Mechanism Of Cyclization Research Articles

Pattern-Based Genome Mining Guides Discovery of the Antibiotic Indanopyrrole A from a Marine Streptomycete.

Terrestrial actinomycetes in the genus Streptomyces have long been recognized as prolific producers of small-molecule natural products, including many clinically important antibiotics and cytotoxic agents. Although Streptomyces can also be isolated from marine environments, their potential for natural product biosynthesis remains underexplored. The MAR4 clade of largely marine-derived Streptomyces has been a rich source of novel halogenated natural products of diverse structural classes. To further explore the biosynthetic potential of this group, we applied pattern-based genome mining, leading to the discovery of the first halogenated pyrroloketoindane natural products, indanopyrrole A (1) and B (2), and the bioinformatic linkage of these compounds to an orphan biosynthetic gene cluster (BCG) in 20 MAR4 genomes. Indanopyrrole A displays potent broad-spectrum antibiotic activity against clinically relevant pathogens. A comparison of the putative indanopyrrole BGC with that of the related compound indanomycin provides new insights into the terminal cyclization and offloading mechanisms in pyrroloketoindane biosynthesis. Broader searches of public databases reveal the rarity of this BGC while also highlighting opportunities for discovering additional compounds in this uncommon class.

Chemical synthesis of 13C-labeled isopentenyl pyrophosphate

Isopentenyl pyrophosphate (IPP) is a key precursor in the biosynthesis of terpenoids, the largest class of natural products. 13C isotope incorporation into the terpenoid scaffolds has been proved to be a powerful chemical probe to track the elusive cyclization mechanism of distinct terpene synthases which are the driving force for the tremendous chemical diversities seen in terpenoid natural products. Here, we present synthetic routes for the preparation of C1 to C5 individually 13C labeled IPP starting from 13C-labeled acetic acid and iodomethane, resulting in five distinct labeled substrates. The 13C labeled IPP will be served as useful chemical probes to elucidate the new cyclization mechanisms catalyzed by those cryptic terpene synthases.

Beyond Photochromism: Alternative Stimuli to Trigger Diarylethenes Switching.

Diarylethenes (DAEs) are typical photochemically reversible type (P-type) photochromic materials with excellent thermal stability and high fatigue resistance and are widely exploited as photo-switches for various applications in molecular devices, data storage, photoresponsive materials, and bioimaging, etc. In recent years, there is an increasing number of reports using heat, acid, electrochemistry, etc. to drive the isomerization reaction of DAEs. The response to two or more different stimuli enables multi-functionality within a single DAE molecule, which would facilitate complex logic-gate operations, multimode data storage, and increased information density. Herein, the recent advances in DAE systems utilizing stimuli "beyond photo" to trigger the isomerization processes from three perspectives: acidochromism, thermochromism, and electrochromism are reviewed. Emphasis is placed on the molecule design strategies and the underlying mechanisms for cyclization and cycloreversion processes addressed by the alternative stimulus. Then the noticeable applications made in multi-stimuli responsive DAE systems are summarized. Additionally, the challenges and opportunities of DAE switches driven by stimuli "beyond photo" in the future are also discussed.

Pattern-based genome mining guides discovery of the antibiotic indanopyrrole A from a marine streptomycetef.

Terrestrial actinomycetes in the genus Streptomyces have long been recognized as prolific producers of small molecule natural products, including many clinically important antibiotics and cytotoxic agents. Although Streptomyces can also be isolated from marine environments, their potential for natural product biosynthesis remains underexplored. The MAR4 clade of largely marine-derived Streptomyces has been a rich source of novel halogenated natural products of diverse structural classes. To further explore the biosynthetic potential of this group, we applied pattern-based genome mining leading to the discovery of the first halogenated pyrroloketoindane natural products, indanopyrrole A (1) and B (2), and the bioinformatic linkage of these compounds to an orphan biosynthetic gene cluster (BCG) in 20 MAR4 genomes. Indanopyrrole A displays potent broad-spectrum antibiotic activity against clinically relevant pathogens. A comparison of the putative indanopyrrole BGC with that of the related compound indanomycin provides new insights into the terminal cyclization and offloading mechanisms in pyrroloketoindane biosynthesis. Broader searches of public databases reveal the rarity of this BGC while also highlighting opportunities for discovering additional compounds in this uncommon class.

