Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster

Computational Modeling of Electrocatalysts for CO2 Reduction: Probing the Role of Primary, Secondary, and Outer Coordination Spheres

ConspectusIn the search for efficient and selective electrocatalysts capable of converting greenhouse gases to value-added products, enzymes found in naturally existing bacteria provide the basis for most approaches toward electrocatalyst design. Ni,Fe-carbon monoxide dehydrogenase (Ni,Fe-CODH) is one such enzyme, with a nickel-iron-sulfur cluster named the C-cluster, where CO2 binds and is converted to CO at high rates near the thermodynamic potential. In this Account, we divide the enzyme's catalytic contributions into three categories based on location and function. We also discuss how computational techniques provide crucial insight into implementing these findings in homogeneous CO2 reduction electrocatalysis design principles. The CO2 binding sites (e.g., Ni and "unique" Fe ion) along with the ligands that support it (e.g., iron-sulfur cluster) form the primary coordination sphere. This is replicated in molecular electrocatalysts via the metal center and ligand framework where the substrate binds. This coordination sphere has a direct impact on the electronic configuration of the catalyst. By computationally modeling a series of Ni and Co complexes with bipyridyl-N-heterocyclic carbene ligand frameworks of varying degrees of planarity, we were able to closely examine how the primary coordination sphere controls the product distribution between CO and H2 for these catalysts. The secondary coordination sphere (SCS) of Ni,Fe-CODH contains residues proximal to the active site pocket that provide hydrogen-bonding stabilizations necessary for the reaction to proceed. Enhancing the SCS when synthesizing new catalysts involves substituting functional groups onto the ligand for direct interaction with the substrate. To analyze the endless possible substitutions, computational techniques are ideal for deciphering the intricacies of substituent effects, as we demonstrated with an array of imidazolium-functionalized Mn and Re bipyridyl tricarbonyl complexes. By examining how the electrostatic interactions between the ligand, substrate, and proton source lowered activation energy barriers, we determined how best to pinpoint the SCS additions. The outer coordination sphere comprises the remaining parts of Ni,Fe-CODH, such as the elaborate protein matrix, solvent interactions, and remote metalloclusters. The challenge in elucidating and replicating the role of the vast protein matrix has understandably led to a localized focus on the primary and secondary coordination spheres. However, certain portions of Ni,Fe-CODH's expansive protein scaffold are suggested to be catalytically relevant despite considerable distance from the active site. Closer studies of these relatively overlooked areas of nature's exceptionally proficient catalysts may be crucial to continually improve upon electrocatalysis protocols. Mechanistic analysis of cobalt phthalocyanines (CoPc) immobilized onto carbon nanotubes (CoPc/CNT) reveals how the active site microenvironment and outer coordination sphere effects unlock the CoPc molecule's previously inaccessible intrinsic catalytic ability to convert CO2 to MeOH. Our research suggests that incorporating the three coordination spheres in a holistic approach may be vital for advancing electrocatalysis toward viability in mitigating climate disruption. Computational methods allow us to closely examine transition states and determine how to minimize key activation energy barriers.

Conformational dynamics of a multienzyme complex in anaerobic carbon fixation

In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO2) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen Clostridium autoethanogenum, characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO2 reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme, which is crucial for CO2 fixation in anaerobic organisms.

The ISC machinery assembles [2Fe-2S] clusters by formation and fusion of [1Fe-1S] precursors

Iron-sulfur clusters are essential metallocofactors synthesized by multiprotein machineries via an unclear multistep process. Here we report a step-by-step dissection of the [2Fe-2S] cluster assembly process by the Escherichia coli iron-sulfur cluster (ISC) assembly machinery using an in vitro reconstituted system and a combination of biochemical and spectroscopic techniques. We show that this process is initiated by iron binding to the scaffold protein IscU, which triggers persulfide insertion by the cysteine desulfurase IscS upon the formation of a complex with IscU. Then, the persulfide is cleaved into sulfide by the ferredoxin Fdx, leading to a [1Fe-1S] precursor. IscU dissociates from IscS, dimerizes and generates a bridging [2Fe-2S] cluster by fusion of two [1Fe-1S] precursors. The IscU dimer ultimately dissociates into a monomer, ready to transfer its [2Fe-2S] cluster to acceptors. These data provide a comprehensive description of the [2Fe-2S] cluster assembly process by the ISC assembly machinery, highlighting the formation of key intermediates through a tightly concerted process.

Distinct Valence States of the [4Fe4S] Cluster Revealed in the Hydrogenase CrHydA1

Iron-sulfur clusters play a crucial role in electron transfer for many essential enzymes, including [FeFe]-hydrogenases. This study focuses on the [4Fe4S] cluster ([4Fe]H) of the minimal [FeFe]-hydrogenase from Chlamydomonas reinhardtii (CrHydA1) and employs advanced spectroscopy, site-directed mutagenesis, molecular dynamics simulations, and QM/MM calculations. We provide insights into the complex electronic structure of [4Fe]H and its role in the catalytic reaction of CrHydA1, serving as paradigm for understanding [FeFe]-hydrogenases. We identified at least two distinct species within the apo-form of CrHydA1, designated 4Fe-R and 4Fe-A, with unique redox potentials and pH sensitivities. Our findings revealed that these species arise from a complex interplay of structural heterogeneity and valence isomer rearrangements, influenced by second-sphere residues. We propose that the interconversion between 4Fe-R and 4Fe-A could provide control over electron transfer in the absence of accessory FeS clusters typically found in other [FeFe]-hydrogenases. The insights gained from this study not only enhance our understanding of [FeFe]-hydrogenases but also provide a crucial foundation for future investigations into analysis of other FeS clusters across diverse biological systems.

Nickel model complexes to mimic carbon monoxide dehydrogenase reactions

Biological CO2/CO interconversion catalyzed at the Ni/Fe heterobimetallic active site of anaerobic carbon monoxide dehydrogenases (CODHs) offers important insights for the design of efficient and selective synthetic catalysts for CO2 capture and utilization (CCU). Notably, this organometallic C1 interconversion process is mediated at a three-coordinate nickel site. Extensive research has been conducted to elucidate the redox and structural changes involved in substrate binding and conversion. The CO2-bound structure of CODH, in particular, has inspired many synthetic studies aimed at exploring key questions, concerning the choice of metal, the role of the unique iron (Feu), and the geometry and oxidation states of both Ni and Feu, as well as CO2/CO exchange mechanism. A better understanding of CODH chemistry promises to reveal and uncover fundamental principles for small molecule activation of first-row transition metal complexes. This mini-review focuses on three key aspects: (1) the coordination environment of the Ni centre in CODH, (2) bioinorganic Ni model systems that provide insight into the biological CO2/CO interconversion at the CODH active site, and (3) recent advances in CODH-inspired catalysis for selective CO2-to-CO conversion.

