本文選題：胞嘧啶 + 團(tuán)簇��； 參考：《曲阜師范大學(xué)》2016年碩士論文

【摘要】：胞嘧啶(Cytosine,簡稱C)學(xué)名為2-羰基-4-氨基嘧啶,它與自然界存在的其它4種堿基分子(鳥嘌呤、腺嘌呤、胸腺嘧啶、尿嘧啶)共同構(gòu)成了重要的生命大分子——核酸(Nucleic Acid)。以胞嘧啶為對象,研究氫鍵的形成和團(tuán)簇結(jié)構(gòu),對于認(rèn)識氫鍵在生物分子中的作用、生物分子結(jié)構(gòu)的形成等都具有十分重要的意義。團(tuán)簇(Clusters)或稱為微團(tuán)簇(Microclusters)被認(rèn)為是物質(zhì)的“第五態(tài)”。團(tuán)簇作為一種新型的物質(zhì)結(jié)構(gòu)其空間尺度跨越范圍大,團(tuán)簇結(jié)構(gòu)的變化也不斷影響著其本身的性質(zhì)。研究團(tuán)簇對我們認(rèn)識凝聚物質(zhì)的性質(zhì)和規(guī)律有很大的價值。氫鍵是原子、分子間形成的一種比較簡單的弱相互作用。氫原子有電負(fù)性差異的C、N、O、F、P等原子都可以組成氫鍵,在非共價鍵中氫鍵的鍵長比較長,強(qiáng)度也并非最強(qiáng),同時氫鍵具有取向性高和形成形式多樣的特點。氫鍵也廣泛存在于各種生命活動中。研究胞嘧啶分子與水分子之間存在的氫鍵,對于研究氫鍵的形成以及人們對于氫鍵的理解都會有很大的幫助。根據(jù)密度泛函理論(DFT)通過計算和對比分析,考察C4H5N3O·(H2O)n(n=1~3)團(tuán)簇結(jié)構(gòu)紅外振動光譜和結(jié)構(gòu)構(gòu)型。本文共分為三個部分。第一部分,介紹胞嘧啶分子的性質(zhì)和用途,對團(tuán)簇這種進(jìn)行了簡介,敘述了氫鍵的作用以及紅外光譜的原理。第二部分,針對本文所涉及的量子化學(xué)計算方法,對量子化學(xué)程序Gaussian、密度泛函理論(DFT)、電子密度拓?fù)浞治?AIM)方法及軟件和PED軟件等進(jìn)行介紹說明。第三部分,采用DFT的B3LYP計算方法,在6-311++G(d,p)基組水平上對C4H5N3O·(H2O)n(n=1~3)的結(jié)構(gòu)進(jìn)行了優(yōu)化并計算振動頻率,研究了C4H5N3O·(H2O)n(n=1~3)分子團(tuán)簇的基態(tài)結(jié)構(gòu)及紅外線光譜。通過對C4H5N3O·(H2O)n(n=1~3)團(tuán)簇進(jìn)行結(jié)構(gòu)優(yōu)化,獲得了該團(tuán)簇的六種穩(wěn)定結(jié)構(gòu)。使用AIM程序分析可知電子密度?的強(qiáng)弱反映了紅移和藍(lán)移的大小。通過AIM程序計算了三種最穩(wěn)定結(jié)構(gòu)的氫鍵臨界點的拓?fù)鋮?shù),C4H5N3O·(H2O)n分子團(tuán)簇中O—H…Y(Y=O、N)和N—H…O的形成是氫鍵作用的結(jié)果。分子團(tuán)簇中O—H…O和N—H…O氫鍵的形成使得原本的O—H…O和N—H…O之間的鍵長變長,同時鍵的強(qiáng)度和伸縮振動頻率均有減小;O—H鍵由于形成O—H…N氫鍵的影響,鍵強(qiáng)增大且長度變短,頻率發(fā)生藍(lán)移。veda4程序?qū)4H5N3O·(H2O)n(n=1~3)團(tuán)簇進(jìn)行了振動頻率的模式指認(rèn),還對該團(tuán)簇序列進(jìn)行了紅外振動光譜分析和振動頻率比較。發(fā)現(xiàn)藍(lán)移型O—H?N氫鍵的形成,該鍵中的O—H鍵發(fā)生變化,伸縮振動頻率變大;原有基團(tuán)O—H、N—H在形成氫鍵之后固有伸縮振動頻率發(fā)生改變,與C4H5N3O分子中相應(yīng)的振動頻率減小。對C4H5N3O·(H2O)n(n=1~3)團(tuán)簇在水溶劑中的紅外光譜振動頻率進(jìn)行了分析。引用原有的理論計算和實驗數(shù)據(jù),再在PBE1PBE/aug-cc-pvtz和B3LYP/6-311++G(d,p)基組水平上,應(yīng)用Gaussian09W軟件分別對C4H5N3O分子進(jìn)行頻率解析和結(jié)構(gòu)的優(yōu)化。兩者對比可知,由于官能團(tuán)振動模式固有頻率的不同,不同基組下計算得到的理論值與實驗數(shù)據(jù)相比,各有最相近數(shù)據(jù)。
[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.
【學(xué)位授予單位】：曲阜師范大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2016
【分類號】：O641.3

【相似文獻(xiàn)】

相關(guān)期刊論文 前10條

1 曹益林,汪]廝，

本文編號：2027526