Stereospecific Reaction Research Articles

PPh3 promoted stereospecific synthesis of ethyl α-chloroacrylates from ethyl trichloroacetate and arylaldehydes

A coupling reaction between arylaldehydes and ethyl trichloroacetate is facilitated by PPh3 under mild conditions to stereospecifically produce (Z)-ethyl α-chloroacrylates. This stereospecific coupling reaction only occurs when the arylaldehyde derivative has an electron-withdrawing substituent. On the other hand, when an electron-donating group is present in the aromatic ring, the aryldichloromethyl derivative is formed as the only product, even at low temperature. The stereospecificity in the coupling reaction was established based on the coupling constants 2JCH and 3JCH in the 13C NMR and crystal-X-ray analysis. From this data we propose that the formation of these compounds occurs through two intermediates initially formed by the reaction between the PPh3 and ethyl trichloroacetate.

Rational Design and Stereodivergent Construction of Enantioenriched Tetrahydro-β-Carbolines Containing Multistereogenic Centers.

Chiral tetrahydro-β-carbolines, as one of the most intriguing subtypes of indole alkaloids, have emerged as the privileged units in plenty of natural products and biologically active molecules with an impressive range of bioactive properties. However, the stereodivergent construction of these valuable skeletons containing multistereogenic centers from readily available starting materials remains very challenging, especially, in view of the introduction of an axial chirality. Herein, we developed an efficient method toward enantioenriched tetrahydro-β-carbolines with readily available tryptophan-derived aldimine esters and allylic carbonates under mild reaction conditions. The reaction proceeds in a sequential fashion involving synergistic Cu/Ir-catalyzed stereodivergent allylation and the Brønsted acid-promoted stereospecific Pictet-Spengler reaction, affording a wide range of chiral tetrahydro-β-carbolines bearing up to four stereogenic centers in good yields with excellent stereoselectivity control. When N-aryl-substituted tryptophan-derived aldimine esters were utilized, notably, a unique C-N heterobiaryl axis could be simultaneously constructed with the formation of the third point stereogenic center in the last cyclization step through dynamic kinetic resolution (DKR). Computational mechanistic studies established a plausible synergistic mechanism for dual Cu/Ir-catalyzed asymmetric allylation and the succeeding protonation-assisted Pictet-Spengler cyclization to complete the annulation. Structure-activity relationship analyses unveil the origins of stereochemistry for the building of one axis and three point stereogenic centers.

α-Halocarbonyls as a Valuable Functionalized Tertiary Alkyl Source.

This review introduces the synthetic organic chemical value of α-bromocarbonyl compounds with tertiary carbons. This α-bromocarbonyl compound with a tertiary carbon has been used primarily only as a radical initiator in atom transfer radical polymerization (ATRP) reactions. However, with the recent development of photo-radical reactions (around 2010), research on the use of α-bromocarbonyl compounds as tertiary alkyl radical precursors became popular (around 2012). As more examples were reported, α-bromocarbonyl compounds were studied not only as radicals but also for their applications in organometallic and ionic reactions. That is, α-bromocarbonyl compounds act as nucleophiles as well as electrophiles. The carbonyl group of α-bromocarbonyl compounds is also attractive because it allows the skeleton to be converted after the reaction, and it is being applied to total synthesis. In our survey until 2022, α-bromocarbonyl compounds can be used to perform a full range of reactions necessary for organic synthesis, including multi-component reactions, cross-coupling, substitution, cyclization, rearrangement, stereospecific reactions, asymmetric reactions. α-Bromocarbonyl compounds have created a new trend in tertiary alkylation, which until then had limited reaction patterns in organic synthesis. This review focuses on how α-bromocarbonyl compounds can be used in synthetic organic chemistry.

Genetic Functionalization of Protein-Based Biomaterials via Protein Fusions.

Proteins implement many useful functions, including binding ligands with unparalleled affinity and specificity, catalyzing stereospecific chemical reactions, and directing cell behavior. Incorporating proteins into materials has the potential to imbue devices with these desirable traits. This review highlights recent advances in creating active materials by genetically fusing a self-assembling protein to a functional protein. These fusion proteins form materials while retaining the function of interest. Key advantages of this approach include elimination of a separate functionalization step during materials synthesis, uniform and dense coverage of the material by the functional protein, and stabilization of the functional protein. This review focuses on macroscale materials and discusses (i) multiple strategies for successful protein fusion design, (ii) successes and limitations of the protein fusion approach, (iii) engineering solutions to bypass any limitations, (iv) applications of protein fusion materials, including tissue engineering, drug delivery, enzyme immobilization, electronics, and biosensing, and (v) opportunities to further develop this useful technique.

