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研究生:曾志踴
研究生(外文):Zhi-Yong Zeng
論文名稱:醯胺分子分子間作用力之取代效應與多肽分子分子間作用力量子化學計算
論文名稱(外文):Quantum Chemistry Calculation of Substituent Effect on Intermolecular Interaction of Amide Molecules and Intermolecular Interaction of Polypeptide
指導教授:趙聖德趙聖德引用關係
口試委員:江志強陳俊杉郭哲來蔡政達
口試日期:2014-11-05
學位類別:碩士
校院名稱:國立臺灣大學
系所名稱:應用力學研究所
學門:工程學門
學類:機械工程學類
論文種類:學術論文
論文出版年:2014
畢業學年度:103
語文別:中文
論文頁數:118
中文關鍵詞:氫鍵甲醯胺乙醯胺丙醯胺N-甲基甲醯胺N-甲基乙醯胺N-甲基丙醯胺多肽beta-摺疊片層振動光譜wB97XDSAPTGaussian09
外文關鍵詞:quantum chemistry calculationhydrogen bondformamideacetamidepropionamideN-methylformamideN-methylacetamideN-methylpropionamidepolypeptidebeta-sheet structurevibrational spectrumwB97XDSAPTGaussian09
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透過以烷基取代醯胺分子以研究對於N-H...O=C型氫鍵的影響,使用軟體為Gaussia09軟體並以wB97XD/aug-cc-pVDZ計算甲醯胺、乙醯胺、丙醯胺、N-甲基甲醯胺、N-甲基乙醯胺與N-甲基丙醯胺單體、二聚體的最佳化構型與振動頻率並計算二聚體間的N-H...O=C型氫鍵的作用力,研究以烷基取代對於單體結構、官能基振動頻率與二聚體氫鍵作用力之影響,另外配合PSI4軟體透過SAPT方法分解分子間氫鍵作用力為靜電能、誘導能、色散能與交換能,以更進一步的分析烷基取代對於N-H...O=C氫鍵的影響。
接著第二部分為多肽模擬beta-摺疊片層結構,我們改以wB97XD/6-31+G*進行計算,最佳化出八種單體結構與對應的反平行beta-摺疊片層結構。討論分子內C5氫鍵變化與反平行beta-摺疊片層結構的分子間氫鍵作用力。
最後為甲醯胺、乙醯胺與丙醯胺模擬光譜的計算,我們透過wB97XD/aug-cc-pVDZ計算簡諧與非簡諧振動頻率,從模擬光譜中可以看到醯胺分子主要官能基的振動型態,且在比較單體與二聚體光譜可用來觀察氫鍵造成振動頻率的紅移情形。接著與實驗比較後,可以驗證模擬結果的正確。

The first part of this research is studying the N-H...O=C type hydrogen bond by substitution alkyl groups on amide molecules. All the quantum chemistry calculations were performed at the wB97XD/aug-cc-pVDZ using the Gaussian 09 program to calculate the intermolecular interaction of formamide dimer, acetamide dimer, propioamide dimer, N-methylformamide dimer, N-methylacetamide dimer, N-methylpropionamide dimer. In addition, PSI4 software was utilized through SAPT method to decompose the intermolecular interaction into four parts, as electrostatic energy; induction energy; dispersion energy; exchange energy, to discuss the alkyl groups how to influence N-H...O=C type hydrogen bond.
The second part is simulating the intermolecular interaction of beta-sheet structure. The method wB97XD/6-31+G* was used to optimize the structure and calculate the intermolecular interaction of antiparallel beta-sheet structure. In this part, we focus on the intramolecular hydrogen bond and intermolecular hydrogen bond of of beta-sheet structure.
We also have carried out the vibrational spectrum of formamide, acetamide and propionamide through harmonic and anharmonic model. IR spectrum calculated by monomers can obtain the functional group. When comparing the vibrational spectrum of the monomer and dimer, we can find the red shift of frequencies due to hydrogen bond. And compare with the experiment, we can confirm our simulation spectrum.


口試委員會審定書……………………………………………………………………#
致謝 I
摘要 II
Abstract III
目錄 V
表目錄 VIII
圖目錄 X
第1章 緒論 1
1.1 研究動機 1
1.2 醯胺分子介紹 3
1.3 分子間作用力介紹 5
1.4 文獻回顧 6
第2章 基本理論介紹 9
2.1 波恩奧本海默近似(Born-Oppenheimerapproximation) 9
2.2 Ab initio 分子軌域理論 12
2.2.1 自洽理論Hartee-Fock approximation(HF) 12
2.2.2 微擾理論Moller-Plesset perturbation theory 15
2.2.3 密度泛函理論 Density functional theory (DFT) 19
2.2.4 耦合簇理論 Coupled Cluster Method(CC) 22
第3章 計算方法與分子命名介紹 24
3.1 取代效應之計算方法介紹 24
3.1.1 醯胺分子單體與命名介紹 26
3.1.2 醯胺分子二聚體介紹與命名介紹 27
3.2 多肽分子量子化學計算 27
3.1 甲醯胺、乙醯胺與丙醯胺振動光譜計算方法介紹 32
第4章 計算結果與討論 34
4.1 取代效應-單體計算結果 34
4.1 取代效應-二聚體計算結果 40
4.1.1 FM-FM、AM-AM與PM-cis-cis系列二聚體分子間作用力結果與討論 40
4.1.2 NMFM-NMFM、NMAM-NMAM、NMPM-cis-cis二聚體分子間作用力結果與討論 43
4.1.3 對氮位置取代的分子間作用力討論 47
4.1.4 PM-trans-trans與NMPM-trans-trans分子間作用力結果 50
第5章 多肽計算結果 54
5.1 單體計算結果 54
5.2 多肽beta-摺疊片層結構分子間作用力計算結果 62
第6章 FM、AM與PM-trans光譜 70
6.1 FM(甲醯胺)振動光譜實驗文獻 70
6.2 FM(甲醯胺)模擬計算振動光譜 75
6.3 AM(乙醯胺)實驗光譜 78
6.4 AM(乙醯胺)模擬計算振動光譜 82
6.5 PM(丙醯胺)振動光譜實驗文獻 84
6.6 PM(丙醯胺)模擬計算振動光譜 87
第7章 結論與未來展望 91
7.1 醯胺分子取代效應結論 91
7.2 多肽模擬beta-摺疊片層結構結論 91
7.3 甲醯胺、乙醯胺與丙醯胺光譜結論 92
7.4 未來展望 92
參考文獻 93
附錄A 99
附錄B 106
附錄C 110


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