Computational studies of the H-cluster of Fe-only hydrogenases: geometric, electronic, and magnetic properties and their dependence on the [Fe4S4] cubane.

The active sites of Fe-only hydrogenases (FeHases) feature an unusual polynuclear iron-sulfur cluster, known as the H-cluster, that consists of a [Fe4S4] cubane linked to a di-iron subunit (the [2Fe]H component) via a bridging cysteine ligand (SCys). While previous computational studies of FeHases employed H-cluster models that only included the [2Fe]H component, we have utilized density functional theory (DFT), in conjunction with the broken-symmetry (BS) approach, to explore the geometric, electronic, and magnetic properties of the entire H-cluster. These calculations have allowed us to evaluate, for the first time, the influence of the [Fe4S4] cubane on the [2Fe]H component of the H-cluster in its active (Hox) and CO-inhibited (Hox-CO) states, both of which are paramagnetic (S=1/2). Our results reveal that the presence of the cubane tunes both the position and the donor strength of the SCys ligand, which, in turn, modulates the internal geometric and electronic structures of the [2Fe]H subcluster. Importantly, the BS methodology provides an accurate description of the exchange interactions within the H-cluster, permitting insight into the electronic origin of the changes in magnetic properties observed experimentally upon conversion of Hox to Hox-CO. Specifically, while the unpaired spin density in the Hox state is localized on the distal Fe center, in the Hox-CO state, it is delocalized over the [2Fe]H component, such that the proximal Fe center acquires significant spin density (where distal and proximal refer to the positions of the Fe centers relative to the cubane). To validate our H-cluster models on the basis of experimental data, two DFT-based approaches and the semiempirical INDO/S method have been employed to compute electron paramagnetic resonance parameters for the H-cluster states. While most computations yield reasonably accurate g values and ligand hyperfine coupling constants (i.e., A values) for the Hox and Hox-CO states, they fail to reproduce the isotropic 57Fe A tensors found experimentally. Finally, extension of the computational methodology employed successfully for the Hox and Hox-CO states to the metastable Hoxphoto state, generated by irradiation of the Hox-CO state at cryogenic temperatures, has allowed us to discriminate between proposed structural models for this species.