Electrophilic Azides for Materials Synthesis and Chemical Biology

Synthesis of Multisubstituted 1,2,3-Triazoles: Regioselective Formation and Reaction Mechanism

A synthetically useful approach to functionalized triazoles is described via the reaction of β-carbonyl phosphonates and azides. 1,4- and 1,5-disubstituted and 1,4,5-trisubstituted triazoles can be regio- and chemoselectively accessed under mild conditions in good to excellent yields (31 examples, up to 99%). A mechanism is proposed that rationalizes the avoidance of the 4-phosphonate byproducts, which is aligned with crystallographic and experimental evidence.

Maltose-Derivatized Fluorescence Turn-On Imaging Probe for Bacteria Detection

We report a maltose-derivatized fluorescence turn-on imaging probe, Mal-Cz, to detect E. coli and Staphylococci. The fluorescence turn-on is achieved through an intramolecular C-H insertion reaction of the perfluoroaryl azide-functionalized carbazole to give a fluorescent product. Confocal fluorescence microscopy confirmed the successful uptake of Mal-Cz by E. coli and Staphylococci upon photoactivation. The Mal-Cz probe could selectively detect E. coli and S. epidermidis in the presence of P. aeruginosa and M. smegmatis without interference from these bacteria. Both the photoactivation and bacteria detection can be accomplished using a hand-held UV lamp at 365 nm, with the limit of detection of 103 CFU/mL by the naked eye. Mal-Cz could also be used to detect E. coli and S. epidermidis spiked in milk by the naked eye under a hand-held UV lamp. The uptake of Mal-Cz requires metabolically active bacteria: the uptake was reduced in stationary phase bacteria and was diminished in bacteria that were killed by heating or treating with antibiotics or sodium azide. The uptake decreased with increasing concentration of added free maltose, indicating that Mal-Cz hijacked the maltose uptake pathways. In E. coli, the maltose transport systems, including maltoporin LamB, maltose binding protein MBP, and the maltose ATP binding cassette (ABC) transporter MalFGK2, are all critical for the transport of Mal-Cz. The uptake was diminished in the deletion mutants ΔLamB, ΔMalE, ΔMalF, and ΔMalK.

A Convenient One-Pot Synthesis of a Sterically Demanding Aniline from Aryllithium Using Trimethylsilyl Azide, Conversion to β-Diketimines and Synthesis of a β-Diketiminate Magnesium Hydride Complex

This work reports the one-pot synthesis of sterically demanding aniline derivatives from aryllithium species utilising trimethylsilyl azide to introduce amine functionalities and conversions to new examples of a common N,N'-chelating ligand system. The reaction of TripLi (Trip = 2,4,6-iPr3-C6H2) with trimethylsilyl azide afforded the silyltriazene TripN2N(SiMe3)2 in situ, which readily reacts with methanol under dinitrogen elimination to the aniline TripNH2 in good yield. The reaction pathways and by-products of the system have been studied. The extension of this reaction to a much more sterically demanding terphenyl system suggested that TerLi (Ter = 2,6-Trip2-C6H3) slowly reacted with trimethylsilyl azide to form a silyl(terphenyl)triazenide lithium complex in situ, predominantly underwent nitrogen loss to TerN(SiMe3)Li in parallel, which afforded TerN(SiMe3)H after workup, and can be deprotected under acidic conditions to form the aniline TerNH2. TripNH2 was furthermore converted to the sterically demanding β-diketimines RTripnacnacH (=HC{RCN(Trip)}2H), with R = Me, Et and iPr, in one-pot procedures from the corresponding 1,3-diketones. The bulkiest proligand was employed to synthesise the magnesium hydride complex [{(iPrTripnacnac)MgH}2], which shows a distorted dimeric structure caused by the substituents of the sterically demanding ligand moieties.

