Mössbauer and Integer-Spin EPR Studies and Spin-Coupling Analysis of the [4Fe-4S]0 Cluster of the Fe Protein from Azotobacter vinelandii Nitrogenase

Permutation symmetry in spin-adapted many-body wave functions

In the domain of exchange-coupled polynuclear transition-metal (PNTM) clusters, local emergent symmetries exist which can be exploited to greatly increase the sparsity of the configuration interaction (CI) eigensolutions of such systems. Sparsity of the CI secular problem is revealed by exploring the site permutation space within spin-adapted many-body bases, and highly compressed wave functions may arise by finding optimal site orderings. However, the factorial cost of searching through the permutation space remains a bottleneck for clusters with a large number of metal centers. In this work, we explore ways to reduce the factorial scaling, by combining permutation and point group symmetry arguments, and using commutation relations between cumulative partial spin and the Hamiltonian operators, . Certain site orderings lead to commuting operators, from which more sparse wave functions arise. Two graphical strategies will be discussed, one to rapidly evaluate the commutators of interest, and one in the form of a tree search algorithm to predict how many and which distinct site permutations are to be analyzed, eliminating redundancies in the permutation space. Particularly interesting is the case of the singlet spin states for which an additional reversal symmetry can be utilized to further reduce the number of distinct site permutations.

Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction

Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes. The prokaryotic DNA repair photolyase PhrB carries a four-iron-four-sulfur cluster ([4Fe4S]) in addition to the catalytic flavin adenine dinucleotide (FAD) and a second cofactor ribolumazine. Our recent study suggested that the [4Fe4S] cluster functions as an electron cache to coordinate two interdependent photoreactions of the FAD and ribolumazine. Here we report the crystallography observations of light-induced responses in PhrB using the cryo-trapping method and in situ serial Laue diffraction at room temperature. We capture strong signals that depict electron density changes arising from quantized electronic movements in the [4Fe4S] cluster. Our data reveal the mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light-induced redox changes. The quantum effects imaged by decomposition of electron density changes have shed light on the emerging roles of metal clusters in proteins.

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.

Enzymatic Fischer-Tropsch-Type Reactions

The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.

The Fe Protein Cycle Associated with Nitrogenase Catalysis Requires the Hydrolysis of Two ATP for Each Single Electron Transfer Event

A central feature of the current understanding of dinitrogen (N₂) reduction by the enzyme nitrogenase is the proposed coupling of the hydrolysis of two ATP, forming two ADP and two Pi, to the transfer of one electron from the Fe protein component to the MoFe protein component, where substrates are reduced. A redox-active [4Fe-4S] cluster associated with the Fe protein is the agent of electron delivery, and it is well known to have a capacity to cycle between a one-electron-reduced [4Fe-4S]¹⁺ state and an oxidized [4Fe-4S]²⁺ state. Recently, however, it has been shown that certain reducing agents can be used to further reduce the Fe protein [4Fe-4S] cluster to a super-reduced, all-ferrous [4Fe-4S]⁰ state that can be either diamagnetic (S = 0) or paramagnetic (S = 4). It has been proposed that the super-reduced state might fundamentally alter the existing model for nitrogenase energy utilization by the transfer of two electrons per Fe protein cycle linked to hydrolysis of only two ATP molecules. Here, we measure the number of ATP consumed for each electron transfer under steady-state catalysis while the Fe protein cluster is in the [4Fe-4S]¹⁺ state and when it is in the [4Fe-4S]⁰ state. Both oxidation states of the Fe protein are found to operate by hydrolyzing two ATP for each single-electron transfer event. Thus, regardless of its initial redox state, the Fe protein transfers only one electron at a time to the MoFe protein in a process that requires the hydrolysis of two ATP.

Spin-Coupled Electron Densities of Iron-Sulfur Cluster Imaged by In Situ Serial Laue Diffraction

Iron-sulfur clusters are inorganic cofactors found in many proteins involved in fundamental biological processes including DNA processing. The prokaryotic DNA repair enzyme PhrB, a member of the protein family of cryptochromes and photolyases, carries a four-iron-four-sulfur cluster [4Fe4S] in addition to the catalytic cofactor flavin adenine dinucleotide (FAD) and a second pigment 6,7-dimethyl-8-ribityllumazine (DMRL). The light-induced redox reactions of this multi-cofactor protein complex were recently shown as two interdependent photoreductions of FAD and DMRL mediated by the [4Fe4S] cluster functioning as an electron cache to hold a fine balance of electrons. Here, we apply the more traditional temperature-scan cryo-trapping technique in protein crystallography and the newly developed technology of in situ serial Laue diffraction at room temperature. These diffraction methods in dynamic crystallography enable us to capture strong signals of electron density changes in the [4Fe4S] cluster that depict quantized electronic movements. The mixed valence layers of the [4Fe4S] cluster due to spin coupling and their dynamic responses to light illumination are observed directly in our difference maps between its redox states. These direct observations of the quantum effects in a protein bound iron-sulfur cluster have thus opened a window into the mechanistic understanding of metal clusters in biological systems.

