Structural Analysis of Cubane-Type Iron Clusters

An Iron-Sulfur Cluster with a Highly Pyramidalized Three-Coordinate Iron Center and a Negligible Affinity for Dinitrogen

Attempts to generate open coordination sites for N2 binding at synthetic Fe-S clusters often instead result in cluster oligomerization. Recently, it was shown for Mo-Fe-S clusters that such oligomerization reactions can be prevented through the use of sterically protective supporting ligands, thereby enabling N2 complex formation. Here, this strategy is extended to Fe-only Fe-S clusters. One-electron reduction of (IMes)3Fe4S4Cl (IMes = 1,3-dimesitylimidazol-2-ylidene) forms the transiently stable edge-bridged double cubane (IMes)6Fe8S8, which loses two IMes ligands to form the face-bridged double-cubane, (IMes)4Fe8S8. The finding that the three supporting IMes ligands do not confer sufficient protection to curtail cluster oligomerization prompted the design of a new N-heterocyclic carbene, SIArMe,iPr (1,3-bis(3,5-diisopropyl-2,6-dimethylphenyl)-2-imidazolidinylidene; abbreviated as SIAr), that features bulky groups strategically placed in remote positions. When the reduction of (SIAr)3Fe4S4Cl or [(SIAr)3Fe4S4(THF)]+ is conducted in the presence of SIAr, the formation of (SIAr)4Fe8S8 is indeed suppressed, permitting characterization of the reduced [Fe4S4]0 product. Surprisingly, rather than being an N2 complex, the product is simply (SIAr)3Fe4S4: a cluster with a three-coordinate Fe site that adopts an unusually pyramidalized geometry. Although (SIAr)3Fe4S4 does not coordinate N2 to any appreciable extent under the surveyed conditions, it does bind CO to form (SIAr)3Fe4S4(CO). This finding demonstates that the binding pocket at the unique Fe is not too small for N2; instead, the exceptionally weak affinity for N2 can be attributed to weak Fe-N2 bonding. The differences in the N2 coordination chemistry between sterically protected Mo-Fe-S clusters and Fe-only Fe-S clusters are discussed.

Valence Localization in Alkyne and Alkene Adducts of Synthetic [Fe4S4]+ Clusters

Reported herein are alkyne and alkene adducts of synthetic [Fe₄S₄]⁺ clusters that model intermediates and inhibitor-bound states in enzymes involved in isoprenoid biosynthesis. Treatment of the N-heterocyclic carbene-ligated cluster [(IMes)₃Fe₄S₄(OEt₂)][BAr^F₄] (IMes = 1,3-dimesitylimidazol-2-ylidene; [BAr^F₄]^- = tetrakis(3,5-bis(trifluoromethyl)phenyl)borate) with phenylacetylene (PhCCH) or cis-cyclooctene (COE) results in displacement of the Et₂O ligand to yield the corresponding π complexes, [(IMes)₃Fe₄S₄(PhCCH)][BAr^F₄] and [(IMes)₃Fe₄S₄(COE)][BAr^F₄]. EPR spectroscopic analysis demonstrates that both clusters are doublets with g_iso > 2 and thus are spectroscopically faithful models of the analogous species characterized in the isoprenoid biosynthetic enzymes IspG and IspH. Structural and Mössbauer spectroscopic analysis reveals that both complexes are best described as [Fe₄S₄]⁺ clusters in which the unique Fe site engages in modest back-bonding to the π-acidic ligand. Paramagnetic NMR studies show that, even at room temperature, the alkyne/alkene-bound Fe centers harbor minority spin and therefore adopt an Fe²⁺ valence. We propose that such valence localization could likewise occur in Fe-S enzymes that interact with π-acidic molecules.

