Nonlocal Poisson-Fermi model for ionic solvent.

We propose a nonlocal Poisson-Fermi model for ionic solvent that includes ion size effects and polarization correlations among water molecules in the calculation of electrostatic potential. It includes the previous Poisson-Fermi models as special cases, and its solution is the convolution of a solution of the corresponding nonlocal Poisson dielectric model with a Yukawa-like kernel function. The Fermi distribution is shown to be a set of optimal ionic concentration functions in the sense of minimizing an electrostatic potential free energy. Numerical results are reported to show the difference between a Poisson-Fermi solution and a corresponding Poisson solution.

[1]  M. A. Vorotyntsev,et al.  Model nonlocal electrostatics. II. Spherical interface , 1978 .

[2]  G. Burton Sobolev Spaces , 2013 .

[3]  Dexuan Xie,et al.  A new analysis of electrostatic free energy minimization and Poisson–Boltzmann equation for protein in ionic solvent , 2015 .

[4]  J L Sussman,et al.  Acetylcholinesterase: electrostatic steering increases the rate of ligand binding. , 1993, Biochemistry.

[5]  Bo Li,et al.  Minimization of Electrostatic Free Energy and the Poisson-Boltzmann Equation for Molecular Solvation with Implicit Solvent , 2009, SIAM J. Math. Anal..

[6]  New Computational Models for Electrostatics of Macromolecules in Solvents , 2006, IEEE Transactions on Magnetics.

[7]  B. Eisenberg Crowded Charges in Ion Channels , 2010, 1009.1786.

[8]  Philippe H. Hünenberger,et al.  Single-Ion Solvation , 2011 .

[9]  Bopp,et al.  Static nonlocal dielectric function of liquid water. , 1996, Physical review letters.

[10]  Jie Liang,et al.  Ionizable side chains at catalytic active sites of enzymes , 2012, European Biophysics Journal.

[11]  Andreas Hildebrandt,et al.  A new numerical method for nonlocal electrostatics in biomolecular simulations , 2010, J. Comput. Phys..

[12]  Jinn-Liang Liu,et al.  Numerical methods for the Poisson-Fermi equation in electrolytes , 2013, J. Comput. Phys..

[13]  Hans-Peter Lenhof,et al.  Electrostatic potentials of proteins in water: a structured continuum approach , 2007, Bioinform..

[14]  G. Kontogeorgis,et al.  Thermodynamic Models for Industrial Applications: From Classical and Advanced Mixing Rules to Association Theories , 2010 .

[15]  M. Gilson,et al.  Prediction of pH-dependent properties of proteins. , 1994, Journal of molecular biology.

[16]  G. Tresset Generalized Poisson-Fermi formalism for investigating size correlation effects with multiple ions. , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[17]  Nathan A. Baker,et al.  Poisson-Boltzmann Methods for Biomolecular Electrostatics , 2004, Numerical Computer Methods, Part D.

[18]  Jinn-Liang Liu,et al.  Poisson-Fermi model of single ion activities in aqueous solutions , 2015 .

[19]  B. Eisenberg A Leading Role for Mathematics in the Study of Ionic Solutions , 2012 .

[20]  Dexuan Xie,et al.  A Modified Nonlocal Continuum Electrostatic Model for Protein in Water and Its Analytical Solutions for Ionic Born Models , 2013 .

[21]  Jinyong Ying,et al.  Analytical solutions of nonlocal Poisson dielectric models with multiple point charges inside a dielectric sphere. , 2016, Physical review. E.

[22]  Ludmil Zikatanov,et al.  Mathematical models for the deformation of electrolyte droplets , 2007 .

[23]  Jinn-Liang Liu,et al.  Correlated ions in a calcium channel model: a Poisson-Fermi theory. , 2013, The journal of physical chemistry. B.

[24]  L. Ridgway Scott,et al.  Efficient Algorithms for a Nonlocal Dielectric Model for Protein in Ionic Solvent , 2013, SIAM J. Sci. Comput..

