Carbon monoxide dehydrogenase reaction mechanism: a likely case of abnormal CO2 insertion to a Ni-H(-) bond

Mixed Valence {Ni2+Ni1+} Clusters as Models of Acetyl Coenzyme A Synthase Intermediates

Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4]n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni2+Ni1+} cluster, [K(12-crown-4)2][1], effectively replicates the coordination number and oxidation state of the proposed "Ared" state of the A-cluster. Addition of carbon monoxide to [1]- allows for isolation of a dinuclear {Ni2+Ni1+(CO)} complex, [K(12-crown-2)n][2] (n = 1-2), which bears similarity to the "ANiFeC" enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1]- is more stable than the Y-conformation by 22 kcal mol-1, and that binding of CO to Ni1+ is barrierless and exergonic by 6 kcal mol-1. UV/vis absorption spectroscopy on [2]- in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2]- promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.

Opportunities for Insight into the Mechanism of Efficient CO2/CO Interconversion at a Nickel-Iron Cluster in CO Dehydrogenase

The reduction of CO2 with low overpotential and high selectivity is a crucial challenge in catalysis. Fortunately, natural systems have evolved enzymes that achieve this catalytic reaction very efficiently at a complex nickel-iron-sulfur cluster within carbon monoxide dehydrogenase (CODH). Extensive biochemical, crystallographic, and spectroscopic work has been done to understand the structures and mechanism involved in the catalytic cycle, which are summarized here from the perspective of mechanistic organometallic chemistry. We highlight the ambiguities in the data and suggest experiments that could lead to clearer understanding of the mechanism and structures of intermediates at the active-site cluster. These include parallel crystallography and spectroscopy, as well as the preparation of synthetic analogues that help to interpret structural and spectroscopic signatures.

Three-Coordinate Nickel and Metal-Metal Interactions in a Heterometallic Iron-Sulfur Cluster

Biological multielectron reactions often are performed by metalloenzymes with heterometallic sites, such as anaerobic carbon monoxide dehydrogenase (CODH), which has a nickel-iron-sulfide cubane with a possible three-coordinate nickel site. Here, we isolate the first synthetic iron-sulfur clusters having a nickel atom with only three donors, showing that this structural feature is feasible. These have a core with two tetrahedral irons, one octahedral tungsten, and a three-coordinate nickel connected by sulfide and thiolate bridges. Electron paramagnetic resonance (EPR), Mössbauer, and superconducting quantum interference device (SQUID) data are combined with density functional theory (DFT) computations to show how the electronic structure of the cluster arises from strong magnetic coupling between the Ni, Fe, and W sites. X-ray absorption spectroscopy, together with spectroscopically validated DFT analysis, suggests that the electronic structure can be described with a formal Ni1+ atom participating in a nonpolar Ni-W σ-bond. This metal-metal bond, which minimizes spin density at Ni1+, is conserved in two cluster oxidation states. Fe-W bonding is found in all clusters, in one case stabilizing a local non-Hund state at tungsten. Based on these results, we compare different M-M interactions and speculate that other heterometallic clusters, including metalloenzyme active sites, could likewise store redox equivalents and stabilize low-valent metal centers through metal-metal bonding.

