Mechanism Of Stereoselectivity Research Articles

Mechanism and Origin of Stereoselectivity of N-Heterocyclic Carbene (NHC)-Catalyzed Transformation Reaction of Benzaldehyde with o-QDM as Key Intermediate: A DFT Study.

N-heterocyclic carbene (NHC)-bound ortho-quinodimethane, served as a nucleophile, has occupied an important position for constructing various all-carbon or heterocyclic compounds and attracted increasing attention for the functionalization of benzylic carbon of aromatic aldehydes, whereas the mechanistic studies on the generation and transformations of dienolate intermediate are rare. In the present study, the mechanism of activation/transformation of aldehyde catalyzed by NHC was theoretically studied using the density functional theory (DFT) method. Based on the calculations, the nucleophilic addition process is the stereoselectivity-determining step with RS-configured product being generated preferentially. Furthermore, non-covalent index (NCI) and atoms-in-molecules (AIM) analyses have been performed to disclose the origin of stereoselectivity, by which the larger number and stronger weak interactions are the key for stabilizing the low-energy transition state and thus leading to the stereoselectivity inducing.

Computational Exploration of 1,2-Carboamine Carbonylation Catalyzed by Nickel.

Nickel-catalyzed carbonylation of alkenes is a stereoselective and regioselective method for the synthesis of amide compounds. Theoretical predictions with density functional theory calculations revealed the mechanism and origin of stereoselectivity and regioselectivity for the nickel-catalyzed carbonylation of norbornene. The carbonylation reaction proceeds through oxidative addition, migration insertion of alkenes, and subsequent reduction elimination to afford cis-carbonylation product. The C-N bond activation of amides is unfavorable because the oxidative addition ability of the C-C bond is stronger than that of the C-N bond. The determining step of stereoselectivity is the migratory insertion of the strained olefin. The structural analysis shows that steroselectivity is controlled by the steric hindrance of methyl groups to olefins and substituents to IMes in ligands.

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.

Disclosing the mechanism and origin of stereoselectivity of the NHC-catalyzed transformation reaction of enals with acyl azolium as a key intermediate

The reaction mechanism and origin of stereoselectivity of the NHC-catalyzed transformation of an acyl azolium intermediate have been theoretically investigated using the DFT method.

Elucidating the mechanism and origin of stereoselectivity in the activation/transformation of an acetic ester catalyzed by an N-heterocyclic carbene.

The activation of an ester by N-heterocyclic carbene (NHC) organocatalysis is an efficient and important approach for generating an NHC-bound enolate intermediate, an important active intermediate in the transformation of carbonyl compounds. Herein, we perform a theoretical study on the NHC-catalyzed activation and transformation reaction of an acetic ester in which the NHC-bound enolate intermediate is a key intermediate. Multiple activation and transformation pathways are proposed and analyzed to identify an energetically favorable pathway. The use of different substrates for the reaction is considered. When a chalcone substrate is used, [4+2] cycloaddition between the enolate intermediate and the chalcone is identified to be both the rate- and stereoselectivity-determining step for the reaction, with the R-configured product being generated as the major isomer. Noncovalent interaction (NCI) and atoms-in-molecules (AIM) analyses are performed to identify the origin of the stereoselectivity of the reaction, and a local reactivity analysis is conducted to explore substrate and catalyst effects on the reaction.

Theoretical investigation of a chiral Brønsted acid (CBA)-catalyzed isomerization reaction of BCB: mechanism and origin of stereoselectivity

The mechanism, role of catalyst and origin of stereoselectivity for the isomerization reaction of BCB catalyzed by a chiral Brønsted acid (CBA) have been revealed in detail using DFT calculations.

