Unsymmetrical cyanine dyes are widely used in biomolecular detection due to their fluorogenic behavior, whereby fluorescence quantum yields can be very low in fluid solution but are significantly enhanced in conformationally restricted environments. Herein we describe a series of fluorinated analogues of the dye thiazole orange that exhibit improved fluorescence quantum yields and photostabilities. In addition, computational studies on these dyes revealed that twisting about the monomethine bridge beyond an interplanar angle of 60° leads to a dark state that decays nonradiatively to the ground state, accounting for the observed fluorogenic behavior. The effects of position and number of fluorine substituents correlates with both observed quantum yield and calculated activation energy for twisting beyond this critical angle.

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).

The use of molecular similarity to develop reliable low-cost quantum mechanical models for use in quantum mechanical/molecular mechanical simulations of chemical reactions is explored, using the H + HF → H2 + F collinear reaction as a test case. The approach first generates detailed quantum chemical data for the reaction center in geometries and electrostatic environments that span those expected to arise during the molecular dynamics simulations. For each geometry and environment, both high- and low-level ab initio calculations are performed. A model is then developed to predict the high-level results using only inputs generated from the low-level theory. The inputs used here are based on principal component analysis of the low-level distributed multipoles, and the model is a simple linear regression. The distributed multipoles are monopoles, dipoles, and quadrupoles at each atomic center, and they summarize the electronic distribution in a manner that is comparable across basis set. The error in the model is dominated by extrapolation from small to large basis sets, with extrapolation from uncorrelated to correlated methods contributing much less error. A single regression can be used to make predictions for a range of reaction-center geometries and environments. For the trial collinear reaction, separate regressions were developed for the transition region and the entrance and exit channels. These models can predict the results of CCSD(T)/cc-pVTZ computations from HF/3-21G distributed multipoles, with an average error for the reaction energy profile of 0.69 kcal/mol.