Computing the electrostatic free-energy of complex molecules: The variational Coulomb field approximation

We introduce a novel approximate electrostatic method yielding the electrostatic fields around a molecule of complex shape embedded in a continuum dielectric solvent and the electrostatic solvation free-energies. This method extends the widely used Coulomb field approximation by supposing that the dielectric displacement can be written as the Coulomb field created by a set of fictitious “image” charges placed on the solute atomic sites. The electrostatic problem is solved by minimizing a polarization density functional with respect to the image charges. The method presents computational advantages which are reminiscent to those of the Coulomb field approximation; in particular, the solvation free-energy can be cast into a form which requires only the evaluation of space integrals limited to the interior of the solute. Its accuracy is demonstrated for simple solutes in water, ion pairs, the Tanford–Kirkwood globular protein model, and small polypeptides. It is shown also that our approach provides a system...

[1]  W. Im,et al.  Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .

[2]  D. Chandler,et al.  GAUSSIAN FIELD MODEL OF DIELECTRIC SOLVATION DYNAMICS , 1996 .

[3]  Alexander A. Rashin,et al.  Hydration phenomena, classical electrostatics, and the boundary element method , 1990 .

[4]  B. Honig,et al.  A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .

[5]  R. Zauhar,et al.  A new method for computing the macromolecular electric potential. , 1985, Journal of molecular biology.

[6]  C. Tanford,et al.  Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres , 1957 .

[7]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

[8]  Arieh Warshel,et al.  CONTINUUM AND DIPOLE-LATTICE MODELS OF SOLVATION , 1997 .

[9]  Richard A. Friesner,et al.  Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation , 1997 .

[10]  Barry Honig,et al.  Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation , 1990 .

[11]  J. Warwicker,et al.  Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.

[12]  R. Gebauer,et al.  Density functional theory of solvation in a polar solvent: extracting the functional from homogeneous solvent simulations. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[13]  Peter G. Wolynes,et al.  Classical solvent dynamics and electron transfer. 1. Continuum theory , 1983 .

[14]  Gregory D. Hawkins,et al.  Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium , 1996 .

[15]  Martin Karplus,et al.  A Smooth Solvation Potential Based on the Conductor-Like Screening Model , 1999 .

[16]  D. Case,et al.  Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.

[17]  J. A. McCammon,et al.  Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods , 1989 .

[18]  S. Hassan,et al.  A General Treatment of Solvent Effects Based on Screened Coulomb Potentials , 2000 .

[19]  A. Warshel,et al.  Calculations of electrostatic interactions in biological systems and in solutions , 1984, Quarterly Reviews of Biophysics.

[20]  P. Schleyer Encyclopedia of computational chemistry , 1998 .

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

[22]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[23]  M. Levitt,et al.  Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. , 1976, Journal of molecular biology.

[24]  Ernest L. Mehler,et al.  A general screened Coulomb potential based implicit solvent model: Calculation of secondary structure of small peptides , 2001 .

[25]  D. Beglov,et al.  Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations , 1997 .

[26]  M. Marchi,et al.  A dielectric continuum molecular dynamics method , 2001 .

[27]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[28]  R. Friesner,et al.  Generalized Born Model Based on a Surface Integral Formulation , 1998 .

[29]  R. Fox,et al.  Classical Electrodynamics, 3rd ed. , 1999 .

[30]  S. Hassan,et al.  A critical analysis of continuum electrostatics: The screened Coulomb potential–implicit solvent model and the study of the alanine dipeptide and discrimination of misfolded structures of proteins , 2002, Proteins.

[31]  Leslie Greengard,et al.  A fast algorithm for particle simulations , 1987 .

[32]  M. Schaefer,et al.  A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution. , 1990, Journal of molecular biology.

[33]  Simone Melchionna,et al.  Electrostatic potential inside ionic solutions confined by dielectrics: a variational approach , 2001 .

[34]  P. Procacci,et al.  A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle , 2002 .

[35]  J. Kirkwood,et al.  Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions , 1934 .

[36]  Stephen C. Harvey,et al.  Finite element approach to the electrostatics of macromolecules with arbitrary geometries , 1993, J. Comput. Chem..

[37]  J. Hynes,et al.  Time-dependent fluorescence solvent shifts, dielectric friction, and nonequilibrium solvation in polar solvents , 1985 .

[38]  J. Apostolakis,et al.  Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions , 1997 .

[39]  W. C. Still,et al.  The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .

[40]  Sangyoub Lee,et al.  Solution reaction path Hamiltonian for reactions in polar solvents. II. Applications , 1988 .

[41]  J. Hynes,et al.  Dynamical theory of proton tunneling transfer rates in solution: general formulation , 1993 .

[42]  C. Brooks,et al.  Novel generalized Born methods , 2002 .

[43]  M. Karplus,et al.  A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .

[44]  M. A. Vorotyntsev,et al.  Electrostatic models in the theory of solutions , 1976 .

[45]  A. Leach Molecular Modelling: Principles and Applications , 1996 .

[46]  B. Roux,et al.  Implicit solvent models. , 1999, Biophysical chemistry.

[47]  Rudolph A. Marcus,et al.  On the Theory of Oxidation‐Reduction Reactions Involving Electron Transfer. I , 1956 .

[48]  Arieh Warshel,et al.  Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution , 1997 .

[49]  Rudolph A. Marcus,et al.  Electrostatic Free Energy and Other Properties of States Having Nonequilibrium Polarization. I , 1956 .

[50]  Ruhong Zhou,et al.  Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .

[51]  B. U. Felderhof Fluctuations of polarization and magnetization in dielectric and magnetic media , 1977 .