A third type of hydrogenase catalyzing H2 activation

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.

Functionalized nickel(II)-iron(II) dithiolates as biomimetic models of [NiFe]-H2ases

To develop the structural and functional modeling chemistry of [NiFe]-H₂ases, a series of new biomimetics for the active site of [NiFe]-H₂ases have been prepared by various synthetic methods. Treatment of the mononuclear Ni complex (pnp)NiCl₂ (pnp = (Ph₂PCH₂)₂NPh) with (dppv)Fe(CO)₂(pdt) (dppv = 1,2-(Ph₂P)₂C₂H₂, pdt = 1,3-propanedithiolate) and KPF₆ gave the dicarbonyl complex [(pnp)Ni(pdt)Fe(CO)₂(dppv)](PF₆)₂ ([1](PF₆)₂). Further treatment of [1](PF₆)₂ and [(dppe)Ni(pdt)Fe(CO)₂(dppv)](BF₄)₂ (dppe = 1,2-(Ph₂P)₂C₂H₄) with the decarbonylation agent Me₃NO and pyridine afforded the novel sp³ C-Fe bond-containing complexes [(pnp)Ni(SCH₂CH₂CHS)Fe(CO)(dppv)]PF₆ ([2]PF₆) and [(dppe)Ni(SCH₂CH₂CHS)Fe(CO)(dppv)]BF₄ ([3]BF₄). More interestingly, the first t-carboxylato complexes [(pnp)Ni(pdt)Fe(CO)(t-O₂CR)(dppv)]PF₆ ([4]PF₆, R = H; [5]PF₆, R = Me; [6]PF₆, R = Ph) could be prepared by reactions of [1]PF₆ with the corresponding carboxylic acids RCO₂H in the presence of Me₃NO, whereas further reactions of [4]PF₆-[6]PF₆ with aqueous HPF₆ and 1.5 MPa H₂ gave rise to the μ-hydride complex [(pnp)Ni(pdt)Fe(CO)(μ-H)(dppv)]PF₆ ([7]PF₆). Except for H₂ activation by t-carboxylato complexes [4]PF₆-[6]PF₆ to give a μ-hydride complex ([7]PF₆), the sp³ C-Fe bond-containing complex [2]PF₆ was found to be a catalyst for proton reduction to H₂ under CV conditions. Furthermore, the chemical reactivity of the μ-hydride complex [7]PF₆ displayed in the e^- transfer reaction with FcPF₆ in the presence of CO, the H₂ evolution reaction with the protonic acid HCl, and the H^- transfer reaction with N-methylacridinium hexafluorophosphate ([NMA]PF₆) was systematically studied. As a result, a series of the expected products such as H₂, ferrocene, the dicarbonyl complex [1](PF₆)₂, the μ-chloro complex [(pnp)Ni(pdt)Fe(CO)(μ-Cl)(dppv)]PF₆ ([8]PF₆), the t-MeCN-coordinated complex [(pnp)Ni(pdt)Fe(CO)(t-MeCN)(dppv)](PF₆)₂ ([9](PF₆)₂) and the H^- transfer product AcrH₂ were produced. While all the newly prepared model complexes were structurally characterized by spectroscopic methods, the molecular structures of some of their representatives were confirmed by X-ray crystallography.

Interspecies Formate Exchange Drives Syntrophic Growth of Syntrophotalea carbinolica and Methanococcus maripaludis

The complete remineralization of organic matter in anoxic environments relies on communities of microorganisms that ferment organic acids and alcohols to CH₄. This is accomplished through syntrophic association of H₂ or formate producing bacteria and methanogenic archaea, where exchange of these intermediates enables growth of both organisms. While these communities are essential to Earth's carbon cycle, our understanding of the dynamics of H₂ or formate exchanged is limited. Here, we establish a model partnership between Syntrophotalea carbinolica and Methanococcus maripaludis. Through sequencing a transposon mutant library of M. maripaludis grown with ethanol oxidizing S. carbinolica, we found that genes encoding the F₄₂₀-dependent formate dehydrogenase (Fdh) and F₄₂₀-dependent methylene-tetrahydromethanopterin dehydrogenase (Mtd) are important for growth. Competitive growth of M. maripaludis mutants defective in either H₂ or formate metabolism verified that, across multiple substrates, interspecies formate exchange was dominant in these communities. Agitation of these cultures to facilitate diffusive loss of H₂ to the culture headspace resulted in an even greater competitive advantage for M. maripaludis strains capable of oxidizing formate. Finally, we verified that an M. maripaludis Δmtd mutant had a defect during syntrophic growth. Together, these results highlight the importance of formate exchange for the growth of methanogens under syntrophic conditions. IMPORTANCE In the environment, methane is typically generated by fermentative bacteria and methanogenic archaea working together in a process called syntrophy. Efficient exchange of small molecules like H₂ or formate is essential for growth of both organisms. However, difficulties in determining the relative contribution of these intermediates to methanogenesis often hamper efforts to understand syntrophic interactions. Here, we establish a model syntrophic coculture composed of S. carbinolica and the genetically tractable methanogen M. maripaludis. Using mutant strains of M. maripaludis that are defective for either H₂ or formate metabolism, we determined that interspecies formate exchange drives syntrophic growth of these organisms. Together, these results advance our understanding of the degradation of organic matter in anoxic environments.

