[NiFe] and [FeFe] Hydrogenases Studied by Advanced Magnetic Resonance Techniques

Perspective: multi-configurational methods in bio-inorganic chemistry

Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the electronic structure and properties of metalloproteins poses significant challenges due to the complex nature of their electronic configurations and strong correlation effects. Multiconfigurational quantum chemistry methods are, in principle, the most appropriate tools for addressing these challenges, offering the capability to capture the inherent multi-reference character and strong electron correlation present in bio-inorganic systems. Yet their computational cost has long hindered wider adoption, making methods such as density functional theory (DFT) the method of choice. However, advancements over the past decade have substantially alleviated this limitation, rendering multiconfigurational quantum chemistry methods more accessible and applicable to a wider range of bio-inorganic systems. In this perspective, we discuss some of these developments and how they have already been used to answer some of the most important questions in bio-inorganic chemistry. We also comment on ongoing developments in the field and how the future of the field may evolve.

Electrostatic [FeFe]-hydrogenase-carbon nitride assemblies for efficient solar hydrogen production

The assembly of semiconductors as light absorbers and enzymes as redox catalysts offers a promising approach for sustainable chemical synthesis driven by light. However, achieving the rational design of such semi-artificial systems requires a comprehensive understanding of the abiotic-biotic interface, which poses significant challenges. In this study, we demonstrate an electrostatic interaction strategy to interface negatively charged cyanamide modified graphitic carbon nitride (NCNCNX) with an [FeFe]-hydrogenase possessing a positive surface charge around the distal FeS cluster responsible for electron uptake into the enzyme. The strong electrostatic attraction enables efficient solar hydrogen (H2) production via direct interfacial electron transfer (DET), achieving a turnover frequency (TOF) of 18 669 h-1 (4 h) and a turnover number (TON) of 198 125 (24 h). Interfacial characterizations, including quartz crystal microbalance (QCM), photoelectrochemical impedance spectroscopy (PEIS), intensity-modulated photovoltage spectroscopy (IMVS), and transient photocurrent spectroscopy (TPC) have been conducted on the semi-artificial carbon nitride-enzyme system to provide a comprehensive understanding for the future development of photocatalytic hybrid assemblies.

Facile electrocatalytic proton reduction by a [Fe-Fe]-hydrogenase bio-inspired synthetic model bearing a terminal CN- ligand

An azadithiolate bridged CN- bound pentacarbonyl bis-iron complex, mimicking the active site of [Fe-Fe] H2ase is synthesized. The geometric and electronic structure of this complex is elucidated using a combination of EXAFS analysis, infrared and Mössbauer spectroscopy and DFT calculations. The electrochemical investigations show that complex 1 effectively reduces H+ to H2 between pH 0-3 at diffusion-controlled rates (1011 M-1 s-1) i.e. 108 s-1 at pH 3 with an overpotential of 140 mV. Electrochemical analysis and DFT calculations suggests that a CN- ligand increases the pKa of the cluster enabling hydrogen production from its Fe(i)-Fe(0) state at pHs much higher and overpotential much lower than its precursor bis-iron hexacarbonyl model which is active in its Fe(0)-Fe(0) state. The formation of a terminal Fe-H species, evidenced by spectroelectrochemistry in organic solvent, via a rate determining proton coupled electron transfer step and protonation of the adjacent azadithiolate, lowers the kinetic barrier leading to diffusion controlled rates of H2 evolution. The stereo-electronic factors enhance its catalytic rate by 3 order of magnitude relative to a bis-iron hexacarbonyl precursor at the same pH and potential.

