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研究生: 梁方廷
Liang, Fang-Ting
論文名稱: 建立有效且快速預測玻璃轉化溫度之方法論
Establishing a Fast and Reasonably Accurate Computational Protocol for the Prediction of Glass Transition Temperature
指導教授: 林昆翰
LIN, KUN-HAN
口試委員: 吳典霖
WU, DIAN-LIN
林祥泰
LIN, XIANG-TAI
學位類別: 碩士
Master
系所名稱: 工學院 - 化學工程學系
Department of Chemical Engineering
論文出版年: 2024
畢業學年度: 112
語文別: 中文
論文頁數: 133
中文關鍵詞: 玻璃轉換溫度分子動力學模擬力場
外文關鍵詞: glass transition temperature, molecular dynamics simulation, force field
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  • 玻璃轉化溫度(Tg)對非晶質(amorphous)有機半導體的熱穩定性和形態穩定性具有重要的影響,尤其在有機發光二極體(organic light-emitting diode ,OLED)元件中,擁有較高Tg的材料會有較好的熱穩定性以延長器件的使用壽命,如果我們能成功預測材料的Tg,可避免合成出的材料不符合足夠高Tg的標準,加速開發具有足夠熱穩定的材料。
    我們改善林昆翰教授等人開發的方法,用分子動力學模擬(molecular dynamics simulation, MD)進行有機小分子Tg的預測,該方法已證明具有一定的準確性。然而此方法對於一個分子的計算成本很高,限制了其在高通量篩選中的應用,因此本研究的第一個目標是維持此方法的預測準確度並且降低其計算成本。
    我們將系統的大小分別從3000個分子(依據林昆翰教授等人的研究)減少到1500、750和375個分子,結果顯示對於林昆翰教授等人所預測的24個有機小分子以375個分子系統對同一個分子進行4次相同的MD模擬,Tg預測平均值可達到一定準確度(實驗值與預測值相比的平均絕對誤差約為18.66°C),同時由於系統分子數量的減少(只有林昆翰教授等人方法的1/8),其計算成本也大幅降低。
    除了較高的計算成本這個缺點外,林昆翰教授等人的方法還有另一個缺陷,即實施MD前的力場參數化過程非常耗時,每個分子平均需要花費六個小時的人力成本,而這種高人力成本的消耗無法有效率地實施高通量篩選。因此,我們開發了以分子積木為概念的半自動生成分子力場的程式,以減少人力成本,並使用此程式建立了39個有機小分子的力場,並進行降低成本後的MD模擬預測 Tg,其預測值與實驗值相比,線性修正過後的平均絕對誤差為26°C。
    我們除了開發一套快速預測Tg的方法外,也建立了一套半自動化建立分子力場的工具,可以快速且可靠的建立分子力場,用於其他類型的MD模擬中。


    The glass transition temperature (Tg) significantly influences the thermal and morphological stability of amorphous organic semiconductors. In an OLED device, the host material with a high Tg is crucial to its lifetime. If we can successfully predict Tg, we can establish a pre-screening process for the development of high Tg material
    The objective of this research is to provide reasonably accurate and cost-effective predictions for organic small molecules using MD simulations. We adopted the approach developed by Kun-Han Lin et al for predicting Tg using molecular dynamics simulation, which has demonstrated satisfactory accuracy. However, the method is computationally demanding, which prevents its use for high-throughput screening. Hence, we aim to reduce its computational cost while retaining its prediction power.
    We gradually reduced the system size from 3000 molecules (Lin’s work) to 1500, 750, and 375 molecules. Our results show that reasonable Tg predictions (MAE: ~22 °C vs exp. values) with MD simulations of 375-molecule system size can be achieved by conducting the same simulation four times for each of the 24 organic small molecules. Meanwhile, the computational cost is significantly reduced due to the much smaller system size (only ⅛ of Kun-Han Lin’s protocol).
    In addition to the high computational cost, Kun-Han Lin’s protocol has another shortcoming– the labor-demanding force-field parameterization process that is crucial for accurate Tg prediction. This step requires six hours of manual labor per molecule, posing a significant obstacle when implementing it in high-throughput screening. Therefore, we developed a semi-automated force-field parameterization scheme based on the concept of molecular building blocks to alleviate the human labor cost. Using this scheme, we established force fields for 39 organic small molecules and conducted MD simulations to predict Tg values. After correction, the predicted Tg values showed an MAE of 26 °C compared to the experimental values.
    In addition to developing a rapid method for predicting Tg, we have also established semi-automated force-field parameterization scheme. This tool enables the quick and reliable creation of molecular force fields for use in MD simulations

    摘要 i ABSTRACT ii 目錄 iv 表目錄 viii 圖目錄 ix 第一章 緒論 1 1.1 玻璃轉化溫度 1 1.2 Tg對有機材料之重要性 3 1.3 分子設計對玻璃轉化溫度的影響 9 1.4 以實驗測量Tg之方法 12 1.5 以模擬預測Tg之方法 16 1.5.1 以定量結構-性質關係、機器學習預測Tg 16 1.5.2 以分子動力學模擬預測Tg 21 1.6 研究動機 29 第二章 研究方法 35 2.1 分子動力學模擬 (molecular dynamics simulation,MD) 35 2.2 力場 (force field) 35 2.3 力場參數化 37 2.4 結構建置與分子動力學模擬預測Tg流程 39 2.5 密度-溫度圖擬和方法 40 2.5.1 分子動力學模擬預測Tg 40 2.5.2 R2-溫度圖定義兩線性回歸範圍 42 2.6 Savitzky-Golay濾波器 43 2.7 stk分子建模工具 44 2.8 Q-Force生成分子力場工具 45 第三章 降低預測玻璃轉化溫度方法的計算成本之探討 46 3.1 花費時間與預測準度 46 3.2 擾動分析 50 3.3 擾動對預測影響分析 54 3.4 降低密度-溫度圖擾動的處理與模擬間擾動的影響 60 3.4.1 模擬間擾動造成預測的不確定性 60 3.4.2 同時消除密度溫度擾動對Tg之影響 62 3.4.3 僅消除密度擾動對Tg之影響 68 3.5 熱平衡時間分析 73 3.6 小結 76 第四章 建立半自動化生成有機分子力場參數工具 77 4.1 前言 77 4.2 以分子積木概念產生有機小分子力場 79 4.2.1 分子積木概念 79 4.2.2 力場參數測試 80 4.2.3 以分子積木構成分子之力場參數驗證 84 4.3 生成力場程式碼架構 90 4.3.1 力場程式碼概述 90 4.3.2 分子積木資料庫之建立 93 4.3.3 程式碼所需輸入資訊及所須先備知識 97 4.3.4 分子積木相連接編號辨別 101 4.3.5 分子積木相連接力場參數資料庫之建立 103 4.3.6 重複原子名稱的修改 105 4.3.7 分子中原子電荷對稱以及尋找對稱的二面角 107 4.4 二面角掃描 110 4.5 單分子的分子動力學模擬驗證 114 4.6 以程式建立有機分子力場與有機小分子之Tg預測 117 4.7 小結 118 第五章 結論 119 參考文獻 121 附錄 128

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