Correlating 3D arrangements of atoms and defects with material properties and functionality forms the core of several scientific disciplines. Here, we determined the 3D coordinates of 6,569 iron and 16,627 platinum atoms in a model iron-platinum nanoparticle system to correlate 3D atomic arrangements and chemical order/disorder with material properties at the single-atom level. We identified rich structural variety and chemical order/disorder including 3D atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show for the first time that experimentally measured 3D atomic coordinates and chemical species with 22 pm precision can be used as direct input for first-principles calculations of material properties such as atomic magnetic moments and local magnetocrystalline anisotropy. This work not only opens the door to determining 3D atomic arrangements and chemical order/disorder of a wide range of nanostructured materials with high precision, but also will transform our understanding of structure-property relationships at the most fundamental level.
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