Cobalt-Catalyzed Regio-, Diastereo- and Enantioselective Reductive Coupling of 1,3-Dienes and Aldehydes.

Catalytic regio-, diastereo- and enantioselective reductive coupling of 1,3-dienes and aldehydes through regio- and enantioselective oxidative cyclization followed by regio- and diastereoselective protonation promoted by a chiral phosphine-cobalt complex is presented. Such processes represent an unprecedented reaction pathway for cobalt catalysis that enable selective transformation of the more substituted alkene in 1,3-dienes, affording a broad scope of bishomoallylic alcohols without the need of pre-formation of stoichiometric amounts of sensitive organometallic reagents in up to 98 % yield, >98 : 2 regioselectivity, >98 : 2 dr and 98 : 2 er. Application of this method to construction of axial stereogenicity and deuterated stereogenic center provided a wide range of multifunctional chiral building blocks that are otherwise difficult to access. DFT calculations revealed the origin of regio- and stereoselectivity as well as a unique oxidative cyclization mechanism for cobalt catalysis.

Research on the dynamics and mechanism of thermal cracking of coal-based endothermic hydrocarbon fuels

Thermal cracking of endothermic hydrocarbon fuels (EHF) plays an important role in the endothermic process when the fuel temperature exceeds the supercritical temperature. To gain a deeper understanding of the thermal cracking behavior of EHF, this work discusses the thermal cracking law and reaction mechanism of coal-based EHF at different temperatures through static thermal cracking experiments, and establishes a total molecular reaction dynamics model containing 34 species and 24-step reactions based on product distribution. The results show that in the temperature range of 450℃ to 500℃, the gas phase yield of the fuel increases linearly from 8 % to 56 %, and the conversion rate reaches up to 96.1 %. The kinetic reaction of thermal cracking conforms to the primary kinetic equation, the cracking rate constant k is between 1.08×10−4∼7.92×10−4 s−1, the activation energy Ea=184.47±11.5 kJ∙mol−1, and the precursor factor lnA=21.61±3.0. Gas phase products include hydrogen, methane, ethane, ethylene, propane and butane. Liquid phase products include paraffins, alkyldecahydronaphthalenes and aromatic hydrocarbons. As the cracking depth increases, the degree of fuel branching first increases and then decreases, up to 0.33. Paraffins and alkyldecahydronaphthalenes are gradually converted into olefins, cyclic olefins, benzene, naphthalene, indene, fluorene and pyrene and other compounds. Based on the product distribution, the reaction mechanism of thermal cracking of coal-based EHF is speculated to include single-molecule β-cracking, bimolecular F-S-S, intramolecular H-transfer, cyclization and isomerization mechanisms.

In Situ Formation of Acidic Comonomer during Thermal Treatment of Copolymers of Acrylonitrile and Its Influence on the Cyclization Reaction.

Binary and ternary copolymers of acrylonitrile (AN), tert-butyl acrylate (TBA), and n-butyl acrylate (BA) are synthesized through conventional radical polymerization in DMSO in the presence of 2-mercaptoethanol. The thermal behavior of binary and ternary copolymers is studied under argon atmosphere and in air. It is demonstrated that the copolymers of AN contain 1-10 mol.% of TBA split isobutylene upon heating above 160 °C, resulting in the formation of the units of acrylic acid in the chain. The carboxylic groups formed in situ are responsible for the ionic mechanism of cyclization, which starts at lower temperatures compared with pure polyacrylonitrile (PAN) or AN copolymer with BA. The activation energy of cyclization through ionic and radical mechanisms depends on copolymer composition. For the ionic mechanism, the activation energy lies in the range ca. 100-130 kJ/mole, while for the radical mechanism, it lies in the range ca. 150-190 kJ/mole. The increase in the TBA molar part in the copolymer is followed by faster consumption of nitrile groups and the evolution of a ladder structure in both binary and ternary copolymers. Thus, the incorporation of a certain amount of TBA in PAN or its copolymer with BA allows tuning the temperature range of cyclization. This feature seems attractive for applications in the production of melt-spun PAN by choosing the appropriate copolymer composition and heating mode.

A Functional Switch Between Asperfumene and Fusicoccadiene Synthase and Entrance to Asperfumene Biosynthesis through a Vicinal Deprotonation-Reprotonation Process.

