DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal-Dioxygen Complexes: Distinct Mechanisms and Reaction Rules

Dioxygenase Chemistry in Nucleophilic Aldehyde Deformylations Utilizing Dicopper O2-Derived Peroxide Complexes

The chemistry of copper-dioxygen complexes is relevant to copper enzymes in biology as well as in (ligand)Cu-O2 (or Cu2-O2) species utilized in oxidative transformations. For overall energy considerations, as applicable in chemical synthesis, it is beneficial to have an appropriate atom economy; both O-atoms of O2(g) are transferred to the product(s). However, examples of such dioxygenase-type chemistry are extremely rare or not well documented. Herein, we report on nucleophilic oxidative aldehyde deformylation reactivity by the peroxo-dicopper(II) species [Cu2II(BPMPO-)(O22-)]1+ {BPMPO-H = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} and [Cu2II(XYLO-)(O22-)]1+ (XYLO- = a BPMPO- analogue possessing bis(2-{2-pyridyl}ethyl)amine chelating arms). Their dicopper(I) precursors are dioxygenase catalysts. The O2(g)-derived peroxo-dicopper(II) intermediates react rapidly with aldehydes like 2-phenylpropionaldehyde (2-PPA) and cyclohexanecarboxaldehyde (CCA) in 2-methyltetrahydrofuran at -90 °C. Warming to room temperature (RT) followed by workup results in good yields of formate (HC(O)O-) along with ketones (acetophenone or cyclohexanone). Mechanistic investigation shows that [Cu2II(BPMPO-)(O22-)]1+ species initially reacts reversibly with the aldehydes to form detectable dicopper(II) peroxyhemiacetal intermediates, for which optical titrations provide the Keq (at -90 °C) of 73.6 × 102 M-1 (2-PPA) and 10.4 × 102 M-1 (CCA). In the reaction of [Cu2II(XYLO-)(O22-)]1+ with 2-PPA, product complexes characterized by single-crystal X-ray crystallography are the anticipated dicopper(I) complex, [Cu2I(XYLO-)]1+ plus a mixed-valent Cu(I)Cu(II)-formate species. Formate was further identified and confirmed by 1H NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) analysis. Using 18O2(g)-isotope labeling the reaction produced a high yield of 18-O incorporated acetophenone as well as formate. The overall results signify that true dioxygenase reactions have occurred, supported by a thorough mechanistic investigation.

Mechanistic insights into the metabolic pathways of vanillin: unraveling cytochrome P450 interaction mechanisms and implications for food safety

Vanillin, a key flavor compound found in vanilla beans, is widely used in the food and pharmaceutical industries for its aromatic properties and potential therapeutic benefits. This study presents a comprehensive quantum chemical analysis to elucidate the interaction mechanisms of vanillin with CYP450 enzymes, with a focus on mechanism-based inactivation. Three potential inactivation pathways were evaluated: aldehyde deformylation, methoxy dealkylation, and acetal formation. Aldehyde deformylation was identified as the most energy-efficient, involving the removal of the aldehyde group from vanillin and leading to the formation of benzyne intermediates that could react with the iron porphyrin moiety of CYP450, potentially resulting in enzyme inactivation. Further investigation into the interactions of vanillin with CYP2E1 and CYP1A2 was conducted using molecular docking and molecular dynamics (MD) simulation. The docking analyses supported the findings from DFT studies, wherein vanillin revealed high binding affinities with the studied isozymes. Moreover, vanillin occupied the main binding site in both isozymes, as evidenced by the inclusion of the heme moiety in their binding mechanisms. Employing a 100 ns molecular dynamics simulation, we scrutinized the interaction dynamics between vanillin and the two isozymes of CYP450. The assessment of various MD parameters along with interaction energies revealed that vanillin exhibited stable trajectories and substantial energy stabilization during its interaction with both CYP450 isozymes. These insights can guide future research and ensure the safe application of vanillin, especially in scenarios where it may interact with CYP450 enzymes.

