Synthesis of a Far‐Red Photoactivatable Silicon‐Containing Rhodamine for Super‐Resolution Microscopy

The rhodamine system is a flexible framework for building small‐molecule fluorescent probes. Changing N‐substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si‐containing analogue of Q‐rhodamine. This probe is the first example of a “caged” Si‐rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red‐shifted to allow multicolor imaging. The dye is a useful label for super‐resolution imaging and constitutes a new scaffold for far‐red fluorogenic molecules.     

In Situ Synthesis of Alkenyl Tetrazines for Highly Fluorogenic Bioorthogonal Live‐Cell Imaging Probes

In spite of the wide application potential of 1,2,4,5‐tetrazines, particularly in live‐cell and in vivo imaging, a major limitation has been the lack of practical synthetic methods. Here we report the in situ synthesis of (E)‐3‐substituted 6‐alkenyl‐1,2,4,5‐tetrazine derivatives through an elimination–Heck cascade reaction. By using this strategy, we provide 24 examples of π‐conjugated tetrazine derivatives that can be conveniently prepared from tetrazine building blocks and related halides. These include tetrazine analogs of biological small molecules, highly conjugated buta‐1,3‐diene‐substituted tetrazines, and a diverse array of fluorescent probes suitable for live‐cell imaging. These highly conjugated probes show very strong fluorescence turn‐on (up to 400‐fold) when reacted with dienophiles such as cyclopropenes and trans‐cyclooctenes, and we demonstrate their application for live‐cell imaging. This work provides an efficient and practical synthetic methodology for tetrazine derivatives and will facilitate the application of conjugated tetrazines, particularly as fluorogenic probes for live‐cell imaging.     

Metal Complexes of a Boron‐Dipyrromethene (BODIPY)‐Tagged N‐Heterocyclic Carbene (NHC) as Luminescent Carbon Monoxide Chemodosimeters

Several metal complexes with a boron dipyrromethene (BODIPY)‐functionalized N‐heterocyclic carbene (NHC) ligand 4 were synthesized. The fluorescence in [( 4 )(SIMes)RuCl₂(ind)] complex is quenched (Φ=0.003), it is weak in [( 4 )PdI₂(Clpy)] (Φ=0.033), and strong in [( 4 )AuI] (Φ=0.70). The BODIPY‐tagged complexes can experience pronounced changes in the brightness of the fluorophore upon ligand‐exchange and ligand‐dissociation reactions. Complexes [( 4 )MX(1,5‐cyclooctadiene)] (M=Rh, Ir; X=Cl, I; Φ=0.008–0.016) are converted into strongly fluorescent complexes [( 4 )MX(CO)₂] (Φ=0.53–0.70) upon reaction with carbon monoxide. The unquenching of the Rh and Ir complexes appears to be a consequence of the decreased electron density at Rh or Ir in the carbonyl complexes. In contrast, the substitution of an iodo ligand in [( 4 )AuI] by an electron‐rich thiolate decreases the brightness of the BODIPY fluorophore, rendering the BODIPY as a highly sensitive probe for changes in the coordination sphere of the transition metal.     

Detection of LacZ‐Positive Cells in Living Tissue with Single‐Cell Resolution

The LacZ gene, which encodes Escherichia coli β‐galactosidase, is widely used as a marker for cells with targeted gene expression or disruption. However, it has been difficult to detect lacZ‐positive cells in living organisms or tissues at single‐cell resolution, limiting the utility of existing lacZ reporters. Herein we present a newly developed fluorogenic β‐galactosidase substrate suitable for labeling live cells in culture, as well as in living tissues. This precisely functionalized fluorescent probe exhibited dramatic activation of fluorescence upon reaction with the enzyme, remained inside cells by anchoring itself to intracellular proteins, and provided single‐cell resolution. Neurons labeled with this probe preserved spontaneous firing, which was enhanced by application of ligands of receptors expressed in the cells, suggesting that this probe would be applicable to investigate functions of targeted cells in living tissues and organisms.     

