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Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.

3-oxidopyridinium ions are water stable and soluble heteroaromatic betaines that behave as latent dipoles and undergo a wide variety of cycloadditions. Research into the cycloaddition reactions of 3-oxidopyridiniums was spearheaded by Alan R. Katritzky and collaborators from the early 1970s until the late 1980s, but they have yet to be used for bioorthogonal applications. Herein we report that 3-oxidopyridiniums can readily react with 4-dibenzocyclooctynol (DIBO), a common bioorthogonal handle, in a [3+2] cycloaddition. The mechanism was investigated by altering the electronics of the reaction by changing the substituent on the 5 position of the pyridinium. Electron-donating 5-substituents have been shown to significantly increase the rate of the reaction, with bimolecular rate constants ranging from 3.3×10-4 s-1 with 5-trifluoromethyl-N-methyl-3-oxidopyridinium to 1.07 M-1 s-1 with 5-amino-N-methyl-3-oxidopyridinium. 3-oxidopyridiniums' appreciable cycloaddition rates and compatibility with bioorthogonally relevant environments give them the potential to be used in a variety of bioconjugation applications. [ABSTRACT FROM AUTHOR]

Over the past decade, bioorthogonal chemistry that facilitates the efficient conjugation of biomolecules has expanded from the copper-catalyzed alkyne-azide cycloadditions to a multitude of diverse reactions, varying additives and reactiona partners, and most often offering better alternatives with faster rates and lower toxicity of employed reactants. Among these, the copper-free strain-promoted cycloaddition reactions have been demonstrated to be more promising, offering a reaction withou toxic metal catalysts and with faster inherent kinetic rate constants. The strain-promoted alkyne-nitrone cycloadditions are easily tunable from both the (strained) alkyne and nitrone perspective, both compounds giving the opportunity to modulate the rate of reaction by substituting various positions. Previously, acyclic nitrones have been evaluated in the strain-promoted alkyne-nitrone reactions; however, they were notably prone to hydrolysis. Some five-membered ring endocyclic nitrones devel oped concomitantly offered the advantage of relatively fast kinetics and better resistance to degradation in aqueous condition and have been successfully used for labelling of biomolecules in living systems. Herein, we have prepared and studied nitrone inspired by the phenanthridine scaffold that efficiently undergo strain-promoted alkyne-nitrone reactions. Phenanthridine nitrones react fast with strained cyclooctynes with large bimolecular rate constants while maintaining bioorthogonality and resistance to hydrolysis. Key words: phenanthridine, bioorthogonal labelling, nitrone, SPANC. Au cours des dix dernieres annees, la chimie bioorthogonale facilitant la conjugaison de biomolecules a permis d'etendre les cycloadditions catalysees par le cuivre d'azotures sur des alcynes a une multitude d'autres reactions qui font intervenir differents additifs et diverses paires de reactifs et qui constituent la plupart du temps une option plus avantageuse pour effectuer des reactions plus rapides, utilisant des reactifs moins toxiques. Parmi celles-ci, les cycloadditions sans cuivre accelerees par la tension de cycle se sont revelees les plus prometteuses, car elles procedent sans catalyseur metallique toxique et presentent des constantes de vitesse cinetique intrinseques plus elevees. Les cycloadditions accelerees par la tension de cycle de nitrones sur des alcynes sont facilement reglables, tant du point de vue de l'alcyne (par la tension de cycle) que de la nitrone, les deux composes offrant la possibilite de moduler la vitesse de reaction par substitution a diverses positions. Des nitrones acycliques ont deja ete evaluees dans le contexte de reactions accelerees par la tension de cycle entre des alcynes et des nitrones. Cependant, elles etaient remarquablement sensibles a l'hydrolyse. Certaines nitrones endocycliques a cinq membres synthetiseesau meme moment offraient l'avantage d'une cinetique relativement rapideet une meilleure resistance a la degradation en conditions aqueuses. Elles s'etaient revelees utiles pour le marquage de biomolecules dans des systemes vivants. Dans le cadre des presents travaux, nous avons etudie des nitrones inspirees de la structure de la phenanthridine qui reagissent efficacement dans les cycloadditions accelerees par la tension de cycle de nitrones sur des alcynes. Les nitrones derivees la phenanthridine reagissent rapidement avec les cyclooctynes, comme en temoignent leurs constantes de vitesse de reaction bimoleculaire elevees, tout en conservant la bioorthogonalite et la resistance a l'hydrolyse. [Traduit par la Redaction] Mots-cles : phenanthridine, marquage bioorthogonal, nitrone, SPANC., Introduction Studying biological processes in their natural environment has been made possible using bioorthogonal reactions that have little impact on metabolism and homeostasis. The challenging task of selectively targeting one [...]