Chemodivergent Staudinger Reactions of Secondary Phosphine Oxides and Application to the Total Synthesis of LL-D05139β Potassium Salt

Unprecedented Staudinger reaction modes of secondary phosphine oxides (SPO) and organic azides are herein disclosed. By the application of various additives, selective nitrogen atom exclusion from the azide group has been achieved. Chlorotrimethylsilane mediates a stereoretentive Staudinger reaction with a 2-N exclusion which provides a valuable method for the synthesis of phosphinic amides and can be considered complementary to the stereoinvertive Atherton-Todd reaction. Alternatively, a 1-N exclusion pathway is promoted by acetic acid to provide the corresponding diazo compound. The effectiveness of this protocol has been further demonstrated by the total synthesis of the diazo-containing natural product LL-D05139β, which was prepared as a potassium salt for the first time in 6 steps and 26.5 % overall yield.

Expedient synthesis of imino-C-nucleoside fleximers featuring a one-pot procedure to prepare aryl triazoles

Nucleoside analogues such as the antiviral agents galidesivir and ribavirin are of synthetic interest. This work reports a "one-pot" preparation of similar fleximers using a bifunctional copper catalyst that generates the aryl azide in situ, which is captured by a terminal alkyne to effect triazole formation.

Azide-Masked Fluorescence Turn-On Probe for Imaging Mycobacteria

A fluorescence turn-on probe, an azide-masked and trehalose-derivatized carbazole (Tre-Cz), was developed to image mycobacteria. The fluorescence turn-on is achieved by photoactivation of the azide, which generates a fluorescent product through an efficient intramolecular C-H insertion reaction. The probe is highly specific for mycobacteria and could image mycobacteria in the presence of other Gram-positive and Gram-negative bacteria. Both the photoactivation and detection can be accomplished using a handheld UV lamp, giving a limit of detection of 10³ CFU/mL, which can be visualized by the naked eye. The probe was also able to image mycobacteria spiked in sputum samples, although the detection sensitivity was lower. Studies using heat-killed, stationary-phase, and isoniazid-treated mycobacteria showed that metabolically active bacteria are required for the uptake of Tre-Cz. The uptake decreased in the presence of trehalose in a concentration-dependent manner, indicating that Tre-Cz hijacked the trehalose uptake pathway. Mechanistic studies demonstrated that the trehalose transporter LpqY-SugABC was the primary pathway for the uptake of Tre-Cz. The uptake decreased in the LpqY-SugABC deletion mutants ΔlpqY, ΔsugA, ΔsugB, and ΔsugC and fully recovered in the complemented strain of ΔsugC. For the mycolyl transferase antigen 85 complex (Ag85), however, only a slight reduction of uptake was observed in the Ag85 deletion mutant ΔAg85C, and no incorporation of Tre-Cz into the outer membrane was observed. The unique intracellular incorporation mechanism of Tre-Cz through the LpqY-SugABC transporter, which differs from other trehalose-based fluorescence probes, unlocks potential opportunities to bring molecular cargoes to mycobacteria for both fundamental studies and theranostic applications.

Mechanistic DFT Study of 1,3-Dipolar Cycloadditions of Azides with Guanidine

Density functional calculations SMD(chloroform)//B3LYP/6-311+G(2d,p) were employed in the computational study of 1,3-dipolar cycloadditions of azides with guanidine. The formation of two regioisomeric tetrazoles and their rearrangement to cyclic aziridines and open-chain guanidine products were modeled. The results suggest the feasibility of an uncatalyzed reaction under very drastic conditions since the thermodynamically preferred reaction path (a), which involves cycloaddition by binding the carbon atom from guanidine to the terminal azide nitrogen atom, and the guanidine imino nitrogen with the inner N atom from the azide, has an energy barrier higher than 50 kcal mol^-1. The formation of the other regioisomeric tetrazole (imino nitrogen interacts with terminal N atom of azide) in direction (b) can be more favorable and proceed under milder conditions if alternative activation of the nitrogen molecule releases (e.g., photochemical activation), or deamination could be achieved because these processes have the highest barrier in the less favorable (b) branch of the mechanism. The introduction of substituents should favorably affect the cycloaddition reactivity of the azides, with the greatest effects expected for the benzyl and perfluorophenyl groups.