N‐Oxide 1,2,4,5‐Tetrazine‐Based High‐Performance Energetic Materials

One route to high density and high performance energetic materials based on 1,2,4,5‐tetrazine is the introduction of 2,4‐di‐N‐oxide functionalities. Based on several examples and through theoretical analysis, the strategy of regioselective introduction of these moieties into 1,2,4,5‐tetrazines has been developed. Using this methodology, various new tetrazine structures containing the N‐oxide functionality were synthesized and fully characterized using IR, NMR, and mass spectroscopy, elemental analysis, and single‐crystal X‐ray analysis. Hydrogen peroxide (50 %) was used very effectively in lieu of the usual 90 % peroxide in this system to generate N‐oxide tetrazine compounds successfully. Comparison of the experimental densities of N‐oxide 1,2,4,5‐tetrazine compounds with their 1,2,4,5‐tetrazine precursors shows that introducing the N‐oxide functionality is a highly effective and feasible method to enhance the density of these materials. The heats of formation for all compounds were calculated with Gaussian 03 (revision D.01) and these values were combined with measured densities to calculate detonation pressures (P) and velocities (ν_D) of these energetic materials (Explo 5.0 v. 6.01). The new oxygen‐containing tetrazines exhibit high density, good thermal stability, acceptable oxygen balance, positive heat of formation, and excellent detonation properties, which, in some cases, are superior to those of 1,3,5‐tritnitrotoluene (TNT), 1,3,5‐trinitrotriazacyclohexane (RDX), and octahydro‐1,3,5,7‐tetranitro‐1,3,5,7‐tetrazocine (HMX).     

New 3‐(Heteroaryl)‐2‐iminocoumarin‐based Borate Complexes: Synthesis,Photophysical Properties,and Rational Functionalization for Biosensing/Biolabeling Applications

Members of a series of boron difluoride complexes with 3‐(heteroaryl)‐2‐iminocoumarin ligands bearing both a phenolic hydroxyl group (acting as a fluorogenic center) and an N‐aryl substituent (acting as a stabilizing moiety) have been synthesized in good yields by applying a straightforward two‐step method. These novel fluorogenic dyes belong to the family of “Boricos” (D. Frath et al., Chem. Commun.­ 2013 , 49, 4908–4910) and are the first examples of phenol‐based fluorophores of which the photophysical properties in the green‐yellow spectral range are dramatically improved by N,N‐chelation of a boron atom. Modulation of their fluorescence properties through reversible chemical modification of their phenol moieties has been demonstrated by the preparation of the corresponding 2,4‐dinitrophenyl (DNP) ethers, which led to a dramatic “OFF‐ON” fluorescence response upon reaction with thiols. Additionally, to expand the scope of these “7‐hydroxy‐Borico” derivatives, particularly in biolabeling, amine or carboxylic acid functionalities amenable to (bio)conjugation have been introduced within their scaffold. Their utility has been demonstrated in the preparation of fluorescent bovine serum albumin (BSA) conjugates and “Borico”‐DOTA‐like scaffolds in an effort to design novel monomolecular multimodal fluorescence‐ radioisotope imaging agents.     

In Situ Localization of Enzyme Activity in Live Cells by a Molecular Probe Releasing a Precipitating Fluorochrome

Current enzyme‐responsive, fluorogenic probes fail to provide in situ information because the released fluorophores tend to diffuse away from the reaction sites. The problem of diffusive signal dilution can be addressed by designing a probe that upon enzyme conversion releases a fluorophore that precipitates. An excited‐state intramolecular proton transfer (ESIPT)‐based solid‐state fluorophore HTPQ was developed that is strictly insoluble in water and emits intense fluorescence in the solid state, with λ _ex/em=410/550 nm, thus making it far better suited to use with a commercial confocal microscope. HTPQ was further utilized in the design of an enzyme‐responsive, fluorogenic probe (HTPQA), targeting alkaline phosphatase (ALP) as a model enzyme. HTPQA makes possible diffusion‐resistant in situ detection of endogenous ALP in live cells. It was also employed in the visualizing of different levels of ALP in osteosarcoma cells and tissue, thus demonstrating its interest for the diagnosis of this type of cancer.     

Coumarin‐Based Fluorogenic Probes for No‐Wash Protein Labeling

A fluorescent protein‐labeling strategy was developed in which a protein of interest (POI) is genetically tagged with a short peptide sequence presenting two Cys residues that can selectively react with synthetic fluorogenic reagents. These fluorogens comprise a fluorophore and two maleimide groups that quench fluorescence until they both undergo thiol addition during the labeling reaction. Novel fluorogens were prepared and kinetically characterized to demonstrate the importance of a methoxy substituent on the maleimide in suppressing reactivity with glutathione, an intracellular thiol, while maintaining reactivity with the dithiol tag. This system allows the rapid and specific labeling of intracellular POIs.     

