Mechanistic Analysis of Bioorthogonal Double Strain-Promoted Alkyne–Nitrone Cycloadditions Involving Dibenzocyclooctadiyne

Abstract

The reactions of nitrones with cyclooctadiynes were studied to establish the relative rates of sequential reactions and to determine the limits and scope of this bioorthogonal chemistry. We have established the second-order rate constants for the consecutive additions of a variety of nitrones onto diyne and studied the structure−activity relationships via Hammett plots. Results show that the addition of the second nitrone to the monointermediate occurs significantly faster than the first, with both reactions being faster than analogous reactions with azides. Computational chemistry supports these observations. The rate of second addition increases with electron-deficient nitrones, as demonstrated by a large rho value of 2.08, suggesting that the reaction rate can be controlled by nitrone selectivity. To further investigate the kinetic parameters of the reaction, dinitrone monomers containing cyclic and diaryl-nitrones were designed for use in oligomerization applications. Oligomerization was used as a probe to test the limits of the reactivity and attempt to isolate monocycloaddition products. The oligomer formed from a cyclic nitrone reacts faster, and detailed MALDI mass spectrometry analysis shows that monoaddition products exist only transiently and are not isolatable. These studies inform on the scope and limits of this chemistry in a variety of applications. We successfully demonstrated bacterial cell wall labeling using heterogeneous dual cycloadditions involving nitrone and azide dipoles, where the nitrone was the faster reacting partner on the bacterial cell surface.

Computational Organic Chemistry: The Frontier for Understanding and Designing Bioorthogonal Cycloadditions

“…In a more recent exploration, the same group investigated the double strain-promoted alkyne–nitrone cycloadditions utilizing the Sondheimer diyne [ 82 ]. This unique diyne has the capacity to react with two units of nitrone, essentially functioning as a crosslinking agent.…”

“…22 Calculated reaction coordinate diagram for the cycloaddition between nitrone dipoles and cyclooctadiyne dipolarophiles. The activation energies are shown for X ═ H. Reprinted with permission from [ 82 ]. Copyright 2023 American Chemical Society …”