The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center

Beyond S and Se: Electrocatalytic Hydrogen Production by Tellurolate-Bridged Co(III)-Mn(I) Heterodinuclear Complexes

In the pursuit of efficient electrocatalysts for the hydrogen evolution reaction (HER), a series of manganese and cobalt heterodinuclear complexes have been synthesized and characterized that have a stark resemblance with the [NiFe]-hydrogenase active site structure. Irradiation of [Mn2(CO)10] in the presence of 1.5 eq of [NaEPh] [E = S, Se, Te] followed by reaction with [Cp*CoCl]2 led to the formation of half-sandwiched trichalcogenate-bridged heterodinuclear complexes [{Mn(CO)3}(μ-EPh)3(CoCp*)] [E = S (C1); Se (C2) and Te (C3)]. The reaction of these heterodinuclear trichalcogenate-bridged complexes with [LiBH4·THF] yielded the corresponding dichalcogenate hydride-bridged heterobimetallic complexes [(CO)3Mn(μ-EPh)2(μ-H)(CoCp*)] [E = S (C5); Se (C6) and Te (C7)], which closely imitate the Ni-R intermediate of [NiFe]-hydrogenase. The resultant complexes (C5-C7) displayed impressive H2 production in DMF in the presence of HBF4, whereas the Te-based complex (C7) showcased the highest TON (184 h-1) with an impressive Faradaic efficiency of >98%. The DFT investigations revealed a unique role of bridging chalcogens in catalysis, wherein, depending on the identity of the chalcogen (S, Se, or Te), protonation could occur via two distinct routes. This study represents a rare example of the full trio of S/Se/Te-based heterodinuclear complexes whose electrocatalytic HER activity has been probed under analogous conditions.

Mononuclear Fe(III) Schiff base antipyrine complexes for catalytic hydrogen generation

Mononuclear Fe(III) complexes containing an antipyrine Schiff base ligand were prepared and fully characterized, demonstrating a planar tetradentate coordination geometry. These complexes were found to be active for the hydrogen evolution reaction. Catalysis occurs at -1.4 V vs. Fc+/Fc, with an overpotential of 700 mV. The complexes are active electrocatalysts with a turnover frequency of 700 s-1. Furthermore, when paired with a chromophore and sacrificial donor, the complexes are active photocatalysts demonstrating >1700 turnovers during 40 hours of irradiation with a quantum yield of up to 5.4%. The catalysts have also been found to operate in natural water samples of varying salinity.

Promising approaches for the assembly of the catalytically active, recombinant Desulfomicrobium baculatum hydrogenase with substitutions at the active site

BACKGROUND

Hydrogenases (H2ases) are metalloenzymes capable of the reversible conversion of protons and electrons to molecular hydrogen. Exploiting the unique enzymatic activity of H2ases can lead to advancements in the process of biohydrogen evolution and green energy production.

RESULTS

Here we created of a functional, optimized operon for rapid and robust production of recombinant [NiFe] Desulfomicrobium baculatum hydrogenase (Dmb H2ase). The conversion of the [NiFeSe] Dmb H2ase to [NiFe] type was performed on genetic level by site-directed mutagenesis. The native dmb operon includes two structural H2ase genes, coding for large and small subunits, and an additional gene, encoding a specific maturase (protease) that is essential for the proper maturation of the enzyme. Dmb, like all H2ases, needs intricate bio-production machinery to incorporate its crucial inorganic ligands and cofactors. Strictly anaerobic, sulfate reducer D. baculatum bacteria are distinct, in terms of their biology, from E. coli. Thus, we introduced a series of alterations within the native dmb genes. As a result, more than 100 elements, further compiled into 32 operon variants, were constructed. The initial requirement for a specific maturase was omitted by the artificial truncation of the large Dmb subunit. The assembly of the produced H2ase subunit variants was investigated both, in vitro and in vivo. This approach resulted in 4 recombinant [NiFe] Dmb enzyme variants, capable of H2 evolution. The aim of this study was to overcome the gene expression, protein biosynthesis, maturation and ligand loading bottlenecks for the easy, fast, and cost-effective delivery of recombinant [NiFe] H2ase, using a commonly available E. coli strains.

