Triplet states of oxa- and thiamonomethine cyanines in complexes with RNA: heavy atom effect and SASA-dependent chromophore shielding

The triplet states of monomethine cyanine dyes (MCDs) in complexes with nucleic acids remain poorly understood, despite their fundamental importance for photochemical applications and for the design of photosensitizers. This work presents the first systematic comparative study of the triplet states of a series of unsymmetrical MCDs containing benzoxazole (oxa-) and benzothiazole (thia-) terminal heterocycles in noncovalent complexes with yeast RNA. Using flash photolysis, triplet–triplet absorption spectra and triplet decay kinetics were measured. A fundamental difference between the two groups of MCDs was discovered: thia derivatives populate the triplet state upon direct photoexcitation (with triplet quantum yields up to ~5.5%), whereas for oxa analogs, intersystem crossing is inefficient and triplets are observed only upon sensitized energy transfer. This effect is qualitatively explained by the enhancement of spin–orbit coupling upon replacement of the oxygen atom with sulfur (the internal heavy atom effect), which was confirmed by quantum chemical calculations. TD-DFT calculations have shown that the spin density of the MCD triplet state is concentrated mainly on the methine bond (with some contributions of N heteroatoms), which should be probably most susceptible to triplet quenchers. The kinetics of triplet state decay for all studied MCDs are biexponential, reflecting the heterogeneity of the RNA-binding sites. Based on the poses obtained by molecular docking, the solvent-accessible surface area of the chromophores (SASA) was calculated for each type of complexes (intercalation, groove binding, hairpin loop). A qualitative correlation between the triplet decay kinetics and SASA was shown: the ”slow” component of the kinetics (hundreds of microseconds) corresponds to a strongly shielded intercalated chromophore (upon complexation, SASA decreases by ~80–85%), while the ”fast” component corresponds to a chromophore localized in the groove (SASA decreases by only ~40–60%). The obtained results offer a new, structure-based approach to predicting the triplet dynamics of dyes in biopolymer microenvironments and provide a basis for the design of ligands with desired photochemical properties.