Prediction of the <i>n</i>‐hexane/water and 1‐octanol/water partition coefficients for environmentally relevant compounds using molecular simulation

Garrido, Nuno M.; Economou, Ioannis G.; Queimada, António J.; Jorge, Miguel; Macedo, Eugénia A.

doi:10.1002/aic.12718

Cited by 49 publications

(52 citation statements)

References 74 publications

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“…By contrast, the partition coefficients for cyclohexane/water partitioning are 1–1.5 log P units skewed in favor of partitioning into water for the most hydrophilic quinone, which may be due to the non-polarizable nature of the force field not accounting for the induced dipoles and quadrupoles in hexane or cyclohexane brought about by the quinone. The magnitude of the error is similar to that found in computational measures of other species which would induce dipoles, such as chlorinated benzene rings in a fixed-charge force field (61, 62). These cases are also found to partition too favorably into water (61, 62).…”

Section: Resultssupporting

confidence: 72%

Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center ofRhodobacter sphaeroides

et al. 2015

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Ubiquinone forms an integral part of the electron transport chain in cellular respiration and photosynthesis across a vast number of organisms. Prior experimental results have shown that the photosynthetic reaction center (RC) from Rhodobacter sphaeroides is only fully functional with a limited set of methoxy-bearing quinones, suggesting that specific interactions with this substituent are required to drive electron transport and the formation of quinol. The nature of these interactions has yet to be determined. Through parameterization of a CHARMM-compatible quinone force field and subsequent molecular dynamics simulations of the quinone-bound RC, we have investigated and characterized the protein interactions with the quinones in the QA and QB sites using both equilibrium simulation and thermodynamic integration. In particular, we identify a specific interaction between the 2-methoxy group of ubiquinone in the QB site and the amide nitrogen of GlyL225 that we implicate in locking the orientation of the 2-methoxy group, thereby tuning the redox potential difference between the quinones occupying the QA and QB sites. Disruption of this interaction leads to weaker binding in a ubiquinone analog that lacks a 2-methoxy group, a finding supported by reverse electron transfer EPR experiments of the QA−QB− biradical and competitive binding assays.

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Section: Resultssupporting

confidence: 72%

Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center ofRhodobacter sphaeroides

et al. 2015

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“…The same force field was used by Garrido et al [32] to predict 1-hexanol/water and 1-octanol/water partition functions for the same chlorobenzenes in agreement with experimental results.…”

Section: Introductionsupporting

confidence: 76%

Prediction of diffusion coefficients of chlorophenols in water by computer simulation

Martins

Parreira

Ramalho

et al. 2015

Fluid Phase Equilibria

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A B S T R A C TIntra-diffusion coefficients of seven chlorophenols (2-chlorophenol, 3-chlorophenol, 4-chlorophenol, 2,4-dichlorophenol, 2,6-dichlorophenol, 2,4,6-dichlorophenol and pentachlorophenol) in water were determined by computer simulation (molecular dynamics) for dilute solutions at three different temperatures and the corresponding mutual diffusion coefficients estimated. The mutual diffusion coefficients of 2-chlorophenol in water agree with the available experimental results from the literature for all the temperatures studied. From the dependence of the diffusion coefficients on temperature, diffusion activation energies were estimated for all the solutes in water. Analyzing the radial distribution functions and spatial distribution functions of water around chlorophenols sites enable a discussion about intermolecular interactions (dominated by hydrogen bonding) between solute and solvent and its importance on the relative magnitude of diffusion coefficients. Finally the mutual diffusion coefficients obtained by simulation were correlated by the well-known Wilke-Chang equation.

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“…Details of the computational procedure were given in the first paper of this series [17], as well as in previous publications [20][21][22][23][24][25]. Briefly, solvation free energies were calculated by the thermodynamic integration (TI) method [26] based on a series of molecular dynamics (MD) simulations carried out using the GROMACS software [27].…”

Section: -Computational Methodsmentioning

confidence: 99%

Predicting hydrophobic solvation by molecular simulation: 2. New united‐atom model for alkanes, alkenes, and alkynes

Jorge

2016

J Comput Chem

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This version is available at https://strathprints.strath.ac.uk/59034/ Strathprints is designed to allow users to access the research output of the University of Strathclyde. Unless otherwise explicitly stated on the manuscript, Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Please check the manuscript for details of any other licences that may have been applied. You may not engage in further distribution of the material for any profitmaking activities or any commercial gain. You may freely distribute both the url (https://strathprints.strath.ac.uk/) and the content of this paper for research or private study, educational, or not-for-profit purposes without prior permission or charge.Any correspondence concerning this service should be sent to the Strathprints administrator: strathprints@strath.ac.ukThe Strathprints institutional repository (https://strathprints.strath.ac.uk) is a digital archive of University of Strathclyde research outputs. It has been developed to disseminate open access research outputs, expose data about those outputs, and enable the management and persistent access to Strathclyde's intellectual output. Predicting Hydrophobic Solvation by Molecular Simulation: 2. New United-atom Model for Alkanes, Alkenes and AlkynesMiguel Jorge* Department of Chemical and Process Engineering, University of Strathclyde, 75 MontroseStreet, Glasgow G1 1XJ, United Kingdom Email -miguel.jorge@strath.ac.uk Abstract: Existing united-atom models for non-polar hydrocarbons lead to systematic deviations in predicted solvation free energies in hydrophobic solvents. In this paper, an improved set of parameters is proposed for alkane molecules that corrects this systematic deviation and accurately predicts solvation free energies in hydrophobic media, while simultaneously providing a very good description of pure liquid densities. The model is then extended to alkenes and alkynes, again yielding very accurate predictions of solvation free energies and densities for these classes of compounds. For alkynes in particular, this work represents the first attempt at a systematic parameterization using the united-atom approach. Averaging over all 95 solute/solvent pairs tested, the mean signed deviation from experimental data is very close to zero, indicating no systematic error in the predictions. The fact that predictions are robust even for relatively large molecules suggests that the new model may be applicable to solvation of non-polar macromolecules without accumulation of errors. The root mean squared deviation of the simulations is only 0.6 kJ/mol, which is lower than the estimated uncertainty in the experimental measurements. This excellent performance constitutes a solid basis upon which a more general model can be parameterized to describe solvation in both polar and non-polar environments.Keywords: Solubility; Molecular Simulation; hydrocarbons; non-polar; free energy -IntroductionPredicting solvation in hydrophobic environments is r...

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Prediction of the n‐hexane/water and 1‐octanol/water partition coefficients for environmentally relevant compounds using molecular simulation

Cited by 49 publications

References 74 publications

Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center ofRhodobacter sphaeroides

Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center ofRhodobacter sphaeroides

Prediction of diffusion coefficients of chlorophenols in water by computer simulation

Predicting hydrophobic solvation by molecular simulation: 2. New united‐atom model for alkanes, alkenes, and alkynes

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