Optical Properties of New Donor–Acceptor Dyes for RNA Imaging: Insights from Ab Initio and H¨uckel’s Model Calculations

Optical properties of 11 donor–acceptor dyes based on pyridinium–indole, pyridinium–indolizine, isoquinolinium–indole, and isoquinolinium–indolizine motifs developed for RNA imaging are investigated using high-level quantum chemistry methods and semi-empirical H¨uckel’s model. The goal of this study is three-fold: (i) to develop and benchmark computational protocols that can be used for computational design and screening of novel dyes; (ii) to explain the trends in optical properties of the model dyes in terms of underlying charge distributions and connectivity; (iii) to propose a strategy for tuning their optical properties by structural modifications. We also present the results for a new dye designed to have red-shifted absorption and emission.