A complete biomimetic iron-sulfur cubane redox series

Synthetic iron-sulfur cubanes are models for biological cofactors, which are essential to delineate oxidation states in the more complex enzymatic systems. However, a complete series of [Fe₄S₄]ⁿ complexes spanning all redox states accessible by 1-electron transformations of the individual iron atoms (n = 0-4+) has never been prepared, deterring the methodical comparison of structure and spectroscopic signature. Here, we demonstrate that the use of a bulky arylthiolate ligand promoting the encapsulation of alkali-metal cations in the vicinity of the cubane enables the synthesis of such a series. Characterization by EPR, ⁵⁷Fe Mössbauer spectroscopy, UV-visible electronic absorption, variable-temperature X-ray diffraction analysis, and cyclic voltammetry reveals key trends for the geometry of the Fe₄S₄ core as well as for the Mössbauer isomer shift, which both correlate systematically with oxidation state. Furthermore, we confirm the S = 4 electronic ground state of the most reduced member of the series, [Fe₄S₄]⁰, and provide electrochemical evidence that it is accessible within 0.82 V from the [Fe₄S₄]²⁺ state, highlighting its relevance as a mimic of the nitrogenase iron protein cluster.

Evidence for Low-Valent Electronic Configurations in Iron-Sulfur Clusters

Although biological iron-sulfur (Fe-S) clusters perform some of the most difficult redox reactions in nature, they are thought to be composed exclusively of Fe²⁺ and Fe³⁺ ions, as well as mixed-valent pairs with average oxidation states of Fe^2.5+. We herein show that Fe-S clusters formally composed of these valences can access a wider range of electronic configurations─in particular, those featuring low-valent Fe¹⁺ centers. We demonstrate that CO binding to a synthetic [Fe₄S₄]⁰ cluster supported by N-heterocyclic carbene ligands induces the generation of Fe¹⁺ centers via intracluster electron transfer, wherein a neighboring pair of Fe²⁺ sites reduces the CO-bound site to a low-valent Fe¹⁺ state. Similarly, CO binding to an [Fe₄S₄]⁺ cluster induces electron delocalization with a neighboring Fe site to form a mixed-valent Fe^1.5+Fe^2.5+ pair in which the CO-bound site adopts partial low-valent character. These low-valent configurations engender remarkable C-O bond activation without having to traverse highly negative and physiologically inaccessible [Fe₄S₄]⁰/[Fe₄S₄]^- redox couples.

Spontaneous assembly of redox-active iron-sulfur clusters at low concentrations of cysteine

Iron-sulfur (FeS) proteins are ancient and fundamental to life, being involved in electron transfer and CO₂ fixation. FeS clusters have structures similar to the unit-cell of FeS minerals such as greigite, found in hydrothermal systems linked with the origin of life. However, the prebiotic pathway from mineral surfaces to biological clusters is unknown. Here we show that FeS clusters form spontaneously through interactions of inorganic Fe²⁺/Fe³⁺ and S^2- with micromolar concentrations of the amino acid cysteine in water at alkaline pH. Bicarbonate ions stabilize the clusters and even promote cluster formation alone at concentrations >10 mM, probably through salting-out effects. We demonstrate robust, concentration-dependent formation of [4Fe4S], [2Fe2S] and mononuclear iron clusters using UV-Vis spectroscopy, ⁵⁷Fe-Mössbauer spectroscopy and ¹H-NMR. Cyclic voltammetry shows that the clusters are redox-active. Our findings reveal that the structures responsible for biological electron transfer and CO₂ reduction could have formed spontaneously from monomers at the origin of life.

Characterization of Fe-S Clusters in Proteins by Mӧssbauer Spectroscopy

⁵⁷Fe Mӧssbauer spectroscopy is unparalleled in the study of Fe-S cluster-containing proteins because of its unique ability to detect all forms of iron. Enrichment of biological samples with the ⁵⁷Fe isotope and manipulation of experimental parameters such as temperature and magnetic field allow for elucidation of the number of Fe-S clusters present in a given protein, their nuclearity, oxidation state, geometry, and ligation environment, as well as any transient states relevant to enzyme chemistry. This chapter is arranged in five sections to help navigate an experimentalist to utilize ⁵⁷Fe Mӧssbauer spectroscopy for delineating the role and structure of biological Fe-S clusters. The first section lays out the tools and technical considerations for the preparation of ⁵⁷Fe-labeled samples. The choice of experimental parameters and their effects on the Mӧssbauer spectra are presented in the following two sections. The last two sections provide a theoretical and practical guide on spectral acquisition and analysis relevant to Fe-S centers.

