3-Trifluoromethyl-3-phenyldiazirine. A new carbene generating group for photolabeling reagents

Direct Photopatterning of Colloidal Quantum Dots with Electronically Optimized Diazirine Cross-Linkers

Colloidal quantum dots (QDs) with a wide color gamut and high luminescent efficiency are promising for next-generation electronic and photonic devices. However, precise and scalable patterning of QDs without degrading their properties and their integration into commercially relevant devices, such as digitally addressable QD light-emitting diode (QLED) displays, remain challenging. Here, we develop electronically optimized diazirine-based cross-linkers for nondestructive, direct photopatterning of QDs and, ultimately, building the active-matrix QLED displays. The key to the cross-linker design is the introduction of electron-donating substituents that permit the formation of ground-state singlet carbenes for air-stable and benign QD photopatterning. Under ambient conditions, these cross-linkers enable the patterning of heavy metal-free QDs at a resolution of over 13,000 pixels per inch using commercial i-line photolithography. The patterned QD layers fully preserved their optical and optoelectronic properties. Pixelated electroluminescent devices with patterned InP/ZnSe/ZnS QD layers show a peak external quantum efficiency of 15.3% and a maximum luminance of about 40,000 cd m-2, outperforming those made by existing QD patterning approaches. We further show the seamless integration of patterned QLEDs with thin-film transistor circuits and the fabrication of dual-color active-matrix displays. These results underscore the importance of designing photochemistry for QD patterning, and promise the implementation of direct photopatterning methods in manufacturing commercial QLED displays and other integrated QD device platforms.

Light-Induced Unlocking Reactivity of Fragments for Fast Target-Guided Synthesis of Carbonic Anhydrase Inhibitors

We showcase the successful combination of photochemistry and kinetic target-guided synthesis (KTGS) for rapidly pinpointing enzyme inhibitors. KTGS is a fragment-based drug discovery (FBDD) methodology in which the biological target (BT) orchestrates the construction of its own ligand from fragments featuring complementary reactive functionalities. Notably, fragments interacting with the protein binding sites leverage their spatial proximity, facilitating a preferential reaction. Consequently, the resulting bivalent ligand exhibits heightened affinity. Within the realm of KTGS strategies, in situ click chemistry stands out as the most widely used to identify potent protein binders. This approach requires significant protein contributions, such as binding interactions and appropriate orientations of fragments, to overcome high activation barriers. This leads to prolonged incubation times and the potential for generating false negatives, thereby limiting this strategy to proteins that are stable enough in buffer. We herein unveil the possibility to integrate photochemistry into the realm of KTGS, accelerating the ligation reaction between fragments to a time scale of minutes. This approach should significantly expand the narrow reactivity window of traditional KTGS reactions, paving the way for the exploration and development of novel photo-KTGS reactions.

Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling

A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.

Photoactivatable mRNA 5' Cap Analogs for RNA-Protein Crosslinking

Chemical modification of messenger RNA (mRNA) has paved the way for advancing mRNA-based therapeutics. The intricate process of mRNA translation in eukaryotes is orchestrated by numerous proteins involved in complex interaction networks. Many of them bind specifically to a unique structure at the mRNA 5'-end, called 5'-cap. Depending on the 5'-terminal sequence and its methylation pattern, different proteins may be involved in the translation initiation and regulation, but a deeper understanding of these mechanisms requires specialized molecular tools to identify natural binders of mRNA 5'-end variants. Here, a series of 8 new synthetic 5'-cap analogs that allow the preparation of RNA molecules with photoreactive tags using a standard in vitro transcription reaction are reported. Two photoreactive tags and four different modification sites are selected to minimize potential interference with cap-protein contacts and to provide complementary properties regarding crosslinking chemistry and molecular interactions. The tailored modification strategy allows for the generation of specific crosslinks with model cap-binding proteins, such as eIF4E and Dcp2. The usefulness of the photoreactive cap analogs is also demonstrated for identifying the cap-binding subunit in a multi-protein complex, which makes them perfect candidates for further development of photoaffinity labeling probes to study more complex mRNA-related processes.

Crosslinking Vinyl-Addition Polynorbornenes via Difunctional Diazirines to Generate Low Dielectric-Constant and Low Dielectric-Loss Thermosets

Thermosets having low dielectric constant (Dk < 3) and low dielectric dissipation factor (Df < 0.003), high glass transition temperature (Tg > 150 °C), and good adhesion to copper are desirable for the low loss layers of the copper clad laminates (CCL) in next generation printed circuit boards. Three different difunctional diazirines are evaluated for both thermal and photochemical crosslinking of a high Tg vinyl-addition polynorbornene resin: poly(5-hexyl-1-norbornene) (poly(HNB)). The substrate polymer, crosslinked by the carbenes generated from the activated diazirines, forms thermosets with Dk < 2.3 and Df < 0.001 at 10 GHz depending on the identity of the diazirine and the loading. The Dk and Df values for one composition are stable for 1600 h at 125 °C in air and for 1400 h at 85 °C and 85% relative humidity, suggesting good long-term reliability of this thermoset. Adhesion of poly(HNB) to copper can be enhanced by priming the copper surface with a diazirine prior to high temperature lamination; peel strength values of greater than 7.5 N cm-1 are achieved. Negative-tone photopatterning of poly(HNB) with diazirines upon exposure to 365 nm light is demonstrated.