The diterpene synthase AfAS was identified from Aspergillus fumigatiaffinis. Its amino acid sequence and-according to a structural model-active site architecture are highly similar to those of the fusicocca-2,10(14)-diene synthase PaFS, but AfAS produces a structurally much more complex diterpene with a novel 6-5-5-5 tetracyclic skeleton called asperfumene. The cyclisation mechanism of AfAS was elucidated through isotopic labelling experiments and DFT calculations. The reaction cascade proceeds in its initial steps through similar intermediates as for the PaFS cascade, but then diverges through an unusual vicinal deprotonation-reprotonation process that triggers a skeletal rearrangement at the entrance to the steps leading to the unique asperfumene skeleton. The structural model revealed only one major difference between the active sites: The PaFS residue F65 is substituted by I65 in AfAS. Intriguingly, site-directed mutagenesis experiments with both diterpene synthases revealed that position 65 serves as a bidirectional functional switch for the biosynthesis of tetracyclic asperfumene versus structurally less complex diterpenes.

Ein funktioneller Wechsel zwischen Asperfumen‐ und Fusicoccadien‐Synthase und Eintritt in die Asperfumen‐Biosynthese durch einen vicinalen Deprotonierungs‐Reprotonierungsprozess

AbstractDie Diterpensynthase AfAS wurde aus Aspergillus fumigatiaffinis identifiziert. Ihre Aminosäuresequenz und – einem Strukturmodell zufolge – die Architektur des aktiven Zentrums sind denen der Fusicocca‐2,10(14)‐dien‐Synthase PaFS sehr ähnlich, AfAS produziert jedoch ein strukturell viel komplexeres Diterpen mit einem neuartigen 6–5–5–5 tetracyclischen Gerüst namens Asperfumen. Der Cyclisierungsmechanismus von AfAS wurde durch Isotopenmarkierungsexperimente und DFT‐Rechnungen aufgeklärt. Die Reaktionskaskade verläuft in ihren ersten Schritten über ähnliche Intermediate wie die PaFS‐Kaskade, divergiert dann aber durch einen ungewöhnlichen vicinalen Deprotonierungs‐Reprotonierungsprozess, der eine Skelettumlagerung am Startpunkt der Stufen auslöst, die zum einzigartigen Asperfumen‐Gerüst führen. Das Strukturmodell zeigte nur einen wesentlichen Unterschied zwischen den aktiven Zentren: Der PaFS‐Rest F65 ist in AfAS durch I65 ersetzt. Interessanterweise zeigten ortsspezifische Mutageneseexperimente mit beiden Diterpensynthasen, dass Position 65 als bidirektionaler funktioneller Schalter für die Biosynthese von tetracyclischem Asperfumen im Vergleich zu strukturell weniger komplexen Diterpenen dient.

Characteristics and competitive mechanisms of polycondensation and cyclization induced by end‐groups in polyamide 6 melt

AbstractPolycondensation and ring‐formation reactions are the main factors that cause instability in the molecular structure of commercial polyamide 6 (PA6) during melting. In this study, the mechanisms and interactions of the ring‐formation and polycondensation reactions induced by various factors were thoroughly investigated. The findings suggest that the average molecular weight of PA6 increased by 20.4% during melting. The total monomer and oligomer content increased by 79.2%, and the ring‐forming reaction was promoted with an increase in temperature. Moreover, a high concentration of the end‐amino in PA6 promoted the ring‐forming reaction, whereas similar concentrations of the end‐amino and end‐carboxyl groups were more conducive to the polycondensation reaction. In short, the nitrogen atoms in the end‐amino group on the PA6 molecular chain attack the carbonyl carbon at different sites, including the carbonyl carbon in the amide bond and the carbonyl carbon in the end‐carboxyl group, which is the key to the strength of the ring‐formation and polycondensation reactions.

Simulation-Guided Engineering Enables a Functional Switch in Selinadiene Synthase toward Hydroxylation.

Engineering sesquiterpene synthases to form predefined alternative products is a major challenge due to their diversity in cyclization mechanisms and our limited understanding of how amino acid changes affect the steering of these mechanisms. Here, we use a combination of atomistic simulation and site-directed mutagenesis to engineer a selina-4(15),7(11)-diene synthase (SdS) such that its final reactive carbocation is quenched by trapped active site water, resulting in the formation of a complex hydroxylated sesquiterpene (selin-7(11)-en-4-ol). Initially, the SdS G305E variant produced 20% selin-7(11)-en-4-ol. As suggested by modeling of the enzyme-carbocation complex, selin-7(11)-en-4-ol production could be further improved by varying the pH, resulting in selin-7(11)-en-4-ol becoming the major product (48%) at pH 6.0. We incorporated the SdS G305E variant along with genes from the mevalonate pathway into bacterial BL21(DE3) cells and demonstrated the production of selin-7(11)-en-4-ol at a scale of 10 mg/L in batch fermentation. These results highlight opportunities for the simulation-guided engineering of terpene synthases to produce predefined complex hydroxylated sesquiterpenes.

