The Challenging in silico Description of Carbon Monoxide Oxidation as Catalyzed by Molybdenum-Copper CO Dehydrogenase

CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme

The aerobic oxidation of carbon monoxide to carbon dioxide is catalysed by the Mo/Cu-containing CO-dehydrogenase enzyme in the soil bacterium Oligotropha carboxidovorans, enabling the organism to grow on the small gas molecule as carbon and energy source. It was shown experimentally that silver can be substituted for copper in the active site of Mo/Cu CODH to yield a functional enzyme. In this study, we employed QM/MM calculations to investigate whether the reaction mechanism of the silver-substituted enzyme is similar to that of the native enzyme. Our results suggest that the Ag-substituted enzyme can oxidize CO and release CO2 following the same reaction steps as the native enzyme, with a computed rate-limiting step of 10.4 kcal/mol, consistent with experimental findings. Surprisingly, lower activation energies for C-O bond formation have been found in the presence of silver. Furthermore, comparison of rate constants for reduction of copper- and silver-containing enzymes suggests a discrepancy in the transition state stabilization upon silver substitution. We also evaluated the effects that differences in the water-active site interaction may exert on the overall energy profile of catalysis. Finally, the formation of a thiocarbonate intermediate along the catalytic pathway was found to be energetically unfavorable for the Ag-substituted enzyme. This finding aligns with the hypothesis proposed for the wild-type form, suggesting that the creation of such species may not be necessary for the enzymatic catalysis of CO oxidation.

Studies Relevant to the Functional Model of Mo-Cu CODH: In Situ Reactions of Cu(I)-L Complexes with Mo(VI) and Synthesis of Stable Structurally Characterized Heterotetranuclear MoVI2CuI2 Complex

In this study, we report the synthesis, characterization, and reactions of Cu(I) complexes of the general form Cu(L)(LigH₂) (LigH₂ = xanthene-based heterodinucleating ligand (E)-3-(((5-(bis(pyridin-2-ylmethyl)amino)-2,7-di-tert-butyl-9,9-dimethyl-9H-xanthen-4-yl)imino)methyl)benzene-1,2-diol); L = PMe₃, PPh₃, CN(2,6-Me₂C₆H₃)). New complexes [Cu(PMe₃)(LigH₂)] and [CuCN(2,6-Me₂C₆H₃)(LigH₂)] were synthesized by treating [Cu(LigH₂)](PF₆) with trimethylphosphine and 2,6-dimethylphenyl isocyanide, respectively. These complexes were characterized by multinuclear NMR spectroscopy, IR spectroscopy, high-resolution mass spectrometry (HRMS), and X-ray crystallography. In contrast, attempted reactions of [Cu(LigH₂)](PF₆) with cyanide or styrene failed to produce isolable crystalline products. Next, the reactivity of these and previously synthesized Cu(I) phosphine and isocyanide complexes with molybdate was interrogated. IR (for isocyanide) and ³¹P NMR (for PPh₃/PMe₃) spectroscopy demonstrates the lack of oxidation reactivity. We also describe herein the first example of a structurally characterized multinuclear complex combining both Mo(VI) and Cu(I) metal ions within the same system. The heterobimetallic tetranuclear complex [Cu₂Mo₂O₄(μ₂-O)(Lig)₂]·HOSiPh₃ was obtained by the reaction of the silylated Mo(VI) precursor (Et₄N)(MoO₃(OSiPh₃)) with LigH₂, followed by the addition of [Cu(NCMe)₄](PF₆). This complex was characterized by NMR spectroscopy, high-resolution mass spectrometry, and X-ray crystallography.

How general is the effect of the bulkiness of organic ligands on the basicity of metal-organic catalysts? H2-evolving Mo oxides/sulphides as case studies

Tailoring the activity of an organometallic catalyst usually requires a targeted ligand design. Tuning the ligand bulkiness and tuning the electronic properties are popular approaches, which are somehow interdependent because substituents of different sizes within ligands can determine inter alia the occurrence of different degrees of inductive effects. Ligand basicity, in particular, turned out to be a key property for the modulation of protonation reactions occurring in vacuo at the metals in complexes bearing organophosphorus ligands; however, when the same reactions take place in a polar organic solvent, their energetics becomes dependent on the trade-off between ligand basicity and bulkiness, with the polarity of the solvent playing a key role in this regard [Bancroft et al., Inorg. Chem., 1986, 25, 3675; Rovaletti et al., J. Phys. Org. Chem., 2018, 31, e3748]. In the present contribution, we carried out molecular dynamics and density functional theory calculations on water-soluble Mo-based catalysts for proton reduction, in order to study the energetics of protonation reactions in complexes where the incipient proton binds a catalytically active ligand (i.e., an oxide or a disulphide). We considered complexes either soaked in water or in a vacuum, and featuring N-based ancillary ligands of different bulkiness (i.e. cages constituted either by pyridine or isoquinoline moieties). Our results show that the energetics of protonation events can be affected by ancillary ligand bulkiness even when the metal center does not play the role of the H⁺ acceptor. In vacuo, protonation at the O or S atom in the α position relative to the metal in complexes featuring the bulky isoquinoline-based ligand is more favored by around 10 kcal mol^-1 when compared to the case of the pyridine-based counterparts, a difference that is almost zero when the same reactions occur in water. Such an outcome is rationalized in light of the different electrostatic properties of complexes bearing ancillary ligands of different sizes. The overall picture from theory indicates that such effects of ligand bulkiness can be relevant for the design of green chemistry catalysts that undergo protonation steps in water solutions.

