The BGY3dM model for the approximation of solvent densities.

We present a new approach for the approximation of solvent densities around solutes of arbitrary shape. Our model represents a three-dimensional (3d) Born-Green-Yvon (BGY) equation for an arbitrary solute immersed into a molecular (M) solvent, the BGY3dM model. It comprises the famous Kirkwood approximation as closure relation. The molecules of the solvent are modeled as rigid bodies by taking the limit of an infinite restoring force for the intramolecular interactions. Furthermore, short-range potentials as well as the long-range Coulomb interaction are taken into account. The resulting integro-differential equations are efficiently solved by a Picard iteration and a solution of the linearized equations using Fourier transformations. We compare the results obtained from the presented BGY3dM method with results obtained by extensive molecular dynamics simulations for a HCl-like model solvent. Furthermore, we apply the method to carbon disulfide as solvent. The overall performance of the method is promising.

[1]  M. Taylor,et al.  Collapse of a ring polymer: Comparison of Monte Carlo and Born–Green–Yvon integral equation results , 1997 .

[2]  Hans Petter Langtangen,et al.  Modern Software Tools for Scientific Computing , 1997, Birkhäuser Boston.

[3]  H. H. Gan,et al.  Application of the integral equation theory of polymers: Distribution function, chemical potential, and mean expansion coefficient , 1993 .

[4]  H. H. Gan,et al.  Integral equations of the correlation functions for polymeric liquids , 1993 .

[5]  J. Kirkwood Statistical Mechanics of Fluid Mixtures , 1935 .

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

[7]  Fumio Hirata,et al.  Potential of Mean Force between Two Molecular Ions in a Polar Molecular Solvent: A Study by the Three-Dimensional Reference Interaction Site Model , 1999 .

[8]  Steven G. Johnson,et al.  The Design and Implementation of FFTW3 , 2005, Proceedings of the IEEE.

[9]  Jane E. G. Lipson,et al.  A BORN-GREEN-YVON EQUATION FOR FLEXIBLE CHAIN-MOLECULE FLUIDS. II: APPLICATIONS TO HARD-SPHERE POLYMERS , 1995 .

[10]  Michael Griebel,et al.  Numerical Simulation in Molecular Dynamics: Numerics, Algorithms, Parallelization, Applications , 2007 .

[11]  Benoît Roux,et al.  An Integral Equation To Describe the Solvation of Polar Molecules in Liquid Water , 1997 .

[12]  William Gropp,et al.  Modern Software Tools in Scientific Computing , 1994 .

[13]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[14]  William Gropp,et al.  Efficient Management of Parallelism in Object-Oriented Numerical Software Libraries , 1997, SciTools.

[15]  Benoît Roux,et al.  NUMERICAL SOLUTION OF THE HYPERNETTED CHAIN EQUATION FOR A SOLUTE OF ARBITRARY GEOMETRY IN THREE DIMENSIONS , 1995 .

[16]  Fumio Hirata,et al.  Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method , 2000 .

[17]  Tamar Schlick,et al.  New Algorithms for Macromolecular Simulation , 2006 .

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

[19]  F. Hirata,et al.  Three-dimensional density profiles of water in contact with a solute of arbitrary shape: a RISM approach , 1998 .

[20]  F. Hirata,et al.  Hydration structure and stability of Met-enkephalin studied by a three-dimensional reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method , 2000 .

[21]  Fumio Hirata,et al.  Potentials of mean force of simple ions in ambient aqueous solution. I. Three-dimensional reference interaction site model approach , 2000 .

[22]  Jane E. G. Lipson,et al.  Collapse of a polymer chain: A Born–Green–Yvon integral equation study , 1996 .

[23]  A. Alastuey,et al.  Decay of correlations in classical fluids with long-range forces , 1985 .

[24]  Ericka Stricklin-Parker,et al.  Ann , 2005 .

[25]  J. Luettmer-Strathmann,et al.  Structure and phase behavior of square-well dimer fluids , 2001 .

[26]  B. Montgomery Pettitt,et al.  Application of an extended RISM equation to dipolar and quadrupolar fluids , 1982 .

[27]  P. Attard An improved kirkwood superposition approximation for three atoms in rolling contact , 1991 .

[28]  J. Fischer,et al.  Classical multicomponent fluid structure near solid substrates : born-green-yvon equation versus density-functional theory , 1990 .

[29]  G. W. Robinson,et al.  Molecular dynamics simulation of liquid carbon disulphide with a harmonic intramolecular potential , 1988 .

[30]  B. Roux,et al.  Solvation Free Energy of Polar and Nonpolar Molecules in Water: An Extended Interaction Site Integral Equation Theory in Three Dimensions , 2000 .

[31]  Jane E. G. Lipson,et al.  A Born-Green-Yvon equation for flexible chain-molecule fluids. I. General formalism and numerical results for short hard-sphere chains , 1995 .

[32]  Phil Attard,et al.  Polymer Born–Green–Yvon equation with proper triplet superposition approximation. Results for hard‐sphere chains , 1995 .

[33]  H. H. Gan,et al.  Integral equation theory of single-chain polymers: Comparison with simulation data for hard-sphere and square-well chains , 1999 .

[34]  A. Singer,et al.  Maximum entropy formulation of the Kirkwood superposition approximation. , 2004, The Journal of chemical physics.

[35]  M. Ikeguchi,et al.  Direct numerical solution of the Ornstein–Zernike integral equation and spatial distribution of water around hydrophobic molecules , 1995 .

[36]  T. Truong,et al.  Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach , 2000 .

[37]  Jane E. G. Lipson,et al.  A site–site Born–Green–Yvon equation for hard sphere dimers , 1994 .

[38]  Fumio Hirata,et al.  Potentials of mean force of simple ions in ambient aqueous solution. II. Solvation structure from the three-dimensional reference interaction site model approach, and comparison with simulations , 2000 .

[39]  David Chandler,et al.  Optimized Cluster Expansions for Classical Fluids. II. Theory of Molecular Liquids , 1972 .