Laboratory Technology Program, Department of Chemistry and Chemical Processing Technologies, Susurluk Vocational School, Bandırma Onyedi Eylul University, 10600, Balıkesir, Turkey.
J Mol Model. 2023 Mar 24;29(4):110. doi: 10.1007/s00894-023-05519-2.
In guest-host interactions, guest molecules used for hydrogen bonding potential of clathrate hydrate cages are involved as "promoters" for hydrogen or methane storage. Among the promoter molecules, there are pinacolone and tert-butylmethyl ether containing oxygen atom, and tert-butyl amine among those containing nitrogen atom. The dimer and trimer interactions of these molecules with the water clusters were investigated. The cooperativity effect, which is a measure of the hydrogen bonding of these oxygen and nitrogen-containing complexes, was calculated and these complexes were analyzed. Moreover, molecular electrostatic potential (MEP) analysis was performed to determine intermolecular interactions. Clusters of several molecules may seem like a non-significant state of matter; however, in systematic studies with small clusters, important results can be obtained. Therefore, it is very useful to work with clusters to understand the properties of the dense phase, and this study aimed to examine the properties of structures, energies, infrared vibration frequencies, and topological parameters, which develop as a result of the interaction of structures in different clusters with water molecules.
The MP2 level was performed using aug-cc-pVDZ basis set calculations for this study. Tight converting criteria were used in the optimization step. Harmonic vibrational modes were calculated at the MP2/aug-cc-pVDZ level. Each minima obtained from the MP2 level was subjected to single-point energy calculations using CCSD(T) levels with the aug-cc-pVDZ basis set by the Gaussian16 package program suite. The topological analyses were performed with non-covalent interaction (NCI). MEP surface of the complex was also composed by Gaussian program using the optimized geometry at a MP2/aug-cc-pvdz level.
在主客体相互作用中,用于笼型水合物笼氢键潜力的客体分子作为氢或甲烷储存的“促进剂”。在促进剂分子中,有含氧原子的二丙酮醇和叔丁基甲基醚,以及含氮原子的叔丁胺。研究了这些分子与水团簇的二聚体和三聚体相互作用。计算了这些含氧和含氮配合物氢键的协同效应(衡量氢键的指标),并对这些配合物进行了分析。此外,还进行了分子静电势(MEP)分析以确定分子间相互作用。几个分子的簇可能看起来是一种不重要的物质状态;然而,在对小簇的系统研究中,可以得到重要的结果。因此,用簇来理解密相的性质是非常有用的,本研究旨在研究不同簇中结构相互作用导致的结构、能量、红外振动频率和拓扑参数的性质。
本研究采用 aug-cc-pVDZ 基组在 MP2 水平上进行计算。在优化步骤中使用了严格的转换标准。在 MP2/aug-cc-pVDZ 水平上计算了谐振动模式。从 MP2 水平获得的每个极小值都通过高斯 16 程序套件的 CCSD(T)水平与 aug-cc-pVDZ 基组进行单点能计算。非共价相互作用(NCI)进行了拓扑分析。用高斯程序也在 MP2/aug-cc-pvdz 水平的优化几何形状上绘制了复合物的 MEP 表面。