Convergence of Kirkwood–Buff Integrals of Ideal and Nonideal Aqueous Solutions Using Molecular Dynamics Simulations

Milzetti, Jasmin; Nayar, Divya; Vegt, Nico F. A. van der

doi:10.1021/acs.jpcb.7b11831

Cited by 71 publications

(85 citation statements)

References 55 publications

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“…Recently, the activity coefficient has been computed by using a modified version of Equation (20) with empirical tail corrections to the RDF. The squares correspond to one data set extracted from [54] with the smallest error bars and that best reproduces the experimental results. For the latter, as well as for our data, the error bars are comparable to the symbol size.…”

Section: Multicomponent Systemsmentioning

confidence: 82%

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations

et al. 2018

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We present an efficient method to obtain bulk isothermal compressibilities (κ T) and Kirkwood-Buff (KB) integrals of single-and multicomponent liquids using fluctuations of the number of molecules obtained from small-sized molecular dynamics simulations. We write finite-size versions of the Ornstein-Zernike and the KB integral equations and include there finite size effects related to the statistical ensemble and the finite integration volumes required in computer simulations. Consequently, we obtain analytical expressions connecting κ T and the KB integrals in the thermodynamic limit (TL) with density fluctuations in the simulated system. We validate the method by calculating various thermodynamic quantities, including the chemical potentials of SPC/E water as a function of the density, and of aqueous urea solutions as a function of the mole fraction. The reported results are in excellent agreement with calculations obtained by using the best computational methods available, thus validating the method as a tool to compute the chemical potentials of dense molecular liquids and mixtures. Furthermore, the present method identifies conditions in which computer simulations can be effectively considered in the TL.

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Section: Multicomponent Systemsmentioning

confidence: 82%

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations

et al. 2018

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“…Here, we work with a single-component fluid and therefore the indices α and β are dropped. The use of an analytic g(r) eliminates errors due to uncertainties in RDFs obtained from molecular dynamics simulations [14,16,17]. The functions w(x) are obtained numerically in tabulated form, and the value of w(x) at any x is obtained by interpolation.…”

Section: Kb Integralsmentioning

confidence: 99%

“…It is important to note that Equations (1) and (2) are identical and yield the same KB integral provided that the subvolume V is convex and the function w(x) corresponding to the shape of V is used. Both approaches (Equation (1) and Equation (2)) have been used in molecular simulation [4][5][6]8,[14][15][16]. The advantage of using Equation (2) is that only the RDF is needed, which is usually computed from a built-in function of Molecular Dynamics software [17].…”

Section: Introductionmentioning

confidence: 99%

Kirkwood–Buff integrals of finite systems: shape effects

et al. 2018

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The Kirkwood-Buff (KB) theory provides an important connection between microscopic density fluctuations in liquids and macroscopic properties. Recently, Krüger et al. derived equations for KB integrals for finite subvolumes embedded in a reservoir. Using molecular simulation of finite systems, KB integrals can be computed either from density fluctuations inside such subvolumes, or from integrals of radial distribution functions (RDFs). Here, based on the second approach, we establish a framework to compute KB integrals for subvolumes with arbitrary convex shapes. This requires a geometric function w(x) which depends on the shape of the subvolume, and the relative position inside the subvolume. We present a numerical method to compute w(x) based on Umbrella Sampling Monte Carlo (MC). We compute KB integrals of a liquid with a model RDF for subvolumes with different shapes. KB integrals approach the thermodynamic limit in the same way: for sufficiently large volumes, KB integrals are a linear function of area over volume, which is independent of the shape of the subvolume.

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“…62−65 For a binary mixture, the thermodynamic factor can be written as 44 where c 1 is the number density of species 1. The finite-size effects of radial distribution functions are corrected for according to the work of van der Vegt and co-workers.…”

Section: Simulation Detailsmentioning

confidence: 99%

“…The finite-size effects of radial distribution functions are corrected for according to the work of van der Vegt and co-workers. 62,63 Kirkwood–Buff coefficients ( G ij ) are computed in the thermodynamic limit using the method of Krüger et al 64,65 …”

Section: Simulation Detailsmentioning

confidence: 99%

Optimizing Nonbonded Interactions of the OPLS Force Field for Aqueous Solutions of Carbohydrates: How to Capture Both Thermodynamics and Dynamics

Jamali

Westen

Moultos

et al. 2018

J. Chem. Theory Comput.

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Knowledge on thermodynamic and transport properties of aqueous solutions of carbohydrates is of great interest for process and product design in the food, pharmaceutical, and biotechnological industries. Molecular simulation is a powerful tool to calculate these properties, but current classical force fields cannot provide accurate estimates for all properties of interest. The poor performance of the force fields is mainly observed for concentrated solutions, where solute–solute interactions are overestimated. In this study, we propose a method to refine force fields, such that solute–solute interactions are more accurately described. The OPLS force field combined with the SPC/Fw water model is used as a basis. We scale the nonbonded interaction parameters of sucrose, a disaccharide. The scaling factors are chosen in such a way that experimental thermodynamic and transport properties of aqueous solutions of sucrose are accurately reproduced. Using a scaling factor of 0.8 for Lennard-Jones energy parameters (ϵ) and a scaling factor of 0.95 for partial atomic charges (q), we find excellent agreement between experiments and computed liquid densities, thermodynamic factors, shear viscosities, self-diffusion coefficients, and Fick (mutual) diffusion coefficients. The transferability of these optimum scaling factors to other carbohydrates is verified by computing thermodynamic and transport properties of aqueous solutions of d-glucose, a monosaccharide. The good agreement between computed properties and experiments suggests that the scaled interaction parameters are transferable to other carbohydrates, especially for concentrated solutions.

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Convergence of Kirkwood–Buff Integrals of Ideal and Nonideal Aqueous Solutions Using Molecular Dynamics Simulations

Cited by 71 publications

References 55 publications

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations

Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations

Kirkwood–Buff integrals of finite systems: shape effects

Optimizing Nonbonded Interactions of the OPLS Force Field for Aqueous Solutions of Carbohydrates: How to Capture Both Thermodynamics and Dynamics

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