Characterizing the Biosynthesis of the [Fe(II)(CN)(CO)2(cysteinate)]- Organometallic Product of the Radical-SAM Enzyme HydG by EPR and Mössbauer Spectroscopy

[FeFe]-hydrogenases employ a catalytic H-cluster, consisting of a [4Fe-4S]H cluster linked to a [2Fe]H subcluster with CO, CN- ligands, and an azadithiolate bridge, which mediates the rapid redox interconversion of H+ and H2. In the biosynthesis of this H-cluster active site, the radical S-adenosyl-l-methionine (radical SAM, RS) enzyme HydG plays the crucial role of generating an organometallic [Fe(II)(CN)(CO)2(cysteinate)]- product that is en route to forming the H-cluster. Here, we report direct observation of this diamagnetic organometallic Fe(II) complex through Mössbauer spectroscopy, revealing an isomer shift of δ = 0.10 mm s-1 and quadrupole splitting of ΔEQ = 0.66 mm s-1. These Mössbauer values are a change from the starting values of δ = 1.15 mm s-1 and ΔEQ = 3.23 mm s-1 for the ferrous "dangler" Fe in HydG. These values of the observed product complex B are in good agreement with Mössbauer parameters for the low-spin Fe2+ ions in synthetic analogues, such as 57Fe Syn-B, which we report here. These results highlight the essential role that HydG plays in converting a resting-state high-spin Fe(II) to a low-spin organometallic Fe(II) product that can be transferred to the downstream maturase enzymes.

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.

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.

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.

Bioinorganic Chemistry on Electrodes: Methods to Functional Modeling

One of the major goals of bioinorganic chemistry has been to mimic the function of elegant metalloenzymes. Such functional modeling has been difficult to attain in solution, in particular, for reactions that require multiple protons and multiple electrons (nH⁺/ne^-). Using a combination of heterogeneous electrochemistry, electrode and molecule design one may control both electron transfer (ET) and proton transfer (PT) of these nH⁺/ne^- reactions. Such control can allow functional modeling of hydrogenases (H⁺ + e^- → 1/2 H₂), cytochrome c oxidase (O₂ + 4 e^- + 4 H⁺ → 2 H₂O), monooxygenases (RR'CH₂ + O₂ + 2 e^- + 2 H⁺ → RR'CHOH + H₂O) and dioxygenases (S + O₂ → SO₂; S = organic substrate) in aqueous medium and at room temperatures. In addition, these heterogeneous constructs allow probing unnatural bioinspired reactions and estimation of the inner- and outer-sphere reorganization energy of small molecules and proteins.

Structural and spectroscopic characterization of CO inhibition of [NiFe]-hydrogenase from Citrobacter sp. S-77

Hydrogenases catalyze the reversible oxidation of H2. Carbon monoxide (CO) is known to be a competitive inhibitor of O2-sensitive [NiFe]-hydrogenases. Although the activities of some O2-tolerant [NiFe]-hydrogenases are unaffected by CO, the partially O2-tolerant [NiFe]-hydrogenase from Citrobacter sp. S-77 (S77-HYB) is inhibited by CO. In this work, the CO-bound state of S77-HYB was characterized by activity assays, spectroscopic techniques and X-ray crystallography. Electron paramagnetic resonance spectroscopy showed a diamagnetic Ni2+ state, and Fourier-transform infrared spectroscopy revealed the stretching vibration of the exogenous CO ligand. The crystal structure determined at 1.77 Å resolution revealed that CO binds weakly to the nickel ion in the Ni-Fe active site of S77-HYB. These results suggest a positive correlation between O2 and CO tolerance in [NiFe]-hydrogenases.

The oxygen-resistant [FeFe]-hydrogenase CbA5H harbors an unknown radical signal

[FeFe]-hydrogenases catalyze the reversible conversion of molecular hydrogen into protons and electrons with remarkable efficiency. However, their industrial applications are limited by their oxygen sensitivity. Recently, it was shown that the [FeFe]-hydrogenase from Clostridium beijerinckii (CbA5H) is oxygen-resistant and can be reactivated after oxygen exposure. In this work, we used multifrequency continuous wave and pulsed electron paramagnetic resonance (EPR) spectroscopy to characterize the active center of CbA5H, the H-cluster. Under oxidizing conditions, the spectra were dominated by an additional and unprecedented radical species. The generation of this radical signal depends on the presence of an intact H-cluster and a complete proton transfer pathway including the bridging azadithiolate ligand. Selective ⁵⁷Fe enrichment combined with isotope-sensitive electron-nuclear double resonance (ENDOR) spectroscopy revealed a spin density distribution that resembles an H-cluster state. Overall, we uncovered a radical species in CbA5H that is potentially involved in the redox sensing of CbA5H.

