Computational Mechanistic Study Research Articles

Copper-catalysed electrophilic carboamination of terminal alkynes with benzyne looked at through the computational lens.

A detailed computational mechanistic study of the copper-catalysed three-component-type electrophilic carboamination of terminal alkynes with benzyne and an archetypal O-benzoylhydroxylamine electrophile is presented. Probing various plausible pathways for relevant elementary steps and scrutinising performance degradation pathways, with the aid of a reliable computational protocol applied to a realistic catalyst model combined with kinetic analysis, identified the pathways preferably traversed in productive catalysis. It entails rapid alkynylcupration of in situ generated benzyne to deliver the arylcopper nucleophile that undergoes amination with the O-benzoylhydroxylamine electrophile to afford copper benzoate. Umpolung-enabled electrophilic amination favours a multistep SN2-type oxidative addition/N-C bond-forming reductive elimination sequence involving a short-lived formal {P^P}CuIII carboxylate amido aryl intermediate. SN2-type displacement of the benzoate leaving group at the arylcopper nucleophile, which represents the catalyst resting state, is predicted to be the turnover limiting step. Alkynolysis transforms copper benzoate back to catalytically competent alkynylcopper. The computational probe of a wider range of substrates reveals that only severely ring-strained C6-arynes, C6-cycloalkynes and electron-deficient cyclopropenes featuring a highly reactive C≡C linkage could replace benzyne. Moreover, strict control of stationary benzyne concentration is indispensable for electrophilic carboamination to ever become achievable.

A New Reaction Mode of 3-Halooxindoles: Acting as C-C-O Three-Atom Components for (3+3) Cycloaddition to Access Indolenine-Fused 2H-1,4-Oxathiines.

Herein, we report an unprecedented implementation of 3-halooxindoles as C-C-O three-atom components for (3+3) cycloaddition with pyridinium 1,4-zwitterionic thiolates, affording structurally diverse indolenine-fused 2H-1,4-oxathiines in moderate to high yields. A combined experimental and computational mechanistic study suggests that the reaction proceeds through addition of a S conjugate to the o-azaxylylene intermediate, followed by O-Michael addition and a sequential retro-Michael addition/pyridine extrusion pathway.

Nickel‐Catalyzed Cycloisomerization of 1,5‐Allenynes

AbstractWe report the Ni‐catalyzed cycloisomerization of 1,5‐allenynes. Substrates containing terminal alkynes afford cyclopentene derivatives, whereas internal alkynes lead to the formation of two consecutive C−C bonds to give fused 5–5 bicyclic compounds. The reaction shows a wide scope. Experimental and computational mechanistic studies suggest a Ni(0)−Ni(II) catalytic cycle. The reaction starts with an oxidative cyclometallation followed by a β‐hydrogen elimination. The trans arrangement of alkenyl and hydride ligands is key to allow formation of the second carbocycle.

Copper-Catalyzed C-H (Phenylsulfonyl)difluoromethylation of Acrylamides: Scope, Mechanism, and Critical Role of Additives.

Herein, we report the Cu-complex catalyzed, native functional group-assisted, and TFA/NMF additives promoted (phenylsulfonyl)difluoromethylation of vinylic C(sp2 )-H bond of acrylamides. Using our in-home designed reagent, this reaction enables the construction of the C(sp2 )-CF2 SO2 Ph bond from simple C-H bond activation by copper catalysis under mild reaction conditions with total Z-selectivity. The versatility of utilized fluorinated group was illustrated by its conversion into value-added CF2 moieties as well as the remarkable =CHF residue. The performed experimental and computational mechanistic studies enabled to identify the true nature of active catalyst and substrate, as well as establish critical roles of TFA and NMF additives. In this reaction, the TFA acts as a promoter of the much-needed CuII /CuII →CuIII /CuI disproportionation, while the NMF facilitates the following ligand exchange and C-C coupling processes. We ruled out the generation of radical intermediates and established the C-H activation to be irreversible and the rate-determining step of the entire process.