Finding Relevant Retrosynthetic Disconnections for Stereocontrolled Reactions.

Machine learning-driven computer-aided synthesis planning (CASP) tools have become important tools for idea generation in the design of complex molecule synthesis but do not adequately address the stereochemical features of the target compounds. A novel approach to automated extraction of templates used in CASP that includes stereochemical information included in the US Patent and Trademark Office (USPTO) and an internal AstraZeneca database containing reactions from Reaxys, Pistachio, and AstraZeneca electronic lab notebooks is implemented in the freely available AiZynthFinder software. Three hundred sixty-seven templates covering reagent- and substrate-controlled as well as stereospecific reactions were extracted from the USPTO, while 20,724 templates were from the AstraZeneca database. The performance of these templates in multistep CASP is evaluated for 936 targets from the ChEMBL database and an in-house selection of 791 AZ designs. The potential and limitations are discussed for four case studies from ChEMBL and examples of FDA-approved drugs.

Development of a Cryogenic Flow Reactor to Optimize Glycosylation Reactions Based on the Active Donor Intermediate.

The development of a continuous flow reactor for stereospecific glycosylation reactions with deoxy sugars is described. This apparatus that permits optimizing the selectivity of glycosylation reactions based on the stability of the activated intermediate is described. By coupling a flow apparatus with HPLC analysis, we can optimize the yield of TsCl-mediated β-linked deoxy sugar construction in a matter of hours. In all cases, results from continuous flow processing translate into improved results in batch-scale reactions, as demonstrated by competition experiments. This is the result of carrying out optimization to identify the ideal temperature for the reaction of the activated intermediate, as opposed to the initial activation conditions. Such an approach allows for the rapid development of highly selective glycosylation reactions in cases in which classical neighboring group participation is not possible.

Helically twisted nanoribbons via stereospecific annulative π-extension reaction employing [7]helicene as a molecular wrench.

Over the past decade, significant progress has been made in synthesizing atomically precise carbon nanostructures, particularly graphene nanoribbons (NRs), employing advanced synthetic methodologies. Despite these advancements, achieving control over the stereochemistry of twisted NRs has proven to be a formidable challenge. This manuscript presents a strategic approach to achieve absolute control over the single-handed helical conformation in a cove-edged NR. This strategy leverages enantiopure helicenes as a molecular wrench, intricately influencing the overall conformation of the NR. [7]helicenes stitched to the terminal K-regions of a conjugated pyrene NR through a stereospecific annulative π-extension reaction to produce a helically twisted NR with an end-to-end twist of 171°. Furthermore, a detailed investigation of the impact of twisting on the conformational population was studied by quantum chemical calculations.

Cytochromes P450 as Tools for Electroenzymatic Synthesis

The electrocatalytic properties of cytochrome P450 2C9 and the cytochrome P450 2C9/FAD and cytochrome P450 2C9/FMN complexes have been studied using a two-electrode system. The system consisted of an enzymatic catalyst electrode modified by the membrane-like compound didodecyldimethylammonium bromide (SPE/DDAB) and a measuring electrode, modified with carbon nanotubes (SPE/CNT). To study the effectiveness of electroenzymatic reactions catalyzed by cytochrome P450 2C9, the nonsteroidal anti-inflammatory drug diclofenac was used as a substrate. Cytochrome P450 2C9 catalyzes the stereospecific hydroxylation reaction to form 4′-hydroxydiclofenac. The metabolite 4′-hydroxydiclofenac was recorded at a potential E=+0.12 (relative to Ag/AgCl).The use of FAD and FMN as low-molecular mediators made it possible to increase the efficiency of electrocatalysis of the SPE/DDAB/CYP2C9/FAD system to 148±10% and SPE/DDAB/CYP2C9/FMN to 113±6% compared to SPE/DDAB/CYP2C9 (100±5%), and also increase the rate of the enzymatic reaction by 1.5 and 1.13 times, respectively.

Algal Kainoid Synthases Exhibit Substrate-Dependent Hydroxylation and Cyclization Activities.

