标题: 关于MOF的反应途径计算中的一些问题 [打印本页] 作者Author: hanmingxi 时间: 2020-8-1 23:53 标题: 关于MOF的反应途径计算中的一些问题 (1):下段中描述的the carboxylic acid binding mode was 5.1 kJ/mol more favorable than the carbonyl mode是指用不同的键合方式后的分子的单点能的对比吗？
To support or refute the interpretation of the experimental results, and obtain atomistic-level insights into the catalytic mechanism, we carried out DFT calculations to search for the reaction pathways. We first investigated the binding mode of levulinic acid on the node of UiO-66, as both the carbonyl and carboxylic acid groups can bind to the open Zr sites. From our calculations, we found that the carboxylic acid binding mode was 5.1 kJ/mol more favorable than the carbonyl mode, and we therefore chose to map out the entire catalytic pathway based on this binding mode. Once levulinic acid is adsorbed on the node, the subsequent nucleophilic attack can occur in two ways (Figure2a): (1) A Langmuir–Hinshelwood type mechanism where the ethoxide adsorbed on the adjacent Zr site is the nucleophile or (2) an Eley–Rideal type mechanism where a free ethanol molecule from the solvent attacks the bound levulinic acid.（2）：下段中的䏻垒是指过渡态和合成后的分子的能量的比较吗？
Our results show that pathway (1) has a much lower energy barrier (96.5 versus 226.1 kJ/mol) than pathway (2) because ethoxide (activated from ethanol by the Zr site) is a much stronger nucleophile than ethanol. We then modeled pathway (1) on the functionalized UiO-66-(COOH)2 catalyst and found that the energy barrier is significantly lower than on unfunctionalized UiO-66 (66.2 vs 96.5 kJ/mol), which agrees with the experimental finding that the reaction rate is much faster on UiO-66-(COOH)2 than UiO-66 (Figure2b).
以下是文章的计算细节：
The starting point of the reaction pathway search was the UiO-66 node with one missing linker defect which created one coordination site on each of the two adjacent Zr atoms. To reduce the system size and speed up the calculations, 5 out of the remaining 11 PhCOOlinker moieties that were far away from the active site (1 on the opposite side of the missing site and another 4 around it) were replaced with HCOO-. Similar truncation approaches have been used and validated on closely related systems. Since the reaction was performed in ethanol solvent and the missing linker moiety PhCOO- has-1 charge, one ethoxide anion and one ethanol molecule were placed on the open sites to keep the system charge neutral and mimic the solvation environment as suggested by previous computational studies. In all the following calculations, the entire system was kept charge neutral. In the UiO-66-(COOH)2 model, one –COOH group was added on one of the linkers near the active site.
All electronic structure calculations were carried out in the Gaussian 16 package (revision A.03) with the M06-L density functional and the DFT-D3 dispersion correction with zero damping. For the geometry optimization and vibrational calculations, the def2-SVP basis set was used for H, C, and O atoms while the SDD effective core potential (ECP) was applied on Zr atoms.During the geometry optimizations, the positions of the terminal C and H atoms on all linkers were held fixed to mimic the crystal environment. Single-point energy refinements at a higher level of theory in which the def2-SVP basis set was replaced by the larger def2-TZVP basis set were performed for all species. The Gibbs free energy reported for each species was the summation of its electronic energy at the higher level of theory and its thermal corrections at the original level of theory. The SMD implicit solvation model with ethanol as solvent was used to describe the solvation effects
第一次研究类似计算，希望有做过类似计算的大神能够回答下，非常感谢