[Characteristic vibration analysis of M-RNA nucleic acid bases complexes (M = Ca+ and Mg+) by DFT].
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 C1M, T1M and U1M (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 C1, at 1,747 and 1,792 cm(-1) for T1, 1,763 and at 1,796 cm(-1) for U1. 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 C1M 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 C1Ca+ and by 110 cm(-1) for C1Mg+. When the stable complexes T1M 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 U1M are formed, the vibration of bond C--O--M turns 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.
Zhang
Xing-Chu
XC
Department of Electromechanical Engineering, Guangzhou Polytechnic of Science and Trade, Guangzhou 511442, China. xingchuz@126.com
Hu
Yi-Hua
YH
Wang
Xiao-Juan
XJ
D002118:Calcium / Q000737:chemistry; D002412:Cations / Q000032:analysis*; D003596:Cytosine / Q000032:analysis; D006801:Humans; D008274:Magnesium / Q000737:chemistry; D008297:Male; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000032:analysis*; D011188:Potassium / Q000737:chemistry; D011743:Pyrimidines / Q000032:analysis*; D011789:Quantum Theory; D012313:RNA; D012964:Sodium / Q000737:chemistry; D013055:Spectrophotometry, Infrared / Q000379:methods*; D013059:Spectrum Analysis, Raman; D013941:Thymine / Q000032:analysis; D014498:Uracil / Q000032:analysis; D014732:Vibration
D002412:Cations; D009696:Nucleic Acids; D011743:Pyrimidines; D014498:Uracil; D012313:RNA; D003596:Cytosine; D012964:Sodium; D008274:Magnesium; D013941:Thymine; D011188:Potassium; D002118:Calcium