Electron paramagnetic resonance spectroscopy revealed an unprecedented radical species in the oxygen-resistant [FeFe]-hydrogenase CbA5H. Analysis of the isotope-sensitive data suggests that it is related to the active site, the H-cluster.

Electronic and Structural Properties of the Double Cubane Iron-Sulfur Cluster

The double-cubane cluster (DCC) refers to an [Fe8S9] iron-sulfur complex that is otherwise only known to exist in nitrogenases. Containing a bridging µ2-S ligand, the DCC in the DCC-containing protein (DCCP) is covalently linked to the protein scaffold via six coordinating cysteine residues. In this study, the nature of spin coupling and the effect of spin states on the cluster’s geometry are investigated computationally. Using density functional theory (DFT) and a broken symmetry (BS) approach to study the electronic ground state of the system, we computed the exchange interaction between the spin-coupled spins of the four FeFe dimers contained in the DCC. This treatment yields results that are in excellent agreement with both computed and experimentally determined exchange parameters for analogously coupled di-iron complexes. Hybrid quantum mechanical (QM)/molecular mechanical (MM) geometry optimizations show that cubane cluster A closest to charged amino acid side chains (Arg312, Glu140, Lys146) is less compact than cluster B, indicating that electrons of the same spin in a charged environment seek maximum separation. Overall, this study provides the community with a fundamental reference for subsequent studies of DCCP, as well as for investigations of other [Fe8S9]-containing enzymes.

Deuteration mechanistic studies of hydrogenase mimics

The role of deuterium in disentangling key steps of the mechanisms of H₂ activation by mimics of hydrogenases is presented. These studies have allowed to a better understanding of the mode of action of the natural enzymes and their mimics.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

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.

Spin Polarization Reveals the Coordination Geometry of the [FeFe] Hydrogenase Active Site in Its CO-Inhibited State

The active site of [FeFe] hydrogenase features a binuclear iron cofactor Fe₂ADT(CO)₃(CN)₂, where ADT represents the bridging ligand aza-propane-dithiolate. The terminal diatomic ligands all coordinate in a basal configuration, and one CO bridges the two irons leaving an open coordination site at which the hydrogen species and the competitive inhibitor CO bind. Externally supplied CO is expected to coordinate in an apical configuration. However, an alternative configuration has been proposed in which, due to ligand rotation, the CN^- bound to the distal Fe becomes apical. Using selective ¹³C isotope labeling of the CN^- and CO_ext ligands in combination with pulsed ¹³C electron-nuclear-nuclear triple resonance spectroscopy, spin polarization effects are revealed that, according to density functional theory calculations, are consistent with only the "unrotated" apical CO_ext configuration.

A Review of Biohydrogen Productions from Lignocellulosic Precursor via Dark Fermentation: Perspective on Hydrolysate Composition and Electron-Equivalent Balance

