A Kirkwood−Buff Derived Force Field for Thiols, Sulfides, and Disulfides

Bentenitis, Nikolaos; Cox, Nicholas; Smith, Paul E.

doi:10.1021/jp904806f

Cited by 29 publications

(37 citation statements)

References 34 publications

(115 reference statements)

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“…81,91,94,[96][97][98][99][100][101] The results showed that without introducing polarization good agreement with experimental KB data can be obtained. The present study demonstrated that the polarizable Drude force field, which was not developed by targeting experimental KB data, can also achieve almost the same degree of accuracy compared to KBFF, except for activity derivative and excess Gibbs free energy, which will be the focus in our future force field optimization efforts.…”

Section: Discussionsupporting

confidence: 55%

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

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Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

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Section: Discussionsupporting

confidence: 55%

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin

Lopes

Roux

et al. 2013

The Journal of Chemical Physics

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“…Details of the force fields are provided elsewhere. [28][29][30][31] All mixtures were simulated with enough molecules to occupy a cubic box of length of Ϸ6 nm, starting from random initial configurations, and were simulated for between 10 and 20 ns.…”

Section: Methodsmentioning

confidence: 99%

“…Similar trends are observed for mixtures of TOL/MOH, MSH/ MOH, and MSM/MOH. 29,30 Mixtures of BEN/TOL and, to some extent, MSH/MSM would be expected to display close to ideal behavior. In contrast, the behavior of BEN/MSH mixtures would be more difficult to predict using basic chemical principles.…”

Section: Molecular Dynamics Simulations Of Symmetric Ideal Solutionsmentioning

confidence: 99%

Kirkwood–Buff integrals for ideal solutions

Ploetz

Bentenitis²,

Smith³

2010

The Journal of Chemical Physics

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The Kirkwood-Buff ͑KB͒ theory of solutions is a rigorous theory of solution mixtures which relates the molecular distributions between the solution components to the thermodynamic properties of the mixture. Ideal solutions represent a useful reference for understanding the properties of real solutions. Here, we derive expressions for the KB integrals, the central components of KB theory, in ideal solutions of any number of components corresponding to the three main concentration scales. The results are illustrated by use of molecular dynamics simulations for two binary solutions mixtures, benzene with toluene, and methanethiol with dimethylsulfide, which closely approach ideal behavior, and a binary mixture of benzene and methanol which is nonideal. Simulations of a quaternary mixture containing benzene, toluene, methanethiol, and dimethylsulfide suggest this system displays ideal behavior and that ideal behavior is not limited to mixtures containing a small number of components.

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“…More details can be found in our recent studies [27,28]. All mixtures are simulated via classical molecular dynamics techniques using the Gromacs program (version 3.3) [29].…”

Section: Simulation Detailsmentioning

confidence: 99%

Developing force fields from the microscopic structure of solutions

Ploetz

Bentenitis

Smith

2010

Fluid Phase Equilibria

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We have been developing force fields designed for the eventual simulation of peptides and proteins using the Kirkwood-Buff (KB) theory of solutions as a guide. KB theory provides exact information on the relative distributions for each species present in solution. This information can also be obtained from computer simulations. Hence, one can use KB theory to help test and modify the parameters commonly used in biomolecular studies. A series of small molecule force fields representative of the fragments found in peptides and proteins have been developed. Since this approach is guided by the KB theory, our results provide a reasonable balance in the interactions between self-association of solutes and solute solvation. Here, we present our progress to date. In addition, our investigations have provided a wealth of data concerning the properties of solution mixtures, which is also summarized. Specific examples of the properties of aromatic (benzene, phenol, p-cresol) and sulfur compounds (methanethiol, dimethylsulfide, dimethyldisulfide) and their mixtures with methanol or toluene are provided as an illustration of this kind of approach.

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A Kirkwood−Buff Derived Force Field for Thiols, Sulfides, and Disulfides

Cited by 29 publications

References 34 publications

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Kirkwood–Buff integrals for ideal solutions

Developing force fields from the microscopic structure of solutions

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