Synthesis and Cu(I)/Mo(VI) Reactivity of a Bifunctional Heterodinucleating Ligand on a Xanthene Platform

In an effort to probe the feasibility of a model of Mo-Cu CODH (CODH = carbon monoxide dehydrogenase) lacking a bridging sulfido group, the new heterodinucleating ligand LH₂ was designed and its Cu(I)/Mo(VI) reactivity was investigated. LH₂ ((E)-3-(((5-(bis(pyridin-2-ylmethyl)amino)-2,7-di-tert-butyl-9,9-dimethyl-9H-xanthen-4-yl)imino)methyl)benzene-1,2-diol) features two different chelating positions bridged by a xanthene linker: bis(pyridyl)amine for Cu(I) and catecholate for Mo(VI). LH₂ was synthesized via the initial protection of one of the amine positions, followed by two consecutive alkylations of the second position, deprotection, and condensation to attach the catechol functionality. LH₂ was found to exhibit dynamic cooperativity between two reactive sites mediated by H-bonding of the catechol protons. In the free ligand, catechol protons exhibit H-bonding with imine (intramolecular) and with pyridine (intermolecular in the solid state). The reaction of LH₂ with [Cu(NCMe)₄]⁺ led to the tetradentate coordination of Cu(I) via all nitrogen donors of the ligand, including the imine. Cu(I) complexes were characterized by multinuclear NMR spectroscopy, high-resolution mass spectrometry (HRMS), X-ray crystallography, and DFT calculations. Cu(I) coordination to the imine disrupted H-bonding and caused rotation away from the catechol arm. The reaction of the Cu(I) complex [Cu(LH₂)]⁺ with a variety of monodentate ligands X (PPh₃, Cl^-, SCN^-, CN^-) released the metal from coordination to the imine, thereby restoring imine H-bonding with the catechol proton. The second catechol proton engages in H-bonding with Cu-X (X = Cl, CN, SCN), which can be intermolecular (XRD) or intramolecular (DFT). The reaction of LH₂ with molybdate [MoO₄]^2- led to incorporation of [Mo^VIO₃] at the catecholate position, producing [MoO₃(L)]^2-. Similarly, the reaction of [Cu(LH₂)]⁺ with [MoO₄]^2- formed the heterodinuclear complex [CuMoO₃(L)]^-. Both complexes were characterized by multinuclear NMR, UV-vis, and HRMS. HRMS in both cases confirmed the constitution of the complexes, containing molecular ions with the expected isotopic distribution.

Functional Expression of a Mo-Cu-Dependent Carbon Monoxide Dehydrogenase (CODH) and Its Use as a Dissolved CO Bio-microsensor

Herein, we report the heterologous expression in Escherichia coli of a Mo-Cu-containing carbon monoxide dehydrogenase (Mo-Cu CODH) from Hydrogenophaga pseudoflava, which resulted in an active protein catalyzing CO oxidation to CO₂. By supplying the E. coli growth medium with Na₂MoO₄ (Mo) and CuSO₄ (Cu), the Mo-Cu CODH metal cofactors precursors, the expressed L-subunit was found to have CO-oxidation activity even without the M- and S- subunits. This successful expression of CO-oxidizing-capable single L-subunit provides direct evidence of its role as the catalytic center of Mo-Cu CODH that has not been discovered and studied before. Subsequently, we used the expressed protein to construct a CO bio-microsensor based on a newly developed fast and sensitive Clark-type CO₂ transducer using an aprotic solvent/ionic liquid electrolyte. The CO bio-microsensor exhibited a linear response to CO concentration in the 0-9 μM range, with a limit of detection (LOD) of 15 nM CO. The sensor uses a mixture of Mo-Cu CODH's L-subunit/Mo, Cu cofactors/methylene blue, confined in the enzyme chamber that is placed in front of a CO₂ transducer. The optimized sensor's sensitivity and performance were retained to levels of at least 80% for 1 week of continuous polarization and operation in an aqueous medium. We have also demonstrated the use of an alkaline front-trap solution to make a completely O₂/CO₂ interference-free microsensor. The CO bio-microsensor developed in this study is potentially useful as an analytical tool for the detection of trace CO in dissolved form for monitoring dissolved CO concentration dynamics in natural or synthetic systems.

Enzymes for Efficient CO2 Conversion

The accumulation of carbon dioxide in the atmosphere as a result of human activities has caused a number of adverse circumstances in the world. For this reason, the proposed solutions lie within the aim of reducing carbon dioxide emissions have been quite valuable. However, as the human activity continues to increase on this planet, the possibility of reducing carbon dioxide emissions decreases with the use of conventional methods. The emergence of compounds than can be used in different fields by converting the released carbon dioxide into different chemicals will construct a fundamental solution to the problem. Although electro-catalysis or photolithography methods have emerged for this purpose, they have not been able to achieve successful results. Alternatively, another proposed solution are enzyme based systems. Among the enzyme-based systems, pyruvate decarboxylase, carbonic anhydrase and dehydrogenases have been the most studied enzymes. Pyruvate dehydrogenase and carbonic anhydrase have either been an expensive method or were incapable of producing the desired result due to the reaction cascade they catalyze. However, the studies reporting the production of industrial chemicals from carbon dioxide using dehydrogenases and in particular, the formate dehydrogenase enzyme, have been remarkable. Moreover, reported studies have shown the existence of more active and stable enzymes, especially the dehydrogenase family that can be identified from the biome. In addition to this, their redesign through protein engineering can have an immense contribution to the increased use of enzyme-based methods in CO₂ reduction, resulting in an enormous expansion of the industrial capacity.