Metal-Metal Bond Umpolung in Heterometallic Extended Metal Atom Chains

Understanding the fundamental properties governing metal–metal interactions is crucial to understanding the electronic structure and thereby applications of multimetallic systems in catalysis, material science, and magnetism. One such property that is relatively underexplored within multimetallic systems is metal–metal bond polarity, parameterized by the electronegativities (χ) of the metal atoms involved in the bond. In heterobimetallic systems, metal–metal bond polarity is a function of the donor–acceptor (Δχ) interactions of the two bonded metal atoms, with electropositive early transition metals acting as electron acceptors and electronegative late transition metals acting as electron donors. We show in this work, through the preparation and systematic study of a series of Mo₂M(dpa)₄(OTf)₂ (M = Cr, Mn, Fe, Co, and Ni; dpa = 2,2′-dipyridylamide; OTf = trifluoromethanesulfonate) heterometallic extended metal atom chain (HEMAC) complexes that this expected trend in χ can be reversed. Physical characterization via single-crystal X-ray diffraction, magnetometry, and spectroscopic methods as well as electronic structure calculations supports the presence of a σ symmetry 3c/3e^– bond that is delocalized across the entire metal-atom chain and forms the basis of the heterometallic Mo₂–M interaction. The delocalized 3c/3e^– interaction is discussed within the context of the analogous 3c/3e^– π bonding in the vinoxy radical, CH₂CHO. The vinoxy comparison establishes three predictions for the σ symmetry 3c/3e^– bond in HEMACS: (1) an umpolung effect that causes the Mo–M interactions to become more covalent as Δχ increases, (2) distortion of the σ bonding and non-bonding orbitals to emphasize Mo–M bonding and de-emphasize Mo–Mo bonding, and (3) an increase in Mo spin population with increasing Mo–M covalency. In agreement with these predictions, we find that the Mo₂···M covalency increases with increasing Δχ of the Mo and M atoms (Δχ_Mo–M increases as M = Cr < Mn < Fe < Co < Ni), an umpolung of the trend predicted in the absence of σ delocalization. We attribute the observed trend in covalency to the decreased energic differential (ΔE) between the heterometal orbital and the σ bonding molecular orbital of the Mo₂ quadruple bond, which serves as an energetically stable, “ligand”-like electron-pair donor to the heterometal ion acceptor. As M is changed from Cr to Ni, the σ bonding and nonbonding orbitals do indeed distort as anticipated, and the spin population of the outer Mo group is increased by at least a factor of 2. These findings provide a predictive framework for multimetallic compounds and advance the current understanding of the electronic structures of molecular heteromultimetallic systems, which can be extrapolated to applications in the context of mixed-metal surface catalysis and multimetallic proteins.

This work describes how use of a metal−metal quadruply bonded metalloligand can reverse expected trends in metal−metal bond polarity through the preparation and systematic study of a novel series of Mo₂M(dpa)₄(OTf)₂ (M = Cr, Mn, Fe, Co, and Ni) heterotrimetallic extended metal atom chain (HEMAC) complexes. These complexes feature a 3c/3e⁻ metal−metal bond that is delocalized across the entire metal atom chain and is compared to the 3c/3e⁻ π bonding in the vinoxyl radical.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H₂, N₂, CO₂, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N₂, CO₂, and CO and the production of H₂ require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N₂ fixation by nitrogenase and H₂ production by hydrogenase as well as CO₂ and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Recent developments on the transformation of CO2 utilising ligand cooperation and related strategies

A portfolio of value-added chemicals, fuels and building block compounds can be envisioned from CO₂ on an industrial scale. The high kinetic and thermodynamic stabilities of CO₂, however, present a significant barrier to its utilisation as a C1 source. In this context, metal-ligand cooperation methodologies have emerged as one of the most dominant strategies for the transformation of the CO₂ molecule over the last decade or so. This review focuses on the advancements in CO₂ transformation using these cooperative methodologies. Different and well-studied ligand cooperation methodologies, such as dearomatisation-aromatisation type cooperation, bimetallic cooperation (M⋯M'; M' = main group or transition metal) and other related strategies are also discussed. Furthermore, the cooperative bond activations are subdivided based on the number of atoms connecting the reactive centre in the ligand framework (spacer/linker length) and the transition metal. Several similarities across these seemingly distinct cooperative methodologies are emphasised. Finally, this review brings out the challenges ahead in developing catalytic systems from these CO₂ transformations.

Electrochemical Studies of CO2 -Reducing Metalloenzymes

Only two enzymes are capable of directly reducing CO₂ : CO dehydrogenase, which produces CO at a [NiFe₄ S₄ ] active site, and formate dehydrogenase, which produces formate at a mononuclear W or Mo active site. Both metalloenzymes are very rapid, energy-efficient and specific in terms of product. They have been connected to electrodes with two different objectives. A series of studies used protein film electrochemistry to learn about different aspects of the mechanism of these enzymes (reactivity with substrates, inhibitors…). Another series focused on taking advantage of the catalytic performance of these enzymes to build biotechnological devices, from CO₂ -reducing electrodes to full photochemical devices performing artificial photosynthesis. Here, we review all these works.