FeII/α-ketoglutarate-dependent dioxygenases (Fe/αKG) make up a large enzyme family that functionalize C-H bonds on diverse organic substrates. Although Fe/αKG homologues catalyze an array of chemically useful reactions, hydroxylation typically predominates. Microalgal DabC uniquely forms a novel C-C bond to construct the bioactive pyrrolidine ring in domoic acid biosynthesis; however, we have identified that this kainoid synthase exclusively performs a stereospecific hydroxylation reaction on its cis substrate regioisomer. Mechanistic and kinetic analyses with native and alternative substrates identified a 20-fold rate increase in DabC radical cyclization over β-hydroxylation with no observable 1,5-hydrogen atom transfer. Moreover, this dual activity was conserved among macroalgal RadC1 and KabC homologues and provided insight into substrate recognition and reactivity trends. Investigation of this substrate-dependent chemistry improves our understanding of kainoid synthases and their biocatalytic application.

Identification of theenantiomeric nature of 2-keto-3-deoxy-galactonate in the catabolic pathway of3,6-anhydro-L-galactose.

A novel metabolic pathway of 3,6-anhydro-L-galactose (L-AHG), the main sugar component in red macroalgae, was first discovered in the marine bacterium Vibrio sp. EJY3. L-AHG is converted to 2-keto-3-deoxy-galactonate (KDGal) in two metabolic steps. Here, we identified the enantiomeric nature of KDGal in the L-AHG catabolic pathway via stereospecific enzymatic reactions accompanying the biosynthesis of enantiopure L-KDGal and D-KDGal. Enantiopure L-KDGal and D-KDGal were synthesized by enzymatic reactions derived from the fungal galacturonate and bacterial oxidative galactose pathways, respectively. KDGal, which is involved in the L-AHG pathway, was also prepared. The results obtained from the reactions with an L-KDGal aldolase, specifically acting on L-KDGal, showed that KDGal in the L-AHG pathway exists in an L-enantiomeric form. Notably, we demonstrated the utilization of L-KDGal by Escherichia coli for the first time. E. coli cannot utilize L-KDGal as the sole carbon source. However, when a mixture of L-KDGal and D-galacturonate was used, E. coli utilized both. Our study suggests a stereoselective method to determine the absolute configuration of a compound. In addition, our results can be used to explore the novel L-KDGal catabolic pathway in E. coli and to construct an engineered microbial platform that assimilates L-AHG or L-KDGal as substrates. KEY POINTS: • Stereospecific enzyme reactions were used to identify enantiomeric nature of KDGal • KDGal in the L-AHG catabolic pathway exists in anL-enantiomeric form • E. coli can utilize L-KDGal as a carbon source when supplied with D-galacturonate.

Synthesis of N–O-Linked Glycosides via Stereospecific Pd-Catalyzed Reaction

Synthesis of N–O-Linked Glycosides via Stereospecific Pd-Catalyzed Reaction

Facile one-pot, domino reaction to synthesize (Z)-2-imino-5-(1-alkyl-2-oxoindolin-3-ylidene)thiazolidin-4-one derivatives and its DFT study for the E/Z confirmation structure

In this publication, we reported an eco-friendly procedure for the efficient synthesis of 2-imino-5-(1-alkyl-2-oxoindolin-3-ylidene) thiazolidin-4-one derivatives with a stereospecific coupling reaction between 2-imino-thiazolidin-4-one (pseudothiohydantoin) and cyano-substituted oxindole derivatives. Thus, a variety of new thiazolidin-oxindole derivatives with potential medicinal applications have been synthesized with an effective and economical method, focusing on sustainable chemistry. The final products have been obtained in excellent yields together with high purity after washing with water and ethanol. This publication is the first easy protocol to be reported for the rapid condensation of pseudothiohydantoin with substituted isatins. In addition, the stereospecificity, which led to the formation of the Z- isomer of the products is validated using computational calculations.

Stereospecific naphthoquinone photoredox reactions: Total syntheses of spirocyclic natural products

This account outlines our recent studies on the photoredox reaction of naphthoquinones. The mechanism consists of three consecutive events triggered by photo-irradiation, (1) hydrogen abstraction by the excited quinone to generate a biradical species, (2) internal single electron transfer (SET) to convert the biradical to the corresponding zwitterion, and (3) oxy-cyclization to give the product. The overall process allows replacement of a C–H bond by a C–O bond in a stereospecific, retentive manner. This photo-induced reaction has a broad scope, enabling otherwise-difficult stereocontrolled synthesis of natural products, as demonstrated by the syntheses of two classes of antibiotics, the spiroxins and the preussomerins. The former targets feature stereogenic spirocyclic ether structures, which were effectively constructed by a photoredox reaction involving 1,5-HAT, while the latter targets featuring stereogenic acetal structures were constructed by a photoredox reaction involving 1,6-HAT. Also described is the synthetic study of the rubromycins, centering attention to the stereospecific construction of the spiroacetal center.