Mechanistic differences between linear vs. spirocyclic dialkyldiazirine probes for photoaffinity labeling

Dialkyldiazirines have emerged as a photo-reactive group of choice for interactome mapping in live cell experiments. Upon irradiation, 'linear' dialkyldiazirines produce dialkylcarbenes which are susceptible to both intramolecular reactions and unimolecular elimination processes, as well as diazoalkanes, which also participate in intermolecular labeling. Cyclobutylidene has a nonclassical bonding structure and is stable enough to be captured in bimolecular reactions. Cyclobutanediazirines have more recently been studied as photoaffinity probes based on cyclobutylidene, but the mechanism, especially with respect to the role of putative diazo intermediates, was not fully understood. Here, we show that photolysis (365 nm) of cyclobutanediazirines can produce cyclobutylidene intermediates as evidenced by formation of their expected bimolecular and unimolecular products, including methylenecyclopropane derivatives. Unlike linear diazirines, cyclobutanediazirine photolysis in the presence of tetramethylethylene produces a [2 + 1] cycloaddition adduct. By contrast, linear diazirines produce diazo compounds upon low temperature photolysis in THF, whereas diazo compounds are not detected in similar photolyses of cyclobutanediazirines. Diazocyclobutane, prepared by independent synthesis, is labile, reactive toward water and capable of protein alkylation. The rate of diazocyclobutane decomposition is not affected by 365 nm light, suggesting that the photochemical conversion of diazocyclobutane to cyclobutylidene is not an important pathway. Finally, chemical proteomic studies revealed that a likely consequence of this primary conversion to a highly reactive carbene is a marked decrease in labeling by cyclobutanediazirine-based probes relative to linear diazirine counterparts both at the individual protein and proteome-wide levels. Collectively, these observations are consistent with a mechanistic picture for cyclobutanediazirine photolysis that involves carbene chemistry with minimal formation of diazo intermediates, and contrasts with the photolyses of linear diazirines where alkylation by diazo intermediates plays a more significant role.

Optimization of fluorinated phenyl azides as universal photocrosslinkers for semiconducting polymers

Fluorinated phenyl azides (FPA) enable photo-structuring of π-conjugated polymer films for electronic device applications. Despite their potential, FPAs have faced limitations regarding their crosslinking efficiency, and more importantly, their impact on critical semiconductor properties, such as charge-carrier mobility. Here, we report that azide photolysis and photocrosslinking can achieve unity quantum efficiencies for specific FPAs. This suggests preferential nitrene insertion into unactivated C‒H bonds over benzazirine and ketenimine reactions, which we attribute to rapid interconversion between the initially formed hot states. Furthermore, we establish a structure‒activity relationship for carrier mobility quenching. The binding affinity of FPA crosslinker to polymer π-stacks governs its propensity for mobility quenching in both PM6 and PBDB-T used as model conjugated polymers. This binding affinity can be suppressed by FPA ring substitution, but varies in a non-trivial way with π-stack order. Utilizing the optimal FPA, photocrosslinking enables the fabrication of morphology-stabilized, acceptor-infiltrated donor polymer networks (that is, PBDB-T: ITIC and PM6: Y6) for solar cells. Our findings demonstrate the exceptional potential of the FPA photochemistry and offer a promising approach to address the challenges of modelling realistic molecular interactions in complex polymer morphologies, moving beyond the limitations of Flory‒Huggins mean field theory.

Regioselective hydroamination of unactivated olefins with diazirines as a diversifiable nitrogen source

Nitrogen-containing compounds, such as amines, hydrazines, and heterocycles, play an indispensable role in medicine, agriculture, and materials. Alkylated derivatives of these compounds, especially in sterically congested environments, remain a challenge to prepare. Here we report a versatile method for the regioselective hydroamination of readily available unactivated olefins with diazirines. Over fifty examples are reported, including the protecting group-free amination of fourteen different natural products. A broad functional group tolerance includes alcohols, ketones, aldehydes, and epoxides. The proximate products of these reactions are diaziridines, which, under mild conditions, are converted to primary amines, hydrazines, and heterocycles. Five target- and diversity-oriented syntheses of pharmaceutical compounds are shown, along with the preparation of a bis-15N diazirine validated in the late-stage isotopic labeling of an RNA splicing modulator candidate. In this work, we report using diazirine (1) as an electrophilic nitrogen source in a regioselective hydroamination reaction, and the diversification of the resulting diaziridines.

Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping

While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints and offer insights into protein structures, unambiguous identification of cross-linked residues hinders data interpretation to the same level that has been achieved with chemical cross-linking (CXL). We address this challenge by developing an in-line system with systematic modulation of light intensity and irradiation time, which allows for a quantitative evaluation of diazirine photolysis and photo-reaction mechanism. Our results reveal a two-step pathway with mainly sequential generation of diazo and carbene intermediates. Diazo intermediate preferentially targets buried polar residues, many of which are inaccessible with known CXL probes for their limited reactivity. Moreover, we demonstrate that tuning light intensity and duration enhances selectivity towards polar residues by biasing diazo-mediated cross-linking reactions over carbene ones. This mechanistic dissection unlocks the full potential of PXL, paving the way for accurate distance mapping against protein structures and ultimately, unveiling protein dynamic behaviors.

Visible Light-Induced Reactions of Diazo Compounds and Their Precursors

In recent years, visible light-induced reactions of diazo compounds have attracted increasing attention in organic synthesis, leading to improvement of existing reactions, as well as to the discovery of unprecedented transformations. Thus, photochemical or photocatalytic generation of both carbenes and radicals provide milder tools toward these key intermediates for many valuable transformations. However, the vast majority of the transformations represent new reactivity modes of diazo compounds, which are achieved by the photochemical decomposition of diazo compounds and photoredox catalysis. In particular, the use of a redox-active photocatalysts opens the avenue to a plethora of radical reactions. The application of these methods to diazo compounds led to discovery of transformations inaccessible by the classical reactivity associated with carbenes and metal carbenes. In most cases, diazo compounds act as radical sources but can also serve as radical acceptors. Importantly, the described processes operate under mild, practical conditions. This Review describes this subfield of diazo compound chemistry, particularly focusing on recent advancements.

Tougher Bioadhesives through Dual Stimulation Strategies

Carbene-based bioadhesives have favourable attributes for tissue adhesion, including non-specific bonding to wet and dry tissues, but suffer from relatively weak fracture strength after photocuring. Light irradiation of carbene-precursor (diazirine) also creates inert side products that are absent under thermal activation. Herein, a dual activation method combines light irradiation at elevated temperatures for the evaluation of diazirine depletion and effects on cohesive properties. A customized photo/thermal-rheometer evaluates viscoelastic properties, correlated to the kinetics of carbene:diazoalkane ratios via 19F NMR). The latter exploits the sensitive -CF3 functional group to determine joule-based light/temperature kinetics on trifluoroaryl diazirine consumption. The combination of heat and photoactivation produced bioadhesives that are 3× tougher compared to control. Dual thermal/light irradiation may be a strategy to improve viscoelastic dissipation and toughness of photo-activated adhesive resins.

