As a cutting-edge technique, fluorescence imaging in the second near-infrared window (NIR-II) is vital for both biomedical research and clinical applications. However, its intravital imaging capacity has been restricted by the extremely limited brightness of NIR-II fluorophores. To address this challenge, we elucidated the inner mechanism of constructing high-performance NIR-II chromophores based on molecular isomer engineering from detailed computational investigations. Herein, three pairs of cis–trans isomers (cis-1, 2, 3 and trans-1, 2, 3) are designed by attaching amino, methoxyl and nitro moieties to different positions on the donor–acceptor-donor molecular skeleton with benzobisthiadiazole as the acceptor and triphenylamine as the donor. All the compounds feature efficient NIR-II emission ranging in 1000–1164 nm, and the photophysical characterizations are regulated by molecular isomer manipulation. Interestingly, fluorescence quantum yields of cis-isomers are higher than those of their trans-counterparts. These enhancements can be attributed to the significant reduction in non-radiative transition, as evidenced by the non-adiabatic excitation energy, non-adiabatic electron coupling and electron-vibration coupling. Meanwhile, fluorophores with nitro terminal group exhibit superior performance facilitated by the prominently intramolecular charge transfer. As a result, cis-3 achieves an optimal brightness maxima of 196.36 M−1 cm−1 at 632 nm. Notably, the energy gap and the hole-electron related H index are respectively identified as strongly relevant to the emission wavelength and brightness, making them capable of evaluating the feasibility of fluorophores as effective NIR-II candidates. These findings highlight the correlations between molecular geometry and luminescent properties, which will inspire more insights into the development of highly efficient NIR-II fluorophores through rational isomer engineering for biomedical applications.
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