Tris(4-azidophenyl)methanol - a novel and multifunctional thiol protecting group

The novel tris(4-azidophenyl)methanol, a multifunctionalisable aryl azide, is reported. The aryl azide can be used as a protecting group for thiols in peptoid synthesis and can be cleaved under mild reaction conditions via a Staudinger reduction. Moreover, the easily accessible aryl azide can be functionalised via copper-catalysed cycloaddition reactions, providing additional opportunities for materials chemistry applications.

Trehalose-Grafted Glycopolymer: Synthesis via the Staudinger Reaction and Capture of Mycobacteria

A new trehalose-grafted poly(2-hydroxyethyl methacrylate) (HEMA) glycopolymer was synthesized via the perfluorophenyl azide (PFPA)-mediated Staudinger reaction between poly(HEMA-co-HEMA-PFPA) and a diphenylphosphine-derivatized trehalose. The reaction occurred rapidly at room temperature without the use of any catalyst, giving the trehalose glycopolymers over 68% yield after 1 h. The grafting density of trehalose can be controlled by the copolymer composition in poly(HEMA-co-HEMA-PFPA), resulting in 6.1% (TP1) or 37% (TP2) at 10:1 and 1:1 HEMA/HEMA-PFPA feed ratio, respectively. The trehalose glycopolymer was covalently attached on glass slides or silicon wafers using a thin film of poly(HEMA-co-HEMA-PFPA) as the adhesion layer, achieved through the C-H insertion reaction of the photogenerated singlet perfluorophenyl nitrene. To demonstrate the ability of the trehalose glycopolymer to capture mycobacteria, arrays of the trehalose glycopolymer were fabricated and treated with Mycobacterium smegmatis. Results from the optical, fluorescence, and scanning electron microscopy showed that mycobacteria were indeed captured on the trehalose glycopolymer. The amount of mycobacteria captured increased with the percent trehalose in the trehalose glycopolymer and also with the concentration of the trehalose glycopolymer. In addition, the captured bacteria could be visualized by the naked eye under the illumination of a hand-held UV lamp.

Targeted activation in localized protein environments via deep red photoredox catalysis

State-of-the-art photoactivation strategies in chemical biology provide spatiotemporal control and visualization of biological processes. However, using high-energy light (λ < 500 nm) for substrate or photocatalyst sensitization can lead to background activation of photoactive small-molecule probes and reduce its efficacy in complex biological environments. Here we describe the development of targeted aryl azide activation via deep red-light (λ = 660 nm) photoredox catalysis and its use in photocatalysed proximity labelling. We demonstrate that aryl azides are converted to triplet nitrenes via a redox-centric mechanism and show that its spatially localized formation requires both red light and a photocatalyst-targeting modality. This technology was applied in different colon cancer cell systems for targeted protein environment labelling of epithelial cell adhesion molecule (EpCAM). We identified a small subset of proteins with previously known and unknown association to EpCAM, including CDH3, a clinically relevant protein that shares high tumour-selective expression with EpCAM.

Diazophosphane HPN2

Diazophosphane HPN₂, a heavy analogue of hydrazoic acid (HN₃), has been synthesized at low temperature (10 K) through photolytic reactions of molecular nitrogen (N₂) with phosphine (PH₃) and phosphaketene (HPCO) under irradiations at 193 and 365 nm, respectively. The characterization of HPN₂ and its isotopologues DPN₂ and HP¹⁵N₂ by matrix-isolation IR and UV-vis spectroscopy is supported by quantum chemical calculations at the CCSD(T)-F12a/cc-pVTZ-F12 level of theory. Upon irradiation at 266 nm, the P-N bond in HPN₂ breaks, whereas its photolysis at 193 nm generates the elusive phosphinyl radical ^•PN₂.