[25]  Godehard Sutmann,et al.  NONLOCAL DIELECTRIC SATURATION IN LIQUID WATER , 1997 .

[26]  Dexuan Xie,et al.  New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics , 2014, J. Comput. Phys..

[27]  D. Whiffen Thermodynamics , 1973, Nature.

[28]  M. Shimizu [Electrolyte solutions]. , 2019, [Kango] Japanese journal of nursing.

[29]  W. Marsden I and J , 2012 .

[30]  J. Barthel,et al.  Physical Chemistry of Electrolyte Solutions: Modern Aspects , 1998 .

[31]  R. Ehrenberg Genes & cells: Octopus adjusts RNA to water temp: Tweaks to genetic messenger offer efficient way to adapt , 2012 .

[32]  Simon Sherman,et al.  Influence of the solvent structure on the electrostatic interactions in proteins. , 2004, Biophysical journal.

[33]  Andreas Hildebrandt,et al.  Biomolecules in a structured solvent : a novel formulation of nonlocal electrostatics and its numerical solution , 2005 .

[34]  A. Kornyshev,et al.  Double layer in ionic liquids: overscreening versus crowding. , 2010, Physical review letters.

[35]  C. A. Kraus The present status of the theory of electrolytes , 1938 .

[36]  N. Shah,et al.  About Pure and Applied Mathematics , 2018 .

[37]  Maria M. Reif,et al.  Single-ion solvation : experimental and theoretical approaches to elusive thermodynamic quantities , 2011 .

[38]  Nathan A. Baker,et al.  Biomolecular electrostatics and solvation: a computational perspective , 2012, Quarterly Reviews of Biophysics.

[39]  M K Gilson,et al.  Energetics of charge–charge interactions in proteins , 1988, Proteins.

[40]  Patrice Koehl,et al.  AQUASOL: An efficient solver for the dipolar Poisson-Boltzmann-Langevin equation. , 2010, The Journal of chemical physics.

[41]  J. H. Robertson,et al.  The chemical physics of solvation. Part A: Theory of solvation edited by R. R. Dogonadze, E. Kalman, A. A. Kornyshev and J. Ulstrup , 1986 .

[42]  H. D. Patton,et al.  The brain and neural function , 1979 .

[43]  Ariel Fernández,et al.  Continuum equations for dielectric response to macro-molecular assemblies at the nano scale , 2004 .

[44]  Yi Jiang,et al.  A Fast Solver for a Nonlocal Dielectric Continuum Model , 2012, SIAM J. Sci. Comput..

[45]  A. Kornyshev,et al.  Effect of Overscreening on the Localization of Hydrated Electrons , 2001 .

[46]  A. L. Horvath Handbook of aqueous electrolyte solutions : physical properties, estimation, and correlation methods , 1985 .

[47]  V. Vlachy Ionic effects beyond Poisson-Boltzmann theory. , 2003, Annual review of physical chemistry.

[48]  F. Young Biochemistry , 1955, The Indian Medical Gazette.

[49]  YunKyong Hyon,et al.  Energy variational analysis of ions in water and channels: Field theory for primitive models of complex ionic fluids. , 2010, The Journal of chemical physics.

[50]  Masaya Nagai,et al.  The intermolecular stretching vibration mode in water isotopes investigated with broadband terahertz time-domain spectroscopy , 2009 .

[51]  Shenggao Zhou,et al.  Ionic size effects: generalized Boltzmann distributions, counterion stratification and modified Debye length , 2013, Nonlinearity.

[52]  Christian D Santangelo Computing counterion densities at intermediate coupling. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[53]  W. Fawcett Liquids, Solutions, and Interfaces: From Classical Macroscopic Descriptions to Modern Microscopic Details , 2004 .

[54]  Malcolm E. Davis,et al.  Electrostatics in biomolecular structure and dynamics , 1990 .

[55]  Mikhail V. Basilevsky,et al.  Nonlocal continuum solvation model with exponential susceptibility kernels , 1998 .

