Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method

Ishii, Yoshiki; Yamamoto, Naoki; Matubayasi, Nobuyuki; Zhang, Bin W.; Cui, Di; Levy, Ronald M.

doi:10.1021/acs.jctc.8b01309

Cited by 18 publications

(37 citation statements)

References 103 publications

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“…To implement the SS model in the context of biomolecular assembly, the simplest approach would be to apply renormalized interactions between each pair of atoms on the biomolecules. However, complications may arise from bonding and geometrical complexities of biomolecules in different configurations (83). For example, most biomolecules possesses both hydrophobic and hydrophilic regions, and extended hydrophobic regions from conformational changes induce very different local solvent structures and fluctuations than seen near hydrophilic regions.…”

Section: Discussionmentioning

confidence: 99%

Short solvent model for ion correlations and hydrophobic association

Gao

Remsing

Weeks

2020

Proc. Natl. Acad. Sci. U.S.A.

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Coulomb interactions play a major role in determining the thermodynamics, structure, and dynamics of condensed-phase systems, but often present significant challenges. Computer simulations usually use periodic boundary conditions to minimize corrections from finite cell boundaries but the long range of the Coulomb interactions generates significant contributions from distant periodic images of the simulation cell, usually calculated by Ewald sum techniques. This can add significant overhead to computer simulations and hampers the development of intuitive local pictures and simple analytic theory. In this paper, we present a general framework based on local molecular field theory to accurately determine the contributions from long-ranged Coulomb interactions to the potential of mean force between ionic or apolar hydrophobic solutes in dilute aqueous solutions described by standard classical point charge water models. The simplest approximation leads to a short solvent (SS) model, with truncated solvent–solvent and solute–solvent Coulomb interactions and long-ranged but screened Coulomb interactions only between charged solutes. The SS model accurately describes the interplay between strong short-ranged solute core interactions, local hydrogen-bond configurations, and long-ranged dielectric screening of distant charges, competing effects that are difficult to capture in standard implicit solvent models.

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Section: Discussionmentioning

confidence: 99%

Short solvent model for ion correlations and hydrophobic association

Gao

Remsing

Weeks

2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The third term takes into account the effect of solvent-solvent correlations (indirect part of the PMF), and is in this work approximated by a combined Percus-Yevick (PY)-type and hypernetted-chain (HNC)-type functional, as it has been done in previous work employing a similar strategy. 28,42,84,85…”

Section: Statistical Mechanical Expression For the Solvation Free Energy And The Energy-representation Theorymentioning

confidence: 99%

Anion–cation contrast of small molecule solvation in salt solutions

Hervø-Hansen

Heyda

Lund

et al. 2022

Phys. Chem. Chem. Phys.

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“…To circumvent the problem of dimensionality within the DFT framework, the method of energy representation was proposed. 1,2,11,13,37 In this method, the solute−solvent distribution is described with respect to the solute−solvent pair interaction v(x) of interest as…”

Section: Structural Features Of the Cavity Particlementioning

confidence: 99%

“…1−3 The endpoints DFT functional can be constructed using onedimensional solute−solvent interaction energy distributions or mixed four-dimensional (energy, position) distributions; this is a significant computational advantage as compared with using full six-dimensional (position, orientation) distributions. 11 In recent years endpoints DFT has been applied to a diverse array of problems in biophysics, polymers, and interfaces. 12,13 In this work, we provide the theoretical foundation of the endpoints DFT method.…”

Section: Introductionmentioning

confidence: 99%

Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals

2020

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Endpoints density functional theory (DFT) provides a framework for calculating the excess chemical potential of a solute in solution using solvent distribution functions obtained from both physical endpoints of a hypothetical charging process which transforms the solvent density from that of the pure liquid to the solution state. In this work, the endpoints DFT equations are formulated in terms of the indirect (solvent-mediated) contribution ω(x) to the solute–solvent potential of mean force, and their connections are established with the conventional DFT expressions which are based on the use of direct correlation functions. ω actually corresponds to the free-energy cost to move a cavity particle (a tagged solvent molecule which interacts with the other solvent molecules but not the solute) from the bulk to the configuration x of a solvent molecule relative to the solute and is a suitable variable to describe the solvent effects on the solute–solvent interactions. HNC and PY type approximations are then used to integrate the DFT charging integral involved in the exact expression for the excess chemical potential. With these approximations, molecular simulations are to be performed at the two endpoints of solute insertion: pure solvent without the solute and the solution system with the fully coupled solute–solvent interaction. An endpoints method thus utilizes the ensembles of intermolecular configurations of physical interest, which are often readily accessible with MD simulations given the present computational power. To illustrate properties of the formulation, we perform simulations of model systems consisting of a cavity particle in an aqueous solution containing a spherical hydrophobic solute of three different sizes from which ω(x) and the solute chemical potential can be calculated using endpoints DFT expressions. These are compared with corresponding results obtained using the approximations needed in order to evaluate the endpoints DFT charging integral when cavity particle simulation data is not available. We analyze a new approximation (two-points quadratic HNC) to the DFT charging integral which captures the correct behavior of the cavity distributions at both endpoints of the solute insertion. The behavior of the cavity particle in simple and complex liquids plays an important role in various theoretical treatments of the solute chemical potential. For pure Lennard-Jones fluids, the free energy to bring a cavity particle from the bulk to the center of a fluid particle is negative. However, for solutes of varying size, this is not generally true for Lennard-Jones fluids or the systems studied in this work. We carry out energetic and structural analyses of the cavity particle in aqueous solution with hydrophobic solutes of varying size and discuss the results in the context of the hydrophobic effect.

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Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method

Cited by 18 publications

References 103 publications

Short solvent model for ion correlations and hydrophobic association

Short solvent model for ion correlations and hydrophobic association

Anion–cation contrast of small molecule solvation in salt solutions

Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals

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