Three-dimensional distribution of individual atoms in the channels of beryl

Single atom detection in nanoporous materials is a significant challenge, particularly due to their sensitivity to electron irradiation. Here, natural beryl (Be3Al2Si6O18) is used as a model system to quantitatively analyse the occupancy of its atomic channels. High-angle annular dark-field imaging in a scanning transmission electron microscope is employed, revealing the presence of Cs atoms within the channels. Through statistical analysis of atomic column intensities and comparison with a series of multislice simulations, we successfully pinpoint the three-dimensional positions of individual Cs atoms. Our findings indicate a non-uniform distribution of Cs atoms in the crystal. Importantly, by extracting both the crystal thickness and atomic positions from a single high-resolution micrograph, we effectively minimize the adverse effects of beam damage. This approach offers a promising pathway for accurately determining the three-dimensional distribution of dopant atoms in various porous materials, opening new possibilities for the study and application of these technologically important materials. Single atom detection in nanoporous materials is challenging due to their sensitivity to electron irradiation. Here, the three-dimensional atomic occupancy of natural beryl is quantitatively analysed using high-angle annular dark-field imaging in a scanning transmission electron microscope and statistical analysis.