Fully Oxidized State of the Oxygen-Tolerant [NiFe] Hydrogenase from Hydrogenophilus thermoluteolus SH: A Quantum Mechanics Cluster and Quantum Mechanics/Molecular Mechanics Study

TL;DR

This paper uses quantum mechanics to study the oxygen-tolerant [NiFe] hydrogenase enzyme, revealing structural and electronic properties that could help design better hydrogen production catalysts.

Contribution

The study identifies a spin-coupled open-shell singlet ground state and a three-center two-electron bond in the oxidized [NiFe] hydrogenase active site.

Findings

The fully oxidized [NiFe] hydrogenase ground state is a spin-coupled open-shell singlet (BS) Ni(III)Fe(III) oxidation state.

A three-center two-electron bond at the active site enhances the enzyme's stability under oxidative conditions.

QM/MM methods provide insights into suitable models for studying metalloproteins.

Abstract

The oxygen tolerance of some [NiFe] hydrogenase enzymes
is crucial
for designing efficient bioinspired catalysts for sustainable hydrogen
production and advancing renewable energy technologies. To investigate
this, we employed a quantum mechanical (QM) cluster model and quantum
mechanics/molecular mechanics (QM/MM) calculations to study the fully
oxidized state of the [NiFe]-hydrogenase from Hydrogenophilus
thermoluteolus SH. Our analysis focused on the structural
and electronic properties of the enzyme’s active site across
different spin states, including closed-shell singlet (CS, S = 0),
high-spin triplet (HS, S = 1), and open-shell singlet broken symmetry
(BS, S = 0). Using a comprehensive structural model (>300 atoms),
we identified the ground state of the fully oxidized enzyme state
to be a spin-coupled BS Ni(III)Fe(III) oxidation state, where residues
beyond the first coordination sphere primarily contribute sterically.
Notably, natural bond order calculations revealed an unusual three-center
two-electron bond at the active site, which may enhance the open-shell
ground state stability and the enzyme’s resilience under oxidative
conditions. Our comparative study of QM and QM/MM methods provides
insights into their performance, facilitating and guiding the choice
of suitable enzyme models when studying other metalloproteins.

The oxygen tolerance of some [NiFe]-hydrogenase
enzymes
is crucial for designing efficient bioinspired catalysts for sustainable
hydrogen production and advancing renewable energy technologies.

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