Density functional theory guide for copolymerization mechanism between allyl radical with radicalophile: photo-driven radical mediated [3 + 2] cyclization.

CONTEXT: The challenge of activating inert allyl monomers for polymerization has persisted, prompting our proposal of the photo-driven radical mediated [3 + 2] cyclization reaction (PRMC). This innovative approach significantly expedites the homopolymerization of multi-allyl monomers, enabling the synthesis of embolic microspheres for hepatocellular carcinoma interventions. PRMC involves allyl monomers to form allylic radicals and then radicals participating in a cycloaddition reaction with unsaturated olefins as radicalophiles to form cyclopentane-based radical products. While extensively studied in the theoretical and experimental homopolymerization, PRMC's application in copolymerization remains unexplored. To address this knowledge gap, we explored the elementary reaction, selecting allyl methyl ether radicals (AMER) and α,ß-unsaturated ketones as radicalophiles for copolymerization investigations by density functional theory (DFT) analysis. We quantified energy differences between ground and excited states of reactants, elucidated frontier molecular orbitals, and assessed thermodynamic data for copolymerization feasibility. We also evaluated the electronic properties of reactants, predicting the reactivity of radicalophiles and the interactions of intermolecular reactions. Additionally, we applied transition state theory and interaction/deformation models and conducted a local orbital analysis to comprehensively study excess electron distribution and gyration radius of cyclic radical product. Our findings offer vital insights into PRMC's potential in copolymerization. This research provides a robust theoretical foundation for practical application, enhancing the polymerization field. METHODS: Based on density functional theory (DFT), the calculations were performed at the M06-2X/6-311 + + G(d,p) level in/by Gaussian 16 package. Subsequently, our analytical results apply time-dependent density-functional theory (TD-DFT) and solvent modeling (SMD). Single-point energy calculations determine the driving force behind the radicals' reaction with radicalophiles. Furthermore, we assessed the electrostatic potential (ESP) of the reactants. The results of the calculations were visualized by the Multiwfn 3.6 and VMD 1.9 programs.

Recent progresses in the cyclization and oxidation of polyketide biosynthesis.

Polyketides represent an important class of natural products, renowned for their intricate structures and diverse biological activities. In contrast to common fatty acids, polyketides possess relatively more rigid carbon skeletons, more complex ring systems, and chiral centers. These structural features are primarily achieved through distinctive enzymatic cyclizations and oxidations as tailoring steps. In this opinion, we discuss the recent progress in deciphering the mechanisms of cyclization and oxidation within polyketide biosynthesis. By shedding light on these enzymatic processes, this article seeks to motivate the community to unravel the remaining mysteries surrounding cyclase and oxidase functionalities and to explore novel polyketide natural products through genome mining.

Total Biosynthesis of Circular Bacteriocins by Merging the Genetic Engineering and Enzymatic Catalysis.

Circular bacteriocins are known for their structural stability and effective antimicrobial properties, positioning them as potential natural food preservatives. However, their widespread application is impeded by restricted availability. This research developed a total biosynthesis platform for circular bacteriocins, with a focus on AS-48 by involving recombinant production of the linear precursor in Escherichia coli, followed by enzymatic cyclization of the precursor into cyclic AS-48 using the ligase butelase-1 in vitro. An important discovery is that, aside from fusion tags, the C-terminal motif LE and LEKKK also could affect the expression yield of the precursor. This biosynthesis platform is both versatile and high-yielding, achieving yields of 10-20 mg/L of AS-48. Importantly, the biosynthetic AS-48 exhibited a secondary structure and antimicrobial activities comparable to those of the native molecules. As such, this work proposes an effective synthetic approach for circular bacteriocins, facilitating their advancement and application in the food industry.

Ordered Carbonaceous Framework Synthesized from Hexaazatrinaphthylene with Enediyne Groups via Solid-State Bergman Cyclization Reaction.

Porous materials synthesized through bottom-up approaches, such as metal-organic frameworks and covalent organic frameworks, have attracted attention owing to their design flexibility for functional materials. However, achieving the chemical and thermal stability of these materials for various applications is challenging considering the reversible coordination bonds and irreversible covalent bonds in their frameworks. Thus, ordered carbonaceous frameworks (OCFs) emerge as a promising class of bottom-up materials with good periodicity, thermal and chemical stability, and electrical conductivity. However, a few OCFs have been reported owing to the limited range of precursor molecules. Herein, we designed a hexaazatrinaphthylene-based molecule with enediyne groups as a precursor molecule for synthesizing an OCF. The solid-state Bergman cyclization of enediyne groups at a low temperature formed a microporous polymer and an OCF, exhibiting redox activity and demonstrating their potential for electrochemical applications. The microporous polymer was used as an active material in sodium-ion batteries, while the OCF was used as an electrochemical capacitor. These findings illustrate the utility of the Bergman cyclization reaction for synthesizing microporous polymers and OCFs with a customizable functionality for broad applications.