Reversible Electron Transfer and Substrate Binding Support [NiFe3S4] Ferredoxin as a Protein-Based Model for [NiFe] Carbon Monoxide Dehydrogenase

The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme catalyzes the reversible and selective interconversion of carbon dioxide (CO₂) to carbon monoxide (CO) with high rates and negligible overpotential. Despite decades of research, many questions remain about this complex metalloenzyme system. A simplified model enzyme could provide substantial insight into biological carbon cycling. Here, we demonstrate reversible electron transfer and binding of both CO and cyanide, a substrate and an inhibitor of CODH, respectively, in a Pyrococcus furiosus (Pf) ferredoxin (Fd) protein that has been reconstituted with a nickel-iron sulfide cluster ([NiFe₃S₄] Fd). The [NiFe₃S₄] cluster mimics the core of the native CODH active site and thus serves as a protein-based structural model of the CODH subsite. Notably, despite binding cyanide, no CO binding is observed for the physiological [Fe₄S₄] clusters in Pf Fd, providing chemical rationale underlying the evolution of a site-differentiated cluster for substrate conversion in native CODH. The demonstration of a substrate-binding metalloprotein model of CODH sets the stage for high-resolution spectroscopic and mechanistic studies correlating the subsite structure and function, ultimately guiding the design of anthropogenic catalysts that harness the advantages of CODH for effective CO₂ reduction.

Residues surrounding the active centre of carbon monoxide dehydrogenase are key in converting [Formula: see text] to CO

The enzyme carbon monoxide dehydrogenase is capable of efficiently converting [Formula: see text] to CO and, therefore, can enable an affordable [Formula: see text] recycling strategy. The reduction of [Formula: see text] occurs at a peculiar nickel-iron-sulfur cluster, following a mechanism that remains little understood. In this study, we have used ab initio molecular dynamics simulations to explore the free energy landscape of the reaction. We predict the existence of a COOH ligand that strongly interacts with the surrounding protein residues and favours a mechanism where a [Formula: see text] molecule is eliminated before CO. We have taken advantages of the insights offered by our simulations to revisit the catalytic mechanism and the role of the residues surrounding the active centre in particular, thus assisting in the design of inorganic catalysts that mimic the enzyme.

A Beginner’s Guide to Thermodynamic Modelling of [FeFe] Hydrogenase

[FeFe] hydrogenases, which are considered the most active naturally occurring catalysts for hydrogen oxidation and proton reduction, are extensively studied as models to learn the important features for efficient H2 conversion catalysis. Using infrared spectroscopy as a selective probe, the redox behaviour of the active site H-cluster is routinely modelled with thermodynamic schemes based on the Nernst equation for determining thermodynamic parameters, such as redox midpoint potentials and pKa values. Here, the thermodynamic models usually applied to [FeFe] hydrogenases are introduced and discussed in a pedagogic fashion and their applicability to additional metalloenzymes and molecular catalysts is also addressed.

A quantum chemical approach for the mechanisms of redox-active metalloenzymes

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes. In our group we have developed an approach that has been applied to a large number of such systems. Hybrid density functional theory (hybrid DFT) has from the start of these investigations been the leading electronic structure tool. An understanding of how the method works in practice has significantly improved the accuracy and applicability. During the past ten years, it has been found that the results for redox enzymes mainly depend on the chosen fraction of exact exchange in the functional, and that a choice of 15% has worked best. The idea has therefore been to vary that fraction over a reasonable range and study the relative energy dependence. For modeling the enzymes, a cluster approach has been developed. In the present review the development of the method we used is described from its start in work on photosystem II, fifteen years ago. Examples from a few recent applications are described, where the metals have been iron, nickel, copper, cobalt or manganese. The results are in excellent agreement with available experiments, and a large number of new predictions have been made.

