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研究生:郭章王
研究生(外文):Chang-wang Kuo
論文名稱:運用密度泛函理論方法研究腺嘌呤外環加成物與胸腺嘧啶間的反應
論文名稱(外文):Interaction of Adenine adducts with Thymine using Density Functional Theory method
指導教授:李錫隆李錫隆引用關係
指導教授(外文):Shyi-Long Lee
學位類別:碩士
校院名稱:國立中正大學
系所名稱:化學所
學門:自然科學學門
學類:化學學類
論文種類:學術論文
論文出版年:2006
畢業學年度:94
語文別:英文
論文頁數:73
中文關鍵詞:外環加成物密度泛函理論方法腺嘌呤
外文關鍵詞:Adenine adductsDFTThymine
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在本次研究中,對於DNA外環加成物和胸腺嘧啶所形成化合物的結構計算,是使用了密度泛函理論方法來做結構幾何最佳化 (B3LYP /6-31+G*)。在此我們考慮了兩種不同的外環加成物, etheno -adenine (εA) 和 ethano -adenine (EA) 和胸腺嘧啶之間的作用關係。而我們認為會有數種穩定的結構形成 : [εA(1)-T, εA(2)-T, εA(3)-T 和 EA(1)-T, EA(2)-T, EA(3)-T] 、 [εA(1)-T(II), εA(2)-T(II), εA(3)-T(II) 以及 EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)]。 在實驗中,用MP2/6-311++G**單點能量的計算方法,對B3LYP的結構最佳化的結果做計算,可以對氫鍵強度的狀況有更佳的表示;並運用Counterpoise方法消除基組重疊誤差(basis set superposition error)。我們同時也將計算出的幾何結構最佳化、能量、以及氫鍵強度和華生-克立克所提出的A-T鹼基對模型做比較分析。
The electronic structure calculations have been performed for DNA adduct-thymine complexes using density functional theory method (B3LYP/6-31+G*). In this work, we have considered two types of adenine adducts; etheno-adenine (εA) and ethano-adenine (EA) to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [εA(1)-T, εA(2)-T, εA(3)-T and EA(1)-T, EA(2)-T, EA(3)-T] and [εA(1)-T(II), εA(2)-T(II), εA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)] have been considered with regards to their interactions. Single point energy calculations at MP2/6-311++G** levels on B3LYP optimized geometries have also been carried out to better estimate the hydrogen bonding strengths. The calculated hydrogen bonding energies are corrected for the basis set superposition error (BSSE), using counterpoise method. We have also compared the differences in its geometrical structures, energetics, and binding energies with Watson-Crick adenine-thymine base pairs (A-T).
CONTENTS……………………………………………………………. I
LIST OF TABLES……………………………………………………… II
LIST OF FIGURES……………………..……………………………... III
中文摘要..................................................................................................IV
Abstract…………………………………………………………………. 1
1. Introduction………………………………………………………….. 2
2. Computational Method & Theoretical Background.......…………….. 8
2-1. Computational Method..…………………………………………..9
2-2. Theoretical Background.……………………………………….. 10
(A) Density Functional Theory (DFT)...…………………………10
(B) B3LYP method……………………………………………….13
(C) Pople Type Split Valence Basis Set…………………………..14
(D) Polarization function…………………………………………14
(E) Diffusion function……………………………………………15
(F) Basis Set Super-position Error………………………………..15
3. Results & Discussion ………………………………………………..17
3-1. Optimized geometries Parameters for DNAadducts-thymine complexes……………………………………………………….18
3-2. Hydrogen Bonding Parameters for DNA adducts-thymine complexes……………………………………………………….53
3-3. Energetics and hydrogen bonding energy strength for for DNA adducts-thymine complexes…………………………………….57
4. Conclusion …………………………………………………………...67
References...…………………………………………………………….71
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