Hydrogenation without a Metal Catalyst: An ab Initio Study on the Mechanism of the Metal-Free Hydrogenase from Methanobacterium thermoautotrophicum

Reversible Hydride Transfer to N,N'-Diarylimidazolinium Cations from Hydrogen Catalyzed by Transition Metal Complexes Mimicking the Reaction of [Fe]-Hydrogenase

[Fe]-hydrogenase is a key enzyme involved in methanogenesis and facilitates reversible hydride transfer from H₂ to N⁵,N¹⁰-methenyltetrahydromethanopterin (CH-H₄MPT⁺). In this study, a reaction system was developed to model the enzymatic function of [Fe]-hydrogenase by using N,N'-diphenylimidazolinium cation (1⁺) as a structurally related alternative to CH-H₄MPT⁺. In connection with the enzymatic mechanism via heterolytic cleavage of H₂ at the single metal active site, several transition metal complex catalysts capable of such activation were utilized in the model system. Reduction of 1[BF₄] to N,N'-diphenylimidazolidine (2) was achieved under 1 atm H₂ at ambient temperature in the presence of an equimolar amount of NEt₃ as a proton acceptor. The proposed catalytic pathways involved the generation of active hydride complexes and subsequent intermolecular hydride transfer to 1⁺. The reverse reaction was accomplished by treatment of 2 with HNMe₂Ph⁺ as the proton source, where [(η⁵-C₅Me₅)Ir{(p-MeC₆H₄SO₂)NCHPhCHPhNH}] was found to catalyze the formation of 1⁺ and H₂ with high efficiency. These results are consistent with the fact that use of 2,6-lutidine in the forward reaction or 2,6-lutidinium in the reverse reaction resulted in incomplete conversion. By combining these reactions using the above Ir amido catalyst, the reversible hydride transfer interconverting 1⁺/H₂ and 2/H⁺ was performed successfully. This system demonstrated the hydride-accepting and hydride-donating modes of biologically relevant N-heterocycles coupled with proton concentration. The influence of substituents on the forward and reverse reactivities was examined for the derivatives of 1⁺ and 2 bearing one para-substituted N-phenyl group.

Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand

A protein, Tm1631 from the hyperthermophilic organism Thermotoga maritima belongs to a domain of unknown function protein family. It was predicted that Tm1631 binds with the DNA and that the Tm1631–DNA complex is an endonuclease repair system with a DNA repair function (Konc et al. PLoS Comput Biol 9(11): e1003341, 2013). We observed that the severely bent, strained DNA binds to the protein for the entire 90 ns of classical molecular dynamics (MD) performed; we could observe no significant changes in the most distorted region of the DNA, where the cleavage of phosphodiester bond occurs. In this article, we modeled the reaction mechanism at the interface between Tm1631 and its proposed ligand, the DNA molecule, focusing on cleavage of the phosphodiester bond. After addition of two Mg²⁺ ions to the reaction center and extension of classical MD by 50 ns (totaling 140 ns), the DNA ligand stayed bolted to the protein. Results from density functional theory quantum mechanics/molecular mechanics (QM/MM) calculations suggest that the reaction is analogous to known endonuclease mechanisms: an enzyme reaction mechanism with two Mg²⁺ ions in the reaction center and a pentacovalent intermediate. The minimum energy pathway profile shows that the phosphodiester bond cleavage step of the reaction is kinetically controlled and not thermodynamically because of a lack of any energy barrier above the accuracy of the energy profile calculation. The role of ions is shown by comparing the results with the reaction mechanisms in the absence of the Mg²⁺ ions where there is a significantly higher reaction barrier than in the presence of the Mg²⁺ ions.Graphical abstract

Pyridylidene-Mediated Dihydrogen Activation Coupled with Catalytic Imine Reduction

In recent years, dihydrogen activation at non-metallic centers has received increasing attention. A system in which dihydrogen is trapped by a pyridylidene intermediate that is generated from a pyridinium salt and a base is now reported. The dihydropyridine formed in this process can act as reducing agent towards organic electrophiles. By coupling the hydrogen-activation step with subsequent hydride transfer from the dihydropyridine to an imine, a catalytic process was established. Treatment of the N-phenylimine of phenyl trifluoromethyl ketone with 5-20 mol% of N-mesityl-3,5-bis(2,6-dimethylphenyl)pyridinium triflate and 0.3-1.0 equivalents of LiN(SiMe3)2 under 50 bar of hydrogen gas resulted in high conversion into the corresponding amine.