Abstract: Epigenetics control numerous cellular processes such as gene transcription, signal transduction, and protein stabilization. An understanding of epigenetic mechanisms can lead to the development of therapeutic agents for various [...]

Strain-promoted alkyne-nitrone cycloaddition (SPANC) reactions represent a bioorthogonal labeling strategy that is both very rapid and at the same time efficient and selective. Nitrones provide increased reaction rates as well as greater susceptibility toward stereoelectronic modification when compared with organic azides. We find that strain-promoted cycloadditions of cyclic nitrones with bicyclo[6.1.0]nonyne react with second-order rate constants as large as 1.49 L [mol.sup.-1] [s.sup.-1] at 25 °C. These reactions display rate constants that are up to 37-fold greater than those of the analogous reactions of benzyl azide with bicyclo[6.1.0]nonyne. We observed that reactions of nitrones with bicyclo[6.1.0]nonyne showed a stronger dependence on substituent effect for the reaction, as evidenced by a larger Hammett ρ value, than that for biaryl-aza-cyclooctanone. We demonstrate the ability to stereoelectronically tune the reactivity of nitrones towards different cyclooctynes in SPANC reactions. This ability to introduce selectivity into different SPANC reactions through substituent provides the opportunity to perform multiple SPANC reactions in one reaction vessel and opens up potential applications in multiplex labeling. Key words: metal-free bioothrogonal cycloadditions, 1,3-dipolar cycloadditions, nitrones, click chemistry, bicyclo[6.1.0]nonyne, strain-promoted alkyne-nitrone cycloaddition (SPANC). La reaction de cycloaddition par catalyse forcee de nitrones a un alcyne ('strain-promoted alkyne-nitrone cycloaddition 'ou SPANC) constitue une methode de marquage a la fois efficace, selective et tres rapide. Les nitrones augmentent les taux de reaction ameliore et la sensibilite aux modifications stereoelectroniques par comparaison avec les azotures organiques. Nous constatons que les reactions de cycloaddition par catalyse forcee de nitrones cycliques au bicyclo[6.1.0]nonyne ont lieu avec des taux de second ordre eleve de 1,49 L [mol.sup.-1] [s.sup.-1] a 25 °C. Ces reactions montrent des valeurs de taux jusqu'a 37 fois plus elevees que celles des reactions similaires de l'azoture de benzyle avec le bicyclo[6.1.0]nonyne. Nous avons observe que les reactions de nitrones avec le bicyclo[6.1.0]nonyne dependaient davantage de substituant sur la reaction, comme l'a montre l'augmentation de la valeur de Hammett ρ, que celles avec la biaryl-aza-cyclooctanone. Nous avons demontre qu'il etait possible d'ajuster stereoelectroniquement la reactivite des nitrones avec differents cyclooctynes dans des reactions de SPANC. Cette aptitude a introduire une selectivite dans differentes reactions de SPANC par l'intermediaires de substituants rend possible la realisation de multiples reactions de SPANC dans un reacteur unique et pourrait eventuellement etre appliquee au marquage multiple. [Traduit par la Redaction] Mots-cles : cycloadditions bioorthogonales sans metal, cycloadditions 1,3-dipolaires, nitrones, chimie 'click', bicyclo[6.1.0]nonyne, cycloaddition par catalyse forcee de nitrones a un alcyne (SPANC)., Introduction The study of complex biological systems at the molecular level requires the use of a powerful and highly selective nonperturbing probe or reporter reactions to produce coherent results with [...]

The benzoin condensation that involves the umpolung coupling of two aldehyde groups has been applied to the formation of functionalized silicon and silicon oxide surfaces using thiamine and other N-heterocyclic carbene (NHC) catalysis in water. This bioorthogonal conjugation of an aldehyde to a modified silicon or silicon oxide surface has been monitored and characterized using X-ray photoelectron spectroscopy and IR spectroscopy. NHC catalysis was found to be efficient in water mediating full conversion of the aldehyde functionalized silicon oxide surfaces at the interface. Key words: 'click' chemistry, benzoin condensation, silicon, surface functionalization. Dans le but de preparer des surfaces de silicium et d'oxydes de silicium fonctionnalisees, on a fait appel a une reaction de condensation de type benzoine impliquant un couplage avec inversion de polarite de deux groupes aldehydes, effectuee en solution aqueuse en presence de thiamine et d'autres carbenes N-heterocycliques (CNH) utilises comme catalyseurs. On a controle la conjugaison bioorthogonale d'un aldehyde a une surface de silicium ou d'oxyde de silicium modifiee et on l'a caracterisee en faisant appel a la spectroscopie photoelectronique des rayons-X et a la spectroscopie infrarouge. On a observe que la catalyse par des carbenes N-heterocycliques est efficace dans l'eau pour conduire a une conversion complete des surfaces d'oxyde de silicium fonctionnalisees par un aldehyde a l'interface. Mots-cles : << chimie a clic >>, condensation de type benzoine, silicium, fonctionnalisation d'une surface. [Traduit par la Redaction], The development of organic reactions on silicon and silicon oxide surfaces is a highly active area of research because of the potential impact of the resulting new materials on applications [...]

