Quantum Chemistry Calculation of Substituent Effect、Stack Effect and Hydration Effect of Double Proton Transfer on Amide and Acid Molecules

我們對甲醯胺或甲酸二聚體執行烷基取代，觀察取代效應對於N-H...O=C型氫鍵以及O-H...O=C型氫鍵的雙質子轉移反應影響。使用Gaussian09 軟體計算各個分子的烯醇式、酮式並最佳化各別的穩定構型，同時計算雙質子轉移反應的過渡態，並以IRC(Intrinsic reaction coordinate)法計算出完整反應路徑以求得正反應能障，觀察並分析烷基取代對質子轉移的影響。另外配合PSI4軟體透過SAPT方法分解分子間作用力，分析分子作用力變化與質子轉移能障的關係。 接著我們進行堆疊效應研究，研究當多個二聚體垂直堆疊時，雙質子轉移反應所受之影響。我們利用簡單的醯胺分子與酸分子結構來進行堆疊，層與層在外側以六環碳相互連接，如同長鏈DNA的外圍骨架般。由此更進一步的了解在堆疊結構下雙質子轉移反應的正反應能障變化。 最後我們進行醯胺或酸二聚體與水分子的水合效應研究，近年研究顯示水分子雖然阻礙了含氮鹼基間的直接質子轉移，卻扮演著雙質子轉移反應中的質子提供者與接收者，水分子透過與含氮鹼基的氫鍵網絡參與了質子轉移過程，針對此種情況我們以醯胺或酸分子來當作簡化模型，計算此種水分子參與的質子轉移路徑正反應能障。同時我們也比較了水分子環繞在二聚體外圍以及內鉗於二聚體間的兩種構型，分析其構型位能以及質子轉移正反應能障有何差異。We studied the N-H...O=C and O-H...O=C type hydrogen bonds by substituting alkyl groups on amide and acid molecules. All the quantum chemistry calculations were performed at Gaussian 09 software to optimize individual keto or enol structures and search the transition state of proton transfer reaction. Meanwhile,we use the IRC(Intrinsic reaction coordinate) method to plot the reaction path in order to obtain the energy barrier. In addition, the PSI4 software was utilized through the SAPT method to decompose the intermolecular interaction into several physically meaningfull terms, to discuss the effect of alkyl groups on the proton transfer reaction. For the stack effect, we use amide and acid molecules in planar structures and use several vertically stacked layers to observe the effect of stacking on proton transfer reaction. Six-carbon ring on the outside is used to bond each layers, similar to the peripheral backbone in DNA double helix. The energy barrier of proton transfer under different stacking structures was also discussed. We also consider the hydration effect on amide and acid of proton transfer reaction. Recent studies have shown that water molecules could hamper direct proton transfer between nitrogenous bases, but it plays the role of proton donor and acceptor during the reaction. Therefore, water molecules can form hydrogen bonding network to be involved in the proton transfer process. In such cases we use amide and acid molecule as a simplified model for analysis. At the same time, the configuration of waters surrounding the dimer or clamping in the hydrogen bonds of the dimer has been discussed