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The interaction between homochiral substituted perylene bisimide (PBI) molecule and the D enantiomer of phenylalanine amino acid was monitored. Spectroscopic transitions of PBI derivative in aqueous solution in the visible range were used to evaluate the presence of D-phenylalanine. UV-visible, fluorescence, FT-IR, and AFM characterizations showed that D-phenylalanine induces significant variations in the chiral perylene derivative aggregation state and the mechanism is enantioselective as a consequence of the 3D analyte structure. Th