Reinforcing thermostability and pH robustness of exo-inulinase facilitated by ReverseTag/ReverseCatcher tagging system.

Enhancing protein stability is pivotal in the field of protein engineering. Protein self-cyclization using peptide a tagging system has emerged as an effective strategy for augmenting the thermostability of target proteins. In this study, we utilized a novel peptide tagging system, ReverseTag/ReverseCatcher, which leverages intramolecular ester bond formation. Initially, we employed GFP as a model to validate the feasibility of cyclization mediated by ReverseTag/ReverseCatcher in improving the protein thermostability. Cyclized GFP (cGFP) retained 30 % of its relative fluorescence after a 30-min incubation at 100 °C, while both GFP and linear GFP (lGFP) completely lost their fluorescence within 5 min. Additionally, we applied this method to exo-inulinase (EXINU), resulting in a variant named cyclized EXINU (cEXINU). The T50 and t1/2 values of cEXINU exhibited significant enhancements of 10 °C and 10 min, respectively, compared to EXINU. Furthermore, post-cyclization, EXINU demonstrated a broad operational pH range from 5 to 10 with sustained catalytic activity, and cEXINU maintained a half-life of 960 min at pH 5 and 9. Molecular dynamics simulations were conducted to elucidate the mechanisms underlying the enhanced thermostability and pH robustness of EXINU following cyclization. This study highlights that cyclization substanitially enhances the stability of both highly stable protein GFP and low-stable protein EXINU, mediated by the ReverseTag/ReverseCatcher tagging system. The ReverseTag/ReverseCatcher tagging system proves to be a potent conjugation method, with potential applications in improving thermostability, pH robustness, and other areas of protein engineering.

Radical-Mediated Trifunctionalization Reactions.

Synthetic radicals have intrinsic power for cascading and multifunctional reactions to construct diverse molecular scaffolds. In the previous review series, we covered 1,2-difunctionalizations, remote 1,3-, 1,4-, 1,5-, 1,6-, and 1,7-difunctionalizations, addition followed by cyclization reactions, and cycloaddition-initiated difunctionalizations. Presented in this paper are radical addition-initiated trifunctionalization reactions of alkenes, alkynes, and their derivatives. After the initial radical addition, there are different pathways, such as group or hydrogen atom transfer, cyclization, and radical coupling, to complete the second and third functionalizations.

Electrochemical radical cation aza-Wacker cyclizations.

Electrochemical or photochemical single-electron oxidation of bench-stable substrates can generate radical cations that offer unique reactivities as intermediates in various bond-formation processes. Such intermediates can potentially take part in both radical and ionic bond formation; however, the mechanisms involved are complicated and not fully understood. Herein, we report electrochemical radical cation aza-Wacker cyclizations under acidic conditions, which are expected to proceed via radical cations generated by single-electron oxidation of alkenes.

Novel oxidative routes to N-arylpyridoindazolium salts.

A novel facile approach to N-arylpyridoindazolium salts is proposed, based on direct oxidation of the ortho-pyridine substituted diarylamines, either using bis(trifluoroacetoxy)iodobenzene as an oxidant, or electrochemically, via potentiostatic oxidation. Electrochemical synthesis occurs under mild conditions; no chemical reagents are required except electric current. Both approaches can be considered as a late-stage functionalization; easily available ortho-pyridyl-substituted diarylamines are used as the precursors.

Palladium(0) and Brønsted Acid Co-catalyzed Enantioselective Hydro-Cyclization of 2,4-Dienyl Hydrazones and Oximes.

The transition metal-catalyzed asymmetric hydro-functionalization of 1,3-dienes has been well explored, but most reactions focus on electron-neutral substrates in an intermolecular manner. Here we first demonstrate that readily available 2,4-dienyl hydrazones and oximes can be efficiently utilized in the hydro-cyclization reaction under co-catalysis of a Brønsted acid and a chiral palladium complex, furnishing multifunctional dihydropyrazones and dihydroisoxazoles, respectively. Diverse substitution patterns for both types of electron-deficient diene compounds are tolerated, and corresponding heterocycles were generally constructed with moderate to excellent enantioselectivity, which can be elaborated to access products with higher molecular complexity and diversity. Control experiments and density functional theory calculations support that α-regioselective protonation of dienyl substrates by acid and concurrent π-Lewis base activation of Pd0 complex is energetically favoured in the formation of active π-allylpalladium intermediates, and an outer-sphere allylic amination or etherification mode is adopted to deliver the observed cyclized products enantioselectively.

