The B3LYP method with 6-31G* basis set was used to predict the geometries of five 9-aminoacridines (9-AA 1(a–e) ), DNA base pairs, and respective complexes. Polarizabilities, charge distribution, frontier molecular orbital (FMO), and dipole moments were used to analyze the nature of interactions that allow reasonable drug diffusion levels. The results showed that charge delocalization, high polarizabilities, and high dipole moments play an important role in intermolecular interactions with DNA. The interactions of 9-AA 1(a–e) with GC are the strongest. 9-AA 1(d) displayed the strongest interaction and 9-AA 1(b) the weakest.