A [RuRu] Analogue of an [FeFe]-Hydrogenase Traps the Key Hydride Intermediate of the Catalytic Cycle

Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges

Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.

Hybrids of [FeFe]- and [NiFe]-H2ase Active Site Models

Complexes of the type (diphosphine)Ni(μ-SR)2Fe(CO)3 are investigated with azadithiolate (adt, HN(CH2S-)2) as the dithiolate. The resulting complexes are hybrid models for the active sites of the [NiFe]- and [FeFe]-hydrogenases. The key complex (dppv)Ni(μ-adt)Fe(CO)3 (3) was prepared from the complex Ni[(SCH2)2NCbz](dppv), which contains a Cbz-protected adt ligand (Cbz = C(O)OCH2Ph, dppv = cis-1,2-(Ph2P)2C2H2). This complex combines with Fe2(CO)9 to give (dppv)Ni[(μ-SCH2)2NCbz]Fe(CO)3, which is readily deprotected to give 3. Complex 3 undergoes protonation at both Fe and N to give successively [(dppv)Ni(μ-adt)FeH(CO)3]+ ([H3]+) and [(dppv)Ni(μ-adtH)FeH(CO)3]2+ ([H3H]2+). The redox properties and dynamics of these complexes resemble previously reported analogues with propanedithiolate. Solutions of [H3]+ readily degrade to [(dppv)Ni[(μ-SCH2)2NCH2]Fe(CO)3]+ ([4]+), which features a methylene group linking N and Fe. Complex [4]+ can be made in high yield by reaction of [H3]+ with CH2O, and this conversion was also demonstrated with 13CH2O. Complex [4]+ undergoes hydrogenolysis by photochemical reaction with H2 to give [(dppv)Ni[(μ-SCH2)2NMe]FeH(CO)3]+, the N-methylated analogue of [H3]+. Upon treatment ith Me3O+, [4]+ undergoes quaternization, giving [(dppv)Ni[(μ-SCH2)2N(Me)CH2]Fe(CO)3]2+. In contrast with the lability of [H3]+, the phosphine-substituted derivative [(dppv)Ni(μ-adt)FeH(CO)2(PPh3)]+ did not degrade. Most complexes were characterized by X-ray crystallography.

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.

Hydrogenase and Nitrogenase: Key Catalysts in Biohydrogen Production

Hydrogen with high energy content is considered to be a promising alternative clean energy source. Biohydrogen production through microbes provides a renewable and immense hydrogen supply by utilizing raw materials such as inexhaustible natural sunlight, water, and even organic waste, which is supposed to solve the two problems of "energy supply and environment protection" at the same time. Hydrogenases and nitrogenases are two classes of key enzymes involved in biohydrogen production and can be applied under different biological conditions. Both the research on enzymatic catalytic mechanisms and the innovations of enzymatic techniques are important and necessary for the application of biohydrogen production. In this review, we introduce the enzymatic structures related to biohydrogen production, summarize recent enzymatic and genetic engineering works to enhance hydrogen production, and describe the chemical efforts of novel synthetic artificial enzymes inspired by the two biocatalysts. Continual studies on the two types of enzymes in the future will further improve the efficiency of biohydrogen production and contribute to the economic feasibility of biohydrogen as an energy source.

Investigating the role of the strong field ligands in [FeFe] hydrogenase: spectroscopic and functional characterization of a semi-synthetic mono-cyanide active site

Artificial maturation of hydrogenases provides a path towards generating new semi-synthetic enzymes with novel catalytic properties. Here enzymes featuring a synthetic asymmetric mono-cyanide cofactor have been prepared using two different hydrogenase scaffolds. Their structure and reactivity was investigated in order to elucidate the design rationale behind the native di-cyanide cofactor, and by extension the second coordination sphere of the active-site pocket. Surprisingly, the choice of host enzyme was found to have a dramatic impact on reactivity. Moreover, the study shows that synthetic manipulations of the active-site can significantly increase inhibitor tolerance, as compared to native [FeFe] hydrogenase, while retaining the enzyme's native capacity for reversible catalysis.

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.