A Multipurpose Metallophore and Its Copper Complexes with Diverse Catalytic Antioxidant Properties to Deal with Metal and Oxidative Stress Disorders: A Combined Experimental, Theoretical, and In Vitro Study

We report the discovery that the molecule 1-(pyridin-2-ylmethylamino)propan-2-ol (HL) can reduce oxidative stress in neuronal C6 glioma cells exposed to reactive oxygen species (O2-•, H2O2, and •OH) and metal (Cu+) stress conditions. Furthermore, its association with Cu2+ generates [Cu(HL)Cl2] (1) and [Cu(HL)2](ClO4)2 (2) complexes that also exhibit antioxidant properties. Potentiometric titration data show that HL can coordinate to Cu2+ in 1:1 and 1:2 Cu2+:ligand ratios, which was confirmed by monocrystal X-ray studies. The subsequent ultraviolet-visible, electrospray ionization mass spectrometry, and electron paramagnetic resonance experiments show that they can decompose a variety of reactive oxygen species (ROS). Kinetic studies revealed that 1 and 2 mimic the superoxide dismutase and catalase activities. Complex 1 promotes the fastest decomposition of H2O2 (kobs = 2.32 × 107 M-1 s-1), efficiently dismutases the superoxide anion (kcat = 3.08 × 107 M-1 s-1), and scavenges the hydroxyl radical (RSA50 = 25.7 × 10-6 M). Density functional theory calculations support the formation of dinuclear Cu-peroxide and mononuclear Cu-superoxide species in the reactions of [Cu(HL)Cl2] with H2O2 and O2•-, respectively. Furthermore, both 1 and 2 also reduce the oxidative stress of neuronal glioma C6 cells exposed to different ROS, including O2•- and •OH.

Mechanistic Insights into Oxidation of Benzaldehyde by Co-Peroxo Complexes

Transition metal-peroxide complexes play a crucial role as intermediates in oxidation reactions. To unravel the mechanism of benzaldehyde oxidation by the Co-peroxo complex, we conducted density functional theory (DFT) calculations. The identified competing mechanisms include nucleophilic attack and hydrogen atom transfer (HAT). The nucleophilic attack pathway involves Co-O cleavage and nucleophilic attack, leading to the formation of the benzoate product. And the HAT pathway comprises O-O cleavage and HAT, ultimately resulting in the benzoate product. DFT calculations revealed that the formation of the end-on Co-superoxo complex 2 through Co-O cleavage, starting from the side-on Co-peroxo complex 1, is much more favorable than the formation of the two-terminal oxyl-radical intermediate 3 through O-O cleavage. Compared with the nucleophilic attack of benzaldehyde by 2, the abstraction of a hydrogen atom from benzaldehyde by 3 requires higher energy. The nature of the nucleophilicity of 2 and 3 accounts for the reactivity of the reaction.

Cyclopentadienone Diphosphine Ruthenium Complex: A Designed Catalyst for the Hydrogenation of Carbon Dioxide to Methanol

The development of homogeneous metal catalysts for the efficient hydrogenation of carbon dioxide (CO2) into methanol (CH3OH) remains a significant challenge. In this study, a new cyclopentadienone diphosphine ligand (CPDDP ligand) was designed, which could coordinate with ruthenium to form a Ru-CPDDP complex to efficiently catalyze the CO2-to-methanol process using dihydrogen (H2) as the hydrogen resource based on density functional theory (DFT) mechanistic investigation. This process consists of three catalytic cycles, stage I (the hydrogenation of CO2 to HCOOH), stage II (the hydrogenation of HCOOH to HCHO), and stage III (the hydrogenation of HCHO to CH3OH). The calculated free energy barriers for the hydrogen transfer (HT) steps of stage I, stage II, and stage III are 7.5, 14.5, and 3.5 kcal/mol, respectively. The most favorable pathway of the dihydrogen activation (DA) steps of three stages to regenerate catalytic species is proposed to be the formate-assisted DA step with a free energy barrier of 10.4 kcal/mol. The calculated results indicate that the designed Ru-CPDDP and Ru-CPDDPEt complexes could catalyze hydrogenation of CO2 to CH3OH (HCM) under mild conditions and that the transition-metal owning designed CPDDP ligand framework be one kind of promising potential efficient catalysts for HCM.

