Predicting Accurate Solvation Free Energy in n-Octanol Using 3D-RISM-KH Molecular Theory of Solvation: Making Right Choices.

Molecular theory of solvation, a.k.a., three-dimensional reference interaction site model theory of solvation with Kovalenko-Hirata closure relation (3D-RISM-KH), is an accurate and fast theory predicting solvation free energy and structure. Here we report a benchmark study of n-octanol solvation free energy calculations using this theory. The choice of correct force field parameters is quintessential for the success of 3D-RISM theory, and we present a guideline to obtain them for n-octanol solvent. Our best prediction of the solvation free energy on a set of 205 small organic molecules supplemented with the so-called "universal correction" scheme yields relative mean unsigned error of 0.94 kcal/mol against the reported database. The best agreement is obtained with the united atom (UA) type force field parametrization of n-octanol with the van der Waals parameters of hydroxyl hydrogen reported by Kobryn et al. [ Kobryn , A. E. ; Kovalenko , A. J. Chem. Phys. 2008 , 129 , 134701 ].

[1]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[2]  M. Plesset,et al.  Note on an Approximation Treatment for Many-Electron Systems , 1934 .

[3]  Mitsuhisa Sato,et al.  Massively parallel implementation of 3D‐RISM calculation with volumetric 3D‐FFT , 2014, J. Comput. Chem..

[4]  A. Kovalenko,et al.  Molecular theory of solvation: Methodology summary and illustrations , 2015, 1510.06520.

[5]  P. Kollman,et al.  Automatic atom type and bond type perception in molecular mechanical calculations. , 2006, Journal of molecular graphics & modelling.

[6]  Maxim V Fedorov,et al.  Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction , 2010, Journal of physics. Condensed matter : an Institute of Physics journal.

[7]  J. Pople,et al.  Self‐Consistent Molecular‐Orbital Methods. IX. An Extended Gaussian‐Type Basis for Molecular‐Orbital Studies of Organic Molecules , 1971 .

[8]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[9]  Fumio Hirata,et al.  An extended rism equation for molecular polar fluids , 1981 .

[10]  A. Kovalenko,et al.  Self-consistent combination of the three-dimensional RISM theory of molecular solvation with analytical gradients and the Amsterdam density functional package. , 2006 .

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

[12]  David L. Mobley,et al.  FreeSolv: a database of experimental and calculated hydration free energies, with input files , 2014, Journal of Computer-Aided Molecular Design.

[13]  A. Kovalenko Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials , 2013 .

[14]  A. D. McLean,et al.  Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18 , 1980 .

[15]  Justin L MacCallum,et al.  Structures of neat and hydrated 1-octanol from computer simulations. , 2002, Journal of the American Chemical Society.

[16]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

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

[18]  William L. Jorgensen,et al.  Optimized intermolecular potential functions for liquid alcohols , 1986 .

[19]  T. Luchko,et al.  Small molecule hydration energy and entropy from 3D-RISM , 2016, Journal of physics. Condensed matter : an Institute of Physics journal.

[20]  H. Sun,et al.  COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds , 1998 .

[21]  Paul Labute,et al.  A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies , 2014, Journal of chemical theory and computation.

[22]  A. E. Kobryn,et al.  Molecular theory of hydrodynamic boundary conditions in nanofluidics. , 2008, The Journal of chemical physics.

[23]  A. Kovalenko,et al.  Octanol-Water Partition Coefficient from 3D-RISM-KH Molecular Theory of Solvation with Partial Molar Volume Correction. , 2015, The journal of physical chemistry. B.

[24]  Fumio Hirata,et al.  Self-consistent description of a metal–water interface by the Kohn–Sham density functional theory and the three-dimensional reference interaction site model , 1999 .

[25]  G. Hessler,et al.  The hpCADD NDDO Hamiltonian: Parametrization , 2017, J. Chem. Inf. Model..

[26]  J. Ilja Siepmann,et al.  Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols , 2001 .

[27]  Khaled M. Elbassioni,et al.  Charge Group Partitioning in Biomolecular Simulation , 2013, J. Comput. Biol..

[28]  David S. Palmer,et al.  Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. , 2015, Chemical reviews.

[29]  Michael J. Frisch,et al.  Semi-direct algorithms for the MP2 energy and gradient , 1990 .

[30]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[31]  Clemens C. J. Roothaan,et al.  New Developments in Molecular Orbital Theory , 1951 .

[32]  Maxim V Fedorov,et al.  Toward a universal model to calculate the solvation thermodynamics of druglike molecules: the importance of new experimental databases. , 2011, Molecular pharmaceutics.

[33]  A. Zhu,et al.  Molecular simulation of water/alcohol mixtures' adsorption and diffusion in zeolite 4A membranes. , 2009, The journal of physical chemistry. B.

[34]  S. L. Mayo,et al.  DREIDING: A generic force field for molecular simulations , 1990 .

[35]  Carlos Simmerling,et al.  Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. , 2010, Journal of chemical theory and computation.

[36]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[37]  B. Montgomery Pettitt,et al.  A dielectrically consistent interaction site theory for solvent—electrolyte mixtures , 1992 .

[38]  J. Pople,et al.  Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .

[39]  Pramod C. Nair,et al.  An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0. , 2011, Journal of chemical theory and computation.

[40]  C. Cramer,et al.  Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. , 2009, The journal of physical chemistry. B.

[41]  Robert J Woods,et al.  Carbohydrate force fields , 2012, Wiley interdisciplinary reviews. Computational molecular science.

[42]  S. Bruzzone,et al.  A RISM approach to the liquid structure and solvation properties of ionic liquids. , 2007, Physical chemistry chemical physics : PCCP.

[43]  T. H. Dunning Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen , 1989 .

[44]  David Chandler,et al.  Density functional theory of nonuniform polyatomic systems. I. General formulation , 1986 .

[45]  A. Kovalenko Multiscale Modeling of Solvation , 2017 .