During the past 20 years, quantum chemistry has grown to be a significant part in the investigation of mechanisms for redox-active enzymes.

First-Principles Calculations on Ni,Fe-Containing Carbon Monoxide Dehydrogenases Reveal Key Stereoelectronic Features for Binding and Release of CO2 to/from the C-Cluster

In view of the depletion of fossil fuel reserves and climatic effects of greenhouse gas emissions, Ni,Fe-containing carbon monoxide dehydrogenase (Ni-CODH) enzymes have attracted increasing interest in recent years for their capability to selectively catalyze the reversible reduction of CO₂ to CO (CO₂ + 2H⁺ + 2e^– CO + H₂O). The possibility of converting the greenhouse gas CO₂ into useful materials that can be used as synthetic building blocks or, remarkably, as carbon fuels makes Ni-CODH a very promising target for reverse-engineering studies. In this context, in order to provide insights into the chemical principles underlying the biological catalysis of CO₂ activation and reduction, quantum mechanics calculations have been carried out in the framework of density functional theory (DFT) on different-sized models of the Ni-CODH active site. With the aim of uncovering which stereoelectronic properties of the active site (known as the C-cluster) are crucial for the efficient binding and release of CO₂, different coordination modes of CO₂ to different forms and redox states of the C-cluster have been investigated. The results obtained from this study highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. In particular, the protonation state of His93 is found to be crucial for promoting the binding or the dissociation of CO₂. The oxidation state of the C-cluster is also shown to be critical. CO₂ binds to C_red2 according to a dissociative mechanism (i.e., CO₂ binds to the C-cluster after the release of possible ligands from Fe_u) when His93 is doubly protonated. CO₂ can also bind noncatalytically to C_red1 according to an associative mechanism (i.e., CO₂ binding is preceded by the binding of H₂O to Fe_u). Conversely, CO₂ dissociates when His93 is singly protonated and the C-cluster is oxidized at least to the C_int redox state.

Density functional theory was used to investigate Ni,Fe-containing carbon monoxide dehydrogenase enzymes. Different coordination modes of the substrate CO₂ to several forms and redox states of the C-cluster—the enzyme active site—were considered. The obtained results highlight the key role of the protein environment in tuning the reactivity and the geometry of the C-cluster. This helps to uncover which stereoelectronic properties of the active site are crucial for the efficient binding and release of CO₂.

Bioinspired Nickel Complexes Supported by an Iron Metalloligand

Nature utilizes multimetallic sites in metalloenzymes to enable multielectron chemical transformations at ambient conditions and low overpotentials. One such example of multimetallic cooperativity can be found in the C-cluster of Ni-carbon monoxide dehydrogenase (CODH), which interconverts CO and CO₂. Toward a potential functional model of the C-cluster, a family of Ni-Fe bimetallic complexes was synthesized that contain direct metal-metal bonding interactions. The complexes were characterized by X-ray crystallography, various spectroscopies (NMR, EPR, UV-vis, Mössbauer), and theoretical calculations. The Ni-Fe bimetallic system has a reversible Fe(III)/Fe(II) redox couple at -2.10 V (vs Fc⁺/Fc). The Fe-based "redox switch" can turn on CO₂ reactivity at the Ni(0) center by leveraging the Ni→Fe dative interaction to attenuate the Ni(0) electron density. The reduced Ni(0)Fe(II) species mediated the formal two-electron reduction of CO₂ to CO, providing a Ni-CO adduct and CO₃^2- as products. During the reaction, an intermediate was observed that is proposed to be a Ni-CO₂ species.

Theoretical Studies of Nickel-Dependent Enzymes

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.