Discovery of drug targets based on traditional Chinese medicine microspheres (TCM-MPs) fishing strategy combined with bio-layer interferometry (BLI) technology

Target discovery of natural products is a key step in the development of new drugs, and it is also a difficult speed-limiting step. In this study, a traditional Chinese medicine microspheres (TCM-MPs) target fishing strategy was developed to discover the key drug targets from complex system. The microspheres are composed of Fe3O4 magnetic nanolayer, oleic acid modified layer, the photoaffinity group (4- [3-(Trifluoromethyl)-3H-diazirin-3-yl] benzoic acid, TAD) layer and active small molecule layer from inside to outside. TAD produces highly reactive carbene under ultraviolet light, which can realize the self-assembly and fixation of drug active small molecules with non-selective properties. Here, taking Shenqi Jiangtang Granules (SJG) as an example, the constructed TCM-MPs was used to fish the related proteins of human glomerular mesangial cells (HMCs) lysate. 28 differential proteins were screened. According to the target analysis based on bioinformatics, GNAS was selected as the key target, which participated in insulin secretion and cAMP signaling pathway. To further verify the interaction effect of GNAS and small molecules, a reverse fishing technique was established based on bio-layer interferometry (BLI) coupled with UHPLC-Q/TOF-MS/MS. The results displayed that 26 small molecules may potentially interact with GNAS, and 7 of them were found to have strong binding activity. In vitro experiments for HMCs have shown that 7 active compounds can significantly activate the cAMP pathway by binding to GNAS. The developed TCM-MPs target fishing strategy combined with BLI reverse fishing technology to screen out key proteins that directly interact with active ingredients from complex target protein systems is significant for the discovery of drug targets for complex systems of TCM.

Cyclopropanation of Alkenes with Halodiazirines as Halocarbene Precursors in Continuous Flow

The cyclopropanation reaction of alkenes with photolytically-generated chlorocarbenes from chlorodiazirines is reported as an effective way to prepare substituted 3-chloro-3-aryl-cyclopropanes. This practical and efficient approach allows the synthesis of various 3-chloro-3-aryl-cyclopropanes (32 examples) in continuous flow in 5-minute residence time under light-emitting diode (LED) irradiation. The conditions using 380 nm LED irradiation were successfully extended to the synthesis of substituted 3-bromo-3-aryl-cyclopropanes (3 examples).

Diazirine Photoprobes for the Identification of Vancomycin-Binding Proteins

Vancomycin's interactions with cellular targets drive its antimicrobial activity and also trigger expression of resistance against the antibiotic. Interaction partners for vancomycin have previously been identified using photoaffinity probes, which have proven to be useful tools for exploring vancomycin's interactome. This work seeks to develop diazirine-based vancomycin photoprobes that display enhanced specificity and bear fewer chemical modifications as compared to previous photoprobes. Using proteins fused to vancomycin's main cell-wall target, d-alanyl-d-alanine, we used mass spectrometry to show that these photoprobes specifically label known vancomycin-binding partners within minutes. In a complementary approach, we developed a Western-blot strategy targeting the vancomycin adduct of the photoprobes, eliminating the need for affinity tags and simplifying the analysis of photolabeling reactions. Together, the probes and identification strategy provide a novel and streamlined pipeline for identifying vancomycin-binding proteins.

Nondestructive Direct Optical Patterning of Perovskite Nanocrystals with Carbene-Based Ligand Cross-Linkers

Microscale patterning of colloidal perovskite nanocrystals (NCs) is essential for their integration in advanced device platforms, such as high-definition displays. However, perovskite NCs usually show degraded optical and/or electrical properties after patterning with existing approaches, posing a critical challenge for their optoelectronic applications. Here we achieve nondestructive, direct optical patterning of perovskite NCs with rationally designed carbene-based cross-linkers and demonstrate their applications in high-performance light-emitting diodes. We reveal that both the photochemical properties and the electronic structures of cross-linkers need to be carefully tailored to the material properties of perovskite NCs. This method produces high-resolution (∼4000 ppi) NC patterns with preserved photoluminescent quantum efficiencies and charge transport properties. Prototype light-emitting diodes with patterned/cross-linked NC layers show a maximum luminance of over 60000 cd m-2 and a peak external quantum efficiency of 16%, among the highest for patterned perovskite electroluminescent devices. Such a material-adapted patterning method enabled by designs from a photochemistry perspective could foster the applications of perovskite NCs in system-level electronic and optoelectronic devices.