Cyclopropylcarbinyl-to-Homoallyl Carbocation Equilibria Influence the Stereospecificity in the Nucleophilic Substitution of Cyclopropylcarbinols

The synthesis of quaternary homoallylic halides and trichloroacetates from cyclopropylcarbinols, as reported by Marek (J. Am. Chem. Soc. 2020, 142, 5543-5548), is one of the few reported examples of stereospecific nucleophilic substitution involving chiral bridged carbocations. However, for the phenyl-substituted substrates, poor specificity is observed and mixtures of diastereomers are obtained. To understand the nature of the intermediates involved and explain the loss of specificity for certain substrates, we have performed a computational investigation of the reaction mechanism using ωB97X-D optimizations and DLPNO-CCSD(T) energy refinements. Our results indicate that cyclopropylcarbinyl cations are stable intermediates in this reaction, while bicyclobutonium structures are high-energy transition structures that are not involved. Instead, multiple rearrangement pathways of cyclopropylcarbinyl cations were located, including ring openings to homoallylic cations. The activation barriers required to reach such structures are correlated to the nature of the substituents; while direct nucleophilic attack on the chiral cyclopropylcarbinyl cations is kinetically favored for most systems, the rearrangements become competitive with nucleophilic attack for the phenyl-substituted systems, leading to a loss of specificity through rearranged carbocation intermediates. As such, stereospecific reactions of chiral cyclopropylcarbinyl cations depend on the energies required to access their corresponding homoallylic structures, from which selectivity is not guaranteed.

Stereospecific Transformations of Alkylboronic Esters Enabled by Direct Boron-to-Zinc Transmetalation.

Chiral secondary organoboronic esters, when activated with t-butyllithium, are shown to undergo efficient stereoretentive transmetalation with either zinc acetate or zinc chloride. This reaction provides chiral secondary alkylzinc reagents that are configurationally stable under practical experimental conditions. The organozinc compounds were found to engage in stereospecific reactions with difluorocarbene, catalytic cross-couplings with palladium-based catalysts, and trifluoromethylation with a copper(III) complex. Mechanistic and computational studies shed light on the inner workings of the transmetalation event.

Photochemical Wolff Rearrangement Initiated Generation and Subsequent α-Chlorination of C1 Ammonium Enolates.

The enantioselective synthesis of α-chlorinated carboxylic acid esters with er up to 99:1 and yields up to 82% was achieved via a one-pot multistep protocol starting from α-diazoketones. This process proceeds via a photochemical Wolff rearrangement, trapping of the generated ketene with a chiral Lewis base catalyst, subsequent enantioselective α-chlorination, and a final nucleophilic displacement of the bound catalyst. The obtained products were successfully utilized for stereospecific nucleophilic displacement reactions with N- and S-nucleophiles.

Interaction between Divalent Copper Fluoride and Carboxamide Group Enabling Stereoretentive Fluorination of Tertiary Alkyl Halides.

Herein, we report Cu-catalyzed stereospecific fluorination involving CsF and α-bromocarboxamides as tertiary alkyl sources that, unlike traditional stereospecific routes involving stereoinversive SN2 reactions, proceeds with retention of stereochemistry. The developed stereospecific Cu-catalyzed reaction is among the most efficient methods for synthesizing fluorinated molecules that possess highly congested stereogenic carbon centers. Mechanistic studies revealed that the combined reactivity of CuF2 and Cs salt is essential for completing the catalytic cycle. Our catalytic system underwent fluorination exclusively with tertiary alkyl bromides and did not react with primary alkyl bromides, indicating that this stereospecific fluorination methodology is suitable for synthesizingfluorinated building blocks possessing stereo-defined F-containing tertiary carbon stereogenic center.

Experimental Evolution Reveals a Novel Ene Reductase That Detoxifies α,β-Unsaturated Aldehydes in Listeria monocytogenes.

