The roles of long-range proton-coupled electron transfer in the directionality and efficiency of [FeFe]-hydrogenases

Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility

Hydrogenases catalyze hydrogen/proton interconversion that is normally electrochemically reversible (having minimal overpotential requirement), a special property otherwise almost exclusive to platinum metals. The mechanism of [NiFe]-hydrogenases includes a long-range proton-coupled electron-transfer process involving a specific Ni-coordinated cysteine and the carboxylate of a nearby glutamate. A variant in which this cysteine has been exchanged for selenocysteine displays two distinct changes in electrocatalytic properties, as determined by protein film voltammetry. First, proton reduction, even in the presence of H2 (a strong product inhibitor), is greatly enhanced relative to H2 oxidation: this result parallels a characteristic of natural [NiFeSe]-hydrogenases which are superior H2 production catalysts. Second, an inflection (an S-shaped "twist" in the trace) appears around the formal potential, the small overpotentials introduced in each direction (oxidation and reduction) signaling a departure from electrocatalytic reversibility. Concerted proton-electron transfer offers a lower energy pathway compared to stepwise transfers. Given the much lower proton affinity of Se compared to that of S, the inflection provides compelling evidence that concerted proton-electron transfer is important in determining why [NiFe]-hydrogenases are reversible electrocatalysts.

Modifying Proton Relay into Bioinspired Dye-Based Coordination Polymer for Photocatalytic Proton-Coupled Electron Transfer

Proton-coupled electron transfer (PCET) imparts an energetic advantage over single electron transfer in activating inert substances. Natural PCET enzyme catalysis generally requires tripartite preorganization of proton relay, substrate-bound active center, and redox mediator, making the processes efficient and precluding side reactions. Inspired by this, a heterogeneous photocatalytic PCET system was established to achieve higher PCET driving forces by modifying proton relays into anthraquinone-based anionic coordination polymers. The proximally separated proton relays and photoredox-mediating anthraquinone moiety allowed pre-assembly of inert substrate between them, merging proton and electron into unsaturated bonds by photoreductive PCET, which enhanced reaction kinetics compared with the counter catalyst without proton relay. This photocatalytic PCET method was applied to a broad-scoped reduction of aryl ketones, unsaturated carbonyls, and aromatic compounds. The distinctive regioselectivities for the reduction of isoquinoline derivatives were found to occur on the carbon-ring sides. PCET-generated radical intermediate of quinoline could be trapped by alkene for proton relay-assisted Minisci addition, forming the pharmaceutical aza-acenaphthene scaffold within one step. When using heteroatom(X)-H/C-H compounds as proton-electron donors, this protocol could activate these inert bonds through photooxidative PCET to afford radicals and trap them by electron-deficient unsaturated compounds, furnishing the direct X-H/C-H functionalization.

Photo-Electro-Biochemical H2 Production Using the Carbon Material-Based Cathode Combined with Genetically Engineered Escherichia coli Whole-Cell Biocatalysis

Abio/bio hybrids, which incorporate biocatalysts that promote efficient and selective material conversions under mild conditions into existing catalytic reactions, have attracted considerable attention for developing new catalytic systems. This study constructed a H2 -forming biocathode based on a carbon material combined with whole-cell biocatalysis of genetically-engineered-hydrogenase-overproducing Escherichia coli for the photoelectrochemical water splitting for clean H2 production. Low-cost and abundant carbon materials are generally not suitable for H2 -forming cathode due to their high overpotential for proton reduction; however, the combination of the reduction of an organic electron mediator on the carbon electrode and the H2 formation with the reduced mediator by the redox enzyme hydrogenase provides a H2 -forming cathodic reaction comparable to that of the noble metal electrode. The present study demonstrates that the recombinant E. coli whole cell can be employed as a part of the H2 -forming biocathode system, and the biocathode system wired with TiO2 photoanode can be a photoelectrochemical water-splitting system without external voltage assistance under natural pH. The findings of this study expand the feasibility of applications of whole-cell biocatalysis and contribute to obtaining solar-to-chemical conversions by abio/bio hybrid systems, especially for low-cost, noble-metal-free, and clean H2 production.

Insights into the Molecular Mechanism of Formaldehyde Inhibition of [FeFe]-Hydrogenases

[FeFe]-hydrogenases are efficient H2 converting biocatalysts that are inhibited by formaldehyde (HCHO). The molecular mechanism of this inhibition has so far not been experimentally solved. Here, we obtained high-resolution crystal structures of the HCHO-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum, showing HCHO reacts with the secondary amine base of the catalytic cofactor and the cysteine C299 of the proton transfer pathway which both are very important for catalytic turnover. Kinetic assays via protein film electrochemistry show the CpI variant C299D is significantly less inhibited by HCHO, corroborating the structural results. By combining our data from protein crystallography, site-directed mutagenesis and protein film electrochemistry, a reaction mechanism involving the cofactor's amine base, the thiol group of C299 and HCHO can be deduced. In addition to the specific case of [FeFe]-hydrogenases, our study provides additional insights into the reactions between HCHO and protein molecules.

