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The FeMo cofactor (FeMoco) of Mo nitrogenase is responsible for reducing dinitrogen to ammonia, but it requires the addition of 3-4 e - /H + pairs before N 2 even binds. A binding site at the Fe2/Fe3/Fe6/Fe7 face of the cofactor has long been suggested based on mutation studies, with Fe2 or Fe6 nowadays being primarily discussed as possibilities. However, the nature of N 2 binding to the cofactor is enigmatic as the metal ions are coordinatively saturated in the resting state with no obvious binding site. Furthermore, the cofactor consists of high-spin Fe(II)/Fe(III) ions (antiferromagnetically coupled but also mixed-valence delocalized), which are not known to bind N 2 . This suggests that an Fe binding site with a different molecular and electronic structure than the resting state must be responsible for the experimentally known N 2 binding in the E 4 state of FeMoco. We have systematically studied N 2 binding to Fe2 and Fe6 sites of FeMoco at the broken-symmetry QM/MM level as a function of the redox-, spin-, and protonation state of the cofactor. The local and global electronic structure changes to the cofactor taking place during redox events, protonation, Fe-S cleavage, hydride formation, and N 2 coordination are systematically analyzed. Localized orbital and quasi-restricted orbital analysis via diamagnetic substitution is used to get insights into the local single Fe ion electronic structure in various states of FeMoco. A few factors emerge as essential to N 2 binding in the calculations: spin-pairing of d xz and d yz orbitals of the N 2 -binding Fe ion, a coordination change at the N 2 -binding Fe ion aided by a hemilabile protonated sulfur, and finally hydride ligation. The results show that N 2 binding to E 0 , E 1 , and E 2 models is generally unfavorable, likely due to the high-energy cost of stabilizing the necessary spin-paired electronic structure of the N 2 -binding Fe ion in a ligand environment that clearly favors high-spin states. The results for models of E 4 , however, suggest a feasible model for why N 2 binding occurs experimentally in the E 4 state. E 4 models with two bridging hydrides between Fe2 and Fe6 show much more favorable N 2 binding than other models. When two hydrides coordinate to the same Fe ion, an increased ligand-field splitting due to octahedral coordination at either Fe2 or Fe6 is found. This altered ligand field makes it easier for the Fe ion to acquire a spin-paired electronic structure with doubly occupied d xz and d yz orbitals that backbond to a terminal N 2 ligand. Within this model for N 2 binding, both Fe2 and Fe6 emerge as possible binding site scenarios. Due to steric effects involving the His195 residue, affecting both the N 2 ligand and the terminal SH - group, distinguishing between Fe2 and Fe6 is difficult; furthermore, the binding depends on the protonation state of His195.

Carbon monoxide (CO) is a well-known inhibitor of nitrogenase activity. Under turnover conditions, CO binds to FeMoco, the active site of Mo nitrogenase. Time-resolved IR measurements suggest an initial terminal CO at 1904 cm -1 that converts to a bridging CO at 1715 cm -1 , and an X-ray structure shows that CO can displace one of the bridging belt sulfides of FeMoco. However, the CO-binding redox state(s) of FeMoco (E n ) and the role of the protein environment in stabilizing specific CO-bound intermediates remain elusive. In this work, we carry out an in-depth analysis of the CO-FeMoco interaction based on quantum chemical calculations addressing different aspects of the electronic structure. (1) The local electronic structure of the Fe-CO bond is studied through diamagnetically substituted FeMoco. (2) A cluster model of FeMoco within a polarizable continuum illustrates how CO binding may affect the spin-coupling between the metal centers. (3) A QM/MM model incorporates the explicit influence of the amino acid residues surrounding FeMoco in the MoFe protein. The QM/MM model predicts both a terminal and a bridging CO in the E 1 redox state. The scaled calculated CO frequencies (1922 and 1716 cm -1 , respectively) are in good agreement with the experimentally observed IR bands supporting CO binding to the E 1 state. Alternatively, an E 2 state QM/MM model, which has the same atomic structure as the CO-bound X-ray structure, features a semi-bridging CO with a scaled calculated frequency (1718 cm -1 ) similar to the bridging CO in the E 1 model.

The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO 2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron-vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO 3 2- or NO 3 - ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO 3 2- or NO 3 - ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe 7 S 8 C(CO 3 )] 2- model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe-Fe and V-Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe 7 S 8 C(CO 3 )] 2- BS7-235 model is compared to our [MoFe 7 S 9 C] - BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E 1 state of FeMoco. Furthermore, V-Fe interactions in FeVco are not as strong compared to Mo-Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.

