Substructural And Vibrational Properties Of Nucleobase

Nucleic acid is the most important biological macromolecules, and the basis of life existence. It is indispensable to the instorage, replication, transcription and identification of genetic information. In radiation biology and radiation medicine, DNA and RNA are the major target of ionizing radiation which induces cell killing or transformation. It is a complex process that rays act on the body, from exposure to biological effects (cancer, etc.). A wide variety of radiation products appear, and the impact of its structure is more and more complex. But it is not genetic unless nucleic loss or change. Therefore, by studying the vibrational properties of the base pairs, one can understand the mechanisms of the radiant DNA and RNA damages.The study of vibrational spectra of molecules is an important tool to explore the properties of molecules. Spectroscopic investigations of biological macromolecules, such as the nucleic acid (NA) bases contained in non-interacting environments or their salvation may help clarify the role of these molecules in biological systems. IR and Raman vibrational spectra are the main two experimental methods, but it is difficult to assign the spectra of poly-atomic molecules because of the complexity resulting from coupling of vibrational modes, molecular interactions, and other effects. So the theoretical calculation of vibrational spectra has an important meaning to comprehend the experimental result. Furthermore, the theoretical calculation can also predict new spectra.Molecular dynamics applicated in bio-molecular research is getting more and more broad, many studies have shown that the study of biological macro molecules by molecular dynamics method is feasible, but only a few molecules have been given the vibration mode and their frequency. Therefore, in this thesis, the molecule dynamic (MD) method will be used to study the structure and spectroscopy of bio-molecules. So we have performed the empirical force field MD to study the vibrational properties of Uracil and Thymine, both the range of uracil spectra and the eigenmodes corresponding to frequencies via FDH are from 86 cm-1 to 3372 cm-1. And the range of thymidine is from 118 cm-1 to 3657 cm-1. Considering biological molecules are in different biological temperatures, the temperature ffect on the structures can not be ignored, so we use the semi-empirical molecular dynamics method to study and list the temperature potential vibration properties of the uracil and thymine molecule, the kinetic energy changes of the amplitude. We have found that the temperature of the uracil molecular structure and vibrational frequencies indeed have a small effect on the structures and vibrational frequencies of the uracil. We also studied the thermal radiation (temperature effect) affect the nature of the uracil and thymine molecule. These results accord with the theoretical expectation that the vibration spectra is independent of temperature.