CONCLUSION

The optimized genetic constructs together with the developed growth and purification procedures appear to be a promising platform for further studies toward fully-active and O2 tolerant, recombinant [NiFeSe] Dmb H2ase, resembling the native Dmb enzyme. It could likely be achieved by selective cysteine to selenocysteine substitution within the active site of the [NiFe] Dmb variant.

Enzymatic and Bioinspired Systems for Hydrogen Production

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.

Heterometallic bond activation enabled by unsymmetrical ligand scaffolds: bridging the opposites

Heterobi- and multimetallic complexes providing close proximity between several metal centers serve as active species in artificial and enzymatic catalysis, and in model systems, showing unique modes of metal-metal cooperative bond activation. Through the rational design of well-defined, unsymmetrical ligand scaffolds, we create a convenient approach to support the assembly of heterometallic species in a well-defined and site-specific manner, preventing them from scrambling and dissociation. In this perspective, we will outline general strategies for the design of unsymmetrical ligands to support heterobi- and multimetallic complexes that show reactivity in various types of heterometallic cooperative bond activation.

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.

Catalytic Mechanism of Competing Proton Transfer Events from Water and Acetic Acid by [CoII(bpbH2)Cl2] for Water Splitting Processes

We performed first principles simulations to explore the water reduction process of the cobalt complex [Co^II(bpbH₂)Cl₂], where bpbH₂ = N,N'-bis(2'-pyridine carboxamide)-1,2-benzene. We considered the sequence steps of electron reduction followed by the proton addition process to observe the hydrogen evolution process. An experimental study of the catalyst showed that the increase in the acetic acid concentration triggers catalytic current and reduction of Co(II) to Co(I), and protonation occurred, yielding a Co(III)-H intermediate. Therefore, we used water and acetic acid as the proton sources. We compare the proton transfer kinetics from both the water and acetic acid. The reduction potentials and proton transfer kinetics from water or acetic acid to the reaction center were studied in a DMF solvent through the implicit solvent model. The first proton transfer from the acetic acid is more favorable, forming a Co^III-H complex and further reducing to Co^II-H. The second proton transfer from water to the Co^II-H moiety requires less free energy than acetic acid and is the rate-limiting step. The nature of the reduction process is also examined through the charge analysis, which reveals that the ligand becomes softer due to the C═O groups.

An open-source framework for fast-yet-accurate calculation of quantum mechanical features

We present the open-source framework kallisto that enables the efficient and robust calculation of quantum mechanical features for atoms and molecules. For a benchmark set of 49 experimental molecular polarizabilities,...

Harnessing selenocysteine to enhance microbial cell factories for hydrogen production

Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.

Common modifications of selenocysteine in selenoproteins

Selenocysteine (Sec), the sulfur-to-selenium substituted variant of cysteine (Cys), is the defining entity of selenoproteins. These are naturally expressed in many diverse organisms and constitute a unique class of proteins. As a result of the physicochemical characteristics of selenium when compared with sulfur, Sec is typically more reactive than Cys while participating in similar reactions, and there are also some qualitative differences in the reactivities between the two amino acids. This minireview discusses the types of modifications of Sec in selenoproteins that have thus far been experimentally validated. These modifications include direct covalent binding through the Se atom of Sec to other chalcogen atoms (S, O and Se) as present in redox active molecular motifs, derivatization of Sec via the direct covalent binding to non-chalcogen elements (Ni, Mb, N, Au and C), and the loss of Se from Sec resulting in formation of dehydroalanine. To understand the nature of these Sec modifications is crucial for an understanding of selenoprotein reactivities in biological, physiological and pathophysiological contexts.

