The origin of differential binding affinity and structural recognition between the inclusion complexes of cyclobis(paraquat-p-phenylene), I4+, and 1,4-substituted phenyl or 4,4’-substituted biphenyl derivatives has been jointly determined by spectrometric techniques and ab initio and semiempirical molecular orbital methods. The unusual boxed geometry and tetracationic charge distribution in 1(4+) are key molecular features which produce strong intermolecular interactions with guest and solvent molecules. Solvation was addressed by including up to 12 acetonitrile molecules in the theoretical model which realigned the predicted gas-phase supramolecular structures and energies into excellent agreement with experiment.