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研究生： 郭展豪
Kuo, Chan-Hao
論文名稱： 鹼基(腺嘌呤、胸腺嘧啶及尿嘧啶) 配對物內相對氫鍵強度與芳香性的理論研究
Theoretical Studies of Relative H-Bonding Strengths and Aromatic Character in Pairing of Nucleobases (Nucleobases =Adenine, Thymine and Uracil)
指導教授： 王小萍
Wang, Shao-Pin
學位類別： 碩士
Master
系所名稱： 理學院 - 化學系
Department of Chemistry
論文出版年： 2010
畢業學年度： 98
語文別： 中文
論文頁數： 76
中文關鍵詞： 鹼基 、天然鍵性軌域 、氫鍵 、芳香性
外文關鍵詞： Nucleobases, NBO, HOMA, Hydrogen bond
相關次數： 點閱：68  下載：2 
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    • DNA(deoxyribonucleic acid)與 RNA(ribonucleic acid) 鹼基對錯配(mismatch)的情況已有許多人作過此探討。對此，吾人認為鹼基對的分子間氫鍵會影響整個核酸的結構和穩定，因此本文利用密度泛涵理論計算 (DFT) 研究腺嘌呤二聚物 (AA) 、尿嘧啶二聚物(UU) 和配對錯合物 (AT)、(AU) 之能量與芳香性。
    藉由各種鹼基之氫鍵錯合物的天然鍵結軌域 (NBO) 分析結果，我們發現氫鍵若由相同原子所形成則可視為同一類，其分子間的距離、E(2) 値和 Δs% 可以有效地與氫鍵的強弱及錯合物的穩定性呈一相關性。而錯配物中氫鍵若不是相同原子所形成將視為不同類，應分開探討其相關性。
    除此之外，本文延續先前實驗室引進的芳香性的簡諧振動模型 (Harmonic Oscillator Model of Aromaticity，HOMA)方法分析錯合物的芳香性，而經Krogowski等人證實外環雙鍵取代基會減弱分子的芳香性。鹼基使用羰基配對形成氫鍵後，錯配物因此有了結構與電子特性上的改變使得鹼基分子的環上芳香性特徵受到改變。而依計算後發現，若形成氫鍵的羰基位在其鹼基分子主要貢獻芳香性量(HOMA)的部位，則整體的芳香性會增加較多。

    Hydrogen-bonded nucleic acids base pairs substantially contribute to the structure and stability of nucleic acids. Our purpose is to understand the interaction between nucleotide bases. We have studied numerous model systems for dimers and mismatched pairs involving adenine (A), thymine (T), and Uracil (U) at density functional theory (DFT).
    The wavefunctions were analyzed by the Natural Bond Orbitals (NBO). If those two-dentate pairing modes were formed by the same functional groups, we can use E(2) (the second order perturbation energy),Δs% (the change of s-orbital contents) and the average intermolecular distances to describe the H-bonding strengths and stability of complexes.
    Furthermore, aromaticity of the ring of three compounds and their complexes was analyzed by the aromaticity index HOMA (Harmonic Oscillator Model of Aromacity). Aromaticity of the bases decreases with an increase of the number of double-bond substituents at the rings. Even if hydrogen bonding is much weaker perturbation than the substituent effect, H-bonds involving C=O groups in mismatched pairs may cause an increase of the aromatic character of the rings, but the increasing value is not identical in the pairs which build of the same compound, such as six uracil dimers. It is regard as whether H-bonds contribute to increasing the ring resonance.

    摘要.............................................................................................................I Abstract.......................................................................................................II 誌謝..........................................................................................................III 目錄..........................................................................................................IV 表目錄......................................................................................................VI 圖目錄.....................................................................................................VII 第一章 緒論...............................................................................................1 第二章 理論背景.......................................................................................2 2-1 氫鍵.....................................................................................................2 2-1-1 超共軛..........................................................................................5 2-1-2 判斷氫鍵......................................................................................6 2-2 π 電子系統.......................................................................................8 2-2-1 共振..............................................................................................8 2-2-2 芳香性..........................................................................................9 2-2-3 共軛氫鍵......................................................................................9 2-2-4 分子間氫鍵與芳香性................................................................11 第三章 計算原理與方法........................................................................13 3-1 計算原理...........................................................................................13 3-1-1 HF 理論方法............................................................................13 3-1-2 DFT 理論方法..........................................................................14 3-1-3 基底...........................................................................................16 3-1-4 分裂基底...................................................................................17 3-1-5 極化函數...................................................................................18 3-1-6 擴散函數.................................................................................. 18 3-1-7 限定自洽場與非限定自洽場...................................................19 3-1-8 天然鍵性軌域 (NBO) .............................................................20 3-1-9 HOMA.....................................................................................22 3-2 計算方法..........................................................................................25 3-2-1 選用軟體...................................................................................25 3-2-2 計算條件...................................................................................25 3-2-3 計算流程...................................................................................26 3-2-4 計算指令...................................................................................26 3-2-5 選用基底...................................................................................27 3-2-6 HOMA 的計算.........................................................................27 第四章 結果與討論................................................................................29 4-1 穩定能分析.......................................................................................29 4-1-1 AT、AU、AA與UU氫鍵錯合物.............................................29 4-1-2 AA與UU氫鍵錯合物的比較.................................................32 4-1-3 AT與AU氫鍵錯合物的比較..................................................42 4-1-4 相關表格..................................................................50 4-2 π 電子系統的極化作用.................................................................55 4-2-1 芳香性的差異............................................................................55 4-2-2 芳香性與穩定能的關係............................................................55 4-2-3 氫鍵對芳香性的影響................................................................56 4-2-4 相關表格....................................................................................66 第五章 結論...........................................................................................70 參考文獻...................................................................................................71

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