A Cascade C(sp3)-H Annulation Involving C(alkyl),C(alkyl)-Palladacycle Intermediates.

C-H bond functionalization involving C,C-palladacycle intermediates provides a unique platform for developing novel reactions. However, the vast majority of studies have been limited to the transformations of C(aryl),C-palladacycles. In sharp contrast, catalytic reactions involving C(alkyl),C(alkyl)-palladacycles have rarely been reported. Herein, we disclose an unprecedented cascade C(sp3)-H annulation involving C(alkyl),C(alkyl)-palladacycles. In this protocol, alkene-tethered cycloalkenyl bromides undergo intramolecular Heck/C(sp3)-H activation to generate C(alkyl),C(alkyl)-palladacycles, which can be captured by α-bromoacrylic acids to afford tricyclic fused pyridinediones. In addition, this strategy can also be applied to indole-tethered cycloalkenyl bromides to construct pentacyclic fused pyridinediones via suquential Heck dearomatization/C(sp3)-H activation/decarboxylative cyclization. Notably, the removal of α-bromoacrylic acids in the reaction of alkene-tethered cycloalkenyl bromides can build an interesting tricyclic skeleton containing a four-membered ring. Preliminary mechanistic experiments indicate that five-membered C(alkyl),C(alkyl)-palladacycles serve as the key intermediates. Meanwhile, density functional theory (DFT) calculations have provided insights into the reaction pathway.

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations.

A steadily increasing number of reports have been published on chemo-enzymatic synthesis methods that integrate biosynthetic enzymatic transformations with chemical conversions. This review focuses on the total synthesis of natural products and classifies the enzymatic reactions into three categories. The total synthesis of five natural products: cotylenol, trichodimerol, chalcomoracin, tylactone, and saframycin A, as well as their analogs, is outlined with an emphasis on comparing these chemo-enzymatic syntheses with the corresponding natural biosynthetic pathways.

Ring opening of photogenerated azetidinols as a strategy for the synthesis of aminodioxolanes.

α-Aminoacetophenones are identified as promising building blocks for the synthesis of highly substituted dioxolanes. The presented strategy is founded on the build and release of molecular strain and achieves a formal transposition of a methyl group. During light irradiation, 3-phenylazetidinols are forged as reaction intermediates, which readily undergo ring opening upon the addition of electron-deficient ketones or boronic acids. Key to the successful development of this two-step process is the identification of a benzhydryl-protecting group, which orchestrates the photochemical Norrish-Yang cyclization and facilitates the subsequent ring opening.

Cooperative NHC and Photoredox Catalyzed Radical Aminoacylation of Alkenes to Tetrahydropyridazines.

Tetrahydropyridazines constitute an important structural motif found in numerous natural products and pharmaceutical compounds. Herein, we report an aminoacylation reaction of alkenes that enables the synthesis of 1,4,5,6-tetrahydropyridazines through cooperative N-heterocyclic carbene (NHC) and photoredox catalysis. This approach involves the 6-endo-trig cyclization of N-centered hydrazonyl radicals, generated via single-electron oxidation of hydrazones, followed by a radical-radical coupling step. The mild process tolerates a wide range of common functional groups and affords a variety of tetrahydropyridazines in moderate to high yields. Preliminary investigations using chiral NHC catalysts demonstrate the potential of this protocol for asymmetric radical reactions.

"Top-down" overexpression optimization of butelase-1 in Escherichia coli and its application in anti-tumor peptides.

Butelase-1, the fastest known Asn/Asp-specific peptide ligase capable of catalyzing peptide ligation and cyclization, holds promising application prospects in the fields of food and biology. However, limited research exists on its recombinant expression and potential applications in peptide drugs. In this study, the activity of recombinantly-produced butelase-1 was enhanced by co-expressing it with a molecular chaperone in the SHuffle T7 strain. By introducing single or multiple synonymous rare codons at the beginning of the coding regions of beta-strand or alpha-helix, in combination with ribosomal binding site engineering, the activity of butelase-1 could be further improved. Consequently, the butelase-1 with a specific activity of 386.93 U/mg and a catalytic efficiency of 11,048 M-1 s-1 was successfully prepared in E. coli, resulting in a total activity of 8183.54 U/L and a yield of about 100 mg/L. This optimized butelase-1 was then used to efficiently cyclize the redesigned anti-cancer peptide lunasin, leading to enhanced bioavailability and anti-cancer effects. Overall, this study not only provided valuable biotechnology strategies for improving the recombinant expression of butelase-1 but also demonstrated a successful application for enhancing the biological efficacy of anti-cancer peptides.

Divergent Synthesis of 17-nor-Cephalotane Diterpenoids through Developed Ynol-diene Cyclization.