The plant essential oil component trans-cinnamaldehyde (t-CIN) exhibits antibacterial activity against a broad range of foodborne pathogenic bacteria, including L. monocytogenes, but its mode of action is not fully understood. In this study, several independent mutants of L. monocytogenes with increased t-CIN tolerance were obtained via experimental evolution. Whole-genome sequencing (WGS) analysis revealed single-nucleotide-variation mutations in the yhfK gene, encoding an oxidoreductase of the short-chain dehydrogenases/reductases superfamily, in each mutant. The deletion of yhfK conferred increased sensitivity to t-CIN and several other α,β-unsaturated aldehydes, including trans-2-hexenal, citral, and 4-hydroxy-2-nonenal. The t-CIN tolerance of the deletion mutant was restored via genetic complementation with yhfK. Based on a gas chromatography-mass spectrometry (GC-MS) analysis of the culture supernatants, it is proposed that YhfK is an ene reductase that converts t-CIN to 3-phenylpropanal by reducing the C=C double bond of the α,β-unsaturated aldehyde moiety. YhfK homologs are widely distributed in Bacteria, and the deletion of the corresponding homolog in Bacillus subtilis also caused increased sensitivity to t-CIN and trans-2-hexenal, suggesting that this protein may have a conserved function to protect bacteria against toxic α,β-unsaturated aldehydes in their environments. IMPORTANCE While bacterial resistance against clinically used antibiotics has been well studied, less is known about resistance against other antimicrobials, such as natural compounds that could replace traditional food preservatives. In this work, we report that the food pathogen Listeria monocytogenes can rapidly develop an elevated tolerance against t-cinnamaldehyde, a natural antimicrobial from cinnamon, by single base pair changes in the yhfK gene. The enzyme encoded by this gene is an oxidoreductase, but its substrates and precise role were hitherto unknown. We demonstrate that the enzyme reduces the double bond in t-cinnamaldehyde and thereby abolishes its antibacterial activity. Furthermore, the mutations linked to t-CIN tolerance increased bacterial sensitivity to a related compound, suggesting that they modify the substrate specificity of the enzyme. Since the family of oxidoreductases to which YhfK belongs is of great interest in the mediation of stereospecific reactions in biocatalysis, our work may also have unanticipated application potential in this field.

Mechanism of Radical Initiation in the Radical SAM Enzyme Superfamily.

Radical S-adenosylmethionine (SAM) enzymes use a site-differentiated [4Fe-4S] cluster and SAM to initiate radical reactions through liberation of the 5'-deoxyadenosyl (5'-dAdo•) radical. They form the largest enzyme superfamily, with more than 700,000 unique sequences currently, and their numbers continue to grow as a result of ongoing bioinformatics efforts. The range of extremely diverse, highly regio- and stereo-specific reactions known to be catalyzed by radical SAM superfamily members is remarkable. The common mechanism of radical initiation in the radical SAM superfamily is the focus of this review. Most surprising is the presence of an organometallic intermediate, Ω, exhibiting an Fe-C5'-adenosyl bond. Regioselective reductive cleavage of the SAM S-C5' bond produces 5'-dAdo• to form Ω, with the regioselectivity originating in the Jahn-Teller effect. Ω liberates the free 5'-dAdo• as the catalytically active intermediate through homolysis of the Fe-C5' bond, in analogy to Co-C5' bond homolysis in B12, which was once viewed as biology's choice of radical generator.

Stereospecific Nickel-Catalyzed Cross-Electrophile Coupling Reaction of Alkyl Mesylates and Allylic Difluorides to Access Enantioenriched Vinyl Fluoride-Substituted Cyclopropanes.

Cross-electrophile coupling reactions involving direct C-O bond activation of unactivated alkyl sulfonates or C-F bond activation of allylic gem-difluorides remain challenging. Herein, we report a nickel-catalyzed cross-electrophile coupling reaction between alkyl mesylates and allylic gem-difluorides to synthesize enantioenriched vinyl fluoride-substituted cyclopropane products. These complex products are interesting building blocks with applications in medicinal chemistry. Density functional theory (DFT) calculations demonstrate that there are two competing pathways for this reaction, both of which initiate by coordination of the electron-deficient olefin to the low-valent nickel catalyst. Subsequently, the reaction can proceed by oxidative addition of the C-F bond of the allylic gem-difluoride moiety or by directed polar oxidative addition of the alkyl mesylate C-O bond.