Electronic Structure Topology Associated Domain is Useful to Minimize the Uncertainty of QM/MM Boundary Charge Transfer Effects

TL;DR

This paper introduces a community-structure-based method using graph theory to identify and minimize charge transfer effects at QM/MM boundaries, improving simulation convergence in protein studies.

Contribution

It proposes the charge transfer topology associated domain (ctTAD) as a novel tool to systematically reduce boundary charge transfer effects in QM/MM simulations.

Findings

ctTAD effectively identifies significant charge transfer regions.

Using ctTAD improves convergence with minimal additional computational cost.

The method offers a new perspective on QM/MM boundary treatment.

Abstract

The charge transfer effect is an important component in the physical description of realistic proteins. In the hybrid quantum mechanical-molecular mechanical (QM/MM) simulations, the significant charge transfer between the QM/MM boundaries could lead to the slow convergence problem with very large QM regions. In this work, we will discuss how community structure in complex network (electronic structure topology associated domain) can be used to measure QM/MM boundary effects and how it can provide a different perspective on well established concepts in available QM/MM simulations. The graph theory is employed to provide an useful solution to distinguish the significant charge transfer regions between the core active site and the surrounding protein environment in the QM/MM simulations. According to community detection algorithm for complex network, the charge transfer topology associated domain (ctTAD) is suggested to provide an alternative tool for systematically minimizing the charge transfer effects of QM/MM boundary with minor computational costs.