Trapping an Oxidized and Protonated Intermediate of the [FeFe]-Hydrogenase Cofactor under Mildly Reducing Conditions

The H-cluster is the catalytic cofactor of [FeFe]-hydrogenase, a metalloenzyme that catalyzes the formation of dihydrogen (H₂). The catalytic diiron site of the H-cluster carries two cyanide and three carbon monoxide ligands, making it an excellent target for IR spectroscopy. In previous work, we identified an oxidized and protonated H-cluster species, whose IR signature differs from that of the oxidized resting state (Hox) by a small but distinct shift to higher frequencies. This "blue shift" was explained by a protonation at the [4Fe-4S] subcomplex of the H-cluster. The novel species, denoted HoxH, was preferentially accumulated at low pH and in the presence of the exogenous reductant sodium dithionite (NaDT). When HoxH was reacted with H₂, the hydride state (Hhyd) was formed, a key intermediate of [FeFe]-hydrogenase turnover. A recent publication revisited our protocol for the accumulation of HoxH in wild-type [FeFe]-hydrogenase, concluding that inhibition by NaDT decay products rather than cofactor protonation causes the spectroscopic "blue shift". Here, we demonstrate that HoxH formation does not require the presence of NaDT (or its decay products), but accumulates also with the milder reductants tris(2-carboxyethyl)phosphine, dithiothreitol, or ascorbic acid, in particular at low pH. Our data consistently suggest that HoxH is accumulated when deprotonation of the H-cluster is impaired, thereby preventing the regain of the oxidized resting state Hox in the catalytic cycle.

Proposed Mechanism for the Biosynthesis of the [FeFe] Hydrogenase H-Cluster: Central Roles for the Radical SAM Enzymes HydG and HydE

Radical S-adenosylmethionine (radical SAM or rSAM) enzymes use their S-adenosylmethionine cofactor bound to a unique Fe of a [4Fe-4S] cluster to generate the "hot" 5'-deoxyadenosyl radical, which drives highly selective radical reactions via specific interactions with a given rSAM enzyme's substrate. This Perspective focuses on the two rSAM enzymes involved in the biosynthesis of the organometallic H-cluster of [FeFe] hydrogenases. We present here a detailed sequential model initiated by HydG, which lyses a tyrosine substrate via a 5'-deoxyadenosyl H atom abstraction from those amino acid's amino group, initially producing dehydroglycine and an oxidobenzyl radical. In this model, two successive radical cascade reactions lead ultimately to the formation of HydG's product, a mononuclear Fe organometallic complex: [Fe(II)(CN)(CO)₂(cysteinate)]^-, with the iron originating from a unique "dangler" Fe coordinated by a cysteine ligand providing a sulfur bridge to another [4Fe-4S] auxiliary cluster in the enzyme. In turn, in this model, [Fe(II)(CN)(CO)₂(cysteinate)]^- is the substrate for HydE, the second rSAM enzyme in the biosynthetic pathway, which activates this mononuclear organometallic unit for dimerization, forming a [Fe₂S₂(CO)₄(CN)₂] precursor to the [2Fe] _H component of the H-cluster, requiring only the completion of the bridging azadithiolate (SCH₂NHCH₂S) ligand. This model is built upon a foundation of data that incorporates cell-free synthesis, isotope sensitive spectroscopies, and the selective use of synthetic complexes substituting for intermediates in the enzymatic "assembly line". We discuss controversies pertaining to this model and some remaining open issues to be addressed by future work.

Remarkable Stability of a Molecular Ruthenium Complex in PEM Water Electrolysis

The dinuclear Ru diazadiene olefin complex, [Ru₂(OTf)(μ-H)(Me₂dad)(dbcot)₂], is an active catalyst for hydrogen evolution in a Polymer Exchange Membrane (PEM) water electrolyser. When supported on high surface area carbon black and at 80 °C, [Ru₂(OTf)(μ-H)(Me₂dad)(dbcot)₂]@C evolves hydrogen at the cathode of a PEM electrolysis cell (400 mA cm⁻², 1.9 V). A remarkable turn over frequency (TOF) of 7800 mol_H2 mol_catalyst⁻¹ h⁻¹ is maintained over 7 days of operation. A series of model reactions in homogeneous media and in electrochemical half cells, combined with DFT calculations, are used to rationalize the hydrogen evolution mechanism promoted by [Ru₂(OTf)(μ-H)(Me₂dad)(dbcot)₂].

