Binding of mono-, di-, and triphosphate, adenosine diphosphate (ADP), and adenosine triphosphatase (ATP) with receptors L1-L3, composed of two [9]aneN(3) units separated by a 2,9-dimethylene-1,10-phenanthroline (L1), a 2,6-dimethylenepyrichne (L2), or a 2,3-dimethylenequinoxaline (L3) spacer, has been studied by means of potentiometric titrations, H-1 and P-31 NMR measurements in aqueous solutions, and molecular modeling calculations. In the case of inorganic phosphates, the binding properties of the receptors appear to be determined by their geometrical features, in particular the distance between the two [9]aneN3 units imposed by the spacer separating the two macrocyclic units. While Li is able to selectively bind triphosphate over di- and monophosphate, L3 selectively coordinates the smaller monophosphate anion. Finally, L2 shows preferential binding of diphosphate. 1H and 31P NMR measurements show that the complexes are essentially stabilized by charge charge and hydrogen-bonding interactions between the anion and the protonated amine groups of the macrocyclic subunits of the receptor's. Molecular dynamics simulations suggest that the larger distance between the two macrocyclic units of L1 allows this receptor to form a larger number of hydrogen-bonding contacts with triphosphate, justifying its selectivity toward this anion. Conversely, in the case of L3, the two facing [9]aneN3 units give rise to a cleft of appropriate dimensions where the small monophosphate anion can be conveniently hosted. Considering nucleotide coordination, L1 is a better receptor for ATP and ADP than L2, thanks to the higher ability of phenanthroline to establish stabilizing pi stacking and hydrophobic interactions with the adenine units of the guests.