Direct observation of a photoinduced nonstabilized nitrile imine structure in the solid state

Tetrazoles: A multi-potent motif in drug design

The unique physicochemical properties and fascinating bioisosterism of tetrazole scaffolds have received significant attention in medicinal chemistry. We report recent efforts using tetrazoles in drug design strategies in this context. Despite the increasing prevalence of tetrazoles in FDA-approved drugs for various conditions such as cancer, bacterial viral and fungal infections, asthma, hypertension, Alzheimer's disease, malaria, and tuberculosis, our understanding of their structure-activity relationships, multifunctional mechanisms, binding modes, and biochemical properties remains limited. We explore the potential of tetrazole bioisosteres in optimising lead molecules for innovative therapies, discussing applications, trends, advantages, limitations, and challenges. Additionally, we assess future research directions to drive further progress in this field.

Template-Directed In Crystallo Photopolymerization of a Donor-Acceptor Cyclopropane: When Everything Falls into Place!

A single-crystal-to-single-crystal solid-state reaction of vinylogous donor-acceptor cyclopropanes is documented. The enantiospecific synthesis of new products, distinct from those obtained in solution, is achieved for the target compounds. Photopolymerization occurred upon X-ray exposure to the crystals. Notably, in one case, this reactivity exhibits selectivity since an ordered arrangement of polymers and unreacted cocrystallized monomeric conformers has been observed. Structural characterization of the complete transformation monitored through single-crystal X-ray diffraction and supported by molecular dynamics simulations sheds light on the subtle role of crystal packing in the reaction process. Moreover, the X-ray diffraction (XRD)-resolved structure of a donor-acceptor cyclopropane intermediate reveals an elongation in bond length that corroborates the existence of the so-called "push-pull effect".

Photo-activatable Reagents for Bioorthogonal Ligation Reactions

Light-induced bioorthogonal reactions offer spatiotemporal control over selective biomolecular labeling. This review covers the recent advances in the design of photo-activatable reagents for bioorthogonal conjugation reactions in living systems. These reagents are stable in the absence of light, but transformed into reactive species upon light illumination, which then undergo rapid ligation reactions. The light wavelength has been tuned from ultraviolet to near infrared to enable efficient photo-activation in reactions in deep tissues. The most prominent photo-activatable reagents are presented, including tetrazoles, tetrazines, 9,10-phenanthrenequinone, diarylsydnones, and others. A particular focus is on the strategies for improving reaction kinetics and biocompatibility accomplished through careful molecular engineering. The utilities of these photo-activatable reagents are illustrated through a broad range of biological applications, including in vivo protein labeling, positron emission tomography (PET) imaging, responsive hydrogels, and fluorescence microscopy. The further development and optimization of these biocompatible photo-activatable reagents should lead to new chemical biology strategies for studying biomolecular structure and function in living systems.

Development of Nonclassical Photoprecursors for Rh2 Nitrenes

Characterization of reactive intermediates in C-H functionalization is challenging due to the fleeting lifetimes of these species. Synthetic photochemistry provides a strategy to generate post-turnover-limiting-step intermediates in catalysis under cryogenic conditions that enable characterization. We have a long-standing interest in the structure and reactivity of Rh2 nitrene intermediates, which are implicated as transient intermediates in Rh2-catalyzed C-H amination. Previously, we demonstrated that Rh2 complexes bearing organic azide ligands can serve as solid-state and in crystallo photoprecursors in the synthesis of transient Rh2 nitrenoids. Complementary solution-phase experiments have not been available due to the weak binding of most organic azides to Rh2 complexes. Furthermore, the volatility of the N2 that is evolved during in crystallo nitrene synthesis from these precursors has prevented the in crystallo observation of C-H functionalization from lattice-confined nitrenes. Motivated by these challenges, here we describe the synthesis and photochemistry of nonclassical nitrene precursors based on sulfilimine ligands. Sulfilimines bind to Rh2 carboxylate complexes more tightly than the corresponding azides, which has enabled the full solid-state and solution-phase characterization of these new complexes. The higher binding affinity of sulfilimine ligands as compared with organic azides has enabled both solution-phase and solid-state nitrene photochemistry. Cryogenic photochemical studies of Rh2 sulfilimine complexes confined within polystyrene thin films demonstrate that sulfilimine photochemistry can be accomplished at low temperature but that C-H amination is rapid at temperatures compatible with N═S photoactivation. The potential of these structures to serve as platforms for multistep in crystallo cascades is discussed.