The roles of chalcogenides in O2 protection of H2ase active sites

At some point, all HER (Hydrogen Evolution Reaction) catalysts, important in sustainable H2O splitting technology, will encounter O2 and O2-damage. The [NiFeSe]-H2ases and some of the [NiFeS]-H2ases, biocatalysts for reversible H2 production from protons and electrons, are exemplars of oxygen tolerant HER catalysts in nature. In the hydrogenase active sites oxygen damage may be extensive (irreversible) as it is for the [FeFe]-H2ase or moderate (reversible) for the [NiFe]-H2ases. The affinity of oxygen for sulfur, in [NiFeS]-H2ase, and selenium, in [NiFeSe]-H2ase, yielding oxygenated chalcogens results in maintenance of the core NiFe unit, and myriad observable but inactive states, which can be reductively repaired. In contrast, the [FeFe]-H2ase active site has less possibilities for chalcogen-oxygen uptake and a greater chance for O2-attack on iron. Exposure to O2 typically leads to irreversible damage. Despite the evidence of S/Se-oxygenation in the active sites of hydrogenases, there are limited reported synthetic models. This perspective will give an overview of the studies of O2 reactions with the hydrogenases and biomimetics with focus on our recent studies that compare sulfur and selenium containing synthetic analogues of the [NiFe]-H2ase active sites.

Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases

Hydrogenases are efficient biocatalysts for H₂ production and oxidation with various potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both production and oxidation processes—albeit primarily biased to the latter—but suffer from being sensitive to O₂.[NiFeSe] hydrogenases are a subclass of [NiFe] hydrogenases with, usually, an increased insensitivity to aerobic environments. In this study we aim to understand the structural causes of the low sensitivity of a [NiFeSe]-hydrogenase, when compared with a [NiFe] class enzyme, by studying the diffusion of O₂. To unravel the differences between the two enzymes, we used computational methods comprising Molecular Dynamics simulations with explicit O₂ and Implicit Ligand Sampling methodologies. With the latter, we were able to map the free energy landscapes for O₂ permeation in both enzymes. We derived pathways from these energy landscapes and selected the kinetically more relevant ones with reactive flux analysis using transition path theory. These studies evidence the existence of quite different pathways in both enzymes and predict a lower permeation efficiency for O₂ in the case of the [NiFeSe]-hydrogenase when compared with the [NiFe] enzyme. These differences can explain the experimentally observed lower inhibition by O₂ on [NiFeSe]-hydrogenases, when compared with [NiFe]-hydrogenases. A comprehensive map of the residues lining the most important O₂ pathways in both enzymes is also presented.

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.

Structure, function, and biosynthesis of nickel-dependent enzymes

Nickel enzymes, present in archaea, bacteria, plants, and primitive eukaryotes are divided into redox and nonredox enzymes and play key functions in diverse metabolic processes, such as energy metabolism and virulence. They catalyze various reactions by using active sites of diverse complexities, such as mononuclear nickel in Ni-superoxide dismutase, glyoxylase I and acireductone dioxygenase, dinuclear nickel in urease, heteronuclear metalloclusters in [NiFe]-carbon monoxide dehydrogenase, acetyl-CoA decarbonylase/synthase and [NiFe]-hydrogenase, and even more complex cofactors in methyl-CoM reductase and lactate racemase. The presence of metalloenzymes in a cell necessitates a tight regulation of metal homeostasis, in order to maintain the appropriate intracellular concentration of nickel while avoiding its toxicity. As well, the biosynthesis and insertion of nickel active sites often require specific and elaborated maturation pathways, allowing the correct metal to be delivered and incorporated into the target enzyme. In this review, the phylogenetic distribution of nickel enzymes will be briefly described. Their tridimensional structures as well as the complexity of their active sites will be discussed. In view of the latest findings on these enzymes, a special focus will be put on the biosynthesis of their active sites and nickel activation of apo-enzymes.