Ancient complexes of iron and sulfur modulate oncogenes and oncometabolism

Inorganic complexes of iron and sulfur, that is, iron-sulfur [FeS] clusters, have played a fundamental role in life on Earth since the prebiotic period. These clusters were involved in elementary reactions leading to the emergence of life and, since then, gained function in processes, such as respiration, replication, transcription, and the immune response. We discuss how three [FeS] proteins involved in the innate immune response play a role in oncogene expression/function and oncometabolism. Our analysis highlights the importance of future research into understanding the [FeS] clusters' roles in cancer progression and proliferation. The outcomes of these studies will help identify new targets and develop new anticancer therapeutics.

Comprehensive structural, infrared spectroscopic and kinetic investigations of the roles of the active-site arginine in bidirectional hydrogen activation by the [NiFe]-hydrogenase 'Hyd-2' from Escherichia coli

The active site of [NiFe]-hydrogenases contains a strictly-conserved pendant arginine, the guanidine head group of which is suspended immediately above the Ni and Fe atoms. Replacement of this arginine (R479) in hydrogenase-2 from E. coli results in an enzyme that is isolated with a very tightly-bound diatomic ligand attached end-on to the Ni and stabilised by hydrogen bonding to the Nζ atom of the pendant lysine and one of the three additional water molecules located in the active site of the variant. The diatomic ligand is bound under oxidising conditions and is removed only after a prolonged period of reduction with H2 and reduced methyl viologen. Once freed of the diatomic ligand, the R479K variant catalyses both H2 oxidation and evolution but with greatly decreased rates compared to the native enzyme. Key kinetic characteristics are revealed by protein film electrochemistry: most importantly, a very low activation energy for H2 oxidation that is not linked to an increased H/D isotope effect. Native electrocatalytic reversibility is retained. The results show that the sluggish kinetics observed for the lysine variant arise most obviously because the advantage of a more favourable low-energy pathway is massively offset by an extremely unfavourable activation entropy. Extensive efforts to establish the identity of the diatomic ligand, the tight binding of which is an unexpected further consequence of replacing the pendant arginine, prove inconclusive.

Probing Substrate Transport Effects on Enzymatic Hydrogen Catalysis: An Alternative Proton Transfer Pathway in Putatively Sensory [FeFe] Hydrogenase

[FeFe] hydrogenases, metalloenzymes catalyzing proton/dihydrogen interconversion, have attracted intense attention due to their remarkable catalytic properties and (bio-)technological potential for a future hydrogen economy. In order to unravel the factors enabling their efficient catalysis, both their unique organometallic cofactors and protein structural features, i.e., "outer-coordination sphere" effects have been intensively studied. These structurally diverse enzymes are divided into distinct phylogenetic groups, denoted as Group A-D. Prototypical Group A hydrogenases display high turnover rates (104-105 s-1). Conversely, the sole characterized Group D representative, Thermoanaerobacter mathranii HydS (TamHydS), shows relatively low catalytic activity (specific activity 10-1 μmol H2 mg-1 min-1) and has been proposed to serve a H2-sensory function. The various groups of [FeFe] hydrogenase share the same catalytic cofactor, the H-cluster, and the structural factors causing the diverging reactivities of Group A and D remain to be elucidated. In the case of the highly active Group A enzymes, a well-defined proton transfer pathway (PTP) has been identified, which shuttles H+ between the enzyme surface and the active site. In Group D hydrogenases, this conserved pathway is absent. Here, we report on the identification of highly conserved amino acid residues in Group D hydrogenases that constitute a possible alternative PTP. We varied two proposed key amino acid residues of this pathway (E252 and E289, TamHydS numbering) via site-directed mutagenesis and analyzed the resulting variants via biochemical and spectroscopic methods. All variants displayed significantly decreased H2-evolution and -oxidation activities. Additionally, the variants showed two redox states that were not characterized previously. These findings provide initial evidence that these amino acid residues are central to the putative PTP of Group D [FeFe] hydrogenase. Since the identified residues are highly conserved in Group D exclusively, our results support the notion that the PTP is not universal for different phylogenetic groups in [FeFe] hydrogenases.

Molecular Catalysis of Energy Relevance in Metal-Organic Frameworks: From Higher Coordination Sphere to System Effects

The modularity and synthetic flexibility of metal-organic frameworks (MOFs) have provoked analogies with enzymes, and even the term MOFzymes has been coined. In this review, we focus on molecular catalysis of energy relevance in MOFs, more specifically water oxidation, oxygen and carbon dioxide reduction, as well as hydrogen evolution in context of the MOF-enzyme analogy. Similar to enzymes, catalyst encapsulation in MOFs leads to structural stabilization under turnover conditions, while catalyst motifs that are synthetically out of reach in a homogeneous solution phase may be attainable as secondary building units in MOFs. Exploring the unique synthetic possibilities in MOFs, specific groups in the second and third coordination sphere around the catalytic active site have been incorporated to facilitate catalysis. A key difference between enzymes and MOFs is the fact that active site concentrations in the latter are often considerably higher, leading to charge and mass transport limitations in MOFs that are more severe than those in enzymes. High catalyst concentrations also put a limit on the distance between catalysts, and thus the available space for higher coordination sphere engineering. As transport is important for MOF-borne catalysis, a system perspective is chosen to highlight concepts that address the issue. A detailed section on transport and light-driven reactivity sets the stage for a concise review of the currently available literature on utilizing principles from Nature and system design for the preparation of catalytic MOF-based materials.

