Recent theoretical predictions of the active site for the observed forms in the catalytic cycle of Ni-Fe hydrogenase

Abstract

Various states or forms of the active site in Ni-Fe hydrogenase, both catalytically active and inactive forms, have been identified and investigated experimentally. Until recently, the geometric structure of each form remained an open question. Several recent theoretical studies with density functional theory have attempted to redress this deficiency. In this commentary, the similarities and differences among the structures proposed by these studies will be addressed.

Probing intermediates in the activation cycle of [NiFe] hydrogenase by infrared spectroscopy: the Ni-SIr state and its light sensitivity

“…OD − ) is expected to affect slightly the values of the kinetic rates. This is in agreement with our results, supports the proposed reaction shown in Scheme 1 and further rules out processes involving a (de)protonation of a coordinating cysteine [30] or the release of a hydron located in the active site [50]. …”

“…The magnitude of the isotope effect in our experiments (kinetic isotope effect of 0.6–1.4, see the electronic supplementary material) was too small to be related to the dissociation of a single hydron species [49],3 as observed for the Ni-C to Ni-L transition [47]. This result therefore suggests that the light-induced effect is not related to a (de)protonation of a coordinating cysteine [30] or a release of a hydron located in the active site [50]. Thus, the (H/D) isotope effect observed in this work can be better explained considering the dislocation of an oxygen-based species [5, 14, 51] that has the potential to be deuterated (e.g.…”

Computational Studies of [NiFe] and [FeFe] Hydrogenases

“…In DFT studies of the mechanism for H 2 activation, this state came out as the most natural candidate for Ni a -C*. 71,81,82,85,87 Hall and co-worker used a comparison of calculated and measured IR frequencies for the CO and CN ligands to make this assignment for Ni a -C*. 86,88 They also suggested that one of the terminal cysteines is protonated.…”

The Activation of Dihydrogen

“…Computational studies on the [NiFe] active site have been performed by a number of workers [198][199][200][201][202][203][204][205][206][207][208][209][210][211][212][213][214]. Theory supports high-spin nickel [189] and suggests that the sulfur atoms of the terminal cysteine ligands act as bases in the heterolytic cleavage of dihydrogen.…”