Literature DB >> 25296776

Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.

Jaydeep P Bardhan1, Matthew G Knepley2.   

Abstract

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

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Year:  2014        PMID: 25296776      PMCID: PMC4193973          DOI: 10.1063/1.4897324

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  36 in total

1.  Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior.

Authors:  Sowmianarayanan Rajamani; Tuhin Ghosh; Shekhar Garde
Journal:  J Chem Phys       Date:  2004-03-01       Impact factor: 3.488

2.  Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions.

Authors:  Jaydeep P Bardhan; Matthew G Knepley
Journal:  J Chem Phys       Date:  2011-09-28       Impact factor: 3.488

3.  Charge asymmetries in hydration of polar solutes.

Authors:  David L Mobley; Janene R Baker; Alan E Barber; Christopher J Fennell; Ken A Dill
Journal:  J Phys Chem B       Date:  2008-02-06       Impact factor: 2.991

4.  Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory.

Authors:  Dezso Boda; Mónika Valiskó; Douglas Henderson; Dirk Gillespie; Bob Eisenberg; Michael K Gilson
Journal:  Biophys J       Date:  2009-02-18       Impact factor: 4.033

5.  Langevin-Debye model for nonlinear electrostatic screening of solvated ions.

Authors:  Haipeng Gong; Karl F Freed
Journal:  Phys Rev Lett       Date:  2009-02-06       Impact factor: 9.161

6.  Theory of the Poisson Green's function for discontinuous dielectric media with an application to protein biophysics.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-10

7.  Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

Authors:  Jaydeep P Bardhan; Pavel Jungwirth; Lee Makowski
Journal:  J Chem Phys       Date:  2012-09-28       Impact factor: 3.488

8.  Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density using proximal Radial Distribution Functions.

Authors:  Bin Lin; Ka-Yiu Wong; Char Hu; Hironori Kokubo; B Montgomery Pettitt
Journal:  J Phys Chem Lett       Date:  2011-06       Impact factor: 6.475

9.  The AGBNP2 Implicit Solvation Model.

Authors:  Emilio Gallicchio; Kristina Paris; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2009-07-31       Impact factor: 6.006

10.  Solvation effect on conformations of 1,2:dimethoxyethane: charge-dependent nonlinear response in implicit solvent models.

Authors:  Abhishek K Jha; Karl F Freed
Journal:  J Chem Phys       Date:  2008-01-21       Impact factor: 3.488

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  3 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.  Accuracy limit of rigid 3-point water models.

Authors:  Saeed Izadi; Alexey V Onufriev
Journal:  J Chem Phys       Date:  2016-08-21       Impact factor: 3.488

3.  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

  3 in total

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