Atomic imaging of zeolite-confined single molecules by electron microscopy

Single-molecule imaging with atomic resolution is a notable method to study various molecular behaviours and interactions1–5. Although low-dose electron microscopy has been proved effective in observing small molecules6–13, it has not yet helped us achieve an atomic understanding of the basic physics and chemistry of single molecules in porous materials, such as zeolites14–16. The configurations of small molecules interacting with acid sites determine the wide applications of zeolites in catalysis, adsorption, gas separation and energy storage17–21. Here we report the atomic imaging of single pyridine and thiophene confined in the channel of zeolite ZSM-5 (ref. 22). On the basis of integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM)23–25, we directly observe the adsorption and desorption behaviours of pyridines in ZSM-5 under the in situ atmosphere. The adsorption configuration of single pyridine is atomically resolved and the S atoms in thiophenes are located after comparing imaging results with calculations. The strong interactions between molecules and acid sites can be visually studied in real-space images. This work provides a general strategy to directly observe these molecular structures and interactions in both the static image and the in situ experiment, expanding the applications of electron microscopy to the further study of various single-molecule behaviours with high resolution.