The most probable time‐averaged conformations of three polyammonium cations Hn2n+ (n = 3–5) formed from the macrocyclic pentamine ligand (2, scorpiand) [derivative of 1,4,8,11‐tetraazacyclotetradecane (cyclam)] were analyzed in order to elucidate an origin of ‘wrong‐way’ amine‐protonation shifts found in some 13C NMR pH‐profiles determined for the acidic H2O/D2O solution. These NMR trends were reproduced quite well in δCs computed for multicomponent shapes of related cations, which were in turn elucidated by the best fitting experimental data to those predicted by the gauge‐independent atomic orbital (GIAO) B3LYP/6‐31G* method, including the IEF‐PCM approach. A consistent DFT methodology of the treatment of such equilibrated cationic mixtures is proposed. Moreover, a few novel ONIOM2‐GIAO B3LYP/6‐31G*:STO‐3G type supermolecular calculations were performed for a simulated presence of bulk water molecules surrounding H525+. Copyright © 2009 John Wiley & Sons, Ltd.