Theoretical Insights Into the Photophysical Properties of the Isomorphic Fluorescent <scp>RNA</scp> Alphabet Derived From the Trifluoromethylthieno[3,4‐d]Pyrimidine Core

ABSTRACT This study offers a comprehensive and systematic theoretical investigation into the photophysical properties of new fluorescent nucleobase analogs, specifically CF3th G, CF3th A, CF3th C, and CF3th U, utilizing density functional theory (DFT) and time‐dependent DFT (TD‐DFT) calculations. These analogs (CF3th‐bases) are generated by trifluoromethylation on the C7 atom of th‐bases, and only CF3th G has just been synthesized experimentally. The nature of the electronic low‐lying singlet transitions are discussed and compared with methylated and unmodified th‐bases. The effects of water solution, deoxryribose conjunction, and base pairing were meticulously examined. It was found that trifluoromethylation leads to an increase in adiabatic ionization potentials (AIPs) and a concomitant decrease in HOMO (H)‐LUMO (L) gaps, highlighting the significant impact of this modification on the electronic properties of nucleobases. Electronic absorption studies reveal red shifts in the S 1 transition energies of CF3th‐bases relative to their parent th‐bases, with enhanced oscillator strengths. All CF3th‐bases exhibit fluorescence in the visible region. The inner shell water molecules were found to significantly impact the photophysical properties of CF3th G‐H3. The deoxyribose conjugation introduces bathochromic shifts and enhancements of oscillator strengths in fluorescence emission processes. Base pairing with natural nucleobases maintains structural stability and it will result in the fluorescence quenching of CF3th C via an intermolecular charge transfer mechanism in gas phase. These findings highlight the significant impact of trifluoromethylation on the electronic and photophysical properties of th‐bases, providing insights into their potential applications in nucleic acid research.