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.