Reactivity of Biarylazacyclooctynones in Copper-Free Click Chemistry

Abstract

The 1,3-dipolar cycloaddition of cyclooctynes with azides, also called “copper-free click chemistry”, is a bioorthogonal reaction with widespread applications in biological discovery. The kinetics of this reaction are of paramount importance for studies of dynamic processes, particularly in living subjects. Here we performed a systematic analysis of the effects of strain and electronics on the reactivity of cyclooctynes with azides through both experimental measurements and computational studies using a density functional theory (DFT) distortion/interaction transition state model. In particular, we focused on biarylazacyclooctynone (BARAC) because it reacts with azides faster than any other reported cyclooctyne and its modular synthesis facilitated rapid access to analogues. We found that substituents on BARAC’s aryl rings can alter the calculated transition state interaction energy of the cycloaddition through electronic effects or the calculated distortion energy through steric effects. Experimental data confirmed that electronic perturbation of BARAC’s aryl rings has a modest effect on reaction rate, whereas steric hindrance in the transition state can significantly retard the reaction. Drawing on these results, we analyzed the relationship between alkyne bond angles, which we determined using X-ray crystallography, and reactivity, quantified by experimental second-order rate constants, for a range of cyclooctynes. Our results suggest a correlation between decreased alkyne bond angle and increased cyclooctyne reactivity. Finally, we obtained structural and computational data that revealed the relationship between the conformation of BARAC’s central lactam and compound reactivity. Collectively, these results indicate that the distortion/interaction model combined with bond angle analysis will enable predictions of cyclooctyne reactivity and the rational design of new reagents for copper-free click chemistry.

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes

“…20). A positive effect on reactivity (1.6 Â faster) upon cyclooctyne fluorination, as in DIFO 8 or BARAC 25 , or upon DIBAC halogenation (up to 2.2 Â faster) 26 further supports this notion. Interestingly, the fast reaction of electron-poor azides with an aliphatic cyclooctyne (BCN) as reported here is highly indicative of an alternative frontier orbital interaction.…”

A New in Vivo Cross-linking Mass Spectrometry Platform to Define Protein–Protein Interactions in Living Cells

“…Although both coppercatalyzed click chemistry and Staudinger ligation were effective, they have proven to be technically challenging (35). In order to develop a more robust methodology, we adopted a copper-free click chemistry reaction using a biotin-tagged strained alkyne BARAC (47). The tests using Azide-A-DSBSO cross-linked standard protein cytochrome C showed that copper-free conjugation was efficient in both phosphate buffer and buffers containing 8 M urea (supplemental Fig.…”

In silico study on the mechanism of formation of hydrazine and nitrogen in the reactions of excess hydroxylamine with 2,4-dinitrophenyl diethyl phosphate

“…40,41 The distortion/interaction model divides the activation energy (DE ‡ ) of a reaction into two parts, Fig. S6 in the ESI †).…”

“…S6 in the ESI †). 40,41 The distortion/interaction model for TS1-a and TS1-b suggests that the favourable distortion energy is mainly responsible for controlling the reaction kinetics rather than the interaction energy (see Fig. S6 in the ESI †).…”