The elucidation of magnetostructural correlations between bridging ligand substitution and strength of magnetic coupling is essential to the development of high-temperature molecule-based magnetic materials. Toward this end, we report the series of tetraoxolene-bridged Fe II 2 complexes [(Me 3 TPyA) 2 Fe 2 ( R L)] n + (Me 3 TPyA = tris(6-methyl-2-pyridylmethyl)amine; n = 2: OMe LH 2 = 3,6-dimethoxy-2,5-dihydroxo-1,4-benzoquinone, Cl LH 2 = 3,6-dichloro-2,5-dihydroxo-1,4-benzoquinone, Na 2 [ NO 2 L] = sodium 3,6-dinitro-2,5-dihydroxo-1,4-benzoquinone; n = 4: SMe 2 L = 3,6-bis(dimethylsulfonium)-2,5-dihydroxo-1,4-benzoquinone diylide) and their one-electron-reduced analogues. Variable-temperature dc magnetic susceptibility data reveal the presence of weak ferromagnetic superexchange between Fe II = +1.2(2) (R = OMe, Cl) and +0.3(1) (R = NO J = +1.2(2) (R = OMe, Cl) and +0.3(1) (R = NO 2 , SMe 2 ) cm -1 . In contrast, X-ray diffraction, cyclic voltammetry, and Mössbauer spectroscopy establish a ligand-centered radical in the reduced complexes. Magnetic measurements for the radical-bridged species reveal the presence of strong antiferromagnetic metal-radical coupling, with J for R = OMe, Cl, NO -1 for R = OMe, Cl, NO 2 , and SMe 2 , respectively. The minimal effects of substituents in the 3- and 6-positions of R L x -• on the magnetic coupling strength is understood through electronic structure calculations, which show negligible spin density on the substituents and associated C atoms of the ring. Finally, the radical-bridged complexes are single-molecule magnets, with relaxation barriers of U for R = OMe, Cl, NO eff = 50(1), 41(1), 38(1), and 33(1) cm -1 for R = OMe, Cl, NO 2 , and SMe 2 , respectively. Taken together, these results provide the first examination of how bridging ligand substitution influences magnetic coupling in semiquinoid-bridged compounds, and they establish design criteria for the synthesis of semiquinoid-based molecules and materials.

Molybdenum-dependent nitrogenase is the most active biological catalyst for dinitrogen reduction. This reaction is catalyzed by a [MoFe 7 S 9 C] cofactor (FeMoco). FeMoco can be described as a double-cubane, with [MoFe 3 S 3 ] and [Fe 4 S 3 ] parts, bound via an interstitial carbide and three bridging sulfides. Model compounds have been synthesized since early studies of the enzyme and Coucouvanis and co-workers demonstrated that [MoFe 3 S 4 ] cubanes are active catalysts for many substrates catalyzed by nitrogenase. These reactions include hydrazine reduction to ammonia and cis-dimethyldiazene reduction to methylamine. Experiments implicated molybdenum as the binding site but the mechanisms have not been studied by theoretical calculations before. Here we present a DFT study of the catalytic reaction mechanisms of hydrazine and cis-dimethyldiazene reduction with a [MoFe 3 S 4 ] cubane. Like in the experiments, molybdenum is revealed as the likely substrate binding site, likely due to the labile ligand on Mo. For the hydrazine mechanism, a reduction event is centered on Fe, specifically on the Fe antiferromagnetically coupled to the mixed-valence pair. After protonation of the distal hydrazine nitrogen, the N-N bond can be cleaved to yield NH 3 and a Mo-bound -NH 2 intermediate. This is followed by another protonation/reduction step to give an -NH 3 intermediate, and finally substituted by the substrate to complete the cycle. The computed mechanisms shed light on the bimetallic cooperativity in these systems where the reduction steps are localized on Fe while the substrate binds to Mo and the reductions require only a free coordination site (on Mo) and a favorable reduction event (to Fe). Although both substrates easily displace the weakly bound acetonitrile ligand, one reduction event is required for hydrazine activation and N-N bond cleavage to give an integer-spin -NH 2 intermediate. An integer-spin -NH 2 intermediate has been observed as a common intermediate for the enzyme reduction of hydrazine and diazene, suggesting a possible link to the enzyme chemistry.

A combination of two elements' (Au, Zn) X-ray absorption spectroscopy (XAS) and time-dependent density functional theory (TD-DFT) allowed the elucidation of differential substitution pathways of Au(I) and Au(III) compounds reacting with biologically relevant zinc fingers (ZnFs). Gold L 3 -edge XAS probed the interaction of gold and the C-terminal Cys 2 HisCys finger of the HIV-1 nucleocapsid protein NCp7, and the Cys 2 His 2 human transcription factor Sp1. The use of model compounds helped assign oxidation states and the identity of the gold-bound ligands. The computational studies accurately reproduced the experimental XAS spectra and allowed the proposition of structural models for the interaction products at early time points. The direct electrophilic attack on the ZnF by the highly thiophilic Au(I) resulted in a linear P-Au-Cys coordination sphere after zinc ejection whereas for the Sp1, loss of PEt 3 results in linear Cys-Au-Cys or Cys-Au-His arrangements. Reactions with Au(III) compounds, on the other hand, showed multiple binding modes. Prompt reaction between [AuCl(dien)] 2+ and [Au(dien)(DMAP)] 3+ with Sp1 showed a partially reduced Au center and a final linear His-Au-His coordination. Differently, in the presence of NCp7, [AuCl(dien)] 2+ readily reduces to Au(I) and changes from square-planar to linear geometry with Cys-Au-His coordination, while [Au(dien)(DMAP)] 3+ initially maintains its Au(III) oxidation state and square-planar geometry and the same first coordination sphere. The latter is the first observation of a "noncovalent" interaction of a Au(III) complex with a zinc finger and confirms early hypotheses that stabilization of Au(III) occurs with N-donor ligands. Modification of the zinc coordination sphere, suggesting full or partial zinc ejection, is observed in all cases, and for [Au(dien)(DMAP)] 3+ this represents a novel mechanism for nucleocapsid inactivation. The combination of XAS and TD-DFT presents the first direct experimental observation that not only compound reactivity, but also ZnF core specificity, can be modulated on the basis of the coordination sphere of Au(III) compounds.

