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Home  >  Volume 26 (March 2014)

23. Density Functional Theory Calculations of The Vibrational Spectra of Deoxy 5’-Monophosphate Nucleotides Using FHI-aims code by A.S. Gidado and G. Babaji. Volume26, (March, 2014), pp153 – 166.
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Abstract

We calculated vibrational frequencies, infrared intensities and total free energies of the most stable conformers of the four nucleotides: Deoxyadenosine '5 -monophosphate, deoxycytidine 5' -monophosphate, deoxyguanosine 5' monophosphate and deoxythymidine 5' -monophosphate. The infrared spectra of these nucleotides have been observed  from about 3700 to about 50 cm−1 and are presented. The spectra were interpreted   with the aid of IRPal 2.0 software. The vibrational frequencies calculated were compared favorably with those reported in the literature. Some of the vibrations observed in the ir-spectra are the stretching vibration of  C-O group which give rise to strong band in the region 1320-1000cm-1, bending vibration of P-H group which give rise to weak band in the region 1250-950cm-1, stretching vibration of C=O group which give rise to strong band  in the region 1690-1720cm-1, out of plane vibration of C-H group which produces medium intensity in the region 865-810cm-1, in plane bending vibration of the NH2 group produces strong intensity in the region 1640-1500cm-1, stretching vibration of O-H group produces variable intensity in the region 3600-3400cm-1 and stretching vibration of C=C group produces weak intensity in the region 1616-1550cm-1. Total free energy for each nucleotide was also calculated with variation of temperature from 25K to 400K in the interval of 25. We have observed that an increase in temperature leads to a decrease in total free energy. This feature is observed in all the nucleotides. Principal moment of inertia as well as the zero point energy for the five nucleotides were also calculated. The results of the zero point energy were also  compared favorably with those reported in the literature. Generalized gradient approximation,[GGA-Perdew–Burke–Ernzerhof (pbe)] exchange-correlation functional of the Density functional theory was employed throughout the work. 

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