Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations

Abstract

The apparently simple dihydrogen formation from protons and electrons (2H + + 2e − ⇄ H 2 ) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H 2 as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni−B and Ni−A states of the [NiFe]hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni−B and Ni−A. However, this process is sufficient to activate only the Ni−B state. H 2 binding to the active site is required to convert Ni−A to the active Ni−SI a state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni−SI r and Ni−SU species, formed respectively from the one-electron reduction of Ni−B and Ni−A. Ni−SI r , depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni−SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni−A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H 2 O and H 2 binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni−B and Ni−A states.

Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations

“…S6. † Notably, the structural optimization of the Ni r -S mOH models revealed an over-elongated bond between the Ni II ion and the bridging sulfur ligand of Cys482, 19,28,35 mOH model (Fig. 3c), in line with available crystallographic data.…”

Successes, challenges, and opportunities for quantum chemistry in understanding metalloenzymes for solar fuels research

“…Structures for the species obtained upon reduction of Ni-A and Ni-B were proposed and specific structural features were shown to impact the reactivation kinetics of the oxidized and inactive states. 331 Similarly, with [NiFe] hydrogenases, distinct mechanisms were proposed for the [FeFe] ones and differ mainly in the protonation sites and H 2 binding. Lately, computational studies together with experimental investigations seem consistent with one scenario.…”

Hydroxy-bridged Active Site States of [NiFe]-Hydrogenase Unraveled by Cryogenic Vibrational Spectroscopy and DFT Computations

“…The corresponding Nir-SµOH Cys60-SH model is shown inFig. S6.Notably, structural optimization of the Nir-SµOH models revealed an over-elongated bond between the Ni II ion and the bridging sulfur ligand of Cys482,19,28,35 whose length depended on the protonation state of the Ni-terminal cysteines. The Nir-SµOH SH , Nir-SµOH Cys60-SH and Nir-SµOH Smodels yielded Ni II •••S(Cys482) distances of 2.7, 2.8 and 3.0 Å, respectively, consistent with an essentially lost coordination.…”