Iron‑sulfur cluster biogenesis and function in Apicomplexa parasites

Iron‑sulfur cluster are ubiquitous and ancient protein cofactors that support a wide array of essential cellular functions. In eukaryotes, their assembly requires specific and dedicated machineries in each subcellular compartment. Apicomplexans are parasitic protists that are collectively responsible for a significant burden on the health of humans and other animals, and most of them harbor two organelles of endosymbiotic origin: a mitochondrion, and a plastid of high metabolic importance called the apicoplast. Consequently, apicomplexan parasites have distinct iron‑sulfur cluster assembly machineries located to their endosymbiotic organelles, as well as a cytosolic pathway. Recent findings have not only shown the importance of iron‑sulfur cluster assembly for the fitness of these parasites, but also highlighted parasite-specific features that may be promising for the development of targeted anti-parasitic strategies.

Transferring enzyme features to molecular CO2 reduction catalysts

Carbon monoxide dehydrogenases and formate dehydrogenases efficiently catalyze the reduction of CO2. In both enzymes, CO2 activation at the metal active site is assisted by proximate amino acids and Fe-S-clusters. Functional features of the enzyme are mimicked in molecular catalysts by redox-active ligands, acidic and charged groups in the ligand periphery, and binuclear scaffolds. These components have all improved the catalytic performance of synthetic systems. Recent studies impart a deeper understanding of the individual contributions of the various functionalities to reactivity and of their combined effects. New catalyst platforms reveal alternate pathways for CO2 reduction, unique intermediates, and strategies for switching selectivity. Design of a wider array of complexes that combine different functional elements is encouraged to further optimize catalysts for CO2 reduction, especially for product formation beyond CO. More diverse bimetallic catalysts are needed to better exploit metal-metal interactions for CO2 conversion.

Composition Determination of Heterometallic Trinuclear Clusters via Anomalous X-ray and Neutron Diffraction

Anomalous X-ray diffraction (AXD) and neutron diffraction can be used to crystallographically distinguish between metals of similar electron density. Despite the use of AXD for structural characterization in mixed metal clusters, there are no benchmark studies evaluating the accuracy of AXD toward assessing elemental occupancy in molecules with comparisons with what is determined via neutron diffraction. We collected resonant diffraction data on several homo and heterometallic clusters and refined their anomalous scattering components to determine metal site occupancies. Theoretical resonant scattering terms for Fe0, Co0, and Zn0 were compared against experimental values, revealing theoretical values are ill-suited to serve as references for occupancy determination. The cluster featuring distinct cation and anion metal compositions [CoCp2*][(tbsL)Fe3(μ3-NAr)] was used to assess the accuracy of different f' references for occupancy determination (f'theoretical ± 15-17%; f'experimental ± 10%). This methodology was applied toward calculating the occupancy of three different clusters: (tbsL)Fe2Zn(py) (6), (tbsL)Fe2Zn(μ3-NAr)(py) (7), and [CoCp*2][(tbsL)Fe2Zn(μ3-NAr)] (8). The first two clusters maintain 100% Fe/Zn site isolation, whereas 8 showed metal mixing within the sites. The large crystal size of 8 enabled collection of neutron diffraction data which was compared against the results found with AXD. The ability of AXD to replicate the metal occupancies as determined by neutron diffraction supports the AXD occupancy methodology developed herein. Furthermore, the advantages innate to AXD (e.g., smaller crystal sizes, shorter collection times, and greater availability of synchrotron resources) versus neutron diffraction further support the need for its development as a standard technique.

Heterobimetallic NiFe Complex for Photocatalytic CO2 Reduction: United Efforts of NiFe Dual Sites

Catalytic CO2 reduction poses a significant challenge for the conversion of CO2 into chemicals and fuels. Ni-Fe carbon monoxide dehydrogenase ([NiFe]-CODH) effectively mediates the reversible conversion of CO2 and CO at a nearly thermodynamic equilibrium potential, highlighting the heterobimetallic cooperation for the design of CO2 reduction catalysts. However, numerous NiFe biomimetic model complexes have realized little success in CO2 reduction catalysis, which underscores the crucial role of precise bimetallic configuration and functionality. Herein, we presented a heterobimetallic NiFe complex for the photocatalytic reduction of CO2 to CO, demonstrating significantly enhanced catalytic performance compared to the homonuclear NiNi catalyst. Photocatalytic and mechanistic investigations revealed that with the assistance of a redox-active phenanthroline ligand, NiFe achieves dual-site activation of CO2 through a pivotal intermediate, NiII(μ-CO22--κC:κO)FeII, where the Lewis acidity of the FeII site plays an important role, as corroborated in the homonuclear FeFe system. This study introduces the first heteronuclear NiFe molecular catalyst capable of efficiently catalyzing the reduction of CO2 to CO, deepening insights into heterobimetallic cooperation and offering a novel strategy for designing highly active and selective CO2 reduction catalysts.

Capturing a methanogenic carbon monoxide dehydrogenase/acetyl-CoA synthase complex via cryogenic electron microscopy

Approximately two-thirds of the estimated one-billion metric tons of methane produced annually by methanogens is derived from the cleavage of acetate. Acetate is broken down by a Ni-Fe-S-containing A-cluster within the enzyme acetyl-CoA synthase (ACS) to carbon monoxide (CO) and a methyl group (CH3+). The methyl group ultimately forms the greenhouse gas methane, whereas CO is converted to the greenhouse gas carbon dioxide (CO2) by a Ni-Fe-S-containing C-cluster within the enzyme carbon monoxide dehydrogenase (CODH). Although structures have been solved of CODH/ACS from acetogens, which use these enzymes to make acetate from CO2, no structure of a CODH/ACS from a methanogen has been reported. In this work, we use cryo-electron microscopy to reveal the structure of a methanogenic CODH and CODH/ACS from Methanosarcina thermophila (MetCODH/ACS). We find that the N-terminal domain of acetogenic ACS, which is missing in all methanogens, is replaced by a domain of CODH. This CODH domain provides a channel for CO to travel between the two catalytic Ni-Fe-S clusters. It generates the binding surface for ACS and creates a remarkably similar CO alcove above the A-cluster using residues from CODH rather than ACS. Comparison of our MetCODH/ACS structure with our MetCODH structure reveals a molecular mechanism to restrict gas flow from the CO channel when ACS departs, preventing CO escape into the cell. Overall, these long-awaited structures of a methanogenic CODH/ACS reveal striking functional similarities to their acetogenic counterparts despite a substantial difference in domain organization.

