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

© 2019 American Chemical Society. 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,...

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Main Authors: Kara E. Ranaghan, Darya Shchepanovska, Simon J. Bennie, Narin Lawan, Stephen J. Macrae, Jolanta Zurek, Frederick R. Manby, Adrian J. Mulholland
Format: Journal
Published: 2019
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http://cmuir.cmu.ac.th/jspui/handle/6653943832/65455
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Institution: Chiang Mai University
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spelling th-cmuir.6653943832-654552019-08-05T04:43:53Z Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution Kara E. Ranaghan Darya Shchepanovska Simon J. Bennie Narin Lawan Stephen J. Macrae Jolanta Zurek Frederick R. Manby Adrian J. Mulholland Chemical Engineering Chemistry Computer Science Social Sciences © 2019 American Chemical Society. 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. 2019-08-05T04:33:36Z 2019-08-05T04:33:36Z 2019-05-28 Journal 15205142 15499596 2-s2.0-85063146980 10.1021/acs.jcim.8b00940 https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85063146980&origin=inward http://cmuir.cmu.ac.th/jspui/handle/6653943832/65455
institution Chiang Mai University
building Chiang Mai University Library
country Thailand
collection CMU Intellectual Repository
topic Chemical Engineering
Chemistry
Computer Science
Social Sciences
spellingShingle Chemical Engineering
Chemistry
Computer Science
Social Sciences
Kara E. Ranaghan
Darya Shchepanovska
Simon J. Bennie
Narin Lawan
Stephen J. Macrae
Jolanta Zurek
Frederick R. Manby
Adrian J. Mulholland
Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution
description © 2019 American Chemical Society. 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.
format Journal
author Kara E. Ranaghan
Darya Shchepanovska
Simon J. Bennie
Narin Lawan
Stephen J. Macrae
Jolanta Zurek
Frederick R. Manby
Adrian J. Mulholland
author_facet Kara E. Ranaghan
Darya Shchepanovska
Simon J. Bennie
Narin Lawan
Stephen J. Macrae
Jolanta Zurek
Frederick R. Manby
Adrian J. Mulholland
author_sort Kara E. Ranaghan
title Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution
title_short Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution
title_full Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution
title_fullStr Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution
title_full_unstemmed Projector-Based Embedding Eliminates Density Functional Dependence for QM/MM Calculations of Reactions in Enzymes and Solution
title_sort projector-based embedding eliminates density functional dependence for qm/mm calculations of reactions in enzymes and solution
publishDate 2019
url https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85063146980&origin=inward
http://cmuir.cmu.ac.th/jspui/handle/6653943832/65455
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