Photoactivation of the Ni-SIr state to the Ni-SIa state in [NiFe] hydrogenase: FT-IR study on the light reactivity of the ready Ni-SIr state and as-isolated enzyme revisited

New insights into the oxidation process from neutron and X-ray crystal structures of an O2-sensitive [NiFe]-hydrogenase

[NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F is an O2-sensitive enzyme that is inactivated in the presence of O2 but the oxidized enzyme can recover its catalytic activity by reacting with H2 under anaerobic conditions. Here, we report the first neutron structure of [NiFe]-hydrogenase in its oxidized state, determined at a resolution of 2.20 Å. This resolution allowed us to reinvestigate the structure of the oxidized active site and to observe the positions of protons in several short hydrogen bonds. X-ray anomalous scattering data revealed that a part of the Ni ion is dissociated from the active site Ni-Fe complex and forms a new square-planar Ni complex, accompanied by rearrangement of the coordinated thiolate ligands. One of the thiolate Sγ atoms is oxidized to a sulfenate anion but remains attached to the Ni ion, which was evaluated by quantum chemical calculations. These results suggest that the square-planar complex can be generated by the attack of reactive oxygen species derived from O2, as distinct from one-electron oxidation leading to a conventional oxidized form of the Ni-Fe complex. Another major finding of this neutron structure analysis is that the Cys17S thiolate Sγ atom coordinating to the proximal Fe-S cluster forms an unusual hydrogen bond with the main-chain amide N atom of Gly19S with a distance of 3.25 Å, where the amide proton appears to be delocalized between the donor and acceptor atoms. This observation provides insight into the contribution of the coordinated thiolate ligands to the redox reaction of the Fe-S cluster.

Understanding 2D-IR Spectra of Hydrogenases: A Descriptive and Predictive Computational Study

[NiFe] hydrogenases are metalloenzymes that catalyze the reversible cleavage of dihydrogen (), a clean future fuel. Understanding the mechanism of these biocatalysts requires spectroscopic techniques that yield insights into the structure and dynamics of the [NiFe] active site. Due to the presence of CO and ligands at this cofactor, infrared (IR) spectroscopy represents an ideal technique for studying these aspects, but molecular information from linear IR absorption experiments is limited. More detailed insights can be obtained from ultrafast nonlinear IR techniques like IRpump−IRprobe and two-dimensional (2D-)IR spectroscopy. However, fully exploiting these advanced techniques requires an in-depth understanding of experimental observables and the encoded molecular information. To address this challenge, we present a descriptive and predictive computational approach for the simulation and analysis of static 2D-IR spectra of [NiFe] hydrogenases and similar organometallic systems. Accurate reproduction of experimental spectra from a first-coordination-sphere model suggests a decisive role of the [NiFe] core in shaping the enzymatic potential energy surface. We also reveal spectrally encoded molecular information that is not accessible by experiments, thereby helping to understand the catalytic role of the diatomic ligands, structural differences between [NiFe] intermediates, and possible energy transfer mechanisms. Our studies demonstrate the feasibility and benefits of computational spectroscopy in the 2D-IR investigation of hydrogenases, thereby further strengthening the potential of this nonlinear IR technique as a powerful research tool for the investigation of complex bioinorganic molecules.

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.