Enzymatic CO2 reduction catalyzed by natural and artificial Metalloenzymes

The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.

Exploring the Frontiers of Heterometallic Systems: the {FeW5} Octahedral Cluster Complex

This research presents the first examples of heterometallic octahedral cluster complexes incorporating both 5d and 3d metals, specifically, tungsten and iron. The key compound, (TBA)2[FeW5Br14] (TBA = tetrabutylammonium), exhibits selective ligand substitution reactions at the iron site when exposed to various solvents. Several {FeW5}-type anions, namely, [FeW5Br14]2-, [FeW5Br13(L)]- (L = H2O, DMSO, CH3CN), and [(FeW5Br13)2O]4-, were revealed and characterized by single-crystal X-ray diffraction analysis. The redox properties of [FeW5Br14]2- were studied and compared with those of [W6Br14]2-. Density functional theory calculations demonstrated that the bonding between Fe and W atoms is fundamentally different from the bonding between 4d (Mo-Mo) or 5d (W-W) metals in isotypic {M6} clusters.

Understanding the role of negative charge in the scaffold of an artificial enzyme for CO2 hydrogenation on catalysis

We have approached the construction of an artificial enzyme by employing a robust protein scaffold, lactococcal multidrug resistance regulator, LmrR, providing a structured secondary and outer coordination spheres around a molecular rhodium complex, [RhI(PEt2NglyPEt2)2]-. Previously, we demonstrated a 2-3 fold increase in activity for one Rh-LmrR construct by introducing positive charge in the secondary coordination sphere. In this study, a series of variants was made through site-directed mutagenesis where the negative charge is located in the secondary sphere or outer coordination sphere, with additional variants made with increasingly negative charge in the outer coordination sphere while keeping a positive charge in the secondary sphere. Placing a negative charge in the secondary or outer coordination sphere demonstrates decreased activity by a factor of two compared to the wild-type Rh-LmrR. Interestingly, addition of positive charge in the secondary sphere, with the negatively charged outer coordination sphere restores activity. Vibrational and NMR spectroscopy suggest minimal changes to the electronic density at the rhodium center, regardless of inclusion of a negative or positive charge in the secondary sphere, suggesting another mechanism is impacting catalytic activity, explored in the discussion.

Chemical Antiquity in Metabolism

ConspectusLife is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.

Generation of Thiosulfate, Selenite, Dithiosulfite, Perthionitrite, Nitric Oxide, and Reactive Chalcogen Species by Binuclear Zinc(II)-Chalcogenolato/-Polychalcogenido Complexes

A comparative bioinspired reactivity study of new binuclear Zn(II) complexes featuring coordinated thiolate, selenolate, trisulfide and diselenide in relation with (i) the generation of reactive sulfur/selenium species (RSS/RSeS), (ii) the oxygen dependent oxidation and disproportionation of polysulfide (Sn2-) to produce sulfite (SO32-), thiosulfate (S2O32-) and sulfide (S2-) by sulfur oxygenase reductase (SOR), and (iii) the reaction of Sn2- with nitrite (NO2-) to generate thionitrite (SNO-), perthionitrite (SSNO-) and nitric oxide (NO), is presented. The binuclear Zn(II)-thiolate/selenolate complexes could react with elemental sulfur to generate RSS/RSeS while similar reactions involving elemental selenium could not generate RSeS. The dizinc(II)-S3 and the dizinc(II)-Se2 complexes could react with dioxygen (O2) to generate binuclear Zn(II) complexes featuring coordinated thiosulfate (S2O32-) and selenite (SeO32-), respectively. Finally, unlike the nonreactive nature of the dizinc(II)-Se2 complex toward NO2-, reaction of the dizinc(II)-S3 complex with NO2- produced a new binuclear Zn(II) complex featuring a coordinated dithiosulfite (S3O2-) along with the formation of perthionitrite (SSNO-), of which the latter subsequently produced nitric oxide (NO) and S42-. The present work, thus, demonstrates the comparative reactivity of a series of binuclear Zn(II)-chalcogenolato/-polychalcogenido complexes for the generation of S2O32-, SeO32-, S3O2-, SSNO-, NO and RSS/RSeS.

Phylogenetic diversity of putative nickel-containing carbon monoxide dehydrogenase-encoding prokaryotes in the human gut microbiome

Although the production of carbon monoxide (CO) within the human body has been detected, only two CO-utilizing prokaryotes (CO utilizers) have been reported in the human gut. Therefore, the phylogenetic diversity of the human gut CO-utilizing prokaryotes remains unclear. Here, we unveiled more than a thousand representative genomes containing genes for putative nickel-containing CO dehydrogenase (pCODH), an essential enzyme for CO utilization. The taxonomy of genomes encoding pCODH was expanded to include 8 phyla, comprising 82 genera and 248 species. In contrast, putative molybdenum-containing CODH genes were not detected in the human gut microbial genomes. pCODH transcripts were detected in 97.3 % (n=110) of public metatranscriptome datasets derived from healthy human faeces, suggesting the ubiquitous presence of prokaryotes bearing transcriptionally active pCODH genes in the human gut. More than half of the pCODH-encoding genomes contain a set of genes for the autotrophic Wood-Ljungdahl pathway (WLP). However, 79 % of these genomes commonly lack a key gene for the WLP, which encodes the enzyme that synthesizes formate from CO2, suggesting that potential human gut CO-utilizing prokaryotes share a degenerated gene set for WLP. In the other half of the pCODH-encoding genomes, seven genes, including putative genes for flavin adenine dinucleotide-dependent NAD(P) oxidoreductase (FNOR), ABC transporter and Fe-hydrogenase, were found adjacent to the pCODH gene. None of the putative genes associated with CO-oxidizing respiratory machinery, such as energy-converting hydrogenase genes, were found in pCODH-encoding genomes. This suggests that the human gut CO utilization is not for CO removal, but potentially for fixation and/or biosynthesis, consistent with the harmless yet continuous production of CO in the human gut. Our findings reveal the diversity and distribution of prokaryotes with pCODH in the human gut microbiome, suggesting their potential contribution to microbial ecosystems in human gut environments.