Reaction Mechanism and Origin of Stereoselectivity in the Fluorination and Trifluoromethylthiolation of 2‐Bromoamides with AgF and AgSCF3

AbstractReactions of chiral α‐bromoamides with AgF readily gave the corresponding 2‐fluorinated amide with retention of configuration. The mechanism and origin of the stereochemistry were rationalized using density functional theory calculations, which suggested a double‐inversion pathway via the formation of an aziridinone intermediate. The computed reaction pathway is consistent with the experimental results. In addition, the stereochemistry in base‐promoted trifluoromethylthiolation of α‐bromoamides using AgSCF3 was examined. The experimental results showed that the reaction proceeds through the generation of a neutral aziridinone intermediate, following the attack of a trifluoromethylthiolate anion at C‐3. The stereoselectivity of C‐3 attack on the aziridinone depended on the steric bulk of substitutes on the α‐position and nitrogen of the amide. The study results show the potential utility of AgF and AgSCF3 in the synthesis of chiral 2‐functionalized amide derivatives and provide mechanistic insights for nucleophilic substitution of 2‐bromoamides.

Theoretical study of an N-heterocyclic carbene-catalyzed annulation reaction between an enal and a β-silyl enone: Mechanism and origin of stereoselectivity

In this study, the mechanism and origin of the stereoselectivity of an N-heterocyclic carbene (NHC)-catalyzed transformation reaction between an enal and a β-silyl enone are systematically investigated using density functional theory (DFT) at the M06-2X level. Multiple pathways are proposed and studied to identify the most energetically favorable mechanism for the reaction. The calculation results show that the most energetically favorable pathway comprises the following processes: nucleophilic addition of NHC to the Si-face of the enal to form a zwitterionic intermediate, two sequential CsHCO3-assisted intramolecular proton shifts to produce an enolate intermediate, Michael-type addition of the enolate intermediate to the β-silyl enone, ring closure to construct a six-membered ring intermediate, and the dissociation of NHC to release the final product. The reaction between the enolate intermediate and the β-silyl enone is identified as the stereoselectivity-determining step, preferentially generating an RS-configured product. Subsequent atoms-in-molecules (AIM) and noncovalent interaction (NCI) analyses verify that the main factor for inducing stereoselectivity is the higher number of noncovalent intermolecular interactions in the low-energy transition state.

Biomimetic asymmetric transamination reactions catalyzed by axial pyroxamine organocatalysts: Mechanism and origin of stereoselectivity

Biomimetic asymmetric transamination reactions have emerged as a focal point within the organocatalysis domain, generating substantial interest. However, the detailed mechanism and origin of stereoselectivity are remains elusive. Within this context, we present an exhaustive theoretical investigation into the detailed mechanism and origin of stereoselectivity governing such reactions between α-keto acids and amines catalyzed by axial pyroxamine. The fundamental reaction pathway can be divided into two stages, i.e. amino transfer stage to form chiral amine product and imine hydration stage for the generation of ketone product. To uncover the mystery of the chiral center produced by protonation in the amino transfer stage, five possible pathways were investigated and compared. This thorough examination unequivocally identifies the HOAc-assisted [1,3]-proton transfer as the pivotal step dictating stereoselectivity within the most energetically advantageous route. Further atoms-in-molecules (AIM) analysis was carried out to predict the origin of stereoselectivity. Notably, the N–H⋯O hydrogen bond interaction occurring between the pyridoxamine catalyst and α-keto acid of substrate has been pinointed as the driving force responsible for the energetical favorability of S-configurational pathway. These insights will be of great value for understanding and rational design of biomimetic organocatalysts for transamination reactions.

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.

