Theoretical Study On Structural Characteristics Of Cytosine - Water Molecules

Cytosine(referred to as C), the scientific name is 4-aminopyrimidin-2(1H)-one, together with the other four bases molecules(guanine, adenine, thymine, uracil) which exist in nature constitute an important biomacromolecules--Nucleic Acid. With cytosine as the object, studying the formation of hydrogen bond and cluster structures has great significance for understanding the role of hydrogen bond in biological molecules and the formation of biological molecules structure.Clusters or called microclusters is considered to be material “fifth states”. As a new material structure, its range across large spatial scales, changes in cluster structure also continue to affect the nature of its own. Researching Clusters has great value for us to understand the nature and regulars of cohesion material.Hydrogen bond is a kind of relatively simple weak interactions shaped between atoms and molecules. A hydrogen atom who has electrone gativity difference of C, N, O, F, P, etc. can be composed of hydrogen bond, in the non covalent bond, the length of hydrogen bond is relatively long, the strength is not the strongest, and hydrogen also has the features of high orientation and variously formed formation.Hydrogen bonds are also existing in a wide variety of life activities. Studying the hydrogen bonds between cytosine molecules and water molecules will offer great help for understanding the hydrogen bonding.We use density functional theory methods(DFT) in quantum chemistry for studying infrared vibration spectra and structure of Cytosine and water molecule clusters. This article is divided into three parts.The first part describes the nature and purpose of cytosine molecules and has carried on the introduction to clusters, recounted the function of hydrogen bond and the principle of infrared spectrum.The second part presents the calculation method of quantum chemistry, the Gaussian software, density functional theory(DFT), topological analysis of electron density, the AIM and PED software.In the third part, the C4H5N3O·(H2O)n(n=1~3) molecule was optimized and vibrational frequency was calculated, C4H5N3O·(H2O)n(n=1~3)clusters of state structures and infrared spectra was researched by using B3 LYP of DFT at the 6-311++G(d, p) level. The six stable structures of C4H5N3O·(H2O)n(n=1~3) clusters can be obtained by optimizing its structure. AIM analysis suggests that the electron density that reflects the strength of a bond has been used to explain the red and blue-shifted. AIM program was used to calculated critical points ’ topological parameters of three most stable structures, in C4H5N3O·(H2O)n(n=1~3) clusters, the formation of O—H?Y(Y=O、N) and N—H?O are due to hydrogen bond. O—H?O and N—H?O hydrogen bond are attributed to the longer length of the original O—H?O and N—H?O bond length, at the same time, the strength and the stretching vibrational frequency are also decreased; while O—H?N hydrogen bond is attributed to the shorter length, the strength and the stretching vibrational frequency are stronger. The IR spectra of C4H5N3O·(H2O)n(n=1~3) clusters were assigned by veda4 software and part of the vibration frequency were compared.The results show that in hydrogen bond O—H?N, the stretching vibration of H relatively affects cytosine molecules, so that the corresponding vibration frequency was blue-shifted; hydrogen bond O—H?O and N—H?O, the stretching vibration of H makes cytosine molecules’ corresponding vibration frequency red-shifted. The cluster of C4H5N3O·(H2O)n(n=1~3) in water solvent has carried on the infrared spectrum analysis of vibration frequency. The structures of cytosine molecules were optimized and their vibrational frequencies were calculated using density functional theory(DFT) at the B3LYP/6-311++G(d, p) level and the PBE1PBE/aug-cc-pvtz basis set level by Gaussian09 W program. With theoretical values and experimental values comparative analysis of the previous, vibrational frequencies are calculated with different basis sets are compared with the experimental values are the most likely value is formed by different vibration mode of groups.