Unravelling the Potential of Ylides in Stabilizing Low-Valent Group 13 Compounds: Theoretical Predictions of Stable, Five-Membered Group 13 (Aluminum and Gallium) Carbenoids Capable of Small-Molecule Activation

Computational investigations provide evidence toward the remarkable ability of strongly electron-donating ylidic functionalities in stabilizing singlet group 13 carbenoids with promising ligand properties. All of the proposed carbenoids are found to be considerably nucleophilic and possess significant singlet-triplet energy separation values. The calculated activation barriers and reaction free energies obtained for the cleavage of different enthalpically strong bonds by these carbenoids are found to be either comparable to or lower than those of the experimentally evaluated aluminum and gallium carbenoids, thereby indicating their potential in small-molecule activation.

Tungsten Enzyme Using Hydrogen as an Electron Donor to Reduce Carboxylic Acids and NAD. ACS Catal 2022;12:8707-8717. [PMID: 35874620 PMCID: PMC9295118 DOI: 10.1021/acscatal.2c02147]

Tungsten-dependent aldehyde oxidoreductases (AORs) catalyze the oxidation of aldehydes to acids and are the only known enzymes reducing non-activated acids using electron donors with low redox potentials. We report here that AOR from Aromatoleum aromaticum (AOR_Aa) catalyzes the reduction of organic acids not only with low-potential Eu(II) or Ti(III) complexes but also with H₂ as an electron donor. Additionally, AOR_Aa catalyzes the H₂-dependent reduction of NAD⁺ or benzyl viologen. The rate of H₂-dependent NAD⁺ reduction equals to 10% of that of aldehyde oxidation, representing the highest H₂ turnover rate observed among the Mo/W enzymes. As AOR_Aa simultaneously catalyzes the reduction of acids and NAD⁺, we designed a cascade reaction utilizing a NAD(P)H-dependent alcohol dehydrogenase to reduce organic acids to the corresponding alcohols with H₂ as the only reductant. The newly discovered W-hydrogenase side activity of AOR_Aa may find applications in either NADH recycling or conversion of carboxylic acids to more useful biochemicals.

Synthesis, Structures and Chemical Reactivity of Dithiolato-Bridged Ni-Fe Complexes as Biomimetics for the Active Site of [NiFe]-Hydrogenases