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.

Metal-Metal Redox Exchange to Produce Heterometallic Manganese-Cobalt Oxo Cubanes via a "Dangler" Intermediate

Pendent metals bound to heterocubanes are components of well-known active sites in enzymes that mediate difficult chemical transformations. Investigations into the specific role of these metal ions, sometimes referred to as "danglers", have been hindered by a paucity of rational synthetic routes to appropriate model structures. To generate pendent metal ions bonded to an oxo cubane through a carboxylate bridge, the cubane Co4(μ3-O)4(OAc)4(t-Bupy)4 (OAc = acetate, t-Bupy = 4-tert-butylpyridine) was exposed to various metal acetate complexes. Reaction with Cu(OAc)2 gave the structurally characterized (by X-ray diffraction) dicopper dangler Cu2Co4(μ4-O)2(μ3-O)2(OAc)6(Cl)2(t-Bupy)4. In contrast, the analogous reaction with Mn(OAc)2 produced the MnIV-containing cubane cation [MnCo3(μ3-O)4(OAc)4(t-Bupy)4]+ by way of a metal-metal exchange that gives Co(OAc)2 and [CoIII(μ-OH)(OAc)]n oligomers as byproducts. Additionally, reaction of the formally CoIV cubane complex [Co4(μ3-O)4(OAc)4(t-Bupy)4][PF6] with Mn(OAc)2 gave the corresponding Mn-containing cubane in 80% yield. A mechanistic examination of the related metal-metal exchange reaction between Co4(μ3-O)4(OBz)4(py)4 (OBz = benzoate) and [Mn(acac)2(py)2][PF6] by ultraviolet-visible (UV-vis) spectroscopy provided support for a process involving rate-determining association of the reactants and electron transfer through a μ-oxo bridge in the adduct intermediate. The rates of exchange correlate with the donor strength of the cubane pyridine and benzoate ligand substituents; more electron-donating pyridine ligands accelerate metal-metal exchange, while both electron-donating and -withdrawing benzoate ligands can accelerate exchange. These experiments suggest that the basicity of the cubane oxo ligands promotes metal-metal exchange reactivity. The redox potentials of the Mn and cubane starting materials and isotopic labeling studies suggest an inner-sphere electron-transfer mechanism in a dangler intermediate.

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.

Properties of the iron-sulfur cluster electron transfer relay in an [FeFe]-hydrogenase that is tuned for H2 oxidation catalysis

[FeFe]-hydrogenases catalyze the reversible oxidation of H2 from electrons and protons at an organometallic active site cofactor named the H-cluster. In addition to the H-cluster, most [FeFe]-hydrogenases possess accessory FeS cluster (F-cluster) relays that function in mediating electron transfer with catalysis. There is significant variation in the structural properties of F-cluster relays among the [FeFe]-hydrogenases; however, it is unknown how this variation relates to the electronic and thermodynamic properties, and thus the electron transfer properties, of enzymes. Clostridium pasteurianum [FeFe]-hydrogenase II (CpII) exhibits a large catalytic bias for H2 oxidation (compared to H2 production), making it a notable system for examining if F-cluster properties contribute to the overall function and efficiency of the enzyme. By applying a combination of multifrequency and potentiometric electron paramagnetic resonance, we resolved two electron paramagnetic resonance signals with distinct power- and temperature-dependent properties at g = 2.058 1.931 1.891 (F2.058) and g = 2.061 1.920 1.887 (F2.061), with assigned midpoint potentials of -140 ± 18 mV and -406 ± 12 mV versus normal hydrogen electrode, respectively. Spectral analysis revealed features consistent with spin-spin coupling between the two [4Fe-4S] F-clusters, and possible functional models are discussed that account for the contribution of coupling to the electron transfer landscape. The results signify the interplay of electronic coupling and free energy properties and parameters of the FeS clusters to the electron transfer mechanism through the relay and provide new insight as to how relays functionally complement the catalytic directionality of active sites to achieve highly efficient catalysis.

Nonheme binuclear transition metal complexes with hydrosulfide and polychalcogenides

The intriguing chemistry of chalcogen (S, Se)-containing ligands and their capability to bridge multiple metal centres have resulted in a plethora of reports on transition metal complexes featuring hydrosulfide (HS-) and polychalcogenides (En2-, E = S, Se). While a large number of such molecules are strictly organometallic complexes, examples of non-organometallic complexes featuring HS- and En2- with N-/O-donor ligands are relatively rare. The general synthetic procedure for the transition metal-hydrosulfido complexes involves the reaction of the corresponding metal salts with HS-/H2S and this is prone to generate sulfido bridged oligomers in the absence of sterically demanding ligands. On the other hand, the synthetic methods for the preparation of transition metal-polychalcogenido complexes include the reaction of the corresponding metal salts with En2- or the two electron oxidation of low-valent metals with elemental chalcogen, often at an elevated temperature and/or for a long time. Recently, we have developed new synthetic methods for the preparation of two new classes of binuclear transition metal complexes featuring either HS-, or Sn2- and Sen2- ligands. The new method for the synthesis of transition metal-hydrosulfido complexes involved transition metal-mediated hydrolysis of thiolates at room temperature (RT), while the method for the synthesis of transition metal-polychalcogenido complexes involved redox reaction of coordinated thiolates and exogenous elemental chalcogens at RT. An overview of the synthetic aspects, structural properties and intriguing reactivity of these two new classes of transition metal complexes is presented.

Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase

The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.

