On the role of density fluctuations in the entropy of a fluid

Wallace, Duane C.

doi:10.1063/1.453158

Cited by 173 publications

(149 citation statements)

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“…29,[51][52][53][54] Here, we focus on the lower order terms, as these are relatively tractable computationally and are expected, based in part on prior applications of IST (see Introduction), to capture much of the physics; higher order terms will be examined in future studies. Subsections II A 1 and II A 2 briefly review IST in order to define notation and provide a basis for the discretization methodology.…”

Section: A Inhomogeneous Solvation Theorymentioning

confidence: 99%

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

Nguyen

Young²,

Gilson³

2012

The Journal of Chemical Physics

302

506

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The displacement of perturbed water upon binding is believed to play a critical role in the thermodynamics of biomolecular recognition, but it is nontrivial to unambiguously define and answer questions about this process. We address this issue by introducing grid inhomogeneous solvation theory (GIST), which discretizes the equations of inhomogeneous solvation theory (IST) onto a threedimensional grid situated in the region of interest around a solute molecule or complex. Snapshots from explicit solvent simulations are used to estimate localized solvation entropies, energies, and free energies associated with the grid boxes, or voxels, and properly summing these thermodynamic quantities over voxels yields information about hydration thermodynamics. GIST thus provides a smoothly varying representation of water properties as a function of position, rather than focusing on hydration sites where solvent is present at high density. It therefore accounts for full or partial displacement of water from sites that are highly occupied by water, as well as for partly occupied and water-depleted regions around the solute. GIST can also provide a well-defined estimate of the solvation free energy and therefore enables a rigorous end-states analysis of binding. For example, one may not only use a first GIST calculation to project the thermodynamic consequences of displacing water from the surface of a receptor by a ligand, but also account, in a second GIST calculation, for the thermodynamics of subsequent solvent reorganization around the bound complex. In the present study, a first GIST analysis of the molecular host cucurbit [7]uril is found to yield a rich picture of hydration structure and thermodynamics in and around this miniature receptor. One of the most striking results is the observation of a toroidal region of high water density at the center of the host's nonpolar cavity. Despite its high density, the water in this toroidal region is disfavored energetically and entropically, and hence may contribute to the known ability of this small receptor to bind guest molecules with unusually high affinities. Interestingly, the toroidal region of high water density persists even when all partial charges of the receptor are set to zero. Thus, localized regions of high solvent density can be generated in a binding site without strong, attractive solute-solvent interactions.

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Section: A Inhomogeneous Solvation Theorymentioning

confidence: 99%

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

Nguyen

Young²,

Gilson³

2012

The Journal of Chemical Physics

302

506

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“…As discussed earlier the excess entropy S ex , defined as the difference between the total entropy (S total ) and the ideal gas entropy (S id ) at the same temperature (T ) and density (ρ), can also be expanded in an infinite series, S ex = S 2 + S 3 + ..... = S 2 + ∆S using Kirkwood factorization 44 of the N-particle distribution function [45][46][47] . S n is the "n" body contribution to the entropy.…”

Section: Excess Entropymentioning

confidence: 99%

Determination of onset temperature from the entropy for fragile to strong liquids

Banerjee

Nandi

Sastry

et al. 2017

The Journal of Chemical Physics

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In this paper we establish a connection between the onset temperature of glassy dynamics with the change in the entropy for a wide range of model systems. We identify the crossing temperature of pair and excess entropies as the onset temperature. Below the onset temperature, the residual multiparticle entropy(RMPE), the difference between excess and pair entropies, becomes positive. The positive entropy can be viewed as equivalent to the larger phase space exploration of the system. The new method of onset temperature prediction from entropy is less ambiguous, as it does not depend on any fitting parameter like the existing methods. Our study also reveals the connection between fragility and the degree of breakdown of the Stokes Einstein (SE) relation.

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“…This factorization leads to an expression of the excess entropy that can be truncated at the two body correlation function which contains the information of both the relative position and orientation of two molecules (details can be found in the literature [14][15][16][17][18][19] and the ESI † ). Even in the simple case of two-body correlations there is still the need to calculate the correlation function for 6 variables.…”

Section: Introductionmentioning

confidence: 99%

The structure of liquid water beyond the first hydration shell

Henao

Büsch

Guàrdia

et al. 2016

Phys. Chem. Chem. Phys.

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There is to date a general consensus on the structure of the first coordination shells of liquid water, namely a tetrahedral short range order of the molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules, and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about ∼6 Å: from a predominantly orientational order at shorter distances to a regime at larger distances of up to ∼9 Å where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.

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On the role of density fluctuations in the entropy of a fluid

Cited by 173 publications

References 2 publications

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

Determination of onset temperature from the entropy for fragile to strong liquids

The structure of liquid water beyond the first hydration shell

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