To develop the structural and functional modeling chemistry of [NiFe]-H2ases, we have carried out a study regarding the synthesis, structural characterization and reactivity of a new series of [NiFe]-H2ase model complexes. Thus, treatment of diphosphine dppb-chelated Ni complex (dppb)NiCl2 (dppb = 1,2-(Ph2P)2C6H4) with (dppv)Fe(CO)2(pdt) (dppv = 1,2-(Ph2P)2C2H2, pdt = 1,3-propanedithiolate) and NaBF4 gave dicarbonyl complex [(dppb)Ni(pdt)Fe(CO)2(dppv)](BF4)2 ([A](BF4)2). Further treatment of [A](BF4)2 with Me3NO and Bu4NCN or KSCN afforded t-cyanido and t-isothiocyanato complexes [(dppb)Ni(pdt)Fe(CO)(t-R)(dppv)]BF4 ([1]BF4, R = CN; [2]BF4, R = NCS), respectively. While azadiphosphine MeN(CH2PPh2)2-chelated t-hydride complex [MeN(CH2PPh2)2Ni(pdt)Fe(CO)(t-H)(dppv)]BF4 ([3]BF4) was prepared by treatment of dicarbonyl complex [MeN(CH2PPh2)2Ni(pdt)Fe(CO)2(dppv)](BF4)2 ([B](BF4)2) with Me3NO and 1.5 MPa of H2, treatment of dicarbonyl complex [B](BF4)2 with Me3NO (without H2) in pyridine resulted in formation of a novel monocarbonyl complex [MeN(CH2PPh2)2Ni(SCHCH2CH2S)Fe(CO)(dppv)]BF4 ([4]BF4) via the unexpected sp3 C-H bond activation reaction. Furthermore, azadiphosphine PhN(CH2PPh2)2-chelated µ-mercapto complex [PhN(CH2PPh2)2Ni(pdt)Fe(CO)(µ-SH)(dppv)]BF4 ([5]BF4) was prepared by treatment of dicarbonyl complex [PhN(CH2PPh2)2Ni(pdt)Fe(CO)2(dppv)](BF4)2 ([C](BF4)2) with Me3NO and H2S gas, whereas treatment of azadiphosphine Ph2CHN(CH2PPh2)2-chelated dicarbonyl complex [Ph2CHN(CH2PPh2)2Ni(pdt)Fe(CO)2(dppe)](BF4)2 ([D](BF4)2, dppe = 1,2-(Ph2P)2C2H4) with Me3NO⋅2H2O gave rise to µ-hydroxo complex [Ph2CHN(CH2PPh2)2Ni(pdt)Fe(CO)(µ-OH)(dppe)]BF4 ([6]BF4). All the possible pathways for formation of the new model complexes are briefly discussed, and their structures were fully characterized by various spectroscopic techniques and for six of them by X-ray crystallography.

Biomimetic models of [Fe]-hydrogenase featuring a 2-acylphenylthiomethyl-6-R-pyridine (R = H or OMe) ligand

A new flexible pyridine ligand (FPL)-based method is developed, by which two novel biomimetic models of [Fe]-H2ase are prepared and their enzyme-like H2/D2 activation functions are studied.

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.

Activation of small molecules by cyclic alkyl amino silylenes (CAASis) and germylenes (CAAGes): a theoretical study

Quantum chemical calculations have been carried out on a series of skeletally modified cyclic alkyl amino silylenes (CAASis) and germylenes (CAAGes) to understand their ligand properties and reactivity towards the activation of a variety of small molecules. The installation of boron or silicon atoms into the ring framework of these silylenes/germylenes led to a dramatic increase in their σ-basicity while the incorporation of ylidic moieties resulted in a sharp reduction of their π-acidity although it did help in increasing the electron donation ability. The calculated values of energy barriers for the activation of H-H, N-H, C-H and Si-H bonds by many of the cyclic silylenes considered here are found to be comparable to those for experimentally evaluated systems, indicating the potential of these computationally designed molecules in small molecule activation and calling for synthetic efforts towards their isolation. Furthermore, activations employing CAAGes are found to be more demanding than those with CAASis which may be attributed to the significantly lower Lewis basicity of the former than the latter.

A Kinetic Study of the Electron-Transfer Reactions of Nickel(III,II) Tripeptide Complexes with Cyano Complexes of Molybdenum, Tungsten, and Iron

Experimentally measured rate constants, k₁₂^obsd, for the reductions of [Ni(III)tripeptides(H₂O)₂] with Fe(CN)₆^4-, Mo(CN)₈^4-, and W(CN)₈^4- are 10² to 10⁵ times faster than the calculated rate constants with the Marcus theory for outer-sphere electron-transfer processes, k₁₂^calc, even when work terms are considered. This gives rise to a kinetic advantage of k₁₂^obsd/k₁₂^calc = 10²-10⁵, which is consistent with an inner-sphere electron-transfer mechanism via a bridged intermediate. In addition, k₁₂^obsd values are nearly independent of the electrochemical driving force of the reactions. This is consistent with one of the two axial water ligands coordinated to [Ni(III)tripeptides(H₂O)₂] being substituted in the rate-limiting step to form bridged intermediates of the type [(CN)_5or7M-(CN)-Ni^III(tripeptide)(H₂O)]^4- with M = Fe^II, Mo^IV, or W^IV. A limiting rate constant of H₂O replacement from [Ni(III)tripeptides(H₂O)₂] of (5 ± 2) × 10⁷ M^-1 s^-1 at 25.0 °C is observed. Electron paramagnetic resonance spectra of Ni(III) peptide complexes in the presence of Fe(CN)₆^3-, Mo(CN)₈^3-, or IrCl₆^3- provide evidence for the cyanide-bridged intermediates. Substitution-limited electron-transfer reactions could serve as an additional criterion for inner-sphere pathways when atom or group transfer does not occur during electron-transfer and when precursor and successor complexes cannot be observed directly.