Fluorescence turn-on by photoligation - bright opportunities for soft matter materials

Photochemical ligation has become an indispensable tool for applications that require spatially addressable functionalisation, both in biology and materials science. Interestingly, a number of photochemical ligations result in fluorescent products, enabling a self-reporting function that provides almost instantaneous visual feedback of the reaction's progress and efficiency. Perhaps no other chemical reaction system allows control in space and time to the same extent, while concomitantly providing inherent feedback with regard to reaction success and location. While photoactivable fluorescent properties have been widely used in biology for imaging purposes, the expansion of the array of photochemical reactions has further enabled its utility in soft matter materials. Herein, we concisely summarise the key developments of fluorogenic-forming photoligation systems and their emerging applications in both biology and materials science. We further summarise the current challenges and future opportunities of exploiting fluorescent self-reporting reactions in a wide array of chemical disciplines.

Lights on 2,5-diaryl tetrazoles: applications and limits of a versatile photoclick reaction

Recently, photoclick chemistry emerged as a powerful tool employed in several research fields, from medicinal chemistry and biology to material sciences. The growing interest in this type of chemical process is justified by the possibility to produce complex molecular systems using mild reaction conditions. However, the elevated spatio-temporal control offered by photoclick chemistry is highly intriguing, as it expands the range of applications. In this context, the light-triggered reaction of 2,5-diaryl tetrazoles with dipolarophiles emerged for its interesting features: excellent stability of the substrates, fast reaction kinetic, and the formation of a highly fluorescent product, fundamental for sensing applications. In the last years, 2,5-diaryl tetrazoles have been extensively employed, especially for bioorthogonal ligations, to label biomolecules and nucleic acids. In this review, we summarized recent applications of this interesting photoclick reaction, with a particular focus on biological fields. Moreover, we described the main limits that affect this system and current strategies proposed to overcome these issues. The general discussion here presented could prompt further optimization of the process and pave the way for the development of new original structures and innovative applications.

Graphical abstract

Sequence-independent activation of photocycloadditions using two colours of light

We exploit two reactive chromophores to establish sequence-independent photochemical activation, employing ortho-methyl benzaldehyde (oMBA) and N,N-(dimethylamino)pyrene aryl tetrazole (APAT) with N-(2-hydroxy)ethyl maleimide (NHEM), without any additives. Critically, the order of the irradiation sequence is irrelevant, as the shorter wavelength does not activate the higher wavelength activated species. Therefore, full sequence-independent λ-orthogonality is achieved through differences in both the reaction quantum yields (Φ r,oMBA and Φ r,APAT) and wavelength-dependent reactivity profiles of the employed chromophores.

Light-Triggered Click Chemistry

The merging of click chemistry with discrete photochemical processes has led to the creation of a new class of click reactions, collectively known as photoclick chemistry. These light-triggered click reactions allow the synthesis of diverse organic structures in a rapid and precise manner under mild conditions. Because light offers unparalleled spatiotemporal control over the generation of the reactive intermediates, photoclick chemistry has become an indispensable tool for a wide range of spatially addressable applications including surface functionalization, polymer conjugation and cross-linking, and biomolecular labeling in the native cellular environment. Over the past decade, a growing number of photoclick reactions have been developed, especially those based on the 1,3-dipolar cycloadditions and Diels-Alder reactions owing to their excellent reaction kinetics, selectivity, and biocompatibility. This review summarizes the recent advances in the development of photoclick reactions and their applications in chemical biology and materials science. A particular emphasis is placed on the historical contexts and mechanistic insights into each of the selected reactions. The in-depth discussion presented here should stimulate further development of the field, including the design of new photoactivation modalities, the continuous expansion of λ-orthogonal tandem photoclick chemistry, and the innovative use of these unique tools in bioconjugation and nanomaterial synthesis.