Phototunable and Photopatternable Polymer Semiconductors

ConspectusIn recent decades, there has been rapid development in the field of polymer semiconductors, particularly those based on conjugated donor-acceptor (D-A) polymers exhibiting high charge mobilities. Furthermore, the application of polymer semiconductors has been successfully extended to a wide range of functional devices, including sensors, photodetectors, radio frequency identification (RFID) tags, electronic paper, skin electronics, and artificial synapses. Over the past few years, there has been a growing focus on stimuli-responsive polymer semiconductors, which have the potential to impart additional functionalities to conventional field-effect transistors, garnering increased attention within the research community. In this context, phototunable polymer semiconductors have received significant attention due to their ability to utilize light as an external stimulus, enabling remote control of device performance with high spatiotemporal resolution. Meanwhile, integration of field-effect transistors with polymer semiconductors can enable the realization of complex functions. To achieve this, precise and controllable patterning of polymer semiconductors becomes essential. In this Account, we discuss our research findings in the context of phototunable and photopatternable polymer semiconductors. These developments encompass the following key aspects: (i) polymer semiconductors, such as poly(diketopyrrolopyrrole-quaterthiophene) (PDPP4T), exhibit phototunability when blended with the photochromic compound hexaarylbiimidazole (HABI). The photo/thermal-responsive field-effect transistors (FETs) can be fabricated using blending thin films. Remarkably, these photo/thermal-responsive transistors can function as photonically programmable and thermally erasable nonvolatile memory devices. (ii) By incorporating photoswitchable groups like azo and spiropyran into the side chains of conjugated D-A polymers, we can create phototunable polymer semiconductors. The reversible isomerization of azo and spiropyran groups significantly influences the charge transport properties of these polymer semiconductors. Consequently, the performance of the resulting FETs can be reversibly tuned through UV/visible or near-infrared light (NIR) irradiation. Notably, the incorporation of two distinct azo groups into the side chains leads to polymer semiconductors with tristable semiconducting states, offering the ability to logically control device performance using light irradiation at three different wavelengths. (iii) Photopatterning of p-type, n-type, and ambipolar semiconductors featuring alkyl side chains can be achieved using a diazirine-based, four-armed photo-cross-linker (4CNN) with a loading concentration of no more than 3% (w/w). Furthermore, the semiconducting performances of FETs with patterned thin films were found to be satisfactorily uniform. Importantly, the cross-linked thin films are robust and show good resistance to organic solvents, which is useful for fabricating all-solution processable multilayer electronic devices. (iv) The introduction of azide groups into the side chains of conjugated polymers results in a single-component semiconducting photoresist. The presence of azide groups renders the side chains with photo-cross-linking ability, enabling the successful formation of uniform patterns, even as small as 5 μm, under UV light irradiation. Benefiting from the single component feature, field-effect transistors with individual patterned thin films display satisfactorily uniform performances. Moreover, this semiconducting photoresist has proven effective for efficiently photopatterning other polymer semiconductors, demonstrating its versatility.

Design of light-responsive amphiphilic self-assemblies: A novel application of the photosensitive diazirine moiety

Diazirine is one of the smallest photo-sensitive moieties discovered to date. When incorporated in the structure of phospholipids, its minimal size has a low impact on the morphology of the resultant liposomes. A DMPC-diazirine analogue was designed and subsequently used to generate liposomes with a lower permeability and a lower phase-transition temperature compared to control DMPC liposomes. Contrary to control liposomes, in the absence of light, the photosensitive nanoparticles retained the cargo (calcein) for at least 10 days. However, upon irradiation, diazirine's conversion triggered the fluorophore release within minutes. The kinetics of the release could be tuned by the power and duration of the irradiation process. The same approach can be used on other nanomaterials, with the final goal of discovering a release profile appropriate not only for therapeutic applications, but also for agrochemicals delivery or cosmoceutics.

Designing photoaffinity tool compounds for the investigation of the DENV NS2B-NS3 protease allosteric binding pocket

Dengue virus (DENV) infection still lacks specific antiviral therapy, making the NS2B-NS3 protease an attractive target for drug development. However, allosteric inhibitors that bind to a site other than the active site still need to be better understood. In this study, we designed and synthesised tool compounds for photoaffinity labelling (PAL) to investigate the binding site of allosteric inhibitors on the DENV protease. These tool compounds contained an affinity moiety, a photoreactive group, and a reporter tag for detection. Upon irradiation, the photoreactive group formed a covalent bond with the protease, allowing for binding site identification. SDS-PAGE-based assays confirmed the qualitative binding of the designed inhibitors to the allosteric pocket, and pull-down experiments validated the interaction. Tryptic protein digestion following liquid chromatography/mass spectrometry analysis further supported the binding of the inhibitor to the proposed pocket revealing photo-attachment to an NS3 loop close to the C-terminus. These results enhance our understanding of allosteric inhibitors and their mechanism of action against the DENV protease. The developed tool compounds and PAL are potent tools for future drug discovery efforts and investigations targeting the DENV protease.

High resolution micro-confocal Raman spectrometer-based photo-affinity microarray technology for the investigation of active ingredients - Target protein recognition strategy

Natural products has been used for the prevention and treatment of diseases for a long history. Research on the bioactive components from natural products and their interaction with target proteins are essential for drug discovery. However, studying the binding ability of natural products' active ingredients to target proteins is usually time-consuming and laborious due to their complex and diverse chemical structures. In this study, we have developed a high resolution micro-confocal Raman spectrometer-based photo-affinity microarray (HRMR-PM) technology for the investigation of active ingredients-target protein recognition strategy. The novel photo-affinity microarray was constructed by photo-cross-linking the small molecule with the photo-affinity group (4-[3-(Trifluoromethyl)-3H-diazirin-3-yl]benzoic acid, TAD) on the photo-affinity linker coated (PALC) slides under 365 nm ultraviolet irradiation. The small molecules on the microarrays with specific binding ability might immobilize target protein, which were characterized by high resolution micro-confocal Raman spectrometer. Using this method, more than a dozen components of Shenqi Jiangtang granules (SJG) were made into small molecule probe (SMP) microarrays. As a result, 8 of them had been identified to have α-glucosidase binding ability according to characteristic Raman shift at about 3060 cm^-1. These compounds were further verified by different small molecule-protein interaction analysis methods, including contact angle D-value, surface plasmon resonance (SPR) and molecular docking. The results showed that Ginsenosides Mb, Formononetin and Gomisin D exhibited the strongest binding ability. In conclusion, the HRMR-PM strategy for investigating the interaction between target proteins and small molecules has the advantages such as high throughput, low sample consumption and fast qualitative characterization. This strategy is universal which can be applied in the study of in vitro binding activity of various types of small molecules to target proteins.

Heteroaromatic Diazirines Are Essential Building Blocks for Material and Medicinal Chemistry

In materials (polymer) science and medicinal chemistry, heteroaromatic derivatives play the role of the central skeleton in development of novel devices and discovery of new drugs. On the other hand, (3-trifluoromethyl)phenyldiazirine (TPD) is a crucial chemical method for understanding biological processes such as ligand-receptor, nucleic acid-protein, lipid-protein, and protein-protein interactions. In particular, use of TPD has increased in recent materials science to create novel electric and polymer devices with comparative ease and reduced costs. Therefore, a combination of heteroaromatics and (3-trifluoromethyl)diazirine is a promising option for creating better materials and elucidating the unknown mechanisms of action of bioactive heteroaromatic compounds. In this review, a comprehensive synthesis of (3-trifluoromethyl)diazirine-substituted heteroaromatics is described.