This paper reviews the current technological development of bio-hydrogen (BioH2) generation, focusing on using lignocellulosic feedstock via dark fermentation (DF). Using the collected reference reports as the training data set, supervised machine learning via the constructed artificial neuron networks (ANNs) imbedded with feed backward propagation and one cross-out validation approach was deployed to establish correlations between the carbon sources (glucose and xylose) together with the inhibitors (acetate and other inhibitors, such as furfural and aromatic compounds), hydrogen yield (HY), and hydrogen evolution rate (HER) from reported works. Through the statistical analysis, the concentrations variations of glucose (F-value = 0.0027) and acetate (F-value = 0.0028) were found to be statistically significant among the investigated parameters to HY and HER. Manipulating the ratio of glucose to acetate at an optimal range (approximate in 14:1) will effectively improve the BioH2 generation (HY and HER) regardless of microbial strains inoculated. Comparative studies were also carried out on the evolutions of electron equivalent balances using lignocellulosic biomass as substrates for BioH2 production across different reported works. The larger electron sinks in the acetate is found to be appreciably related to the higher HY and HER. To maintain a relative higher level of the BioH2 production, the biosynthesis needs to be kept over 30% in batch cultivation, while the biosynthesis can be kept at a low level (2%) in the continuous operation among the investigated reports. Among available solutions for the enhancement of BioH2 production, the selection of microbial strains with higher capacity in hydrogen productions is still one of the most phenomenal approaches in enhancing BioH2 production. Other process intensifications using continuous operation compounded with synergistic chemical additions could deliver additional enhancement for BioH2 productions during dark fermentation.

Catalytically-active porous assembly with dynamic pulsating motion for efficient exchange of products and reagents

Despite recent advances in the use of porous materials as efficient heterogeneous catalysts which operate through effectively trapping reagents in a well-defined space, continuously uptaking reagents to substitute products in the cavity for efficient product turnover still remains challenging. Here, a porous catalyst is endowed with 'breathing' characteristics by thermal stimulus, which can enable the efficient exchange of reagents and products through reversible stacking from inflated aromatic hexamers to contracted trimeric macrocycles. The contracted super-hydrophobic tubular interior with pyridine environment exhibits catalytic activity towards a nucleophilic aromatic substitution reaction by promoting interactions between concentrated reagents and active sites. Subsequent expansion facilitates the exchange of products and reagents, which ensures the next reaction. The strategy of mesoporous modification with inflatable transition may provide a new insight for construction of dynamic catalysts.

Synthesis, characterization, and some properties of two types of new [Fe]-H2ase models containing a 4-phosphatopyridine or a 4-phosphatoguanosinepyridine moiety

The novel [Fe]-H₂ase active site framework-containing model 6 was first prepared and structurally characterized.

The monoiron anionfac-[Fe(CO)3I3]−and its organic aminium salts: their preparation, CO-release, and cytotoxicity

The anionfac-[Fe(CO)₃I₃]⁻undergoes rapid decomposition to release CO and involve iodine radical. The CO-release can be tuned by its cations. The radical causes severe cytotoxicity which may endow the anion a great potential as an anticancer drug.

Benzenedithiolate-bridged MoFe complexes: structures, oxidation states, and reactivities

The benzenedithiolate-bridged MoFe complexes were synthesized and the oxidation states of the metal centers elucidated.

Spectroscopic and biochemical insight into an electron-bifurcating [FeFe] hydrogenase

Abstract

The heterotrimeric electron-bifurcating [FeFe] hydrogenase (HydABC) from Thermotoga maritima (Tm) couples the endergonic reduction of protons (H⁺) by dihydronicotinamide adenine dinucleotide (NADH) (∆G⁰ ≈ 18 kJ mol⁻¹) to the exergonic reduction of H⁺ by reduced ferredoxin (Fd_red) (∆G⁰ ≈ − 16 kJ mol⁻¹). The specific mechanism by which HydABC functions is not understood. In the current study, we describe the biochemical and spectroscopic characterization of TmHydABC recombinantly produced in Escherichia coli and artificially maturated with a synthetic diiron cofactor. We found that TmHydABC catalyzed the hydrogen (H₂)-dependent reduction of nicotinamide adenine dinucleotide (NAD⁺) in the presence of oxidized ferredoxin (Fd_ox) at a rate of  ≈17 μmol NADH min⁻¹ mg⁻¹. Our data suggest that only one flavin is present in the enzyme and is not likely to be the site of electron bifurcation. FTIR and EPR spectroscopy, as well as FTIR spectroelectrochemistry, demonstrated that the active site for H₂ conversion, the H-cluster, in TmHydABC behaves essentially the same as in prototypical [FeFe] hydrogenases, and is most likely also not the site of electron bifurcation. The implications of these results are discussed with respect to the current hypotheses on the electron bifurcation mechanism of [FeFe] hydrogenases. Overall, the results provide insight into the electron-bifurcating mechanism and present a well-defined system for further investigations of this fascinating class of [FeFe] hydrogenases.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-019-01747-1) contains supplementary material, which is available to authorized users.

