Electronic Structure Studies of Iron-Sulfur Clusters: from Model Compounds to the Active Site of Nitrogenase

Abstract

Iron-sulfur (FeS) clusters are omnipresent in nature, where they are involved in a variety of tasks, such as electron transfer, DNA repair, Fe storage, and substrate activation. The enzyme nitrogenase contains one of the largest known biological FeS clusters. Nitrogenase is responsible for the conversion of inert N₂ gas to bioavailable ammonia, a reaction that is copied by the industrial Haber-Bosch process. However, despite decades of research, little is known about the molecular mechanism behind enzymatic N<sub<2</sub> reduction. The active site of nitrogenase is the iron-molybdenum cofactor (FeMoco, [MoFe₇S₉C]) in the MoFe protein, which contains a unique &mu;₆-C^4- center. The complex electronic structure of FeMoco pushes state-of-the-art quantum mechanical methods to their limits, therefore, smaller model compounds are often explored with high-level methods. The present work studies FeS clusters ranging from monomeric and dimeric FeS model compounds up to the FeMoco cluster, which has eight metal centers. The results are based on quantum chemical calculations and put into context of experimental observables. <br> The study is divided into four parts, each focusing on different characteristics of FeS clusters: (i) S and Se are compared as bridging ligands in [Fe₂X₂]^2+,1+ (X = S,Se) synthetic model compounds. The electronic structure is calculated with the complete active space self-consistent field method (CASSCF). S&rarr;Se substitution is shown to reduce the antiferromagnetic coupling strength between the Fe centers, which can be related to a decrease in Heisenberg exchange and vibronic coupling and an increase in double exchange. Se-bridged Fe centers are relevant to nitrogenase, because selective replacement of S with Se is used to probe the electronic structure in FeMoco with element-specific techniques. (ii) Cysteine (Cys) and serine (Ser) are compared as terminal ligands for the [Fe₂X₂]¹⁺ ferredoxins from <i>Clostridium pasteurianum</i> (<i>Cp</i>) and <i>Aquifex aeolicus</i> (<i>Aae</i>). According to density functional theory (DFT) cluster models, the valence-localized electronic structure (Fe²⁺Fe³⁺) is stabilized with only Cys terminal ligands, while Cys&rarr;Ser replacement stabilizes a valence-delocalized electronic structure (Fe^2.5+Fe^2.5+). Cys&rarr;Ser variants of the ferredoxins from <i>Cp</i> and <i>Aae</i> are the only known examples for valence-delocalized [Fe₂X₂]¹⁺ clusters, but valence-delocalization is frequently encountered in higher-nuclearity FeS clusters, such as FeMoco. (iii) The electronic structure of FeMoco in the E₀ resting state of the MoFo protein is analyzed in detail and compared to the FeVco, the active site in the alternative V nitrogenase. The proteins are modeled with a cluster model and a quantum mechanics/molecular mechanics (QM/MM) model, where DFT in is used for the QM part. It is shown that the energy of a given spin-coupling pattern is related to the antiferromagnetic coupling strength between Fe pairs. It is further shown that the MoFe and the VFe protein are responsible for distinct charge distributions in the respective active sites, which may be related to their distinct reactivities. (iv) Binding of the inhibitor carbon monoxide (CO) to the active site of nitrogenase is explored with a QM/MM model. The results of the E₁ redox state model of the MoFe protein are consistent with experimental CO vibrational frequencies. No large differences were observed between the Mo and the V nitrogenase models, even though V nitrogenase has been reported to bind CO without enzymatic reduction.