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

Dominique A. Wappett, Lars Goerigk

2023Journal of Chemical Theory and Computation56 citationsDOIOpen Access PDF

Abstract

)-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.

Topics & Concepts

Benchmark (surveying)BenchmarkingDensity functional theoryBasis setSet (abstract data type)Range (aeronautics)Computer scienceDispersion (optics)Statistical physicsComputational chemistryChemistryPhysicsMaterials scienceQuantum mechanicsGeographyMarketingGeodesyComposite materialBusinessProgramming languageEnzyme Structure and FunctionMetalloenzymes and iron-sulfur proteinsEnzyme Catalysis and Immobilization
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