Cooperative Asymmetric Dual Catalysis Involving a Chiral N-Heterocyclic Carbene Organocatalyst and Palladium in an Annulation Reaction: Mechanism and Origin of Stereoselectivity

The increasing number of examples on cooperative dual catalysis involving organocatalysts and transition metal catalysts indicate their wider acceptance and utility in synthetic applications. In such reactions, the concurrent activation of substrates is likely to present mechanistic complexities. In one of the studies, designed for intermolecular annulation aimed at making a biologically important class of benzazepines, chiral N-heterocyclic carbenes engage an enal in the form of a Breslow intermediate (nucleophilic partner) and Pd(0) activates rac-vinyl benzoxazinanone as a Pd-π-allyl intermediate (electrophile). Given the current importance and the lack of molecular insights on the origin of high enantio-/diastereoselectivities and cooperativity in such dual catalytic reactions, we have undertaken a detailed computational investigation using density functional theory. The kinetically most accessible Pd-π-allyl intermediate from the (S)- and (R)-vinyl benzoxazinanone is found to be Cre and Csi (where re and si denote the open prochiral faces through which the nucleophile can add), respectively. An energetically favorable change in configuration from Csi to Cre, via a PPh3-induced π–σ–π isomerization, suggests that an enantioconvergent mechanism was responsible for the enrichment of the desired Cre Pd-π-allyl species. Ready availability of Cre and the higher energy transition state (TS) for the alternative nucleophilic addition to the Csi is responsible for the high ee (computed >99%, experimental 99%). Improved shape complementarity between the chiral electrophile and nucleophile in the most preferred C–C bond formation TS as well as the noncovalent interactions (C–H··· π, π···π, and H-bonding) therein dictates the diastereoselectivity. An intramolecular C–N bond formation to the final annulated product is the turnover-determining TS. Molecular insights and energetic features, as obtained through our computations, are found to be in concert with several experimental observations, even beyond the sense and extent of stereoselectivities.

Role of mutations in a chemoenzymatic enantiodivergent C(sp3)-H insertion: exploring the mechanism and origin of stereoselectivity.

New-to-nature enzymes have emerged as powerful catalysts in recent years for streamlining various stereoselective organic transformations. While synthetic strategies employing engineered enzymes have witnessed proliferating success, there is limited clarity on the mechanistic front and more so when considering molecular-level insights into the role of selected mutations, dramatically escalating catalytic competency and selectivity. We have investigated the mechanism and correlation between mutations and exquisite stereoselectivity of a lactone carbene insertion into the C(sp3)-H bond of substituted aniline, catalyzed by two mutants of a cytochrome P450 variant, "P411" (engineered through directed evolution) in which the axial cysteine has been mutated to serine, utilizing various computational tools. The pivotal role of S264 and L/R328 mutations in the active site has been delineated computationally using two cluster models, thus rationalizing the enantiodivergence. This report provides much-needed insights into the origin of enantiodivergence, furnishing a mechanistic framework for understanding the anchoring effects of H-bond donor residues with the lactone ring. This study is expected to have important implications in the rational design of stereodivergent enzymes and toward successful in silico enzyme designing.

NHC-catalyzed N[sbnd]H functionalization/cycloaddition reaction of indole aldehyde and ketone: A DFT perspective

We have theoretically investigated the mechanism and origin of stereoselectivity in N-heterocyclic carbene (NHC)-catalyzed NH functionalization/cycloaddition reaction of indole aldehyde and ketone. The outcome of theoretical study shows that the formal [4 + 2] cycloaddition determines the stereoselectivity and the formation of R-configured product is more favorable, which aligns with the experimental results. The stronger interaction between two interactive fragments disclosed by distortion/interaction analysis governs the stereoselectivity. The types and strength of such interaction are further qualitatively and quantitatively recognized by NCI and AIM analyses.

Site- and Enantioselective Manganese-Catalyzed Benzylic C-H Azidation of Indolines.

