Cofactor-Free Dioxygenases-Catalyzed Reaction Pathway via Proton-Coupled Electron Transfer

Mechanisms of C(sp3)-H Functionalization of Acetonitrile or Acetone with Alkynes: A DFT Investigation

The mechanisms for the C(sp3)-H activation and addition reactions between acetonitrile (or acetone) and alkynes have been investigated with the M06-2X-D3/ma-def2-TZVP method and basis set. The SMD (solvation model based on solute electron density) model was applied to simulate the solvent effect. In the first and second reactions, 2-phenylbut-3-yn-2-ol reacted with acetonitrile and acetone, respectively. First, the C(sp3)-H activations of acetonitrile and acetone could be achieved by PhCOO• and t-BuO• radicals. Then, addition reactions converted 2-phenylbut-3-yn-2-ol into final products P1 and P2. Gibbs free energy surfaces of these two reactions suggest that blue lines would be the favorable paths with lower Gibbs energy barriers, and the terminal C atom of the C≡C bond is the best reactive site. Moreover, the analysis of the IRI (Interaction Region Indicator) reveals the Z- and E-configuration transformations. While in the third and fourth reactions, methyl(2-(phenylethynyl)phenyl)sulfane has interactions with acetonitrile and acetone via some paths, respectively. Gibbs free energy profiles show that the C10 atom, rather than the C11 atom, has priority, and the blue lines are favorable. Furthermore, the action mode of Na2HPO4 could reduce the energy barrier and benefit the reaction. vdW (van der Waals) interactions play an important role in the choice for the reactive site. In the fifth (or sixth) reaction, it happened between 1-(2-(methylthio)phenyl)-3-phenylprop-2-yn-1-one and acetontrile (or acetone) to yield the final product P5 (or P6). The computational results uncovered the blue line is the best path, and the choice for the reactive site depends on the vdW interactions, which reveals the origin of selectivity. In addition, the investigation for the byproducts have been carried out, and these can explain the reason that only the main product is produced. Both of those can agree with the experimental results. The localized orbital locator (LOL) isosurfaces, Laplacian bond order (LBO), electron density of the bond critical point (ρBCP), electron spin density isosurface graphs, and IRI graphs can be used to analyze the structure and reveal the reaction substances.

Unraveling proton-coupled electron transfer in cofactor-free oxidase- and oxygenase-catalyzed oxygen activation: a theoretical view

Oxygen plays a crucial role in the metabolic processes of non-anaerobic organisms. However, a detailed understanding of how triplet oxygen participates in the enzymatic oxidation of organic compounds involved in life processes is still lacking. It is noteworthy that recent studies have found that cofactor-free oxidase- and oxygenase-catalyzed oxygen activation occurs through proton-coupled electron transfer (PCET), which is significantly different from the previously proposed single electron transfer (SET) mechanism. Herein, we summarize the recent advances in the general mechanism of catalytic activation reactions of triplet oxygen by these enzymes. We believe that this review not only helps in providing a deep understanding of the processes involved in oxygen metabolism in organisms but also provides valuable theoretical reference data for designing more efficient enzyme mutants for treating diseases and handling environmental pollution in the future.

Alkali metal hydroxide-catalyzed mechanisms of Csp-H silylation of alkynes: a DFT investigation

Mechanisms for the Csp-H silylation between prop-2-yn-1-ylcyclohexane and triethylsilane, catalyzed by MOH/MH (M = Na or K), were investigated at the M06-L-D3/ma-def2-TZVP level. The SMD model was applied to simulate the solvent effect of 1,2-dimethoxyethane (DME). Computational results suggested that the Csp-H activation of prop-2-yn-1-ylcyclohexane could be achieved by MOH to generate R-CC-M compounds, which continued to react with triethylsilane to yield the final product: (3-cyclohexylprop-1-yn-1-yl) triethylsilane. Moreover, analysis of the Gibbs free energy surface of the three reactions suggested that a path with the participation of LiOH had the highest energy barrier, which was consistent with experimental results showing that only a small amount of product had been formed. The obtained KH could interact readily with the H2O molecule with a much lower energy barrier (0.6 kcal mol-1) than that using the path with prop-2-yn-1-ylcyclohexane. Furthermore, compared to MOH, MH could catalyze the reaction with lower energy barriers, and the reactions became exothermic, thereby benefiting the reaction. Finally, the mechanism for obtaining the byproduct (prop-1-yn-1-ylcyclohexane) was posited: it had a higher energy barrier than the path to yield the main product. Frontier orbital, noncovalent interactions (NCI), Fukui function and dual descriptor analyses could be used to analyze the structure and reveal the reaction substances.

