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Title: Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

Authors:
;
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1222508
Alternate Identifier(s):
OSTI ID: 1420696
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Published Article
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Name: Journal of Chemical Physics Journal Volume: 141 Journal Issue: 13; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics
Country of Publication:
United States
Language:
English

Citation Formats

Bardhan, Jaydeep P., and Knepley, Matthew G. Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions. United States: N. p., 2014. Web. doi:10.1063/1.4897324.
Bardhan, Jaydeep P., & Knepley, Matthew G. Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions. United States. https://doi.org/10.1063/1.4897324
Bardhan, Jaydeep P., and Knepley, Matthew G. Tue . "Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions". United States. https://doi.org/10.1063/1.4897324.
@article{osti_1222508,
title = {Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions},
author = {Bardhan, Jaydeep P. and Knepley, Matthew G.},
abstractNote = {},
doi = {10.1063/1.4897324},
journal = {Journal of Chemical Physics},
number = 13,
volume = 141,
place = {United States},
year = {Tue Oct 07 00:00:00 EDT 2014},
month = {Tue Oct 07 00:00:00 EDT 2014}
}

Journal Article:
Free Publicly Available Full Text
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https://doi.org/10.1063/1.4897324

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Cited by: 20 works
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Works referenced in this record:

Charge Asymmetries in Hydration of Polar Solutes
journal, February 2008

  • Mobley, David L.; Barber, Alan E.; Fennell, Christopher J.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 8
  • DOI: 10.1021/jp709958f

Using simulation to study solvation in water
journal, January 2001

  • Lynden-Bell, R. M.; Rasaiah, J. C.; Noworyta, J. P.
  • Pure and Applied Chemistry, Vol. 73, Issue 11
  • DOI: 10.1351/pac200173111721

Ions and Inhibitors in the Binding Site of HIV Protease: Comparison of Monte Carlo Simulations and the Linearized Poisson-Boltzmann Theory
journal, February 2009


Beyond the no-slip boundary condition
journal, October 2011


Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior
journal, March 2004

  • Rajamani, Sowmianarayanan; Ghosh, Tuhin; Garde, Shekhar
  • The Journal of Chemical Physics, Vol. 120, Issue 9
  • DOI: 10.1063/1.1644536

Dependence of ion hydration on the sign of the ion’s charge
journal, January 2005

  • Grossfield, Alan
  • The Journal of Chemical Physics, Vol. 122, Issue 2
  • DOI: 10.1063/1.1829036

Understanding the Surface Potential of Water
journal, April 2011

  • Kathmann, Shawn M.; Kuo, I-Feng William; Mundy, Christopher J.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 15
  • DOI: 10.1021/jp1116036

The Free Energy of Hydration of Gaseous Ions, and the Absolute Potential of the Normal Calomel Electrode
journal, February 1939

  • Latimer, Wendell M.; Pitzer, Kenneth S.; Slansky, Cyril M.
  • The Journal of Chemical Physics, Vol. 7, Issue 2
  • DOI: 10.1063/1.1750387

Nonlocal Dielectric Saturation in Liquid Water
journal, November 1997


Solvation effect on conformations of 1,2:dimethoxyethane: Charge-dependent nonlinear response in implicit solvent models
journal, January 2008

  • Jha, Abhishek K.; Freed, Karl F.
  • The Journal of Chemical Physics, Vol. 128, Issue 3
  • DOI: 10.1063/1.2815764

Molecular Interactions in Solution: An Overview of Methods Based on Continuous Distributions of the Solvent
journal, November 1994

  • Tomasi, Jacopo; Persico, Maurizio
  • Chemical Reviews, Vol. 94, Issue 7
  • DOI: 10.1021/cr00031a013

Electrostatics in biomolecular structure and dynamics
journal, May 1990

  • Davis, Malcolm E.; McCammon, J. Andrew
  • Chemical Reviews, Vol. 90, Issue 3
  • DOI: 10.1021/cr00101a005

Incorporating Dipolar Solvents with Variable Density in Poisson-Boltzmann Electrostatics
journal, December 2008


Solvation of complex molecules in a polar liquid: An integral equation theory
journal, June 1996

  • Beglov, Dmitrii; Roux, Benoît
  • The Journal of Chemical Physics, Vol. 104, Issue 21
  • DOI: 10.1063/1.471557

Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
journal, September 2011

  • Bardhan, Jaydeep P.; Knepley, Matthew G.
  • The Journal of Chemical Physics, Vol. 135, Issue 12
  • DOI: 10.1063/1.3641485

Reevaluation of the Born model of ion hydration
journal, December 1985

  • Rashin, Alexander A.; Honig, Barry
  • The Journal of Physical Chemistry, Vol. 89, Issue 26
  • DOI: 10.1021/j100272a006

Nonlinear response effects in continuum models of the hydration of ions
journal, February 2002

