Simulating nuclear and electronic quantum effects in enzymes

TL;DR

This paper discusses recent computational advancements enabling the simulation of both electronic and nuclear quantum effects in enzymes, providing detailed insights into enzymatic reactions previously computationally infeasible.

Contribution

It reviews recent algorithmic and hardware developments that make ab initio path integral molecular dynamics feasible for large biological systems.

Findings

Recent algorithms accelerate quantum simulations of enzymes

Simulations now feasible for large enzymatic systems

Enhanced understanding of enzyme reactivity mechanisms

Abstract

An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics (AIMD) simulations while the latter can be included by performing ab initio path integral molecular dynamics (AI-PIMD) simulations. Both AIMD and AI-PIMD simulations have traditionally been computationally prohibitive for large enzymatic systems. Recent developments in streaming computer architectures and new algorithms to accelerate path integral simulations now make these simulations practical for biological systems, allowing elucidation of enzymatic reactions in unprecedented detail. In this chapter, we summarize these recent developments and discuss practical considerations for applying AIMD and AI-PIMD simulations to enzymes.