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.

Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum

Living biological systems display a fascinating ability to self-organize their metabolism. This ability ultimately determines the metabolic robustness that is fundamental to controlling cellular behavior. However, fluctuations in metabolism can affect cellular homeostasis through transient oscillations. For example, yeast cultures exhibit rhythmic oscillatory behavior in high cell-density continuous cultures. Oscillatory behavior provides a unique opportunity for quantitating the robustness of metabolism, as cells respond to changes by inherently compromising metabolic efficiency. Here, we quantify the limits of metabolic robustness in self-oscillating autotrophic continuous cultures of the gas-fermenting acetogen Clostridium autoethanogenum Online gas analysis and high-resolution temporal metabolomics showed oscillations in gas uptake rates and extracellular byproducts synchronized with biomass levels. The data show initial growth on CO, followed by growth on CO and H2 Growth on CO and H2 results in an accelerated growth phase, after which a downcycle is observed in synchrony with a loss in H2 uptake. Intriguingly, oscillations are not linked to translational control, as no differences were observed in protein expression during oscillations. Intracellular metabolomics analysis revealed decreasing levels of redox ratios in synchrony with the cycles. We then developed a thermodynamic metabolic flux analysis model to investigate whether regulation in acetogens is controlled at the thermodynamic level. We used endo- and exo-metabolomics data to show that the thermodynamic driving force of critical reactions collapsed as H2 uptake is lost. The oscillations are coordinated with redox. The data indicate that metabolic oscillations in acetogen gas fermentation are controlled at the thermodynamic level.

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.

Structural characterization of HypX responsible for CO biosynthesis in the maturation of NiFe-hydrogenase

Several accessory proteins are required for the assembly of the metal centers in hydrogenases. In NiFe-hydrogenases, CO and CN- are coordinated to the Fe in the NiFe dinuclear cluster of the active center. Though these diatomic ligands are biosynthesized enzymatically, detail mechanisms of their biosynthesis remain unclear. Here, we report the structural characterization of HypX responsible for CO biosynthesis to assemble the active site of NiFe hydrogenase. CoA is constitutionally bound in HypX. Structural characterization of HypX suggests that the formyl-group transfer will take place from N10-formyl-THF to CoA to form formyl-CoA in the N-terminal domain of HypX, followed by decarbonylation of formyl-CoA to produce CO in the C-terminal domain though the direct experimental results are not available yet. The conformation of CoA accommodated in the continuous cavity connecting the N- and C-terminal domains will interconvert between the extended and the folded conformations for HypX catalysis.

CNS and CNP Iron(II) Mono-Iron Hydrogenase (Hmd) Mimics: Role of Deprotonated Methylene(acyl) and the trans-Acyl Site in H2 Heterolysis

We report syntheses and H₂ activation involving model complexes of mono-iron hydrogenase (Hmd) derived from acyl-containing pincer ligand precursors bearing thioether (CNS^Pre) or phosphine (CNP^Pre) donor sets. Both complexes feature pseudo-octahedral iron(II) dicarbonyl units. While the CNS pincer adopts the expected mer-CNS (pincer) geometry, the CNP ligand unexpectedly adopts the fac-CNP coordination geometry. Both complexes exhibit surprisingly acidic methylene C-H bond (reversibly de/protonated by a bulky phenolate), which affords a putative dearomatized pyridinate-bound intermediate. Such base treatment of Fe-CNS also results in deligation of the thioether sulfur donor, generating an open coordination site trans from the acyl unit. In contrast, Fe-CNP maintains a CO ligand trans from the acyl site both in the parent and dearomatized complexes (the -PPh₂ donor is cis to acyl). The dearomatized mer-Fe-CNS was competent for H₂ activation (5 atm D_2(g) plus phenolate as base), which is attributed to both the basic site on the ligand framework and the open coordination site trans to the acyl donor. In contrast, the dearomatized fac-Fe-CNP was not competent for H₂ activation, which is ascribed to the blocked coordination site trans from acyl (occupied by CO ligand). These results highlight the importance of both (i) the open coordination site trans to the organometallic acyl donor and (ii) a pendant base in the enzyme active site.

