Cargando…

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

[Image: see text] We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO–CC...

Descripción completa

Detalles Bibliográficos
Autores principales: Wappett, Dominique A., Goerigk, Lars
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688432/
https://www.ncbi.nlm.nih.gov/pubmed/37943578
http://dx.doi.org/10.1021/acs.jctc.3c00558
_version_ 1785152170265411584
author Wappett, Dominique A.
Goerigk, Lars
author_facet Wappett, Dominique A.
Goerigk, Lars
author_sort Wappett, Dominique A.
collection PubMed
description [Image: see text] We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO–CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob’s ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
format Online
Article
Text
id pubmed-10688432
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher American Chemical Society
record_format MEDLINE/PubMed
spelling pubmed-106884322023-12-01 Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set Wappett, Dominique A. Goerigk, Lars J Chem Theory Comput [Image: see text] We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO–CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob’s ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics. American Chemical Society 2023-11-09 /pmc/articles/PMC10688432/ /pubmed/37943578 http://dx.doi.org/10.1021/acs.jctc.3c00558 Text en © 2023 American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Wappett, Dominique A.
Goerigk, Lars
Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set
title Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set
title_full Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set
title_fullStr Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set
title_full_unstemmed Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set
title_short Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set
title_sort benchmarking density functional theory methods for metalloenzyme reactions: the introduction of the mme55 set
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10688432/
https://www.ncbi.nlm.nih.gov/pubmed/37943578
http://dx.doi.org/10.1021/acs.jctc.3c00558
work_keys_str_mv AT wappettdominiquea benchmarkingdensityfunctionaltheorymethodsformetalloenzymereactionstheintroductionofthemme55set
AT goerigklars benchmarkingdensityfunctionaltheorymethodsformetalloenzymereactionstheintroductionofthemme55set