Structural reasons for the formation of multicomponent products and the influence of high pressure

(S)-(-)-1-Phenylethanaminium 4-(2,4,6-triisopropylbenzoyl)benzoate (S-PEATPBB) undergoes a photochemical reaction in its crystalline form upon UV irradiation and forms three different products: the first product is the result of a Yang cyclization with the participation of the δ-H atom of o-isopropyl (product D) and the second and third products are obtained via a Norrish-Yang reaction with the involvement of the γ-H atom of 2-isopropyl (product P) and 6-isopropyl (product Z). These products are formed in different proportions (D > P >> Z). The path and kinetics of the reaction were monitored step-by-step using crystallographic methods, both under ambient and high-pressure conditions. The reactivity of S-PEATPBB depends strongly on the geometry of the reaction centre and the volume of the reaction cavity. Due to the geometrical preferences making the cyclization reaction easier to proceed, product D dominates over the other products, while the formation of product Z becomes difficult or almost impossible at high pressure. The reaction proceeds with an increase of the unit-cell volume, which, suppressed by high pressure, results in a significant decrease of the reaction rate. The crystal lattice of S-PEATPBB shows high elasticity. The quality of the partially reacted crystal remains the same after decompression from 0.75 GPa to 0.1 MPa.

In crystallo organometallic chemistry

X-ray crystallography is an invaluable tool in design and development of organometallic catalysis, but application typically requires species to display sufficiently high solution concentrations and lifetimes for single crystalline samples to be obtained. In crystallo organometallic chemistry relies on chemical reactions that proceed within the single-crystal environment to access crystalline samples of reactive organometallic fragments that are unavailable by alternate means. This highlight describes approaches to in crystallo organometallic chemistry including (a) solid-gas reactions between transition metal complexes in molecular crystals and diffusing small molecules, (b) reactions of organometallic complexes within the extended lattices of metal-organic frameworks (MOFs), and (c) intracrystalline photochemical transformations to generate reactive organometallic fragments. Application of these methods has enabled characterization of catalytically important transient species, including σ-alkane adducts of transition metals, metal alkyl intermediates implicated in metal-catalyzed carbonylations, and reactive M-L multiply bonded species involved in C-H functionalization chemistry. Opportunities and challenges for in crystallo organometallic chemistry are discussed.

C-H Amination Mediated by Cobalt Organoazide Adducts and the Corresponding Cobalt Nitrenoid Intermediates

Treatment of (^ArL)CoBr (^ArL = 5-mesityl-1,9-(2,4,6-Ph₃C₆H₂)dipyrrin) with a stoichiometric amount of 1-azido-4-(tert-butyl)benzene N₃(C₆H₄-p-^tBu) furnished the corresponding four-coordinate organoazide-bound complex (^ArL)CoBr(N₃(C₆H₄-p-^tBu)). Spectroscopic and structural characterization of the complex indicated redox innocent ligation of the organoazide. Slow expulsion of dinitrogen (N₂) was observed at room temperature to afford a ligand functionalized product via a [3 + 2] annulation, which can be mediated by a high-valent nitrene intermediate such as a Co^III iminyl (^ArL)CoBr(^•N(C₆H₄-p-^tBu)) or Co^IV imido (^ArL)CoBr(N(C₆H₄-p-^tBu)) complex. The presence of the proposed intermediate and its viability as a nitrene group transfer reagent are supported by intermolecular C-H amination and aziridination reactivities. Unlike (^ArL)CoBr(N₃(C₆H₄-p-^tBu)), a series of alkyl azide-bound Co^II analogues expel N₂ only above 60 °C, affording paramagnetic intermediates that convert to the corresponding Co-imine complexes via α-H-atom abstraction. The corresponding N₂-released structures were observed via single-crystal-to-crystal transformation, suggesting formation of a Co-nitrenoid intermediate in solid-state. Alternatively, the alkyl azide-bound congeners supported by a more sterically accessible dipyrrinato scaffold ^tBuL (^tBuL = 5-mesityl-(1,9-di-tert-butyl)dipyrrin) facilitate intramolecular 1,3-dipolar cycloaddition as well as C-H amination to furnish 1,2,3-dihydrotriazole and substituted pyrrolidine products, respectively. For the C-H amination, we observe that the temperature required for azide activation varies depending on the presence of weak C-H bonds, suggesting that the alkyl azide adducts serve as viable species for C-H amination when the C-H bonds are (1) proximal to the azide moiety and (2) sufficiently weak to be activated.