Strain-promoted cycloadditions of diazo compounds with dibenzocyclooctyne proceed with second-order rate constants of >10 L [mol.sup.-1] [s.sup.-1] at 25°C. These reactions display rate constants that are comparable or greater than those of the analogous reactions of nitrones or azides with cyclooctynes. Key words: metal-free click chemistry, diazo compounds, 1,3-dipolar cycloaddition, dibenzocyclooctyne, rate constants. Les cycloadditions catalysees par une tension de composes diazo avec le dibenzocyclooctyne se produisent avec des constantes de vitesse du deuxieme ordre superieures a 10 L [mol.sup.-1] [s.sup.-1], a 25°C. Les constantes de vitesse de ces reactions sont comparables ou superieures a celles de reactions analogues de nitrones ou d'azotures sur les cyclooctynes. Mots-cles: chimie par cliquage sans metal, composes diazo, cycloaddition 1,3-dipolaire, dibenzocyclooctyne, constantes de vitesse. [Traduit par la Redaction], Introduction 'Click chemistry' was first coined by Kolb et al. in 2001, (1) and has come to describe chemical reactions that are rapid, selective, thermodynamically favourable, and devoid of side [...]

Short laser pulse technology has significantly contributed to biomedical research, especially via nonlinear optical microscopy. Coherent anti-Stokes Raman scattering (CARS) microscopy is a label-free, chemical-selective method that is growing in importance as improved methods and light sources develop. Here we discuss different approaches to laser source development for CARS microscopy and highlight the advantages of a multimodal CARS microscope, illustrated by selected applications in biomedical research. [c] 2010 Optical Society of America OCIS codes: 170.5810, 180.4315, 300.6230.

Abstract: The hepatitis C virus (HCV) replicates on a membrane protein complex composed of viral proteins, replicating RNA, and altered cellular membranes. Small-molecule inhibitors of cellular lipid-cholesterol metabolism such as [...]

Laser flash photolysis at 300 nm was used in studying the photochemistry of 2-methoxy-2-methyl-5,5-dipropyl-delta(super 3)-1,3,4-oxadiazoline and 2,2-dimethoxy-5,5-dipropyl-delta(super 3)-1,3,4-oxadiazoline. Results indicate that photolysis leads to the formation of 4-diazoheptane and 4-heptanone. Yields of 4-diazoheptane in CH2Cl2 are higher than in pentane and the former can be trapped with 1-pentene to form a pyrazoline or with methanol to form 4-methoxyheptane.

Reactions of dimethoxycarbene (2), a carbonyl group equivalent, with cyclic perchlorinated olefins and ketones were analyzed. Dimethoxycarbene (2) was generated from 7,7-dimethoxynorbornadienes, dimethoxydiazirine, hexamethoxycyclopropane and 2,2-dimethoxy-5,5-dimethyl-delta-1,3,4-oxadiazoline. Results show that dimethoxycarbene reacts with perchloro olefins by overall nucleophilic substitution resulting in ion pair intermediates. The latter is subjected to nucleophilic substitution by Cl- either at Me of (MeO)2C+R to afford esters and MeCl or at Cl to afford a ketene acetal and Cl2.

Oxadiazoline precursors were used to generate four different cyclohexylidenes. Dual wavelength steady state photolysis experiments were used to determine the photoproducts. Rate constants for rearrangement of the carbenes were estimated by intercepting them with pyridine in LFP experiments. The results showed that the steady state photolysis of the oxadiazolines led to the same carbenes, via diazoalkane intermediates.

Heteroatom transfer reactions from oxiranes and thiiranes to several carbenes with varied structures and philicity are studied. The carbene compounds are benzylchlorocarbene, phenylchlorocarbene and methoxyphenylcarbene which are all ambiphilic and have singlet ground states. Results show that absolute rate constants for heteroatom transfers from propylene oxide and propylene sulfide to the carbenes were in the range of 10 raised to the fourth power to 10 raised to the tenth power/Ms at 22 degrees C. They follow the free energy relationship law with respect to the carbene philicity parameter m(sub cxy).

The fragmentation of N(1')-methyl-2-(1-hydroxybenzyl)thiamin (MBzT) is a first-order reaction and involves the protonation of the pyrimidine. The fragmentation of MBzT involves an initial loss of the C(2-alpha) proton of the pyrimidine to give an intermediate enamine. This zwitterion suffers cleavage at the C-N bond but no benzaldehyde is formed. However in alkaline solutions 2-(1-hydroxybenzyl)thiamin gives benzaldehyde and thiamin.