Hydrogen activation by [NiFe]-hydrogenases

Bioinspired and biomolecular catalysts for energy conversion and storage

Metalloenzymes are remarkable for facilitating challenging redox transformations with high efficiency and selectivity. In the area of alternative energy, scientists aim to capture these properties in bioinspired and engineered biomolecular catalysts for the efficient and fast production of fuels from low-energy feedstocks such as water and carbon dioxide. In this short review, efforts to mimic biological catalysts for proton reduction and carbon dioxide reduction are highlighted. Two important recurring themes are the importance of the microenvironment of the catalyst active site and the key role of proton delivery to the active site in achieving desired reactivity. Perspectives on ongoing and future challenges are also provided.

Recent developments in electrochemical investigations into iron carbonyl complexes relevant to the iron centres of hydrogenases

In this brief review mainly based on our own work, we summarised the electrochemical investigations into those iron carbonyl complexes relevant to the iron centres of [FeFe]-and [Fe]-hydrogenases in the following aspects: (i) electron transfer (E) coupled with a chemical reaction (C), EC process, (ii) two-electron process with potential inversion (EC_isoE), and (iii) proton-coupled electron transfer (PCET) and the role of an internal base group in the non-coordination sphere. Through individual examples, these processes involved in the electrochemistry of the iron carbonyl complexes are discussed. In probing the complexes involving a two-electron process with potential inversion, the co-existence of one- and two-electron for a complex is demonstrated by incorporating intramolecularly a ferrocenyl group(s) into the complex. Our studies on proton reduction catalysed by three diiron complexes involving the PCET mechanism are also summarised. Finally, perspectives of the electrochemical study in iron carbonyl complexes inspired by the iron-containing enzymes are mentioned in the sense of developing mimics of low overpotentials for hydrogen evolution through exploiting the PCET effect.

H2 activation by hydrogenase-inspired NiFe catalyst using frustrated Lewis pair: effect of buffer and halide ion in the heterolytic H-H bond cleavage

Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production. We investigate the reaction mechanism of H₂ activation in an aqueous solution by the recently developed NiFe complex (Ogo et al. Sci. Adv. 2020, 6, eaaz8181) using density functional theory (DFT) calculation. Our computational results showed that H₂ is activated using frustrated Lewis pair. That is, H₂ binds to the Fe site of the NiFe complex, acting as a Lewis acid, while the added buffer, acting as Lewis base, abstracts protons to form a hydride complex. Furthermore, the higher basicity in the proton abstraction reaction characterises reaction more exergonic and lowers the reaction barrier. In addition, in the proton abstraction by the water molecule, the reaction barrier was lowered when anion such as Cl⁻ is in the vicinity of the water. Understanding the chemical species that contribute to the catalytic process in cooperation with the metal catalyst at the atomic level should help to maximise the function of the catalyst.

Hydrogen is a clean fuel alternative to fossil fuels, and it is vital to develop catalysts for its efficient activation and production.

Biosynthetic Approaches towards the Design of Artificial Hydrogen-Evolution Catalysts

Hydrogen is a clean and sustainable form of fuel that can minimize our heavy dependence on fossil fuels as the primary energy source. The need of finding greener ways to generate H₂ gas has ignited interest in the research community to synthesize catalysts that can produce H₂ by the reduction of H⁺ . The natural H₂ producing enzymes hydrogenases have served as an inspiration to produce catalytic metal centers akin to these native enzymes. In this article we describe recent advances in the design of a unique class of artificial hydrogen evolving catalysts that combine the features of the active site metal(s) surrounded by a polypeptide component. The examples of these biosynthetic catalysts discussed here include i) assemblies of synthetic cofactors with native proteins; ii) peptide-appended synthetic complexes; iii) substitution of native cofactors with non-native cofactors; iv) metal substitution from rubredoxin; and v) a reengineered Cu storage protein into a Ni binding protein. Aspects of key design considerations in the construction of these artificial biocatalysts and insights gained into their chemical reactivity are discussed.

Therapeutic Efficacy of Molecular Hydrogen: A New Mechanistic Insight

Background:

Molecular hydrogen (H₂) is now recognized as a therapeutic gas for the treatment of numerous diseases including neurodegenerative diseases, metabolic disorders, and inflammatory diseases. Non-polar, neutral H₂ is assumed to have health benefits facilitated by its passive diffusion across the human body immediately after administration and is considered a safe therapeutic inert gas that does not interfere with physiological enzymatic reactions. The effects of H₂ on mammalian cells are assumed to be based on non-enzymatic reactions with Reactive Oxygen Species (ROS) exhibiting extremely high reactivity. However, many reports on therapeutic applications of H₂ have the limitation to regard H2 only as a scavenger for the hydroxyl radical and peroxynitrite.