In situ synthesis, crystal structures, topology and photoluminescent properties of poly[di-μ-aqua-di-aqua-[μ3-4-(1H-tetra-zol-1-id-5-yl)benzoato-κ4 O:O,O':O'']barium(II)] and poly[μ-aqua-di-aqua-[μ3-4-(1H-tetra-zol-1-id-5-yl)benzoato-κ4 O:O,O':O']strontium(II)]

Two alkaline-earth coordination compounds, [Ba(C8H4N4O2)(H2O)4] n , (I), and [Sr(C8H4N4O2)(H2O)3] n , (II), from the one-pot hydrolysis transformation of benzoyl chloride and the in situ self-assembled [2 + 3] cyclo-addition of nitrile are presented. These coordination compounds are prepared by reacting 4-cyano-benzoyl chloride with divalent alkaline-earth salts (BaCl2 and SrCl2) in aqueous solution under hydro-thermal conditions. The mononuclear coordination compounds (I) and (II) show the same mode of coordination of the organic ligands. The cohesion of the crystalline structures is provided by hydrogen bonds and π-stacking inter-actions, thus forming three-dimensional supra-molecular networks. The two compounds have a three-dimensional (3,6)-connected topology, and the structural differences between them is in the number of water mol-ecules around the alkaline earth metals. Having the same emission frequencies, the compounds exhibit photoluminescence properties with a downward absorption value from (I) to (II).

Modular activatable bioorthogonal reagents

The bioorthogonal reaction toolbox contains approximately two-dozen unique chemistries that permit selective tagging and probing of biomolecules. Over the past two decades, significant effort has been devoted to optimizing and discovering bioorthogonal reagents that are faster, fluorogenic, and orthogonal to the already existing bioorthogonal repertoire. Conversely, efforts to explore bioorthogonal reagents whose reactivity can be controlled in space and/or time are limited. The "activatable" bioorthogonal reagents that do exist are often unimodal, meaning that their reagent's activation method cannot be easily modified to enable activation with red-shifted wavelengths, enzymes, or metabolic-byproducts and ions like H₂O₂ or Fe³⁺. Here, we summarize the available activatable bioorthogonal reagents with a focus on our recent addition: modular caged cyclopropenes. We designed caged cyclopropenes to be unreactive to their bioorthogonal partner until they are activated through the removal of the cage by light, an enzyme, or another reaction partner. To accomplish this, their structure includes a nitrogen atom at the cyclopropene C3 position that is decorated with the desired caging group through a carbamate linkage. This 3-N cyclopropene system can allow control of cyclopropene reactivity using a multitude of already available photo- and enzyme-caging groups. Additionally, this cyclopropene scaffold can enable metabolic-byproduct or ion activation of bioorthogonal reactions.

Photoinducible Oncometabolite Detection

Dysregulated metabolism can fuel cancer by altering the production of bioenergetic building blocks and directly stimulating oncogenic gene-expression programs. However, relatively few optical methods for the direct study of metabolites in cells exist. To address this need and facilitate new approaches to cancer treatment and diagnosis, herein we report an optimized chemical approach to detect the oncometabolite fumarate. Our strategy employs diaryl tetrazoles as cell-permeable photoinducible precursors to nitrileimines. Uncaging these species in cells and cell extracts enables them to undergo 1,3-dipolar cycloadditions with endogenous dipolarophile metabolites such as fumarate to form pyrazoline cycloadducts that can be readily detected by their intrinsic fluorescence. The ability to photolytically uncage diaryl tetrazoles provides greatly improved sensitivity relative to previous methods, and enables the facile detection of dysregulated fumarate metabolism through biochemical activity assays, intracellular imaging, and flow cytometry. Our studies showcase an intersection of bioorthogonal chemistry and metabolite reactivity that can be applied for biological profiling, imaging, and diagnostics.

