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

Quantum Chemistry Calculation of Substituent Effect on Intermolecular Interaction of Amide Molecules and Intermolecular Interaction of Polypeptide

曾志踴(Zhi-Yong Zeng)

指導教授 ： 趙聖德

國立臺灣大學/工學院/應用力學研究所/碩士(2014年)

https://doi.org/10.6342/NTU.2014.01772

摘要

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。

關鍵字

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 ； wB97XD ； SAPT ； Gaussian09

並列摘要

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.

並列關鍵字

quantum chemistry calculation ； hydrogen bond ； formamide ； acetamide ； propionamide ； N-methylformamide ； N-methylacetamide ； N-methylpropionamide ； polypeptide ； beta-sheet structure ； vibrational spectrum ； wB97XD ； SAPT ； Gaussian09

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