Influence of selenium yeast on the growth, selenium uptake and mineral composition of Coriolus versicolor mushroom

The ability of Coriolus versicolor medicinal mushroom to grow and accumulate selenium during submerged cultivation in a selenium-fortified medium is examined in this paper. For selenium supplementation, commercial selenium yeast was used. Control, nonenriched sample and reference cultures cultivated in the medium enriched with commercial yeast Saccharomyces cerevisiae were also prepared. The mushroom demonstrated a high ability to accumulate selenium from the added source (around 970 and 1,300 µg/g of dry mycelium weight for samples enriched with selenium in a concentration of 10 and 20 mg Se/L, respectively). The addition of selenium significantly (p ≤ .05) increased the biomass yield, whereas the addition of nonenriched yeast had no significant (p ≤ .05) impact. Furthermore, regression analysis showed statistically significant (p ≤ .05) and positive correlations between the content of Se and Fe (r = .92), Se and Cu (r = .92), Se and Mn (r = .98), and Se and Sr (r = .96), suggesting that selenium incorporation was followed by incorporation of these elements, and led to mineral enrichment of the obtained mycelium. Methanol extracts prepared from mycelium biomass demonstrated a better inhibitory effect on Gram-positive bacterial strains with minimal inhibitory concentrations between <0.3125 and 40 mg/ml. The obtained results showed that selenium yeast could be used for obtaining a potential novel food supplement: mushroom biomass with high selenium content and enhanced mineral composition.

Coupling natural systems with synthetic chemistry for light-driven enzymatic biocatalysis

Visible light-driven redox reactions have been widely adopted for the production of chemicals to combat energy shortage and global warming. Key elements of such a reaction system include a photosensitizer, a catalyst, and an electron source. In this review, we introduce the small molecules and nanoparticles that are widely used as photosensitizers, as well as the development of a photosensitizer protein that is based on the expansion of genetic code, with a fluorescent protein that is used as a scaffold. Visible light-driven enzymes using proteins as photosensitizers or as catalysts such as carbon monoxide dehydrogenase (CODH), formic acid dehydrogenase (FDH), hydrogenase, nitrogenase, cytochrome P450 BM3, and alkane synthase are then described. CODH can be coupled with photosensitizing nanoparticles to reduce CO₂ to CO, and hydrogenase can produce H₂ using high-energy electrons produced from dye-sensitized nanoparticles. When water-soluble zinc porphyrin is coupled with FDH, visible light drives CO₂ to produce formic acid. Nitrogenase can reduce N₂ to NH₃ using CdS nanoparticle as photosensitizer. Cytochrome P450 BM3 can be enhanced by a visible light-driven redox system and thus by hydroxylate lauric acid or fatty acids. CvFAP, an alkane synthase, can decarboxylate palmitic acid to pentadecane under blue light excitation. Moreover, we describe a genetically encoded photosensitive protein, which mimics the function of natural photosynthesis and catalyzes the conversion of CO₂ to CO when covalently attached with a Ni-terpyridine complex.

Catalytic H2 evolution/oxidation in [FeFe]-hydrogenase biomimetics: account from DFT on the interplay of related issues and proposed solutions

A DFT overview on selected issues regarding diiron catalysts related to [FeFe]-hydrogenase biomimetic research, with implications for both energy conversion and storage strategies.

Electrocatalytic proton-reduction behaviour of telluride-capped triiron clusters: tuning of overpotentials and stabilization of redox states relative to lighter chalcogenide analogues

Electrocatalytic proton reduction catalyzed by [Fe₃(CO)₉(μ₃-Te)₂], and a number of its phosphine and diphosphine derivatives, has been studied.

