Leskourová Aneta, Kolář Michal H
Department of Physical Chemistry, University of Chemistry and Technology, Prague, Czech Republic.
J Comput Chem. 2022 May 5;43(12):864-869. doi: 10.1002/jcc.26841. Epub 2022 Mar 17.
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 -hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the -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 -hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.
部分原子电荷属于计算化学的关键概念。然而，在某些情况下，它们在描述分子静电学方面存在不足。一个这样的例子是σ-空穴，即位于卤素和其他原子上的正静电势区域。在分子力学中，σ-空穴通常被建模为一个位于卤素原子核外、带有正部分电荷的伪原子。在此我们提出一个问题，即该伪原子在多大程度上影响分子中其他原子的部分电荷。为此，我们全面分析了ZINC数据库中2300多个卤代分子通过受限静电势（RESP）方法计算得到的部分电荷，并将它们与包含伪原子的RESP拟合电荷进行了比较。我们表明，伪原子改善了绝大多数分子的电荷拟合。被建模为偏心电荷的σ-空穴会影响距离卤素三个共价键范围内的原子。