Graphene Supported Rhodium Nanoparticles for Enhanced Electrocatalytic Hydrogen Evolution Reaction

Current research on catalysts for proton exchange membrane fuel cells (PEMFC) is based on obtaining higher catalytic activity than platinum particle catalysts on porous carbon. In search of a more sustainable catalyst other than platinum for the catalytic conversion of water to hydrogen gas, a series of nanoparticles of transition metals viz., Rh, Co, Fe, Pt and their composites with functionalized graphene such as RhNPs@f-graphene, CoNPs@f-graphene, PtNPs@f-graphene were synthesized and characterized by SEM and TEM techniques. The SEM analysis indicates that the texture of RhNPs@f-graphene resemble the dispersion of water droplets on lotus leaf. TEM analysis indicates that RhNPs of <10 nm diameter are dispersed on the surface of f-graphene. The air-stable NPs and nanocomposites were used as electrocatalyts for conversion of acidic water to hydrogen gas. The composite RhNPs@f-graphene catalyses hydrogen gas evolution from water containing p-toluene sulphonic acid (p-TsOH) at an onset reduction potential, E_p, −0.117 V which is less than that of PtNPs@f-graphene (E_p, −0.380 V) under identical experimental conditions whereas the onset potential of CoNPs@f-graphene was at E_p, −0.97 V and the FeNPs@f-graphene displayed onset potential at E_p, −1.58 V. The pure rhodium nanoparticles, RhNPs also electrocatalyse at E_p, −0.186 V compared with that of PtNPs at E_p, −0.36 V and that of CoNPs at E_p, −0.98 V. The electrocatalytic experiments also indicate that the RhNPs and RhNPs@f-graphene are stable, durable and they can be recycled in several catalytic experiments after washing with water and drying. The results indicate that RhNPs and RhNPs@f-graphene are better nanoelectrocatalysts than PtNPs and the reduction potentials were much higher in other transition metal nanoparticles. The mechanism could involve a hydridic species, Rh-H⁻ followed by interaction with protons to form hydrogen gas.

Asymmetry in the Ligand Coordination Sphere of the [FeFe] Hydrogenase Active Site Is Reflected in the Magnetic Spin Interactions of the Aza-propanedithiolate Ligand

[FeFe] hydrogenases are very active enzymes that catalyze the reversible conversion of molecular hydrogen into protons and electrons. Their active site, the H-cluster, contains a unique binuclear iron complex, [2Fe]_H, with CN^- and CO ligands as well as an aza-propane-dithiolate (ADT) moiety featuring a central amine functionality that mediates proton transfer during catalysis. We present a pulsed ¹³C-ENDOR investigation of the H-cluster in which the two methylene carbons of ADT are isotope labeled with ¹³C. We observed that the corresponding two ¹³C hyperfine interactions are of opposite sign and corroborated this finding using density functional theory calculations. The spin polarization in the ADT ligand is shown to be linked to the asymmetric coordination of the distal iron site with its terminal CN^- and CO ligands. We propose that this asymmetry is relevant for the enzyme reactivity and is related to the (optimal) stabilization of the iron-hydride intermediate in the catalytic cycle.