Resolution of Low-Energy States in Spin-Exchange Transition-Metal Clusters: Case Study of Singlet States in [Fe(III)4S4] Cubanes

Polynuclear transition-metal (PNTM) clusters owe their catalytic activity to numerous energetically low-lying spin states and stable oxidation states. The characterization of their electronic structure represents one of the greatest challenges of modern chemistry. We propose a theoretical framework that enables the resolution of targeted electronic states with ease and apply it to two [Fe(III)₄S₄] cubanes. Through direct access to their many-body wave functions, we identify important correlation mechanisms and their interplay with the geometrical distortions observed in these clusters, which are core properties in understanding their catalytic activity. The simulated magnetic coupling constants predicted by our strategy allow us to make qualitative connections between spin interactions and geometrical distortions, demonstrating its predictive power. Moreover, despite its simplicity, the strategy provides magnetic coupling constants in good agreement with the available experimental ones. The complexes are intrinsically frustrated anti-ferromagnets, and the obtained spin structures together with the geometrical distortions represent two possible ways to release spin frustration (spin-driven Jahn–Teller distortion). Our paradigm provides a simple, yet rigorous, route to uncover the electronic structure of PNTM clusters and may be applied to a wide variety of such clusters.

Probing the All-Ferrous States of Methanogen Nitrogenase Iron Proteins

The Fe protein of nitrogenase reduces two C1 substrates, CO₂ and CO, under ambient conditions when its [Fe₄S₄] cluster adopts the all-ferrous [Fe₄S₄]⁰ state. Here, we show disparate reactivities of the nifH- and vnf-encoded Fe proteins from Methanosarcina acetivorans (designated MaNifH and MaVnfH) toward C1 substrates in the all-ferrous state, with the former capable of reducing both CO₂ and CO to hydrocarbons, and the latter only capable of reducing CO to hydrocarbons at substantially reduced yields. EPR experiments conducted at varying solution potentials reveal that MaVnfH adopts the all-ferrous state at a more positive reduction potential than MaNifH, which could account for the weaker reactivity of the MaVnfH toward C1 substrates than MaNifH. More importantly, MaVnfH already displays the g = 16.4 parallel-mode EPR signal that is characteristic of the all-ferrous [Fe₄S₄]⁰ cluster at a reduction potential of -0.44 V, and the signal reaches 50% maximum intensity at a reduction potential of -0.59 V, suggesting the possibility of this Fe protein to access the all-ferrous [Fe₄S₄]⁰ state under physiological conditions. These results bear significant relevance to the long-lasting debate of whether the Fe protein can utilize the [Fe₄S₄]^0/2+ redox couple to support a two-electron transfer during substrate turnover which, therefore, is crucial for expanding our knowledge of the reaction mechanism of nitrogenase and the cellular energetics of nitrogenase-based processes.

From Synthetic to Biological Fe4 S4 Complexes: Redox Properties Correlated to Function of Radical S-Adenosylmethionine Enzymes

By employing the computational protocol for calculation of reduction potentials of the Fe₄ S₄ -containing species validated using a representative series of well-defined synthetic complexes, we focused on redox properties of two prototypical radical SAM enzymes to reveal how they transform SAM into the reactive 5'-deoxyadenosyl radical, and how they tune this radical for its proper biological function. We found the reduction potential of SAM is indeed elevated by 0.3-0.4 V upon coordination to Fe₄ S₄ , which was previously speculated in the literature. This makes a generation of 5'-deoxyadenosyl radical from SAM less endergonic (by ca. 7-9 kcal mol^-1 ) and hence more feasible in both enzymes as compared to the identical process in water. Furthermore, our calculations indicate that the enzyme-bound 5'-deoxyadenosyl radical has a significantly lower reduction potential than in referential aqueous solution, which may help the enzymes to suppress potential side redox reactions and simultaneously elevate its proton-philic character, which may, in turn, promote the radical hydrogen-atom abstraction ability.

Homoleptic mono-, di-, and tetra-iron complexes featuring phosphido ligands: a synthetic, structural, and spectroscopic study

We report the first series of homoleptic phosphido iron complexes synthesized by treating either the β-diketiminato complex [(Dippnacnac)FeCl₂Li(dme)₂] (Dippnacnac = HC[(CMe)N(C₆H₃-2,6-iPr₂)]₂) or [FeBr₂(thf)₂] with an excess of phosphides R₂PLi (R = tBu, tBuPh, Cy, iPr). Reaction outcomes depend strongly on the bulkiness of the phosphido ligands. The use of tBu₂PLi precursor led to an anionic diiron complex 1 encompassing a planar Fe₂P₂ core with two bridging and two terminal phosphido ligands. An analogous reaction employing less sterically demanding phosphides, tBuPhPLi and Cy₂PLi yielded diiron anionic complexes 2 and 3, respectively, featuring a short Fe-Fe interaction supported by three bridging phosphido groups and one additional terminal R₂P^- ligand at each iron center. Further tuning of the P-substrates bulkiness gave a neutral phosphido complex 4 possessing a tetrahedral Fe₄ cluster core held together by six bridging iPr₂P moieties. Moreover, we also describe the first homoleptic phosphanylphosphido iron complex 5, which features an iron center with low coordination provided by three tBu₂P-P(SiMe₃)^- ligands. The structures of compounds 1-5 were determined by single-crystal X-ray diffraction and 1-3 by ¹H NMR spectroscopy. Moreover, the electronic structures of 1-3 were interrogated using zero-field Mössbauer spectroscopy and DFT methods.

