Polysaccharide monooxygenases (PMOs) use a type-2 copper center to activate O₂ for the selective hydroxylation of one of the two C-H bonds of glycosidic linkages. Our electron paramagnetic resonance (EPR) analysis and molecular dynamics (MD) simulations suggest the unprecedented dynamic roles of the loop containing the residue G89 (G89 loop) on the active site structure and reaction cycle of starch-active PMOs (AA₁₃ PMOs). In the Cu(II) state, the G89 loop could switch between an open and closed conformation, which is associated with the binding and dissociation of an aqueous ligand in the distal site, respectively. The conformation of the G89 loop influences the positioning of the copper center on the preferred substrate of AA₁₃ PMOs. The dissociation of the distal ligand results in the bending of the T-shaped core of the Cu(II) active site, which could help facilitate its reduction to the active Cu(I) state. In the Cu(I) state, the G89 loop is in the closed conformation with a confined copper center, which could allow for efficient O₂ binding. In addition, the G89 loop remains in the closed conformation in the Cu(II)-superoxo intermediate, which could prevent off-pathway superoxide release via exchange with the distal aqueous ligand. Finally, at the end of the reaction cycle, aqueous ligand binding to the distal site could switch the G89 loop to the open conformation and facilitate product release.

An efficient Pd/ETM (ETM = electron transfer mediator)-cocatalyzed stereoselective oxidative carbocyclization of dienallenes under aerobic oxidation conditions has been developed to afford six-membered heterocycles. The use of a bifunctional cobalt complex [Co(salophen)-HQ] as hybrid ETM gave a faster aerobic oxidation than the use of separated ETMs, indicating that intramolecular electron transfer between the hydroquinone unit and the oxidized metal macrocycle occurs. In this way, a class of important cis-1,4-disubstituted six-membered heterocycles, including dihydropyran and tetrahydropyridine derivatives were obtained in high diastereoselectivity with good functional group compatibility. The experimental and computational (DFT) studies reveal that the pendent olefin does not only act as an indispensable element for the initial allene attack involving allenic C(sp(3))-H bond cleavage, but it also induces a face-selective reaction of the olefin of the allylic group, leading to a highly diastereoselective formation of the product. Finally, the deuterium kinetic isotope effects measured suggest that the initial allenic C(sp(3))-H bond cleavage is the rate-limiting step, which was supported by DFT calculations.

A catalyst system of mononuclear manganese precursor 3 combined with potassium alkoxide served as a superior catalyst compared with our previously reported manganese homodinuclear catalyst 2 a for esterification of not only tertiary aryl amides, but also tertiary aliphatic amides. On the basis of stoichiometric reactions of 3 and potassium alkoxide salt, kinetic studies, and density functional theory (DFT) calculations, we clarified a plausible reaction mechanism in which in situ generated manganese-potassium heterodinuclear species cooperatively activates the carbonyl moiety of the amide and the OH moiety of the alcohols. We also revealed details of the reaction mechanism of our previous manganese homodinuclear system 2 a, and we found that the activation free energy (Delta G(not equal)) for the manganese-potassium heterodinuclear complex catalyzed esterification of amides is lower than that for the manganese homodinuclear system, which was consistent with the experimental results. We further applied our catalyst system to deprotect the acetyl moiety of primary and secondary amines.

Electrophilic F/CF3/SCF3 transfer reactions have recently emerged as a promising strategy to introduce fluorine substituents to organic compounds at mild conditions with high reactivity and selectivity. Several safe and stable electrophilic reagents have been introduced and have found interesting applications in synthetic chemistry. To control the reactivity and selectivity of these reactions, metal catalysts are typically used in combination with the reagents. Herein, we describe our recent efforts to elucidate the detailed mechanisms and origins of selectivity for a number of metal-catalyzed electrophilic F/CF3/SCF3 transfer reactions using density functional theory calculations. Focus is on reactions employing hypervalent fluoroiodine and nitrogen-based reagents, with zinc or rhodium as the metal catalysts. The roles of the metal ions are discussed, and some novel mechanistic ideas have emerged from these calculations that can have bearing on other reactions for introducing fluorinecontaining groups.

