利用第一原理進行分子動力學模擬探討氯化甲烷二聚體分子組成之結構

Abstract

本研究探討氯化甲烷(Chlorinated)四面二聚體結構利用第一原理(ab initio)進行分子動力學模擬的相關參數擬合以及空間局部堆疊結構，其中包括一氯甲烷(Chloromethane)、二氯甲烷(Dichloromethane)、三氯甲烷(Chloroform)、四氯甲烷(Tetrachloromethane)的分子動力學模擬。我們針對氯化甲烷四面體結構的二聚體做了一系列的分類，從中選取了最佳化的二聚體構型，並從量子計算中建立的MP2/aug-cc-PVQZ單體最佳化分子結構以及利用微擾理論(Møller-Plesset Perturbation Theory, MP2)選取MP2方法並且使用aug-cc-PVQZ的基底去做勢能擬合以及力場的建構，並且使用PSI4軟體中的SAPT 2+3(Symmetry-Adapted Perturbation Theory) 將建構出來的力場構型進行能量計算並且與MP2比較，進行二聚體間能量的拆解得出交換能、誘導能、靜電能以及色散能，藉此去更深入了解各個作用能其吸引力和排斥力對於氯化甲烷二聚體分子的占比影響。 以第一原理量子化學計算所建構的力場用於分子動力學模擬，我們使用5-sites model方法去分析氯化甲烷極性分子二聚體結構並且搭配使用Lennard-Jones Potential Function加上庫倫作用項(Coulombic terms)去對力場的建構以及二聚體曲線勢能擬合，並帶入牛頓方程式進行分子動力學模擬，藉此得到相關熱力學性質。模擬時使用徑向分布函數(Radial Distribution Function)、速度自相關函數(Velocity Autocorrelation Function)、擴散係數(Diffusion Constant)和黏滯係數(Viscosity)等相關性質進行模擬，計算溫度從三相點(Triple Point)沿著汽化點(Bolling Point)到臨界點(Critical Point)進行熱力學性質曲線分析。並且近一步探討了空間局部結構的部分，使用方向相關函數(Orientational Correlation Function, OCF)和空間分布函數(Spatial Distribution Function, SDF)進行模擬得出與角度相關的徑向分布函數關係，並將結果與現有文獻之實驗值進行比較，本研究顯示出以量子化學計算所建構的力場在分子動力學模擬中有不錯的精準度與可靠性。

This study investigates the parameter fitting and spatial local stacking structure of chlorinated methane (Chlorinated) tetrahedral dimers using first-principles (ab initio) molecular dynamics simulations, including chloromethane, dichloromethane, chloroform, and tetrachloromethane. We classified a series of dimer structures and selected the optimized dimer configuration. The potential energy and force field were constructed using the MP2 method and aug-cc-PVQZ basis set, and the energy was calculated using the Symmetry-Adapted Perturbation Theory (SAPT) 2+3 method in the PSI4 software. The inter-dimer energy was decomposed into exchange, induction, electrostatic, and dispersion energies to further understand the proportionate influence of attractive and repulsive forces on the chlorinated methane dimer molecules. The first-principles quantum chemical calculations were used to construct the force field for molecular dynamics simulations. We used the 5-sites model to analyze the polar molecular dimer structure of chlorinated methane and used the Lennard-Jones potential function with Coulombic terms to construct the force field and curve-fitting for the dimer potential energy. The Newtonian equations were used to perform molecular dynamics simulations to obtain relevant thermodynamic properties. The simulations included the radial distribution function, velocity autocorrelation function, diffusion constant, and viscosity to calculate the thermodynamic properties along the temperature curve from the triple point to the critical point. Additionally, the local spatial structure was explored using the orientational correlation function and spatial distribution function to obtain the angular radial distribution function relationship, which was compared with experimental values in existing literature. This study demonstrates the accuracy and reliability of the force field constructed using quantum chemical calculations in molecular dynamics simulations.