Structural Transformations in Crystals Induced by Radiation and Pressure. Part 7. Molecular and Crystal Geometries as Factors Deciding about Photochemical Reactivity under Ambient and High Pressures

We studied the photochemical reactivity of salts of 4-(2,4,6-triisopropylbenzoyl)benzoic acid with propane-1,2-diamine (1), methanamine (2), cyclohexanamine (3), and morpholine (4), for compounds (1), (3), and (4) at 0.1 MPa and for compounds (1) and (2) at 1.3 GPa and 1.0 GPa, respectively. The changes in the values of the unit cell parameters after UV irradiation and the values of the intramolecular geometrical parameters indicated the possibility of the occurrence of the Norrish–Yang reaction in the case of all the compounds. The analysis of the intramolecular geometry and free spaces revealed which o-isopropyl group takes part in the reaction. For (1), the same o-isopropyl group should be reactive at ambient and high pressures. In the case of (2), high pressure caused the phase transition from the space group I2/a with one molecule in the asymmetric unit cell to the space group P1¯ with two asymmetric molecules. The analysis of voids indicated that the Norrish–Yang reaction is less probable for one of the two molecules. For the other molecule, the intramolecular geometrical parameters showed that except for the Norrish–Yang reaction, the concurrent reaction leading to the formation of a five-membered ring can also proceed. In (3), both o-isopropyl groups are able to react; however, the bigger volume of a void near 2-isopropyl may be the factor determining the reactivity. For (4), only one o-isopropyl should be reactive.

Improved Photoinduced Fluorogenic Alkene-Tetrazole Reaction for Protein Labeling

The 1,3-dipolar cycloaddition reaction between an alkene and a tetrazole represents one elegant and rare example of fluorophore-forming bioorthogonal chemistry. This is an attractive reaction for imaging applications in live cells that requires less intensive washing steps and/or needs spatiotemporal resolutions. In the present work, as an effort to improve the fluorogenic property of the alkene-tetrazole reaction, an aromatic alkene (styrene) was investigated as the dipolarophile. Over 30-fold improvement in quantum yield of the reaction product was achieved in aqueous solution. According to our mechanistic studies, the observed improvement is likely due to an insufficient protonation of the styrene-tetrazole reaction product. This finding provides useful guidance to the future design of alkene-tetrazole reactions for biological studies. Fluorogenic protein labeling using the styrene-tetrazole reaction was demonstrated both in vitro and in vivo. This was realized by the genetic incorporation of an unnatural amino acid containing the styrene moiety. It is anticipated that the combination of styrene with different tetrazole derivatives can generally improve and broaden the application of alkene-tetrazole chemistry in real-time imaging in live cells.

Stereoelectronic Effects in Cl2 Elimination from Binuclear Pt(III) Complexes

Halogen photoelimination is the critical energy-storing step of metal-catalyzed HX-splitting photocycles. Homo- and heterobimetallic Pt(III) complexes display among the highest quantum efficiencies for halogen elimination reactions. Herein, we examine in detail the mechanism and energetics of halogen elimination from a family of binuclear Pt(III) complexes featuring meridionally coordinated Pt(III) trichlorides. Transient absorption spectroscopy, steady-state photocrystallography, and far-infrared vibrational spectroscopy suggest a halogen elimination mechanism that proceeds via two sequential halogen-atom-extrusion steps. Solution-phase calorimetry experiments of the meridional complexes have defined the thermodynamics of halogen elimination, which show a decrease in the photoelimination quantum efficiency with an increase in the thermochemically defined Pt-X bond strength. Conversely, when compared to an isomeric facial Pt(III) trichloride, a much more efficient photoelimination is observed for the fac isomer than would be predicted based on thermochemistry. This difference in the fac vs mer isomer photochemistry highlights the importance of stereochemistry on halogen elimination efficiency and points to a mechanism-based strategy for achieving halogen elimination reactions that are both efficient and energy storing.

