To understand the effect of chemical modification on the stability and proton electron coupling in neutral radical molecules with a proton electron-transfer (PET) state, we investigate a nickel dithiolene complex with cyano-substituted pyrazine skeletons using experimental and theoretical methods. A Pourbaix diagram constructed from absorption spectroscopic and cyclic voltammetric measurements strongly suggests that the PET state of the complex is significantly more stable compared with that of the nonsubstituted complex. Theoretical calculations predicted that the introduction of electron-withdrawing groups leads to stabilization of the PET state mainly because of a greater delocalized electron distribution in the molecule. Crystallographic studies, with the support of theoretical calculations, revealed that the degree of coupling between protons and electrons varies depending on the Hammett sigma value of the substituents; the electronic state of the nonsubstituted complex appears to be most sensitive to the protonated state mainly owing to the spatially confined a-electron system.