Fluorinated Aliphatic Diazirines: Preparation, Characterization, and Model Photolabeling Studies

The previously unknown difluoromethyl diazirines and the previously neglected trifluoromethyl-aliphatic diazirines were synthesized and characterized. Model photolabeling experiments and biological studies showed that these compounds could indeed be used as photoaffinity labels.

Photoreactive bioorthogonal lipid probes and their applications in mammalian biology

Lipids are an important class of biological molecules that possess many critical physiological functions, which enable the optimal survival of all organisms, including humans. While the role of lipids in the formation of biological cellular membranes and as a source of energy is fairly well understood, the cellular signalling pathways that lipids modulate in mammals are, in comparison, poorly characterized mechanistically and/or largely unknown. In an effort to dissect these mammalian cellular pathways regulated by signalling lipids and map hitherto unknown protein-lipid interactions, the last two decades have seen tremendous progress in the development of multifunctional lipid probes that, in conjunction with well-established bioorthogonal chemistries and chemoproteomics platforms, has almost exponentially expanded our knowledge in this field. In this review, we focus on the various photoreactive bioorthogonal lipid probes described in the literature, and briefly summarize the different photo-crosslinking groups and bioorthogonal chemistries used by them. Furthermore, we report specific case examples of such photoreactive bioorthogonal lipid probes, and discuss the new biological pathways and insights that have emerged from their use through chemoproteomics in mammalian cells. Finally, we highlight the challenges associated with the use of lipid probes in biological systems, and highlight their importance in the discovery and mechanistic understanding of lipid signalling pathways in the years to come.

Molecular Design of Diazo Compound for Carbene-Mediated Cross-Linking of Hole-Transport Polymer in QLED with Reduced Energy Barrier and Improved Charge Balance

Polymeric hole-transport materials (HTMs) have been widely used in quantum-dot light-emitting diodes (QLEDs). However, their solution processability normally causes interlayer erosion and unstable film state, leading to undesired device performance. Besides, the imbalance of hole and electron transport in QLEDs also damages the device interfaces. In this study, we designed a bis-diazo compound, X1, as carbene cross-linker for polymeric HTM. Irradiated by ultraviolet and heating, a poly[(9,9-dioctylfluorenyl-2,7-diyl)-alt(4,4'-(N-(4-butylphenyl))] (TFB)/X1 blend can achieve fast "electronically clean" cross-linking with ∼100% solvent resistance. The cross-linking reduced the stacking behaviors of TFB and thus led to a lower hole-transport mobility, whereas it was a good match of electron mobility. The carbene-mediated TFB cross-linking also downshifted the HOMO level from -5.3 to -5.5 eV, delivering a smaller hole-transport energy barrier. Benefiting from these, the cross-linked QLED showed enhanced device performances over the pristine device, with EQE, power efficiency, and current efficiency being elevated by nearly 20, 15, and 83%, respectively. To the best of our knowledge, this is the first report about a bis-diazo compound based carbene cross-linker built into a polymeric HTM for a QLED with enhanced device performance.

Photoaffinity labeling and bioorthogonal ligation: Two critical tools for designing "Fish Hooks" to scout for target proteins

Small molecules remain an important category of therapeutic agents. Their binding to different proteins can lead to both desired and undesired biological effects. Identification of the proteins that a drug binds to has become an important step in drug development because it can lead to safer and more effective drugs. Parent bioactive molecules can be converted to appropriate probes that allow for visualization and identification of their target proteins. Typically, these probes are designed and synthesized utilizing some or all of five major tools; a photoactivatable group, a reporter tag, a linker, an affinity tag, and a bioorthogonal handle. This review covers two of the most challenging tools, photoactivation and bioorthogonal ligation. We provide a historical and theoretical background along with synthetic routes to prepare them. In addition, the review provides comparative analyses of the available tools that can assist decision making when designing such probes. A survey of most recent literature reports is included as well to identify recent trends in the field.

Base Mediated Diazirination via Iodine(III) Reagents

Herein, we described an efficient method for the construction of highly functionalized diazirines from the carbohydrazide and diazo-substituted hypervalent iodine reagents. Unambiguous transformation has been designed with user applicable and easy practicable conditions. Remarkably, d-glucose, menthol, aspirin, proline, and lithocholic acid were efficiently diazirinated. Furthermore, the method is mild, robust, and highly selective, which successfully converted a variety of aryl, alkyl, benzyl, and heterocyclic hydrazides into the corresponding diazirine derivatives.

Charting the Chemical and Mechanistic Scope of Light-Triggered Protein Ligation

The creation of discrete, covalent bonds between a protein and a functional molecule like a drug, fluorophore, or radiolabeled complex is essential for making state-of-the-art tools that find applications in basic science and clinical medicine. Photochemistry offers a unique set of reactive groups that hold potential for the synthesis of protein conjugates. Previous studies have demonstrated that photoactivatable desferrioxamine B (DFO) derivatives featuring a para-substituted aryl azide (ArN₃) can be used to produce viable zirconium-89-radiolabeled monoclonal antibodies (⁸⁹Zr-mAbs) for applications in noninvasive diagnostic positron emission tomography (PET) imaging of cancers. Here, we report on the synthesis, ⁸⁹Zr-radiochemistry, and light-triggered photoradiosynthesis of ⁸⁹Zr-labeled human serum albumin (HSA) using a series of 14 different photoactivatable DFO derivatives. The photoactive groups explore a range of substituted, and isomeric ArN₃ reagents, as well as derivatives of benzophenone, a para-substituted trifluoromethyl phenyl diazirine, and a tetrazole species. For the compounds studied, efficient photochemical activation occurs inside the UVA-to-visible region of the electromagnetic spectrum (∼365-450 nm) and the photochemical reactions with HSA in water were complete within 15 min under ambient conditions. Under standardized experimental conditions, photoradiosynthesis with compounds 1-14 produced the corresponding ⁸⁹ZrDFO-PEG₃-HSA conjugates with decay-corrected isolated radiochemical yields between 18.1 ± 1.8% and 62.3 ± 3.6%. Extensive density functional theory (DFT) calculations were used to explore the reaction mechanisms and chemoselectivity of the light-induced bimolecular conjugation of compounds 1-14 to protein. The photoactivatable DFO-derivatives operate by at least five distinct mechanisms, each producing a different type of bioconjugate bond. Overall, the experimental and computational work presented here confirms that photochemistry is a viable option for making diverse, functionalized protein conjugates.

