The enantioselective interactions between chiral tetra-amidic receptors and nucleosides have been investigated by the ESI-IT-MS and ESI-FT-ICR-MS methodologies. Configurational effects on the CID fragmentation of diastereomeric [M (H) (2) aEuro cent HaEuro cent A] (+) aggregates (A = 2'-deoxycytidine dC, citarabine (ara-C) were found to be mostly offset by isotope effect in [S (X) (2) aEuro cent HaEuro cent A] (+) (X = H, D) differently from the results obtained on the analogues (A = cytidine C and gemcitabine G). This result points the involvement of two different nucleoside/tetraamide isoforms. The structural differences of the [M (H) (2) aEuro cent HaEuro cent A] (+) (A = C and G) complexes vs. the [M (H) (2) aEuro cent HaEuro cent A] (+) (dC and ara-C) ones is fully confirmed by the kinetics of their uptake of the 2-aminobutane enantiomers, measured by FT-ICR mass spectrometry. Indeed, uptake of the 2-aminobutane enantiomers by [M (H) (n) aEuro cent HaEuro cent A] (+) (n = 1,2; A = dC and ara-C) complexes is reversible, while that by [M (H) (n) aEuro cent HaEuro cent A] (+) (n = 1,2; A = C and G) is not. The most encouraging result concerning the measured fragmentation and kinetic differences between C and ara-C, that are just epimers, indicates the possibility to subtly modulate the non-covalent drug/receptor interactions, through the electronic properties of the 2'-substituent on the nucleoside furanose ring, and furthermore on its three-dimensional position.