  • Sandberg, Lars; Edholm, Olle
  • The Journal of Chemical Physics, Vol. 116, Issue 7
  • DOI: 10.1063/1.1435566

Accurate Evaluation of Electrostatics for Macromolecules in Solution
journal, January 2003

  • Chern, I-Liang; Liu, Jian-Guo; Wang, Wei-Cheng
  • Methods and Applications of Analysis, Vol. 10, Issue 2
  • DOI: 10.4310/MAA.2003.v10.n2.a9

Evolving interfaces via gradients of geometry-dependent interior Poisson problems: application to tumor growth
journal, February 2005


Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation
journal, February 1994

  • Zhou, Huan‐Xiang
  • The Journal of Chemical Physics, Vol. 100, Issue 4
  • DOI: 10.1063/1.466406

Dipolar Poisson-Boltzmann Equation: Ions and Dipoles Close to Charge Interfaces
journal, August 2007


Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
journal, September 1990

  • Sharp, Kim A.; Honig, Barry.
  • The Journal of Physical Chemistry, Vol. 94, Issue 19
  • DOI: 10.1021/j100382a068

Estimation of Absolute Free Energies of Hydration Using Continuum Methods:  Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions
journal, November 2005

  • Rizzo, Robert C.; Aynechi, Tiba; Case, David A.
  • Journal of Chemical Theory and Computation, Vol. 2, Issue 1
  • DOI: 10.1021/ct050097l

Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions
journal, July 1934

  • Kirkwood, John G.
  • The Journal of Chemical Physics, Vol. 2, Issue 7
  • DOI: 10.1063/1.1749489

Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
journal, August 2008

  • Gong, H.; Hocky, G.; Freed, K. F.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 32
  • DOI: 10.1073/pnas.0804506105

Novel Formulation of Nonlocal Electrostatics
journal, September 2004


Interpreting the Coulomb-field approximation for generalized-Born electrostatics using boundary-integral equation theory
journal, October 2008

  • Bardhan, Jaydeep P.
  • The Journal of Chemical Physics, Vol. 129, Issue 14
  • DOI: 10.1063/1.2987409

Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations
journal, June 1997

  • Nina, Mafalda; Beglov, Dmitri; Roux, Benoît
  • The Journal of Physical Chemistry B, Vol. 101, Issue 26
  • DOI: 10.1021/jp970736r

Numerical solution of boundary-integral equations for molecular electrostatics
journal, March 2009

  • Bardhan, Jaydeep P.
  • The Journal of Chemical Physics, Vol. 130, Issue 9
  • DOI: 10.1063/1.3080769

Dynamical model of oscillatory zoning in plagioclase with nonlinear partition relation
journal, January 1996

  • L'Heureux, Ivan; Fowler, Anthony D.
  • Geophysical Research Letters, Vol. 23, Issue 1
  • DOI: 10.1029/95GL03327

Nonlocal nonlinear static dielectric response of polar liquids
journal, June 1998


A phenomenological and extended continuum approach for modelling non-equilibrium flows
journal, July 2007

  • Mizzi, S.; Barber, R. W.; Emerson, D. R.
  • Continuum Mechanics and Thermodynamics, Vol. 19, Issue 5
  • DOI: 10.1007/s00161-007-0054-9

Nonlinear Poisson Equation for Heterogeneous Media
journal, August 2012


Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions
journal, June 2011

  • Lin, Bin; Wong, Ka-Yiu; Hu, Char
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 13
  • DOI: 10.1021/jz200609v

Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
journal, February 1994

  • Sitkoff, Doree; Sharp, Kim A.; Honig, Barry
  • The Journal of Physical Chemistry, Vol. 98, Issue 7
  • DOI: 10.1021/j100058a043

Charge Hydration Asymmetry: The Basic Principle and How to Use It to Test and Improve Water Models
journal, August 2012

  • Mukhopadhyay, Abhishek; Fenley, Andrew T.; Tolokh, Igor S.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 32
  • DOI: 10.1021/jp305226j

Langevin-Debye Model for Nonlinear Electrostatic Screening of Solvated Ions
journal, February 2009


On the Theory of Strong Electrolyte Solutions
journal, November 1934

  • Kirkwood, John G.
  • The Journal of Chemical Physics, Vol. 2, Issue 11
  • DOI: 10.1063/1.1749393

Electrostatic models in the theory of solutions
journal, January 1976

  • Kharkats, Yu. I.; Kornyshev, A. A.; Vorotyntsev, M. A.
  • Journal of the Chemical Society, Faraday Transactions 2, Vol. 72
  • DOI: 10.1039/f29767200361

Convergence of Molecular and Macroscopic Continuum Descriptions of Ion Hydration
journal, August 2000

  • Ashbaugh, Henry S.
  • The Journal of Physical Chemistry B, Vol. 104, Issue 31
  • DOI: 10.1021/jp0015067