The Elusive Mononitrosylated [Fe4 S4 ] Cluster in Three Redox States

Iron-sulfur clusters are well-established targets in biological nitric oxide (NO) chemistry, but the key intermediate in these processes-a mononitrosylated [Fe4 S4 ] cluster-has not been fully characterized in a protein or a synthetic model thereof. Here, we report the synthesis of a three-member redox series of isostructural mononitrosylated [Fe4 S4 ] clusters. Mononitrosylation was achieved by binding NO to a 3 : 1 site-differentiated [Fe4 S4 ]+ cluster; subsequent oxidation and reduction afforded the other members of the series. All three clusters feature a local high-spin Fe3+ center antiferromagnetically coupled to 3 [NO]- . The observation of an anionic NO ligand suggests that NO binding is accompanied by formal electron transfer from the cluster to NO. Preliminary reactivity studies with the monocationic cluster demonstrate that exposure to excess NO degrades the cluster, supporting the intermediacy of mononitrosylated intermediates in NO sensing/signaling.

Characterization of a Nitrogenase Iron Protein Substituted with a Synthetic [Fe4 Se4 ] Cluster

The Fe protein of nitrogenase plays multiple roles in substrate reduction and cluster maturation via its redox-active [Fe₄ S₄ ] cluster. Here we report the synthesis and characterization of a water-soluble [Fe₄ Se₄ ] cluster that is used to substitute the [Fe₄ S₄ ] cluster of the Azotobacter vinelandii Fe protein (AvNifH). Biochemical, EPR and XAS/EXAFS analyses demonstrate the ability of the [Fe₄ Se₄ ] cluster to adopt the super-reduced, all-ferrous state upon its incorporation into AvNifH. Moreover, these studies reveal that the [Fe₄ Se₄ ] cluster in AvNifH already assumes a partial all-ferrous state ([Fe₄ Se₄ ]⁰ ) in the presence of dithionite, where its [Fe₄ S₄ ] counterpart in AvNifH exists solely in the reduced state ([Fe₄ S₄ ]¹⁺ ). Such a discrepancy in the redox properties of the AvNifH-associated [Fe₄ Se₄ ] and [Fe₄ S₄ ] clusters can be used to distinguish the differential redox requirements for the substrate reduction and cluster maturation of nitrogenase, pointing to the utility of chalcogen-substituted FeS clusters in future mechanistic studies of nitrogenase catalysis and assembly.

Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH3)4]q, q = -2, -1, +2, +3

Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe(SCH₃)₄]^2-/1-/2+/3+ using multireference (CASSCF, MRCISD), and coupled cluster [CCSD(T)] methodologies. We show that the nature of the Fe-S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe(SCH₃)₄] complexes offer a physical rationale for the relative stabilization, structure, and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe(SCH₃)₄]^2-/1- complexes and covalent in [Fe(SCH₃)₄]^2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe(SCH₃)₄]^2- → [Fe(SCH₃)₄]^- (i.e., Fe^II → Fe^III) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe(SCH₃)₄]²⁺ → [Fe(SCH₃)₄]³⁺ of 16.6 eV, almost half of the ionization potential of Fe²⁺. The ionic versus covalent bond character influences the Fe-S bond strength and length, that is, ionic Fe-S bonds are longer than covalent ones by about 0.2 Å (for Fe^II) and 0.04 Å (for Fe^II). Finally, the average Fe-S heterolytic bond strength is 6.7 eV (Fe^II) and 14.6 eV (Fe^III) at the RCCSD(T) level of theory.

Dinitrogen binding and activation at a molybdenum-iron-sulfur cluster

The Fe-S clusters of nitrogenases carry out the life-sustaining conversion of N₂ to NH₃. Although progress continues to be made in modelling the structural features of nitrogenase cofactors, no synthetic Fe-S cluster has been shown to form a well-defined coordination complex with N₂. Here we report that embedding an [MoFe₃S₄] cluster in a protective ligand environment enables N₂ binding at Fe. The bridging [MoFe₃S₄]₂(μ-η¹:η¹-N₂) complex thus prepared features a substantially weakened N-N bond despite the relatively high formal oxidation states of the metal centres. Substitution of one of the [MoFe₃S₄] cubanes with an electropositive Ti metalloradical induces additional charge transfer to the N₂ ligand with generation of Fe-N multiple-bond character. Structural and spectroscopic analyses demonstrate that N₂ activation is accompanied by shortened Fe-S distances and charge transfer from each Fe site, including those not directly bound to N₂. These findings indicate that covalent interactions within the cluster play a critical role in N₂ binding and activation.