Proton Transfer Mechanisms in Bimetallic Hydrogenases

Hydrogenases are metalloenzymes that catalyze proton reduction and H₂ oxidation with outstanding efficiency. They are model systems for bioinorganic chemistry, including low-valent transition metals, hydride chemistry, and proton-coupled electron transfer. In this Account, we describe how photochemistry and infrared difference spectroscopy can be used to identify the dynamic hydrogen-bonding changes that facilitate proton transfer in [NiFe]- and [FeFe]-hydrogenase.[NiFe]-hydrogenase binds a heterobimetallic nickel/iron site embedded in the protein by four cysteine ligands. [FeFe]-hydrogenase carries a homobimetallic iron/iron site attached to the protein by only a single cysteine. Carbon monoxide and cyanide ligands in the active site facilitate detailed investigations of hydrogenase catalysis by infrared spectroscopy because of their strong signals and redox-dependent frequency shifts. We found that specific redox-state transitions in [NiFe]- and [FeFe]-hydrogenase can be triggered by visible light to record extremely sensitive "light-minus-dark" infrared difference spectra monitoring key amino acid residues. As these transitions are coupled to protonation changes, our data allowed investigation of dynamic hydrogen-bonding changes that go well beyond the resolution of protein crystallography.In [NiFe]-hydrogenase, photolysis of the bridging hydride ligand in the Ni-C state was followed by infrared difference spectroscopy. Our data clearly indicate the formation of a protonated cysteine residue as well as hydrogen-bonding changes involving a glutamic acid residue and a "dangling water" molecule. These findings are in excellent agreement with crystallographic analyses of [NiFe]-hydrogenase. In [FeFe]-hydrogenase, an external redox dye was used to accumulate the Hred state. Infrared difference spectra indicate hydrogen-bonding changes involving two glutamic acid residues and a conserved arginine residue. While crystallographic analyses of [FeFe]-hydrogenase in the oxidized state failed to explain the rapid proton transfer because of a breach in the succession of residues, our findings facilitated a precise molecular model of discontinued proton transfer.Comparing both systems, our data emphasize the role of the outer coordination sphere in bimetallic hydrogenases: we suggest that protonation of a nickel-ligating cysteine in [NiFe]-hydrogenase causes the notable preference toward H₂ oxidation. On the contrary, proton transfer in [FeFe]-hydrogenase involves an adjacent cysteine as a relay group, promoting both H₂ oxidation and proton reduction. These observations may guide the design of organometallic compounds that mimic the catalytic properties of hydrogenases.

Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations

The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H₂/H⁺ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, ⁵⁷Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site.

Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two Ni^IIFe^II and Ni^IIIFe^II resting states, contributing in combination with DFT modeling to rationalized structural candidates.

The large subunit of the regulatory [NiFe]-hydrogenase from Ralstonia eutropha - a minimal hydrogenase?

Chemically synthesized compounds that are capable of facilitating the reversible splitting of dihydrogen into protons and electrons are rare in chemists' portfolio. The corresponding biocatalysts – hydrogenases – are, however, abundant in the microbial world. [NiFe]-hydrogenases represent a major subclass and display a bipartite architecture, composed of a large subunit, hosting the catalytic NiFe(CO)(CN)₂ cofactor, and a small subunit whose iron–sulfur clusters are responsible for electron transfer. To analyze in detail the catalytic competence of the large subunit without its smaller counterpart, we purified the large subunit HoxC of the regulatory [NiFe]-hydrogenase of the model H₂ oxidizer Ralstonia eutropha to homogeneity. Metal determination and infrared spectroscopy revealed a stoichiometric loading of the metal cofactor. This enabled for the first time the determination of the UV-visible extinction coefficient of the NiFe(CO)(CN)₂ cofactor. Moreover, the absence of disturbing iron–sulfur clusters allowed an unbiased look into the low-spin Fe²⁺ of the active site by Mössbauer spectroscopy. Isolated HoxC was active in catalytic hydrogen–deuterium exchange, demonstrating its capacity to activate H₂. Its catalytic activity was drastically lower than that of the bipartite holoenzyme. This was consistent with infrared and electron paramagnetic resonance spectroscopic observations, suggesting that the bridging position between the active site nickel and iron ions is predominantly occupied by water-derived ligands, even under reducing conditions. In fact, the presence of water-derived ligands bound to low-spin Ni²⁺ was reflected by the absorption bands occurring in the corresponding UV-vis spectra, as revealed by time-dependent density functional theory calculations conducted on appropriate in silico models. Thus, the isolated large subunits indeed represent simple [NiFe]-hydrogenase models, which could serve as blueprints for chemically synthesized mimics. Furthermore, our data point to a fundamental role of the small subunit in preventing water access to the catalytic center, which significantly increases the H₂ splitting capacity of the enzyme.

Spectroscopic investigation of an isolated [NiFe]-hydrogenase large subunit enables a unique view of the NiFe(CO)(CN)₂ cofactor.

Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy

A [NiFe] hydrogenase (H₂ ase) is a proton-coupled electron transfer enzyme that catalyses reversible H₂ oxidation; however, its fundamental proton transfer pathway remains unknown. Herein, we observed the protonation of Cys546-SH and Glu34-COOH near the Ni-Fe site with high-sensitivity infrared difference spectra by utilizing Ni-C-to-Ni-L and Ni-C-to-Ni-SI_a photoconversions. Protonated Cys546-SH in the Ni-L state was verified by the observed SH stretching frequency (2505 cm^-1 ), whereas Cys546 was deprotonated in the Ni-C and Ni-SI_a states. Glu34-COOH was double H-bonded in the Ni-L state, as determined by the COOH stretching frequency (1700 cm^-1 ), and single H-bonded in the Ni-C and Ni-SI_a states. Additionally, a stretching mode of an ordered water molecule was observed in the Ni-L and Ni-C states. These results elucidate the organized proton transfer pathway during the catalytic reaction of a [NiFe] H₂ ase, which is regulated by the H-bond network of Cys546, Glu34, and an ordered water molecule.

Comprehensive reaction mechanisms at and near the Ni-Fe active sites of [NiFe] hydrogenases

[NiFe] hydrogenase (H2ase) catalyzes the oxidation of dihydrogen to two protons and two electrons and/or its reverse reaction. For this simple reaction, the enzyme has developed a sophisticated but intricate mechanism with heterolytic cleavage of dihydrogen (or a combination of a hydride and a proton), where its Ni-Fe active site exhibits various redox states. Recently, thermodynamic parameters of the acid-base equilibrium for activation-inactivation, a new intermediate in the catalytic reaction, and new crystal structures of [NiFe] H2ases have been reported, providing significant insights into the activation-inactivation and catalytic reaction mechanisms of [NiFe] H2ases. This Perspective provides an overview of the reaction mechanisms of [NiFe] H2ases based on these new findings.

Development of air-stable hydrogen evolution catalysts

Obtaining abundant pure hydrogen by reduction of water has an important implication in the development of clean and renewable energy. Hence research focused on the development of non-noble metal based facile and energy efficient catalysts for proton reduction is on the rise. However, for practical utilization, it is necessary that these complexes function unabated in the presence of atmospheric oxygen and other common contaminants in abundant water sources. There has been very little activity towards the development of oxygen-tolerant hydrogen producing catalysts. This article aims to draw attention to this issue of oxygen sensitivity in the HER and highlights the development of a few air-stable HER catalysts (enzymatic as well as artificial) elaborating the challenges involved and the techniques discovered to overcome this significant deterrent to large-scale hydrogen production by electrolysis from abundant water sources.

Equilibrium between inactive ready Ni-SIr and active Ni-SIa states of [NiFe] hydrogenase studied by utilizing Ni-SIr-to-Ni-SIa photoactivation

Previously, the Ni-SI_r state of [NiFe] hydrogenase was found to convert to the Ni-SI_a state by light irradiation. Herein, large activation energies and a large kinetic isotope effect were obtained for the reconversion of the Ni-SI_a state to the Ni-SI_r state after the Ni-SI_r-to-Ni-SI_a photoactivation, suggesting that the Ni-SI_a state reacts with H₂O and leaves a bridging hydroxo ligand for the Ni-SI_r state.

First-principles computation of electron transfer and reaction rate at a perovskite cathode for hydrogen production

The focus of this research is on the electron transfer and its reaction rate at the perovskite cathode of a photoelectrochemical cell for hydrogen production. By employing the density functional theory (DFT), the electron density, projected density of states (PDOS), electron distribution and electron transfer path between [Fe-Fe] hydrogenase and the perovskite cathode can be obtained. Simulation results show that the perovskite cathode is better than traditional cathodes for hydrogen production. Before transmission to the [Fe-Fe] hydrogenase, electron clouds mainly aggregate at the periphery of amine molecules. Simulations also show that the key to hydrogen production at the perovskite structure lies in the organic molecules. Electrons are transferred to the hydrocarbon structural chain before reaching the Fe atoms. The Rice, Ramsperger, Kassel and Marcus (RRKM) theory was used to predict the reaction rates at different temperatures. It was found that the reaction rates are in good agreement with the experimental results. This research provides more physical insight into the electron transfer mechanism during the hydrogen production process.