We have used experimental studies and DFT calculations to investigate the IrIII-catalyzed isomerization of allylic alcohols into carbonyl compounds, and the regiospecific isomerization–chlorination of allylic alcohols into α-chlorinated carbonyl compounds. The mechanism involves a hydride elimination followed by a migratory insertion step that may take place at Cβ but also at Cα with a small energy-barrier difference of 1.8 kcal mol−1. After a protonation step, calculations show that the final tautomerization can take place both at the Ir center and outside the catalytic cycle. For the isomerization–chlorination reaction, calculations show that the chlorination step takes place outside the cycle with an energy barrier much lower than that for the tautomerization to yield the saturated ketone. All the energies in the proposed mechanism are plausible, and the cycle accounts for the experimental observations.

Herein, we report the synthesis of 2,3-dihydropyrroles via an iron-catalyzed intramolecular nucleophilic cyclization of alpha-allenic sulfonamides. A highly diastereoselective variant of the reaction was also developed with the use of 1,2-disubstituted allenamides, which afforded 2,3-dihydropyrroles with diastereomeric ratios of >98:2. Insight into the mechanism was gained through a detailed DFT study, which elucidates the reaction mechanism and rationalizes the high chemoselectivity and diastereoselectivity.

A highly selective palladium-catalyzed hydroborylative carbocyclization of bisallenes to afford seven-membered rings has been established. This ring-closing coupling reaction showed good functional group compatibility with high chemo- and regioselectivity, as seven-membered ring 3 was the only product obtained. The extensive use of different linkers, including nitrogen, oxygen, malononitrile, and malonate, showed a broad substrate scope for this approach. A one-pot cascade reaction was realized by trapping the primary allylboron compound with an aldehyde, affording a diastereomerically pure alcohol and a quaternary carbon center by formation of a new C-C bond. A comprehensive mechanistic DFT investigation is also presented. The calculations suggest that the reaction proceeds via a concerted hydropalladation pathway from a Pd(0)-olefin complex rather than via a pathway involving a defined palladium hydride species. The reaction was significantly accelerated by the coordination of the pendant olefin, as well as the introduction of suitable substituents in the bridge, due to the Thorpe-Ingold effect.

Density functional theory calculations were performed to study the detailed reaction mechanisms of rhodium-catalyzed oxyaminofluorination and oxyaminotrifluoromethylthiolation of diazocarbonyl compounds with electrophilic N-F and N-SCF3-based reagents. The calculations show that the operating mechanisms for the two reactions are identical. The catalytic cycle starts with N-2 dissociation to provide a rhodium-carbene intermediate, followed by nucleophilic attack of tetrahydrofuran on the carbene and a rhodium coordination change generating a rhodium-enolate intermediate. Subsequent electrophilic attack introduces the fluorine or the SCF3 moiety, and it is followed by nucleophilic attack of the remaining amino group to yield the final product.

The reaction mechanisms of rhodium-catalyzed geminal oxyfluorination and oxytrifluoromethylation of diazo-carbonyl compounds with fluoro-benziodoxole and Togni reagents are investigated by means of density functional theory calculations. It is shown that the two reactions follow very similar mechanisms, involving N-2 dissociation to form a Rh-carbene intermediate, alcohol insertion and proton transfer resulting in a stable Rh-enol intermediate, and concerted proton transfer/electrophilic addition of the hypervalent iodine reagent to the enol. Isomerization of the hypervalent iodine takes then place before a ligand coupling affords the final product. The role of the dirhodium catalyst in facilitating the various steps of the reaction is discussed. The presented mechanisms are consistent with available experimental information, and the obtained insights allow for extension to other reactions involving hypervalent iodine reagents.