Origin of Chemoselectivity of Halohydrin Dehalogenase-Catalyzed Epoxide Ring-Opening Reactions

By performing molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and QM cluster calculations, the origin of chemoselectivity of halohydrin dehalogenase (HHDH)-catalyzed ring-opening reactions of epoxide with the nucleophilic reagent NO2- has been explored. Four possible chemoselective pathways were considered, and the computed results indicate that the pathway associated with the nucleophilic attack on the Cα position of epoxide by NO2- is most energetically favorable and has an energy barrier of 12.9 kcal/mol, which is close to 14.1 kcal/mol derived from experimental kinetic data. A hydrogen bonding network formed by residues Ser140, Tyr153, and Arg157 can strengthen the electrophilicity of the active site of the epoxide substrate to affect chemoselectivity. To predict the energy barrier trends of the chemoselective transition states, multiple analyses including distortion analysis and electrophilic Parr function (Pk+) analysis were carried out with or without an enzyme environment. The obtained insights should be valuable for the rational design of enzyme-catalyzed and biomimetic organocatalytic epoxide ring-opening reactions with special chemoselectivity.

DFT investigation of the DDQ-catalytic mechanism for constructing C-O bonds

In this study, we investigated the photo-catalytic mechanisms for the construction of C-O bonds from arenes (benzene, 2',6'-dimethyl-[1,1'-biphenyl]-2-carboxylic acid, or 2,4-dichloro-1-fluorobenzene), catalyzed by 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ). All the structures for the Gibbs free surfaces were calculated at the M06-2X-D3/ma-def2-SVP level in the SMD solvent model. Also, TDDFT calculations of DDQ were performed at the PBE1PBE-D3/ma-def2-SVP level in the SMD solvent model. The computational results indicated that DDQ, serving as a photo-catalyst, would be excited under visible light of 450 nm, aligning well with experimental observations as reflected in the UV-vis spectrum. Gibbs free energy surface analyses of the three reactions suggested that the path involving 3DDQ* activating the reactant (-COOH, H2O, or CH3OH) is favorable. Additionally, the role of O2 was investigated, revealing that it could facilitate the recycling of DDQ by lowering the energy barrier for the conversion of the DDQH˙ radical (not DDQH2) into DDQ. The use of ρhole and ρele can reveal the photo-catalytic reaction and charge transfer processes, while localized orbital locator isosurfaces and electron spin density isosurface graphs were employed to analyze structures and elucidate the single electron distribution. These computational results offer valuable insights into the studied interactions and related processes, shedding light on the mechanisms governing C-O bond formation from arenes catalyzed by DDQ.

Mechanism and Origin of Stereoselectivity for the NHC-Catalyzed Desymmetrization Reaction for the Synthesis of Axially Chiral Biaryl Aldehydes

Organocatalytic desymmetrization reaction is a powerful tool for constructing axial chirality, but the theoretical study on the origin of stereoselectivity still lags behind even now. In this work, the N-heterocyclic carbene (NHC)-catalyzed desymmetrization reaction of biaryl frameworks for the synthesis of axially chiral aldehydes has been selected and theoretically investigated by using density functional theory (DFT). The fundamental pathway involves several steps, i.e., desymmetrization, formation of Breslow oxidation, esterification, and NHC regeneration. The desymmetrization and formation of Breslow processes have been identified as stereoselectivity-determining and rate-determining steps. Further weak interaction analyses proved that the C-H···O hydrogen bond and C-H···π interactions are responsible for the stability of the key stereoselective desymmetrization transition states. This research contributes to understanding the nature of NHC-catalyzed desymmetrization reactions for the synthesis of axially chiral compounds.

Chiral Oxazaborolidinium Ion (COBI)-Catalyzed Reaction of Aldimine with Tributyltin Cyanide: Mechanism and Origin of Stereoselectivity

By conducting density functional theory (DFT) calculations, the detailed reaction mechanisms of aldimines with tributyltin cyanide under the catalytic influence of chiral oxazaborolidinium ion (COBI) have been uncovered. Three potential reaction pathways were examined, and two stereoselective routes were determined for the most energetically favorable mechanism. In the primary route, a proton is transferred from the COBI catalyst to the aldimine substrate, which is then followed by the C-C bond formation to produce the final product. Subsequently, NBO analyses of the stereoselectivity-determining transition states were conducted to identify the crucial role of hydrogen bond interactions in controlling stereoselectivity. These computed findings should prove invaluable in comprehending the detailed mechanisms and underlying origins of stereoselectivity for COBI-mediated reactions of this type.