Molecular Engineering Enables Bright Carbon Dots for Super‐Resolution Fluorescence Imaging and In Vivo Optogenetics

Abstract Improving the fluorescence quantum yield (QY) of carbon dots (CDs) is essential for expanding their applications. Understanding the photoluminescence mechanism of CDs can provide valuable insights for QY improvement. In this study, it is demonstrated that polarization facilitated the surface state emission of CDs through a single decay pathway, while hydrogen bonding (HB) is identified as a factor that hindered the surface state emission of CDs through non‐radiative decay. Following an in‐depth evaluation of these mechanisms, the QY of CDs is markedly enhanced by engineering molecules onto their surfaces. This strategy not only eliminated HB but also promoted polarization‐induced charge transfer. Notably, the QY of the yellow‐emitting CD is elevated to 98.1%. Capitalizing on their long‐term stability, excellent water solubility, two‐photon excitation capacity, and non‐toxicity, the engineered CDs are successfully applied in dual‐color super‐resolution fluorescence imaging in living cells, two‐photon imaging of zebrafish, and optogenetic regulation in the deep brain of freely‐moving animals.