Mechanistic Insights into Nitrile Activation by Cobalt(III)-Hydroperoxo Intermediates: The Influence of Ligand Basicity

The versatile applications of nitrile have led to the widespread use of nitrile activation in the synthesis of pharmacologically and industrially valuable compounds. We reported the activation of nitriles using mononuclear cobalt(III)-hydroperoxo complexes, [CoIII(Me3-TPADP)(O2H)(RCN)]2+ [R = Me (2) and Ph (2Ph)], to form cobalt(III)-peroxyimidato complexes, [CoIII(Me3-TPADP)(R-C(=NH)O2)]2+ [R = Me (3) and Ph (3Ph)]. The independence of the rate on the nitrile concentration and the positive Hammett value of 3.2(2) indicated that the reactions occur via an intramolecular nucleophilic attack of the hydroperoxide ligand to the coordinated nitrile carbon atom. In contrast, the previously reported cobalt(III)-hydroperoxo complex, [CoIII(TBDAP)(O2H)(CH3CN)]2+ (2TBDAP), exhibited the deficiency of reactivity toward nitrile. The comparison of pKa values and redox potentials of 2 and 2TBDAP showed that Me3-TPADP had a stronger ligand field strength than that of TBDAP. The density functional theory calculations for 2 and 2TBDAP support that the strengthened ligand field in 2 is mainly due to the replacement of two tert-butyl amine donors in TBDAP with methyl groups in Me3-TPADP, resulting in the compression of the Co-Nax bond lengths. These results provide mechanistic evidence of nitrile activation by the cobalt(III)-hydroperoxo complex and indicate that the basicity dependent on the ligand framework contributes to the ability of nitrile activation.

Recent advances in computational studies on Cu-catalyzed aerobic reactions: cooperation of copper catalysts and dioxygen

O2, one of the ideal oxidants, suffers from low solubility, low oxidizability, low selectivity and a triplet ground state when applied in organic synthesis. Biomimetic copper catalysis has been demonstrated to be a powerful method for activating and transforming O2 to conduct aerobic reactions for a long time. On the other hand, the structures of Cu-O2 complexes are complex with diverse downstream reactions, whereas active copper intermediates were rarely identified by experimental methods, making the mechanisms of many Cu-catalyzed aerobic reactions far from clear. In this context, computational studies emerged as an effective alternative to mechanistic studies on Cu-catalyzed aerobic reactions. This review introduces the relevant computational studies since 2012, focusing on showing the cooperation of copper catalysts and O2 in dehydrogenation, oxygenation and coupling reactions.

Quantum DFT methods to explore the interaction of 1-Adamantylamine with pristine, and P, As, Al, and Ga doped BN nanotubes

Nanostructures, nowadays, found growing applications in different scientific and industrial areas. Nano-coins, nanosheets, and nanotubes are used in medical applications as sensors or drug delivery substances. The aim of this study is to explore the adsorption of 1-Adamantylamine drug on the pristine armchair boron nitride nanotubes (BNNTs) with BNNT(5,5), BNNT(6,6), and BNNT(7,7) chirality along with the P, As, Al and Ga-doped BNNTs, using the quantum mechanical density functional methods. Considering the fact that dispersion effects are important in the case of weak Van der Waals interactions, computations have been done using B3LYP hybrid functional with the implementation of the D3(BJ) empirical dispersion correction methods. Quantum theory of atoms in molecules, natural bonding orbitals, and Kohn-Sham orbitals were used to investigate the nature and type of the adsorption process. The results showed that, while the adsorption of 1-Adamantylamine on the outer surface of pristine BNNT is physical in nature, doping can improve the ability of detracted BN to adsorb the drug through chemical bonds. Also, it was found that, by increasing the radius of the BNNT the adsorption energy was decreased. In conclusion, results of the present work suggest that, Ga doped nanotube, due the chemisorption, is not an ideal nanotube in drug delivery of 1-Adamantylamine drug, whereas, the other studied cases physiosorbed the drug, and may not have serious problem in release of the 1-Adamantylamine drug.