Relayed Heteroatom Group Transfer: A Structural Reorganization between Bisthioester and Triaminophosphine to α,α-Disulfenylamide.

Simultaneous multiple displacements of organic molecules can lead to a large structural reconstruction with increased complexity that would be difficult to access otherwise. Whereas double displacement such as olefin metathesis is well-established, higher-order versions remain much more challenging, because of their intrinsic thermodynamic disadvantages. Here, we describe a newly discovered relayed heteroatom group transfer process between bisthioesters and triaminophosphines as an unusual example of a formal triple displacement. Through the oxygen/nitrogen exchange between the two simple starting materials, in addition to the 1,2-sulfur migration of a putative carbene intermediate, an organized relocation of the O/S/N groups proceeded to give a variety of α,α-disulfenylamides with excellent efficiency under ambient conditions. The experimental and computational mechanistic studies revealed the sequence of the relayed group shifts via an α,α-disulfenyl phosphonium enolate intermediate as well as the dual role of triaminophosphine as both an oxygen acceptor and a nitrogen donor.

Highly Enantioselective 6π Photoelectrocyclizations Engineered by Hydrogen Bonding.

Photochemical electrocyclization reactions are valued for both their ability to produce structurally complex molecules and their central role in elucidating fundamental mechanistic principles of photochemistry. We present herein a highly enantioselective 6π photoelectrocyclization catalyzed by a chiral Ir(III) photosensitizer. This transformation was successfully realized by engineering a strong hydrogen-bonding interaction between a pyrazole moiety on the catalyst and a basic imidazolyl ketone on the substrate. To shed light on the origin of stereoinduction, we conducted a comprehensive investigation combining experimental and computational mechanistic studies. Results from density functional theory calculations underscore the crucial role played by the prochirality and the torquoselectivity in the electrocyclization process as well as the steric demand in the subsequent [1,4]-H shift step. Our findings not only offer valuable guidance for developing chiral photocatalysts but also serve as a significant reference for achieving high levels of enantioselectivity in the 6π photoelectrocyclization reaction.

A Formal Exchange Reaction between Ketones and Vinyl Ethers with Solid Catalysts

AbstractThe formal exchange of functional groups in internal positions of two different molecules is of interest in synthetic chemistry, as a simple retrosynthetic strategy. Here the formal exchange reaction between internal α-methylene ketones and vinyl ethers, retaining the original C–O bonds is presented. This process offers a new route for the synthesis of vinyl ethers in one step from ketones, including 1,3-diketones, under mild reaction conditions. Besides, the reaction is catalyzed by reusable cheap solids and can be carried out in flow for 20 days without signs of catalyst depletion. Combined experimental and computational mechanistic studies unveil the key role of carbonyl–enol equilibria.

“Stepwise or concerted or a hybrid mechanism for berberine bridge enzyme?”: A computational mechanistic study by QM-MM and QM methods

Berberine bridge enzyme (BBE) is a plant-based amine oxidase that catalyzes conversion of (S)-reticuline into (S)-scoulerine using flavin as cofactor in a stereospecific way in an alkaloid biosynthesis pathway. Based on the active site enzyme variants, a concerted mechanism was proposed involving hydride transfer, proton transfer, and substrate cyclization processes in a single step. In this mechanism, Glu417 residue acts as the catalytic base which deprotonates the phenolic proton of the substrate while a hydride ion transfers from the substrate to flavin and the substrate cyclizes. However, based on solvent and substrate deuterium kinetic isotope effect studies, it was proposed that the oxidation process occurs in a stepwise fashion in which a hydride ion transfer from substrate to flavin first, then cyclization of the substrate occurs together with the proton transfer process. In this study, we formulated computational models to elucidate the oxidation mechanism of (S)-reticuline into (S)-scoulerine using the crystal structure of enzyme complexed with (S)-reticuline. Both QM and QM-MM calculations revealed that a hybrid of concerted and stepwise mechanisms might be operative during the catalysis. It was found that a concerted hydride-proton transfer processes occurs forming a reactive intermediate which subsequently cyclize without an energy barrier as a decoupled step.

