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

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.

Identifying a key spot for electron mediator-interaction to tailor CO dehydrogenase's affinity

Fe‒S cluster-harboring enzymes, such as carbon monoxide dehydrogenases (CODH), employ sophisticated artificial electron mediators like viologens to serve as potent biocatalysts capable of cleaning-up industrial off-gases at stunning reaction rates. Unraveling the interplay between these enzymes and their associated mediators is essential for improving the efficiency of CODHs. Here we show the electron mediator-interaction site on ChCODHs (Ch, Carboxydothermus hydrogenoformans) using a systematic approach that leverages the viologen-reactive characteristics of superficial aromatic residues. By enhancing mediator-interaction (R57G/N59L) near the D-cluster, the strategically tailored variants exhibit a ten-fold increase in ethyl viologen affinity relative to the wild-type without sacrificing the turn-over rate (kcat). Viologen-complexed structures reveal the pivotal positions of surface phenylalanine residues, serving as external conduits for the D-cluster to/from viologen. One variant (R57G/N59L/A559W) can treat a broad spectrum of waste gases (from steel-process and plastic-gasification) containing O2. Decoding mediator interactions will facilitate the development of industrially high-efficient biocatalysts encompassing gas-utilizing enzymes.

Efficient, Light-Driven Reduction of CO2 to CO by a Carbon Monoxide Dehydrogenase-CdSe/CdS Nanorod Photosystem

The solar conversion of CO₂ to low carbon fuels has been heralded as a potential solution to combat the rise in greenhouse gas emissions. Here we report the first light-driven activation of [NiFe] CODH II from Carboxydothermus hydrogenoformans for the reduction of CO₂ to CO. To accomplish this, a hybrid photosystem composed of CODH II and CdSe/CdS dot-in-rod nanocrystals was developed. By incorporating a low-potential redox mediator to assist electron transfer, quantum yields up to 19% and turnover frequencies of 9 s^-1 were achieved. These results represent a new standard in efficient CO₂ reduction by an enzyme-based photocatalytic systems. Furthermore, successful photoactivation of CODH II allows for future exploration into the enzyme's not fully understood mechanism.

A Pyrene-Triazacyclononane Anchor Affords High Operational Stability for CO2 RR by a CNT-Supported Histidine-Tagged CODH

An original 1-acetato-4-(1-pyrenyl)-1,4,7-triazacyclononane (AcPyTACN) was synthesized for the immobilization of a His-tagged recombinant CODH from Rhodospirillum rubrum (RrCODH) on carbon-nanotube electrodes. The strong binding of the enzyme at the Ni-AcPyTACN complex affords a high current density of 4.9 mA cm-2 towards electroenzymatic CO2 reduction and a high stability of more than 6×106  TON when integrated on a gas-diffusion bioelectrode.

Protein-based models offer mechanistic insight into complex nickel metalloenzymes

There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.

Understanding the local chemical environment of bioelectrocatalysis

Bioelectrochemistry employs an array of high-surface-area meso- and macroporous electrode architectures to increase protein loading and the electrochemical current response. While the local chemical environment has been studied in small-molecule and heterogenous electrocatalysis, conditions in enzyme electrochemistry are still commonly established based on bulk solution assays, without appropriate consideration of the nonequilibrium conditions of the confined electrode space. Here, we apply electrochemical and computational techniques to explore the local environment of fuel-producing oxidoreductases within porous electrode architectures. This improved understanding of the local environment enabled simple manipulation of the electrolyte solution by adjusting the bulk pH and buffer pKa to achieve an optimum local pH for maximal activity of the immobilized enzyme. When applied to macroporous inverse opal electrodes, the benefits of higher loading and increased mass transport were employed, and, consequently, the electrolyte adjusted to reach −8.0 mA ⋅ cm−2 for the H2 evolution reaction and −3.6 mA ⋅ cm−2 for the CO2 reduction reaction (CO2RR), demonstrating an 18-fold improvement on previously reported enzymatic CO2RR systems. This research emphasizes the critical importance of understanding the confined enzymatic chemical environment, thus expanding the known capabilities of enzyme bioelectrocatalysis. These considerations and insights can be directly applied to both bio(photo)electrochemical fuel and chemical synthesis, as well as enzymatic fuel cells, to significantly improve the fundamental understanding of the enzyme–electrode interface as well as device performance.