A Terminal Imido Complex of an Iron-Sulfur Cluster

We report the synthesis and characterization of the first terminal imido complex of an Fe-S cluster, (IMes)₃ Fe₄ S₄ =NDipp (2; IMes=1,3-dimesitylimidazol-2-ylidene, Dipp=2,6-diisopropylphenyl), which is generated by oxidative group transfer from DippN₃ to the all-ferrous cluster (IMes)₃ Fe₄ S₄ (PPh₃ ). This two-electron process is achieved by formal one-electron oxidation of the imido-bound Fe site and one-electron oxidation of two IMes-bound Fe sites. Structural, spectroscopic, and computational studies establish that the Fe-imido site is best described as a high-spin Fe³⁺ center, which is manifested in its long Fe-N(imido) distance of 1.763(2) Å. Cluster 2 abstracts hydrogen atoms from 1,4-cyclohexadiene to yield the corresponding anilido complex, demonstrating competency for C-H activation.

Heterologous Expression and Engineering of the Nitrogenase Cofactor Biosynthesis Scaffold NifEN

NifEN plays a crucial role in the biosynthesis of nitrogenase, catalyzing the final step of cofactor maturation prior to delivering the cofactor to NifDK, the catalytic component of nitrogenase. The difficulty in expressing NifEN, a complex, heteromultimeric metalloprotein sharing structural/functional homology with NifDK, is a major challenge in the heterologous expression of nitrogenase. Herein, we report the expression and engineering of Azotobacter vinelandii NifEN in Escherichia coli. Biochemical and spectroscopic analyses demonstrate the integrity of the heterologously expressed NifEN in composition and functionality and, additionally, the ability of an engineered NifEN variant to mimic NifDK in retaining the matured cofactor at an analogous cofactor-binding site. This is an important step toward piecing together a viable pathway for the heterologous expression of nitrogenase and identifying variants for the mechanistic investigation of this enzyme.

Mutation effects on charge transport through the p58c iron-sulfur protein

Growing experimental evidence indicates that iron–sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [Fe₄S₄] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [Fe₄S₄] protein, and its p58c domain (which contains an [Fe₄S₄] cluster) plays a role in the initiation of DNA replication. The Y345C mutation in p58c is linked to gastric tumors and may influence the protein-mediated charge transport. The complexity of protein–DNA systems, and the intricate electronic structure of [Fe₄S₄] clusters, have impeded progress into understanding functional charge transport in these systems. In this study, we built force fields to describe the high potential [Fe₄S₄] cluster in both oxidation states. The parameterization is compatible with AMBER force fields and enabled well-balanced molecular dynamics simulations of the p58c–RNA/DNA complex relevant to the initiation of DNA replication. Using the molecular mechanics Poisson–Boltzmann and surface area solvation method on the molecular dynamics trajectories, we find that the p58c mutation induces a modest change in the p58c–duplex binding free energy in agreement with recent experiments. Through kinetic modeling and analysis, we identify key features of the main charge transport pathways in p58c. In particular, we find that the Y345C mutation partially changes the composition and frequency of the most efficient (and potentially relevant to the biological function) charge transport pathways between the [Fe₄S₄] cluster and the duplex. Moreover, our approach sets the stage for a deeper understanding of functional charge transfer in [Fe₄S₄] protein–DNA complexes.

Functional electron transfer between the [Fe₄S₄] cluster and the nucleic acid is impacted by a Y345C mutation in the p58c subunit of human primase.

