title: Simulating Nuclear and Electronic Quantum Effects in Enzymes.
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.
authors: Rutgers University, Piscataway, NJ, United States.
authors: L
authors: L
authors: Wang
authors: School of Natural Sciences, University of California, Merced, CA, United States.
authors: C M
authors: CM
authors: Isborn
authors: Stanford University, Stanford, CA, United States. Electronic address: tmarkland@stanford.edu.
authors: T E
authors: TE
authors: Markland
mesh_terms: D000465:Algorithms; D000818:Animals; D004798:Enzymes / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D004798:Enzymes
keywords: Ab initio molecular dynamics; Density functional theory; Nuclear quantum effects; Path integral molecular dynamics; QM/MM