As part of ongoing studies of the effects of O-donor ligands based on pyridine-2,6-dicarboxylic acid N-oxide on the geometry, topology and dimensionality of their metal complexes, the salt (H9a-acr)2(pydco)·2H2O (1) and two new coordination complexes with formulas, {(H9a-acr)2[Cu(pydco)2(H2O)2]·4H2O} (2), and {(H9a-acr)2[Ni(pydco)2(H2O)2]·4H2O} (3) (where H2pydco = pyridine-2,6-dicarboxylic acid N-oxide and 9a-acr = 9-aminoacridine) have been synthesized by proton transfer from H2pydco to 9a-acr. The structures of 1-3 were characterized by elemental analysis, infrared spectroscopy and X-ray diffraction methods. Thermogravimetric analysis (TGA) was also carried out on compounds 1 and 2. All three compounds have similar crystal packing, features, namely alternating 2D cationic and anionic layers which are held together by an extensive network of hydrogen bonds and π-stacking interactions to create three-dimensional supramolecular architectures. Despite the different conditions of temperature and stoichiometric ratio in the synthesis of complexes 2 and 3, the products are isostructural and Cu2+ and Ni2+ have distorted octahedral geometry with two (pydco)2- ions coordinated as chelating bidentate ligands. In all three compounds, protonated 9-aminoacridiunium cations are arranged in an anti-parallel stacking mode. This behavior is described and analyzed via density functional theory (DFT) calculations, molecular electrostatic potential (MEP) tools and the NCI method.