Nitrogenase is one of the most fascinating enzymes in nature, being responsible for all biological nitrogen reduction. Despite decades of research, it is among the enzymes in bioinorganic chemistry whose mechanism is the most poorly understood. The MoFe protein of nitrogenase contains an iron-molybdenum-sulfur cluster, FeMoco, where N 2 reduction takes place. The resting state of FeMoco has been characterized by crystallography, multiple spectroscopic techniques, and theory (broken-symmetry density functional theory), and all heavy atoms are now characterized. The cofactor charge, however, has been controversial, the electronic structure has proved enigmatic, and little is known about the mechanism. While many computational studies have been performed on FeMoco, few have taken the protein environment properly into account. In this study, we put forward QM/MM models of the MoFe protein from Azotobacter vinelandii, centered on FeMoco. By a detailed analysis of the FeMoco geometry and comparison to the atomic resolution crystal structure, we conclude that only the [MoFe 7 S 9 C] 1- charge is a possible resting state charge. Further, we find that of the three lowest energy broken-symmetry solutions of FeMoco, the BS7-235 spin isomer (where 235 refers to Fe atoms that are "spin-down") is the only one that can be reconciled with experiment. This is revealed by a comparison of the metal-metal distances in the experimental crystal structure, a rare case of spin-coupling phenomena being visible through the molecular structure. This could be interpreted as the enzyme deliberately stabilizing a specific electronic state of the cofactor, possibly for tuning specific reactivity on specific metal atoms. Finally, we show that the alkoxide group on the Mo-bound homocitrate must be protonated under resting state conditions, the presence of which has implications regarding the nature of FeMoco redox states as well as for potential substrate reduction mechanisms.

Despite decades of research, the structure-activity relationship of nitrogenase is still not understood. Only recently was the full molecular structure of the FeMo cofactor (FeMoco) revealed, but the charge and metal oxidation states of FeMoco have been controversial. With the recent identification of the interstitial atom as a carbide and the more recent revised oxidation-state assignment of the molybdenum atom as Mo(III), here we revisit the Mössbauer properties of FeMoco. By a detailed error analysis of density functional theory-computed isomer shifts and computing isomer shifts relative to the P-cluster, we find that only the charge of [MoFe 7 S 9 C] 1- fits the experimental data. In view of the recent Mo(III) identification, the charge of [MoFe 7 S 9 C] 1- corresponds to a formal oxidation-state assignment of Mo(III)3Fe(II)4Fe(III), although due to spin delocalization, the physical oxidation state distribution might also be interpreted as Mo(III)1Fe(II)4Fe(2.5)2Fe(III), according to a localized orbital analysis of the M S = 3/2 broken symmetry solution. These results can be reconciled with the recent spatially resolved anomalous dispersion study by Einsle et al. that suggests the Mo(III)3Fe(II)4Fe(III) distribution, if some spin localization (either through interactions with the protein environment or through vibronic coupling) were to take place.

Herein, a systematic study of [L2Fe2S2](n) model complexes (where L = bis(benzimidazolato) and n = 2-, 3-, 4-) has been carried out using iron and sulfur K-edge X-ray absorption (XAS) and iron Kβ and valence-to-core X-ray emission spectroscopies (XES). These data are used as a test set to evaluate the relative strengths and weaknesses of X-ray core level spectroscopies in assessing redox changes in iron-sulfur clusters. The results are correlated to density functional theory (DFT) calculations of the spectra in order to further support the quantitative information that can be extracted from the experimental data. It is demonstrated that due to canceling effects of covalency and spin state, the information that can be extracted from Fe Kβ XES mainlines is limited. However, a careful analysis of the Fe K-edge XAS data shows that localized valence vs delocalized valence species may be differentiated on the basis of the pre-edge and K-edge energies. These findings are then applied to existing literature Fe K-edge XAS data on the iron protein, P-cluster, and FeMoco sites of nitrogenase. The ability to assess the extent of delocalization in the iron protein vs the P-cluster is highlighted. In addition, possible charge states for FeMoco on the basis of Fe K-edge XAS data are discussed. This study provides an important reference for future X-ray spectroscopic studies of iron-sulfur clusters.