Benchmark of density functionals for the calculation of the redox potential of Fe3+/Fe2+ within protein coordination shells

Risnita Vicky Listyarini, Diana Sofia Gesto, Pedro Paiva, Maria João Ramos, Pedro Alexandrino Fernandes

Research output: Contribution to journalArticle

Abstract

Iron is a very important transition metal often found in proteins. In enzymes specifically, it is often found at the core of reaction mechanisms, participating in the reaction cycle, more often than not in oxidation/reduction reactions, where it cycles between its most common Fe(III)/Fe(II) oxidation states. QM and QM/MM computational methods that study these catalytic reaction mechanisms mostly use density functional theory (DFT) to describe the chemical transformations. Unfortunately, density functional is known to be plagued by system-specific and property-specific inaccuracies that cast a shadow of uncertainty over the results. Here we have modeled 12 iron coordination complexes, using ligands that represent amino acid sidechains, and calculated the accuracy with which the most common density functionals reproduce the redox properties of the iron complexes (specifically the electronic component of the redox potential at 0 K, ΔEelecFe3+/Fe2+), using the same property calculated with CCSD(T)/CBS as reference for the evaluation. A number of hybrid and hybrid-meta density functionals, generally with a large % of HF exchange (such as BB1K, mPWB1K, and mPW1B95) provided systematically accurate values for ΔEelecFe3+/Fe2+, with MUEs of ~2 kcal/mol. The very popular B3LYP density functional was found to be quite precise as well, with a MUE of 2.51 kcal/mol. Overall, the study provides guidelines to estimate the inaccuracies coming from the density functionals in the study of enzyme reaction mechanisms that involve an iron cofactor, and to choose appropriate density functionals for the study of the same reactions.

Original languageEnglish
Article number391
JournalFrontiers in Chemistry
Volume7
Issue numberJUN
DOIs
Publication statusPublished - 1 Jan 2019

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Iron
Proteins
Redox reactions
Coordination Complexes
Enzymes
Computational methods
Transition metals
Density functional theory
Ligands
Amino Acids
Oxidation
Oxidation-Reduction

Keywords

  • Benchmaking
  • DFT
  • Iron
  • Quantum-chemical calculations
  • Redox potencial

Cite this

Listyarini, Risnita Vicky ; Gesto, Diana Sofia ; Paiva, Pedro ; Ramos, Maria João ; Fernandes, Pedro Alexandrino. / Benchmark of density functionals for the calculation of the redox potential of Fe3+/Fe2+ within protein coordination shells. In: Frontiers in Chemistry. 2019 ; Vol. 7, No. JUN.
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Benchmark of density functionals for the calculation of the redox potential of Fe3+/Fe2+ within protein coordination shells. / Listyarini, Risnita Vicky; Gesto, Diana Sofia; Paiva, Pedro; Ramos, Maria João; Fernandes, Pedro Alexandrino.

In: Frontiers in Chemistry, Vol. 7, No. JUN, 391, 01.01.2019.

Research output: Contribution to journalArticle

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AU - Ramos, Maria João

AU - Fernandes, Pedro Alexandrino

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