Nickel-catalyzed defluorinative asymmetric cyclization of Trifluoromethyl-substituted 1,6-Enynes: Insights from DFT calculations on the reaction mechanism and selectivity

Density functional theory (DFT) calculations were employed to elucidate the mechanism and selectivity of nickel-catalyzed defluorinative asymmetric cyclization reactions of trifluoromethyl-substituted 1,6-enynes. The results indicate that the product is formed via a stepwise addition cyclization mechanism, including sequential steps of ligand coordination, transmetalation, ligand exchange, alkyne insertion, olefin insertion, β-F elimination, another transmetalation, and a final ligand exchange. The regioselectivity is primarily governed by the alkyne insertion step, where electrostatic interactions strongly favor 1,2-insertion of the carbon-carbon triple bond over 2,1-insertion. The enantioselectivity is largely determined during the insertion step of the olefin insertion step, with the (S)-product forming preferentially over the (R)-product due to stronger non-covalent interactions between the ligand and the substrate, minimal catalyst conformational distortion, and enhanced electronic interactions between the catalyst and the substrate.

Mechanism of Intramolecular Cyclization of Quaternary Ammonium Salts Containing a β,γ-Unsaturated Fragment and Various π4 Fragments

Mechanism of Intramolecular Cyclization of Quaternary Ammonium Salts Containing a β,γ-Unsaturated Fragment and Various π4 Fragments

Competing Domino Knoevenagel-Cyclization Sequences with N-Arylcinnamylamines.

Domino Knoevenagel-cyclization reactions of N-arylcinnamylamines were carried out with active methylene reagents, which took place with five competing cyclization mechanisms: intramolecular hetero Diels-Alder reaction, stepwise polar [2 + 2] cycloaddition, styryl or aza-Diels-Alder reactions followed by rearomatization, and [1,5]-hydride shift-6-endo cyclization. In the stepwise aza-Diels-Alder reaction, the N-vinylpyridinium moiety acted as an azadiene, producing a condensed heterocycle with tetrahydroquinolizinium and tetrahydroquiniline subunits. Antiproliferative activity with low micromolar IC50 values was identified for some of the novel scaffolds.

One‐Pot Triple and Mixed Double Michael Addition of Activated Alkenes to 2‐Oxindole and 7‐Aza‐2‐Oxindole: Synthesis of C‐3/N‐Functionalized Carbon Rich 2‐Oxindole and 7‐Aza‐2‐Oxindole Derivatives

AbstractA simple, efficient, and atom‐economical, one‐pot triple Michael Addition of activated alkenes to 2‐oxindole, 7‐aza‐2‐ indolone, and N‐methyl‐5‐bromo‐7‐aza‐2‐indolone has been developed. Significantly, multifunctionalities have also been achieved via one‐pot mixed Michael addition using the equimolar amount of two different activated alkenes. The reaction provided C‐3 and N‐functionalized carbon‐rich 7‐aza‐2‐oxindole derivatives. The scope of the reaction using diverse activated alkenes has been tested to provide the title compounds. The structure of the representative compounds has been established by the XRD method. Synthetic transformation of representative compounds is demonstrated to provide the respective 3‐spirooctane‐2‐oxindole derivatives in excellent yield. A plausible mechanism for cyclization is provided.

Catalytic Mechanism and Heterologous Biosynthesis Application of Sesquiterpene Synthases.

Sesquiterpenes comprise a diverse group of natural products with a wide range of applications in cosmetics, food, medicine, agriculture, and biofuels. Heterologous biosynthesis is increasingly employed for sesquiterpene production, aiming to overcome the limitations associated with chemical synthesis and natural extraction. Sesquiterpene synthases (STSs) play a crucial role in the heterologous biosynthesis of sesquiterpene. Under the catalysis of STSs, over 300 skeletons are produced through various cyclization processes (C1-C10 closure, C1-C11 closure, C1-C6 closure, and C1-C7 closure), which are responsible for the diversity of sesquiterpenes. According to the cyclization types, we gave an overview of advances in understanding the mechanism of STSs cyclization from the aspects of protein crystal structures and site-directed mutagenesis. We also summarized the applications of engineering STSs in the heterologous biosynthesis of sesquiterpene. Finally, the bottlenecks and potential research directions related to the STSs cyclization mechanism and application of modified STSs were presented.

