Literature DB >> 24058212

Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach.

Bo Li1, Xiaoliang Cheng, Zhengfang Zhang.   

Abstract

In an implicit-solvent description of molecular solvation, the electrostatic free energy is given through the electrostatic potential. This potential solves a boundary-value problem of the Poisson-Boltzmann equation in which the dielectric coefficient changes across the solute-solvent interface-the dielectric boundary. The dielectric boundary force acting on such a boundary is the negative first variation of the electrostatic free energy with respect to the location change of the boundary. In this work, the concept of shape derivative is used to define such variations and formulas of the dielectric boundary force are derived. It is shown that such a force is always in the direction toward the charged solute molecules.

Entities:  

Keywords:  dielectric boundary force; implicit solvent; shape derivative; the Poisson–Boltzmann equation

Year:  2011        PMID: 24058212      PMCID: PMC3778505          DOI: 10.1137/110826436

Source DB:  PubMed          Journal:  SIAM J Appl Math        ISSN: 0036-1399            Impact factor:   2.080


  29 in total

Review 1.  Generalized born models of macromolecular solvation effects.

Authors:  D Bashford; D A Case
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

Review 2.  The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology.

Authors:  F Fogolari; A Brigo; H Molinari
Journal:  J Mol Recognit       Date:  2002 Nov-Dec       Impact factor: 2.137

3.  Calculation of the Maxwell stress tensor and the Poisson-Boltzmann force on a solvated molecular surface using hypersingular boundary integrals.

Authors:  Benzhuo Lu; Xiaolin Cheng; Tingjun Hou; J Andrew McCammon
Journal:  J Chem Phys       Date:  2005-08-22       Impact factor: 3.488

4.  Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms.

Authors:  Jason A Wagoner; Nathan A Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2006-05-18       Impact factor: 11.205

5.  Application of the level-set method to the implicit solvation of nonpolar molecules.

Authors:  Li-Tien Cheng; Joachim Dzubiella; J Andrew McCammon; Bo Li
Journal:  J Chem Phys       Date:  2007-08-28       Impact factor: 3.488

Review 6.  Areas, volumes, packing and protein structure.

Authors:  F M Richards
Journal:  Annu Rev Biophys Bioeng       Date:  1977

7.  Mean-field description of ionic size effects with nonuniform ionic sizes: a numerical approach.

Authors:  Shenggao Zhou; Zhongming Wang; Bo Li
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-08-01

8.  Yukawa-Field Approximation of Electrostatic Free Energy and Dielectric Boundary Force.

Authors:  Hsiao-Bing Cheng; Li-Tien Cheng; Bo Li
Journal:  Nonlinearity       Date:  2011-11

9.  Differential geometry based solvation model I: Eulerian formulation.

Authors:  Zhan Chen; Nathan A Baker; G W Wei
Journal:  J Comput Phys       Date:  2010-11-01       Impact factor: 3.553

10.  Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach.

Authors:  Li-Tien Cheng; Zhongming Wang; Piotr Setny; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2009-10-14       Impact factor: 3.488

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  21 in total

1.  A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson-Boltzmann electrostatics.

Authors:  Hui Sun; Jiayi Wen; Yanxiang Zhao; Bo Li; J Andrew McCammon
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

2.  Variational Implicit Solvation with Solute Molecular Mechanics: From Diffuse-Interface to Sharp-Interface Models.

Authors:  Bo Li; Yanxiang Zhao
Journal:  SIAM J Appl Math       Date:  2013       Impact factor: 2.080

3.  Electrostatic forces in the Poisson-Boltzmann systems.

Authors:  Li Xiao; Qin Cai; Xiang Ye; Jun Wang; Ray Luo
Journal:  J Chem Phys       Date:  2013-09-07       Impact factor: 3.488

4.  Numerical interpretation of molecular surface field in dielectric modeling of solvation.

Authors:  Changhao Wang; Li Xiao; Ray Luo
Journal:  J Comput Chem       Date:  2017-03-20       Impact factor: 3.376

5.  Dielectric pressure in continuum electrostatic solvation of biomolecules.

Authors:  Qin Cai; Xiang Ye; Ray Luo
Journal:  Phys Chem Chem Phys       Date:  2012-10-23       Impact factor: 3.676

Review 6.  Interacting ions in biophysics: real is not ideal.

Authors:  Bob Eisenberg
Journal:  Biophys J       Date:  2013-05-07       Impact factor: 4.033

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

Authors:  Changhao Wang; Jun Wang; Qin Cai; Zhilin Li; Hong-Kai Zhao; Ray Luo
Journal:  Comput Theor Chem       Date:  2013-11-15       Impact factor: 1.926

8.  DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.

Authors:  Lin Li; Arghya Chakravorty; Emil Alexov
Journal:  J Comput Chem       Date:  2017-01-28       Impact factor: 3.376

9.  LS-VISM: A software package for analysis of biomolecular solvation.

Authors:  Shenggao Zhou; Li-Tien Cheng; Hui Sun; Jianwei Che; Joachim Dzubiella; Bo Li; J Andrew McCammon
Journal:  J Comput Chem       Date:  2015-03-12       Impact factor: 3.376

10.  Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.

Authors:  Saeed Izadi; Boris Aguilar; Alexey V Onufriev
Journal:  J Chem Theory Comput       Date:  2015-08-21       Impact factor: 6.006

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