Ligand-Bound CO2 as a Nonclassical Route toward Efficient Photocatalytic CO2 Reduction with a Ni N-Confused Porphyrin

Implementing the synergistic effects between the metal and the ligand has successfully streamlined the energetics for CO2 activation and gained high catalytic activities, establishing the important breakthroughs in photocatalytic CO2 reduction. Herein, we describe a Ni(II) N-confused porphyrin complex (NiNCP) featuring an acidic N-H group. It is readily deprotonated and exists in an anion form during catalysis. Owing to this functional site, NiNCP gave rise to an outstanding turnover number (TON) as high as 217,000 with a 98% selectivity for CO2 reduction to CO, while the parent Ni(II) porphyrin (NiTPP) was found to be nearly inactive. Our mechanistic analysis revealed a nonclassical reaction pattern where CO2 was effectively activated via the attack of the Lewis-basic ligand. The resulting ligand-bound CO2 adduct could be further reduced to produce CO. This new metal-ligand synergistic effect is anticipated to inspire the design of highly active catalysts for small molecule activations.

Weak Bimetal Coupling-Assisted MN4 Catalyst for Enhanced Carbon Dioxide Reduction Reaction

The design of multimetal catalysts holds immense significance for efficient CO2 capture and its conversion into economically valuable chemicals. Herein, heterobimetallic catalysts (MiMo)L were exploited for the CO2 reduction reactions (CO2RR) using relativistic density functional theory (DFT). The octadentate Pacman-like polypyrrolic ligand (H4L) accommodates two metal ions (Mo, W, Nd, and U) inside (Mi) and outside (Mo) its month, rendering a weak bimetal coupling-assisted MN4 catalytically active site. Adsorption reactions have access to energetically stable coordination modes of -OCO, -OOC, and -(OCO)2, where the donor atom(s) are marked in bold. Among all of the species, (UiMoo)L releases the most energy. Along CO2RR, it favors to produce CO. The high-efficiency CO2 reduction is attributed to the size matching of U with the ligand mouth and the effective manipulation of the electron density of both ligand and bimetals. The mechanism in which heterobimetals synergetically capture and reduce CO2 has been postulated. This establishes a reference in elaborating on the complicated heterogeneous catalysis.

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.

Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation

Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.

Bioinspired Binickel Catalyst for Carbon Dioxide Reduction: The Importance of Metal-ligand Cooperation

Catalyst design for the efficient CO2 reduction reaction (CO2RR) remains a crucial challenge for the conversion of CO2 to fuels. Natural Ni-Fe carbon monoxide dehydrogenase (NiFe-CODH) achieves reversible conversion of CO2 and CO at nearly thermodynamic equilibrium potential, which provides a template for developing CO2RR catalysts. However, compared with the natural enzyme, most biomimetic synthetic Ni-Fe complexes exhibit negligible CO2RR catalytic activities, which emphasizes the significance of effective bimetallic cooperation for CO2 activation. Enlightened by bimetallic synergy, we herein report a dinickel complex, NiIINiII(bphpp)(AcO)2 (where NiNi(bphpp) is derived from H2bphpp = 2,9-bis(5-tert-butyl-2-hydroxy-3-pyridylphenyl)-1,10-phenanthroline) for electrocatalytic reduction of CO2 to CO, which exhibits a remarkable reactivity approximately 5 times higher than that of the mononuclear Ni catalyst. Electrochemical and computational studies have revealed that the redox-active phenanthroline moiety effectively modulates the electron injection and transfer akin to the [Fe3S4] cluster in NiFe-CODH, and the secondary Ni site facilitates the C-O bond activation and cleavage through electron mediation and Lewis acid characteristics. Our work underscores the significant role of bimetallic cooperation in CO2 reduction catalysis and provides valuable guidance for the rational design of CO2RR catalysts.

Generation and Reactivity of Polychalcogenide Chains in Binuclear Cobalt(II) Complexes

A series of six binuclear Co(II)-thiolate complexes, [Co2(BPMP)(S-C6H4-o-X)2]1+ (X = OMe, 2; NH2, 3), [Co2(BPMP)(μ-S-C6H4-o-O)]1+ (4), and [Co2(BPMP)(μ-Y)]1+ (Y = bdt, 5; tdt, 6; mnt, 7), has been synthesized from [Co2(BPMP)(MeOH)2(Cl)2]1+ (1a) and [Co2(BPMP)(Cl)2]1+ (1b), where BPMP1- is the anion of 2,6-bis[[bis(2-pyridylmethyl)amino]methyl]-4-methylphenol. While 2 and 3 could allow the two-electron redox reaction of the two coordinated thiolates with elemental sulfur (S8) to generate [Co2(BPMP)(μ-S5)]1+ (8), the complexes, 4-7, could not undergo a similar reaction. An analogous redox reaction of 2 with elemental selenium ([Se]) produced [{Co2(BPMP)(μ-Se4)}{Co2(BPMP)(μ-Se3)}]2+ (9a) and [Co2(BPMP)(μ-Se4)]1+ (9b). Further reaction of these polychalcogenido complexes, 8 and 9a/9b, with PPh3 allowed the isolation of [Co2(BPMP)(μ-S)]1+ (10) and [Co2(BPMP)(μ-Se2)]1+ (11), which, in turn, could be converted back to 8 and 9a upon treatment with S8 and [Se], respectively. Interestingly, while the redox reaction of the polyselenide chains in 9a and 11 with S8 produced 8 and [Se], the treatment of 8 with [Se] gave back only the starting material (8), thus demonstrating the different redox behavior of sulfur and selenium. Furthermore, the reaction of 8 and 9a/9b with activated alkynes and cyanide (CN-) allowed the isolation of the complexes, [Co2(BPMP)(μ-E2C2(CO2R)2)]1+ (E = S: 12a, R = Me; 12b, R = Et; E = Se: 13a, R = Me; 13b, R = Et) and [Co2(BPMP)(μ-SH)(NCS)2] (14), respectively. The present work, thus, provides an interesting synthetic strategy, interconversions, and detailed comparative reactivity of binuclear Co(II)-polychalcogenido complexes.

