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Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

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Abstract

All-atom molecular dynamics simulations were used to predict water-cyclohexane distribution coefficients \(D_{cw}\) of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in \(\log D_{cw}\) of almost 4 log units and an overall signed error of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental \(D_{cw}\) data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.

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Acknowledgments

OB was supported in part by Grant ACI-1443054 from the National Science Foundation. BII was supported in part by Grants ANR-10-LABX-33 (LabEx LERMIT) and ANR-14-JAMR-0002-03 (JPIAMR) from the French National Research Agency (ANR).

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Authors and Affiliations

  1. Department of Physics, Arizona State University, P.O. Box 871504, Tempe, AZ, 85287-1504, USA

    Ian M. Kenney & Oliver Beckstein

  2. Center for Biological Physics, Arizona State University, P.O. Box 871504, Tempe, AZ, 85287-1504, USA

    Oliver Beckstein

  3. Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette, France

    Bogdan I. Iorga

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  1. Ian M. Kenney
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  2. Oliver Beckstein
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Correspondence to Oliver Beckstein or Bogdan I. Iorga.

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Kenney, I.M., Beckstein, O. & Iorga, B.I. Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. J Comput Aided Mol Des 30, 1045–1058 (2016). https://doi.org/10.1007/s10822-016-9949-5

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