Probing Site Occupancy of Rare-Earth Elements in Zoned Apatite via Three-Dimensional Electron Diffraction Coupled with Focused Ion Beam Sampling

Apatite serves as one of the host minerals for rare earth elements (REE). Elucidating the site preference of REE within the apatite structure is critical for understanding their enrichment mechanisms, ore-forming processes, and potential utilization. Single-crystal X-ray diffraction (SCXRD) is a key technique in such research. However, natural apatite commonly exhibits compositional zoning, and the sample size requirements of SCXRD often hinder the characterization of structural variations among different zones. Consequently, there is a pressing need in Earth sciences for analytical techniques capable of quantitative structural analysis at the micron scale. Three-dimensional electron diffraction (3DED) can resolve crystal structures of nanoscale crystals, yet its application has long been constrained by dynamical scattering effects that compromise diffraction intensity accuracy. In this study, 3DED combined with focused ion beam (FIB) microsampling was employed to successfully determine the crystal structures of both high and low REE concentration zones in zoned apatite from the Scientific Drilling Project YSDP-4 drill core in Sihedang Town, Lingyuan City, western Liaoning Province. The refined crystal chemical formulas show excellent consistency with electron probe microanalysis (EPMA) data. The refinement results reveal that as established in the literature, REE incorporation into apatite primarily occurs via two known coupled substitution mechanisms: REE 3+ + Si 4+ = Ca 2+ + P 5+ . The 3DED structural refinements are in strong agreement with trends in relative elemental contents obtained by EPMA, demonstrating the reliability and significant potential of 3DED for quantitative site occupancy analysis in micromineralogy. This approach provides a new pathway for determining the occurrence states of trace elements in electron beam-sensitive nano- to micron-sized minerals.