Flexible-boundary QM/MM calculations: II. Partial charge transfer across the QM/MM boundary that passes through a covalent bond

Abstract

Recently, based on the principle of electronic chemical potential equalization and the principle of charge conservation, we proposed a flexible-boundary scheme that allows both partial charge transfer and self-consistent polarization between the quantum mechanical (QM) and molecular mechanical (MM) subsystems in QM/MM calculations; the scheme was applied to study the atomic charges in selected ion–solvent complexes. In the present contribution, we further extend the flexible-boundary treatment to handle the QM/MM boundary passing through covalent bonds. We find that the flexible-boundary redistributed charge and dipole schemes yield reasonable agreement with full-QM calculations for a number of molecular ions and amino acids with charged side chains. Using the full-QM results as reference, the mean unsigned deviations are computed to be 0.06 e for atomic partial charges of the QM atoms, 0.11 e for the amounts of charge transfer between the QM and MM subsystems, and 0.016 A for the lengths of the covalent bonds that directly connect the QM and MM subsystems. The results indicate the importance of accounting for partial charge transfer across the QM/MM boundary when the QM subsystems are charged.