The efficient recovery of rare earth elements from associated rare-earth-bearing phosphate ores is of paramount importance for expanding the supply of rare earth resources. In contrast to conventional studies that focus on extracting rare earths either from phosphate concentrates or from phosphogypsum generated during the sulfuric acid wet-process, this study takes as its subject the rare-earth-enriched residue—an intermediate product obtained after the selective leaching of phosphorus via the hydrochloric acid route—from a rare-earth-bearing phosphate ore in Zhijin, Guizhou Province. The occurrence states, leaching behavior, and kinetic mechanisms of rare earth elements within this residue were systematically elucidated. Analyses using scanning electron microscopy coupled with energy-dispersive spectroscopy (SEM–EDS) and aberration-corrected scanning transmission electron microscopy (STEM) reveal that rare earth elements are hosted in residual fluorapatite and newly formed CaF
2 through isomorphic substitution. The substitution of REE
3+ for Ca
2+ induces lattice contraction in CaF
2, with the interplanar spacing decreasing from 0.27 nm to 0.26 nm. Through single-factor experiments and response surface methodology (RSM) optimization, the optimal leaching conditions were determined to be a temperature of 80 °C, a leaching time of 120 min, a hydrochloric acid dosage of 160% of the theoretical requirement, a solid–liquid ratio of 1:6, and a agitation speed of 500 r·min
−1. Under these conditions, the leaching efficiency of rare earth elements reached as high as 92.69%. Kinetic analysis indicates that the leaching process follows the shrinking-core model, with the rate controlled by diffusion through the solid product layer. The apparent activation energy was calculated to be 37.2 kJ·mol
−1, characteristic of a diffusion-controlled process. Furthermore, response surface analysis of variance confirms that leaching temperature and time are the most significant factors influencing rare earth leaching. This study elucidates, from multiple perspectives, the leaching mechanism of rare earth elements from enriched residues within a hydrochloric acid system, thereby providing important theoretical support for the efficient recovery and process optimization of rare earth resources from associated phosphate ores.
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