Evidence of Atypical Structural Flexibility of the Active Site Surrounding of an [FeFe] Hydrogenase from Clostridium beijerinkii

[FeFe] hydrogenase from Clostridium beijerinkii (CbHydA1) is an unusual hydrogenase in that it can withstand prolonged exposure to O₂ by reversibly converting into an O₂-protected, inactive state (H_inact). It has been indicated in the past that an atypical conformation of the "SC₃₆₇CP" loop near the [2Fe]_H portion of the six-iron active site (H-cluster) allows the Cys367 residue to adopt an "off-H⁺-pathway" orientation, promoting a facile transition of the cofactor to H_inact. Here, we investigated the electronic structure of the H-cluster in the oxidized state (H_ox) that directly converts to H_inact under oxidizing conditions and the related CO-inhibited state (H_ox-CO). We demonstrate that both states exhibit two distinct forms in electron paramagnetic resonance (EPR) spectroscopy. The ratio between the two forms is pH-dependent but also sensitive to the buffer choice. Our IR and EPR analyses illustrate that the spectral heterogeneity is due to a perturbation of the coordination environment of the H-cluster's [4Fe4S]_H subcluster without affecting the [2Fe]_H subcluster. Overall, we conclude that the observation of two spectral components per state is evidence of heterogeneity of the environment of the H-cluster likely associated with conformational mobility of the SCCP loop. Such flexibility may allow Cys367 to switch rapidly between off- and on-H⁺-pathway rotamers. Consequently, we believe such structural mobility may be the key to maintaining high enzymatic activity while allowing a facile transition to the O₂-protected state.

Phonon-assisted electron-proton transfer in [FeFe] hydrogenases: Topological role of clusters

[FeFe] hydrogenases are enzymes that have acquired a unique capacity to synthesize or consume molecular hydrogen (H2). This function relies on a complex catalytic mechanism involving the active site and two distinct electron and proton transfer networks working in concert. By an analysis based on terahertz vibrations of [FeFe] hydrogenase structure, we are able to predict and identify the existence of rate-promoting vibrations at the catalytic site and the coupling with functional residues involved in reported electron and proton transfer networks. Our findings suggest that the positioning of the cluster is influenced by the response of the scaffold to thermal fluctuations, which in turn drives the formation of networks for electron transfer through phonon-assisted mechanisms. Thus, we address the problem of linking the molecular structure to the catalytic function through picosecond dynamics, while raising the functional gain brought by the cofactors or clusters, using the concept of fold-encoded localized vibrations.

A personal account on 25 years of scientific literature on [FeFe]-hydrogenase

[FeFe]-hydrogenases are gas-processing metalloenzymes that catalyze H₂ oxidation and proton reduction (H₂ release) in microorganisms. Their high turnover frequencies and lack of electrical overpotential in the hydrogen conversion reaction has inspired generations of biologists, chemists, and physicists to explore the inner workings of [FeFe]-hydrogenase. Here, we revisit 25 years of scientific literature on [FeFe]-hydrogenase and propose a personal account on 'must-read' research papers and review article that will allow interested scientists to follow the recent discussions on catalytic mechanism, O₂ sensitivity, and the in vivo synthesis of the active site cofactor with its biologically uncommon ligands carbon monoxide and cyanide. Focused on-but not restricted to-structural biology and molecular biophysics, we highlight future directions that may inspire young investigators to pursue a career in the exciting and competitive field of [FeFe]-hydrogenase research.

Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway

Hydrogenases are H₂ converting enzymes that harbor catalytic cofactors in which iron (Fe) ions are coordinated by biologically unusual carbon monoxide (CO) and cyanide (CN^- ) ligands. Extrinsic CO and CN^- , however, inhibit hydrogenases. The mechanism by which CN^- binds to [FeFe]-hydrogenases is not known. Here, we obtained crystal structures of the CN^- -treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum. The high resolution of 1.39 Å allowed us to distinguish intrinsic CN^- and CO ligands and to show that extrinsic CN^- binds to the open coordination site of the cofactor where CO is known to bind. In contrast to other inhibitors, CN^- treated crystals show conformational changes of conserved residues within the proton transfer pathway which could allow a direct proton transfer between E279 and S319. This configuration has been proposed to be vital for efficient proton transfer, but has never been observed structurally.

