Substrate and metal control of barrier heights for oxo transfer to Mo and W bis-dithiolene sites

Elucidating the Mechanism of Tetrahydrofuran-Diol Formation through Os(VI)-Catalyzed Oxidative Cyclization of 5,6-Dihydroxyalkenes Ligated by Citric Acid

A computational study is reported here on the mechanism of tetrahydrofuran (THF)-diol formation from the Os(VI)-catalyzed oxidative cyclization of 5,6-dihydroxyalkene ligated with citric acid and in the presence of Bro̷nsted acid. Initiated by Os(VI) dioxo citrate formation, coordination of co-oxidant pyridine-N-oxide (PNO) and protonation of its oxo group generate the active catalyst. The catalytic cycle commences through successive steps, including dihydroxyalkene addition to the active catalyst in a concerted mechanism to form hexacoordinated alkoxy-protonated PNO-complexed Os(VI) bisglycolate as a turnover-limiting step (TLS), cyclization to Os(IV) THF-diolate, reoxidation to Os(VI) THF-diolate, and hydrolysis via a dissociative mechanism to furnish the THF-diol and regenerate the active species, sustaining the catalytic cycle through an Os(VI)/Os(IV) cycle. Despite the overall exergonic nature of catalytic cycle (ΔGrcycle = -45.0 kcal/mol), the TLS is accelerated by the formation of an open-valence 16-electron Os(VI) intermediate but decelerated by the undesired formation of a saturated/hexacoordinate 18-electron Os(VI) intermediate. Bro̷nsted acid plays crucial roles in the formation of Os(VI) citrate and the active catalyst, impediment of the second cycle, and the cyclization step. Additionally, besides its role as a co-oxidant, and in the presence of acid, PNO is found to assist the insertion of dihydroxyalkene and, importantly, in releasing the THF-diol to regenerate the active intermediate.

Resonance Raman spectroscopy of pyranopterin molybdenum enzymes

Resonance Raman spectroscopy (rR) is a powerful spectroscopic probe that is widely used for studying the geometric and electronic structure of metalloproteins. In this focused review, we detail how resonance Raman spectroscopy has contributed to a greater understanding of electronic structure, geometric structure, and the reaction mechanisms of pyranopterin molybdenum enzymes. The review focuses on the enzymes sulfite oxidase (SO), dimethyl sulfoxide reductase (DMSOR), xanthine oxidase (XO), and carbon monoxide dehydrogenase. Specifically, we highlight how Mo-Ooxo, Mo-Ssulfido, Mo-Sdithiolene, and dithiolene CC vibrational modes, isotope and heavy atom perturbations, resonance enhancement, and associated Raman studies of small molecule analogs have provided detailed insight into the nature of these metalloenzyme active sites.

S K-edge XAS of CuII, CuI, and ZnII oxidized Dithiolene complexes: Covalent contributions to structure and the Jahn-Teller effect

Reduced dithiolene ligands are bound to high valent Mo centers in the active site of the oxotransferase family of enzymes. Related model complexes have been studied with great insight by Prof. Holm and his colleagues. This study focuses on the other limit of dithiolene chemistry: an investigation of the 2-electron oxidized dithiolene bound to low-valent late transition metal (TM) ions (ZnII, CuI, and CuII). The bonding descriptions of the oxidized dithiolene [N,N-dimethyl piperazine 2,3-dithione (Me2Dt0)] complexes are probed using S K-edge X-ray absorption spectroscopy (XAS) and the results are correlated to density functional theory (DFT) calculations. These experimentally supported calculations are then extended to explain the different geometric structures of the three complexes. The ZnII(Me2Dt0)2 complex has only ligand-ligand repulsion so it is stabilized at the D2d symmetry limit. The CuI(Me2Dt0)2 complex has additional weak backbonding thus distorts somewhat from D2d toward D2h symmetry. The CuII(Me2Dt0)2 complex has a strong σ donor bond that leads to both a large Jahn-Teller stabilization to D2h and an additional covalent contribution to the geometry. The combined strong stabilization results in the square planar, D2h structure. This study quantifies the competition between the ligand-ligand repulsion and the change in electronic structures in determining the final geometric structures of the oxidized dithiolene complexes, and provides quantitative insights into the Jahn-Teller stabilization energy and its origin.

Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily

Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Predominance of the second cycle in homogeneous Os-catalyzed dihydroxylation: the nature of Os(vi) → Os(viii) reoxidation and unprecedented roles of amine-N-oxides

Our detailed DFT study of Os-catalyzed alkene dihydroxylation revealed that the reaction predominantly proceeds via a second cycle initiated by the formation of a putative Os(viii)trioxoglycolate as a highly reactive intermediate.

Ru-catalysed oxidative cyclisation of 1,5-dienes: an unprecedented role for the co-oxidant

The Ru-mediated oxidative cyclisation of 1,5-dienes to furnish 2,5-dihydroxyalkyl-substituted tetrahydrofuran-diols (THF-diols) represents a practical approach for the synthesis of many bioactive natural products. In the current study, we reported profound findings obtained by density functional theory (DFT) simulations, and they were consistent with the experimental conditions. The results set out a catalytic cycle within intermediacy of NaIO₄-complexed Ru(vi) species. Importantly, the co-oxidant played a critical role in the cyclisation step and subsequently the release of THF-diols. Following the formation of Ru(vi) glycolate, cyclisation and THF-diol release proceeded through NaIO₄-coordinated Ru(vi) intermediates, outpacing the Ru(viii) glycolate or THF-diolate intermediates and subsequently entering “second cycle” type pathways. The results indicated a cycle involving Ru(viii)/Ru(vi)/Ru(iv)/Ru(vi) rather than Ru(viii)/Ru(vi)/Ru(viii)/Ru(vi)/Ru(viii). Additionally, the existence of an electron-withdrawing group (EWG) on one of the double bonds of 1,5-dienes revealed that the regioselectivity of the Ru-catalysed oxidative cyclisation was predominantly initiated at the electron-rich alkene. Overall, this study offers new insights, which were ignored by earlier experimentalists and theoreticians, into the Ru-catalysed functionalizations of alkenes and 1,5-dienes.

The Ru-mediated oxidative cyclisation of 1,5-dienes to THF-diols proceeds with the intermediacy of NaIO₄-complexed Ru(vi) species and offers new insights into the Ru-catalysed functionalizations of alkenes and 1,5-dienes.

Molybdenum and Tungsten Cofactors and the Reactions They Catalyze

The last 20 years have seen a dramatic increase in our mechanistic understanding of the reactions catalyzed by pyranopterin Mo and W enzymes. These enzymes possess a unique cofactor (Moco) that contains a novel ligand in bioinorganic chemistry, the pyranopterin ene-1,2-dithiolate. A synopsis of Moco biosynthesis and structure is presented, along with our current understanding of the role Moco plays in enzymatic catalysis. Oxygen atom transfer (OAT) reactivity is discussed in terms of breaking strong metal-oxo bonds and the mechanism of OAT catalyzed by enzymes of the sulfite oxidase (SO) family that possess dioxo Mo(VI) active sites. OAT reactivity is also discussed in members of the dimethyl sulfoxide (DMSO) reductase family, which possess des-oxo Mo(IV) sites. Finally, we reveal what is known about hydride transfer reactivity in xanthine oxidase (XO) family enzymes and the formate dehydrogenases. The formal hydride transfer reactivity catalyzed by xanthine oxidase family enzymes is complex and cleaves substrate C-H bonds using a mechanism that is distinct from monooxygenases. The chapter primarily highlights developments in the field that have occurred since ~2000, which have contributed to our collective structural and mechanistic understanding of the three canonical pyranopterin Mo enzymes families: XO, SO, and DMSO reductase.