Ammonium hydrogen bis[4-(2-phenyl-2H-tetrazol-5-yl)benzoate]

The title salt, NH4 +·H+·2C14H9N4O2 −, is composed of an ammonium cation with a strong intermolecular negatively charge-assisted hydrogen-bonded acid/conjugate base-pair monoanion. The carboxylic acid H atom is located on an inversion center, while the N atom of the ammonium cation is located on a twofold rotation axis. In the crystal, the N—H bonds of each ammonium cation act as donors with carboxylate O-atom acceptors to form chains along the a-axis direction. The chains are linked by offset π–π interactions [intercentroid distances = 3.588 (2) and 3.686 (2) Å], forming layers parallel to the ab plane.

2-Aryl-5-carboxytetrazole as a New Photoaffinity Label for Drug Target Identification

Photoaffinity labels are powerful tools for dissecting ligand-protein interactions, and they have a broad utility in medicinal chemistry and drug discovery. Traditional photoaffinity labels work through nonspecific C-H/X-H bond insertion reactions with the protein of interest by the highly reactive photogenerated intermediate. Herein, we report a new photoaffinity label, 2-aryl-5-carboxytetrazole (ACT), that interacts with the target protein via a unique mechanism in which the photogenerated carboxynitrile imine reacts with a proximal nucleophile near the target active site. In two distinct case studies, we demonstrate that the attachment of ACT to a ligand does not significantly alter the binding affinity and specificity of the parent drug. Compared with diazirine and benzophenone, two commonly used photoaffinity labels, in two case studies ACT showed higher photo-cross-linking yields toward their protein targets in vitro based on mass spectrometry analysis. In the in situ target identification studies, ACT successfully captured the desired targets with an efficiency comparable to the diazirine. We expect that further development of this class of photoaffinity labels will lead to a broad range of applications across target identification, and validation and elucidation of the binding site in drug discovery.

Photo-Triggered Click Chemistry for Biological Applications

In the last decade and a half, numerous bioorthogonal reactions have been developed with a goal to study biological processes in their native environment, i.e., in living cells and animals. Among them, the photo-triggered reactions offer several unique advantages including operational simplicity with the use of light rather than toxic metal catalysts and ligands, and exceptional spatiotemporal control through the application of an appropriate light source with pre-selected wavelength, light intensity and exposure time. While the photoinduced reactions have been studied extensively in materials research, e.g., on macromolecular surface, the adaptation of these reactions for chemical biology applications is still in its infancy. In this chapter, we review the recent efforts in the discovery and optimization the photo-triggered bioorthogonal reactions, with a focus on those that have shown broad utility in biological systems. We discuss in each cases the chemical and mechanistic background, the kinetics of the reactions and the biological applicability together with the limiting factors.

Tracking reaction dynamics in solution by pump–probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering)

TRXL and TRXAS are powerful techniques for real-time probing of structural and electronic dynamics of photoinduced reactions in solution phase.

Bond-shift isomers: the co-existence of allenic and propargylic phenylnitrile imines

Two bond-shift isomers of phenylnitrile imine resulting from photochemistry of 5-phenyltetrazole.

Photocrystallographic observation of halide-bridged intermediates in halogen photoeliminations

Polynuclear transition metal complexes, which frequently constitute the active sites of both biological and chemical catalysts, provide access to unique chemical transformations that are derived from metal-metal cooperation. Reductive elimination via ligand-bridged binuclear intermediates from bimetallic cores is one mechanism by which metals may cooperate during catalysis. We have established families of Rh2 complexes that participate in HX-splitting photocatalysis in which metal-metal cooperation is credited with the ability to achieve multielectron photochemical reactions in preference to single-electron transformations. Nanosecond-resolved transient absorption spectroscopy, steady-state photocrystallography, and computational modeling have allowed direct observation and characterization of Cl-bridged intermediates (intramolecular analogues of classical ligand-bridged intermediates in binuclear eliminations) in halogen elimination reactions. On the basis of these observations, a new class of Rh2 complexes, supported by CO ligands, has been prepared, allowing for the isolation and independent characterization of the proposed halide-bridged intermediates. Direct observation of halide-bridged structures establishes binuclear reductive elimination as a viable mechanism for photogenerating energetic bonds.