Facile Functionalization of Carbon Electrodes for Efficient Electroenzymatic Hydrogen Production

Enzymatic electrocatalysis holds promise for new biotechnological approaches to produce chemical commodities such as molecular hydrogen (H₂). However, typical inhibitory limitations include low stability and/or low electrocatalytic currents (low product yields). Here we report a facile single-step electrode preparation procedure using indium-tin oxide nanoparticles on carbon electrodes. The subsequent immobilization of a model [FeFe]-hydrogenase from Clostridium pasteurianum ("CpI") on the functionalized carbon electrode permits comparatively large quantities of H₂ to be produced in a stable manner. Specifically, we observe current densities of >8 mA/cm² at -0.8 V vs the standard hydrogen electrode (SHE) by direct electron transfer (DET) from cyclic voltammetry, with an onset potential for H₂ production close to its standard potential at pH 7 (approximately -0.4 V vs. SHE). Importantly, hydrogenase-modified electrodes show high stability retaining ∼92% of their electrocatalytic current after 120 h of continuous potentiostatic H₂ production at -0.6 V vs. SHE; gas chromatography confirmed ∼100% Faradaic efficiency. As the bioelectrode preparation method balances simplicity, performance, and stability, it paves the way for DET on other electroenzymatic reactions as well as semiartificial photosynthesis.

From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf

Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP⁺ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.

Fundamentals and recent progress in bioelectrochemical system-assisted biohythane production

Biohythane, a balanced mixture of 10%-30% v/v of hydrogen and 70%-90% v/v of methane, could be the backbone of an all-purpose future energy supply. Recently, bioelectrochemical systems (BES) became a new sensation among environmental biotechnology processes with the potential to sustainably generate biohythane. Therefore, to unleash its full potential for scaling up, researchers are consistently improving microbial metabolic pathways, novel reactors, and electrode designs. This review presents a detailed analysis of recently discovered fundamental mechanisms and science and engineering intervention of different strategies to improve the biohythane composition and production rate from BES. However, several milestones are to be achieved, for instance, improving electrode kinetics using efficient catalysts, engineered microbial communities, and improved reactor configurations, for commercializing this sustainable technology. Thus, a future perspective section is included to recommend novel research lines, mainly focusing on the microbial communities and the efficient electrocatalysts, to enhance reactor performance.

The Contribution of Proton-Donor pKa on Reactivity Profiles of [FeFe]-hydrogenases

The [FeFe]-hydrogenases are enzymes that catalyze the reversible activation of H₂ coupled to the reduction–oxidation of electron carriers. Members of the different taxonomic groups of [FeFe]-hydrogenases display a wide range of preference, or bias, for H₂ oxidation or H₂ production reactions, despite sharing a common catalytic cofactor, or H-cluster. Identifying the properties that control reactivity remains an active area of investigation, and models have emerged that include diversity in the catalytic site coordination environments and compositions of electron transfer chains. The kinetics of proton-coupled electron transfer at the H-cluster might be expected to be a point of control of reactivity. To test this hypothesis, systematic changes were made to the conserved cysteine residue that functions in proton exchange with the H-cluster in the three model enzymes: CaI, CpII, and CrHydA1. CaI and CpII both employ electron transfer accessory clusters but differ in bias, whereas CrHydA1 lacks accessory clusters having only the H-cluster. Changing from cysteine to either serine (more basic) or aspartate (more acidic) modifies the sidechain pKa and thus the barrier for the proton exchange step. The reaction rates for H₂ oxidation or H₂ evolution were surveyed and measured for model [FeFe]-hydrogenases, and the results show that the initial proton-transfer step in [FeFe]-hydrogenase is tightly coupled to the control of reactivity; a change from cysteine to more basic serine favored H₂ oxidation in all enzymes, whereas a change to more acidic aspartate caused a shift in preference toward H₂ evolution. Overall, the changes in reactivity profiles were profound, spanning 10⁵ in ratio of the H₂ oxidation-to-H₂ evolution rates. The fact that the change in reactivity follows a common trend implies that the effect of changing the proton-transfer residue pKa may also be framed as an effect on the scaling relationship between the H-cluster di(thiolmethyl)amine (DTMA) ligand pKa and E_m values of the H-cluster. Experimental observations that support this relationship, and how it relates to catalytic function in [FeFe]-hydrogenases, are discussed.

