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研究生:張瑞娟
研究生(外文):Chang jui chuan
論文名稱:自然界穩定存在貝他髮夾之氧氣分子氧化反應之理論計算研究
論文名稱(外文):Theoretical Investigation of Oxygen Molecule-Mediated Oxidation Reactions of a Nature Occurring β-hairpin
指導教授:李豐穎
指導教授(外文):Feng-Yin LI
學位類別:碩士
校院名稱:國立中興大學
系所名稱:化學系所
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:2008
畢業學年度:96
語文別:英文
論文頁數:48
中文關鍵詞:從頭計算氧氣加成貝他髮夾阿法碳自由基
外文關鍵詞:ab initiooxygen-adductionβ-hairpinαC-centered radical
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本研究利用量化從頭計算(ab initio) 方法成功計算氧氣加成在一集中於阿法碳的自由基,從一自然界穩定存在的貝他髮夾之反應,與它的產物過氧化自由基之一系列複雜反應。
在反應機制中的所有相關分子結構都是以量化從頭計算方法中的B3LYP/6-31G(d)層次和半經驗式方法的PM3層次做計算。當氧氣加成在阿法碳自由基反應後,受到周遭殘基氫鍵的影響,使得整體結構並沒有很大的改變。唯有在受到攻擊的殘基及其附近才有較劇烈的改變,但其它殘基僅有微小變動,因此整體結構改變不大。
從熱力學的角度來看,本反應可觀察到進行氧氣加成反應的優先順序,氧氣加成阿法碳自由基很容易形成過氧化自由基與其它接下來的一系列反應,例如阿法碳和貝他碳鍵的斷裂,阿法碳和氮的鍵結因水存在而產生水解的斷裂,這些都會導致貝他髮夾序列骨幹斷裂。
We have successfully investigated the oxygen-adduction reaction of the αC-centered radical of a nature occurring β-hairpin (PDB code:1UAO) and its product peroxyl radical that a series of the complex reactions. All the structures of the related molecules in the reaction mechanism were used ab initio method at B3LYP/6-31G(d) level and Semi-empirical method at PM3 level. After oxygen-adducted αC-centered radical reaction, it does not undergo large-scale structural change due to the intramolecular interaction between surrounding residues, such as the H-bonding. Only the local conformation changes of the attacked and the adjacent residues were observed. The oxygen adduction of the αC-centered radical happen easily to form peroxyl peptide radical and follow by a series of complex reactions, such as the Cα-Cβ fragmentation and Cα-N bond hydrolysis, that cause backbone fragmentation in the hairpin.
Acknowledgement---------------------------------------------------------------------------i
Abstract-----------------------------------------------------------------------------------------ii
Contents----------------------------------------------------------------------------------------iv
Tables--------------------------------------------------------------------------------------------vi
Figures-----------------------------------------------------------------------------------------vii
Schemes---------------------------------------------------------------------------------------viii
Chapter 1 Introduction------------------------------------------------------------------01
Chapter 2 Theoretical Background-------------------------------------------------07
2.1 The Born-Oppenheimer approximation--------------------------------------------07
2.2 Density-Functional Theory----------------------------------------------------------08
2.2.1 The Hohenberg-Kohn theorems---------------------------------------------08
2.2.2 Exchange and correlation----------------------------------------------------10
2.2.3 The Kohn-Sham equations-------------------------------------------------- 11
2.2.4 Hybrid functionals -----------------------------------------------------------13
2.3 Basis sets------------------------------------------------------------------------------13
2.3.1 Slater-type orbital-------------------------------------------------------------14
2.3.2 Gaussian Type Orbital--------------------------------------------------------16
2.3.3 Double-ξ, Triple-ξ, Quadruple-ξ------------------------------------------- 16
2.3.4 Polarization functions---------------------------------------------------------17
2.3.5 Diffusion functions-----------------------------------------------------------18
2.4 Semi-empirical quantum chemistry method-------------------------------------18
2.4.1 Parameterized Model number 3 (PM3)-----------------------------------19
Chapter 3 Model and Computational Method ------------------------------21
Chapter 4 Results and Discussion-------------------------------------------------23
4.1 Hydrogen bond-----------------------------------------------------------------------26
4.2 Bond Dissociation Energy and Entropy-------------------------------------------31
4.3 Mulliken atomic charge and Molecular frontier orbital ------------------------36
4.4 Peroxyl radical reactive with lipid -------------------------------------------------41
Chapter 5 Conclusions ----------------------------------------------------------------43
References------------------------------------------------------------------------------------44
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