Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field. Kenney, I. M., Beckstein, O., & Iorga, B. I. Journal of Computer-Aided Molecular Design, 30(11):1045–1058, 2016. doi abstract bibtex All-atom molecular dynamics (MD) simulations were used to predict water-cyclohexane distribution coefficients Dcw of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the trans- ferable all-atom OPLS-AA force field, which required the derivation of new param- eters 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 per- turbation with thermodynamic integration. This protocol resulted in an overall root mean square error (RMSE) in log Dcw of almost 4 log units and an overall signed er- ror of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error sug- gests a systematic error but the experimental Dcw 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.
@article{kenney_prediction_2016,
title = {Prediction of cyclohexane-water distribution coefficients for the {SAMPL5} data set using molecular dynamics simulations with the {OPLS}-{AA} force field},
volume = {30},
doi = {10.1007/s10822-016-9949-5},
abstract = {All-atom molecular dynamics (MD) simulations were used to predict water-cyclohexane distribution coefficients Dcw of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the trans- ferable all-atom OPLS-AA force field, which required the derivation of new param- eters 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 per- turbation with thermodynamic integration. This protocol resulted in an overall root mean square error (RMSE) in log Dcw of almost 4 log units and an overall signed er- ror of −3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error sug- gests a systematic error but the experimental Dcw 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.},
number = {11},
journal = {Journal of Computer-Aided Molecular Design},
author = {Kenney, Ian M. and Beckstein, Oliver and Iorga, Bogdan I.},
year = {2016},
pages = {1045--1058},
}
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