The interaction of AMP, ADP, ATP and related phosphate, diphosphate and triphosphate anions with the positively charged forms of the HL ligand, constituted by a tren molecule functionalized with a pyrimidine residue, was studied by potentiometric titrations, affording the stability constants of the formed anion complexes, (31)P and (1)H NMR spectroscopy in aqueous solutions and modelling calculations. The equilibrium data show that electrostatic forces make an important, but not decisive contribution, to the stability of the anion complexes. For nucleotides, (1)H NMR spectra showed that the formation of pi-stacking interactions between nucleotide adenine and ligand pyrimidine moieties contribute to the stability of these complexes, being very important for those complexes of higher stability. The synergistic action of the different binding groups of the polyfunctional HL receptor leads to a marked recognition of ADP over ATP with a selectivity coefficient as high as 116 at pH 3.3, which is unprecedented in the context of synthetic receptor in water. According to modelling calculations, such exceptional binding selectivity has a strong relation with the increase of stability experienced by ADP complexes upon ADP protonation. A similar phenomenon is observed for HAMP(-) whose interaction with H(3)L(2+) is at least as strong as that of the more charged HATP(3) anion, which is another rare occurrence.