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This study uses density functional theory to investigate boron nitride nanoclusters functionalized with amino acids for enhanced binding of bisphenols A (BPA) and Z (BPZ) to mimic the estrogen-related receptor gamma. Three categories of nanoclusters were examined: pristine B₁₂N₁₂, and those which were germanium-doped for boron or nitrogen. The study reveals that hydrogen bonding patterns and molecular stability are significantly influenced by the type of functional group and the specific amino acids involved. Ge-doping generally enhances the binding stability and spontaneity of the nanocluster–amino acid–bisphenol complexes, with Glu 275 emerging as the most stable binding site. The analysis of electronic properties such as energy gap, ionization potential, electron affinity, and chemical hardness before and after bisphenol binding indicates a general trend of increased reactivity, particularly in Ge-doped nanoclusters. The findings highlight the potential of these nanocluster composites in applications requiring high reactivity and electron mobility, such as pollutant removal and drug delivery.