Ueber Wärmeleitung in verdünnten Gasen
journal, January 1898


Gradient models in molecular biophysics: progress, challenges, opportunities
journal, January 2013

  • Bardhan, Jaydeep P.
  • Journal of the Mechanical Behavior of Materials, Vol. 22, Issue 5-6
  • DOI: 10.1515/jmbm-2013-0024

Nonlocal continuum electrostatic theory predicts surprisingly small energetic penalties for charge burial in proteins
journal, September 2011

  • Bardhan, Jaydeep P.
  • The Journal of Chemical Physics, Vol. 135, Issue 10
  • DOI: 10.1063/1.3632995

Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies
journal, June 2009

  • Purisima, Enrico O.; Sulea, Traian
  • The Journal of Physical Chemistry B, Vol. 113, Issue 24
  • DOI: 10.1021/jp9020799

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
journal, July 1983

  • Brooks, Bernard R.; Bruccoleri, Robert E.; Olafson, Barry D.
  • Journal of Computational Chemistry, Vol. 4, Issue 2
  • DOI: 10.1002/jcc.540040211

Biomolecular electrostatics—I want your solvation (model)
journal, January 2012


A fast solver for nonlocal electrostatic theory in biomolecular science and engineering
conference, January 2011

  • Bardhan, Jaydeep P.; Hildebrandt, Andreas
  • Proceedings of the 48th Design Automation Conference on - DAC '11
  • DOI: 10.1145/2024724.2024904

Rapid Prediction of Solvation Free Energy. 2. The First-Shell Hydration (FiSH) Continuum Model
journal, April 2010

  • Corbeil, Christopher R.; Sulea, Traian; Purisima, Enrico O.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 5
  • DOI: 10.1021/ct9006037

The electric potential of a macromolecule in a solvent: A fundamental approach
journal, November 1991

  • Juffer, AndréH; Botta, Eugen F. F.; van Keulen, Bert A. M.
  • Journal of Computational Physics, Vol. 97, Issue 1
  • DOI: 10.1016/0021-9991(91)90043-K

Electrostatic Interactions in Macromolecules: Theory and Applications
journal, June 1990


Unravelling the solvent response to neutral and charged solutes
journal, January 2007


On the origin of the electrostatic potential difference at a liquid-vacuum interface
journal, December 2008

  • Harder, Edward; Roux, Benoît
  • The Journal of Chemical Physics, Vol. 129, Issue 23
  • DOI: 10.1063/1.3027513

Adaptive Finite Element Modeling Techniques for the Poisson-Boltzmann Equation
journal, January 2012


Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies
journal, September 2012

  • Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee
  • The Journal of Chemical Physics, Vol. 137, Issue 12
  • DOI: 10.1063/1.4752735

Implicit solvent models
journal, April 1999


Field strength dependence of dielectric saturation in liquid water
journal, November 1990

  • Alper, Howard E.; Levy, Ronald M.
  • The Journal of Physical Chemistry, Vol. 94, Issue 22
  • DOI: 10.1021/j100385a008

Symmetry breaking in induced-charge electro-osmosis over polarizable spheroids
journal, June 2007

  • Yossifon, G.; Frankel, I.; Miloh, T.
  • Physics of Fluids, Vol. 19, Issue 6
  • DOI: 10.1063/1.2746847

Variational Implicit Solvation with Poisson–Boltzmann Theory
journal, March 2014

  • Zhou, Shenggao; Cheng, Li-Tien; Dzubiella, Joachim
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 4
  • DOI: 10.1021/ct401058w

An Accurate Surface Formulation for Biomolecule Electrostatics in Non-Ionic Solutions
conference, January 2005

  • Altman, M. D.; Bardhan, J. P.; White, J. K.
  • 2005 IEEE Engineering in Medicine and Biology 27th Annual Conference
  • DOI: 10.1109/IEMBS.2005.1616269

Free Energy of Ionic Hydration
journal, January 1996

  • Hummer, Gerhard; Pratt, Lawrence R.; García, Angel E.
  • The Journal of Physical Chemistry, Vol. 100, Issue 4
  • DOI: 10.1021/jp951011v

Introducing Charge Hydration Asymmetry into the Generalized Born Model
journal, March 2014

  • Mukhopadhyay, Abhishek; Aguilar, Boris H.; Tolokh, Igor S.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 4
  • DOI: 10.1021/ct4010917

Evaluation of Hydration Free Energy by Level-Set Variational Implicit-Solvent Model with Coulomb-Field Approximation
journal, February 2013

  • Guo, Zuojun; Li, Bo; Dzubiella, Joachim
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 3
  • DOI: 10.1021/ct301087w

The AGBNP2 Implicit Solvation Model
journal, July 2009

  • Gallicchio, Emilio; Paris, Kristina; Levy, Ronald M.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 9
  • DOI: 10.1021/ct900234u