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

• Main Authors: Kai-Lun Shen, 沈凱綸
• Other Authors: Sheng-Der Chao
• Format: Others
• Language: zh-TW
• Published: 2016
• Online Access: http://ndltd.ncl.edu.tw/handle/nqn627

碩士 === 國立臺灣大學 === 應用力學研究所 === 104 === 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.