Spectroscopic Characterization of an Eight-Iron Nitrogenase Cofactor Precursor that Lacks the "9th Sulfur"

Nitrogenases catalyze the reduction of N₂ to NH₄ ⁺ at its cofactor site. Designated the M-cluster, this [MoFe₇ S₉ C(R-homocitrate)] cofactor is synthesized via the transformation of a [Fe₄ S₄ ] cluster pair into an [Fe₈ S₉ C] precursor (designated the L-cluster) prior to insertion of Mo and homocitrate. We report the characterization of an eight-iron cofactor precursor (designated the L*-cluster), which is proposed to have the composition [Fe₈ S₈ C] and lack the "9^th sulfur" in the belt region of the L-cluster. Our X-ray absorption and electron spin echo envelope modulation (ESEEM) analyses strongly suggest that the L*-cluster represents a structural homologue to the l-cluster except for the missing belt sulfur. The absence of a belt sulfur from the L*-cluster may prove beneficial for labeling the catalytically important belt region, which could in turn facilitate investigations into the reaction mechanism of nitrogenases.

Iron-sulfur clusters have no right angles

Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4S4 cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4S4: coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues. Furthermore, computational tools were developed to assist researchers when refining Fe4S4-containing proteins.

Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [FeIII4 S4 (SAr)4 ]

An unprecedented, super oxidized all-ferric iron-sulfur cubanoid cluster with all terminal thiolates, Fe₄ S₄ (STbt)₄ (3) [Tbt=2,4,6-tris{bis(trimethylsilyl)methyl}phenyl], has been isolated from the reaction of the bis-thiolate complex Fe(STbt)₂ (2) with elemental sulfur. This cluster 3 has been characterized by X-ray crystallography, zero-field ⁵⁷ Fe Mössbauer spectroscopy, cyclic voltammetry, and other relevant physico-chemical methods. Based on all the data, the electronic ground state of the cluster has been assigned to be S_tot =0.

Synthesis and crystal structure of new K and Rb selenido/tellurido ferrate cluster compounds

In the course of a systematic study of alkali iron chalcogenido salts containing clusters [Fe4 Q 8] a series of new mixed-valent potassium and rubidium selenido and tellurido ferrates(II/III) was synthesized by carefully heating the pure elements enclosed in sample tubes under an argon atmosphere up to maximum temperatures of 800–900 °C. Their crystal structures have been determined by means of single crystal X-ray diffraction. The mixed-valent FeII/III tellurido ferrates A 7[Fe4Te8] form three different structure types. All structures contain tetramers of four edge sharing [FeTe4] tetrahedra, which are connected by common edges to form only slightly distorted tetrahedral [Fe4Te8]7− anions (‘stella quadrangula’) with a [Fe4Te4] cubane core. In all cases, these anions are surrounded by 26 alkali cations, which are located at the eight corners and the midpoints of the six faces and 12 edges of a cube. The three crystal structures can thus be described by three different packings of cuboid moieties: The monoclinic rubidium compound Rb7[Fe4Te8] (space group C2/c, a = 2000.16(7), b = 897.79(3), c = 1768.12(6) pm, β = 117.4995(10)°, Z = 4, R1 = 0.0296) is isotypic to the known cesium tellurido and sulfido ferrates Cs7[Fe4(S/Te)8]. Depending on the temperature, K7[Fe4Te8] forms two different but closely related new structure types: The tetragonal r.t. modification (space group P42/nmc, a = 1222.25(14), c = 872.1(2) pm, Z = 2, R1 = 0.0583) crystallizes in a supergroup of the orthorhombic l.t. (100 K) form (space group Pbcn, a = 1715.5, b = 866.76(3), c = 1715.50(7) pm, Z = 4, R1 = 0.0160). In all structures, the cluster centered cubes are stacked to form columns along the short (≈870 pm) axis. These columns are themselves densely packed with 4 (both K compounds) and 6 (A = Rb) adjacent face-sharing columns. According to these arrangements of cluster-centered cubes, a relation of the packing of K/Rb cations and cluster anions with the simple cubic packing can be established applying the crystallographic group-subgroup formalism. Attempts to synthesize the corresponding selenium compound K7[Fe4Se8] resulted in the formation of the likewise mixed-valent compound K6[Fe4Se8]. Despite the modified composition, the new orthorhombic structure (space group Pbcn, a = 1632.62(6), b = 821.10(3), c = 1592.75(6) pm, Z = 4, R1 = 0.0540) is almost isotypic to the l.t. form of K7[Fe4Te8], the only difference being a missing K site. K5Fe2Te5 crystallizes in a new structure type (cubic, space group Pa3̅, a = 1709.02(5) pm, Z = 4, R1 = 0.0594). According to K5Fe2Te5=K15[Fe3Te7]2(Te), its structure contains mixed-valent cuboidal trimers [Fe3Te7](6/7)− and isolated telluride ions, which are coordinated by cubes of K+ cations.