The 1,3-Dipolar Cycloaddition From Conception to Quantum Chemical Design

The 1,3‐dipolar cycloaddition (1,3‐DCA) reaction, conceptualized by Rolf Huisgen in 1960, has proven immensely useful in organic, material, and biological chemistry. The uncatalyzed, thermal transformation is generally sluggish and unselective, but the reactivity can be enhanced by means of metal catalysis or by the introduction of either predistortion or electronic tuning of the dipolarophile. These promoted reactions generally go with a much higher reactivity, selectivity, and yields, often at ambient temperatures. The rapid orthogonal reactivity and compatibility with aqueous and physiological conditions positions the 1,3‐DCA as an excellent bioorthogonal reaction. Quantum chemical calculations have been critical for providing an understanding of the physical factors that control the reactivity and selectivity of 1,3‐DCAs. In silico derived design principles have proven invaluable for the design of new dipolarophiles with tailored reactivity. This review discusses everything from the conception of the 1,3‐DCA all the way to the state‐of‐the‐art methods and models used for the quantum chemical design of novel (bioorthogonal) reagents.

Development of a bioorthogonal fluorescence-based assay for assessing drug uptake and delivery in bacteria

Bioorthogonal chemistry can facilitate the development of fluorescent probes that can be used to sensitively and specifically detect the presence of biological targets. In this study, such an assay was developed to evaluate the uptake and delivery of antimicrobials into Escherichia coli, building on and extending previous work which utilised more resource intensive LCMS detection. The bacteria were genetically engineered to express streptavidin in the periplasmic or cytoplasmic compartments, which was used to localise a bioorthogonal probe (BCN-biotin). Azido-compounds which are delivered to these compartments react with the localised BCN-biotin–streptavidin in a concentration-dependent manner via a strain-promoted alkyne–azide cycloaddition. The amount of azido-compound taken up by bacteria was determined by quantifying unreacted BCN-biotin–streptavidin via an inverse electron demand Diels–Alder reaction between remaining BCN-biotin and a tetrazine-containing fluorescent dye. Following optimisation and validation, the assay was used to assess uptake of liposome-formulated azide-functionalised luciferin and cefoxitin. The results demonstrated that formulation into cationic liposomes improved the uptake of azide-functionalised compounds into the periplasm of E. coli, providing insight on the uptake mechanism of liposomes in the bacteria. This newly developed bioorthogonal fluorescence plate-reader based assay provides a bioactivity-independent, medium-to-high throughput tool for screening compound uptake/delivery.

Bioorthogonal alkyne–azide and alkyne–tetrazine chemistries were used to assess drug uptake in bacteria. Azido-drug reacts with streptavidin bound alkyne-biotin within bacteria, the remaining unreacted alkyne is then quantified with a tetrazine-dye.

Chemical versatility of azide radical: journey from a transient species to synthetic accessibility in organic transformations

The generation of azide radical (N₃˙) occurs from its precursors primarily via a single electron transfer (SET) process or homolytic cleavage by chemical methods or advanced photoredox/electrochemical methods. This in situ generated transient open-shell species has unique characteristic features that set its reactivity. In the past, the azide radical was widely used for various studies in radiation chemistry as a 1e^- oxidant of biologically important molecules, but now it is being exploited for synthetic applications based on its addition and intermolecular hydrogen atom transfer (HAT) abilities. Due to the significant role of nitrogen-containing molecules in synthesis, drug discovery, biological, and material sciences, the direct addition onto unsaturated bonds for the simultaneous construction of C-N bond with other (C-X) bonds are indeed worth highlighting. Moreover, the ability to generate O- or C-centered radicals by N₃˙ via electron transfer (ET) and intermolecular HAT processes is also well documented. The purpose of controlling the reactivity of this short-lived intermediate in organic transformations drives us to survey: (i) the history of azide radical and its structural properties (thermodynamic, spectroscopic, etc.), (ii) chemical reactivities and kinetics, (iii) methods to produce N₃˙ from various precursors, (iv) several significant azide radical-mediated transformations in the field of functionalization with unsaturated bonds, C-H functionalization via HAT, tandem, and multicomponent reaction with a critical analysis of underlying mechanistic approaches and outcomes, (v) concept of taming the reactivity of azide radicals for potential opportunities, in this review.

