies of 17 small organic molecules based on the geometric flow solvation model. The results of our study provide insights on the parameterization, accuracy, and predictive power of this new implicit solvent model.
Copyright © 2012 Wiley Periodicals, Inc.

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Year:  2012        PMID: 23212974      PMCID: PMC3578971          DOI: 10.1002/jcc.23181

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  23 in total

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10.  Correlating solvation free energies and surface tensions of hydrocarbon solutes.

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  13 in total

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3.  Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies.

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4.  Exploring accurate Poisson-Boltzmann methods for biomolecular simulations.

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5.  Improvements to the APBS biomolecular solvation software suite.

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6.  An efficient second-order poisson-boltzmann method.

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Journal:  J Comput Chem       Date:  2019-02-18       Impact factor: 3.376

7.  DG-GL: Differential geometry-based geometric learning of molecular datasets.

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9.  Multiscale multiphysics and multidomain models--flexibility and rigidity.

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Journal:  J Chem Phys       Date:  2013-11-21       Impact factor: 3.488

Review 10.  A review of mathematical representations of biomolecular data.

Authors:  Duc Duy Nguyen; Zixuan Cang; Guo-Wei Wei
Journal:  Phys Chem Chem Phys       Date:  2020-02-26       Impact factor: 3.676

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