Effect of Redox-Inactive Metal Ion-Nickel(III) Interactions on the Redox Properties and Proton-Coupled Electron Transfer Reactivity

Mononuclear nickel(II) and nickel(III) complexes of a bisamidate-bisalkoxide ligand, (NMe₄)₂[Ni^II(HMPAB)] (1) and (NMe₄)[Ni^III(HMPAB)] (2), respectively, have been synthesized and characterized by various spectroscopic techniques including X-ray crystallography. The reaction of redox-inactive metal ions (Mⁿ⁺ = Ca²⁺, Mg²⁺, Zn²⁺, Y³⁺, and Sc³⁺) with 2 resulted in 2-Mⁿ⁺ adducts, which was assessed by an array of spectroscopic techniques including X-ray absorption spectroscopy (XAS), electron paramagnetic resonance (EPR), and reactivity studies. The X-ray structure of Ca²⁺ coordinated to Ni(III) complexes, 2-Ca²⁺T, was determined and exhibited an average Ni-Ca distance of 3.1253 Å, close to the metal ions' covalent radius. XAS analysis of 2-Ca²⁺ and 2-Y³⁺ in solution further revealed an additional coordination to Ca and Y in the 2-Mⁿ⁺ adducts with shortened Ni-M distances of 2.15 and 2.11 Å, respectively, implying direct bonding interactions between Ni and Lewis acids (LAs). Such a short interatomic distance between Ni(III) and M is unprecedented and was not observed before. EPR analysis of 2 and 2-Mⁿ⁺ species, moreover, displayed rhombic signals with g_av > 2.12 for all complexes, supporting the +III oxidation state of Ni. The Ni^III/Ni^II redox potential of 2 and 2-Mⁿ⁺ species was determined, and a plot of E_1/2 of 2-Mⁿ⁺ versus pK_a of [M(H₂O)_n]^m+ exhibited a linear relationship, implying that the Ni^III/Ni^II potential of 2 can be tuned with different redox-inactive metal ions. Reactivity studies of 2 and 2-Mⁿ⁺ with different 4-X-2,6-ditert-butylphenol (4-X-DTBP) and other phenol derivatives were performed, and based on kinetic studies, we propose the involvement of a proton-coupled electron transfer (PCET) pathway. Analysis of the reaction products after the reaction of 2 with 4-OMe-DTBP showed the formation of a Ni(II) complex (1a) where one of the alkoxide arms of the ligand is protonated. A pK_a value of 24.2 was estimated for 1a. The reaction of 2-Mⁿ⁺ species was examined with 4-OMe-DTBP, and it was observed that the k₂ values of 2-Mⁿ⁺ species increase by increasing the Lewis acidity of redox-inactive metal ions. However, the obtained k₂ values for 2-Mⁿ⁺ species are much lower compared to the k₂ value for 2. Such a variation of PCET reactivity between 2 and 2-Mⁿ⁺ species may be attributed to the interactions between Ni(III) and LAs. Our findings show the significance of the secondary coordination sphere effect on the PCET reactivity of Ni(III) complexes and furnish important insights into the reaction mechanism involving high-valent nickel species, which are frequently invoked as key intermediates in Ni-mediated enzymatic reactions, solar-fuel catalysis, and biomimetic/synthetic transformation reactions.

Informing geometric deep learning with electronic interactions to accelerate quantum chemistry

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. However, existing machine learning techniques are challenged by the scarcity of training data when exploring unknown chemical spaces. We overcome this barrier by systematically incorporating knowledge of molecular electronic structure into deep learning. By developing a physics-inspired equivariant neural network, we introduce a method to learn molecular representations based on the electronic interactions among atomic orbitals. Our method, OrbNet-Equi, leverages efficient tight-binding simulations and learned mappings to recover high-fidelity physical quantities. OrbNet-Equi accurately models a wide spectrum of target properties while being several orders of magnitude faster than density functional theory. Despite only using training samples collected from readily available small-molecule libraries, OrbNet-Equi outperforms traditional semiempirical and machine learning-based methods on comprehensive downstream benchmarks that encompass diverse main-group chemical processes. Our method also describes interactions in challenging charge-transfer complexes and open-shell systems. We anticipate that the strategy presented here will help to expand opportunities for studies in chemistry and materials science, where the acquisition of experimental or reference training data is costly.

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.

The hangman effect boosts hydrogen production by a manganese terpyridine complex

The manganese terpyridine complex 1 with a coordinated carboxylate in the axial position was obtained in situ. By virtue of a hangman effect, complex 1 catalyzes electrochemical hydrogen evolution from phenol in acetonitrile solution with a turnover frequency of 525 s^-1 at a low overpotential of ca. 230 mV.

Use of Protein Engineering to Elucidate Electron Transfer Pathways between Proteins and Electrodes

Herein, we review protein engineering tools for electron transfer enhancement and investigation in bioelectrochemical systems. We present recent studies in the field while focusing on how electron transfer investigation and measurements were performed and discuss the use of protein engineering to interpret electron transfer mechanisms.