On the basis of a novel ynol-diene cyclization developed as a rapid access to tropone unit, the first divergent strategy to 17-nor-cephalotane diterpenoids has been successfully established. Combining with a bioinspired stereoselective dual hydrogenation, the divergent total synthesis of (+)-3-deoxyfortalpinoid F, (+)-harringtonolide, (-)-fortalpinoids M/N/P, and analog (-)-20-deoxocephinoid P have been achieved in 14-17 linear longest steps starting from commercially available materials.

Gold-Catalyzed Diyne-Ene Annulation for the Synthesis of Polysubstituted Benzenes through Formal [3+3] Approach with Amide as the Critical Co-Catalyst.

The one-step synthesis of tetra-substituted benzenes was accomplished via gold-catalyzed diyne-ene annulation. Distinguished from prior modification methods, this novel strategy undergoes formal [3+3] cyclization, producing polysubstituted benzenes with exceptional efficiency.  The critical factor enabling this transformation was the introduction of amides, which were reported for the first time in gold catalysis as covalent nucleophilic co-catalysts.  This interesting protocol not only offers a new strategy to achieve functional benzenes with high efficiency, but also enlightens potential new reaction pathways within gold-catalyzed alkyne activation processes.

PICKAPEP: An application for parameter calculation and visualization of cyclized and modified peptidomimetics.

The interest in peptides and especially in peptidomimetic structures has risen enormously in the past few years. Novel modification strategies including nonnatural amino acids, sophisticated cyclization strategies, and side chain modifications to improve the pharmacokinetic properties of peptides are continuously arising. However, a calculator tool accompanying the current development in peptide sciences towards modified peptides is missing. Herein, we present the application PICKAPEP, enabling the virtual construction and visualization of peptidomimetics ranging from well-known cyclized and modified peptides such as ciclosporin A up to fully self-designed peptide-based structures with custom amino acids. Calculated parameters include the molecular weight, the water-octanol partition coefficient, the topological polar surface area, the number of rotatable bonds, and the peptide SMILES code. To our knowledge, PICKAPEP is the first tool allowing users to add custom amino acids as building blocks and also the only tool giving the possibility to process large peptide libraries and calculate parameters for multiple peptides at once. We believe that PICKAPEP will support peptide researchers in their work and will find wide application in current as well as future peptide drug development processes. PICKAPEP is available open source for Windows and Mac operating systems (https://urldefense.com/v3/__https://www.research-collection.ethz.ch/handle/20.500.11850/681174__;!!N11eV2iwtfs!qt5f_2lNd6IZUDH1HVSVwg0zYzS8-nFazQ8c61jS5GaD5vkVS5C3igyfh3haJRnaX8ugW7o9VWUiCihPqcptmaWoqwYf9LvZTQ$).

Asymmetric Total Synthesis of Euphordraculoate A and Pedrolide.

Here we report the asymmetric total syntheses of two rearranged tigliane diterpenoids, euphordraculoate A and pedrolide. A reductive dihydroxylation cascade and Nazarov cyclization were performed to generate euphordraculoate A, which was subjected to a cascade of Eu-promoted dienyl enolization, intramolecular Diels-Alder reaction and enol-ketone tautomerization to afford pedrolide, a pathway consistent with our proposal for the biogenesis of pedrolide.

The West Nile virus genome harbors essential riboregulatory elements with conserved and host-specific functional roles.

West Nile virus (WNV) is an arthropod-borne, positive-sense RNA virus that poses an increasing global threat due to warming climates and lack of effective therapeutics. Like other enzootic viruses, little is known about how host context affects the structure of the full-length RNA genome. Here, we report a complete secondary structure of the entire WNV genome within infected mammalian and arthropod cell lines. Our analysis affords structural insights into multiple, conserved aspects of flaviviral biology. We show that the WNV genome folds with minimal host dependence, and we prioritize well-folded regions for functional validation using structural homology between hosts as a guide. Using structure-disrupting, antisense locked nucleic acids, we then demonstrate that the WNV genome contains riboregulatory structures with conserved and host-specific functional roles. These results reveal promising RNA drug targets within flaviviral genomes, and they highlight the therapeutic potential of ASO-LNAs as both WNV-specific and pan-flaviviral therapeutic agents.

Recent Progress in Free Radical Transformations of Allenamides.

Allenamides are special allenes, and the unique reactivity, selectivity (both stereoselective and regionally selective) and stability of allenamides have been widely studied. In this review, the development of the free radical transformation of allenamides over the last few years will be summarized. This review discusses in detail in three parts: intermolecular radical addition to C- X (X = N, S, O, Se) bonds, metal salt mediated cyclization of allenamides, and photocatalytic cyclization of allenamides. In addition, reasonable details of the mechanisms are provided for the vast majority of these transformations.