[56]  D. Fraenkel Computing excess functions of ionic solutions: the smaller-ion shell model versus the primitive model. 1. Activity coefficients. , 2015, Journal of chemical theory and computation.

[57]  Helen Pearson Protein engineering: The fate of fingers , 2008, Nature.

[58]  Chun Liu,et al.  An Introduction of Elastic Complex Fluids: An Energetic Variational Approach , 2009 .

[59]  Yi Jiang,et al.  A nonlocal modified Poisson-Boltzmann equation and finite element solver for computing electrostatics of biomolecules , 2016, J. Comput. Phys..

[60]  Hyunjoong Kim,et al.  Functional Analysis I , 2017 .

[61]  W. Kunz Specific Ion Effects , 2009 .

[62]  Udo Kaatze,et al.  Hydrogen network fluctuations and dielectric spectrometry of liquids , 2002 .

[63]  Y. Levin,et al.  Electrostatic correlations: from plasma to biology , 2002 .

[64]  S. Subramaniam,et al.  Treatment of electrostatic effects in proteins: Multigrid‐based newton iterative method for solution of the full nonlinear poisson–boltzmann equation , 1994, Proteins.

[65]  Nathan A. Baker,et al.  Improving implicit solvent simulations: a Poisson-centric view. , 2005, Current opinion in structural biology.

[66]  Y. C. Zhou,et al.  Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes II: size effects on ionic distributions and diffusion-reaction rates. , 2011, Biophysical journal.

[67]  M. Muir Physical Chemistry , 1888, Nature.

[68]  Maik Moeller,et al.  Introduction to Electrodynamics , 2017 .

[69]  B. Eisenberg Interacting ions in biophysics: real is not ideal. , 2013, Biophysical journal.

[70]  B. Li,et al.  Continuum electrostatics for ionic solutions with non-uniform ionic sizes , 2009 .

[71]  Joseph F. Zemaitis,et al.  Handbook of aqueous electrolyte thermodynamics : theory & application , 1986 .

[72]  F. Namavar,et al.  Effect of the ordered interfacial water layer in protein complex formation: A nonlocal electrostatic approach. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[73]  M. N. Levy,et al.  Berne & Levy Physiology , 1998 .

[74]  D. Gillespie A review of steric interactions of ions: Why some theories succeed and others fail to account for ion size , 2015 .

[75]  Roberto Cammi,et al.  Continuum solvation models in chemical physics : from theory to applications , 2007 .

[76]  Frank W. Newell,et al.  Physiology and Biophysics , 1966 .

[77]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[78]  Jinn-Liang Liu,et al.  Numerical methods for a Poisson-Nernst-Planck-Fermi model of biological ion channels. , 2015, Physical review. E, Statistical, nonlinear, and soft matter physics.

[79]  Roderick MacKinnon,et al.  Energetic optimization of ion conduction rate by the K+ selectivity filter , 2001, Nature.

[80]  Buyukdagli Sahin,et al.  Nonlocal and nonlinear electrostatics of a dipolar Coulomb fluid , 2014, Journal of physics. Condensed matter : an Institute of Physics journal.

[81]  D. Boda Monte Carlo Simulation of Electrolyte Solutions in Biology: In and Out of Equilibrium , 2014 .

[82]  H. Brooks,et al.  Medical physiology , 1961 .

[83]  M. A. Vorotyntsev,et al.  Model nonlocal electrostatics. I , 1978 .

[84]  Jinn-Liang Liu,et al.  Poisson-Nernst-Planck-Fermi theory for modeling biological ion channels. , 2014, The Journal of chemical physics.

[85]  Ricardo M. Pytkowicz,et al.  Activity coefficients in electrolyte solutions , 1979 .

[86]  Jinn-Liang Liu,et al.  Analytical models of calcium binding in a calcium channel. , 2014, The Journal of chemical physics.

[87]  R Blossey,et al.  Novel formulation of nonlocal electrostatics. , 2004, Physical review letters.