Energetics for the Mechanism of Nickel-Containing Carbon Monoxide Dehydrogenase

Nickel-containing carbon monoxide (CO) dehydrogenase is an enzyme that catalyzes the important reversible carbon dioxide reduction. Several high-resolution structures have been determined at various stages of the reduction, which can be used as good starting points for the present computational study. The cluster model is used in combination with a systematic application of the density functional theory as recently described. The results are in very good agreement with experimental evidence. There are a few important results. To explain why the X-ray structure for the reduced C_red1 state has an empty site on nickel, it is here suggested that the cluster has been over-reduced by X-rays and is therefore not the desired reduced state, which instead contains a bound CO on nickel. After an additional reduction, a hydride bound to nickel is suggested to play a role. In order to obtain energetics in agreement with experiments, it is concluded that one sulfide bridge in the Ni-Fe cluster should be protonated. The best test of the accuracy obtained is to compare the computed rate for reduction using -0.6 V with that for oxidation using -0.3 V, where good agreement was obtained. Obtaining a mechanism that is easily reversible is another demanding aspect of the modeling. Nickel oscillates between nickel(II) and nickel(I), while nickel(0) never comes in.

Carbon Monoxide Dehydrogenases

Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of CO with water to CO₂, two electrons, and two protons. Two classes of CODHs exist, having evolved from different scaffolds featuring active sites built from different transition metals. The basic properties of both classes are described in this overview chapter.

Selective Transformation of CO2 to CO at a Single Nickel Center

Carbon dioxide conversion mediated by transition metal complexes continues to attract much attention because of its future potential utilization as a nontoxic and inexpensive C1 source for the chemical industry. Given the presence of nickel in natural systems that allow for extremely efficient catalysis, albeit in an Fe cluster arrangement, studies that focus on selective CO₂ conversion with synthetic nickel species are currently of considerable interest in our group. In this Account, the selective conversion of CO₂ to carbon monoxide occurring at a single nickel center is discussed. The chemistry is based on a series of related nickel pincer complexes with attention to the uniqueness of the coordination geometry, which is crucial in allowing for particular reactivity toward CO₂. Our research is inspired by the efficient enzymatic CO₂ catalysis occurring at the active site of carbon monoxide dehydrogenase. Since the binding and reactivity toward CO₂ are controlled in part by the geometry of a L₃Ni scaffold, we have explored the chemistry of low-valent nickel supported by PP^MeP and PNP ligands, in which a pseudotetrahedral or square-planar geometry is accommodated. Two isolated nickel-CO₂ adducts, (PP^MeP)Ni(η²-CO₂-κ C) (2) and {Na(12-C-4)₂}{(PNP)Ni(η¹-CO₂-κ C)} (7), clearly demonstrate that the geometry of the nickel ion is crucial in the binding of CO₂ and its level of activation. In the case of a square-planar nickel center supported by a PNP ligand, a series of bimetallic metallacarboxylate Ni-μ-CO₂-κ C, O-M species (M = H, Na, Ni, Fe) were synthesized, and their structural features and reactivity were studied. Protonation cleaves the C-O bond, resulting in the formation of a nickel(II) monocarbonyl complex. By sequential reduction, the corresponding mono- and zero-valent Ni-CO species were produced. The reactivities of three nickel carbonyl species toward various iodoalkanes and CO₂ were explored to address whether their corresponding reactivities could be controlled by the number of valence d electrons. In particular, a (PNP)Ni(0)-CO species (13) shows immediate reactivity toward CO₂ but displays multiple product formation. By incorporation of a -CMe₂- bridging unit, a structurally rigidified ^acriPNP ligand was newly designed and produced. This ligand modification was successful in preparing the T-shaped nickel(I) metalloradical species 9 exhibiting open-shell reactivity due to the sterically exposed nickel center possessing a half-filled d _{x²- y²} orbital. More importantly, the selective addition of CO₂ to a nickel(0)-CO species was enabled to afford a nickel(II)-carboxylate species (22) with the expulsion of CO(g). Finally, the (^acriPNP)Ni system provides a synthetic cycle in the study of the selective conversion of CO₂ to CO that involves two-electron reduction of Ni-CO followed by the direct addition of CO₂ to release the coordinated CO ligand.

