A density functional investigation of the interaction between calcium and magnesium univalent cations and RNA pyrimidine base (cytosine,thymine and uracil) was performed to determinE_geometric coordinates and free energies for all possible stable isomers at B3LYP/6-311+G(2df,2p) level.The most stable isomers C 1M,T 1M and U 1M (M=Ca⁺ and Mg⁺) with the lowest free energy among the same pyrimidine base tautomers were calculated to determine the characters of infrared vibrations.According to the results,two characteristic infrared vibrations at wave numbers 1 684 and 1 765 cm^-1 were found for single pyrimidine base C 1,at 1 747 and 1 792 cm^-1 for T 1,1 763 and at 1 796 cm^-1 for U 1.In addition,spectrum shifts were found when the cations interact with the pyrimidine base tautomers.For deeper analysis,we found that when the stable complexes are formed,the cations are prone to act on the oxygen atoms,and cause the vibrational frequencies to change,the spectral lines belonging to the vibration of C—O—M turn out to redshift and the others turn out to blueshift.When the stable complex C 1M is formed,the characteristic infrared vibration at 1 684 cm^-1 mainly caused by the ring’s vibration turns out to blueshift about 10 cm^-1,and the another characteristic vibration of 1 765 cm^-1 caused by vibration of bond C—O with oxygen atom acting on cations directly turns out to redshift by 112 cm^-1 for complex C 1Ca+ and by 110 cm^-1 for C 1Mg⁺.When the stable complexes T 1M are formed,the characteristic vibration of bond C—O—M turns out to redshift about 130 cm^-1 and the vibration of bond C—O turns out to blueshift about 55 cm-1 .When the stable complexes U 1M are formed,the vibration of bond C—O—M truns out to redshift about 90 cm^-1 and about 50 cm^-1 for another C—O.The characteristic infrared vibration frequencies are changed obviously when tautomers act on the cations,which is mainly because cations take part in molecule’s vibrations and change the force constants and reduced masses.