Examination of the Magneto-Structural Effects of Hangman Groups on Ferric Porphyrins by EPR

Ferric hangman porphyrins are bioinspired models for haem hydroperoxidase enzymes featuring an acid/base group in close vicinity to the metal center, which results in improved catalytic activity for reactions requiring O-O bond activation. These functional biomimics are examined herein with a combination of EPR techniques to determine the effects of the hanging group on the electronics of the ferric center. These results are compared to those for ferric octaethylporphyrin chloride [Fe(OEP)Cl], tetramesitylporphyrin chloride [Fe(TMP)Cl], and the pentafluorophenyl derivative [Fe(TPFPP)Cl], which were also examined herein to study the electronic effects of various substituents. Frequency-domain Fourier-transform THz-EPR combined with field domain EPR in a broad frequency range from 9.5 to 629 GHz allowed the determination of zero-field splitting parameters, revealing minor rhombicity E/D and D values in a narrow range of 6.24(8) to 6.85(5) cm^-1. Thus, the hangman porphyrins display D values in the expected range for ferric porphyrin chlorides, though D appears to be correlated with the Fe-Cl bond length. Extrapolating this trend to the ferric hangman porphyrin chlorides, for which no crystal structure has been reported, indicates a slightly elongated Fe-Cl bond length compared to the non-hangman equivalent.

Extending electron paramagnetic resonance to nanoliter volume protein single crystals using a self-resonant microhelix

Electron paramagnetic resonance (EPR) spectroscopy on protein single crystals is the ultimate method for determining the electronic structure of paramagnetic intermediates at the active site of an enzyme and relating the magnetic tensor to a molecular structure. However, crystals of dimensions typical for protein crystallography (0.05 to 0.3mm) provide insufficient signal intensity. In this work, we present a microwave self-resonant microhelix for nanoliter samples that can be implemented in a commercial X-band (9.5 GHz) EPR spectrometer. The self-resonant microhelix provides a measured signal-to-noise improvement up to a factor of 28 with respect to commercial EPR resonators. This work opens up the possibility to use advanced EPR techniques for studying protein single crystals of dimensions typical for x-ray crystallography. The technique is demonstrated by EPR experiments on single crystal [FeFe]-hydrogenase (Clostridium pasteurianum; CpI) with dimensions of 0.3 mm by 0.1 mm by 0.1 mm, yielding a proposed g-tensor orientation of the H_ox state.

Can carbene decorated [FeFe]-hydrogenase model complexes catalytically produce dihydrogen? An insight from theory

Cyclic alkyl amino carbene (CAAC) anchored [FeFe]-hydrogenase model complex featuring rotated conformation at one of the iron centers are found to be promising candidate for effective production of dihydrogen. A stepwise comparison of the complete mechanism using the CAAC stabilized model complex [1]⁰ has been performed with that of an experimentally isolated one ([2]⁰). Interestingly, the reduction events involved in the catalytic cycles are found to be more favorable than those previously reported for a similar experimentally known system. Furthermore, the computed ΔpK_a values indicate that the distal iron center with a vacant coordination site is more basic compared to the amino nitrogen atom of the azadithiolate bridge. We also made an attempt to determine the oxidation states of the iron centers for the intermediates involved in the catalytic cycles on the basis of the computed Mössbauer isomer shift and Mulliken spin density values.

Mössbauer Spectroscopy and Theoretical Studies of Iron Bimetallic Complexes Showing Electrocatalytic Hydrogen Evolution