Mechanism of photocatalytic CO2 reduction to HCO2H by a robust multifunctional iridium complex

The tetradentate PNNP-type IrIII complex Mes-IrPCY2 ([Cl-IrIII-H]+) is reported to be an efficient catalyst for the reduction of CO2 to formate with excellent selectivity under visible light irradiation. Density functional calculations have been carried out to elucidate the mechanism and the origin of selectivity in the present work. Calculations suggest that the double-reduced complex 1-H (1[IrI-H]0) demonstrates higher activity than the single-reduced complex 2-H (2[IrIII(L˙-)-H]+), possibly owing to the higher hydride donor ability of the former compared to the latter; thus 1-H functions as the active species in the overall CO2 reduction reaction. In the HCOO- formation pathway, the hydride of 1-H performs a nucleophilic attack on CO2via an outer-sphere fashion to generate species 1-OCHO (1[IrI-OCHO]0), which then releases HCOO- to produce an IrI intermediate. A subsequent protonation and chloride coordination of the Ir center leads to the regeneration of catalyst 1[Cl-IrIII-H]+. For the CO production, a nucleophilic attack on CO2 takes place by the Ir atom of 1-Hvia an inner-sphere manner to afford complex O2C-3-H (1[O2C-IrIII-H]0), followed by a two-proton-one-electron reduction to furnish the OC-2-H complex (2[OC-IrIII(L˙-)-H]+) after liberating a H2O. Ultimately, CO is released to form 2-H. The stronger nucleophilicity as well as smaller steric hindrance of the hydride than the Ir atom of the active species 1-H (1[IrI-H]0) is found to account for the favoring of formate formation over CO formation. Meanwhile, the CO2 reduction reaction is calculated to be preferred over the hydrogen evolution reaction, and this is consistent with the experimental product distributions.

Redox-Active Ligand Assisted Multielectron Catalysis: A Case of Electrocatalyzed CO2-to-CO Conversion

The selective reduction of carbon dioxide remains a significant challenge due to the complex multielectron/proton transfer process, which results in a high kinetic barrier and the production of diverse products. Inspired by the electrostatic and H-bonding interactions observed in the second sphere of the [NiFe]-CODH enzyme, researchers have extensively explored these interactions to regulate proton transfer, stabilize intermediates, and ultimately improve the performance of catalytic CO2 reduction. In this work, a series of cobalt(II) tetraphenylporphyrins with varying numbers of redox-active nitro groups were synthesized and evaluated as CO2 reduction electrocatalysts. Analyses of the redox properties of these complexes revealed a consistent relationship between the number of nitro groups and the corresponding accepted electron number of the ligand at -1.59 V vs. Fc+/0. Among the catalysts tested, TNPPCo with four nitro groups exhibited the most efficient catalytic activity with a turnover frequency of 4.9 × 104 s-1 and a catalytic onset potential 820 mV more positive than that of the parent TPPCo. Furthermore, the turnover frequencies of the catalysts increased with a higher number of nitro groups. These results demonstrate the promising design strategy of incorporating multielectron redox-active ligands into CO2 reduction catalysts to enhance catalytic performance.

Decorated Vesicles as Prebiont Systems (a Hypothesis)

Decorated vesicles in deep, seafloor basalts form abiotically, but show at least four life-analogous features, which makes them a candidate for origin of life research. These features are a physical enclosure, carbon-assimilatory catalysts, semi-permeable boundaries, and a source of usable energy. The nanometer-to-micron-sized spherules on the inner walls of decorated vesicles are proposed to function as mineral proto-enzymes. Chemically, these structures resemble synthetic FeS clusters shown to convert CO2, CO and H2 into methane, formate, and acetate. Secondary phyllosilicate minerals line the vesicles' inner walls and can span openings in the vesicles and thus can act as molecular sieves between the vesicles' interior and the surrounding aquifer. Lastly, basalt glass in the vesicle walls takes up protons, which replace cations in the silicate framework. This results in an inward proton flux, reciprocal outward flux of metal cations, more alkaline pH inside the vesicle than outside, and production of more phyllosilicates. Such life-like features could have been exploited to move decorated vesicles toward protolife systems. Decorated vesicles are proposed as study models of prebiotic systems that are expected to have existed on the early Earth and Earth-like exoplanets. Their analysis can lead to better understanding of changes in planetary geocycles during the origin of life.

A CuICoII cryptate for the visible light-driven reduction of CO2

Among the rare bimetallic complexes known for the reduction of CO2, CoIICoII and ZnIICoII hexamine cryptates are described as efficient photocatalysts. In close relation to the active sites of natural, CO2-reducing enzymes, we recently reported the asymmetric cryptand {NSNN}m ({NSNN}m = N[(CH2)2SCH2(m-C6H4)CH2NH(CH2)2]3N) comprising distinct sulphur- and nitrogen-rich binding sites and the corresponding CuIMII (MII = CoII, NiII, CuII) complexes. To gain insight into the effect of metals in different oxidation states and sulphur-incorporation on the photocatalytic activity, we herein investigate the CuICoII complex of {NSNN}m as catalyst for the visible light-driven reduction of CO2. After 24 h irradiation with LED light of 450 nm, CuICoII-{NSNN}m shows a high efficiency for the photocatalytic CO2-to-CO conversion with 9.22 μmol corresponding to a turnover number of 2305 and a high selectivity of 98% over the competing H2 production despite working in an acetonitrile/water (4 : 1) mixture. Experiments with mononuclear counterparts and computational studies show that the high activity can be attributed to synergistic catalysis between Cu and Co. Furthermore, it was shown that an increase of the metal distance results in the loss of synergistic effects and rather single-sited Co catalysis is observed.

The Moon-Forming Impact and the Autotrophic Origin of Life

The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.

Construction of multiple metagenome assembled genomes containing carbon monoxide dehydrogenases from anaerobic carbon monoxide enrichment cultures

Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes. Hydrogenogenic CO utilizers employ carbon monoxide dehydrogenase (CODH) and energy-converting hydrogenase (ECH) to oxidize CO and reduce protons to produce H2. Those prokaryotes constitute a rare biosphere and are difficult to detect even with PCR amplification and with metagenomic analyses. In this study, anaerobic CO-enrichment cultures followed by construction of metagenome assembled genomes (MAGs) detected high-quality MAGs from potential hydrogenogenic CO utilizers. Of 32 MAGs constructed, 5 were potential CO utilizer harboring CODH genes. Of the five MAGs, two were classified into the genus Thermolithobacter on the basis of 16S rRNA sequence identity, related to Carboxydocella tharmautotrophica 41, with an average nucleotide identity (ANI) of approximately 72%. Additionally, two were related to Geoglobus acetivorans with ANI values ranging from 75 to 77% to G. acetivorans SBH6, and one MAG was identified as Desulfotomaculum kuznetsovii with an ANI > 96% to D. kuznetsovii DSM 6115. The two Thermolithobacter MAGs identified in this study contained CODH-ECH gene clusters, and were therefore identified as potential hydrogenogenic CO utilizers. However, these MAGs harbored three CODH gene clusters that showed distinct physiological functions in addition to CODH-ECH gene clusters. In total, the five potential CO utilizer MAGs contained sixteen CODH genes. Among those CODHs, four sets did not cluster with any known CODH protein sequences (with an identity of > 90%), and the CODH database was expanded.

