A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo Cu CO-dehydrogenases

Fully Oxidized State of the Oxygen-Tolerant [NiFe] Hydrogenase from Hydrogenophilus thermoluteolus SH: A Quantum Mechanics Cluster and Quantum Mechanics/Molecular Mechanics Study

The oxygen tolerance of some [NiFe] hydrogenase enzymes is crucial for designing efficient bioinspired catalysts for sustainable hydrogen production and advancing renewable energy technologies. To investigate this, we employed a quantum mechanical (QM) cluster model and quantum mechanics/molecular mechanics (QM/MM) calculations to study the fully oxidized state of the [NiFe]-hydrogenase from Hydrogenophilus thermoluteolus SH. Our analysis focused on the structural and electronic properties of the enzyme's active site across different spin states, including closed-shell singlet (CS, S = 0), high-spin triplet (HS, S = 1), and open-shell singlet broken symmetry (BS, S = 0). Using a comprehensive structural model (>300 atoms), we identified the ground state of the fully oxidized enzyme state to be a spin-coupled BS Ni(III)Fe(III) oxidation state, where residues beyond the first coordination sphere primarily contribute sterically. Notably, natural bond order calculations revealed an unusual three-center two-electron bond at the active site, which may enhance the open-shell ground state stability and the enzyme's resilience under oxidative conditions. Our comparative study of QM and QM/MM methods provides insights into their performance, facilitating and guiding the choice of suitable enzyme models when studying other metalloproteins.

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.

Azo-oximate metal-carbonyl to metallocarboxylic acid via the intermediate Ir(III) radical congener: quest for co-ligand driven stability of open- and closed-shell complexes

The redox non-innocent behavior of the diaryl-azo-oxime ligand L^NOH1 has been accentuated via the synthesis of metastable anion radical complexes of type trans-[Ir(L^NO˙-)Cl(CO)(PPh₃)₂] 2 (CO is trans to azo group of the ligand) by the oxidative coordination reaction of 1 with Vaska's complex. The stereochemical role of co-ligands vis-à-vis the interplay of π-bonding has been found to be decisive in controlling the aptitude of the coordinated redox non-innocent ligand to accept or reject an electron. This has been clarified via the isolation of quite a few complexes as well as the failure to synthesize some others. The oxidized analogues of type trans-[Ir(L^NO-)Cl(CO)(PPh₃)₂]⁺2+ (CO and azo group of the ligand are trans) as well as its cis isomer cis-[Ir(L^NO-)Cl(CO)(PPh₃)₂]⁺3+ (CO and azo group of the ligand are cis) have been structurally characterized but the radical anion congener of the latter could not be synthesized. Furthermore, the closed shell complexes [Ir(L^NO-)Cl₂(PPh₃)₂] 4 and [Ir(L^NO-)₂Cl(PPh₃)] 5 have been well characterized by diffraction as well as spectral techniques but their corresponding azo anion radical complexes could not be isolated and this is attributed to the trans influence of ancillary ligands. The anion radical complexes trans-[Ir(L^NO˙-)Cl(CO)(PPh₃)₂] 2 may be rapidly transformed to the metallocarboxylic acids trans-[Ir(L^NO-)Cl(CO₂H)(PPh₃)₂] 6via a proton-coupled electron transfer (PCET) process, thereby demonstrating the role of odd electron over the coordinated ligand framework to trigger metal-mediated carbonyl to carboxylic acid functionalization. Complexes 6 are further stabilized via intramolecular -CO₂H⋯ON- (carboxylic acid⋯oximato) H-bonding. The optoelectronic properties as well as the origin of transitions in the complexes were analyzed by TD-DFT and theoretical analysis, which further disclose that the odd electron in trans-[Ir(L^NO˙-)Cl(CO)(PPh₃)₂] 2 is primarily azo-oxime centric with very low contribution from the iridium center.

Can water act as a nucleophile in CO oxidation catalysed by Mo/Cu CO-dehydrogenase? Answers from theory

The aerobic CO dehydrogenase from Oligotropha carboxidovorans is an environmentally crucial bacterial enzyme for maintenance of subtoxic concentration of CO in the lower atmosphere, as it allows for the oxidation of CO to CO₂ which takes place at its Mo−Cu heterobimetallic active site. Despite extensive experimental and theoretical efforts, significant uncertainties still concern the reaction mechanism for the CO oxidation. In this work, we used the hybrid quantum mechanical/molecular mechanical approach to evaluate whether a water molecule present in the active site might act as a nucleophile upon formation of the new C−O bond, a hypothesis recently suggested in the literature. Our study shows that activation of H₂O can be favoured by the presence of the Mo=O_eq group. However, overall our results suggest that mechanisms other than the nucleophilic attack by Mo=O_eq to the activated carbon of the CO substrate are not likely to constitute reactive channels for the oxidation of CO by the enzyme.

QM/MM study of the binding of H2 to MoCu CO dehydrogenase: development and applications of improved H2 van der Waals parameters

The MoCu CO dehydrogenase enzyme not only transforms CO into CO₂ but it can also oxidise H₂. Even if its hydrogenase activity has been known for decades, a debate is ongoing on the most plausible mode for the binding of H₂ to the enzyme active site and the hydrogen oxidation mechanism. In the present work, we provide a new perspective on the MoCu-CODH hydrogenase activity by improving the in silico description of the enzyme. Energy refinement—by means of the BigQM approach—was performed on the intermediates involved in the dihydrogen oxidation catalysis reported in our previously published work (Rovaletti, et al. “Theoretical Insights into the Aerobic Hydrogenase Activity of Molybdenum–Copper CO Dehydrogenase.” Inorganics 7 (2019) 135). A suboptimal description of the H₂–HN(backbone) interaction was observed when the van der Waals parameters described in previous literature for H₂ were employed. Therefore, a new set of van der Waals parameters is developed here in order to better describe the hydrogen–backbone interaction. They give rise to improved binding modes of H₂ in the active site of MoCu CO dehydrogenase. Implications of the resulting outcomes for a better understanding of hydrogen oxidation catalysis mechanisms are proposed and discussed.

A W/Cu Synthetic Model for the Mo/Cu Cofactor of Aerobic CODH Indicates That Biochemical CO Oxidation Requires a Frustrated Lewis Acid/Base Pair

Constructing synthetic models of the Mo/Cu active site of aerobic carbon monoxide dehydrogenase (CODH) has been a long-standing synthetic challenge thought to be crucial for understanding how atmospheric concentrations of CO and CO₂ are regulated in the global carbon cycle by chemolithoautotrophic bacteria and archaea. Here we report a W/Cu complex that is among the closest synthetic mimics constructed to date, enabled by a silyl protection/deprotection strategy that provided access to a kinetically stabilized complex with mixed O^2-/S^2- ligation between (bdt)(O)W^VI and Cu^I(NHC) (bdt = benzene dithiolate, NHC = N-heterocyclic carbene) sites. Differences between the inorganic core's structural and electronic features outside the protein environment relative to the native CODH cofactor point to a biochemical CO oxidation mechanism that requires a strained active site geometry, with Lewis acid/base frustration enforced by the protein secondary structure. This new mechanistic insight has the potential to inform synthetic design strategies for multimetallic energy storage catalysts.

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.