X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases

[NiFe] hydrogenases are complex model enzymes for the reversible cleavage of dihydrogen (H₂). However, structural determinants of efficient H₂ binding to their [NiFe] active site are not properly understood. Here, we present crystallographic and vibrational‐spectroscopic insights into the unexplored structure of the H₂‐binding [NiFe] intermediate. Using an F₄₂₀‐reducing [NiFe]‐hydrogenase from Methanosarcina barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold that tunes the [NiFe] active site for efficient H₂ binding and conversion. The protein matrix also directs H₂ diffusion to the [NiFe] site via two gas channels and allows the distribution of electrons between functional protomers through a subunit‐bridging FeS cluster. Our findings emphasize the relevance of an atypical Ni coordination, thereby providing a blueprint for the design of bio‐inspired H₂‐conversion catalysts.

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.

Crystal structure of NiFe(CO)5[tris(pyridyl-meth-yl)aza-phosphatrane]: a synthetic mimic of the NiFe hydrogenase active site incorporating a pendant pyridine base

The reaction of Ni(TPAP)(COD) {where TPAP = [(NC5H4)CH2]3P(NC2H4)3N} with Fe(CO)5 resulted in the isolation of the title heterobimetallic NiFe(TPAP)(CO)5 complex di-μ-carbonyl-tricarbon-yl[2,8,9-tris-(pyridin-2-yl-meth-yl)-2,5,8,9-tetra-aza-1-phosphabi-cyclo-[3.3.3]undeca-ne]ironnickel, [FeNi(C24H30N7P)(CO)5]. Characterization of the complex by 1H and 31P NMR as well as IR spectroscopy are presented. The structure of NiFe(TPAP)(CO)5 reveals three terminally bound CO mol-ecules on Fe0, two bridging CO mol-ecules between Ni0 and Fe0, and TPAP coordinated to Ni0. The Ni-Fe bond length is 2.4828 (4) Å, similar to that of the reduced form of the active site of NiFe hydrogenase (∼2.5 Å). Additionally, a proximal pendant base from one of the non-coordinating pyridine groups of TPAP is also present. Although involvement of a pendant base has been cited in the mechanism of NiFe hydrogenase, this moiety has yet to be incorporated in a structurally characterized synthetic mimic with key structural motifs (terminally bound CO or CN ligands on Fe). Thus, the title complex NiFe(TPAP)(CO)5 is an unique synthetic model for NiFe hydrogenase. In the crystal, the complex mol-ecules are linked by C-H⋯O hydrogen bonds, forming undulating layers parallel to (100). Within the layers, there are offset π-π [inter-centroid distance = 3.2739 (5) Å] and C-H⋯π inter-actions present. The layers are linked by further C-H⋯π inter-actions, forming a supra-molecular framework.

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.

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.

Characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough

The [NiFeSe] hydrogenases are a subgroup of the well-characterized family of [NiFe] hydrogenases, in which a selenocysteine is a ligand to the nickel atom in the binuclear NiFe active site instead of cysteine. These enzymes display very interesting catalytic properties for biological hydrogen production and bioelectrochemical applications: high H₂ production activity, bias for H₂ evolution, low H₂ inhibition, and some degree of O₂ tolerance. Here we describe the methodologies employed to study the [NiFeSe] hydrogenase isolated from the sulfate-reducing bacteria D. vulgaris Hildenborough and the creation of a homologous expression system for production of variant forms of the enzyme.

Oxygen uptake in complexes related to [NiFeS]- and [NiFeSe]-hydrogenase active sites

The NiFe hydrogenase biomimetics are protected from oxygen invaders by sulfur and selenium castle guards.