O2 sensitivity and H2 production activity of hydrogenases-A review

Hydrogenases are metalloproteins capable of catalyzing the interconversion between molecular hydrogen and protons and electrons. The iron-sulfur clusters within the enzyme enable rapid relay of electrons which are either consumed or generated at the active site. Their unparalleled catalytic efficiency has attracted attention, especially for potential use in H₂ production and/or fuel cell technologies. However, there are limitations to using hydrogenases, especially due to their high O₂ sensitivity. The subclass, called [FeFe] hydrogenases, are particularly more vulnerable to O₂ but proficient in H₂ production. In this review, we provide an overview of mechanistic and protein engineering studies focused on understanding and enhancing O₂ tolerance of the enzyme. The emphasis is on ongoing studies that attempt to overcome O₂ sensitivity of the enzyme while it catalyzes H₂ production in an aerobic environment. We also discuss pioneering attempts to utilize the enzyme in biological H₂ production and other industrial processes, as well as our own perspective on future applications.

Formate hydrogenlyase: A group 4 [NiFe]-hydrogenase in tandem with a formate dehydrogenase

Hydrogenase enzymes are currently under the international research spotlight due to emphasis on biologically produced hydrogen as one potential energy carrier to relinquish the requirement for 'fossil fuel' derived energy. Three major classes of hydrogenase exist in microbes all able to catalyze the reversible oxidation of dihydrogen to protons and electrons. These classes are defined by their active site metal content: [NiFe]-; [FeFe]- and [Fe]-hydrogenases. Of these the [NiFe]-hydrogenases have links to ancient forms of metabolism, utilizing hydrogen as the original source of reductant on Earth. This review progresses to highlight the Group 4 [NiFe]-hydrogenase enzymes that preferentially generate hydrogen exploiting various partner enzymes or ferredoxin, while in some cases translocating ions across biological membranes. Specific focus is paid to Group 4A, the Formate hydrogenlyase complexes. These are the combination of a six or nine subunit [NiFe]-hydrogenase with a soluble formate dehydrogenase to derived electrons from formate oxidation for proton reduction. The incidence, physiology, structure and biotechnological application of these complexes will be explored with attention on Escherichia coli Formate Hydrogenlyase-1 (FHL-1).

Nickel-Iron Dithiolato Hydrides Derived from H2 Activation by Their μ-Hydroxo Ligand-Containing Analogues

Here, we describe the synthesis and characterization of the two μ-hydrido models of [NiFe]H₂ases prepared from a new type of H₂ activation by the corresponding two μ-hydroxo models. In addition, another μ-hydrido model prepared by the anionic exchange between one of the two μ-hydrido models and KPF₆ is also reported. Interestingly, the synthesis of the two μ-hydrido models from H₂ activation represents the first functional modeling of the H₂ activation catalyzed by the [NiFe]H₂ase (Ni-SIr)_I state to give the Ni-R state.

Complex Multimeric [FeFe] Hydrogenases: Biochemistry, Physiology and New Opportunities for the Hydrogen Economy

Hydrogenases are key enzymes of the energy metabolism of many microorganisms. Especially in anoxic habitats where molecular hydrogen (H₂) is an important intermediate, these enzymes are used to expel excess reducing power by reducing protons or they are used for the oxidation of H₂ as energy and electron source. Despite the fact that hydrogenases catalyze the simplest chemical reaction of reducing two protons with two electrons it turned out that they are often parts of multimeric enzyme complexes catalyzing complex chemical reactions with a multitude of functions in the metabolism. Recent findings revealed multimeric hydrogenases with so far unknown functions particularly in bacteria from the class Clostridia. The discovery of [FeFe] hydrogenases coupled to electron bifurcating subunits solved the enigma of how the otherwise highly endergonic reduction of the electron carrier ferredoxin can be carried out and how H₂ production from NADH is possible. Complexes of [FeFe] hydrogenases with formate dehydrogenases revealed a novel enzymatic coupling of the two electron carriers H₂ and formate. These novel hydrogenase enzyme complex could also contribute to biotechnological H₂ production and H₂ storage, both processes essential for an envisaged economy based on H₂ as energy carrier.

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.