Design of oligothiophene-based tetrazoles for laser-triggered photoclick chemistry in living cells

A 405 nm light-activatable terthiophene-based tetrazole was designed that reacts with a fumarate dipolarophile with the second-order rate constant k2 exceeding 10(3) M(-1) s(-1). The utility of this laser-activatable tetrazole in imaging microtubules in a spatiotemporally controlled manner in live cells was demonstrated.

Nucleophilic trapping nitrilimine generated by photolysis of diaryltetrazole in aqueous phase

Nitrilimine generated by photolysis of diaryltetrazole in aqueous phase under mild conditions was trapped by nucleophiles including amines and thioalcohols. The representative products were characterized, while products with all 20 natural amino acids and a peptide were observed by MALDI-TOF mass spectroscopy. Competitive studies showed that this reaction also occurred in the presence of acrylamide. These results provided new information for understanding the potential side reactions when tetrazole-alkene pairs were used as a bioorthogonal reaction in labeling proteins and related studies in buffered systems.

Bioorthogonal chemistry: strategies and recent developments

The use of covalent chemistry to track biomolecules in their native environment-a focus of bioorthogonal chemistry-has received considerable interest recently among chemical biologists and organic chemists alike. To facilitate wider adoption of bioorthogonal chemistry in biomedical research, a central effort in the last few years has been focused on the optimization of a few known bioorthogonal reactions, particularly with respect to reaction kinetics improvement, novel genetic encoding systems, and fluorogenic reactions for bioimaging. During these optimizations, three strategies have emerged, including the use of ring strain for substrate activation in the cycloaddition reactions, the discovery of new ligands and privileged substrates for accelerated metal-catalysed reactions, and the design of substrates with pre-fluorophore structures for rapid "turn-on" fluorescence after selective bioorthogonal reactions. In addition, new bioorthogonal reactions based on either modified or completely unprecedented reactant pairs have been reported. Finally, increasing attention has been directed toward the development of mutually exclusive bioorthogonal reactions and their applications in multiple labeling of a biomolecule in cell culture. In this feature article, we wish to present the recent progress in bioorthogonal reactions through the selected examples that highlight the above-mentioned strategies. Considering increasing sophistication in bioorthogonal chemistry development, we strive to project several exciting opportunities where bioorthogonal chemistry can make a unique contribution to biology in the near future.

Fluorogenic, two-photon-triggered photoclick chemistry in live mammalian cells

The tetrazole-based photoclick chemistry has provided a powerful tool to image proteins in live cells. To extend photoclick chemistry to living organisms with improved spatiotemporal control, here we report the design of naphthalene-based tetrazoles that can be efficiently activated by two-photon excitation with a 700 nm femtosecond pulsed laser. A water-soluble, cell-permeable naphthalene-based tetrazole was identified that reacts with acrylamide with the effective two-photon cross-section for the cycloaddition reaction determined to be 3.8 GM. Furthermore, the use of this naphthalene-tetrazole for real-time, spatially controlled imaging of microtubules in live mammalian cells via the fluorogenic, two-photon-triggered photoclick chemistry was demonstrated.

Nitrile imines: matrix isolation, IR spectra, structures, and rearrangement to carbodiimides