A manganese-catalyzed highly site- and enantioselective benzylic C-H azidation of indolines has been described. The practical method is applicable for azidation of a tertiary benzylic C-H bond with good functional group tolerance, allowing facile access to structurally diverse tertiary azide-containing indolines in high efficiency with excellent site-, chemo-, and enantioselectivity. The generality of the method was further demonstrated by site- and enantioselective azidation of the secondary benzylic C-H bond for a range of secondary azide-containing indolines. The benzylic C-H azidation method allows to straightforwardly and enantioselectively install a variety of nitrogen-based functional groups and diverse bioactive molecules at the C3 position of indoline frameworks through post-azidation manipulations. Gram-scale synthesis was also demonstrated, further highlighting the synthetic potential of the method. Mechanistic studies by combined experiments and computations elucidated the reaction mechanism and origins of stereoselectivity.

Theoretical investigation on cobalt-catalyzed hydroacylation reaction: Mechanism and origin of stereoselectivity

In the present study, the mechanism of a cobalt-catalyzed hydroacylation reaction between aldehydes and 1,6-enynes and the origin of its stereoselectivity have been systematically investigated using the DFT calculational method. Two possible reaction mechanisms have been investigated: one that starts with oxidative addition of the aldehyde (aldehyde-first) or one that starts with oxidative cyclization of the 1,6-enyne (enyne-first). The computational results show that the aldehyde-first mechanism is energetically more favorable than is the enyne-first mechanism. The aldehyde-first mechanism contains several steps: oxidative addition, acyl migratory insertion, alkene insertion, and reductive elimination. Based on the calculations, the alkene insertion is the stereoselectivity-determining step, generating the S-configured product preferentially. The key to inducing the observed stereoselectivity is the lesser distortion of the structure of the lower-energy transition state that leads to the S-configured product.

Mechanism and Origin of Stereoselectivity of Ni-Catalyzed Cyclization/Carboxylation of Bromoalkynes with CO2.

Bromoalkynes play important roles in coupling reactions because they can show obvious stereoselectivity to form E- and Z-isomers when substituents are different. However, the origin of the stereoselectivity in the bromoalkynes reaction is still unclear. Density functional theory (DFT) calculations were performed to provide an in-depth study of the reaction mechanism, clarifying the mechanistic details of the main reaction and the origin of the stereoselectivity. By comparing the syn-insertion mechanism of alkynes and the radical pathway, it is indicated that the electrostatic effect caused by the different charge distributions of the reactants is the main reason that Ni(I) species are more prone to syn-insertion of alkynes than Ni(II) species. In addition, the lower reaction energy barrier in the radical pathway suggests that it is more advantageous in terms of kinetics. The bond between Ni(I) species and alkenylation products has two directions to generate products of different configurations, which are the direct stereoselectivity-determining stages. The distortion/interaction analysis shows that the distortion energy mainly affects the product configuration, and the steric hindrance is the main factor controlling the stereoselectivity.

Elucidating a Complicated Enantioselective Metabolic Profile: A Study From Rats to Humans Using Optically Pure Doxazosin.

Doxazosin (DOX) is prescribed as a racemic drug for the clinical treatment of benign prostatic hyperplasia and hypertension. Recent studies found that the two enantiomers of DOX exhibit differences in blood concentration and pharmacological effects. However, the stereoselective metabolic characteristics and mechanisms for DOX are not yet clear. Herein, we identified 34 metabolites of DOX in rats based on our comprehensive and effective strategy. The relationship among the metabolites and the most discriminative metabolites between (−)-DOX and (+)-DOX administration was analyzed according to the kinetic parameters using state-of-the-art multivariate statistical methods. To elucidate the enantioselective metabolic profile in vivo and in vitro, we carefully investigated the metabolic characteristics of metabolites after optically pure isomers administration in rat plasma, rat liver microsomes (RLMs) or human liver microsomes (HLMs), and recombinant human cytochrome P450 (CYP) enzymes. As a result, the differences of these metabolites were found based on their exposure and elimination rate, and the metabolic profile of (±)-DOX was more similar to that of (+)-DOX. Though the metabolites identified in RLMs and HLMs were the same, the metabolic profiles of the metabolites from (−)-DOX and (+)-DOX were greatly different. Furthermore, four human CYP enzymes could catalyze DOX to produce metabolites, but their preferences seemed different. For example, CYP3A4 highly specifically and selectively catalyzed the formation of the specific metabolite (M22) from (−)-DOX. In conclusion, we established a comprehensive metabolic system using pure optical isomers from in vivo to in vitro, and the complicated enantioselectivity of the metabolites of DOX was clearly shown. More importantly, the comprehensive metabolic system is also suitable to investigate other chiral drugs.

