Determination of solvation free energies by adaptive expanded ensemble molecular dynamics.

A new method of calculating absolute free energies is presented. It was developed as an extension to the expanded ensemble molecular dynamics scheme and uses probability density estimation to continuously optimize the expanded ensemble parameters. The new method is much faster as it removes the time-consuming and expertise-requiring step of determining balancing factors. Its efficiency and accuracy are demonstrated for the dissolution of three qualitatively very different chemical species in water: methane, ionic salts, and benzylamine. A recently suggested optimization scheme by Wang and Landau [Phys. Rev. Lett. 86, 2050 (2001)] was also implemented and found to be computationally less efficient than the proposed adaptive expanded ensemble method.

[1]  Sven P. Jacobsson,et al.  Solubility of Organic Compounds in Water/Octanol Systems. A Expanded Ensemble Molecular Dynamics Simulation Study of log P Parameters , 2001 .

[2]  Yizhak Marcus,et al.  Thermodynamics of solvation of ions. Part 5.—Gibbs free energy of hydration at 298.15 K , 1991 .

[3]  S. Nosé.  A molecular dynamics method for simulations in the canonical ensemble , 1984 .

[4]  P. A. Bash,et al.  Free energy calculations by computer simulation. , 1987, Science.

[5]  Rahman,et al.  Molecular-dynamics study of atomic motions in water. , 1985, Physical review. B, Condensed matter.

[6]  William L. Jorgensen,et al.  Gas‐phase and liquid‐state properties of esters, nitriles, and nitro compounds with the OPLS‐AA force field , 2001, J. Comput. Chem..

[7]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[8]  Arieh Ben-Naim,et al.  Solvation thermodynamics of nonionic solutes , 1984 .

[9]  Molecular Simulation of Phase Equilibria for Water−n-Butane and Water−n-Hexane Mixtures , 2000 .

[10]  R. Lynden-Bell,et al.  Chemical potentials of water and organic solutes in imidazolium ionic liquids: a simulation study , 2002 .

[11]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[12]  Charles L. Brooks,et al.  λ‐dynamics: A new approach to free energy calculations , 1996 .

[13]  P Buchwald,et al.  Octanol-water partition: searching for predictive models. , 1998, Current medicinal chemistry.

[14]  William L. Jorgensen,et al.  Optimized intermolecular potential functions for liquid hydrocarbons , 1984 .

[15]  D. Chipman.  Computation of p K a from Dielectric Continuum Theory , 2002 .

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

[17]  G. Torrie,et al.  Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .

[18]  Alexander P. Lyubartsev,et al.  Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study , 1994 .

[19]  Christian Bartels,et al.  Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations , 1997 .

[20]  A. Lyubartsev,et al.  New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles , 1992 .

[21]  K. Heinzinger.  Computer simulations of aqueous electrolyte solutions , 1985 .

[22]  M. Mezei.  Polynomial path for the calculation of liquid state free energies from computer simulations tested on liquid water , 1992 .

[23]  J. Banavar,et al.  Computer Simulation of Liquids , 1988 .

[24]  William L. Jorgensen,et al.  OPLS ALL-ATOM MODEL FOR AMINES : RESOLUTION OF THE AMINE HYDRATION PROBLEM , 1999 .

[25]  Lee,et al.  New Monte Carlo algorithm: Entropic sampling. , 1993, Physical review letters.

[26]  Mark E. Tuckerman,et al.  Reversible multiple time scale molecular dynamics , 1992 .

[27]  Gerrit Schüürmann.  Prediction of Henry's law constant of benzene derivatives using quantum chemical continuum‐solvation models , 2000 .

[28]  William L. Jorgensen,et al.  Perfluoroalkanes: Conformational Analysis and Liquid-State Properties from ab Initio and Monte Carlo Calculations , 2001 .

[29]  J. Andrew McCammon,et al.  Calculations of Relative Hydration Free Energies: A Comparative Study Using Thermodynamic Integration and an Extrapolation Method Based on a Single Reference State , 2000 .

[30]  Berg,et al.  Multicanonical ensemble: A new approach to simulate first-order phase transitions. , 1992, Physical review letters.

[31]  Gregory C. Rutledge,et al.  Chemical potential of model benzene fluids using expanded ensemble Monte Carlo simulations , 1999 .

[32]  M. Mezei.  Adaptive umbrella sampling: Self-consistent determination of the non-Boltzmann bias , 1987 .

[33]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[34]  T. Straatsma,et al.  Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations , 1988 .

[35]  Peter A. Kollman,et al.  FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .

[36]  Expanded ensemble Monte Carlo calculations of free energy for closed, stretched and confined lattice polymers , 1999 .

[37]  William L. Jorgensen,et al.  Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes , 1998 .

[38]  D. Landau,et al.  Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.

[39]  Shuichi Nosé,et al.  Constant-temperature molecular dynamics , 1990 .

[40]  D. Beveridge,et al.  Free energy via molecular simulation: applications to chemical and biomolecular systems. , 1989, Annual review of biophysics and biophysical chemistry.

[41]  Arup K. Ghose,et al.  Estimating aqueous solvation and lipophilicity of small organic molecules: A comparative overview of atom/group contribution methods , 2000 .

[42]  R. Hooft,et al.  An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol , 1992 .

[43]  Hoover,et al.  Canonical dynamics: Equilibrium phase-space distributions. , 1985, Physical review. A, General physics.

[44]  Peter T. Cummings,et al.  Quantitative comparison and optimization of methods for evaluating the chemical potential by molecular simulation , 1997 .

[45]  Peter A. Kollman,et al.  Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method qualitative estimates of free energy changes , 1997, J. Comput. Chem..

[46]  A. Izenman.  Review Papers: Recent Developments in Nonparametric Density Estimation , 1991 .