Abstract
The geometric structures, the interaction energies, the vibrational characteristics, and the electronic structures of the complexes of the isoguanine (isoG) quintet coordinated with mono valent cations (Na^+^, K^+^, Rb^+^, and Cs^+^) have been studied based on the nonplanar models. The geometry of the local minimum structure of the Na^+^‐isoG quintet complex deviates significantly from the planar structure. The geometric characteristics of the Na^+^‐isoG quintet complex support the experimental findings that Na^+^ is unlikely to induce the formation of the isoG quintet‐based pentaplexes. Similar to the guanine tetraplexes, the ionic selectivity of the isoG quintet‐based pentaplexes is largely dominated by the hydration energy of the cations. After hydration correction, the positive value of the free energy difference for the formation of the Na^+^‐isoG quintet complex (Δ__G__^f^) suggests that the isoG quintet is unable to capture the hydrated Na^+^. The negative values of Δ__G__^f^ for the K^+^ and Rb^+^ complexes implies that both ions have the tendency to be inserted into the isoG pentaplexes. This study suggests that, to elucidate the high Cs^+^ selectivity of isoG pentaplexes, it is necessary to extend the model from the isoG quintet to the isoG decamer. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007.