The chiral pyridoxal-catalyzed biomimetic Mannich reaction: the mechanism and origin of stereoselectivity

A biomimetic organocatalyst with a pyridoxal-like structure is one of the most successful examples of catalyzing organic reactions under mild conditions in an asymmetric synthesis field.

Insights into Organoamine-Catalyzed Asymmetric Synthesis of Axially Chiral Allenoates Using Morita-Baylis-Hillman Carbonates and Trisubstituted Allenoates: Mechanism and Origin of Stereoselectivity.

A computational study was performed to explore the possible mechanisms of β-isocinchonine-catalyzed asymmetric C(sp2)-H allylation of trisubstituted allenoates using Morita-Baylis-Hillman (MBH) carbonates for synthesis of axially chiral tetrasubstituted allenoates. The calculated results indicate that the most energetically favorable pathway includes (1) nucleophilic attack on MBH carbonate by β-isocinchonine, (2) BocO- dissociation, (3) stereoselective formation of the C-C bond, and (4) regeneration of the catalyst. By tracking the orbital overlap/interaction changes, the half shoulder-to-head orbital overlap mode can be smoothly switched to a head-to-head orbital overlap mode for the key C-C σ bond formation, which is also identified as the stereoselectivity-determining process. Further distortion/interaction, noncovalent interaction (NCI), and atom-in-molecule (AIM) analyses demonstrate that C-H···O and C-H···π interactions should be key for controlling the axial and central chirality. This work would be useful for rational design of organocatalytic allylic alkylation reactions for synthesis of axially chiral compounds in the future.

Identification of four ene reductases and their preliminary exploration in the asymmetric synthesis of (R)-dihydrocarvone and (R)-profen derivatives

The ene reductases (ERs) from the old yellow enzymes (OYEs) family have the ability to reduce activated alkenes to generate up to two stereocenters, therefore they have been received extensive attention as powerful biocatalysts. In this study, through gene mining, four ERs were identified from the genomes of Ensifer adhaerens, Pseudomonas fluorescens, and Pseudomonas veronil. The biocatalytic properties of these four ERs were identified, and their applications in the synthesis process of dihydrocarvone and profen derivatives were further evaluated. Among them, three ERs (EaER2, PvER1, and PvER2) belonging to the classic OYEs showed the best catalytic activity at 30 °C and pH 7.0 (100 mM potassium phosphate buffer) and the PfER2, which belongs to the thermophilic-like OYEs exhibited the best catalytic at 40 °C and pH 7.0 (100 mM potassium phosphate buffer). When exploring the influence of organic solvents on the catalytic efficiency, it was found that the four ERs were more sensitive to toluene and had tolerance to several other selected organic solvents. In addition, EaER2, PfER2, PvER1 and PvER2 showed excellent catalytic activity toward carvone, and the stereoselectivity of PvER2 toward carvone could reach up to 88.7 % de. EaER2 and PfER2 can catalyze the synthesis of a variety of profen derivatives with a stereoselectivity over 99 % ee. Moreover, through homology modeling and molecular docking, we preliminarily explained the mechanism of catalytic activity and stereoselectivity of the four ERs, which provided a solid base on the rational design of their stereo-preference in the future. The discovery of EaER2, PfER2, PvER1, and PvER2 provides four new enzyme sources for the study of the OYEs family and enriches the biocatalytic toolbox of ERs. Our exploration of the enzymatic properties of these four ERs will provide the sufficient data basis for future research and industrialization progress.