Mössbauer spectroscopy and density functional theory (DFT) calculations are reported for the mononuclear Fe-nitrosyl complex [Fe( N, N'-bis(2-mercaptoethyl)-1,4-diazacycloheptane)NO] {[Fe(bme-dach)(NO)] (1)} and the series of dithiolate-bridged dinuclear complexes M-Fe(CO)Cp [M = Fe(bme-dach)(NO) (1-A), Ni(bme-dach) (2-A), and Co(bme-dach)(NO) (3-A)], in which M is a metallo-ligand to Fe(CO)Cp⁺ (Fe'_Cp). The latter is an organometallic fragment in which Fe is coordinated by one CO and one cyclopentadienyl ligand. Complexes 1-A and 2-A were previously shown to have electrocatalytic hydrogen evolution activity. Mononuclear {Fe-NO}⁷ complex 1, with overall spin of ¹/₂, has an isomer shift of 0.23(2) mm/s [Δ E_Q = 1.37(2) mm/s] and magnetic hyperfine couplings of {-38 T, -26.8 T, 8.6 T}. In complexes 2-A and 3-A, Fe'(CO)Cp⁺ has a diamagnetic ground state and δ = 0.33(2) mm/s (Δ E_Q ≈ 1.78 mm/s), consistent with a low-spin Fe^II site. In contrast, in complex 1-A, M = Fe(bme-dach)(NO) (i.e., complex 1) the magnetic hyperfine interactions of both metallo-ligand, M, and low-spin Fe'_Cp are perturbed and Fe'_Cp exhibits small magnetic hyperfine interactions, although its isomer shift and quadrupole splittings are largely unaltered. The DFT calculations for 1-A are in agreement with the paramagnetism observed for the Fe'(CO)Cp⁺ iron site.

Control of the overpotential of a [FeFe] hydrogenase mimic by a synthetic second coordination sphere

Hydrogen as a renewable fuel is viable when produced sustainably via proton reduction catalysis (PRC). Many homogeneous electrocatalysts perform PRC with high rates, but they all require a large overpotential to drive the reaction. Natural hydrogenase enzymes achieve reversible PRC with potentials close to the thermodynamic equilibrium through confinement of the active site in a well-defined protein pocket. Inspired by nature, we report a strategy that relies on the selective encapsulation of a synthetic hydrogenase mimic in a novel supramolecular cage. Catalyst confinement decreases the PRC overpotential by 150 mV, and is proposed to originate from the cationic cage stabilizing anionic reaction intermediates within the catalytic cycle.

FeMo Heterobimetallic Dithiolate Complexes: Investigation of Their Electron Transfer Chemistry and Reactivity toward Acids, a Density Functional Theory Rationalization

The electrochemical behavior of complexes [FeMo(CO)₅(κ²-dppe)(μ-pdt)] (1) and [FeMo(CO)₄(MeCN)(κ²-dppe)(μ-pdt)] (2), in the absence and in the presence of acid, has been investigated. The reduction of 1 follows at slow scan rates, in CH₂Cl₂-[NBu₄][PF₆] and acid-free media, an EC_revE mechanism that is supported by cyclic voltammetry (CV) experiments and digital CV simulations. In MeCN-[NBu₄][PF₆], the electrochemical reduction of 1 is the same as in dichloromethane and follows an ECE mechanism at slow scan rates, but with a positive shift of the redox potentials. In contrast, the oxidation of 1 is strongly solvent-dependent. In dichloromethane, the oxidation of 1 is reversible and involves a single electron, while in acetonitrile, it is irreversible at moderate and slow scan rates ( v ≤ ca. 1 V s^-1), and some chemical reversibility is apparent at higher scan rates ( v = 10 V s^-1). Density functional theory calculations revealed that the chemical step in the EC_revE mechanism corresponds to the dissociation of one PPh₂ end of the diphosphine ligand and the transfer of the semibridging CO to the Fe atom, similarly to the mechanism observed in the FeFe analogue complex. However, in the case of 1, the subsequent coordination of the phosphine ligand to the other metal is an unfavorable process.

Hydrogenases

Hydrogenases catalyze the simple yet important interconversion between H₂ and protons and electrons. Found throughout prokaryotes, lower eukaryotes, and archaea, hydrogenases are used for a variety of redox and signaling purposes and are found in many different forms. This diverse group of metalloenzymes is divided into [NiFe], [FeFe], and [Fe] variants, based on the transition metal contents of their active sites. A wide array of biochemical and spectroscopic methods has been used to elucidate hydrogenases, and this along with a general description of the main enzyme types and catalytic mechanisms is discussed in this chapter.