Dynamic Pt-OH-·H2O-Ag species mediate coupled electron and proton transfer for catalytic hydride reduction of 4-nitrophenol at the confined nanoscale interface

Generally, the catalytic transformation of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) at heterogeneous metal surfaces follows a Langmuir-Hinshelwood (L-H) mechanism when sodium borohydride (NaBH₄) is used as the sacrificial reductant. Herein, with Pt-Ag bimetallic nanoparticles confined in dendritic mesoporous silica nanospheres (DMSNs) as a model catalyst, we demonstrated that the conversion of 4-NP did not pass through the direct hydrogen transfer route with the hydride equivalents being supplied by borohydride via the bimolecular L-H mechanism, since Fourier transform infrared (FTIR) spectroscopy with the use of isotopically labeled reactants (NaBD₄ and D₂O) showed that the final product of 4-AP was composed of protons (or deuterons) that originated from the solvent water (or heavy water). Combined characterization by X-ray photoelectron spectroscopy (XPS), ¹H nuclear magnetic resonance (NMR) and the optical excitation and photoluminescence spectrum evidenced that the surface hydrous hydroxide complex bound to the metal surface (also called structural water molecules, SWs), due to the space overlap of p orbitals of two O atoms in SWs, could form an ensemble of dynamic interface transient states, which provided the alternative electron and proton transfer channels for selective transformation of 4-NP. The cationic Pt species in the Ag-Pt bimetallic catalyst mainly acts as a dynamic adsorption center to temporally anchor SWs and related reactants, and not as the active site for hydrogen activation.

Combining metal-metal cooperativity, metal-ligand cooperativity and chemical non-innocence in diiron carbonyl complexes

Several metalloenzymes, including [FeFe]-hydrogenase, employ cofactors wherein multiple metal atoms work together with surrounding ligands that mediate heterolytic and concerted proton-electron transfer (CPET) bond activation steps. Herein, we report a new dinucleating PNNP expanded pincer ligand, which can bind two low-valent iron atoms in close proximity to enable metal-metal cooperativity (MMC). In addition, reversible partial dearomatization of the ligand's naphthyridine core enables both heterolytic metal-ligand cooperativity (MLC) and chemical non-innocence through CPET steps. Thermochemical and computational studies show how a change in ligand binding mode can lower the bond dissociation free energy of ligand C(sp3)-H bonds by ∼25 kcal mol-1. H-atom abstraction enabled trapping of an unstable intermediate, which undergoes facile loss of two carbonyl ligands to form an unusual paramagnetic (S = ) complex containing a mixed-valent iron(0)-iron(i) core bound within a partially dearomatized PNNP ligand. Finally, cyclic voltammetry experiments showed that these diiron complexes show catalytic activity for the electrochemical hydrogen evolution reaction. This work presents the first example of a ligand system that enables MMC, heterolytic MLC and chemical non-innocence, thereby providing important insights and opportunities for the development of bimetallic systems that exploit these features to enable new (catalytic) reactivity.

Iron Complexes of a Proton-Responsive SCS Pincer Ligand with a Sensitive Electronic Structure

Sulfur/carbon/sulfur pincer ligands have an interesting combination of strong-field and weak-field donors, a coordination environment that is also present in the nitrogenase active site. Here, we explore the electronic structures of iron(II) and iron(III) complexes with such a pincer ligand, bearing a monodentate phosphine, thiolate S donor, amide N donor, ammonia, or CO. The ligand scaffold features a proton-responsive thioamide site, and the protonation state of the ligand greatly influences the reduction potential of iron in the phosphine complex. The N-H bond dissociation free energy, derived from the Bordwell equation, is 56 ± 2 kcal/mol. Electron paramagnetic resonance (EPR) spectroscopy and superconducting quantum interference device (SQUID) magnetometry measurements show that the iron(III) complexes with S and N as the fourth donors have an intermediate spin (S = 3/2) ground state with a large zero field splitting, and X-ray absorption spectra show a high Fe-S covalency. The Mössbauer spectrum changes drastically with the position of a nearby alkali metal cation in the iron(III) amido complex, and density functional theory calculations explain this phenomenon through a change between having the doubly occupied orbital as dz2 or dyz, as the former is more influenced by the nearby positive charge.

Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Di-iron hydrogenases are a class of enzymes that are capable of reducing protons to form molecular hydrogen with high efficiency. In addition to the catalytic site, these enzymes have evolved dedicated pathways to transport protons and electrons to the reaction center. Here, we present a detailed study of the most likely proton transfer pathway in such an enzyme using QM/MM molecular dynamics simulations. The protons are transported through a channel lined out from the protein exterior to the di-iron active site, by a series of hydrogen-bonded, weakly acidic or basic, amino acids and two incorporated water molecules. The channel shows remarkable flexibility, which is an essential feature to quickly reset the hydrogen-bond direction in the channel after each proton passing. Proton transport takes place via a “hole” mechanism, rather than an excess proton mechanism, the free energy landscape of which is remarkably flat, with a highest transition state barrier of only 5 kcal/mol. These results confirm our previous assumptions that proton transport is not rate limiting in the H₂ formation activity and that cysteine C299 may be considered protonated at physiological pH conditions. Detailed understanding of this proton transport may aid in the ongoing attempts to design artificial biomimetic hydrogenases for hydrogen fuel production.

