Uracil, Hydrated Uracil Structure And Vibrational Properties,

We all know that ionizing radiation breeding, cancer therapy by proton and heavy ion are the leading field of science in 21th century. At the same time people pay more and more attention to the radiation effects coming from the universe, medical treatment and the new biological varieties produced by ionizing radiation. Theoretically, it is the foundation of radiation biology and radiology to study the radiation damage to the organism, and this is an important leading field which relates to the crossed subject of nuclear physics, biology, chemistry, medicine and so on.The studies of molecular biology of nucleic acid are mostly concentrated on its structure and function. With the theoretical and experimental development in recent decade years, this area has become the most prolific area in molecular biology. Deoxyribonucleic acid and ribonucleic acid bases are the most important constituents of DNA and RNA, respectively. In radiation biochemistry and radiation medicine, DNA and RNA are main targets of ionizing radiation which will lead to the damage or mutation of cells, as the effect of ionizing radiation is very complex, and the radiant production of cells is various. Among the damages of DNA and RNA on their components, only the losing of base pairs or their mutation can influence on genetic results, 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. There are many experimental and theoretical studies on some basic biological molecules, such as base pairs, their derivatives or compounds. IR and Raman vibrational spectra are the main two experimental methods, but it is difficult to assign the spectra of polyatomic 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 experiment result and to predict new spectra.There are many methods to describe the motions of the molecules, such as quantum chemical methods and empirical molecular dynamics simulation. The former mainly includes HF method, ab initio method, and so on. As for the most accurate quantum chemical methods, the main problem is the large of computations which needs a lot of memory and time, and the using of scale factor would increase the uncertainty of the calculated results. Since there have been already many reports on the studying of large biological molecules used by MD method. All these reports imply that it is feasible for MD to study the large biological molecules. However, as so far, they haven't given the eigenmodes and frequencies in detail. Therefore in this thesis the molecule dynamic (MD) method will be used to study the structure and spectroscopy of biomolecules. So we have developed the empirical force field MD to study the vibrational properties of Uracil, and have given both the range of its spectra from 126cm-1 to 3370cm-1 and the eigenmodes corresponding to frequencies via FDH. The calculation results agree well with experimental data. It also compensates for the frequencies of experimental data that haven't been detected. It is the first time to report the Uracil's vibrational frequencies and eigenmodes calculated by MD method; considering that all biological molecules are in certain liquid state, we also investigate the structural and vibrational frequencies of Uracil in hydrated form, and we find that the hydration bonds have important effect on the structural and vibrational properties of uracil; at the same time, we find there are several special frequencies which are less influenced by hydration effect; we also explore the influences of heat radiation on uracil.