Emerging Applications of Aryl Trifluoromethyl Diazoalkanes and Diazirines in Synthetic Transformations

Aryl trifluoromethyl diazoalkanes and diazirines have become unique as reactants in synthetic methodology. As privileged compounds containing CF₃ groups and ease of synthetic access, aryl trifluoromethyl diazoalkanes and diazirines have been highlighted for their versatility in applications toward a wide range of synthetic transformations. This Perspective highlights the synthetic applications of these reactants as precursors of stabilized metal carbenes, i.e., donor-acceptor-substituted ones.

Electronically optimized diazirine-based polymer crosslinkers

Electronically optimized bis-diazirine crosslinkers allow aliphatic polymers to be crosslinked with up to 10-fold improved efficacy, relative to earlier designs. Activation is achieved using modest temperatures or through UV or visible light.

Photodecarboxylative Amination of Redox-Active Esters with Diazirines

Diazirines have been recently demonstrated to serve as electrophilic amination reagents that afford diaziridines, versatile heterocycles that are readily transformed into amines, hydrazines, and nitrogen-containing heterocycles. Here, we report the photodecarboxylative amination of redox-active esters with diazirines using inexpensive photoactivators under mild conditions with an enhanced scope for primary substrates. The stability of diazirines to blue light is demonstrated, paving the way for further research into other photochemical amination methods with these unique heterocycles.

Comparison of photoactivatable crosslinkers for in-gel immunoassays

While fluorescence readout is a key detection modality for hydrogel-based immunoassays, background fluorescence due to autofluorescence or non-specific antibody interactions impairs the lower limit of detection of fluorescence immunoassays. Chemical modifications to the hydrogel structure impact autofluorescence and non-specific interactions. Benzophenone is a common photoactivatable molecule, and benzophenone methacrylamide (BPMA) has been used for cross-linking protein in polyacrylamide (PA) hydrogels. However, previous studies have suggested that the aromatic structure of benzophenone can contribute to increased autofluorescence and non-specific hydrophobic interactions with unbound fluorescent probes. Here, we synthesize diazirine methacrylamide (DZMA) as an alternative photoactivatable molecule to crosslink into PA hydrogels for in-gel protein capture for in-gel immunoassays. We hypothesize that the less hydrophobic structure of diazirine (based on previously reported predicted and experimental log P values) exhibits both reduced autofluorescence and non-specific hydrophobic interactions. We find that while equal concentrations of DZMA and BPMA result in lower protein target photocapture in the diazirine configuration, increasing the DZMA concentration up to 12 mM improves in-gel protein capture to be on par with previously reported and characterized 3 mM BPMA hydrogels. Furthermore, despite the higher concentration of diazirine, we observe negligible autofluorescence signal and a 50% reduction in immunoassay fluorescence background signal in diazirine gels compared to BPMA gels resulting in comparable signal-to-noise ratios (SNR) of the probed protein target. Finally, we test the utility of DZMA for single-cell immunoblotting in an open microfluidic device and find that protein migrates ∼1.3× faster in DZMA hydrogels than in BPMA hydrogels. However, in DZMA hydrogels we detect only 15% of the protein signal compared to BPMA hydrogels suggesting that the diazirine chemistry results in greater protein losses following electrophoretic separations. We establish that while diazirine has lower background fluorescence signal, which may potentially improve immunoassay performance, the lower capture efficiency of diazirine reduces its utility in open microfluidic systems susceptible to sample losses.

A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites

The role of metabolite-responsive riboswitches in regulating gene expression in bacteria is well known and makes them useful systems for the study of RNA-small molecule interactions. Here, we study the PreQ₁ riboswitch system, assessing sixteen diverse PreQ₁-derived probes for their ability to selectively modify the class-I PreQ₁ riboswitch aptamer covalently. For the most active probe (11), a diazirine-based photocrosslinking analog of PreQ₁, X-ray crystallography and gel-based competition assays demonstrated the mode of binding of the ligand to the aptamer, and functional assays demonstrated that the probe retains activity against the full riboswitch. Transcriptome-wide mapping using Chem-CLIP revealed a highly selective interaction between the bacterial aptamer and the probe. In addition, a small number of RNA targets in endogenous human transcripts were found to bind specifically to 11, providing evidence for candidate PreQ₁ aptamers in human RNA. This work demonstrates a stark influence of linker chemistry and structure on the ability of molecules to crosslink RNA, reveals that the PreQ₁ aptamer/ligand pair are broadly useful for chemical biology applications, and provides insights into how PreQ₁, which is similar in structure to guanine, interacts with human RNAs.

Synthesis of photoactivable oligosaccharide derivatives from 1,2-cyclic carbamate building blocks and study of their interaction with carbohydrate-binding proteins

Despite the broad occurrence of carbohydrate-protein interactions in biology, the low binding affinities of such interactions hamper the characterization of carbohydrate binding sites in the absence of three-dimensional structural models. To allow the identification of proteins interacting with specific carbohydrate epitopes, we have developed new photoactivable oligosaccharide probes. Oligosaccharides containing the 1,2-cyclic carbamate group were attached to building blocks with a primary amino group to yield the corresponding urea derivatives. Cyclic carbamates of lactose, and 3- and 2'-fucosyl lactose, were used for the conjugation with building blocks containing photoactivable diazirine, benzophenone or aryl azido groups. The resulting oligosaccharide derivatives were tested for binding to Erythrina cristagalli lectin (ECL), Aleuria aurantia lectin (AAL) and Ulex europaeus agglutinin-I (UEA I). We found that ligands containing an aryl azido photoactivable group were successfully attached to lectins. The photoactivation reaction preserved lectin integrity, as no sign of protein degradation was visible. Mass spectrometric analysis confirmed the covalent binding of between one to three oligosaccharide probes, which matched with the expected carbohydrate-binding properties of the lectins tested. The conjugation of cyclic carbamate-derivatized oligosaccharides with photoactivable aryl azido groups thus represents a convenient approach to study protein-carbohydrate interactions.