Anion Binding and Oxidative Modification at the Molybdenum Cofactor of Formate Dehydrogenase from Rhodobacter capsulatus Studied by X-ray Absorption Spectroscopy

Formate dehydrogenase (FDH) enzymes are versatile catalysts for CO₂ conversion. The FDH from Rhodobacter capsulatus contains a molybdenum cofactor with the dithiolene functions of two pyranopterin guanine dinucleotide molecules, a conserved cysteine, and a sulfido group bound at Mo(VI). In this study, we focused on metal oxidation state and coordination changes in response to exposure to O₂, inhibitory anions, and redox agents using X-ray absorption spectroscopy (XAS) at the Mo K-edge. Differences in the oxidative modification of the bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor relative to samples prepared aerobically without inhibitor, such as variations in the relative numbers of sulfido (Mo═S) and oxo (Mo═O) bonds, were observed in the presence of azide (N₃^-) or cyanate (OCN^-). Azide provided best protection against O₂, resulting in a quantitatively sulfurated cofactor with a displaced cysteine ligand and optimized formate oxidation activity. Replacement of the cysteine ligand by a formate (HCO₂^-) ligand at the molybdenum in active enzyme is compatible with our XAS data. Cyanide (CN^-) inactivated the enzyme by replacing the sulfido ligand at Mo(VI) with an oxo ligand. Evidence that the sulfido group may become protonated upon molybdenum reduction was obtained. Our results emphasize the role of coordination flexibility at the molybdenum center during inhibitory and catalytic processes of FDH enzymes.

Mechanism of Os-Catalyzed Oxidative Cyclization of 1,5-Dienes

The oxidative cyclization of 1,5-dienes by metal-oxo species is a powerful method for stereocontrolled synthesis of tetrahydrofuran diols (THF-diols), structural motifs present in many bioactive natural products. Oxidative cyclization of (2E,6E)-octa-2,6-diene catalyzed by OsO₄/NMO has been studied using density functional theory (DFT) calculations (M06-2X/aug-cc-pVDZ/Hay-Wadt VDZ (n+1) ECP), highlighting the remarkable effect of acid on the fate of the first intermediate, an Os(VI) dioxoglycolate. A strong acid promotes cyclization of the Os(VI) dioxoglycolate, or its NMO complex, through protonation of an oxo ligand to give more electrophilic species. By contrast, in the absence of acid, reoxidation may occur to afford the Os(VIII) trioxoglycolate, which is shown to favor conventional "second cycle" dihydroxylation reactivity rather than cyclization. The results of the calculations are consistent with experimental results for reactions of OsO₄/NMO with 1,5-dienes with acid (oxidative cyclization) and without acid (second cycle osmylation/dihydroxylation). Detailed evaluation of potential catalytic cycles supports oxidation of the cyclized Os(IV) THF-diolate intermediate to the corresponding Os(VI) species followed by slow hydrolysis and, finally, regeneration of OsO₄.

Synthesis of a dinuclear europium(iii) complex through deprotonation and oxygen-atom transfer of trimethylamine N-oxide

A dinuclear europium complex was synthesized via unprecedented deprotonation and oxygen-atom transfer of Me₃NO.

Mechanistic investigation of trimethylamine-N-oxide reduction catalysed by biomimetic molybdenum enzyme models

In this paper, we report a theoretical investigation of the reduction reaction mechanism of Me3NO using molybdenum containing systems that are functional and structural analogues of trimethylamine N-oxide reductase mononuclear molybdenum enzyme. The reactivity of the monooxomolybdenum(IV) benzenedithiolato complex and its derivatives to carbamoyl (t-BuNHCO) and acylamino (t-BuCONH) substituents on the benzene rings in both cis and trans arrangements was explored. The calculated energy profiles describing the steps of two mechanisms of attack considered viable (named cis- and trans-attack) by the Me3NO substrate at cis and trans positions with respect to the oxo ligand show that the attack on cis is energetically more favourable than the attack on trans. Along the pathway for the cis-attack the first step of the reaction, that is rate-determining for all the studied compounds, is the approach of the substrate to the Mo centre in cis to the oxo ligand that causes a distortion of the initial square-pyramidal geometry of the complex. The reaction steps involved in the trans position attack were also explored. Calculations confirm that, as previously suggested, the introduction of ligands able to form intramolecular NH···S hydrogen bonds accelerates the reduction of the Me3NO substrate and contributes to the tuning of the reactivity of molybdoenzyme models.