A biomimetic study for S/Se oxygenation in Ni(μ-EPh)(μ-SN₂)Fe, (E = S or Se; SN₂ = Me-diazacycloheptane-CH₂CH₂S); Fe = (η⁵-C₅H₅)Fe^II(CO) complexes related to the oxygen-damaged active sites of [NiFeS]/[NiFeSe]-H₂ases is described. Mono- and di-oxygenates (major and minor species, respectively) of the chalcogens result from exposure of the heterobimetallics to O₂; one was isolated and structurally characterized to have Ni–O–Se_Ph–Fe–S connectivity within a 5-membered ring. A compositionally analogous mono-oxy species was implicated by ν(CO) IR spectroscopy to be the corresponding Ni–O–S_Ph–Fe–S complex; treatment with O-abstraction agents such as P(o-tolyl)₃ or PMe₃ remediated the O damage. Computational studies (DFT) found that the lowest energy isomers of mono-oxygen derivatives of Ni(μ-EPh)(μ-SN₂)Fe complexes were those with O attachment to Ni rather than Fe, a result consonant with experimental findings, but at odds with oxygenates found in oxygen-damaged [NiFeS]/[NiFeSe]-H₂ase structures. A computer-generated model based on substituting ^–SMe for the N-CH₂CH₂S^– sulfur donor of the N₂S suggested that constraint within the chelate hindered O-atom uptake at that sulfur site.

Selenium at the redox interface of the genome, metabolome and exposome

Selenium (Se) is a redox-active environmental mineral that is converted to only a small number of metabolites and required for a relatively small number of mammalian enzymes. Despite this, dietary and environmental Se has extensive impact on every layer of omics space. This highlights a need for global network response structures to provide reference for targeted, hypothesis-driven Se research. In this review, we survey the Se research literature from the perspective of the responsive physical and chemical barrier between an organism (functional genome) and its environment (exposome), which we have previously termed the redox interface. Recent advances in metabolomics allow molecular phenotyping of the integrated genome-metabolome-exposome structure. Use of metabolomics with transcriptomics to map functional network responses to supplemental Se in mice revealed complex network responses linked to dyslipidemia and weight gain. Central metabolic hubs in the network structure in liver were not directly linked to transcripts for selenoproteins but were, instead, linked to transcripts for glucose transport and fatty acid β-oxidation. The experimental results confirm the survey of research literature in showing that Se interacts with the functional genome through a complex network response structure. The results imply that systematic application of data-driven integrated omics methods to models with controlled Se exposure could disentangle health benefits and risks from Se exposures and also serve more broadly as an experimental paradigm for exposome research.

Selenium versus sulfur: Reversibility of chemical reactions and resistance to permanent oxidation in proteins and nucleic acids

This review highlights the contributions of Jean Chaudière to the field of selenium biochemistry. Chaudière was the first to recognize that one of the main reasons that selenium in the form of selenocysteine is used in proteins is due to the fact that it strongly resists permanent oxidation. The foundations for this important concept was laid down by Al Tappel in the 1960's and even before by others. The concept of oxygen tolerance first recognized in the study of glutathione peroxidase was further advanced and refined by those studying [NiFeSe]-hydrogenases, selenosubtilisin, and thioredoxin reductase. After 200 years of selenium research, work by Marcus Conrad and coworkers studying glutathione peroxidase-4 has provided definitive evidence for Chaudière's original hypothesis (Ingold et al., 2018) [36]. While the reaction of selenium with oxygen is readily reversible, there are many other examples of this phenomenon of reversibility. Many reactions of selenium can be described as "easy in - easy out". This is due to the strong nucleophilic character of selenium to attack electrophiles, but then this reaction can be reversed due to the strong electrophilic character of selenium and the weakness of the selenium-carbon bond. Several examples of this are described.

An extracellular [NiFe] hydrogenase mediating iron corrosion is encoded in a genetically unstable genomic island in Methanococcus maripaludis

