胞嘧啶—水分子团簇结构特性理论研究

发布时间：2018-06-16 17:28

本文选题：胞嘧啶 + 团簇　；参考：《曲阜师范大学》2016年硕士论文

【摘要】：胞嘧啶(Cytosine,简称C)学名为2-羰基-4-氨基嘧啶,它与自然界存在的其它4种碱基分子(鸟嘌呤、腺嘌呤、胸腺嘧啶、尿嘧啶)共同构成了重要的生命大分子——核酸(Nucleic Acid)。以胞嘧啶为对象,研究氢键的形成和团簇结构,对于认识氢键在生物分子中的作用、生物分子结构的形成等都具有十分重要的意义。团簇(Clusters)或称为微团簇(Microclusters)被认为是物质的“第五态”。团簇作为一种新型的物质结构其空间尺度跨越范围大,团簇结构的变化也不断影响着其本身的性质。研究团簇对我们认识凝聚物质的性质和规律有很大的价值。氢键是原子、分子间形成的一种比较简单的弱相互作用。氢原子有电负性差异的C、N、O、F、P等原子都可以组成氢键,在非共价键中氢键的键长比较长,强度也并非最强,同时氢键具有取向性高和形成形式多样的特点。氢键也广泛存在于各种生命活动中。研究胞嘧啶分子与水分子之间存在的氢键,对于研究氢键的形成以及人们对于氢键的理解都会有很大的帮助。根据密度泛函理论(DFT)通过计算和对比分析,考察C4H5N3O·(H2O)n(n=1~3)团簇结构红外振动光谱和结构构型。本文共分为三个部分。第一部分,介绍胞嘧啶分子的性质和用途,对团簇这种进行了简介,叙述了氢键的作用以及红外光谱的原理。第二部分,针对本文所涉及的量子化学计算方法,对量子化学程序Gaussian、密度泛函理论(DFT)、电子密度拓扑分析(AIM)方法及软件和PED软件等进行介绍说明。第三部分,采用DFT的B3LYP计算方法,在6-311++G(d,p)基组水平上对C4H5N3O·(H2O)n(n=1~3)的结构进行了优化并计算振动频率,研究了C4H5N3O·(H2O)n(n=1~3)分子团簇的基态结构及红外线光谱。通过对C4H5N3O·(H2O)n(n=1~3)团簇进行结构优化,获得了该团簇的六种稳定结构。使用AIM程序分析可知电子密度?的强弱反映了红移和蓝移的大小。通过AIM程序计算了三种最稳定结构的氢键临界点的拓扑参数,C4H5N3O·(H2O)n分子团簇中O—H…Y(Y=O、N)和N—H…O的形成是氢键作用的结果。分子团簇中O—H…O和N—H…O氢键的形成使得原本的O—H…O和N—H…O之间的键长变长,同时键的强度和伸缩振动频率均有减小;O—H键由于形成O—H…N氢键的影响,键强增大且长度变短,频率发生蓝移。veda4程序对C4H5N3O·(H2O)n(n=1~3)团簇进行了振动频率的模式指认,还对该团簇序列进行了红外振动光谱分析和振动频率比较。发现蓝移型O—H?N氢键的形成,该键中的O—H键发生变化,伸缩振动频率变大;原有基团O—H、N—H在形成氢键之后固有伸缩振动频率发生改变,与C4H5N3O分子中相应的振动频率减小。对C4H5N3O·(H2O)n(n=1~3)团簇在水溶剂中的红外光谱振动频率进行了分析。引用原有的理论计算和实验数据,再在PBE1PBE/aug-cc-pvtz和B3LYP/6-311++G(d,p)基组水平上,应用Gaussian09W软件分别对C4H5N3O分子进行频率解析和结构的优化。两者对比可知,由于官能团振动模式固有频率的不同,不同基组下计算得到的理论值与实验数据相比,各有最相近数据。
[Abstract]:Cytosine (C) is called 2- carbonyl -4- amino pyrimidine, which together with other 4 other basic molecules in nature (guanine, adenine, thymine, uracil) constitute an important major life molecule, nucleic acid (Nucleic Acid). Cytosine is used as the object to study the formation of hydrogen bonds and cluster structure of hydrogen bonds in life. The role of the molecule and the formation of the molecular structure are of great significance. Clusters (Clusters) or Microclusters are considered to be the "fifth states" of matter. As a new type of material structure, clusters have a large span of space, and the changes of cluster structure constantly affect their properties. The cluster is of great value to our understanding of the properties and laws of condensed matter. Hydrogen bonds are a relatively simple weak interaction between atoms and molecules. C, N, O, F, P and other atoms of hydrogen atoms can form hydrogen bonds. The bond length of hydrogen bonds in the non covalent bonds is longer, and the intensity is not the strongest, and the hydrogen bond is at the same time. The hydrogen bonds are also widely distributed in various life activities. The hydrogen bonds between the cytosine molecules and the water molecules are widely used to study the formation of hydrogen bonds and the understanding of hydrogen bonds. According to the density functional theory (DFT), the calculation and comparison analysis of C4H5 N3O. (H2O) n (n=1~3) cluster structure IR vibrational spectrum and structural configuration. This paper is divided into three parts. The first part introduces the properties and uses of cytosine molecules. The cluster is introduced, the action of hydrogen bond and the principle of infrared spectrum are described. The second part is about quantum chemistry calculation method involved in this paper, and quantum Chemical program Gaussian, density functional theory (DFT), electronic density topology analysis (AIM) method and software and PED software are introduced. The third part, using the B3LYP calculation method of DFT, the structure of C4H5N3O / (H2O) n is optimized and the vibration frequency is calculated at the level of the 6-311++G (D, P) base group. The base state structure and infrared spectrum of the molecular clusters. By optimizing the structure of the C4H5N3O (H2O) n (n=1~3) cluster, six stable structures of the cluster are obtained. Using the AIM program, we can see that the strength of the electron density reflects the size of the red shift and the blue shift. The topology of the hydrogen bond points of the three most stable structures is calculated by the AIM program. Parameter, O - H in C4H5N3O. (H2O) n cluster. Y (Y=O, N) and N - H... The formation of O is the result of hydrogen bonding. The O - H in molecular clusters. O and N - H... The formation of the hydrogen bond of O makes the original O - H... O and N - H... The bond length between O becomes longer, and the bond strength and stretching vibration frequency decrease. O - H bond is formed by O - H. The influence of N hydrogen bond, the bond strength increases and the length becomes shorter, the frequency blue shift.Veda4 program makes the mode identification of the vibrational frequency of the C4H5N3O (H2O) n (n=1~3) cluster, and also carries out the infrared vibration spectrum analysis and the vibration frequency comparison of the cluster sequence. The formation of the blue shift O H N hydrogen bond is found, the O H bond in the bond is changed and the telescopic vibration is changed. The dynamic frequency of the original group O - H, N - H changed after the formation of hydrogen bonds, and the corresponding vibration frequencies in the C4H5N3O molecule decreased. The vibration frequency of the infrared spectrum of C4H5N3O (H2O) n (n=1~3) cluster in water solvent was analyzed. The original theoretical calculation and experimental data were quoted, and then PBE1PBE/aug-cc-pv, and then PBE1PBE/aug-cc-pv. At the level of TZ and B3LYP/6-311++G (D, P) base group, the frequency analysis and structure optimization of C4H5N3O molecules are used respectively by Gaussian09W software. The comparison shows that the theoretical values calculated under different base groups have the most similar data compared with the experimental data, because of the difference of the natural frequency of the functional group vibration mode.
【学位授予单位】：曲阜师范大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：O641.3

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