DFT Study on the Interaction of Tris(benzene-1,2-dithiolato)molybdenum Complex with Water. A Hydrolysis Mechanism Involving a Feasible Seven-Coordinate Aquomolybdenum Intermediate

In the present work, the reactivity of the tris(benzene-1,2-dithiolato)molybdenum complex ([Mo(bdt)₃]) toward water is studied by means of the density functional theory (DFT). DFT calculations were performed using the M06, B3P86, and B3PW91 hybrid functionals for comparison purposes. The M06 method was employed to elucidate the reaction pathway, relative stability of the intermediate products, nature of the Mo-S bond cleavage, and electronic structure of the involved molybdenum species. This functional was also used to study the transference of electrons from the molybdenum center toward the ligands. The reaction pathway confirms that [Mo(bdt)₃] undergoes hydrolysis, yielding dihydroxo-bis(benzene-1,2-dithiolato)molybdenum complex ([Mo(OH)₂(bdt)₂]) and benzenedithiol. The reaction takes place through seven transition structures, one of them involving an aquo seven-coordinate molybdenum intermediate stabilized by a lone pair (LP) LP_O→LP_Mo hyperconjugative interaction. This heptacoordinate species allows understanding of the observed oxygen atom exchange between water and tertiary phosphines mediated by these complexes. Calculations also show that [Mo(C₂H₄S₂)₃] and [Mo(OH)₂(C₂H₄S₂)₂] have d² and d⁰ electronic configuration, and hence an electron pair must be transferred during the course of the hydrolysis. The frontier molecular orbital (FMO) analysis concludes that the electron pair is transferred in the rupture of the second Mo-S bond, from the occupied donating Mo d_x²-y² orbital to the unoccupied C₂H₄(SH)₂ S-C σ* ligand orbital. This result is supported by the bond dissociation energy calculations, which demonstrate that the neutral dissociation of the second Mo-S bond is energetically the more favorable.

Solution, Solid, and Gas Phase Studies on a Nickel Dithiolene System: Spectator Metal and Reactor Ligand

The syntheses of cationic nickel complexes using N,N'-dimethyl piperazine 2,3-dithione (Me2Dt(0)) and N,N'-diisopropyl piperazine 2,3-dithione ((i)Pr2Dt(0)) ligands are reported. These ligands were used in synthesizing bis and tris(dithione)Ni(II) complexes as tetrafluoroborate or hexafluorophosphate salts, i.e., [Ni((i)Pr2Dt(0))2][BF4]2 ([1a][BF4]2), [Ni((i)Pr2Dt(0))2][PF6]2 ([1a][PF6]2), [Ni(Me2Dt(0))2][BF4]2 ([1b][BF4]2), [Ni((i)Pr2Dt(0))3][BF4]2 ([2a][BF4]2), and [Ni((i)Pr2Dt(0))3][PF6]2 ([2a][PF6]2), respectively. Complex [2a][PF6]2 was isolated from a methanolic solution of [1a][PF6]2. Compound [1a][BF4]2 crystallizes in a trigonal crystal system (space group, P31/c) and exhibits unique packing features, whereas [2a][BF4]2 crystallizes in a monoclinic (P21/n) space group. Cyclic voltammograms of [1a][BF4]2 and [1b][BF4]2 are indicative of four reduction processes associated with stepwise single-electron reduction of the ligands. Spectroelectrochemical experiments on [1a][BF4]2 exhibit an intervalence charge transfer (IVCT) transition as a spectroscopic signature of the mixed-valence [Ni((i)Pr2Dt(0))((i)Pr2Dt(1-))](-) species. Analysis of this IVCT band suggests that this ligand based mixed valence complex, [Ni((i)Pr2Dt(0))((i)Pr2Dt(1-))](-), behaves more like a traditional class II/III metal based mixed-valence complex. The density functional theory (DFT) and time dependent DFT calculations provide a theoretical framework for understanding the electronic structures and the nature of excited states of the target compounds that are consistent with their spectroscopic and redox properties. Vibrational spectra of [1a](2+) and [2a](2+) were investigated as discrete species in the gas phase using infrared multiple photon dissociation (IRMPD) spectroscopy.

Sulfido and cysteine ligation changes at the molybdenum cofactor during substrate conversion by formate dehydrogenase (FDH) from Rhodobacter capsulatus

Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO(-)) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Mo-ligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH.

