Rescaling of Point Charges as a Way to Improve the Simple-to-Use Electrostatic Embedding Scheme Developed to Explore Enzyme Activity with QM-Oriented Software

Computer-aided exploration of enzymatic reactions, which still leaves many important questions open, calls for robust and accurate techniques of molecular modeling. One of the most intriguing issues related to enzymatic reactions is the role of electrostatic interactions established between the reacting moiety and its enzymatic environment. In order to evaluate these interactions, we previously devised a QM/MM scheme based on electrostatic embedding of the reaction kernel, treated by quantum chemistry, into the enzymatic surroundings represented by point charges [A. Prah et al., ACS Catal. 2019, 9, 1231.]. The method features remarkable simplicity and reliably predicts the effect of electrostatics on enzyme catalysis. Yet, this simplified approach has pitfalls; in particular, it tends to overestimate the attracting force between the electrons and the surrounding point chargesan effect named electron spill-outimpairing the accuracy of evaluated electrostatic interactions. Herein, by using statistical methods together with reference quantum calculations, we critically assess the impact of this pitfall and propose a very simple but effective correction based on attenuation of point charges near the QM–MM boundary depending on their distance from the quantum subsystem. We demonstrate that the proposed correction can significantly improve the accuracy of computed energies of electrostatic interactions between the reaction kernel and its enzyme surroundings, thereby representing an important methodological advance of our electrostatic embedding approach. Noteworthily, the optimal attenuation scheme can vary among the considered systemsin particular, it is sensitive to the net charge of the reaction kernelsuggesting the scheme be tuned individually for each considered enzymatic reaction following the presented workflow.