Methods:

Apart from this proposed principle, a new possible mechanism of H₂ activation and consumption in mammalian cells is considered in this review, which is specifically focused on the mitochondrial complex I that has a close evolutionary relationship with energy-converting, membrane-bound [NiFe]-hydrogenases (MBH). Notably, the possibility that H2 may function as both electron and proton donor in the ubiquinone-binding chamber of complex I is discussed.

Results:

H₂ is proposed to act as the rectifier of the mitochondrial electron flow in the disordered or pathological state when the accumulation of electrons leads to ROS production, specifically during the re-supply of O₂ after hypoxia in the mitochondria.

Conclusion:

Furthermore, H₂ is proposed to convert the quinone intermediates to the fully reduced ubiquinol, thereby increasing the antioxidant capacity of the quinone pool as well as preventing the generation of ROS.

Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase

The Mo/Cu-dependent CO dehydrogenase from O. carboxydovorans is an enzyme that is able to catalyse CO oxidation to CO 2 ; moreover, it also expresses hydrogenase activity, as it is able to oxidize H 2 . Here, we have studied the dihydrogen oxidation catalysis by this enzyme using QM/MM calculations. Our results indicate that the equatorial oxo ligand of Mo is the best suited base for catalysis. Moreover, extraction of the first proton from H 2 by means of this basic centre leads to the formation of a Mo–OH–Cu I H hydride that allows for the stabilization of the copper hydride, otherwise known to be very unstable. In light of our results, two mechanisms for the hydrogenase activity of the enzyme are proposed. The first reactive channel depends on protonation of the sulphur atom of a Cu-bound cysteine residues, which appears to favour the binding and activation of the substrate. The second reactive channel involves a frustrated Lewis pair, formed by the equatorial oxo group bound to Mo and by the copper centre. In this case, no binding of the hydrogen molecule to the Cu center is observed but once H 2 enters into the active site, it can be split following a low-energy path.

Metalloproteins in the Biology of Heterocysts

Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.

Computational analyses, molecular dynamics, and mutagenesis studies of unprocessed form of [NiFe] hydrogenase reveal the role of disorder for efficient enzyme maturation

Biological production and oxidation of hydrogen is mediated by hydrogenases, key enzymes for these energy-relevant reactions. Synthesis of [NiFe] hydrogenases involves a complex series of biochemical reactions to assemble protein subunits and metallic cofactors required for enzyme function. A final step in this biosynthetic pathway is the processing of a C-terminal tail (CTT) from its large subunit, thus allowing proper insertion of nickel in the unique NiFe(CN)₂CO cofactor present in these enzymes. In silico modelling and Molecular Dynamics (MD) analyses of processed vs. unprocessed forms of Rhizobium leguminosarum bv. viciae (Rlv) hydrogenase large subunit HupL showed that its CTT (residues 582-596) is an intrinsically disordered region (IDR) that likely provides the required flexibility to the protein for the final steps of proteolytic maturation. Prediction of pKa values of ionizable side chains in both forms of the enzyme's large subunit also revealed that the presence of the CTT strongly modify the protonation state of some key residues around the active site. Furthermore, MD simulations and mutant analyses revealed that two glutamate residues (E27 in the N-terminal region and E589 inside the CTT) likely contribute to the process of nickel incorporation into the enzyme. Computational analysis also revealed structural details on the interaction of Rlv hydrogenase LSU with the endoprotease HupD responsible for the removal of CTT.

QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases

[NiFe]-hydrogenases are highly efficient catalysts for the heterolytic splitting of molecular hydrogen (H₂). The heterobimetallic cysteine-coordinated active site of these enzymes is covered by a highly conserved arginine residue, whose role in the reaction is not fully resolved yet. The structural and catalytic role of this arginine is investigated here using QM/MM calculations with various exchange-correlation functionals. All of them give a very consistent picture of the thermodynamics of H₂ oxidation. The concept of the presence of a neutral arginine and its direct involvement as a Frustrated Lewis Pair (FLP) in the reaction is critically evaluated. The arginine, however, would exist in its standard protonation state and perform a critical role in positioning and slightly polarizing the substrate H₂. It is not directly involved in the heterolytic processing of H₂ but guides its approach and reduces its flexibility during binding. Upon substitution of the positively charged arginine by a charge-conserving lysine residue, the H₂ binding position remains unaffected. However, critical hydrogen bonding interactions with nearby aspartate residues are lost. In addition, the H₂ polarization is unfavorable and the reduced side-chain volume may negatively affect the kinetics of the catalytic process.

Reaction Coordinate Leading to H2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory

[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (Hhyd) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that Hhyd is the catalytic state one step prior to H2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H2 bond formation by [FeFe]-hydrogenases.