Bioinspired Framework Catalysts: From Enzyme Immobilization to Biomimetic Catalysis

Enzymatic catalysis has fueled considerable interest from chemists due to its high efficiency and selectivity. However, the structural complexity and vulnerability hamper the application potentials of enzymes. Driven by the practical demand for chemical conversion, there is a long-sought quest for bioinspired catalysts reproducing and even surpassing the functions of natural enzymes. As nanoporous materials with high surface areas and crystallinity, metal-organic frameworks (MOFs) represent an exquisite case of how natural enzymes and their active sites are integrated into porous solids, affording bioinspired heterogeneous catalysts with superior stability and customizable structures. In this review, we comprehensively summarize the advances of bioinspired MOFs for catalysis, discuss the design principle of various MOF-based catalysts, such as MOF-enzyme composites and MOFs embedded with active sites, and explore the utility of these catalysts in different reactions. The advantages of MOFs as enzyme mimetics are also highlighted, including confinement, templating effects, and functionality, in comparison with homogeneous supramolecular catalysts. A perspective is provided to discuss potential solutions addressing current challenges in MOF catalysis.

Breaking bonds and breaking rules: inert-bond activation by [(iPr3P)Ni]5H4 and catalytic stereospecific norbornene dimerization

The facile carbon atom abstraction reaction by [(ⁱPr₃P)Ni]₅H₆ (1) with various terminal alkenes to give [(ⁱPr₃P)Ni]₅H₄(μ₅-C) (2) occurs via a common highly reactive intermediate [(ⁱPr₃P)Ni]₅H₄ (3), which was isolated by the reaction of 1 with norbornene. Temperature dependent ¹H and ³¹P{¹H} NMR chemical shifts of 3 are consistent with a thermally populated triplet excited state only 2 kcal mol^-1 higher energy than the diamagnetic ground state. Complex 3 catalyzes the dimerization of norbornene to stereoselectively provide exclusively (Z) anti-(bis-2,2'-norbornylidene).

Deciphering the role and mechanism of nano zero-valent iron on medium chain fatty acids production from CO2 via chain elongation in microbial electrosynthesis

The integrated system of microbial electrosynthesis (MES) coupled with chain elongation has been considered a promising platform for carboxylic acids production. However, this biotechnology is still in its infancy, and many limitations are needed to be transcended, such as low electron transfer efficiency between cathode and microbes. In this study, nano zero-valent iron (NZVI) was employed to improve carboxylic acid production in the integrated system, and the promotion mechanisms were revealed. Results suggested that the highest production concentrations of acetate, butyrate, and caproate were observed at 7.5 g/L optimized NZVI dosage, increasing the total yield and coulomb efficiency by 23.7 % and 40.3 % compared to the control. Mechanism studies indicated that the hydrogen and electron released by the anaerobic corrosion of NZVI could be used as additional reducing equivalents, thereby enhancing the electron transfer performance. Besides, NZVI was also proven to facilitate the formation of electroactive biofilms according to the results of biofilm characterization and total DNA. In functional microbes' respect, the moderate NZVI enriched the chain elongator in biofilm, like Clostridium_sensu-stricto_12, and upregulated the activities of key enzymes of homoacetogenesis and chain elongation metabolic pathways, like carbon-monoxide dehydrogenase and hydroxyacyl-CoA dehydratase. This study provided the evidence and revealed how NZVI assisted carboxylic acid production from CO₂ via chain elongation in MES.

Bio-Inspired Bimetallic Cooperativity Through a Hydrogen Bonding Spacer in CO2 Reduction

At the core of carbon monoxide dehydrogenase (CODH) active site two metal ions together with hydrogen bonding scheme from amino acids orchestrate the interconversion between CO₂ and CO. We have designed a molecular catalyst implementing a bimetallic iron complex with an embarked second coordination sphere with multi-point hydrogen-bonding interactions. We found that, when immobilized on carbon paper electrode, the dinuclear catalyst enhances up to four fold the heterogeneous CO₂ reduction to CO in water with an improved selectivity and stability compared to the mononuclear analogue. Interestingly, quasi-identical catalytic performances are obtained when one of the two iron centers was replaced by a redox inactive Zn metal, questioning the cooperative action of the two metals. Snapshots of X-ray structures indicate that the two metalloporphyrin units tethered by a urea group is a good compromise between rigidity and flexibility to accommodate CO₂ capture, activation, and reduction.

The bio-inspired heterogeneous single-cluster catalyst Ni100-Fe4S4 for enhanced electrochemical CO2 reduction to CH4

Electrochemical conversion of CO₂-to-CH₄ is a process of converting the inert greenhouse gas into energy molecules. It offers great promise for the transformation of carbon-neutral economy. However, achieving high CH₄ activity and selectivity remains a major challenge because the electrochemical reduction of CO₂-to-CH₄ is accompanied by various C₁ intermediates at the catalytic site, involving multiple proton-coupled electron transfer processes. Herein, different from the traditional designing strategy, we propose a bio-inspired theoretical design approach to construct a heterogeneous single-cluster catalyst Ni100-Fe₄S₄ at the atomic level, which may show high CO₂ electroreduction performance. Combined with the crystallographic data and theoretical calculations, Ni100-Fe₄S₄ and CO dehydrogenase exhibit highly similar catalytic geometric active centers and CO₂ binding modes. By exploring the origin of the catalytic activity of this biomimetic structure, we found that the activation of CO₂ on Ni100-Fe₄S₄ theoretically exceeds that on natural CO dehydrogenase. Density functional theory calculations reveal that the dehydrogenase enzyme-liked Fe-Ni active site serves as an electron enrichment 'electro-bridge' (an electron-rich highly active catalytic site), which can activate CO₂ molecules efficiently and stabilize various intermediates in multistep elementary reactions to selectively produce CH₄ at a low overpotential (0.13 eV). The calculated CO₂ electroreduction pathways are well consistent with the nickel-based catalytic materials reported in experimental studies. Our work showcases and highlights the rational design of high-performance catalytic materials via the biomimetic methodology at the atomic level.

