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The catalytic cycle for H2 oxidation in [NiFe] D. gigas hydrogenase has been investigated through density functional theory (DFT) calculations on a wide variety of redox and protonated structures of the active site model, (CO)(CN)2Fe(μ-SMe)2Ni(SMe)2. DFT calculations on a series of known LFe(CO)(CN)(L‘) n - (L = Cp or Cp*, L‘ = CN, CO, CNCH3; n = 0, 1, 2) complexes are used to calibrate the calculated CO bond distances with the measured IR stretching frequency. By combining this calibration curve with the energy and CO bond distance of the DFT calculations on the active site model and the experimental IR frequencies on the enzyme, the redox states and structures of active site species have been determined:  Ni-B is a Ni(III)−Fe(II) species, Ni-SI(a) is a Ni(II)−Fe(II) species, Ni-SI(b) has a protonated terminal sulfur (Ni bound), Ni-R is a Ni(II)−Fe(II) dihydrogen complex with H2 bound at Fe, and Ni-C is a Ni(III)−Fe(II) species with an Fe−H−Ni bridge. The latter species returns to Ni-SI through a Ni(I)−Fe(II) intermediate, which is potentially observable. Protonation of the Ni bound terminal sulfur results in a folding of the Fe(μ-S)2Ni framework. Dihydrogen activation is more exothermic on the Ni(III) species than on the corresponding Ni(II) or Ni(I) species. Our final set of proposed structures are consistent with IR, EPR, ENDOR, and XAS measurements for these species, and the correlation coefficient between the measured CO frequency in the enzyme and the CO distance calculated for the model species is 0.905.

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The cubane [4Fe-4S] is the most common multinuclear metal center in nature for electron transfer and storage. Using electrospray, we produced a series of gaseous doubly charged cubane-type complexes, [Fe4S4L4]2- (L = -SC2H5, -SH, -Cl, -Br, -I) and the Se-analogues [Fe4Se4L4]2- (L = -SC2H5, -Cl), and probed their electronic structures with photoelectron spectroscopy and density functional calculations. The photoelectron spectral features are similar among all the seven species investigated, revealing a weak threshold feature due to the minority spins on the Fe centers and confirming the low-spin two-layer model for the [4Fe-4S](2+) core and its "inverted level scheme". The measured adiabatic detachment energies, which are sensitive to the terminal ligand substitution, provide the intrinsic oxidation potentials of the [Fe4S4L4]2- complexes. The calculations revealed a simple correlation between the electron donor property of the terminal thiolate as well as the bridging sulfide with the variation of the intrinsic redox potentials. Our data provide intrinsic electronic structure information of the [4Fe-4S] cluster and the molecular basis for understanding the protein and solvent effects on the redox properties of the [4Fe-4S] active sites.