Hydride state accumulation in native [FeFe]-hydrogenase with the physiological reductant H2 supports its catalytic relevance

Small molecules in solution may interfere with mechanistic investigations, as they can affect the stability of catalytic states and produce off-cycle states that can be mistaken for catalytically relevant species. Here we show that the hydride state (H_hyd), a proposed central intermediate in the catalytic cycle of [FeFe]-hydrogenase, can be formed in wild-type [FeFe]-hydrogenases treated with H₂ in absence of other, non-biological, reductants. Moreover, we reveal a new state with unclear role in catalysis induced by common low pH buffers.

Studies of enzymatic catalysis often rely on non-biological reagents, which may affect catalytic intermediates and produce off-cycle states. Here the influence of buffer and reductant on key intermediates of [FeFe]-hydrogenase are explored.

Reversible or Irreversible Catalysis of H+/H2 Conversion by FeFe Hydrogenases

Studies of molecular catalysts traditionally aim at understanding how a certain mechanism allows the reaction to be fast. A distinct question, which has only recently received attention in the case of bidirectional molecular catalysts, is how much thermodynamic driving force is required to achieve fast catalysis in either direction of the reaction. "Reversible" catalysts are bidirectional catalysts that work either way in response to even a small departure from equilibrium and thus do not waste input free energy as heat; conversely, "irreversible" catalysts require a large driving force to proceed at an appreciable rate [Fourmond et al. Nat. Rev. Chem. 2021, 5, 348-360]. Numerous mechanistic rationales for these contrasting behaviors have been proposed. To understand the determinants of catalytic (ir)reversibility, we examined the steady-state, direct electron transfer voltammetry of a particular FeFe hydrogenase, from Thermoanaerobacter mathranii, which is very unusual in that it irreversibly catalyzes H₂ oxidation and production: a large overpotential is required for the reaction to proceed in either direction [Land et al. Chem. Sci. 2020, 11, 12789-12801]. In contrast to previous hypotheses, we demonstrate that in this particular enzyme catalytic irreversibility can be explained without invoking slow interfacial electron transfer or variations in the mechanism: the observed kinetics is fully consistent with the same catalytic pathway being used in both directions of the reaction.

Multiple-Site Concerted Proton-Electron Transfer in a Manganese-Based Complete Functional Model for [FeFe]-Hydrogenase

The active site of [FeFe]-hydrogenase (H₂ ase) is preorganized with an amine (azadithiolate) as a proton relay and a [4Fe4S] subunit as an electron reservoir, which together lower the overpotential for proton reduction and hydrogen oxidation by multiple-site concerted proton-electron transfer (MS-CPET). Herein, we report a mononuclear manganese complex, fac-[Mn(CO)₃ (6-(2-hydroxyphenol)-2-pyridine-2-quinoline) Br] (1), as a rare model to fully mimic the functions of the H₂ ase. In 1, a redox-active bidentate ligand with a pendent phenol replicates the roles of the electron reservoir and the proton relay in the enzyme. Experimental and theoretical studies revealed two consecutive MS-CPET processes in the catalytic cycle, in each of which an electron stored in the reductive ligand and a proton at the proximal phenol moiety are transferred to the Mn center in a concerted way. By virtue of this mechanism, complex 1 exhibited a low overpotential comparable to that of natural enzyme in electrochemical hydrogen production using phenol as a proton source.

Some fundamental insights into biological redox catalysis from the electrochemical characteristics of enzymes attached directly to electrodes

This article outlines examples of where electrochemical investigations of electrocatalysis by proteins immobilised on an electrode reveal fundamental information about electron-proton coupling in catalysis and provide a new way to energise, control and observe multi-enzyme cascades.

Surface electronic states mediate concerted electron and proton transfer at metal nanoscale interfaces for catalytic hydride reduction of -NO2 to -NH2

Concerted electron and proton transfer is a key step for the reversible conversion of molecular hydrogen in both heterogeneous nanocatalysis and metalloenzyme catalysis. However, its activation mechanism involving electron and proton transfer kinetics remains elusive. With the most widely used catalytic hydride reduction of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) as a model reaction, we evaluate the catalytic activity of noble metal nanoparticles (NPs) trapped in porous silica in aqueous NaBH4 solution. By virtue of a novel combination of catalyst design, reaction kinetics, isotope labeling, and multiple spectroscopic techniques, the real catalytic site for the conversion of -NO2 to -NH2 is identified to be the water-hydroxyl transition metal complex, which could further react with NaBH4 to form a new triangular configuration metal complex of H3B-water-hydroxyl with dynamic features. It yields an ensemble of surface electronic states (SESs) though space overlapping of p orbitals of one B and several O atoms (including the O atoms of 4-NP), which could act as an alternative channel for concerted electron and proton transfer. This work highlights the critical role of the conceptual SESs model in heterogeneous catalysis to tune the chemical reactivity and also sheds light on the intricate working of the [FeFe]-hydrogenases.

