Electronic and Structural Properties of the Double Cubane Iron-Sulfur Cluster

Abstract

The double-cubane cluster (DCC) refers to an [Fe8S9] iron-sulfur complex that is otherwise only known to exist in nitrogenases. Containing a bridging µ2-S ligand, the DCC in the DCC-containing protein (DCCP) is covalently linked to the protein scaffold via six coordinating cysteine residues. In this study, the nature of spin coupling and the effect of spin states on the cluster’s geometry are investigated computationally. Using density functional theory (DFT) and a broken symmetry (BS) approach to study the electronic ground state of the system, we computed the exchange interaction between the spin-coupled spins of the four FeFe dimers contained in the DCC. This treatment yields results that are in excellent agreement with both computed and experimentally determined exchange parameters for analogously coupled di-iron complexes. Hybrid quantum mechanical (QM)/molecular mechanical (MM) geometry optimizations show that cubane cluster A closest to charged amino acid side chains (Arg312, Glu140, Lys146) is less compact than cluster B, indicating that electrons of the same spin in a charged environment seek maximum separation. Overall, this study provides the community with a fundamental reference for subsequent studies of DCCP, as well as for investigations of other [Fe8S9]-containing enzymes.

Review on the QM/MM Methodologies and Their Application to Metalloproteins

“…Note that it could be very useful any additional experimental data on the E n states to further restrict the mechanistic possibilities of FeMo cofactor for comparison with the calculated data. Nonetheless, the published studies propose a pathway to clarify the mechanism of nitrogenase catalytic role [167][168][169][170][171][172][173][174][175][176][177][178].…”

Cation dependence of enniatin B/membrane-interactions assessed using surface-enhanced infrared absorption spectroscopy

“…Geometry optimization and vibrational analysis using normal mode analysis of the EBn:M z+ complexes was performed with the functional BP86 [43,44] in Gaussian16 [45] . Based on related studies on complexes of (alkali) metals and organic molecules, [46,47] C, N, O and H atoms were treated using the 6-31g* basis set, [48] and the alkaline and alkaline earth metal ions were described using def2-TZVP basis set [49] together with its core potential [50] for Cs + . In addition n-pentadecane was specified as solvent in a polarizable continuum model to mimic the hydrophobic parts of the membrane.…”

Multiscale QM/MM modelling of catalytic systems with ChemShell

“…95 Feng et al used QM/MM calculations to provide insight into how the reactivity of the SAM enzyme Dph2 is affected by the electronic state of the [4Fe-4S] cluster. 96 More complicated still are the double-cubane cluster protein, 97 featuring an [Fe 8 S 9 ] complex, and the iron-molybdenum cofactor (FeMoco) in molybdenum-dependent nitrogenase [98][99][100] and iron-vanadium cofactor in vanadium-dependent nitrogenase. 101 Thorhallson and Bjornsson have used QM/MM calculations with ChemShell to explore the energy surface of reduced states of FeMoco, showing how the electronic structure changes along a proposed redox-state cycle.…”