3‐aryl‐6‐methoxy‐2‐oxo‐1,2‐dihydroquinoline‐4‐carbonitriles as Solvent and pH Independent Green Fluorescent Dyes

Highly fluorescent and stable 3‐aryl‐6‐methoxy‐2‐oxoquinoline‐4‐carbonitriles 6 (λ_exc = 408 nm and λ_em = 510 nm) were synthesized starting from appropriate arylmalonates 2 . Ring closure reaction with p‐anisidine gave 4‐hydroxyquinolones 3 , which could be bis‐chlorinated to yield quinolines 4 . Regioselective hydrolysis produced reactive 4‐chloroquinolones 5 , which were converted to green fluorescent 4‐cyano quinolones 6 using toluenesulfinates as catalysts.     

New Red‐Emitting Tetrazine‐Phenoxazine Fluorogenic Labels for Live‐Cell Intracellular Bioorthogonal Labeling Schemes

The synthesis of a set of tetrazine‐bearing fluorogenic dyes suitable for intracellular labeling of proteins in live cells is presented. The red excitability and emission properties ensure minimal autofluorescence, while through‐bond energy‐transfer‐based fluorogenicity reduces nonspecific background fluorescence of unreacted dyes. The tetrazine motif efficiently quenches fluorescence of the phenoxazine core, which can be selectively turned on chemically upon bioorthogonal inverse‐electron‐demand Diels–Alder reaction with proteins modified genetically with strained trans‐cyclooctenes.     

Unveiling the Triplet State of a 4‐Amino‐7‐Nitrobenzofurazan Derivative in Cyclohexane

The nitrobenzofurazan (NBD) moiety has gained tremendous popularity over the last decades due to its fluorogenic nature. Indeed, upon interaction with aliphatic amines, it generates a stable fluorescent adduct, which has been used for protein and lipid labeling. In fact the 4‐amino substituted NBD belongs to the broad family of intramolecular charge transfer molecules, with the amino group acting as an electron donor upon photoexcitation, and the nitro group as an electron acceptor. Although the singlet excited state of 4‐amino NBD derivatives has been abundantly studied, investigation of its triplet manifold is scarce and even the absence of intersystem crossing for this type of molecules has been suggested. However, intramolecular charge transfer molecules are known to undergo intersystem crossing and high phosphorescence quantum yields have been reported in a nonpolar solvent. In the present paper, we have investigated the photophysical and photochemical properties of N‐hexyl‐7‐nitrobenzo[c][1,2,5]xadiazole‐4‐amine. We have shown the existence of a triplet state for this molecule in cyclohexane via nanosecond laser flash photolysis. Interestingly, deactivation of the triplet state leads to photoproducts formation, which are only present in the absence of oxygen.     

Synthesis and Self‐Assembly of Novel s‐Tetrazine‐Based Gelator

The design, synthesis and self‐assembly of new symmetrical 3,6‐bis(4‐(3,4,5‐tris(dodecyloxy)benzoate)phenyl)‐1,2,4,5‐tetrazine were described. The novel gelator, sym‐tetrazine, was prepared by addition reaction of 4‐cyanophenol with hydrazine monohydrate followed by oxidation reaction to afford the corresponding 3,6‐bis(4‐hydroxyphenyl)‐1,2,4,5‐tetrazine which was then subjected to esterification reaction with 3,4,5‐tris(dodecyloxy)benzoic acid. The chemical structure of the sym‐tetrazine gelator was confirmed by elemental analysis, fourier‐transform infrared spectroscopy (FT‐IR), and nuclear magnetic resonance (¹H‐ and ¹³C‐NMR) spectral measurements. It was confirmed to exhibit relatively strong gelation ability to produce supramolecular assemblies in several polar alcoholic organic solvents, such as butanol, octanol, and 1,6‐dihydroxyhexane. The π‐π stacking and van der Waals mediated self‐assembly of tetrazine‐based organogelator were studied by scanning electron microscopy images of the xerogel to reveal that the obtained organogel consists of fibrillar aggregates. Investigation of FT‐IR and concentration‐dependent ¹H‐NMR spectra confirm that the intermolecular van der Waals interactions and π‐π stacking were the key driving forces for self‐assembly during gelation process of s‐tetrazine molecules.     

