Molecular Engineering of Torsional Potentials in Fluorogenic Dyes via Electronic Substituent Effects

Abstract

Fluorogenic dyes such as thiazole orange (TO) and malachite green have been used in live cellular imaging due to their low quantum yield in solution but large fluorescence enhancements when bound to cellular nucleic acids or to a specific surface-expressed protein partner. Better understanding of the structure-property relationships that establish this fluorogenic behavior could benefit the design of improved dyes. In TO the fluorogenic properties are related to twisting of the dye, following electronic excitation in solution, from an emissive planar structure to a nonemissive twisted structure. Herein we develop a computational approach to identify electron acceptor/donor substitution patterns that impart desirable properties to the dye, such as inducing spectral shifts while maintaining an excited-state torsional surface that will lead to fluorogenic behavior. Additivity of substituent effects, on properties such as spectral shifts and excited-state torsional barriers, is tested and found to be sufficiently accurate that it can be used to identify promising dye candidates. Although additivity suggests an underlying linearity in the substituent effects, additional simplifications stemming from linearity could not be identified. The approach is tested on TO, considering seven different substituents at seven substitution positions, to identify fluorogenic dyes that will span a range of wavelengths. Additivity allows quantum chemical calculations on singly substituted molecules (49 molecules) to be used to make estimates for all substitution patterns (nearly 10(6) molecules).

Relation of molecular structure to Franck–Condon bands in the visible-light absorption spectra of symmetric cationic cyanine dyes

“…The second problem arises from the complex potential energy surface (PES) for those cyanines that undergo fast trans-cis photoisomerization from the ES, involving C-C bond rotations along the polymethine chain [19,20,[50][51][52]. The problem here is that the transition is no longer truly adiabatic, and the R ES most relevant for computing transition energies is not a relaxed geometry but a pseudo-stationary FC point on the PES [53,54,31].…”

A two-state model of twisted intramolecular charge-transfer in monomethine dyes

“…[1][2][3] In several cases, the steady-state fluorescence quantum yield increases by four orders of magnitude or more upon binding to biomolecules.…”

Bond alternation, polarizability, and resonance detuning in methine dyes

“…10 The molecular structures of fluorogenic dyes are related to those of dyes with high optical nonlinearities, as members of both classes contain heterocyclic rings separated by an unsaturated carbon bridge. 11,12 Dyes containing this structural motif are sometimes called "Brooker dyes" after L.G.S. Brooker, whose work enhanced our early understanding of color-structure relationships in these systems.…”