Molecular dinuclear ruthenium complexes deposited on conducting carbon serve as active sites for the evolution of hydrogen from neutral water in a Polymer Exchange Membrane (PEM) water electrolyser.

Surprising Condensation Reactions of the Azadithiolate Cofactor

Azadithiolate, a cofactor found in all [FeFe]-hydrogenases, is shown to undergo acid-catalyzed rearrangement. Fe₂ [(SCH₂ )₂ NH](CO)₆ self-condenses to give Fe₆ [(SCH₂ )₃ N]₂ (CO)₁₇ . The reaction, which is driven by loss of NH₄ ⁺ , illustrates the exchange of the amine group. X-ray crystallography reveals that three Fe₂ (SR)₂ (CO)_x butterfly subunits interconnected by the aminotrithiolate [N(CH₂ S)₃ ]^3- . Mechanistic studies reveal that Fe₂ [(SCH₂ )₂ NR](CO)₆ participate in a range of amine exchange reactions, enabling new methodologies for modifying the adt cofactor. Ru₂ [(SCH₂ )₂ NH](CO)₆ also rearranges, but proceeds further to give derivatives with Ru-alkyl bonds Ru₆ [(SCH₂ )₃ N][(SCH₂ )₂ NCH₂ ]S(CO)₁₇ and [Ru₂ [(SCH₂ )₂ NCH₂ ](CO)₅ ]₂ S.

Diversifying Metal-Ligand Cooperative Catalysis in Semi-Synthetic [Mn]-Hydrogenases

The reconstitution of [Mn]-hydrogenases using a series of MnI complexes is described. These complexes are designed to have an internal base or pro-base that may participate in metal-ligand cooperative catalysis or have no internal base or pro-base. Only MnI complexes with an internal base or pro-base are active for H2 activation; only [Mn]-hydrogenases incorporating such complexes are active for hydrogenase reactions. These results confirm the essential role of metal-ligand cooperation for H2 activation by the MnI complexes alone and by [Mn]-hydrogenases. Owing to the nature and position of the internal base or pro-base, the mode of metal-ligand cooperation in two active [Mn]-hydrogenases is different from that of the native [Fe]-hydrogenase. One [Mn]-hydrogenase has the highest specific activity of semi-synthetic [Mn]- and [Fe]-hydrogenases. This work demonstrates reconstitution of active artificial hydrogenases using synthetic complexes differing greatly from the native active site.

Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study

Splitting of molecular hydrogen (H₂) into bridging and terminal hydrides is a common step in transition metal chemistry. Herein, we propose a novel organometallic platform for cleavage of multiple H₂ molecules, which combines metal centers capable of stabilizing multiple oxidation states, and ligands bearing positioned pendant basic groups. Using quantum chemical modeling, we show that low-valent, early transition metal diniobium(ii) complexes with diphosphine ligands featuring pendant amines can favorably uptake up to 8 hydrogen atoms, and that the energetics are favored by the formation of intramolecular dihydrogen bonds. This result suggests new possible strategies for the development of hydrogen scavenger molecules that are able to perform reversible splitting of multiple H₂ molecules.

[FeFe]-Hydrogenases: maturation and reactivity of enzymatic systems and overview of biomimetic models

[FeFe]-hydrogenases recieved increasing interest in the last decades. This review summarises important findings regarding their enzymatic reactivity as well as inorganic models applied as electro- and photochemical catalysts.

Heterodinuclear nickel(ii)-iron(ii) azadithiolates as structural and functional models for the active site of [NiFe]-hydrogenases

