Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes

To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory...

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Published inPeerJ physical chemistry Vol. 2; p. e8
Main Authors Sirirak, Jitnapa, Lawan, Narin, Van der Kamp, Marc W., Harvey, Jeremy N., Mulholland, Adrian J.
Format Journal Article
LanguageEnglish
Published PeerJ Inc 20.05.2020
Subjects
Biochemical Modeling
Enzyme-Catalyzed Reactions
Quantum Chemical Methods
Reaction energy calculation
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Abstract To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol −1 , respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol −1 ), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol −1 ). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.
AbstractList To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol−1, respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol−1), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol−1). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.
To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent chemical steps catalyzed by commonly studied enzymes) were calculated. The methods tested included several popular Density Functional Theory (DFT) functionals, second-order Møller Plesset perturbation theory (MP2) and its spin-component scaled variant (SCS-MP2), and coupled cluster singles and doubles and perturbative triples (CCSD(T)). Different basis sets were tested. CCSD(T)/aug-cc-pVTZ results for all 20 reactions were used to benchmark the other methods. It was found that MP2 and SCS-MP2 reaction energy calculation results are similar in quality to CCSD(T) (mean absolute error (MAE) of 1.2 and 1.3 kcal mol −1 , respectively). MP2 calculations gave a large error in one case, and are more subject to basis set effects, so in general SCS-MP2 calculations are a good choice when CCSD(T) calculations are not feasible. Results with different DFT functionals were of reasonably good quality (MAEs of 2.5–5.1 kcal mol −1 ), whereas popular semi-empirical methods (AM1, PM3, SCC-DFTB) gave much larger errors (MAEs of 11.6–14.6 kcal mol −1 ). These results should be useful in guiding methodological choices and assessing the accuracy of QM/MM calculations on enzyme-catalyzed reactions.
ArticleNumber e8
Author Van der Kamp, Marc W.
Mulholland, Adrian J.
Lawan, Narin
Harvey, Jeremy N.
Sirirak, Jitnapa
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  fullname: Sirirak, Jitnapa
  organization: Department of Chemistry, Faculty of Science, Silpakorn University, Nakhon Pathom, Thailand
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  givenname: Narin
  surname: Lawan
  fullname: Lawan, Narin
  organization: Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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  organization: School of Biochemistry, University of Bristol, Bristol, United Kingdom
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  givenname: Jeremy N.
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  organization: Department of Chemistry, KU Leuven, Leuven, Belgium
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  givenname: Adrian J.
  surname: Mulholland
  fullname: Mulholland, Adrian J.
  organization: Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
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Snippet To assess the accuracy of different quantum mechanical methods for biochemical modeling, the reaction energies of 20 small model reactions (chosen to represent...
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SubjectTerms Biochemical Modeling
Enzyme-Catalyzed Reactions
Quantum Chemical Methods
Reaction energy calculation
Title Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes
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