Asymmetric formal C–C bond insertion into aldehydes via copper-catalyzed diyne cyclization

The formal C–C bond insertion into aldehydes is an attractive methodology for the assembly of homologated carbonyl compounds. However, the homologation of aldehydes has been limited to diazo approach and the enantioselective reaction was rarely developed. Herein, we report an asymmetric formal C–C bond insertion into aldehydes through diyne cyclization strategy. In the presence of Cu(I)/SaBOX catalyst, this method leads to the efficient construction of versatile axially chiral naphthylpyrroles in moderate to excellent yields with good to excellent enantioselectivities. This protocol represents a rare example of asymmetric formal C–C bond insertion into aldehydes using non-diazo approach. The combined experimental and computational mechanistic studies reveal the reaction mechanism, origin of regioselectivity and stereoselectivity. Notably, the chiral phosphine ligand derived from synthesized axially chiral skeleton was proven to be applicable to asymmetric catalysis.

Effect of ligand coordination on the mechanism and regioselectivity of cobalt-catalyzed hydroboration/cyclization of 1,6-enynes

The 3d transition metal-catalyzed cyclization of enynes provides a sustainable and useful strategy for the construction of cyclic compounds. Controlling the regioselectivity is a central challenge for the hydrofunctionalization of multiply unsaturated substrates such as 1,6-enynes. Herein, we report a computational mechanistic study of the cobalt-catalyzed hydroboration/cyclization of 1,6-enynes in the presence of three representative ligands including bidentate nitrogen ligand and phosphine ligand as well as tridentate nitrogen-based ligand. A detailed analysis is carried out on the ligand-substrate interactions to understand the effect of ligand coordination on the mechanism and regioselectivity. Our results indicate that although the initial catalyst-substrate complexes adopt the pseudo-trigonal bipyramidal geometries for the two nitrogen-based ligands, there is a remarkable difference in the free energy surfaces. The steric repulsions and hydrogen bonding interactions between the substrate and the ligand play important roles in regulating the competing migration insertion. Energy decomposition analyses are further performed for the subsequent σ-bond metathesis to illustrate the impacts of steric and electronic effects on the regioselectivity and the electrostatics and orbital interactions are disclosed to be the dominant factors. This work provides a deeper understanding of the specific structural and electronic properties of the cobalt complexes and their potential influences on the reactivity and selectivity.

Origin of Enantio- and Chemoselectivity in the Synthesis of Spirocycles via Palladium/Xu-Phos-Catalyzed Cascade Heck/Remote C(sp2)-H Alkylation: A Computational Mechanistic Study.

Density functional theory (DFT) calculations were performed to study the mechanism and factors affecting the enantio-, regio-, and chemoselectivities in the palladium/Xu-Phos-catalyzed cascade Heck/remote C(sp2)-H alkylation reaction. The active catalyst is found to be able to sustain coordination with P and S atoms and can adapt its coordination mode to accommodate the significant steric hindrance between the ligand and substrate, unlike previous findings that showed coordination with P and O atoms. The reaction is established to occur in sequence through the oxidative addition of the aryl iodide to Pd(0), intramolecular alkene insertion, C(sp2)-H bond activation, and C(sp2)-C(sp3) bond reductive elimination. The C(sp2)-C(sp3) bond reductive elimination is identified as the rate-determining step, and the intramolecular alkene insertion as the enantioselectivity-determining step. The high enantioselectivity originates from the stronger electronic interaction between the catalyst and substrate; the exclusive 5-exo-regioselectivity is due to the stronger nucleophilicity of the terminal alkene carbon atom, and the chemoselectivity of C-H activation over carboiodination is driven by thermodynamics.

Hydrogenation of CO2 by a Bifunctional PC(sp3 )P Iridium(III) Pincer Complex Equipped with Tertiary Amine as a Functional Group.