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

Remote Ligand Modifications Tune Electronic Distribution and Reactivity in Site-Differentiated, High-Spin Iron Clusters: Flipping Scaling Relationships

We report the synthesis, characterization, and reactivity of [LFe₃O(^RArIm)₃Fe][OTf]₂, the first Hammett series of a site-differentiated cluster. The cluster reduction potentials and CO stretching frequencies shift as expected on the basis of the electronic properties of the ligand: electron-donating substituents result in more reducing clusters and weaker C-O bonds. However, unusual trends in the energetics of their two sequential CO binding events with the substituent σ_p parameters are observed. Specifically, introduction of electron-donating substituents suppresses the first CO binding event (ΔΔH by as much as 7.9 kcal mol^-1) but enhances the second (ΔΔH by as much as 1.9 kcal mol^-1). X-ray crystallography, including multiple-wavelength anomalous diffraction, Mössbauer spectroscopy, and SQUID magnetometry, reveal that these substituent effects result from changes in the energetic penalty associated with electronic redistribution within the cluster, which occurs during the CO binding event.

Spectroscopic Description of the E1 State of Mo Nitrogenase Based on Mo and Fe X-ray Absorption and Mössbauer Studies

Mo nitrogenase (N2ase) utilizes a two-component protein system, the catalytic MoFe and its electron-transfer partner FeP, to reduce atmospheric dinitrogen (N2) to ammonia (NH3). The FeMo cofactor contained in the MoFe protein serves as the catalytic center for this reaction and has long inspired model chemistry oriented toward activating N2. This field of chemistry has relied heavily on the detailed characterization of how Mo N2ase accomplishes this feat. Understanding the reaction mechanism of Mo N2ase itself has presented one of the most challenging problems in bioinorganic chemistry because of the ephemeral nature of its catalytic intermediates, which are difficult, if not impossible, to singly isolate. This is further exacerbated by the near necessity of FeP to reduce native MoFe, rendering most traditional means of selective reduction inept. We have now investigated the first fundamental intermediate of the MoFe catalytic cycle, E1, as prepared both by low-flux turnover and radiolytic cryoreduction, using a combination of Mo Kα high-energy-resolution fluorescence detection and Fe K-edge partial-fluorescence-yield X-ray absorption spectroscopy techniques. The results demonstrate that the formation of this state is the result of an Fe-centered reduction and that Mo remains redox-innocent. Furthermore, using Fe X-ray absorption and 57Fe Mössbauer spectroscopies, we correlate a previously reported unique species formed under cryoreducing conditions to the natively formed E1 state through annealing, demonstrating the viability of cryoreduction in studying the catalytic intermediates of MoFe.

Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein

The Fe protein of nitrogenase catalyzes the ambient reduction of CO₂ when its cluster is present in the all-ferrous, [Fe₄ S₄ ]⁰ oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO₂ . Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe₄ S₄ ]⁰ and [Fe₄ S₄ ]⁺ states point to a possible asymmetric functionality of a highly conserved Arg pair in CO₂ binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the "proximal" Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C-O bond. These results provide important mechanistic and structural insights into CO₂ activation by a surface-exposed, scaffold-held [Fe₄ S₄ ] cluster.

Structural Analysis of a Nitrogenase Iron Protein from Methanosarcina acetivorans: Implications for CO2 Capture by a Surface-Exposed [Fe4S4] Cluster

This work reports the crystal structure of a previously uncharacterized Fe protein from a methanogenic organism, which provides important insights into the structural properties of the less-characterized, yet highly interesting archaeal nitrogenase enzymes. Moreover, the structure-derived implications for CO₂ capture by a surface-exposed [Fe₄S₄] cluster point to the possibility of developing novel strategies for CO₂ sequestration while providing the initial insights into the unique mechanism of FeS-based CO₂ activation.