Extracellular Electron Transfer Enables Cellular Control of Cu(I)-Catalyzed Alkyne-Azide Cycloaddition

Extracellular electron transfer (EET) is an anaerobic respiration process that couples carbon oxidation to the reduction of metal species. In the presence of a suitable metal catalyst, EET allows for cellular metabolism to control a variety of synthetic transformations. Here, we report the use of EET from the electroactive bacterium Shewanella oneidensis for metabolic and genetic control over Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC). CuAAC conversion under anaerobic and aerobic conditions was dependent on live, actively respiring S. oneidensis cells. The reaction progress and kinetics were manipulated by tailoring the central carbon metabolism. Similarly, EET-CuAAC activity was dependent on specific EET pathways that could be regulated via inducible expression of EET-relevant proteins: MtrC, MtrA, and CymA. EET-driven CuAAC exhibited modularity and robustness in the ligand and substrate scope. Furthermore, the living nature of this system could be exploited to perform multiple reaction cycles without regeneration, something inaccessible to traditional chemical reductants. Finally, S. oneidensis enabled bioorthogonal CuAAC membrane labeling on live mammalian cells without affecting cell viability, suggesting that S. oneidensis can act as a dynamically tunable biocatalyst in complex environments. In summary, our results demonstrate how EET can expand the reaction scope available to living systems by enabling cellular control of CuAAC.

Replacing amine by azide: Dopamine azide polymerization triggered by sodium periodate

Polydopamine (PDA) have been widely described for a range of biomedical and surface engineering applications. However the structure of PDA remains elusive due to the insoluble nature of the polymer....

Research fronts of Chemical Biology

Over the past decades, researchers have witnessed substantially increasing and ever-growing interests and efforts in Chemical Biology studies, thanks to the development of genome and epi-genome sequencing (revealing potential drug targets), synthetic chemistry (producing new medicines), bioorthogonal chemistry (chemistry in living systems) and high-throughput screening technologies (in vitro cell systems, protein binding assays and phenotypic assays). This report presents literature search results for current research in Chemical Biology, to explore basic principles, summarize recent advances, identify key challenges, and provide suggestions for future research (with a focus on Chemical Biology in the context of human health and diseases). Chemical Biology research can positively contribute to delivering a better understanding of the molecular and cellular mechanisms that accompany pathology underlying diseases, as well as developing improved methods for diagnosis, drug discovery, and therapeutic delivery. While much progress has been made, as shown in this report, there are still further needs and opportunities. For instance, pressing challenges still exist in selecting appropriate targets in biological systems and adopting more rational design strategies for the development of innovative and sustainable diagnostic technologies and medical treatments. Therefore, more than ever, researchers from different disciplines need to collaborate to address the challenges in Chemical Biology.

Synthesis of Azaylide-Based Amphiphiles by the Staudinger Reaction

Catalyst- and reagent-free reactions are powerful tools creating various functional molecules and materials. However, such chemical bonds are usually hydrolysable or require specific functional groups, which limits their use in aqueous media. Herein, we report the development of new amphiphiles through the Staudinger reaction. Simple mixing of chlorinated aryl azide with a hydrophilic moiety and various triarylphosphines (PAr3) gave rise to azaylide-based amphiphiles NPAr3, rapidly and quantitatively. The obtained NPAr3 formed ca. 2 nm-sized spherical aggregates (NPAr3)_n in water. The hydrolysis of NPAr3 was significantly suppressed as compared with those of non-chlorinated amphiphiles nNPAr3. Computational studies revealed that the stability is mainly governed by the decrease in LUMO around the phosphorus atom owing to the o-substituted halogen groups. Furthermore, hydrophobic dyes such as Nile red and BODIPY were encapsulated by the spherical aggregates (NPAr3)_n in water.

Bioorthogonal Reactions of Triarylphosphines and Related Analogues

Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.

