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研究生：	陳怡魁 Chen, Yi-Kui
論文名稱：	以天然鍵性軌域分析來研究腺嘌呤與胸腺嘧啶雙聚物的自由基化合物之互變反應 Studying tautomeric reactions of radical compounds of adenine thymine base pair by Nature Bond Orbital analysis
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：	153
中文關鍵詞：	質子轉移、天然鍵性軌域、氫鍵
外文關鍵詞：	proton transfer, NBO, hydrogen bond
相關次數：	點閱：83 下載：1
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DNA鹼基對會發生特別的互變機制，可能造成基因碼的錯亂，而DNA鹼基對的radical anion/cation 有可能加速這種互變機制的速度，並且使的基因碼發生變異。我們利用量子力學來研究 adenine thymine base pair(AT) 質子轉移的反應機制，為了將來有助於DNA鹼基對的研究。
在本研究中，我們使用分子計算的密度泛函述理論(density functional theory) [DFT/6-31+G(d)] ，對AT radical anion和cation的二步質子轉移反應機制的起始物、過度態、中間產物和最終產物做研究。由電荷分佈和Spin的結果，我們可以推測轉移的是質子或是氫原子。
此外，我們也做了natural bond orbital 的分析，希望由E2值和電子結構獲得有關此反應的更多資訊，其中我們發現到，當A-T base pair變成radical anion時，在thymine上的氧會從keton form變為enol form，而且在路徑一的第一個質子轉移過程中，只有beta spin的電子結構發生改變，所以此反應的活化能特別的低。

The tautomerism, which takes place in DNA base pairing, might lead to confusing genetic coding. In the charged DNA pairing radicals, either radical cations or anions, the rates of tautomerism processes would increase and, consequently, changes of genetic codes become noteworthy. The proton transferring mechanism reported for the adenine thymine base pair have been subjected to quantum mechanic studies in order to lay the foundation for future studies in DNA pairing.
Through molecular calculations at density function level [DFT/6-31G(d)], the initiator, transition state(s), intermediate and final products involved in two-step proton migration mechanism have been studied. From the result of electronic distribution and spin, we assumed a proton or hydrogen atom was transferred.
Furthermore, we performed analysis of the natural bond orbital to obtain information about this reaction by E2 value and electronic structure. We found out that the oxygen of thymine transformed from ketone form to enol form in transforming from A-T base pair to a radical anion.

摘要.............................................................................................................I
Abstract.....................................................................................................Ⅱ
誌謝..........................................................................................................III
目錄..........................................................................................................IV
表目錄.....................................................................................................VII
圖目錄.....................................................................................................XII

第一章 緒論..............................................................................................1
第二章 理論背景......................................................................................2
2-1 DNA的突變........................................................................................2
第三章 計算原理與方法..........................................................................6
3-1 計算原理.............................................................................................6
 3-1-1  HF 理論方法..............................................................................6
 3-1-2  DFT 理論方法............................................................................7
 3-1-3  基底.............................................................................................9
 3-1-4  分裂基底...................................................................................10
 3-1-5  極化函數...................................................................................11
 3-1-6  擴散函數.................................................................................. 11
 3-1-7  限定自洽場與非限定自洽場...................................................12
 3-1-8  天然鍵性軌域 (NBO) .............................................................13
3-2 計算方法..........................................................................................16
 3-2-1  選用軟體...................................................................................16
3-2-2  計算條件.....................................................................................16
 3-2-3  計算流程...................................................................................17
 3-2-4  計算指令...................................................................................18
 3-2-5  選用基底...................................................................................18
第四章 結果與討論................................................................................19
4-1  Adenine-Thymine base pair............................................................19
4-1-1 反應路徑.......................................................................................19
4-1-2 結構與能量.............................................................................. .......24
4-1-3 天然鍵性軌域（NBO）分析....................................................... ..29
4-1-3-1 A-T Normal Form....................................................................... ...29
4-1-3-2 A-T Transition state........................................................................33
4-1-3-2 A-T Tautomeric Form.....................................................................35
4-2 A-T Radical Anion…………………………………………………….37
4-2-1 反應路徑.............................................................................. .. .........37
4-2-2 結構與能量.......................................................................... .. .........37
4-2-3 天然鍵性軌域（NBO）分析............................................. .. .........48
4-2-3-1 Normal Form..................................................................................48
4-2-3-2 Transition State 1-1........................................................................52
4-2-3-3 Transition State 1-2........................................................................55
4-2-3-4 Single-Proton-Transferred-Form-1(SPT1) ....................................58
4-2-3-5 Single-Proton-Transferred-Form-2(SPT2) ....................................61
4-2-3-6 Transition State 2-1........................................................................64
4-2-3-7 Transition State 2-2........................................................................66
4-2-3-8 Tautomeric Form............................................................................69
4-3 A-T Radical Cation...............................................................................72
4-3-1 反應路徑..........................................................................................72
4-3-2 結構與能量......................................................................................72
4-3-3 天然鍵性軌域（NBO）分析.........................................................80
4-3-3-1 Normal Form.................................................................................80
4-3-3-2 Transition State 1-1........................................................................83
4-3-3-3 Transition State 1-2........................................................................85
4-3-3-4 Single-Proton-Transferred-Form-1(SPT1) ....................................88
4-3-3-5 Single-Proton-Transferred-Form-2(SPT2) ....................................90
4-3-3-6 Transition State 2-1........................................................................93
4-3-3-7 Transition State 2-2........................................................................95
4-3-3-8 Tautomeric Form...........................................................................98
第五章  結論..........................................................................................101
參考文獻..................................................................................................152

                                    

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校內：2012-08-02公開
校外：2012-08-02公開

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