Total correlation function integrals and isothermal compressibilities from molecular simulations

Wedberg, Rasmus; Peters, Günther H.J.; Abildskov, Jens

doi:10.1016/j.fluid.2008.07.011

Cited by 14 publications

(8 citation statements)

References 16 publications

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“…For methanol and tert -butyl alcohol, values of ln γ w for nondilute mixtures were obtained by employing an excess Gibbs energy ( G E ) model for the corresponding binary mixture. The G E models were obtained using a fluctuation solution theory , approach to analyze MD simulations of the water/methanol and water/ tert -butyl alcohol mixtures as described previously. − In this approach, the binary mixtures were simulated at a few compositions, and the pair radial distribution functions, g ij ( r ), where ij denotes the molecular pair, were calculated. The total correlation function integrals, H ij , which are defined by H i j = normalρ ∫ 0 ∞ r 2 ( g i j false( r false) − 1 ) .25em normald r were obtained by integrating the radial distribution functions.…”

Section: Methodsmentioning

confidence: 99%

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

2012

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In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method relies on determining the water content of the bulk phase and uses a combination of Kirkwood-Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme structure and flexibility.

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Section: Methodsmentioning

confidence: 99%

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

2012

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“…Other methods not relying on correction terms are also available in the literature for the calculation of the KBI. A method that is mostly used in engineering applications is the fitting of the structured part of the RDF or the KBI to obtain improved results over R-KBIs. An equivalent approach to the computation of eq (with the ω( r , R ) corresponding to the same shape as that of the subvolume) is to directly compute the particle number fluctuations in inserted sub-boxes, as suggested by Schnell et al , These methods were implemented and tested by Ganguly and van der Vegt on urea–water and methanol–water systems.…”

Section: Theorymentioning

confidence: 99%

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

2018

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The computation of Kirkwood-Buff integrals (KBIs) using molecular simulations of closed systems is challenging due to finite system-size effects. One of the problems involves the incorrect asymptotic behavior of the radial distribution function. Corrections to rectify such effects have been proposed in the literature. This study reports a systematic comparison of the proposed corrections (as given by Ganguly et al. J. Chem. Theory Comput. 2013, 9, 1347-1355 and Krüger et al. J. Phys. Chem. Lett. 2013, 4, 4-7) to assess the asymptotic behavior of the RDFs, the KBIs, as well as the estimation of thermodynamic quantities for ideal urea-water and nonideal modified-urea-water mixtures using molecular dynamics simulations. The results show that applying the KBI correction suggested by Krüger et al. on the RDF corrected with the Ganguly et al. correction (denoted as B-KBI) yields improved KBI convergence for the ideal and nonideal aqueous mixtures. Different averaging regions in the running KBIs (correlated or long-range) are assessed, and averaging over the correlated region for large system sizes is found to be robust toward the change in the degree of solvent nonideality and concentration, providing good estimates of thermodynamic quantities. The study provides new insights into improving the KBI convergence, the suitability of different averaging regions in KBIs to estimate thermodynamic properties, as well as the applicability of correction methods to achieve KBI convergence for nonideal aqueous binary mixtures.

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“…Note that this approach has only been successfully tested on pure fluids. The main limitation of both methods (Christensen et al 2007a;Christensen et al 2007b;Christensen et al 2007c;Wedberg, Peters, and Abildskov 2008) is that they apply only to systems where the TCF tails can be approximated by the model equations, which may not be true in general.…”

Section: Long Range Modelingmentioning

confidence: 99%

- Global and Local Properties of Mixtures: An Expanded Paradigm for the Study of Mixtures

2016

Fluctuation Theory of Solutions

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Total correlation function integrals and isothermal compressibilities from molecular simulations

Cited by 14 publications

References 16 publications

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

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

- Global and Local Properties of Mixtures: An Expanded Paradigm for the Study of Mixtures

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