Divergent functionalization of α,β-enones: catalyst-free access to β-azido ketones and β-amino α-diazo ketones

A simple and practical method for the azidation of β-fluoroalkyl α,β-unsaturated ketones to access a wide variety of fluorinated nitrogenous carbonyl compounds is developed. Different from existing precedents, neither a metallic nor an organic catalyst was involved in our strategy. Judicious choice of solvents allows for the modulation of the reaction outcomes, delivering β-azido ketones or β-amino α-diazo ketones. The reaction system features environmental friendliness, mild conditions, simplicity and excellent functional group tolerance.

Electrophilic Aminating Agents in Total Synthesis

Classical amination methods involve the reaction of a nitrogen nucleophile with an electrophilic carbon center; however, in recent years, umpoled strategies have gained traction where the nitrogen source acts as an electrophile. A wide range of electrophilic aminating agents are now available, and these underpin a range of powerful C−N bond‐forming processes. In this Review, we highlight the strategic use of electrophilic aminating agents in total synthesis.

Iron-catalyzed stereoselective haloamidation of amide-tethered alkynes

In this work, by using N-methoxybenzamides as efficient acyl nitrene precursors, an iron-catalyzed formal cis-haloamidation of alkyne is reported. Without assistance of additives, the reaction worked well in the presence of 50 mol% FeCl3 or FeBr3, leading to a series of chloro/bromo-containing isoindolin-5-ones with high efficiency and wide reaction scope. In the reaction, the iron-facilitated haloamidation proceeds through a halo anion-participating concerted [3+2] cyclization to release the final products. The key intermediate ferric acyl nitrene A is generated in situ from a formal removal of MeOH.

Taming the reactivity of alkyl azides by intramolecular hydrogen bonding: site-selective conjugation of unhindered diazides

The intramolecular hydrogen bonding in the α-azido secondary acetamides (α-AzSAs) enabled site-selective integration onto the diazide modular hubs even without steric hindrance.

Divergent Synthesis of γ-Amino Acid and γ-Lactam Derivatives from meso-Glutaric Anhydrides

The first divergent synthesis of both γ-amino acid and γ-lactam derivatives from meso-glutaric anhydrides is described. The organocatalytic desymmetrisation with TMSN₃ relies on controlled generation of a nucleophilic ammonium azide species mediated by a polystyrene-bound base to promote efficient silylazidation. After Curtius rearrangement of the acyl azide intermediate to access the corresponding isocyanate, hydrolysis/alcoholysis provided uniformly high yields of γ-amino acids and their N-protected counterparts. The same intermediates were shown to undergo an unprecedented decarboxylation-cyclisation cascade in situ to provide synthetically useful yields of γ-lactam derivatives without using any further activating agents. Mechanistic insights invoke the intermediacy of an unconventional γ-N-carboxyanhydride (γ-NCA) in the latter process. Among the examples prepared using this transformation are 8 APIs/molecules of considerable medicinal interest.

π-Extended Coumarins Derived with Nonhydrolyzable Iminophosphoranes as Two-Photon-Excited Fluorophores

Novel coumarin-iminophosphorane (IPP) fluorophores that have stable resonance contributions from aza-ylides were formed by using the nonhydrolysis Staudinger reaction. The N═P formation reaction kinetics obey the conventional Staudinger reaction. The absorption and emission profiles of the coumarin-IPP derivatives can be fine-tuned: an electron-donating group at PPh₃ enhances absorption and fluorescence, whereas an electron-withdrawing group at C-3 drives absorption and emission peaks toward blue-light wavelengths. Two-photon adsorption, accompanied by anti-Stokes fluorescence, is achieved under near-infrared femtosecond laser excitation.

Tuning activation and self-immolative properties of the bioorthogonal alkene–azide click-and-release strategy

Combinations of aryl azides and trans-cyclooctenes have been studied in a bioorthogonal click-and-release strategy, with two reaction pairings rapidly releasing phenol at micromolar concentrations.