Certain methanogens deteriorate steel surfaces through a process called microbiologically influenced corrosion (MIC). However, the mechanisms of MIC, whereby methanogens oxidize zerovalent iron (Fe⁰), are largely unknown. In this study, Fe⁰-corroding Methanococcus maripaludis strain OS7 and its derivative (strain OS7mut1) defective in Fe⁰-corroding activity were isolated. Genomic analysis of these strains demonstrated that the strain OS7mut1 contained a 12-kb chromosomal deletion. The deleted region, termed "MIC island", encoded the genes for the large and small subunits of a [NiFe] hydrogenase, the TatA/TatC genes necessary for the secretion of the [NiFe] hydrogenase, and a gene for the hydrogenase maturation protease. Thus, the [NiFe] hydrogenase may be secreted outside the cytoplasmic membrane, where the [NiFe] hydrogenase can make direct contact with Fe⁰, and oxidize it, generating hydrogen gas: Fe⁰ + 2 H⁺ → Fe²⁺ + H₂. Comparative analysis of extracellular and intracellular proteomes of strain OS7 supported this hypothesis. The identification of the MIC genes enables the development of molecular tools to monitor epidemiology, and to perform surveillance and risk assessment of MIC-inducing M. maripaludis.

From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production

Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.

The oxygen reduction reaction on [NiFe] hydrogenases

Oxygen tolerance capacity is critical for hydrogen oxidation/evolution catalysts.

Site preferences in hetero-metallic [Fe9-xNix] clusters: a combined crystallographic, spectroscopic and theoretical analysis

The reaction of mixtures of Fe(O₂CMe)₂·2H₂O and Ni(O₂CMe)₂·4H₂O of various compositions with di-2-pyridyl ketone (py₂CO, dpk) in MeCN under an inert atmosphere afforded a family of hetero-metallic enneanuclear clusters with general formula [Fe_9-xNi_x(μ₄-OH)₂(O₂CMe)₈(py₂CO₂)₄] (2, x = 1.00; 3: x = 6.02; 4, x = 7.46; 5, x = 7.81). Clusters 2-5 are isomorphous to the homo-metallic [Fe₉] cluster (1) previously reported by some of us, and also isostructural to the known homo-metallic [Ni₉] cluster. All four clusters contain a central M^II ion in an unusual 8-coordinate site and eight peripheral M^II ions in distorted octahedral environments. The distribution of Fe^II and Ni^II ions over these two distinct coordination sites in 2-5 can be established through a combination of X-ray fluorescence and Mössbauer spectroscopies, which show that Fe^II preferentially occupies the unique 8-coordinate metal site while Ni^II accumulates in the octahedral holes. Density functional theory indicates that the distribution of ions across the two sites arises not from any intrinsic preference of the Fe^II ions for the 8-coordinate sites, but rather because of the large ligand field stabilization energy available to Ni^II in octahedral coordination.

Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.

Photoelectrocatalytic H2 evolution in water with molecular catalysts immobilised on p-Si via a stabilising mesoporous TiO2 interlayer

A versatile platform for the immobilisation of molecular catalysts on a readily-prepared Si photocathode with a mesoporous TiO₂ layer is reported.

The development of photoelectrodes capable of light-driven hydrogen evolution from water is an important approach for the storage of solar energy in the form of a chemical energy carrier. However, molecular catalyst-based photocathodes remain scarcely reported and typically suffer from low efficiencies and/or stabilities due to inadequate strategies for interfacing the molecular component with the light-harvesting material. In this study, we report the straightforward preparation of a p-silicon|mesoporous titania|molecular catalyst photocathode assembly that is active towards proton reduction in aqueous media with an onset potential of +0.4 V vs. RHE. The mesoporous TiO₂ scaffold acts as an electron shuttle between the silicon and the catalyst, while also stabilising the silicon from passivation and enabling a high loading of molecular catalysts (>30 nmol (geometrical cm)^–2). When a Ni bis(diphosphine)-based catalyst is anchored on the surface of the electrode, a high turnover number of ∼1 × 10³ was obtained from photoelectrolysis under UV-filtered simulated solar irradiation at 1 Sun after 24 h at pH 4.5. Notwithstanding its aptitude for molecular catalyst immobilisation, the p-Si|TiO₂ photoelectrode showed great versatility towards different catalysts and pH conditions, with photoelectrocatalytic H₂ generation also being achieved with platinum and a hydrogenase as catalyst, highlighting the flexible platform it represents for many potential reductive catalysis transformations.