Direct CO2 Addition to a Ni(0)-CO Species Allows the Selective Generation of a Nickel(II) Carboxylate with Expulsion of CO

Addition of CO₂ to a low-valent nickel species has been explored with a newly designed ^acriPNP pincer ligand (^acriPNP^- = 4,5-bis(diisopropylphosphino)-2,7,9,9-tetramethyl-9H-acridin-10-ide). This is a crucial step in understanding biological CO₂ conversion to CO found in carbon monoxide dehydrogenase (CODH). A four-coordinate nickel(0) state was reliably accessed in the presence of a CO ligand, which can be prepared from a stepwise reduction of a cationic {(^acriPNP)Ni(II)-CO}⁺ species. All three Ni(II), Ni(I), and Ni(0) monocarbonyl species were cleanly isolated and spectroscopically characterized. Addition of electrons to the nickel(II) species significantly alters its geometry from square planar toward tetrahedral because of the filling of the d_x²-y² orbital. Accordingly, the CO ligand position changes from equatorial to axial, ∠N-Ni-C of 176.2(2)° to 129.1(4)°, allowing opening of a CO₂ binding site. Upon addition of CO₂ to a nickel(0)-CO species, a nickel(II) carboxylate species with a Ni(η¹-CO₂-κC) moiety was formed and isolated (75%). This reaction occurs with the concomitant expulsion of CO(g). This is a unique result markedly different from our previous report involving the flexible analogous PNP ligand, which revealed the formation of multiple products including a tetrameric cluster from the reaction with CO₂. Finally, the carbon dioxide conversion to CO at a single nickel center is modeled by the successful isolation of all relevant intermediates, such as Ni-CO₂, Ni-COOH, and Ni-CO.

Sterically Stabilized Terminal Hydride of a Diiron Dithiolate

The kinetically robust hydride [t-HFe₂(Me₂pdt)(CO)₂(dppv)₂]⁺ ([t-H1]⁺) (Me₂pdt^2- = Me₂C(CH₂S^-)₂; dppv = cis-1,2-C₂H₂(PPh₂)₂) and related derivatives were prepared with ⁵⁷Fe enrichment for characterization by NMR, FT-IR, and NRVS. The experimental results were rationalized using DFT molecular modeling and spectral simulations. The spectroscopic analysis was aimed at supporting assignments of Fe-H vibrational spectra as they relate to recent measurements on [FeFe]-hydrogenase enzymes. The combination of bulky Me₂pdt^2- and dppv ligands stabilizes the terminal hydride with respect to its isomerization to the 5-16 kcal/mol more stable bridging hydride ([μ-H1]⁺) with t_1/2(313.3 K) = 19.3 min. In agreement with the nOe experiments, the calculations predict that one methyl group in [t-H1]⁺ interacts with the hydride with a computed CH···HFe distance of 1.7 Å. Although [t-H⁵⁷1]⁺ exhibits multiple NRVS features in the 720-800 cm^-1 region containing the bending Fe-H modes, the deuterated [t-D⁵⁷1]⁺ sample exhibits a unique Fe-D/CO band at ∼600 cm^-1. In contrast, the NRVS spectra for [μ-H⁵⁷1]⁺ exhibit weaker bands near 670-700 cm^-1 produced by the Fe-H-Fe wagging modes coupled to Me₂pdt^2- and dppv motions.

Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase

QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

When the inhibitor tells more than the substrate: the cyanide-bound state of a carbon monoxide dehydrogenase

An integral approach including experimental and theoretical analysis has been carried out with the wild-type and engineered CODHII_Ch variant to assess the parameters that control the C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> N stretching frequency.