Reversible hydrogen storage in the form of stable and mostly harmless chemical substances such as formic acid (FA) is a cornerstone of a fossil fuels-free economy. In the past, we have reported a primary amine-functionalized bifunctional iridium(III)-PC(sp3 )P pincer complex as a mild and chemoselective catalyst for the additive-free decomposition of neat formic acid. In this manuscript, we report on the successful application of a redesigned complex bearing tertiary amine functionality as a catalyst for mild hydrogenation of CO2 to formic acid. The catalyst demonstrates TON up to 6×104 and TOF up to 1.7×104 h-1 . In addition to the practical value of the catalyst, experimental and computational mechanistic studies provide the rationale for the design of improved next-generation catalysts.

Modular synthesis of 1,2-azaborines via ring-opening BN-isostere benzannulation.

1,2-Azaborines represent a unique class of benzene isosteres that have attracted interest for developing pharmaceuticals with better potency and bioavailability. However, it remains a long-standing challenge to prepare monocyclic 1,2-azaborines, particularly multi-substituted ones, in an efficient and modular manner. Here we report a straightforward method to directly access diverse multi-substituted 1,2-azaborines from readily available cyclopropyl imines/ketones and dibromoboranes under relatively mild conditions. The reaction is scalable, shows a broad substrate scope, and tolerates a range of functional groups. The utility of this method is demonstrated in the concise syntheses of BN isosteres of a PD-1/PD-L1 inhibitor and pyrethroid insecticide, bifenthrin. Combined experimental and computational mechanistic studies suggest that the reaction pathway involves boron-mediated cyclopropane ring-opening and base-mediated elimination, followed by an unusual low-barrier 6π-electrocyclization accelerated by the BN/CC isomerism. This method is anticipated to find applications for the synthesis of BN-isostere analogues in medicinal chemistry, and the mechanistic insights gained here may guide developing other boron-mediated electrocyclizations.

Palladium/Norbornene-Catalyzed Direct Vicinal Di-Carbo-Functionalization of Indoles: Reaction Development and Mechanistic Study.

Methods that can simultaneously install multiple different functional groups to heteroarenes via C-H functionalizations are valuable for complex molecule synthesis, which, however, remain challenging to realize. Here we report the development of vicinal di-carbo-functionalization of indoles in a site- and regioselective manner, enabled by the palladium/norbornene (Pd/NBE) cooperative catalysis. The reaction is initiated by the Pd(II)-mediated C3-metalation and specifically promoted by the C1-substituted NBEs. The mild, scalable, and robust reaction conditions allow for a good substrate scope and excellent functional group tolerance. The resulting C2-arylated C3-alkenylated indoles can be converted to diverse synthetically useful scaffolds. The combined experimental and computational mechanistic study reveals the unique role of the C1-substituted NBE in accelerating the turnover-limiting oxidative addition step.

Palladium/Norbornene‐Catalyzed Direct Vicinal Di‐Carbo‐Functionalization of Indoles: Reaction Development and Mechanistic Study

AbstractMethods that can simultaneously install multiple different functional groups to heteroarenes via C−H functionalizations are valuable for complex molecule synthesis, which, however, remain challenging to realize. Here we report the development of vicinal di‐carbo‐functionalization of indoles in a site‐ and regioselective manner, enabled by the palladium/norbornene (Pd/NBE) cooperative catalysis. The reaction is initiated by the Pd(II)‐mediated C3‐metalation and specifically promoted by the C1‐substituted NBEs. The mild, scalable, and robust reaction conditions allow for a good substrate scope and excellent functional group tolerance. The resulting C2‐arylated C3‐alkenylated indoles can be converted to diverse synthetically useful scaffolds. The combined experimental and computational mechanistic study reveals the unique role of the C1‐substituted NBE in accelerating the turnover‐limiting oxidative addition step.