Nitrogenase iron (Fe) proteins reduce CO₂ to CO and/or hydrocarbons under ambient conditions. Here, we report a 2.4-Å crystal structure of the Fe protein from Methanosarcina acetivorans (MaNifH), which is generated in the presence of a reductant, dithionite, and an alternative CO₂ source, bicarbonate. Structural analysis of this methanogen Fe protein species suggests that CO₂ is possibly captured in an unactivated, linear conformation near the [Fe₄S₄] cluster of MaNifH by a conserved arginine (Arg) pair in a concerted and, possibly, asymmetric manner. Density functional theory calculations and mutational analyses provide further support for the capture of CO₂ on MaNifH while suggesting a possible role of Arg in the initial coordination of CO₂ via hydrogen bonding and electrostatic interactions. These results provide a useful framework for further mechanistic investigations of CO₂ activation by a surface-exposed [Fe₄S₄] cluster, which may facilitate future development of FeS catalysts for ambient conversion of CO₂ into valuable chemical commodities.

Site-Specific Oxidation State Assignments of the Iron Atoms in the [4Fe:4S]2+/1+/0 States of the Nitrogenase Fe-Protein

The nitrogenase iron protein (Fe-protein) contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+, and 0. Here, we use spatially resolved anomalous dispersion (SpReAD) refinement to determine oxidation assignments for the individual irons for each state. Additionally, we report the 1.13-Å resolution structure for the ADP bound Fe-protein, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]1+ state, our analysis identifies a solvent exposed, delocalized Fe2.5+ pair and a buried Fe2+ pair. We propose that ATP binding by the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe pair becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. In the [4Fe:4S]0 and [4Fe:4S]2+ states, the SpReAD analysis supports oxidation states assignments for all irons in these clusters of Fe2+ and valence delocalized Fe2.5+ , respectively.

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.

The Fe Protein: An Unsung Hero of Nitrogenase

Although the nitrogen-fixing enzyme nitrogenase critically requires both a reductase component (Fe protein) and a catalytic component, considerably more work has focused on the latter species. Properties of the catalytic component, which contains two highly complex metallocofactors and catalyzes the reduction of N2 into ammonia, understandably making it the “star” of nitrogenase. However, as its obligate redox partner, the Fe protein is a workhorse with multiple supporting roles in both cofactor maturation and catalysis. In particular, the nitrogenase Fe protein utilizes nucleotide binding and hydrolysis in concert with electron transfer to accomplish several tasks of critical importance. Aside from the ATP-coupled transfer of electrons to the catalytic component during substrate reduction, the Fe protein also functions in a maturase and insertase capacity to facilitate the biosynthesis of the two-catalytic component metallocofactors: fusion of the [Fe8S7] P-cluster and insertion of Mo and homocitrate to form the matured [(homocitrate)MoFe7S9C] M-cluster. These and key structural-functional relationships of the indispensable Fe protein and its complex with the catalytic component will be covered in this review.

Emerging critical roles of Fe-S clusters in DNA replication and repair

Fe-S clusters are partners in the origin of life that predate cells, acetyl-CoA metabolism, DNA, and the RNA world. The double helix solved the mystery of DNA replication by base pairing for accurate copying. Yet, for genome stability necessary to life, the double helix has equally important implications for damage repair. Here we examine striking advances that uncover Fe-S cluster roles both in copying the genetic sequence by DNA polymerases and in crucial repair processes for genome maintenance, as mutational defects cause cancer and degenerative disease. Moreover, we examine an exciting, controversial role for Fe-S clusters in a third element required for life - the long-range coordination and regulation of replication and repair events. By their ability to delocalize electrons over both Fe and S centers, Fe-S clusters have unbeatable features for protein conformational control and charge transfer via double-stranded DNA that may fundamentally transform our understanding of life, replication, and repair. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Cofactor composition and function of a H2-sensing regulatory hydrogenase as revealed by Mössbauer and EPR spectroscopy

The regulatory hydrogenase (RH) from Ralstonia eutropha H16 acts as a sensor for the detection of environmental H₂ and regulates gene expression related to hydrogenase-mediated cellular metabolism. In marked contrast to prototypical energy-converting [NiFe] hydrogenases, the RH is apparently insensitive to inhibition by O₂ and CO. While the physiological function of regulatory hydrogenases is well established, little is known about the redox cycling of the [NiFe] center and the nature of the iron-sulfur (FeS) clusters acting as electron relay. The absence of any FeS cluster signals in EPR had been attributed to their particular nature, whereas the observation of essentially only two active site redox states, namely Ni-SI and Ni-C, invoked a different operant mechanism. In the present work, we employ a combination of Mössbauer, FTIR and EPR spectroscopic techniques to study the RH, and the results are consistent with the presence of three [4Fe-4S] centers in the small subunit. In the as-isolated, oxidized RH all FeS clusters reside in the EPR-silent 2+ state. Incubation with H₂ leads to reduction of two of the [4Fe-4S] clusters, whereas only strongly reducing agents lead to reduction of the third cluster, which is ascribed to be the [4Fe-4S] center in 'proximal' position to the [NiFe] center. In the two different active site redox states, the low-spin Fe^II exhibits distinct Mössbauer features attributed to changes in the electronic and geometric structure of the catalytic center. The results are discussed with regard to the spectral characteristics and physiological function of H₂-sensing regulatory hydrogenases.