Carbon monoxide dehydrogenase (CODH) is a key enzyme for reversible CO interconversion. To elucidate structural and mechanistic details of CO binding at the CODH active site (C-cluster), cyanide is frequently used as an iso-electronic substitute and inhibitor. However, previous studies revealed conflicting results on the structure of the cyanide-bound complex and the mechanism of cyanide-inhibition. To address this issue in this work, we have employed IR spectroscopy, crystallography, site directed mutagenesis, and theoretical methods to analyse the cyanide complex of the CODH from Carboxydothermus hydrogenoformans (CODHII_Ch). IR spectroscopy demonstrates that a single cyanide binds to the Ni ion. Whereas the inhibitor could be partially removed at elevated temperature, irreversible degradation of the C-cluster occurred in the presence of an excess of cyanide on the long-minute time scale, eventually leading to the formation of [Fe(CN)₆]^4– and [Ni(CN)₄]^2– complexes. Theoretical calculations based on a new high-resolution structure of the cyanide-bound CODHII_Ch indicated that cyanide binding to the Ni ion occurs upon dissociation of the hydroxyl ligand from the Fe₁ subsite of the C-cluster. The hydroxyl group is presumably protonated by Lys563 which, unlike to His93, does not form a hydrogen bond with the cyanide ligand. A stable deprotonated ε-amino group of Lys563 in the cyanide complex is consistent with the nearly unchanged C Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> N stretching in the Lys563Ala variant of CODHII_Ch. These findings support the view that the proton channel connecting the solution phase with the active site displays a strict directionality, controlled by the oxidation state of the C-cluster.

CO and CN- syntheses by [FeFe]-hydrogenase maturase HydG are catalytically differentiated events

The synthesis and assembly of the active site [FeFe] unit of [FeFe]-hydrogenases require at least three maturases. The radical S-adenosyl-l-methionine HydG, the best characterized of these proteins, is responsible for the synthesis of the hydrogenase CO and CN(-) ligands from tyrosine-derived dehydroglycine (DHG). We speculated that CN(-) and the CO precursor (-):CO2H may be generated through an elimination reaction. We tested this hypothesis with both wild type and HydG variants defective in second iron-sulfur cluster coordination by measuring the in vitro production of CO, CN(-), and (-):CO2H-derived formate. We indeed observed formate production under these conditions. We conclude that HydG is a multifunctional enzyme that produces DHG, CN(-), and CO at three well-differentiated catalytic sites. We also speculate that homocysteine, cysteine, or a related ligand could be involved in Fe(CO)x(CN)y transfer to the HydF carrier/scaffold.

The Mössbauer Parameters of the Proximal Cluster of Membrane-Bound Hydrogenase Revisited: A Density Functional Theory Study

An unprecedented [4Fe-3S] cluster proximal to the regular [NiFe] active site has recently been found to be responsible for the ability of membrane-bound hydrogenases (MBHs) to oxidize dihydrogen in the presence of ambient levels of oxygen. Starting from proximal cluster models of a recent DFT study on the redox-dependent structural transformation of the [4Fe-3S] cluster, ⁵⁷Fe Mössbauer parameters (electric field gradients, isomer shifts, and nuclear hyperfine couplings) were calculated using DFT. Our results revise the previously reported correspondence of Mössbauer signals and iron centers in the [4Fe-3S]³⁺ reduced-state proximal cluster. Similar conflicting assignments are also resolved for the [4Fe-3S]⁵⁺ superoxidized state with particular regard to spin-coupling in the broken-symmetry DFT calculations. Calculated ⁵⁷Fe hyperfine coupling (HFC) tensors expose discrepancies in the experimental set of HFC tensors and substantiate the need for additional experimental work on the magnetic properties of the MBH proximal cluster in its reduced and superoxidized redox states.

Investigations by Protein Film Electrochemistry of Alternative Reactions of Nickel-Containing Carbon Monoxide Dehydrogenase

Protein film electrochemistry has been used to investigate reactions of highly active nickel-containing carbon monoxide dehydrogenases (CODHs). When attached to a pyrolytic graphite electrode, these enzymes behave as reversible electrocatalysts, displaying CO2 reduction or CO oxidation at minimal overpotential. The O2 sensitivity of CODH is suppressed by adding cyanide, a reversible inhibitor of CO oxidation, or by raising the electrode potential. Reduction of N2O, isoelectronic with CO2, is catalyzed by CODH, but the reaction is sluggish, despite a large overpotential, and results in inactivation. Production of H2 and formate under highly reducing conditions is consistent with calculations predicting that a nickel-hydrido species might be formed, but the very low rates suggest that such a species is not on the main catalytic pathway.

