Vibrational Properties Of Deoxynucletides Molecule: A First Principles Study

In this paper, the first-principles density functional theory are used to simulate the geometric structures and calculate the phonon vibrational property、Infrared spectroscopy、Raman spectrum of four periodical boundary conditions deoxynucleotide unit cell, which are corresponding to four kinds of basic group(Adenine、Guanine、Cytosine、Thymine). It is revealed that the vibrational frequency have a great differences among four kinds of deoxynucleotide unit cell according to our research. We found out that there are several strong absorption peak for periodical d GMP and d TMP molecules near the frequency of 3000 cm-1.For d GMP,the characteristic frequency is f=3029.47cm-1, absorption strength is 35.18(D/A**2/amu) correspondingly. For d TMP, the characteristic frequency is f=3004.59cm-1, absorption strength is 35.18(D/A**2/amu). The IR absorption for the other two molecules is weak. We found that each of d AMP and d TMP have three characteristic absorption peak, while d GMP and d CMP have two absorption peak in the region of 900cm-1—1300 cm-1. In addition, we calculated the phonon frequency 、 phonon dispersion curves and phonon density of states, we discover that in the high frequency region, there are three branches of phonon dispersion curve for d CMP and d AMP, but d GMP and d TMP just have two. Finally, compare the Raman spectrum of non-periodic deoxynucleotide molecule with periodical boundary deoxynucleotide unit cell, we found that the positions of Raman spectroscopy peak are similar in the low frequency part, but in the high frequency part, the Raman spectroscopy peak of the periodical boundary conditions deoxynucleotide unit cell move towards to the low frequency part according to the non-periodic deoxynucleotide molecule.In summary, by calculating and analyzing the infrared absorption spectrum、phonon dispersion curves、phonon density of states and Raman spectrum of four kinds of periodical boundary deoxynucleotide unit cell. We can not only distinguish deoxynucleotide molecules from each other by the different absorption characteristic frequency in infrared spectrum, but also can find the connection and difference between them.