Evolution in the understanding of [Fe]-hydrogenase

Hydrogenases catalyse redox reactions with molecular hydrogen, either as substrate or product. The enzymes harness hydrogen as a reductant using metals that are abundant and economical, namely, nickel and iron, and should provide new pointers for the economic use of hydrogen in manmade devices. The most recently discovered and perhaps the most enigmatic of the hydrogenases is the [Fe]-hydrogenase, used by certain microorganisms in the pathway that reduces carbon dioxide to methane. Since its discovery some twenty years ago, [Fe]-hydrogenase has consistently provided structural and mechanistic surprises, often requiring complete re-evaluation of its mechanism of action. This tutorial review combines recent advances in X-ray crystallography and other analytical techniques, as well as in computational studies and in chemical synthesis to provide a platform for understanding this remarkable enzyme type.

Amidine dications: isolation and [Fe]-hydrogenase-related hydrogenation

This commmunication demonstrates the preparation, isolation, and full characterization of superelectrophilic salts based on amidine dications in organic solvent, as their triflate salts. These dications are highly activated toward regiospecific reaction with hydrogen gas under mild conditions in the presence of a metal catalyst (Pd/C), mimicking the behavior of the natural substrate, N⁵,N¹⁰-methenyltetrahydromethanopterin, in the iron−sulfur cluster-free [Fe]-hydrogenase.

Carbon Monoxide as Intrinsic Ligand to Iron in the Active Site of [Fe]-Hydrogenase

Structural and spectroscopic studies on [Fe]-hydrogenase revealed an active site mononuclear low spin iron coordinated by the Cys176 sulfur, two CO, and the sp2 hybridized nitrogen of a 2-pyridinol compound with back bonding properties similar to those of cyanide. Thus, [Fe]-hydrogenases are endowed with an iron-ligation pattern related to that found in the active site of [NiFe]- and [FeFe]-hydrogenases although the three hydrogenases and the enzymes involved in their posttranslational maturation have evolved independently and although CO and cyanide ligands are not found in any other metallo-enzymes. Obviously, low-spin iron complexed with thiolate(s), CO, and cyanide or a cyanide functional analogue plays an essential role in H2 activation.

The exchange activities of [Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases

[Fe] hydrogenase (iron-sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min(-1) mg(-1)). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors.

Reversible, metal-free hydrogen activation

Although reversible covalent activation of molecular hydrogen (H2) is a common reaction at transition metal centers, it has proven elusive in compounds of the lighter elements. We report that the compound (C6H2Me3)2PH(C6F4)BH(C6F5)2 (Me, methyl), which we derived through an unusual reaction involving dimesitylphosphine substitution at a para carbon of tris(pentafluorophenyl) borane, cleanly loses H2 at temperatures above 100 degrees C. Preliminary kinetic studies reveal this process to be first order. Remarkably, the dehydrogenated product (C6H2Me3)2P(C6F4)B(C6F5)2 is stable and reacts with 1 atmosphere of H2 at 25 degrees C to reform the starting complex. Deuteration studies were also carried out to probe the mechanism.

UV-A/blue-light inactivation of the 'metal-free' hydrogenase (Hmd) from methanogenic archaea

H2-forming methylenetetrahydromethanopterin dehydrogenase (Hmd) is an unusual hydrogenase present in many methanogenic archaea. The homodimeric enzyme dubbed 'metal-free' hydrogenase does not contain iron-sulfur clusters or nickel and thus differs from [Ni-Fe] and [Fe-Fe] hydrogenases, which are all iron-sulfur proteins. Hmd preparations were found to contain up to 1 mol iron per 40 kDa subunit, but the iron was considered to be a contaminant as none of the catalytic and spectroscopic properties of the enzyme indicated that it was an essential component. Hmd does, however, harbour a low molecular mass cofactor of yet unknown structure. We report here that the iron found in Hmd is most probably functional after all. Further investigation was initiated by the discovery that Hmd is inactivated upon exposure to UV-A (320-400 nm) or blue-light (400-500 nm). Enzyme purified in the dark exhibited an absorption spectrum with a maximum at approximately 360 nm and which mirrored its sensitivity towards light. In UV-A/blue-light the enzyme was bleached. The cofactor extracted from active Hmd was also light sensitive. It showed an UV/visible spectrum similar to that of the active enzyme and was bleached upon exposure to light. Photobleached cofactor no longer had the ability to reconstitute active Hmd from the apoenzyme. When purified in the dark, Hmd consistently contained per monomer about one Fe, which was tightly bound to the cofactor. The iron was released from the enzyme and from the cofactor upon light inactivation. Hmd activity was inhibited by high concentrations of CO and CO protected the enzyme from light inactivation indicating that the iron in Hmd is of functional importance. Therefore, reference to Hmd as 'metal-free' hydrogenase is no longer appropriate.