Mössbauer spectroscopy of Fe/S proteins

Iron-sulfur (Fe/S) clusters are structurally and functionally diverse cofactors that are found in all domains of life. (57)Fe Mössbauer spectroscopy is a technique that provides information about the chemical nature of all chemically distinct Fe species contained in a sample, such as Fe oxidation and spin state, nuclearity of a cluster with more than one metal ion, electron spin ground state of the cluster, and delocalization properties in mixed-valent clusters. Moreover, the technique allows for quantitation of all Fe species, when it is used in conjunction with electron paramagnetic resonance (EPR) spectroscopy and analytical methods. (57)Fe-Mössbauer spectroscopy played a pivotal role in unraveling the electronic structures of the "well-established" [2Fe-2S](2+/+), [3Fe-4S](1+/0), and [4Fe-4S](3+/2+/1+/0) clusters and -more-recently- was used to characterize novel Fe/S clustsers, including the [4Fe-3S] cluster of the O2-tolerant hydrogenase from Aquifex aeolicus and the 3Fe-cluster intermediate observed during the reaction of lipoyl synthase, a member of the radical SAM enzyme superfamily.

Characterization of [4Fe-4S] cluster vibrations and structure in nitrogenase Fe protein at three oxidation levels via combined NRVS, EXAFS, and DFT analyses

Azotobacter vinelandii nitrogenase Fe protein (Av2) provides a rare opportunity to investigate a [4Fe-4S] cluster at three oxidation levels in the same protein environment. Here, we report the structural and vibrational changes of this cluster upon reduction using a combination of NRVS and EXAFS spectroscopies and DFT calculations. Key to this work is the synergy between these three techniques as each generates highly complementary information and their analytical methodologies are interdependent. Importantly, the spectroscopic samples contained no glassing agents. NRVS and DFT reveal a systematic 10-30 cm(-1) decrease in Fe-S stretching frequencies with each added electron. The "oxidized" [4Fe-4S](2+) state spectrum is consistent with and extends previous resonance Raman spectra. For the "reduced" [4Fe-4S](1+) state in Fe protein, and for any "all-ferrous" [4Fe-4S](0) cluster, these NRVS spectra are the first available vibrational data. NRVS simulations also allow estimation of the vibrational disorder for Fe-S and Fe-Fe distances, constraining the EXAFS analysis and allowing structural disorder to be estimated. For oxidized Av2, EXAFS and DFT indicate nearly equal Fe-Fe distances, while addition of one electron decreases the cluster symmetry. However, addition of the second electron to form the all-ferrous state induces significant structural change. EXAFS data recorded to k = 21 Å(-1) indicates a 1:1 ratio of Fe-Fe interactions at 2.56 Å and 2.75 Å, a result consistent with DFT. Broken symmetry (BS) DFT rationalizes the interplay between redox state and the Fe-S and Fe-Fe distances as predominantly spin-dependent behavior inherent to the [4Fe-4S] cluster and perturbed by the Av2 protein environment.

Techniques for functional and structural modeling of nitrogenase

Synthetic compounds play an important role in developing our understanding of nitrogenase enzymes, and over the years, a multitude of new metal-containing compounds have been created using nitrogenase as an inspiration. The techniques for handling coordination compounds in organic solvents are different than those commonly encountered in a biochemistry or molecular biology laboratory. This chapter describes the precautions that are essential for successful synthesis of air- and moisture-sensitive synthetic compounds and gives details of the synthesis of some coordinatively unsaturated iron-dinitrogen and iron-sulfide compounds of interest in nitrogenase research.

Density functional theory study of an all ferrous 4Fe-4S cluster

The all-ferrous, carbene-capped Fe(4)S(4) cluster, synthesized by Deng and Holm (DH complex), has been studied with density functional theory (DFT). The geometry of the complex was optimized for several electronic configurations. The lowest energy was obtained for the broken-symmetry (BS) configuration derived from the ferromagnetic state by reversing the spin projection of one of the high spin (S(i) = 2) irons. The optimized geometry of the latter configuration contains one unique and three equivalent iron sites, which are both structurally and electronically clearly distinguishable. For example, a distinctive feature of the unique iron site is the diagonal Fe···S distance, which is 0.3 Å longer than for the equivalent irons. The calculated (57)Fe hyperfine parameters show the same 1:3 pattern as observed in the Mössbauer spectra and are in good agreement with experiment. BS analysis of the exchange interactions in the optimized geometry for the 1:3, M(S) = 4, BS configuration confirms the prediction of an earlier study that the unique site is coupled to the three equivalent ones by strong antiferromagnetic exchange (J > 0 in J Σ(j<4)Ŝ(4)·Ŝ(j)) and that the latter are mutually coupled by ferromagnetic exchange (J' < 0 in J' Σ(i<j<4)Ŝ(i)·Ŝ(j)). In combination, these exchange couplings stabilize an S = 4 ground state in which the composite spin of the three equivalent sites (S(123) = 6) is antiparallel to the spin (S(4) = 2) of the unique site. Thus, DFT analysis supports the idea that the unprecedented high value of the spin of the DH complex and, by analogy, of the all-ferrous cluster of the Fe-protein of nitrogenase, results from a remarkably strong dependence of the exchange interactions on cluster core geometry. The structure dependence of the exchange-coupling constants in the Fe(II)-(μ(3)-S)(2)-Fe(II) moieties of the all-ferrous clusters is compared with the magneto-structural correlations observed in the data for dinuclear copper complexes. Finally, we discuss two all-ferric clusters in the light of the results for the all-ferrous cluster.