Intramolecular Long‐Distance Nucleophilic Reactions as a Rapid Fluorogenic Switch Applicable to the Detection of Enzymatic Activity

Long‐distance intramolecular nucleophilic reactions are promising strategies for the design of fluorogenic probes to detect enzymatic activity involved in lysine modifications. However, such reactions have been challenging and hence have not been established. In this study, we have prepared fluorogenic peptides that induce intramolecular reactions between lysine nucleophiles and electrophiles in distal positions. These peptides contain a lysine and fluorescence‐quenched fluorophore with a carbonate ester, which triggers nucleophilic transesterification resulting in fluorogenic response. Transesterification occurred under mild aqueous conditions despite the presence of a long nine‐amino‐acid spacer between the lysine and fluorophore. In addition, one of the peptides showed the fastest reaction kinetics with a half‐life time of 3.7 min. Furthermore, the incorporation of this fluorogenic switch into the probes allowed rapid fluorogenic detection of histone deacetylase (HDAC) activity. These results indicate that the transesterification reaction has great potential for use as a general fluorogenic switch to monitor the activity of lysine‐targeting enzymes.     

A fluorogenic ‘click’ reaction of azidoanthracene derivatives

Fluorogenic reactions have broad applications in biolabeling, combinatorial synthesis of fluorescent dyes, and materials development. It was recently reported that the highly selective and efficient Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction can be employed in designing new types of fluorogenic reactions. In this study, we report a fluorogenic reaction using anthracene azides as starting materials. The fluorescence of the anthryl core can be greatly inhibited upon introducing electron-donating azido groups in the proximity. Such weakly fluorescent anthracene azides demonstrate high reactivity with a variety of alkynes under the CuAAC conditions producing a strongly fluorescent triazole product with high quantum yields. This reaction can be used in the synthesis and screening of fluorescent dyes combinatorially. Compared with most existing methods, the fluorogenic CuAAC reaction is a much milder and simpler technique to prepare large libraries of fluorescent dyes without further purification. In order to demonstrate the efficiency of using anthracene azides for biolabeling applications, both small molecules and biomolecules including the multialkyne-derivatized cowpea mosaic virus and tobacco mosaic virus had been studied.     

Metal‐Free Synthetic Approach to 3‐Monosubstituted Unsymmetrical 1,2,4,5‐Tetrazines Useful for Bioorthogonal Reactions

A facile, efficient and metal‐free synthetic approach to 3‐monosubstituted unsymmetrical 1,2,4,5‐tetrazines is presented. Dichloromethane (DCM) is for the first time recognized as a novel reagent in the synthetic chemistry of tetrazines. Using this novel approach 11 3‐aryl/alkyl 1,2,4,5‐tetrazines were prepared in excellent yields (up to 75 %). The mechanism of this new reaction, including the role of DCM in the tetrazine ring formation, has been investigated by ¹³C labeling of DCM, and is also presented and discussed as well as the photophysical and electrochemical properties.     

Synthesis of 7‐Azido‐3‐Formylcoumarin – A Key Precursor in Bioorthogonally Applicable Fluorogenic Dye Synthesis

Coumarins represent an important group of natural products and a common part of various drugs and fluorescent dyestuffs. Herein, we present the synthesis of a coumarin that can serve as a key starting material in the design and synthesis of bioorthogonally applicable fluorogenic dyes. The synthesis of 7‐azido‐3‐formylcoumarin started from 7‐diallylaminocoumarin. This allyl protected aminocoumarin is otherwise hard to obtain by conventional methods but was conveniently accessed in good yields by a sequential, Wittig‐reaction–UV isomerization process. This sequential approach was studied in more details and applied for the synthesis of a series of substituted coumarins even in one‐pot.     

Fluorogenic Strain‐Promoted Alkyne–Diazo Cycloadditions

Fluorogenic reactions, in which non‐ or weakly fluorescent reagents produce highly fluorescent products, are attractive for detecting a broad range of compounds in the fields of bioconjugation and material sciences. Herein, we report that a dibenzocyclooctyne derivative modified with a cyclopropenone moiety (Fl‐DIBO) can undergo fast strain‐promoted cycloaddition reactions under catalyst‐free conditions with azides, nitrones, nitrile oxides, as well as mono‐ and disubstituted diazo‐derivatives. Although the reaction with nitrile oxides, nitrones, and disubstituted diazo compounds gave cycloadducts with low quantum yield, monosubstituted diazo reagents produced 1H‐pyrazole derivatives that exhibited an approximately 160‐fold fluorescence enhancement over Fl‐DIBO combined with a greater than 10 000‐fold increase in brightness. Concluding from quantum chemical calculations, fluorescence quenching of 3H‐pyrazoles, which are formed by reaction with disubstituted diazo‐derivatives, is likely due to the presence of energetically low‐lying (n,π*) states. The fluorogenic probe Fl‐DIBO was successfully employed for the labeling of diazo‐tagged proteins without detectable background signal. Diazo‐derivatives are emerging as attractive reporters for the labeling of biomolecules, and the studies presented herein demonstrate that Fl‐DIBO can be employed for visualizing such biomolecules without the need for probe washout.     