Development of an Environment-Friendly and Electrochemical Method for the Synthesis of an Oxadiazole Drug-Scaffold That Targets Poly(ADP-Ribose)Polymerase in Human Breast Cancer Cells

The development of environment-friendly new Poly-adenosine diphosphate (ADP)-ribose Polymerase (PARP) inhibitors are highly essential because of their involvement in the survival of cancer cells. Therefore, a library of indazolyl-substituted-1,3,4-oxadiazoles known to inhibit PARP in cancer cells was synthesized by a green protocol. Furthermore, the cytotoxic effects of these compounds were evaluated in human MCF-7 breast cancer (BC) cells, which revealed that the compound 2-(3-bromo-4-nitrophenyl)-5-(1-methyl-1H-indazol-3-yl)-1,3,4-oxadiazole (8) inhibited viability with an IC50 value of 1.57 µM. Since the oxadiazole structure was extensively used in medicinal chemistry applications, the reported environment-friendly protocol was superior to the conventional method. Further, computational mechanistic studies revealed that the oxadiazole ring formation occurred spontaneously when compared to the conventional method. Additionally, the in silico bioinformatic studies of oxadiazole binding towards PARP1 showed that compound 8 could bind to PARP1 with higher binding energy (BE) of −7.29 kcal/mol when compound to compound 5s (BE = −7.17 kcal/mol), a known PARP cleavage oxadiazole structure (2-(3,4-Dimethoxybenzyl)-5-(3-(2-fluoro-3-methylpyridin-4-yl)phenyl)-1,3,4-oxadiazole) indicative of the improvement in the optimization process. In conclusion, a newer indazolyl-oxadiazole compound is reported, which could serve as a lead in developing PARP inhibitors in BC cells.

Enantiospecific Synthesis of Aniline-Derived Sulfonimidamides.

Reaction of sulfonimidoyl fluorides with anilines and Ca(NTf2)2 results in the formation of chiral sulfonimidamides. The reaction proceeds with inversion of the stereocenter at a sulfur atom. Enantiospecificity of the reaction was observed for all studied non-heterocyclic anilines. Combined experimental and computational mechanistic studies highlight chelate-type coordination of the sulfonimidoyl group to Ca(NTf2)2 and the formation of a SN2-like transition state, in which leaving F- coordinates with the Ca2+ ion.

Regio- and Enantioselective Catalytic δ-C-H Amidation of Dioxazolones Enabled by Open-Shell Copper-Nitrenoid Transfer.

Controlling regio- and enantioselectivity in C-H functionalization reactions is of paramount importance due to their versatile synthetic utilities. Herein, we describe a new approach for the asymmetric δ-C(sp3)-H amidation catalysis of dioxazolones using a Cu(I) precursor with a chiral bisoxazoline ligand to access six-membered lactams with high to excellent regio- and enantioselectivity (up to >19:1 rr and >99:1 er). Combined experimental and computational mechanistic studies unveiled that the open-shell character of the postulated Cu-nitrenoids enables the regioselective hydrogen atom abstraction and subsequent enantio-determining radical rebound of the resulting carbon radical intermediates. The synthetic utility of this asymmetric cyclization was demonstrated in the diastereoselective introduction of additional functional groups into the chiral δ-lactam skeleton as well as in the rapid access to biorelevant azacyclic compounds.

Catalytic Asymmetric Hydrogen Atom Transfer: Enantioselective Hydroamination of Alkenes.

We report a highly enantioselective radical-based hydroamination of enol esters with sulfonamides jointly catalyzed by an Ir photocatalyst, Brønsted base, and tetrapeptide thiol. This method is demonstrated for the formation of 23 protected β-amino-alcohol products, achieving selectivities up to 97:3 er. The stereochemistry of the product is set through selective hydrogen atom transfer from the chiral thiol catalyst to a prochiral C-centered radical. Structure-selectivity relationships derived from structural variation of both the peptide catalyst and olefin substrate provide key insights into the development of an optimal catalyst. Experimental and computational mechanistic studies indicate that hydrogen-bonding, π-π stacking, and London dispersion interactions are contributing factors for substrate recognition and enantioinduction. These findings further the development of radical-based asymmetric catalysis and contribute to the understanding of the noncovalent interactions relevant to such transformations.

Oxidative Dehydrogenation of Propane on Boron Phosphate: A Computational Mechanistic Study

Oxidative Dehydrogenation of Propane on Boron Phosphate: A Computational Mechanistic Study