The modular nature of all-ferrous edge-bridged double cubanes

Two all-ferrous, edge-bridged 8Fe-8S clusters, one capped with carbenes (2) and the other with phosphenes (3), have been characterized by (57)Fe Mossbauer spectroscopy. The clusters have diamagnetic ground states that yield spectra consisting of one quadrupole doublet with a large splitting (25% of absorption) and one (3) or two (2) doublets with much smaller splittings (75% of absorption). These patterns closely resemble those observed for all-ferrous 4Fe-4S clusters. Structurally, the 4Fe-4S fragments of 2 and 3 are remarkably similar to all-ferrous 4Fe-4S clusters, sharing with them the characteristic 3:1 pattern of the iron sites, a differentiation that has been shown previously to reflect spontaneous distortions of the cluster core. These spectroscopic and geometric similarities suggest that the diamagnetic ground state of the 8Fe-8S cluster results from antiferromagnetic exchange coupling of two identical 4Fe-4S modules, each carrying spin S(4Fe) = 4. The iron atoms with the largest quadrupole splittings are located at the opposite ends of the body diagonal containing the bridging sulfides.

Cubane-type Co4S4 clusters: synthesis, redox series, and magnetic ground states

The recent demonstration that the carbene cluster [Fe(4)S(4)(Pr(i)(2)NHCMe(2))(4)] (9) is an accurate structural and electronic analogue of the fully reduced cluster of the iron protein of Azotobacter vinelandii nitrogenase, including a common S = 4 ground state, raises the issue of the existence and magnetism of other [M(4)S(4)L(4)](z) clusters, none of which are known with transition metals other than iron. The system CoCl(2)/Pr(i)(3)P/(Me(3)Si)(2)S/THF assembles [Co(4)S(4)(PPr(i)(3))(4)] (3), which is converted to [Co(4)S(4)(Pr(i)(2)NHCMe(2))(4)] (5) upon reaction with carbene. The clusters support the redox series [3](1-/0/1+) and [5](0/1+/2+); monocations (4, 6) have been isolated by chemical oxidation. Redox potentials and substitution reactions indicate that the carbene is the more effective electron donor to tetrahedral Fe(II) and Co(II) sites. Clusters 3-6 have the same overall cubane-type geometry as 9. Neutral clusters 3 and 5 have an S = 3 ground state. As with the S = 4 state of 9 with local spins S(Fe) = 2, the septet spin state can be described in terms of the coupling of three parallel and one antiparallel spins S(Co) = 3/2. The octanuclear clusters [Co(8)S(8)(PPr(i)(3))(6)](0,1+) were isolated as minor byproducts of the formation and chemical oxidation of 3. The clusters exhibit a rhomb-bridged noncubane (RBNC) structure, whereas clusters with the Fe(8)S(8) core possess edge-bridged double-cubane (EBDC) stereochemistry. There are two structural solutions for the M(8)S(8) core in the form of topological isomers whose stability may depend on valence electron count. A conceptual model for the RBNC <--> EBDC interconversion is presented. (Pr(i)(2)NHCMe(2) = C(11)H(20)N(2) = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene).

Mössbauer, electron paramagnetic resonance, and theoretical studies of a carbene-based all-ferrous Fe4S4 cluster: electronic origin and structural identification of the unique spectroscopic site

It is well established that the cysteinate-coordinated [Fe(4)S(4)] cluster of the iron protein of nitrogenase from Azotobacter vinelandii (Av2) can attain the all-ferrous core oxidation state. Mössbauer and electron paramagnetic resonance (EPR) studies have shown that the all-ferrous cluster has a ground-state spin S = 4 and an effective 3:1 site symmetry in the spin structure and (57)Fe quadrupole interactions. Recently, Deng and Holm reported the synthesis of [Fe(4)S(4)(Pr(i)(2)NHCMe(2))(4)],(2) (1; Pr(i)(2)NHCMe(2) = 1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene) and showed that the all-ferrous carbene-coordinated cluster is amenable to physicochemical studies. Mössbauer and EPR studies of 1, reported here, reveal that the electronic structure of this complex is strikingly similar to that of the protein-bound cluster, suggesting that the ground-state spin and the 3:1 site ratio are consequences of spontaneous distortions of the cluster core. To gain insight into the origin of the peculiar ground state of the all-ferrous clusters in 1 and Av2, we have studied a theoretical model that is based on a Heisenberg-Dirac-van Vleck Hamiltonian whose exchange-coupling constants are a function of the Fe-Fe distances. By combining the exchange energies with the elastic deformation energies in the harmonic approximation, we obtain for a T(2) distortion a minimum with spin S = 4 and a C(3v) core structure in which one iron is unique and three irons are equivalent. This minimum has all of the spectroscopic and structural characteristics of the all-ferrous clusters of 1 and Av2. Our analysis maps the unique spectroscopic iron site to a specific site in the X-ray structure of the [Fe(4)S(4)](0) core both in complex 1 and in Av2.