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.

Sulfide and transition metals - A partnership for life

Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.

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.

The Solvent-Exposed Fe-S D-Cluster Contributes to Oxygen-Resistance in Desulfovibrio vulgaris Ni-Fe Carbon Monoxide Dehydrogenase

Ni-Fe CO-dehydrogenases (CODHs) catalyze the conversion between CO and CO₂ using a chain of Fe-S clusters to mediate long-range electron transfer. One of these clusters, the D-cluster, is surface-exposed and serves to transfer electrons between CODH and external redox partners. These enzymes tend to be extremely O₂-sensitive and are always manipulated under strictly anaerobic conditions. However, the CODH from Desulfovibrio vulgaris (Dv) appears unique: exposure to micromolar concentrations of O₂ on the minutes-time scale only reversibly inhibits the enzyme, and full activity is recovered after reduction. Here, we examine whether this unusual property of Dv CODH results from the nature of its D-cluster, which is a [2Fe-2S] cluster, instead of the [4Fe-4S] cluster observed in all other characterized CODHs. To this aim, we produced and characterized a Dv CODH variant where the [2Fe-2S] D-cluster is replaced with a [4Fe-4S] D-cluster through mutagenesis of the D-cluster-binding sequence motif. We determined the crystal structure of this CODH variant to 1.83-Å resolution and confirmed the incorporation of a [4Fe-4S] D-cluster. We show that upon long-term O₂-exposure, the [4Fe-4S] D-cluster degrades, whereas the [2Fe-2S] D-cluster remains intact. Crystal structures of the Dv CODH variant exposed to O₂ for increasing periods of time provide snapshots of [4Fe-4S] D-cluster degradation. We further show that the WT enzyme purified under aerobic conditions retains 30% activity relative to a fully anaerobic purification, compared to 10% for the variant, and the WT enzyme loses activity more slowly than the variant upon prolonged aerobic storage. The D-cluster is therefore a key site of irreversible oxidative damage in Dv CODH, and the presence of a [2Fe-2S] D-cluster contributes to the O₂-tolerance of this enzyme. Together, these results relate O₂-sensitivity with the details of the protein structure in this family of enzymes.

Selective Oxidation of H2 and CO by NiIr Catalyst in Aqueous Solution: A DFT Mechanistic Study

One of the challenges in utilizing hydrogen gas (H₂) as a sustainable fossil fuel alternative is the inhibition of H₂ oxidation by carbon monoxide (CO), which is involved in the industrial production of H₂ sources. To solve this problem, a catalyst that selectively oxidizes either CO or H₂ or one that co-oxidizes H₂ and CO is needed. Recently, a NiIr catalyst [Ni^IICl(X)Ir^IIICl(η⁵-C₅Me₅)], (X = N,N'-dimethyl-3,7-diazanonane-1,9-dithiolate), which efficiently and selectively oxidizes either H₂ or CO depending on the pH, has been developed (Angew. Chem. Int. Ed. 2017, 56, 9723-9726). In the present work, density functional theory (DFT) calculations are employed to elucidate the pH-dependent reaction mechanisms of H₂ and CO oxidation catalyzed by this NiIr catalyst. During H₂ oxidation, our calculations suggest that dihydrogen binds to the Ir center and generates an Ir(III)-dihydrogen complex, followed by subsequent isomerization to an Ir(V)-dihydride species. Then, a proton is abstracted by a buffer base, CH₃COO^-, resulting in the formation of a hydride complex. The catalytic cycle completes with electron transfer from the hydride complex to a protonated 2,6-dichlorobenzeneindophenol (DCIP) and a proton transfer from the oxidized hydride complex to a buffer base. The CO oxidation mechanism involves three distinct steps, i.e., (1) formation of a metal carbonyl complex, (2) formation of a metallocarboxylic acid, and (3) conversion of the metallocarboxylic acid to a hydride complex. The formation of the metallocarboxylic acid involves nucleophilic attack of OH^- to the carbonyl-C followed by a large structural change with concomitant cleavage of the Ir-S bond and rotation of the COOH group along the NiIr axis. During the conversion of the metallocarboxylic acid to the hydride complex, intramolecular proton transfer followed by removal of CO₂ leads to the formation of the hydride complexes. In addition, the barrier heights for the binding of small molecules (H₂, OH^-, H₂O, and CO) to Ir were calculated, and the results indicated that dissociation from Ir is a faster process than the binding of H₂O and H₂. These calculations indicate that H₂ oxidation is inhibited by CO and OH^- and thus prefers acidic conditions. In contrast, the CO oxidation reactions occur more favorably under basic conditions, as the formation of the metallocarboxylic acid involves OH^- attack to a carbonyl-C and the binding of OH^- to Ni largely stabilizes the triplet spin state of the complex. Taken together, these calculations provide a rationale for the experimentally observed pH-dependent, selective oxidations of H₂ and CO.

