使用第一原理與分子動力學模擬探討三氯甲烷與三溴甲烷之阿波羅構型

Using Ab initio and Molecular Dynamics Simulations to explore the Apollo Configurations of Chloroform and Bromoform Molecules

游景翔(Ching-Hsiang Yu)

指導教授 ： 趙聖德

國立臺灣大學/工學院/應用力學研究所/碩士(2022年)

https://doi.org/10.6342/NTU202202843

摘要

在近期文獻中針對氯仿的局部結構有爭論，於是我們在量子力學計算中首先以MP2/aug-cc-PVQZ對三氯甲烷與三溴甲烷的單體分子結構進行最佳化，並使用包含BSSE(Basis-Set Superposition Error)修正的自洽理論(Hartee-Fock, HF)、微擾理論(Møller-Plesset Perturbation Theory)與耦合簇理論(Coupled Cluster Method, CC)進行三氯甲烷與三溴甲烷的二聚體間分子作用力計算，且搭配Krishnan’s medium size和Dunning’s correlation consistent的基底進行二聚體分子結構最佳化，最後將MP2與CCSD(T)的各種基底之計算結果進行比較。進行最佳化過程後，可得10種三氯甲烷與8種三溴甲烷的構型，其中以MP2方法對前者使用aug-cc-PVQZ基底且對後者使用aug-cc-PVTZ基底來求得完整勢能曲線，並使用SAPT0方法將勢能以誘導能、靜電能、交換能及色散能組成，以了解各構型分子間排斥力和吸引力之影響。
在分子動力學模擬中，我們使用5-sites model搭配Lennard-Jones potential function及庫倫項，並對10種三氯甲烷與8種三溴甲烷的二聚體構型勢能曲線進行擬合及建構力場，將其代入牛頓方程式來進行分子動力學模擬。計算過程中，模擬溫度從三相點沿著汽化曲線至臨界點，以求得在各溫度下分子之徑向分佈函數(Radial Distribution Function, RDF)、速度自相關函數(Velocity Autocorrelation Function, VAF)、擴散係數(Diffusion Constant)與黏滯係數(Viscosity Coefficient)。且在三氯甲烷與三溴甲烷的局部結構部分，我們模擬方向相關函數(Orientation Correlation Function)與對相關函數(Pair Correlation Function)，並與學長在2021年時所模擬的結果來進行比較，以上模擬結果與實驗值都有一定的準確度，可證明以量子化學為基礎所計算的力場進行分子動力學模擬有一定程度之可靠度，以詳細分析氯仿在局部結構的探討。

關鍵字

三氯甲烷 ； 三溴甲烷 ； 分子動力學模擬 ； 自洽理論 ； 微擾理論 ； 耦合簇理論 ； 徑向分佈函數 ； 速度自相關函數 ； 擴散係數 ； 黏滯係數 ； 方向相關函數 ； 對相關函數 ； Gaussian09套裝軟體

並列摘要

There is a debate about the local structure of chloroform in the recent literature, so we first optimized the monomer molecular structures of chloroform and bromoform with MP2/aug-cc-PVQZ in quantum mechanical calculations, and used Hartee-Fock theory, Møller-Plesset Perturbation Theory and Coupled Cluster Theory are included the BSSE (Basis-Set Superposition Error) correction to calculate the molecular force between the dimers of chloroform and bromomethane, including the use of Krishnan's medium size and Dunning's correlation consistent substrate. Finally, the calculated results of MP2 and CCSD(T) for various bases are compared. After the optimization process, we obtained 10 configurations of chloroform by MP2/aug-cc-PVQZ and 8 configurations of bromomethane by MP2/aug-cc-PVTZ, and use SAPT0 method to combine potential energy into induction energy, electrostatic energy, exchange energy and dispersion energy to understand the influence of repulsion and attraction between molecules of each configuration.
In the molecular dynamics simulation, we use the 5-sites model with the Lennard-Jones potential function and Coulomb term, and fit the potential energy curves of 10 chloroform configurations and 8 bromoform configurations, finally, constructed a force field , which is substituted into Newton's equations for molecular dynamics simulations. In the calculation process, the simulated temperature is from the triple point along the vaporization curve to the critical point to obtain the Radial Distribution Function、Velocity Autocorrelation Function、Diffusion Constant and Viscosity Coefficient of each temperature. And in the local structure of chloroform and bromoform, we simulated the Orientation Correlation Function and the Pair Correlation Function, and compared them with the results simulated by the senior in 2021. The above simulation results and experimental values have a good accuracy, which can be proved Molecular dynamics simulations based on the force fields calculated on the basis of quantum chemistry have a certain degree of reliability to analyze the local structure of chloroform in detail.

並列關鍵字

chloroform ； bromoform ； molecular dynamics simulation ； Hartee-Fock theory ； Møller-Plesset Perturbation Theory ； coupled cluster theory ； radial distribution function ； velocity autocorrelation function ； diffusion coefficient ； viscosity coefficient ； orientation Correlation Function ； pair correlation function ； Gaussian09 software

參考文獻

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