To develop the biomimetic chemistry of [NiFe]-H₂ases, the first azadithiolato-bridged NiFe model complexes [CpNi{(μ-SCH₂)₂NR}Fe(CO)(diphos)]BF₄ (5, R = Ph, diphos = dppv; 6, 4-ClC₆H₄, dppv; 7, 4-MeC₆H₄, dppv; 8, CO₂CH₂Ph, dppe; 9, H, dppe) have been synthesized via well-designed synthetic routes. Thus, treatment of RN[CH₂S(O)CMe]₂ with t-BuONa followed by reaction of the resulting intermediates RN(CH₂SNa)₂ with (dppv)Fe(CO)₂Cl₂ or (dppe)Fe(CO)₂Cl₂ gave the N-substituted azadithiolato-chelated Fe complexes [RN(CH₂S)₂]Fe(CO)₂(diphos) (1, R = Ph, diphos = dppv; 2, 4-ClC₆H₄, dppv; 3, 4-MeC₆H₄, dppv; 4, CO₂CH₂Ph, dppe). Further treatment of 1–4 with nickelocene in the presence of HBF₄·Et₂O afforded the corresponding N-substituted azadithiolato-bridged NiFe model complexes 5–8, while treatment of 8 with HBF₄·Et₂O resulted in formation of the parent azadithiolato-bridged model complex 9. While all the new complexes 1–9 were characterized by elemental analysis and spectroscopy, the molecular structures of model complexes 6–8 were confirmed by X-ray crystallographic study. In addition, model complexes 7 and 9 were found to be catalysts for H₂ production with moderate i_cat/i_p and overpotential values from TFA under CV conditions.

The first azadithiolato-bridged NiFe model complexes with a general formula [CpNi{(μ-SCH₂)₂NR}Fe(CO)(diphos)]BF₄ have been synthesized, characterized, and for some of them found to be catalysts for proton reduction to H₂ under CV conditions.

New Phosphorous-Based [FeFe]-Hydrogenase Models

[FeFe]-hydrogenases have attracted research for more than twenty years as paragons for the design of new catalysts for the hydrogen evolution reaction (HER). The bridging dithiolate comprising a secondary amine as bridgehead is the key element for the reactivity of native [FeFe]-hydrogenases and was therefore the midpoint of hundreds of biomimetic hydrogenase models. However, within those mimics, phosphorous is barely seen as a central element in the azadithiolato bridge despite being the direct heavier homologue of nitrogen. We herein synthesized three new phosphorous based [FeFe]-hydrogenase models by reacting dithiols (HSCH2)2P(O)R (R = Me, OEt, OPh) with Fe3(CO)12. All synthesized mimics show catalytic reactivity regarding HER and change their mechanisms depending on the strength of the used acid. In all presented mimics, the oxide is the center of reactivity, independent of the nature of the bridgehead. However, the phosphorous atom might be reduced by the methods we present herein to alter the reactivity of the model compounds towards protons and oxygen.

Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts

Hybrid protein-organometallic catalysts are being explored for selective catalysis of a number of reactions, because they utilize the complementary strengths of proteins and of organometallic complex. Herein, we present an artificial hydrogenase, StrepH2, built by incorporating a biotinylated [Fe-Fe] hydrogenase organometallic mimic within streptavidin. This strategy takes advantage of the remarkable strength and specificity of biotin-streptavidin recognition, which drives quantitative incorporation of the biotinylated diironhexacarbonyl center into streptavidin, as confirmed by UV/Vis spectroscopy and X-ray crystallography. FTIR spectra of StrepH2 show characteristic peaks at shift values indicative of interactions between the catalyst and the protein scaffold. StrepH2 catalyzes proton reduction to hydrogen in aqueous media during photo- and electrocatalysis. Under photocatalytic conditions, the protein-embedded catalyst shows enhanced efficiency and prolonged activity compared to the isolated catalyst. Transient absorption spectroscopy data suggest a mechanism for the observed increase in activity underpinned by an observed longer lifetime for the catalytic species Fe^I Fe⁰ when incorporated within streptavidin compared to the biotinylated catalyst in solution.

A catalytically active [Mn]-hydrogenase incorporating a non-native metal cofactor

Nature carefully selects specific metal ions for incorporation into the enzymes that catalyze the chemical reactions necessary for life. Hydrogenases, enzymes that activate molecular H₂, exclusively utilize Ni and Fe in [NiFe]-, [FeFe]-, and [Fe]-hydrogeanses. However, other transition metals are known to activate or catalyze the production of hydrogen in synthetic systems. Here, we report the development of a biomimetic model complex of [Fe]-hydrogenase that incorporates a Mn, as opposed to a Fe, metal center. This Mn complex is able to heterolytically cleave H₂ as well as catalyze hydrogenation reactions. Incorporation of the model into an apoenzyme of [Fe]-hydrogenase results in a [Mn]-hydrogenase with enhanced occupancy-normalized activity over an analogous semi-synthetic [Fe]-hydrogenase. These findings represent the first instance of a non-native metal hydrogenase showing catalytic functionality and demonstrate that hydrogenases based on a manganese active site are viable.

Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses

[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined ⁵⁷Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective ⁵⁷Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a ⁵⁷Fe salt and in vitro maturation with a synthetic diiron site precursor containing ⁵⁷Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H₂ turnover.

A low-valent dinuclear ruthenium diazadiene complex catalyzes the oxidation of dihydrogen and reversible hydrogenation of quinones

The dinuclear ruthenium complex [Ru2H(μ-H)(Me2dad)(dbcot)2] contains a 1,4-dimethyl-diazabuta-1,3-diene (Me2dad) as a non-innocent bridging ligand between the metal centers to give a [Ru2(Me2dad)] core. In addition, each ruthenium is bound to one dibenzo[a,e]cyclooctatetraene (dbcot) ligand. This Ru dimer converts H2 to protons and electrons. It also catalyzes reversibly under mild conditions the selective hydrogenation of vitamins K2 and K3 to their corresponding hydroquinone equivalents without affecting the C[double bond, length as m-dash]C double bonds. Mechanistic studies suggest that the [Ru2(Me2dad)] moiety, like hydrogenases, reacts with H2 and releases electrons and protons stepwise.

The Molecular Proceedings of Biological Hydrogen Turnover

Over the past two decades, the bioinorganic chemistry of hydrogenases has attracted much interest from basic and applied research. Hydrogenases are highly efficient metalloenzymes that catalyze the reversible reduction of protons to molecular hydrogen (H₂) in all domains of life. Their iron- and nickel-based cofactors represent promising blueprints for the design of biomimetic, synthetic catalysts. In this Account, we address the molecular proceedings of hydrogen turnover with [FeFe]-hydrogenases. The active site cofactor of [FeFe]-hydrogenases ("H-cluster") comprises a unique diiron complex linked to a [4Fe-4S] cluster via a single cysteine. Since it was discovered that a synthetic analogue of the diiron site can be incorporated into apoprotein in vitro to yield active enzyme, significant progress has been made toward a comprehensive understanding of hydrogenase catalysis. The diiron site carries three to four carbon monoxide (CO) and two cyanide (CN^-) ligands that give rise to intense infrared (IR) absorption bands. These bands are sensitive reporters of the electron density across the H-cluster, which can be addressed by infrared spectroscopy to follow redox and protonation changes at the cofactor. Synthetic variation of the metal-bridging dithiolate ligand at the diiron site, as well as site-directed mutagenesis of amino acids, provides access to the proton pathways toward the cofactor. Quantum chemical calculations are employed to specifically assign IR bands to vibrational modes of the diatomic ligands and yield refined H-cluster geometries. Here, we provide an overview of recent research on [FeFe]-hydrogenases with emphasis on experimental and computational IR studies. We describe advances in attenuated total reflection Fourier transform infrared spectroscopy (ATR FTIR) and protein film electrochemistry, as well as density functional theory (DFT) calculations. Key cofactor species are discussed in terms of molecular geometry, redox state, and protonation. Isotope editing is introduced as a tool to evaluate the cofactor geometry beyond the limits of protein crystallography. In particular, the role of proton-coupled electron transfer (PCET) in the generation of catalytically relevant redox species is addressed. We propose that site-selective protonation of the H-cluster biases surplus electrons either to the [4Fe-4S] cluster or to the diiron site. Protonation of the [4Fe-4S] cluster prevents premature reduction at the diiron site and stabilizes a reactive, terminal hydride. The observed H-cluster species are assigned to rapid H₂ conversion or to reactions possibly involved in activity regulation and cellular H₂ sensing. In the catalytic cycle of [FeFe]-hydrogenases, an H-cluster geometry is preserved that features a bridging CO ligand. PCET levels the redox potential for two steps of sequential cofactor reduction. The concept of consecutive PCET at a geometrically inert cofactor with tight control of electron and proton localization may inspire the design of a novel generation of biomimetic catalysts for the production of H₂ as a fuel.