Disclosure of Key Stereoelectronic Factors for Efficient H₂ Binding and Cleavage in the Active Site of [NiFe]-Hydrogenases

Abstract

A comparative analysis of a series of DFT models of [NiFe]-hydrogenases, ranging from minimal NiFe clusters to very large systems including both the first and second coordination sphere of the bimetallic cofactor, was carried out with the aim of unraveling which stereoelectronic properties of the active site of [NiFe]-hydrogenases are crucial for efficient H2 binding and cleavage. H2 binding to the Ni-SIa redox state is energetically favored (by 4.0 kcal mol(-1)) only when H2 binds to Ni, the NiFe metal cluster is in a low spin state, and the Ni cysteine ligands have a peculiar seesaw coordination geometry, which in the enzyme is stabilized by the protein environment. The influence of the Ni coordination geometry on the H2 binding affinity was then quantitatively evaluated and rationalized analyzing frontier molecular orbitals and populations. Several plausible reaction pathways leading to H2 cleavage were also studied. It turned out that a two-step pathway, where H2 cleavage takes place on the Ni-SIa redox state of the enzyme, is characterized by very low reaction barriers and favorable reaction energies. More importantly, the seesaw coordination geometry of Ni was found to be a key feature for facile H2 cleavage. The discovery of the crucial influence of the Ni coordination geometry on H2 binding and activation in the active site of [NiFe]-hydrogenases could be exploited in the design of novel biomimetic synthetic catalysts.

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation

“…Notwithstanding the significant experimental and theoretical studies applied to the mechanism of [NiFe(Se)]-hydrogenases, definitive experimental evidence for the site of H 2 binding is lacking, though most models support Ni in this function [89,90]. Reaction intermediates isolated under catalytic conditions have been modeled into a mechanism of activation, but many of the details are unresolved [6,118,120,121].…”

“…5) [122]. Alternatively, experimental and theoretical models propose initial H 2 binding and activation can occur at the Fe site, when the Ni is modeled as high spin Ni II [120,121,123]. Cleavage is proposed to result in PT to one of the coordinating thiolate or selenate groups, and subsequently to nearby conserved Glu [116].…”

A Threonine Stabilizes the NiC and NiR Catalytic Intermediates of [NiFe]-hydrogenase

“…The proposed catalytic cycle of the enzymes involves three intermediates (NiSI, NiC, and NiR) that have only been detected under non-catalytic conditions (2,4). The most commonly accepted mechanism suggests that H 2 binds the nickel ion in the NiSI state to yield NiR (both are in the Ni(II) state) (5). NiR would contain a Ni-Fe bridging hydride ligand.…”

“…Several proton pathways have nonetheless been proposed on the basis of crystallographic and theoretical studies (10 -17). In standard [NiFe]-hydrogenases from Desulfovibrio species, some of the proposed pathways start with a Glu residue L in the large subunit 5 of the Desulfovibrio fructosovorans (Df) 6 enzyme). An alternative pathway not involving this Glu and starting with an Arg is proposed in a study of the [NiFe] enzyme from Thiocapsa roseopersicina (17).…”

“…To address the role of Thr-18 S , we studied the kinetic (H 2 production/oxidation and HDE reactions), spectroscopic (EPR, 5 A residue X is noted X L or X S when it is located in the large or in the small subunit, respectively. 6 The abbreviations used are: Df, D. fructosovorans; PT, proton transfer; HDE, H/D exchange.…”