Discovery of a Fungal P450 with an Unusual Two-Step Mechanism for Constructing a Bicyclo[3.2.2]nonane Skeleton.

The successful biomimetic or chemoenzymatic synthesis of target natural products (NPs) and their derivatives relies on enzyme discovery. Herein, we discover a fungal P450 BTG5 that can catalyze the formation of a bicyclo[3.2.2]nonane structure through an unusual two-step mechanism of dimerization and cyclization in the biosynthesis of beticolin 1, whose bicyclo[3.2.2]nonane skeleton connects an anthraquinone moiety and a xanthone moiety. Further investigation reveals that BTG5-T318 not only determines the substrate selectivity but also alters the catalytic reactions, which allows the separation of the reaction to two individual steps, thereby understanding its catalytic mechanism. It reveals that the first heterodimerization undergoes the common oxidation process for P450s, while the second uncommon formal redox-neutral cyclization step is proved as a redox-mediated reaction, which has never been reported. Therefore, this work advances our understanding of P450-catalyzed reactions and paves the way for expansion of the diversity of this class of NPs through synthetic biology.

Functional and Mechanistic Characterization of the 4,5-diepi-Isoishwarane Synthase from the Liverwort Radula lindenbergiana.

The microbial type sesquiterpene synthase RlMTPSL4 from the liverwort Radula lindenbergiana was investigated for its products, showing the formation of several sesquiterpene hydrocarbons. The main product was structurally characterized as the new compound 4,5-diepi-isoishwarane, while the side products included the known hydrocarbons germacrene A, α-selinene, eremophilene and 4,5-diepi-aristolochene. The cyclization mechanism towards 4,5-diepi-isoishwarane catalyzed by RlMTPSL4 was investigated through isotopic labeling experiments, revealing the stereochemical course for the deprotonation step to the neutral intermediate germacrene A, a reprotonation for its further cyclization, and a 1,2-hydride shift along the cascade. The absolute configuration of 4,5-diepi-isoishwarane was determined using a stereoselective deuteration approach, revealing an absolute configuration typically observed for a microbial type sesquiterpene.

Palladium(0) π-Lewis Base Catalysis: Concept and Development.

The development of a new catalytic strategy plays a vital role in modern organic chemistry since it permits bond formation in an unprecedented and more efficient manner. Although the application of preformed metal complexes as π-base-activated reagents have enabled diverse transformations elegantly, the concept and strategy by directly utilizing transition metals as efficient π-Lewis base catalysts remain underdeveloped, especially in the field of asymmetric catalysis. Here, we outline our perspective on the discovery of palladium(0) as an efficient π-Lewis base catalyst, which is capable of increasing the highest occupied molecular orbital (HOMO) energy of both electron-neutral and electron-deficient 1,3-dienes and 1,3-enynes upon flexible η2-complexes formed in situ and resultant π-backdonation. Thus, fruitful carbon-carbon-forming reactions with diverse electrophiles can be achieved enantioselectively in a vinylogous addition pattern, which is conceptually different from the classical oxidative cyclization mechanism. Emphasis will be given to the concept and mechanism elucidation, catalytic features, and reaction design together with perspective on the further development of this emerging field.

Synthesis of 1,1'-Bicarbazoles by Sequential Iron(III)- and Palladium(II)-Catalyzed Oxidative Coupling Reactions.

The iron(III)-catalyzed oxidative coupling of diarylamines to 2,2'-bis(arylamino)-1,1'-biaryls and subsequent twofold palladium(II)-catalyzed oxidative cyclization provide a convergent synthetic route to 1,1'-bicarbazoles. Screening a range of different palladium(II) salts led to palladium(II) acetate, pivalate, and hexafluoroacetylacetonate as the most efficient catalysts. Remarkably, the twofold palladium(II)-catalyzed oxidative cyclization can also be performed under argon. The mechanism for the oxidative cyclization under an inert gas presumably involves regeneration of the catalytically active palladium(II) species by oxidative addition of pivalic acid.