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arXiv · 2201.00890

The Effect of Off-Center $\sigma$-Hole on the Atom-Centered Partial Charges in Halogenated Molecules

Aneta Leskourová·Michal H. Kolář
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Abstract

Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the $\sigma$-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the $\sigma$-hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the Restricted Electrostatic Potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The $\sigma$-hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.

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Aneta Leskourová, Michal H. Kolář. 2022-01-03. The Effect of Off-Center $\sigma$-Hole on the Atom-Centered Partial Charges in Halogenated Molecules. https://arxiv.org/abs/2201.00890

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