Reversible catalysis

We describe as 'reversible' a bidirectional catalyst that allows a reaction to proceed at a significant rate in response to even a small departure from equilibrium, resulting in fast and energy-efficient chemical transformation. Examining the relation between reaction rate and thermodynamic driving force is the basis of electrochemical investigations of redox reactions, which can be catalysed by metallic surfaces and biological or synthetic molecular catalysts. This relation has also been discussed in the context of biological energy transduction, regarding the function of biological molecular machines that harness chemical reactions to do mechanical work. This Perspective describes mean-field kinetic modelling of these three types of systems - surface catalysts, molecular catalysts of redox reactions and molecular machines - with the goal of unifying concepts in these different fields. We emphasize that reversibility should be distinguished from other figures of merit, such as rate or directionality, before its design principles can be identified and used to engineer synthetic catalysts.

Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F₄₃₀. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.

Site-selective protonation of the one-electron reduced cofactor in [FeFe]-hydrogenase

Hydrogenases are bidirectional redox enzymes that catalyze hydrogen turnover in archaea, bacteria, and algae. While all types of hydrogenase show H2 oxidation activity, [FeFe]-hydrogenases are excellent H2 evolution catalysts as well. Their active site cofactor comprises a [4Fe-4S] cluster covalently linked to a diiron site equipped with carbon monoxide and cyanide ligands. The active site niche is connected with the solvent by two distinct proton transfer pathways. To analyze the catalytic mechanism of [FeFe]-hydrogenase, we employ operando infrared spectroscopy and infrared spectro-electrochemistry. Titrating the pH under H2 oxidation or H2 evolution conditions reveals the influence of site-selective protonation on the equilibrium of reduced cofactor states. Governed by pKa differences across the active site niche and proton transfer pathways, we find that individual electrons are stabilized either at the [4Fe-4S] cluster (alkaline pH values) or at the diiron site (acidic pH values). This observation is discussed in the context of the complex interdependence of hydrogen turnover and bulk pH.

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.

Proton-Coupled Electron Transfer Guidelines, Fair and Square

Proton-coupled electron transfer (PCET) reactions are fundamental to energy transformation reactions in natural and artificial systems and are increasingly recognized in areas such as catalysis and synthetic chemistry. The interdependence of proton and electron transfer brings a mechanistic richness of reactivity, including various sequential and concerted mechanisms. Delineating between different PCET mechanisms and understanding why a particular mechanism dominates are crucial for the design and optimization of reactions that use PCET. This Perspective provides practical guidelines for how to discern between sequential and concerted mechanisms based on interpretations of thermodynamic data with temperature-, pressure-, and isotope-dependent kinetics. We present new PCET-zone diagrams that show how a mechanism can switch or even be eliminated by varying the thermodynamic (ΔGPT° and ΔGET°) and coupling strengths for a PCET system. We discuss the appropriateness of asynchronous concerted PCET to rationalize observations in organic reactions, and the distinction between hydrogen atom transfer and other concerted PCET reactions. Contemporary issues and future prospects in PCET research are discussed.

Catalytic bias in oxidation-reduction catalysis

Cataytic bias refers to the propensity of a reaction catalyst to effect a different rate acceleration in one direction versus the other in a chemical reaction under non-equilibrium conditions. In biocatalysis, the inherent bias of an enzyme is often advantagous to augment the innate thermodynamics of a reaction to promote efficiency and fidelity in the coordination of catabolic and anabolic pathways. In industrial chemical catalysis a directional cataltyic bias is a sought after property in facilitating the engineering of systems that couple catalysis with harvest and storage of for example fine chemicals or energy compounds. Interestingly, there is little information about catalytic bias in biocatalysis likely in large part due to difficulties in developing tractible assays sensitive enough to study detailed kinetics. For oxidation-reduction reactions, colorimetric redox indicators exist in a range of reduction potentials to provide a mechanism to study both directions of reactions in a fairly facile manner. The current short review attempts to define catalytic bias conceptually and to develop model systems for defining the parameters that control catalytic bias in enzyme catalyzed oxidation-reduction catalysis.

Characterization of a putative sensory [FeFe]-hydrogenase provides new insight into the role of the active site architecture

[FeFe]-hydrogenases are known for their high rates of hydrogen turnover, and are intensively studied in the context of biotechnological applications. Evolution has generated a plethora of different subclasses with widely different characteristics. The M2e subclass is phylogenetically distinct from previously characterized members of this enzyme family and its biological role is unknown. It features significant differences in domain- and active site architecture, and is most closely related to the putative sensory [FeFe]-hydrogenases. Here we report the first comprehensive biochemical and spectroscopical characterization of an M2e enzyme, derived from Thermoanaerobacter mathranii. As compared to other [FeFe]-hydrogenases characterized to-date, this enzyme displays an increased H2 affinity, higher activation enthalpies for H+/H2 interconversion, and unusual reactivity towards known hydrogenase inhibitors. These properties are related to differences in active site architecture between the M2e [FeFe]-hydrogenase and "prototypical" [FeFe]-hydrogenases. Thus, this study provides new insight into the role of this subclass in hydrogen metabolism and the influence of the active site pocket on the chemistry of the H-cluster.