Activation of dihydrogen without transition metals

The metal-free hydrogenase from methanogenic archaea (Hmd) is a unique enzyme: it catalyzes the reaction of its substrate, methenyl-tetrahydromethanopterin, with molecular hydrogen without the aid of a transition metal. In other words, Hmd is currently the only example of a purely organic hydrogenation catalyst. Recent results from various fields have shed new light on this enzyme. In biochemistry, there is experimental proof that a tightly bound (and metal-free) cofactor exists. Ab initio calculations have revealed that the concerted action of the Lewis-acidic substrate and a Brønsted-base appears to induce facile heterolysis of the hydrogen molecule. In chemical model studies, a transition-metal-free hydrogenation of ketones was achieved in the presence of catalytic base. Taken together, the experimental results available to date point to an enzymatic mechanism in which the hydrogen molecule is heterolyzed by the joint action of the Lewis-acidic substrate methenyl-tetrahydromethanopterin and a Brønsted-base in the active site (i.e. by bifunctional catalysis).

Re-face stereospecificity of methylenetetrahydromethanopterin and methylenetetrahydrofolate dehydrogenases is predetermined by intrinsic properties of the substrate

Four different dehydrogenases are known that catalyse the reversible dehydrogenation of N5,N10-methylenetetrahydromethanopterin (methylene-H4MPT) or N5,N10-methylenetetrahydrofolate (methylene-H4F) to the respective N5,N10-methenyl compounds. Sequence comparison indicates that the four enzymes are phylogenetically unrelated. They all catalyse the Re-face-stereospecific removal of the pro-R hydrogen atom of the coenzyme's methylene group. The Re-face stereospecificity is in contrast to the finding that in solution the pro-S hydrogen atom of methylene-H4MPT and of methylene-H4F is more reactive to heterolytic cleavage. For a better understanding we determined the conformations of methylene-H4MPT in solution and when enzyme-bound by using NMR spectroscopy and semiempirical quantum mechanical calculations. For the conformation free in solution we find an envelope conformation for the imidazolidine ring, with the flap at N10. The methylene pro-S C-H bond is anticlinal and the methylene pro-R C-H bond is synclinal to the lone electron pair of N10. Semiempirical quantum mechanical calculations of heats of formation of methylene-H4MPT and methylene-H4F indicate that changing this conformation into an activated one in which the pro-S C-H bond is antiperiplanar, resulting in the preformation of the leaving hydride, would require a deltadeltaH(f) of +53 kJ mol-1 for methylene-H4MPT and of +51 kJ mol-1 for methylene-H4F. This is almost twice the energy required to force the imidazolidine ring in the enzyme-bound conformation of methylene-H4MPT (+29 kJ mol-1) or of methylene-H4F (+35 kJ mol-1) into an activated conformation in which the pro-R hydrogen atom is antiperiplanar to the lone electron pair of N10. The much lower energy for pro-R hydrogen activation thus probably predetermines the Re-face stereospecificity of the four dehydrogenases. Results are also presented explaining why the chemical reduction of methenyl-H4MPT+ and methenyl-H4F+ with NaBD4 proceeds Si-face-specific, in contrast to the enzyme-catalysed reaction.

The metal-free hydrogenase from methanogenic archaea: evidence for a bound cofactor

The hmd gene, which encodes the metal-free hydrogenase in methanogenic archaea, was heterologously expressed in Escherichia coli. The overproduced enzyme was completely inactive. High activity could, however, be induced by the addition of ultrafiltrate from active enzyme denatured in 8 M urea. The active fraction in the ultrafiltrate was heat-labile and migrated on gel filtration columns with an apparent molecular mass well below 1000 Da.