Multiscale Modeling of Solvation

Abstract

Statistical-mechanical, reference interaction site model (RISM) molecular theory of solvation is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. Beginning with a force field of site interaction potentials between solution species, it uses a diagrammatic analysis of the solvation free energy to construct integral equations for 3-D spatial correlation functions of molecular interaction sites in the statistical-mechanical ensemble. With the solvation structure so obtained at the level of molecular simulation, 3D-RISM-KH further yields the solvation thermodynamics at once as a simple integral of the correlation functions which is obtained by performing thermodynamic integration analytically. The latter allows analytical differentiation of the free energy functional and thus self-consistent coupling in various multiscale approaches. 3D-RISM-KH has been coupled with the KS-DFT and CASSCF quantum chemistry methods in a self-consistent field description of electronic structure, geometry optimization, nanochemistry, and photochemistry in solution. The multiple time step molecular dynamics of biomolecules steered by effective solvation forces obtained from the 3D-RISM-KH theory, accelerated by the generalized solvation force extrapolation, and stabilized by the optimized isokinetic Nosé-Hoover chain (OIN) thermostat, enables gigantic outer time steps up to tens picoseconds to accurately calculate equilibrium properties.

Effective Interactions and Adsorption of Heterocyclic Aromatic Hydrocarbons in Kaolinite Organic Solutions Studied by 3D-RISM-KH Molecular Theory of Solvation

“…70 The performance and accuracy of the RISM and 3D-RISM theories is well studied and documented. 41,71 More information on the molecule−surface interactions of acridine and benzothiophene with kaolinite could be obtained in Figure 5, where the isosurfaces of the density distribution functions of N, S, and C sites of these HACs are presented. From the examination of the isosurfaces, it is clear that the bitumen fragments exhibit strong adsorption at the exposed active sites of the edges of the kaolinite nanoparticle.…”

“…Special approximations with analytical features that properly represent physical characteristics of the system, such as longrange asymptotics and short-range features of the correlation functions related to the solvation structure and thermodynamics, are used instead. In the current work, the 3D-RISM integral equation (eq 1) is complemented with the Kovalenko and Hirata (KH) closure approximation, 41,54,56,57,59 which is a combination of the so-called hypernetted chain (HNC) and the mean spherical approximation (MSA) 60 where g γ uv (r)=h γ uv (r) + 1 is the 3D density distribution function and u γ uv (r) is the 3D interaction potential between site γ of solvent "v" and the whole solute molecule "u". The interaction term, −βu γ uv (r), between solute "u" and solvent site γ is specified by a molecular force field and scaled by the inverse thermodynamic temperature β =( k B T) −1 .…”

To Pass or Not To Pass: Predicting the Blood–Brain Barrier Permeability with the 3D-RISM-KH Molecular Solvation Theory

“…23−26 A detailed description of the theory is presented elsewhere. 27−29 The 3D-RISM-KH theory describes a molecule using a six-dimensional vector composed of three positional { r } and three orientational {Θ} degrees of freedom in the molecular Ornstein–Zernike equation, developing to the pair correlation functions (PCF) of r and Θ of liquids. The 3D distribution functions of solvent interaction sites around a solute molecule of arbitrary shape are obtained from the 3D-RISM integral equation.…”

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

“…Details of 3D-RISM[16,36–38], its implementation in AmberTools[39,40], and analytic temperature derivatives[41,42], in particular, three-dimensional generalization of the analytical derivatives[43] can be found elsewhere. Here we briefly summarize the 3D-RISM theory and the use of temperature derivatives to calculate solvation energy and entropy contributions to the total solvation free energy.…”