Covalent functionalization of polypropylene filters with diazirine-photosensitizer conjugates producing visible light driven virus inactivating materials

The SARS-CoV-2 pandemic has highlighted the weaknesses of relying on single-use mask and respirator personal protective equipment (PPE) and the global supply chain that supports this market. There have been no major innovations in filter technology for PPE in the past two decades. Non-woven textiles used for filtering PPE are single-use products in the healthcare environment; use and protection is focused on preventing infection from airborne or aerosolized pathogens such as Influenza A virus or SARS-CoV-2. Recently, C-H bond activation under mild and controllable conditions was reported for crosslinking commodity aliphatic polymers such as polyethylene and polypropylene. Significantly, these are the same types of polymers used in PPE filtration systems. In this report, we take advantage of this C-H insertion method to covalently attach a photosensitizing zinc-porphyrin to the surface of a melt-blow non-woven textile filter material. With the photosensitizer covalently attached to the surface of the textile, illumination with visible light was expected to produce oxidizing 1O2/ROS at the surface of the material that would result in pathogen inactivation. The filter was tested for its ability to inactivate Influenza A virus, an enveloped RNA virus similar to SARS-CoV-2, over a period of four hours with illumination of high intensity visible light. The photosensitizer-functionalized polypropylene filter inactivated our model virus by 99.99% in comparison to a control.

Photoaffinity labelling strategies for mapping the small molecule-protein interactome

Nearly all FDA approved drugs and bioactive small molecules exert their effects by binding to and modulating proteins. Consequently, understanding how small molecules interact with proteins at an molecular level is a central challenge of modern chemical biology and drug development. Complementary to structure-guided approaches, chemoproteomics has emerged as a method capable of high-throughput identification of proteins covalently bound by small molecules. To profile noncovalent interactions, established chemoproteomic workflows typically incorporate photoreactive moieties into small molecule probes, which enable trapping of small molecule-protein interactions (SMPIs). This strategy, termed photoaffinity labelling (PAL), has been utilized to profile an array of small molecule interactions, including for drugs, lipids, metabolites, and cofactors. Herein we describe the discovery of photocrosslinking chemistries, including a comparison of the strengths and limitations of implementation of each chemotype in chemoproteomic workflows. In addition, we highlight key examples where photoaffinity labelling has enabled target deconvolution and interaction site mapping.

Structure-function relationships in aryl diazirines reveal optimal design features to maximize C-H insertion

Diazirine reagents allow for the ready generation of carbenes upon photochemical, thermal, or electrical stimulation. Because carbenes formed in this way can undergo rapid insertion into any nearby C-H, O-H or N-H bond, molecules that encode diazirine functions have emerged as privileged tools in applications ranging from biological target identification and proteomics through to polymer crosslinking and adhesion. Here we use a combination of experimental and computational methods to complete the first comprehensive survey of diazirine structure-function relationships, with a particular focus on thermal activation methods. We reveal a striking ability to vary the activation energy and activation temperature of aryl diazirines through the rational manipulation of electronic properties. Significantly, we show that electron-rich diazirines have greatly enhanced efficacy toward C-H insertion, under both thermal and photochemical activation conditions. We expect these results to lead to significant improvements in diazirine-based chemical probes and polymer crosslinkers.

An Efficient Diazirine-Based Four-Armed Cross-linker for Photo-patterning of Polymeric Semiconductors

A diazirine-based four-armed cross-linker (4CNN) with a tetrahedron geometry is presented for efficient patterning of polymeric semiconductors by photo-induced carbene insertion. After blending of 4CNN with no more than 3 % (w/w), photo-patterning of p-, n-, and ambipolar semiconducting polymers with side alkyl chains was achieved; regular patterns with size as small as 5 μm were prepared with appropriate photomasks after 365 nm irradiation for just 40 s. The interchain packing order and the thin film morphology were nearly unaltered after the cross-linking and the semiconducting properties of the patterned thin films were mostly retained. A complementary-like inverter with a gain value of 112 was constructed easily by two steps of photo-patterning of the p-type and n-type semiconducting polymers. The results show that 4CNN is a new generation of cross-linker for the photo-patterning of polymeric semiconductors for all-solution-processible flexible electronic devices.

Validation of Trifluoromethylphenyl Diazirine Cholesterol Analogues As Cholesterol Mimetics and Photolabeling Reagents

Aliphatic diazirine analogues of cholesterol have been used previously to elaborate the cholesterol proteome and identify cholesterol binding sites on proteins. Cholesterol analogues containing the trifluoromethylphenyl diazirine (TPD) group have not been reported. Both classes of diazirines have been prepared for neurosteroid photolabeling studies and their combined use provided information that was not obtainable with either diazirine class alone. Hence, we prepared cholesterol TPD analogues and used them along with previously reported aliphatic diazirine analogues as photoaffinity labeling reagents to obtain additional information on the cholesterol binding sites of the pentameric Gloeobacter ligand-gated ion channel (GLIC). We first validated the TPD analogues as cholesterol substitutes and compared their actions with those of previously reported aliphatic diazirines in cell culture assays. All the probes bound to the same cholesterol binding site on GLIC but with differences in photolabeling efficiencies and residues identified. Photolabeling of mammalian (HEK) cell membranes demonstrated differences in the pattern of proteins labeled by the two classes of probes. Collectively, these date indicate that cholesterol photoaffinity labeling reagents containing an aliphatic diazirine or TPD group provide complementary information and will both be useful tools in future studies of cholesterol biology.