Embedding a Ruthenium-Based Structural Mimic of the [Fe]-Hydrogenase Cofactor into Papain

We describe the synthesis of the ruthenacyclic carbamoyl complexes [Ru(2-NHC(O)C₅H₃NMe)(CO)₂( o,o-Me₂-C₆H₃S)(L)] (L = H₂O or MeCN), which have a labile water or acetonitrile ligand at their sixth coordination sites. Steric bulk around the ruthenium center is essential in preventing isomerization and dimerization, and embedding within papain can be achieved via coordination of its sole free cysteine residue. The observed chemistry parallels that of the natural [Fe]-hydrogenase.

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.

Structural Mimics of the [Fe]-Hydrogenase: A Complete Set for Group VIII Metals

A set of structural mimics of the [Fe]-hydrogenase active site comprising all the group VIII metals, viz., [M(2-NHC(O)C₅H₄N)(CO)₂(2-S-C₅H₄N)], has been synthesized. They exist as a mixture of isomers in solution, and the relative stability of the isomers depends on the nature of the metal and the substituent at the 6-position of the pyridine ligand.

Sources and Fates of Carbamyl Phosphate: A Labile Energy-Rich Molecule with Multiple Facets

Carbamyl phosphate (CP) is well-known as an essential intermediate of pyrimidine and arginine/urea biosynthesis. Chemically, CP can be easily synthesized from dihydrogen phosphate and cyanate. Enzymatically, CP can be synthesized using three different classes of enzymes: (1) ATP-grasp fold protein based carbamyl phosphate synthetase (CPS); (2) Amino-acid kinase fold carbamate kinase (CK)-like CPS (anabolic CK or aCK); and (3) Catabolic transcarbamylase. The first class of CPS can be further divided into three different types of CPS as CPS I, CPS II, and CPS III depending on the usage of ammonium or glutamine as its nitrogen source, and whether N-acetyl-glutamate is its essential co-factor. CP can donate its carbamyl group to the amino nitrogen of many important molecules including the most well-known ornithine and aspartate in the arginine/urea and pyrimidine biosynthetic pathways. CP can also donate its carbamyl group to the hydroxyl oxygen of a variety of molecules, particularly in many antibiotic biosynthetic pathways. Transfer of the carbamyl group to the nitrogen group is catalyzed by the anabolic transcarbamylase using a direct attack mechanism, while transfer of the carbamyl group to the oxygen group is catalyzed by a different class of enzymes, CmcH/NodU CTase, using a different mechanism involving a three-step reaction, decomposition of CP to carbamate and phosphate, transfer of the carbamyl group from carbamate to ATP to form carbamyladenylate and pyrophosphate, and transfer of the carbamyl group from carbamyladenylate to the oxygen group of the substrate. CP is also involved in transferring its phosphate group to ADP to generate ATP in the fermentation of many microorganisms. The reaction is catalyzed by carbamate kinase, which may be termed as catabolic CK (cCK) in order to distinguish it from CP generating CK. CP is a thermally labile molecule, easily decomposed into phosphate and cyanate, or phosphate and carbamate depending on the pH of the solution, or the presence of enzyme. Biological systems have developed several mechanisms including channeling between enzymes, increased affinity of CP to enzymes, and keeping CP in a specific conformation to protect CP from decomposition. CP is highly important for our health as both a lack of, or decreased, CP production and CP accumulation results in many disease conditions.

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.

Unique Spectroscopic Properties of the H-Cluster in a Putative Sensory [FeFe] Hydrogenase

Sensory type [FeFe] hydrogenases are predicted to play a role in transcriptional regulation by detecting the H₂ level of the cellular environment. These hydrogenases contain the hydrogenase domain with distinct modifications in the active site pocket, followed by a Per-Arnt-Sim (PAS) domain. As yet, neither the physiological function nor the biochemical or spectroscopic properties of these enzymes have been explored. Here, we present the characterization of an artificially maturated, putative sensory [FeFe] hydrogenase from Thermotoga maritima (HydS). This enzyme shows lower hydrogen conversion activity than prototypical [FeFe] hydrogenases and a reduced inhibition by CO. Using FTIR spectroelectrochemistry and EPR spectroscopy, three redox states of the active site were identified. The spectroscopic signatures of the most oxidized state closely resemble those of the H_ox state from the prototypical [FeFe] hydrogenases, while the FTIR spectra of both singly and doubly reduced states show large differences. The FTIR bands of both the reduced states are strongly red-shifted relative to the H_ox state, indicating reduction at the diiron site, but with retention of the bridging CO ligand. The unique functional and spectroscopic features of HydS are discussed with regard to the possible role of altered amino acid residues influencing the electronic properties of the H-cluster.