The good, the neutral, and the positive: buffer identity impacts CO2 reduction activity by nickel(ii) cyclam

Development of new synthetic catalysts for CO2 reduction has been a central focus of chemical research efforts towards mitigating rising global carbon dioxide levels. In parallel with generating new molecular systems, characterization and benchmarking of these compounds across well-defined catalytic conditions are essential. Nickel(ii) cyclam is known to be an active catalyst for CO2 reduction to CO. The degree of selectivity and activity has been found to differ widely across electrodes used and upon modification of the ligand environment, though without a molecular-level understanding of this variation. Moreover, while proton transfer is key for catalytic activity, the effects of varying the nature of the proton donor remain unclear. In this work, a systematic investigation of the electrochemical and light-driven catalytic behaviour of nickel(ii) cyclam under different aqueous reaction conditions has been performed. The activity and selectivity are seen to vary widely depending on the nature of the buffering agent, even at a constant pH, highlighting the importance of proton transfer for catalysis. Buffer binding to the nickel center is negatively correlated with selectivity, and cationic buffers show high levels of selectivity and activity. These results are discussed in the context of molecular design principles for developing increasingly efficient and selective catalysts. Moreover, identifying these key contributors towards activity has implications for understanding the role of the conserved secondary coordination environments in naturally occurring CO2-reducing enzymes, including carbon monoxide dehydrogenase and formate dehydrogenase.

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.

Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase

The C-cluster of the enzyme carbon monoxide dehydrogenase (CODH) is a structurally distinctive Ni-Fe-S cluster employed to catalyze the reduction of CO₂ to CO as part of the Wood-Ljungdahl carbon fixation pathway. Using X-ray crystallography, we have observed unprecedented conformational dynamics in the C-cluster of the CODH from Desulfovibrio vulgaris, providing the first view of an oxidized state of the cluster. Combined with supporting spectroscopic data, our structures reveal that this novel, oxidized cluster arrangement plays a role in avoiding irreversible oxidative degradation at the C-cluster. Furthermore, mutagenesis of a conserved cysteine residue that binds the C-cluster in the oxidized state but not in the reduced state suggests that the oxidized conformation could be important for proper cluster assembly, in particular Ni incorporation. Together, these results lay a foundation for future investigations of C-cluster activation and assembly, and contribute to an emerging paradigm of metallocluster plasticity.

Fast and Selective Photoreduction of CO2 to CO Catalyzed by a Complex of Carbon Monoxide Dehydrogenase, TiO2, and Ag Nanoclusters

Selective, visible-light-driven conversion of CO₂ to CO with a turnover frequency of 20 s^-1 under visible light irradiation at 25 °C is catalyzed by an aqueous colloidal system comprising a pseudoternary complex formed among carbon monoxide dehydrogenase (CODH), silver nanoclusters stabilized by polymethacrylic acid (AgNCs-PMAA), and TiO₂ nanoparticles. The photocatalytic assembly, which is stable over several hours and for at least 250000 turnovers of the enzyme's active site, was investigated by separate electrochemical (dark) and fluorescence measurements to establish specific connectivities among the components. The data show (a) that a coating of AgNCs-PMAA on TiO₂ greatly enhances its ability as an electrode for CODH- based electrocatalysis of CO₂ reduction and (b) that the individual Ag nanoclusters interact directly and dynamically with the enzyme surface, most likely at exposed cysteine thiols. The results lead to a model for photocatalysis in which the AgNCs act as photosensitizers, CODH captures the excited electrons for catalysis, and TiO₂ mediates hole transfer from the AgNC valence band to sacrificial electron donors. The results greatly increase the benchmark for reversible CO₂ reduction under ambient conditions and demonstrate that, with such efficient catalysts, the limiting factor is the supply of photogenerated electrons.