The structures and reactivities of nitrile imines are subjects of continuing debate. Several nitrile imines were generated photochemically or thermally and investigated by IR spectroscopy in Ar matrices at cryogenic temperatures (Ph-CNN-H 6, Ph-CNN-CH(3)17, Ph-CNN-SiMe(3)23, Ph-CNN-Ph 29, Ph(3)C-CNN-CPh(3)34, and the boryl-CNN-boryl derivative 39). The effect of substituents on the structures and IR absorptions of nitrile imines was investigated computationally at the B3LYP/6-31G* level. IR spectra were analyzed in terms of calculated anharmonic vibrational spectra and were generally in very good agreement with the calculated spectra. Infrared spectra were found to reflect the structures of nitrile imines accurately. Nitrile imines with IR absorptions above 2200 cm(-1) have essentially propargylic structures, possessing a CN triple bond (typically PhCNNSiMe(3)23, PhCNNPh 29, and boryl-CNN-boryl 39). Nitrile imines with IR absorptions below ca. 2200 cm(-1) are more likely to be allenic (e.g., HCNNH 1, PhCNNH 6, HCNNPh 43, PhCNNCH(3)17, and Ph(3)C-CNN-CPh(3)34). All nitrile imines isomerize to the corresponding carbodiimides both thermally and photochemically. Monosubstituted carbodiimides isomerize thermally to the corresponding cyanamides (e.g., Ph-N═C═N-H 5 → Ph-NH-CN 8), which are therefore the thermal end products for nitrile imines of the types RCNNH and HCNNR. This tautomerization is reversible under flash vacuum thermolysis conditions.

Photoinducible bioorthogonal chemistry: a spatiotemporally controllable tool to visualize and perturb proteins in live cells

Visualization in biology has been greatly facilitated by the use of fluorescent proteins as in-cell probes. The genes coding for these wavelength-tunable proteins can be readily fused with the DNA coding for a protein of interest, which enables direct monitoring of natural proteins in real time inside living cells. Despite their success, however, fluorescent proteins have limitations that have only begun to be addressed in the past decade through the development of bioorthogonal chemistry. In this approach, a very small bioorthogonal tag is embedded within the basic building blocks of the cell, and then a variety of external molecules can be selectively conjugated to these pretagged biomolecules. The result is a veritable palette of biophysical probes for the researcher to choose from. In this Account, we review our progress in developing a photoinducible, bioorthogonal tetrazole-alkene cycloaddition reaction ("photoclick chemistry") and applying it to probe protein dynamics and function in live cells. The work described here summarizes the synthesis, structure, and reactivity studies of tetrazoles, including their optimization for applications in biology. Building on key insights from earlier reports, our initial studies of the reaction have revealed full water compatibility, high photoactivation quantum yield, tunable photoactivation wavelength, and broad substrate scope; an added benefit is the formation of fluorescent cycloadducts. Subsequent studies have shown fast reaction kinetics (up to 11.0 M(-1) s(-1)), with the rate depending on the HOMO energy of the nitrile imine dipole as well as the LUMO energy of the alkene dipolarophile. Moreover, through the use of photocrystallography, we have observed that the photogenerated nitrile imine adopts a bent geometry in the solid state. This observation has led to the synthesis of reactive, macrocyclic tetrazoles that contain a short "bridge" between two flanking phenyl rings. This photoclick chemistry has been used to label proteins rapidly (within ∼1 min) both in vitro and in E. coli . To create an effective interface with biology, we have identified both a metabolically incorporable alkene amino acid, homoallylglycine, and a genetically encodable tetrazole amino acid, p-(2-tetrazole)phenylalanine. We demonstrate the utility of these two moieties, respectively, in spatiotemporally controlled imaging of newly synthesized proteins and in site-specific labeling of proteins. Additionally, we demonstrate the use of the photoclick chemistry to perturb the localization of a fluorescent protein in mammalian cells.

Mass spectrometry studies of the retro-cycloaddition reaction of pyrrolidino and 2-pyrazolinofullerene derivatives under negative ESI conditions

Substituted pyrrolidino- and 3-alkyl-2-pyrazolinofullerenes ionize under ESI and MALDI mass spectrometry conditions and negative mode of detection undergoing mass spectral fragmentations, which can be easily correlated with the reported results for the thermal and electrochemical retro-cycloaddition reactions of these compounds. 2-Pyrazolinofullerenes lead directly to a [60]fullerene product ion formed through a retro-cycloaddition process regardless of the substituents attached at the carbon and nitrogen atoms of the heterocyclic ring. These results are different from whose reported for the thermal and electrochemical processes. In contrast, pyrrolidinofullerenes undergo different fragmentative reactions depending upon the substituents (hydrogen, alkyl, or acyl) attached at the nitrogen atom of the heterocyclic ring leading eventually to the pristine C(60) in the last step of the fragmentation pathway.