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J Chem Inf Model. 2018 Mar 26;58(3):579-590. doi: 10.1021/acs.jcim.7b00663. Epub 2018 Mar 7.

Machine Learning of Partial Charges Derived from High-Quality Quantum-Mechanical Calculations.

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Laboratory of Physical Chemistry , ETH Zurich , Vladimir-Prelog-Weg 2 , 8093 Zurich , Switzerland.


Parametrization of small organic molecules for classical molecular dynamics simulations is not trivial. The vastness of the chemical space makes approaches using building blocks challenging. The most common approach is therefore an individual parametrization of each compound by deriving partial charges from semiempirical or ab initio calculations and inheriting the bonded and van der Waals (Lennard-Jones) parameters from a (bio)molecular force field. The quality of the partial charges generated in this fashion depends on the level of the quantum-chemical calculation as well as on the extraction procedure used. Here, we present a machine learning (ML) based approach for predicting partial charges extracted from density functional theory (DFT) electron densities. The training set was chosen with the goal to provide a broad coverage of the known chemical space of druglike molecules. In addition to the speed of the approach, the partial charges predicted by ML are not dependent on the three-dimensional conformation in contrast to the ones obtained by fitting to the electrostatic potential (ESP). To assess the quality and compatibility with standard force fields, we performed benchmark calculations for the free energy of hydration and liquid properties such as density and heat of vaporization.

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