The complexation and electrochemical behavior of redox-dependent ionophores in the presence of various alkylammonium ions were examined with calix[4]arenediquinone compounds. In spite of the small Ligating pore, semi-empirical calculation and H-1 NMR spectra showed that calix[4]arenediquinones were able to form complexes with protonated amine-type guests by virtue of three or four hydrogen bonds between the guest and carbonyl oxygen atoms in the host molecules. As a result of encapsulation, the structure of the calixarenes underwent a large conformational change, especially in the lower rim, which was rearranged to provide a symmetrically tetragonal binding environment. In addition, the reduction potential of the quinone moiety shifted to the positive direction. The magnitude of the potential shift depended on the strength of the hydrogen bond with the quinone. Therefore, the acidity and capability of forming multiple hydrogen bonds were predominant factors among other properties of the guest. The cooperative shortening effect of neighboring hydrogen bonds between the ammonium ion and carbonyl oxygen atoms produced an extra enhancement by making the redox center easily reducible and fast proton transfer possible.