Abstract
Application of a small radius of the hydrogen atom in molecular-mechanical models of hydrogen bonding improves the estimate of the solvation free energy of organic substances. At the same time, the density and evaporation heat of the bulk water vary slightly and are close to experimental values. Blind testing drug candidates in the SAMPL6 simulation competition showed that using the same Lennard-Jones hydrogen parameters for the hydroxyl, hydroxycarbonyl, amino, and amide groups is enough to predict log P octanol–water with MAE 0.67 and RMSD 0.75.
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Acknowledgements
The author is grateful to Yuri Kravatsky for providing computer resources. This work has been carried out with the financial support of the Molecular and Cellular Biology Program of the Russian Academy of Sciences under award number 01201456592 and by grant of the Russian Foundation for Basic Research under award number 1804-01376.
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Nikitin, A. Non-zero Lennard-Jones parameters for the Toukan–Rahman water model: more accurate calculations of the solvation free energy of organic substances. J Comput Aided Mol Des 34, 437–441 (2020). https://doi.org/10.1007/s10822-019-00256-2
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DOI: https://doi.org/10.1007/s10822-019-00256-2