The synthesis and characterization of 2-((pyridine-2-yl)methylamino)naphthalene-1,4-dione (H-1), 2-((thiophen-2-yl)methylamino)naphthalene-1,4-dione (H-2) and 2-((pyridine/thiophen-2-yl)ethylamino)naphthalene-1,4-dione (H-3 and H-4) have been carried out. Molecular recognition abilities of these ligands toward transition metal ions in methanol, methanol–water, methanol–triethylamine or methanol–water–triethylamine mixtures, stoichiometries and association constants of H-1 and H-3 have been determined. It has been shown that H-1 and H-3 coordinate to metal ions via two nitrogen atoms and oxygen and exhibit remarkable selectivity towards Cu²⁺ ions in methanol or methanol–water mixtures, the complexation being accompanied by a color change from orange to intense blue. LOD (Limit of Detection) of Cu²⁺ with H-1, H-3 are 1.48 × 10⁻⁸ mol L⁻¹ and 1.59 × 10⁻⁸ mol L⁻¹ respectively. The vibrational spectra, ¹H NMR chemical shifts and optical properties of H-1 to H-4 derived from density functional theory are also presented.