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A dicarbonylruthenium(II) complex containing bidentate 2-(2-pyridyl)-1,8-naphthyridine, as well as monodentate aqua and chlorido ligands, were isolated and characterized using spectroscopic techniques and single crystal X-ray diffraction. These data indicate that geometrical isomerization occurs during the substitution reaction involving a superacid. Density functional theory (DFT) calculations were performed on the plausible geometrical isomers. The DFT-optimized structures and calculated infrared spectra suggest that the experimentally obtained structure is stable.