Tetrazine Carbon Nanotubes for Pretargeted In Vivo “Click‐to‐Release” Bioorthogonal Tumour Imaging

The bioorthogonal inverse‐electron‐demand Diels–Alder (IEDDA) cleavage reaction between tetrazine and trans‐cyclooctene (TCO) is a powerful way to control the release of bioactive agents and imaging probes. In this study, a pretargeted activation strategy using single‐walled carbon nanotubes (SWCNTs) that bear tetrazines (TZ@SWCNTs) and a TCO‐caged molecule was used to deliver active effector molecules. To optimize a turn‐on signal by using in vivo fluorescence imaging, we developed a new fluorogenic near‐infrared probe that can be activated by bioorthogonal chemistry and image tumours in mice by caging hemicyanine with TCO (tHCA). With our pretargeting strategy, we have shown selective doxorubicin prodrug activation and instantaneous fluorescence imaging in living cells. By combining a tHCA probe and a pretargeted bioorthogonal approach, real‐time, non‐invasive tumour visualization with a high target‐to‐background ratio was achieved in a xenograft mice tumour model. The combined advantages of enhanced stability, kinetics and biocompatibility, and the superior pharmacokinetics of tetrazine‐functionalised SWCNTs could allow application of targeted bioorthogonal decaging approaches with minimal off‐site activation of fluorophore/drug.     

Radical trans‐Hydroboration of Alkynes with N‐Heterocyclic Carbene Boranes

Hydroboration of internal alkynes with N‐heterocyclic carbene boranes (NHC‐boranes) occurs to provide stable NHC (E)‐alkenylboranes upon thermolysis in the presence of di‐tert‐butyl peroxide. The E isomer results from an unusual trans‐hydroboration, and the E/Z selectivity is typically high (90:10 or greater). Evidence suggests that this hydroboration occurs by a radical‐chain reaction involving addition of an NHC‐boryl radical to an alkyne to give a β‐NHC‐borylalkenyl radical. Ensuing hydrogen abstraction from the starting NHC‐borane provides the product and returns the starting NHC‐boryl radical. Experiments suggest that the observed trans‐selectivity results from kinetic control in the hydrogen‐transfer reaction.     

Comparison of conventional and synchrotron X‐ray structure deter­minations of the adduct 1,2,4,5‐tetrahydroxybenzene–2,5‐dihydroxy‐1,4‐benzoquinone (1/1) and a conventional X‐ray structure determination of 1,2,4,5‐tetrahydroxybenzene monohydrate

The X‐ray structure of 1,2,4,5‐tetra­hydroxy­benzene (benzene‐1,2,4,5‐tetrol) monohydrate, C₆H₆O₄·H₂O, (I), reveals columns of 1,2,4,5‐tetra­hydroxy­benzene parallel to the b axis that are separated by 3.364 (12) and 3.453 (11) Å. Molecules in adjacent columns are tilted relative to each other by 27.78 (8)°. Water mol­ecules fill the channels between the columns and are involved in hydrogen‐bonding interactions with the 1,2,4,5‐tetra­hydroxy­benzene mol­ecules. The crystal structure of the adduct 1,2,4,5‐tetra­hydroxy­benzene–2,5‐di­hydroxy‐1,4‐benzo­quinone (1/1), C₆H₆O₄·C₆H₄O₄, (II), reveals alternating mol­ecules of 1,2,4,5‐tetra­hydroxy­benzene and 2,5‐di­hydroxy‐1,4‐benzo­quinone (both lying on inversion centers), and a zigzag hydrogen‐bonded network connecting mol­ecules in three dimensions. For compound (II), the conventional X‐ray determination, (IIa), is in very good agreement with the synchrotron X‐ray determination, (IIb). When differences in data collection temperatures are taken into account, even the displacement parameters are in very good agreement.