Pathways of selective catalytic CO2 two-step reduction on di-iron, di-cobalt and iron-cobalt disulfide carbonyls – an electronic structure study

The mixed iron–cobalt disulfide hexacarbonyl provides a selective route in the two step carbon dioxide reduction to formic acid.

Reactivation of the Ready and Unready Oxidized States of [NiFe]-Hydrogenases: Mechanistic Insights from DFT Calculations

The apparently simple dihydrogen formation from protons and electrons (2H⁺ + 2e^- ⇄ H₂) is one of the most challenging reactions in nature. It is catalyzed by metalloenzymes of amazing complexity, called hydrogenases. A better understanding of the chemistry of these enzymes, especially that of the [NiFe]-hydrogenases subgroup, has important implications for production of H₂ as alternative sustainable fuel. In this work, reactivation mechanism of the oxidized and inactive Ni-B and Ni-A states of the [NiFe]-hydrogenases active site has been investigated using density functional theory. Results obtained from this study show that one-electron reduction and protonation of the active site promote the removal of the bridging hydroxide ligand contained in Ni-B and Ni-A. However, this process is sufficient to activate only the Ni-B state. H₂ binding to the active site is required to convert Ni-A to the active Ni-SI_a state. Here, we also propose a reasonable structure for the spectroscopically well-characterized Ni-SI_r and Ni-SU species, formed respectively from the one-electron reduction of Ni-B and Ni-A. Ni-SI_r, depending on the pH at which the reaction occurs, features a bridging hydroxide ligand or a water molecule terminally coordinated to the Ni atom, whereas in Ni-SU a water molecule is terminally coordinated to the Fe atom, and the Cys64 residue is oxidized to sulfenate. The sulfenate oxygen atom in the Ni-A state affects the stereoelectronic properties of the binuclear cluster by modifying the coordination geometry of Ni, and consequently, by switching the regiochemistry of H₂O and H₂ binding from the Ni to the Fe atom. This effect is predicted to be at the origin of the different reactivation kinetics of the oxidized and inactive Ni-B and Ni-A states.

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H₂ as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s^-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.

Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2

Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

Infrared Characterization of the Bidirectional Oxygen-Sensitive [NiFe]-Hydrogenase from E. coli

[NiFe]-hydrogenases are gas-processing metalloenzymes that catalyze the conversion of dihydrogen (H2) to protons and electrons in a broad range of microorganisms. Within the framework of green chemistry, the molecular proceedings of biological hydrogen turnover inspired the design of novel catalytic compounds for H2 generation. The bidirectional “O2-sensitive” [NiFe]-hydrogenase from Escherichia coli HYD-2 has recently been crystallized; however, a systematic infrared characterization in the presence of natural reactants is not available yet. In this study, we analyze HYD-2 from E. coli by in situ attenuated total reflection Fourier-transform infrared spectroscopy (ATR FTIR) under quantitative gas control. We provide an experimental assignment of all catalytically relevant redox intermediates alongside the O2- and CO-inhibited cofactor species. Furthermore, the reactivity and mutual competition between H2, O2, and CO was probed in real time, which lays the foundation for a comparison with other enzymes, e.g., “O2-tolerant” [NiFe]-hydrogenases. Surprisingly, only Ni-B was observed in the presence of O2 with no indications for the “unready” Ni-A state. The presented work proves the capabilities of in situ ATR FTIR spectroscopy as an efficient and powerful technique for the analysis of biological macromolecules and enzymatic small molecule catalysis.

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.

Hydrogen bonding effect between active site and protein environment on catalysis performance in H2-producing [NiFe] hydrogenases

The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol^-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H⁺/e^- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction. The variety of hydrogen bonds (H-bonds) between the amino acids and the active site is hypothesised to be the main reason for such stability: H-bonds not only work as electrostatic attractive forces that influence the charge redistribution, but more importantly, they act as an electron 'pull' taking electrons from the active site towards the amino acids. Moreover, the electron 'pull' effect through H-bonds via the S^- in cysteine residues shows a larger influence on the energy profile than that via the CN^- ligands on Fe.