Proteome adaptations of the organohalide-respiring Desulfitobacterium hafniense strain DCB-2 to various energy metabolisms

Introduction

Desulfitobacterium hafniense was isolated for its ability to use organohalogens as terminal electron acceptors via organohalide respiration (OHR). In contrast to obligate OHR bacteria, Desulfitobacterium spp. show a highly versatile energy metabolism with the capacity to use different electron donors and acceptors and to grow fermentatively. Desulfitobacterium genomes display numerous and apparently redundant members of redox enzyme families which confirm their metabolic potential. Nonetheless, the enzymes responsible for many metabolic traits are not yet identified.

Methods

In the present work, we conducted an extended proteomic study by comparing the proteomes of Desulfitobacterium hafniense strain DCB-2 cultivated in combinations of electron donors and acceptors, triggering five alternative respiratory metabolisms that include OHR, as well as fermentation. Tandem Mass Tag labelling proteomics allowed us to identify and quantify almost 60% of the predicted proteome of strain DCB-2 (2,796 proteins) in all six growth conditions. Raw data are available via ProteomeXchange with identifier PXD030393.

Results and discussion

This dataset was analyzed in order to highlight the proteins that were significantly up-regulated in one or a subset of growth conditions and to identify possible key players in the different energy metabolisms. The addition of sodium sulfide as reducing agent in the medium - a very widespread practice in the cultivation of strictly anaerobic bacteria - triggered the expression of the dissimilatory sulfite reduction pathway in relatively less favorable conditions such as fermentative growth on pyruvate, respiration with H₂ as electron donor and OHR conditions. The presence of H₂, CO₂ and acetate in the medium induced several metabolic pathways involved in carbon metabolism including the Wood-Ljungdahl pathway and two pathways related to the fermentation of butyrate that rely on electron-bifurcating enzymes. While the predicted fumarate reductase appears to be constitutively expressed, a new lactate dehydrogenase and lactate transporters were identified. Finally, the OHR metabolism with 3-chloro-4-hydroxyphenylacetate as electron acceptor strongly induced proteins encoded in several reductive dehalogenase gene clusters, as well as four new proteins related to corrinoid metabolism. We believe that this extended proteomic database represents a new landmark in understanding the metabolic versatility of Desulfitobacterium spp. and provides a solid basis for addressing future research questions.

Nickel Complexes Bearing ONS Chelating Ligands: A Promising Contender for In Vitro Cytotoxicity Effects on Human Pancreatic Cancer MIA-PaCa-2 Cells

The highly chronic human pancreatic cancer cell is one of the major reasons for cancerous death. Nickel complexes are recently gaining interest in anticancer activities on different types of cancer cells. Hence, in this study, we synthesized and characterized a series of ONS donor ligands [2-HO-C₆H₄-CH═N-(C₆H₄)-SH] (L1), [2-OH-3-OMe-C₆H₃-CH═N-(C₆H₄)-SH] (L2), [2-OH-3,5-(C(Me)₃)₂-C₆H₂-CH═N-(C₆H₄)-SH] (L3), [2-OH-C₆H₄-CH═N-(C₆H₄)-SMe] (L4), [2-OH-3-OMe-C₆H₃-CH═N-(C₆H₄)-SMe] (L5), [2-OH-3,5-(C(Me)₃)₂-C₆H₂-CH═N-(C₆H₄)-SMe] (L6) and their Ni(II) metal complexes [(MeOH)Ni(L1-L1-4H)] (1), [(MeOH)Ni(L2-L2-4H)] (2), [(MeOH)Ni(L3-L3-4H)] (3), [(L4-H)₂Ni] (4), [(L5-H)₂Ni] (5), and [(L6-H)₂Ni] (6). The single-crystal X-ray diffraction data of complexes 1 and 4 were collected to elucidate the geometry around the metal center. The anticancer activity of complexes 1-6 was investigated on human pancreatic cancer cell line MIA-PaCa-2, which revealed that complexes 4 and 6 were the most significantly effective in decreasing the cell viability of cancer cells at the lowest dose. The structure parameters obtained from single-crystal X-ray diffraction data are found to be in good agreement with the data from density functional theory and Hirshfeld surface analysis for complex 1.

Structural Insights into Microbial One-Carbon Metabolic Enzymes Ni-Fe-S-Dependent Carbon Monoxide Dehydrogenases and Acetyl-CoA Synthases

Ni-Fe-S-dependent carbon monoxide dehydrogenases (CODHs) are enzymes that interconvert CO and CO₂ by using their catalytic Ni-Fe-S C-cluster and their Fe-S B- and D-clusters for electron transfer. CODHs are important in the microbiota of animals such as humans, ruminants, and termites because they can facilitate the use of CO and CO₂ as carbon sources and serve to maintain redox homeostasis. The bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is responsible for acetate production via the Wood-Ljungdahl pathway, where acetyl-CoA is assembled from two CO₂-derived one-carbon units. A Ni-Fe-S A-cluster is key to this chemistry. Whereas acetogens use the A- and C-clusters of CODH/ACS to produce acetate from CO₂, methanogens use A- and C-clusters of an acetyl-CoA decarbonylase/synthase complex (ACDS) to break down acetate en route to CO₂ and methane production. Here we review some of the recent advances in understanding the structure and mechanism of CODHs, CODH/ACSs, and ACDSs, their unusual metallocofactors, and their unique metabolic roles in the human gut and elsewhere.

Bioelectrocatalytic CO2 Reduction by Redox Polymer-Wired Carbon Monoxide Dehydrogenase Gas Diffusion Electrodes

The development of electrodes for efficient CO₂ reduction while forming valuable compounds is critical. The use of enzymes as catalysts provides the advantage of high catalytic activity in combination with highly selective transformations. We describe the electrical wiring of a carbon monoxide dehydrogenase II from Carboxydothermus hydrogenoformans (ChCODH II) using a cobaltocene-based low-potential redox polymer for the selective reduction of CO₂ to CO over gas diffusion electrodes. High catalytic current densities of up to -5.5 mA cm^-2 are achieved, exceeding the performance of previously reported bioelectrodes for CO₂ reduction based on either carbon monoxide dehydrogenases or formate dehydrogenases. The proposed bioelectrode reveals considerable stability with a half-life of more than 20 h of continuous operation. Product quantification using gas chromatography confirmed the selective transformation of CO₂ into CO without any parasitic co-reactions at the applied potentials.

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.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.