New Trends in Diaziridine Formation and Transformation (a Review)

This review focuses on diaziridine, a high strained three-membered heterocycle with two nitrogen atoms that plays an important role as one of the most important precursors of diazirine photoaffinity probes, as well as their formation and transformation. Recent research trends can be grouped into three categories, based on whether they have examined non-substituted, N-monosubstituted, or N,N-disubstituted diaziridines. The discussion expands on the conventional methods for recent applications, the current spread of studies, and the unconventional synthesis approaches arising over the last decade of publications.

Monolithic optical microlithography of high-density elastic circuits

Polymeric electronic materials have enabled soft and stretchable electronics. However, the lack of a universal micro/nanofabrication method for skin-like and elastic circuits results in low device density and limited parallel signal recording and processing ability relative to silicon-based devices. We present a monolithic optical microlithographic process that directly micropatterns a set of elastic electronic materials by sequential ultraviolet light-triggered solubility modulation. We fabricated transistors with channel lengths of 2 micrometers at a density of 42,000 transistors per square centimeter. We fabricated elastic circuits including an XOR gate and a half adder, both of which are essential components for an arithmetic logic unit. Our process offers a route to realize wafer-level fabrication of complex, high-density, and multilayered elastic circuits with performance rivaling that of their rigid counterparts.

Structure, Bonding, and Photoaffinity Labeling Applications of Dialkyldiazirines

Dialkyldiazirine photoaffinity probes are unparalleled tools for the study of small molecule–protein interactions. Here we summarize the basic principles of structure, bonding, and photoreactivity of dialkyldiazirines, current methods for their synthesis, and their practical application in photoaffinity labeling experiments. We demonstrate the unique utility of dialkyldiazirine probes in the context of our recent photoaffinity crosslinking-mass spectrometry analysis to reveal a hidden cholesterol binding site in the Hedgehog morphogen proteins.

1 Introduction

2 Structure, Bonding, and Spectral Properties

3 Photoreactivity

4 Synthesis

5 Application in Photoaffinity Labeling

6 Discovery of a Cholesterol–Hedgehog Protein Interface

7 Conclusions and Outlook

Evaluation of fully-functionalized diazirine tags for chemical proteomic applications

The use of photo-affinity reagents for the mapping of noncovalent small molecule-protein interactions has become widespread. Recently, several 'fully-functionalized' (FF) chemical tags have been developed wherein a photoactivatable capture group, an enrichment handle, and a functional group for synthetic conjugation to a molecule of interest are integrated into a single modular tag. Diazirine-based FF tags in particular are increasingly employed in chemical proteomic investigations; however, despite routine usage, their relative utility has not been established. Here, we systematically evaluate several diazirine-containing FF tags, including a terminal diazirine analog developed herein, for chemical proteomic investigations. Specifically, we compared the general reactivity of five diazirine tags and assessed their impact on the profiles of various small molecules, including fragments and known inhibitors revealing that such tags can have profound effects on the proteomic profiles of chemical probes. Our findings should be informative for chemical probe design, photo-affinity reagent development, and chemical proteomic investigations.

Synthesis, X-ray Structure Determination, and Comprehensive Photochemical Characterization of (Trifluoromethyl)diazirine-Containing TRPML1 Ligands

Potential (trifluoromethyl)diazirine-based TRPML1 ion channel ligands were designed and synthesized, and their structures were determined by single-crystal X-ray diffraction analysis. Photoactivation studies via ¹⁹F NMR spectroscopy and HPLC-MS analysis revealed distinct kinetical characteristics in selected solvents and favorable photochemical properties in an aqueous buffer. These photoactivatable TRPML activators represent useful and valuable tools for TRPML photoaffinity labeling combined with mass spectrometry.

Flexible polyfluorinated bis-diazirines as molecular adhesives

Motivated by a desire to develop flexible covalent adhesives that afford some of the same malleability in the adhesive layer as traditional polymer-based adhesives, we designed and synthesized two flexible, highly fluorinated bis-diazirines. Both molecules are shown to function as effective crosslinkers for polymer materials, and to act as strong adhesives when painted between two polymer objects of low surface energy, prior to thermal activation. Data obtained from lap-shear experiments suggests that greater molecular flexibility is correlated with improved mechanical compliance in the adhesive layer.

Recent Perspectives on Rearrangement Reactions of Ylides via Carbene Transfer Reactions

Among the available methods to increase the molecular complexity, sigmatropic rearrangements occupy a distinct position in organic synthesis. Despite being known for over a century sigmatropic rearrangement reactions of ylides via carbene transfer reaction have only recently come of age. Most of the ylide mediated rearrangement processes involve rupture of a σ-bond and formation of a new bond between π-bond and negatively charged atom followed by simultaneous redistribution of π-electrons. This minireview describes the advances in this research area made in recent years, which now opens up metal-catalyzed enantioselective sigmatropic rearrangement reactions, metal-free photochemical rearrangement reactions and novel reaction pathways that can be accessed via ylide intermediates.

Probing the Mechanism of Photoaffinity Labeling by Dialkyldiazirines through Bioorthogonal Capture of Diazoalkanes

Dialkyldiazirines have emerged as reagents of choice for biological photoaffinity labeling studies. The mechanism of crosslinking has dramatic consequences for biological applications where instantaneous labeling is desirable, as carbene insertions display different chemoselectivity and are much faster than competing mechanisms involving diazo or ylide intermediates. Here, deuterium labeling and diazo compound trapping experiments are employed to demonstrate that both carbene and diazo mechanisms operate in the reactions of a dialkyldiazirine motif that is commonly utilized for biological applications. For the fraction of intermolecular labeling that does involve a carbene mechanism, direct insertion is not necessarily involved, as products derived from a carbonyl ylide are also observed. We demonstrate that a strained cycloalkyne can intercept diazo compound intermediates and serve as a bioorthogonal probe for studying the contribution of the diazonium mechanism of photoaffinity labeling on a model protein under aqueous conditions.