A 10(6)-fold enhancement in N2-binding affinity of an Fe2(μ-H)2 core upon reduction to a mixed-valence Fe(II)Fe(I) state

Transient hydride ligands bridging two or more iron centers purportedly accumulate on the iron-molybdenum cofactor (FeMoco) of nitrogenase, and their role in the reduction of N2 to NH3 is unknown. One role of these ligands may be to facilitate N2 coordination at an iron site of FeMoco. Herein, we consider this hypothesis and describe the preparation of a series of diiron complexes supported by two bridging hydride ligands. These compounds bind either one or two molecules of N2 depending on the redox state of the Fe2(μ-H)2 unit. An unusual example of a mixed-valent Fe(II)(μ-H)2Fe(I) is described that displays a 10(6)-fold enhancement of N2 binding affinity over its oxidized congener, quantified by spectroscopic and electrochemical techniques. Furthermore, these compounds show promise as functional models of nitrogenase as substantial amounts of NH3 are produced upon exposure to proton and electron equivalents. The Fe(μ-H)Fe(N2) sub-structure featured herein was previously unknown. This subunit may be relevant to consider in nitrogenases during turnover.

[FeFe] hydrogenase: protonation of {2Fe3S} systems and formation of super-reduced hydride states

The synthesis and crystallographic characterization of a complex possessing a well-defined {2Fe3S(μ-H)} core gives access to a paramagnetic bridging hydride with retention of the core geometry. Chemistry of this 35-electron species within the confines of a thin-layer FTIR spectro-electrochemistry cell provides evidence for a unprecedented super-reduced Fe(I)(μ-H)Fe(I) intermediate.

Nickel-dependent metalloenzymes

This review describes the functions, structures, and mechanisms of nine nickel-containing enzymes: glyoxalase I, acireductone dioxygenase, urease, superoxide dismutase, [NiFe]-hydrogenase, carbon monoxide dehydrogenase, acetyl-coenzyme A synthase/decarbonylase, methyl-coenzyme M reductase, and lactate racemase. These enzymes catalyze their various chemistries by using metallocenters of diverse structures, including mononuclear nickel, dinuclear nickel, nickel-iron heterodinuclear sites, more complex nickel-containing clusters, and nickel-tetrapyrroles. Selected other enzymes are active with nickel, but the physiological relevance of this metal specificity is unclear. Additional nickel-containing proteins of undefined function have been identified.

Investigations of the efficient electrocatalytic interconversions of carbon dioxide and carbon monoxide by nickel-containing carbon monoxide dehydrogenases

Carbon monoxide dehydrogenases (CODH) play an important role in utilizing carbon monoxide (CO) or carbon dioxide (CO2) in the metabolism of some microorganisms. Two distinctly different types of CODH are distinguished by the elements constituting the active site. A Mo-Cu containing CODH is found in some aerobic organisms, whereas a Ni-Fe containing CODH (henceforth simply Ni-CODH) is found in some anaerobes. Two members of the simplest class (IV) of Ni-CODH behave as efficient, reversible electrocatalysts of CO2/CO interconversion when adsorbed on a graphite electrode. Their intense electroactivity sets an important benchmark for the standard of performance at which synthetic molecular and material electrocatalysts comprised of suitably attired abundant first-row transition elements must be able to operate. Investigations of CODHs by protein film electrochemistry (PFE) reveal how the enzymes respond to the variable electrode potential that can drive CO2/CO interconversion in each direction, and identify the potential thresholds at which different small molecules, both substrates and inhibitors, enter or leave the catalytic cycle. Experiments carried out on a much larger (Class III) enzyme CODH/ACS, in which CODH is complexed tightly with acetyl-CoA synthase, show that some of these characteristics are retained, albeit with much slower rates of interfacial electron transfer, attributable to the difficulty in making good electronic contact at the electrode. The PFE results complement and clarify investigations made using spectroscopic investigations.