Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution

Journal of Chemical Information and Modeling
Kara E RanaghanAdrian J Mulholland

Abstract

Combined quantum mechanics/molecular mechanics (QM/MM) methods are increasingly widely utilized in studies of reactions in enzymes and other large systems. Here, we apply a range of QM/MM methods to investigate the Claisen rearrangement of chorismate to prephenate, in solution, and in the enzyme chorismate mutase. Using projector-based embedding in a QM/MM framework, we apply treatments up to the CCSD(T) level. We test a range of density functional QM/MM methods and QM region sizes. The results show that the calculated reaction energetics are significantly more sensitive to the choice of density functional than they are to the size of the QM region in these systems. Projector-based embedding of a wave function method in DFT reduced the 13 kcal/mol spread in barrier heights calculated at the DFT/MM level to a spread of just 0.3 kcal/mol, essentially eliminating dependence on the functional. Projector-based embedding of correlated ab initio methods provides a practical method for achieving high accuracy for energy profiles derived from DFT and DFT/MM calculations for reactions in condensed phases.

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Citations

May 17, 2019·The Journal of Chemical Physics·Moritz Bensberg, Johannes Neugebauer
Jul 9, 2020·Journal of Computational Chemistry·Oscar A Douglas-GallardoEsteban Vöhringer-Martinez
Jun 10, 2019·The Journal of Chemical Physics·Moritz Bensberg, Johannes Neugebauer
Jun 27, 2019·Physical Chemistry Chemical Physics : PCCP·Bodee NuthoThanyada Rungrotmongkol
Feb 20, 2021·Organic & Biomolecular Chemistry·Reynier SuardíazAdrian J Mulholland
Mar 1, 2020·Current Opinion in Structural Biology·Benjamin R JaggerAdrian J Mulholland
Mar 6, 2021·The Journal of Physical Chemistry. a·Giovanni MacettiAlessandro Genoni
Jul 1, 2021·The Journal of Physical Chemistry. a·Giovanni Macetti, Alessandro Genoni
May 20, 2020·Journal of Chemical Theory and Computation·Moritz Bensberg, Johannes Neugebauer
May 28, 2019·Journal of Chemical Information and Modeling·Habibah A WahabZoe Cournia
Jan 31, 2020·Journal of Chemical Theory and Computation·Nicolás O FogliaDarío A Estrin
Jan 7, 2022·Journal of Chemical Information and Modeling·Narin LawanPimchai Chaiyen

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