DFT study on the oxygen transfer mechanism in nitroethenediamine based H2-receptor antagonists using the bis-dithiolene complex as the model catalyst for N-oxide reductase enzyme

Nitroethenediamine is an important functional unit, which is present in H2-receptor antagonists. These drugs show low bioavailability due to the bacterial degradation caused by the N-oxide reductase type of enzymes present in the human colon. Quantum chemical studies have been carried out to elucidate the mechanism of metabolic degradation of nitroethenediamine in the active site of N-oxide reductase. Three different pathways have been explored for the N-oxide bond cleavage by the model system, Mo(IV) bis-dithiolene complex [Mo(OMe)(mdt)2](-), (where mdt=1,2-dimethyl-ethene-1,2-dithiolate) using B3LYP/6-311+G(d,p) and M06/6-311+G(d,p) Density Functional Theory methods. The oxygen atom transfer from the nitrogen atom of nitroethenediamine to the Mo(IV) complex, involves simultaneous weakening of the N-oxide bond and the formation of Mo-O bond through a least motion path. During this transfer, Mo center is converted from a square pyramidal geometry to a distorted octahedral geometry, to facilitate the process of oxygen atom transfer. The energy barrier for the oxygen atom transfer from the imine tautomer has been estimated to be 25.9kcal/mol however, the overall reaction has been found to be endothermic. On the other hand, oxygen transfer reaction from the nitronic acid tautomer requires 30.5kcal/mol energy leading to a highly exothermic metabolite (M-1) directly hence, this path can be considered thermodynamically favorable for this metabolite. The alternative path involving the oxygen atom transfer from the enamine tautomer requires comparatively a higher energy barrier (32.6kcal/mol) and leads to a slightly endothermic metabolite. This study established the structural and energetic details associated with the Mo(IV) bis-dithiolene complex that catalyzes the degradation of nitroethenediamine based drug molecules.

Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on monooxo Mo(IV) and bisoxo Mo(VI) bis-dithiolenes: insights into the mechanism of oxo transfer in sulfite oxidase and its relation to the mechanism of DMSO reductase

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [Mo(IV)O(bdt)2](2-) and [Mo(VI)O2(bdt)2](2-) (bdt = benzene-1,2-dithiolate(2-)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of previously studied dimethyl sulfoxide reductase (DMSOr) models. DFT calculations supported by the data are extended to evaluate the reaction coordinate for oxo transfer to a phosphite ester substrate. Three possible transition states are found with the one at lowest energy, stabilized by a P-S interaction, in good agreement with experimental kinetics data. Comparison of both oxo transfer reactions shows that in DMSOr, where the oxo is transferred from the substrate to the metal ion, the oxo transfer induces electron transfer, while in SO, where the oxo transfer is from the metal site to the substrate, the electron transfer initiates oxo transfer. This difference in reactivity is related to the difference in frontier molecular orbitals (FMO) of the metal-oxo and substrate-oxo bonds. Finally, these experimentally related calculations are extended to oxo transfer by sulfite oxidase. The presence of only one dithiolene at the enzyme active site selectively activates the equatorial oxo for transfer, and allows facile structural reorganization during turnover.

Why is the molybdenum-substituted tungsten-dependent formaldehyde ferredoxin oxidoreductase not active? A quantum chemical study

Formaldehyde ferredoxin oxidoreductase is a tungsten-dependent enzyme that catalyzes the oxidative degradation of formaldehyde to formic acid. The molybdenum ion can be incorporated into the active site to displace the tungsten ion, but is without activity. Density functional calculations have been employed to understand the incapacitation of the enzyme caused by molybdenum substitution. The calculations show that the enzyme with molybdenum (Mo-FOR) has higher redox potential than that with tungsten, which makes the formation of the Mo(VI)=O complex endothermic by 14 kcal/mol. Following our previously suggested mechanism for this enzyme, the formaldehyde substrate oxidation was also investigated for Mo-FOR using the same quantum-mechanics-only model, except for the displacement of tungsten by molybdenum. The calculations demonstrate that formaldehyde oxidation occurs via a sequential two-step mechanism. Similarly to the tungsten-catalyzed reaction, the Mo(VI)=O species performs the nucleophilic attack on the formaldehyde carbon, followed by proton transfer in concert with two-electron reduction of the metal center. The first step is rate-limiting, with a total barrier of 28.2 kcal/mol. The higher barrier is mainly due to the large energy penalty for the formation of the Mo(VI)=O species.