Biomimetic chemistry of iron, nickel, molybdenum, and tungsten in sulfur-ligated protein sites

Biomimetic inorganic chemistry has as its primary goal the synthesis of molecules that approach or achieve the structures, oxidation states, and electronic and reactivity features of native metal-containing sites of variant nuclearity. Comparison of properties of accurate analogues and these sites ideally provides insight into the influence of protein structure and environment on intrinsic properties as represented by the analogue. For polynuclear sites in particular, the goal provides a formidable challenge for, with the exception of iron-sulfur clusters, all such site structures have never been achieved and few have even been closely approximated by chemical synthesis. This account describes the current status of the synthetic analogue approach as applied to the mononuclear sites in certain molybdoenzymes and the polynuclear sites in hydrogenases, nitrogenase, and carbon monoxide dehydrogenases.

Spectroscopic evidence for an all-ferrous [4Fe-4S]0 cluster in the superreduced activator of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans

The key enzyme of the fermentation of glutamate by Acidaminococcus fermentans, 2-hydroxyglutaryl-coenzyme A dehydratase, catalyzes the reversible syn-elimination of water from (R)-2-hydroxyglutaryl-coenzyme A, resulting in (E)-glutaconylcoenzyme A. The dehydratase system consists of two oxygen-sensitive protein components, the activator (HgdC) and the actual dehydratase (HgdAB). Previous biochemical and spectroscopic studies revealed that the reduced [4Fe-4S]+ cluster containing activator transfers one electron to the dehydratase driven by ATP hydrolysis, which activates the enzyme. With a tenfold excess of titanium(III) citrate at pH 8.0 the activator can be further reduced, yielding about 50% of a superreduced [4Fe-4S]0 cluster in the all-ferrous state. This is inferred from the appearance of a new Mössbauer spectrum with parameters delta = 0.65 mm/s and deltaE(Q) = 1.51-2.19 mm/s at 140 K, which are typical of Fe(II)S4 sites. Parallel-mode electron paramagnetic resonance (EPR) spectroscopy performed at temperatures between 3 and 20 K showed two sharp signals at g = 16 and 12, indicating an integer-spin system. The X-band EPR spectra and magnetic Mössbauer spectra could be consistently simulated by adopting a total spin S(t) = 4 for the all-ferrous cluster with weak zero-field splitting parameters D = -0.66 cm(-1) and E/D = 0.17. The superreduced cluster has apparent spectroscopic similarities with the corresponding [4Fe-4S]0 cluster described for the nitrogenase Fe-protein, but in detail their properties differ. While the all-ferrous Fe-protein is capable of transferring electrons to the MoFe-protein for dinitrogen reduction, a similar physiological role is elusive for the superreduced activator. This finding supports our model that only one-electron transfer steps are involved in dehydratase catalysis. Nevertheless we discuss a common basic mechanism of the two diverse systems, which are so far the only described examples of the all-ferrous [4Fe-4S]0 cluster found in biology.

The structure of the 2[4Fe-4S] ferredoxin from Pseudomonas aeruginosa at 1.32-A resolution: comparison with other high-resolution structures of ferredoxins and contributing structural features to reduction potential values

The structure of the 2[4Fe-4S] ferredoxin (PaFd) from Pseudomonas aeruginosa, which belongs to the Allochromatium vinosum (Alvin) subfamily, has been determined by X-ray crystallography at 1.32-A resolution, which is the highest up to now for a member of this subfamily of Fds. The main structural features of PaFd are similar to those of AlvinFd. However, the significantly higher resolution of the PaFd structure makes possible a reliable comparison with available high-resolution structures of [4Fe-4S]-containing Fds, in an effort to rationalize the unusual electrochemical properties of Alvin-like Fds. Three major factors contributing to the reduction potential values of [4Fe-4S]2+/+ clusters of Fds, namely, the surface accessibility of the clusters, the N-H...S hydrogen-bonding network, and the volume of the cavities hosting the clusters, are extensively discussed. The volume of the cavities is introduced in the present work for the first time, and can in part explain the very negative potential of cluster I of Alvin-like Fds.