A Low-Valent Iron Imido Heterocubane Cluster: Reversible Electron Transfer and Catalysis of Selective C-C Couplings

Enzymes and cofactors with iron-sulfur heterocubane core structures, [Fe4 S4 ], are often found in nature as electron transfer reagents in fundamental catalytic transformations. An artificial heterocubane with a [Fe4 N4 ] core is reported that can reversibly store up to four electrons at very negative potentials. The neutral [Fe4 N4 ] and the singly reduced low-valent [Fe4 N4 ](-) heterocubanes were isolated and fully characterized. The low-valent species bears one unpaired electron, which is localized predominantly at one iron center in the electronic ground state but fluctuates with increasing temperatures. The electrons stored or released by the [Fe4 N4 ]/[Fe4 N4 ](-) redox couple can be used in reductive or oxidative CC couplings and even allow catalytic one-pot reactions, which show a remarkably enhanced selectivity in the presence of the [Fe4 N4 ] heterocubanes.

Reactivity of an All-Ferrous Iron-Nitrogen Heterocubane under Reductive and Oxidative Conditions

The reactivity of the all-ferrous FeN heterocubane [Fe4 (Ntrop)4 ] (1) with i) Brønsted acids, ii) σ-donors, iii) σ-donors/π-acceptors, and iv) one-electron oxidants has been investigated (trop = 5H-dibenzo[a,d]cyclo-hepten-5-yl). 1 showed self-re-assembling after reactions with i) and proved surprisingly inert in reactions with ii) and iii), with the exception of CO. Reductive and oxidative cluster degradation was observed in reactions with CO and TEMPO, respectively. These reactions yielded new cluster compounds, namely a trinuclear bis(μ3 -imido) 48 electron complex in the former case and a tetranuclear all ferric μ-oxo-μ-imido species in the latter case. Characterization techniques include NMR and in situ IR spectroscopy, single crystal X-ray analysis, Mössbauer spectroscopy, cyclic voltammetry, magnetic susceptibility measurements, and DFT calculations.

A convenient route to synthetic analogues of the oxidized form of high-potential iron-sulfur proteins

An amide-bound [Fe4S4](3+) cluster, [Fe4S4{N(SiMe3)2}4](-) (1), was found to serve as a convenient precursor for synthetic analogues of the oxidized form of high-potential iron-sulfur proteins. Treatment of 1 with 4 equiv of bulky thiols led to replacement of the amide ligands with thiolates, giving rise to a series of [Fe4S4(SR)4](-) clusters (R = Dmp (2a), Tbt (2b), Eind (2c), Dxp (2d), Dpp (2e); Dmp = 2,6-di(mesityl)phenyl, Tbt = 2,4,6-tris[bis(trimethylsilyl)methyl]phenyl, Eind = 1,1,3,3,5,5,7,7-octaethyl-s-hydrindacen-4-yl, Dxp = 2,6-di(m-xylyl)phenyl, Dpp = 2,6-diphenylphenyl). These clusters were characterized by the mass spectrum, the EPR spectrum, and X-ray crystallography. The redox potentials of the [Fe4S4](3+/2+) couple, -0.82 V (2a), -0.86 V (2b), -0.84 V (2c), -0.74 V (2d), and -0.63 V (2e) vs Ag/Ag(+) in THF, are significantly more negative than that of [Fe4S4(SPh)4](-/2-) (-0.21 V).