Imaging molecular structures and interactions by enhanced confinement effect in electron microscopy

Mengmeng Ma, Qinnan Yu, Jiayi Zhang, Xiao Chen (), Wenbo Li, Xianlin Qu, Xuliang Zhang, Jiale Feng, Fei Wei, Jianyu Yuan, Tao Cheng, Sheng Dai, Yi Wang (), Bin Song () and Boyuan Shen ()
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Mengmeng Ma: Soochow University
Qinnan Yu: Soochow University
Jiayi Zhang: Soochow University
Xiao Chen: Tsinghua University
Wenbo Li: East China University of Science and Technology
Xianlin Qu: Nanjing University of Aeronautics and Astronautics
Xuliang Zhang: Soochow University
Jiale Feng: Soochow University
Fei Wei: Tsinghua University
Jianyu Yuan: Soochow University
Tao Cheng: Soochow University
Sheng Dai: East China University of Science and Technology
Yi Wang: Nanjing University of Aeronautics and Astronautics
Bin Song: Soochow University
Boyuan Shen: Soochow University

Nature Communications, 2025, vol. 16, issue 1, 1-9

Abstract: Abstract Atomic imaging of molecules and intermolecular interactions are of great significance for a deeper understanding of the basic physics and chemistry in various applications, but it is still challenging in electron microscopy due to their thermal mobility and beam sensitivity. Confinement effect and low-dose imaging method may efficiently help us achieve stable high-resolution resolving of molecules and their interactions. Here, we propose a general strategy to image the confined molecules and evaluate the strengths of host-guest interactions in three material systems by low-dose electron microscopy. Then, we change the guest molecules to analyze how each kind of interaction strength influences the imaging quality of these molecules by using a same parameter, the aspect ratios of imaged molecular projections. In the material systems of perovskites (ionic) and zeolites with adsorbed molecules (van der Waals), we can obtain a clear image of molecular configurations by enhancing host-guest interactions. Even in metal organic framework (coordination) system, the atomic structures and bonds of aromatics can be achieved. These results provide a general description on the relation between molecular images and interactions, making it possible to study more molecular behaviors in wide applications by real-space imaging.

Date: 2025
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DOI: 10.1038/s41467-025-57816-4

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