本文藉由全原子模型的分子動力學模擬，研究三羧酸衍生物(tricarboxylic acid derivatives)之1,3,5-tris(carboxymethoxy) benzene(TCMB, C6H3(OCH2COOH)3)於金表面的動態行為。首先針對單一個三羧酸衍生物吸附於Au(111)表面所產生之形貌圖形作一探討，可發現該分子在金表面會形成四種不同構形(conformations)，且分子上之官能基與基板會產生鎖與鑰匙(Lock-and-Key)效應，進而使分子能更穩定的存在於基板上，故鎖與鑰匙效應更會使分子的擴散及轉動行為受到限制。單一個三羧酸衍生物置於Au(100)及Au(110)等不同排列表面時，可發現該分子吸附於排列結構相異之表面後，其擴散的方向也會有所差異，由軌跡圖的觀察可得知分子置於(100)平面時容易沿<110>方向移動，為各排列基板中擴散範圍最廣的一種，而當分子置於(110)平面時，則容易沿[1&#299;0]方向移動。
由於以上的研究發現分子構形的不同及基板表面不同將直接影響分子在基板上的運動行為，因此為更深入了解三羧酸衍生物分子於基板上形成薄膜時之運動特性，本文更深入討論三羧酸衍生物分子單層膜於不同溫度下吸附在Au(111)表面的運動行為，在升溫過程中經由分子間吸附能(Cohesive energy)及分子與Au(111)基板間吸附能的計算，可發現吸附能在某些特定溫度下會產生明顯變化，並可經由結構上的觀察發現單層膜在此特定溫度下，會產生明顯變形及破壞，最後並藉由均方位移(MSD)、擴散係數(D)、金與單層膜間距及吸附能之統計，針對三羧酸衍生物單層膜在某些特定溫度下，分別探討單層膜移動行為及單層膜擴散性質。

The dynamical behaviors of tricarboxylic acid derivative, 1,3,5-tris(carbox- ymethoxy) benzene[TCMB, C6H3(OCH2COOH)3] on an Au surface is investigated by molecular dynamics. A TCMB molecule adsorbed on the Au(111) substrate is first probed into the structure arrangement. It founds that there are four possible conformations of the TCMB molecule that is adsorbed on the Au(111) substrate. The main difference on its conformation is the orientation of its functional group, which lead the molecule that forms the lock-and-key (LAK) behavior and prompts the molecule that become more stable on the substrate. As this result, the LAK behavior directly affects the trajectories of movement and dynamical behaviors.
Another topic is to observe the behavior of TCMB molecule on Au(110) and Au(100) surface, respectively. As well as the result of the TCMB molecule adsorbed on the Au(111) substrate, it also shows a different behavior on dynamical behaviors when the TCMB molecule adsorbed on the Au(110) and Au(100) substrate. Moreover, we found that the diffusion direction of TCMB molecule is dependent on the arrangement of the adsorbed surface. From the observation of the trajectory of the TCMB molecule, we found that diffusion range is most wide on Au(100) plane. The translational direction of TCMB molecule tend to move on the <110> direction as the molecule is migrate on the Au(100) plane, whereas that tend to move on the [1&#299;0] direction as the molecule is migrate on the Au(110) plane.
From the description above, we know that TCMB molecule with different conformations on different plane of surface arrangement displays different trajectories of movement and dynamical behaviors. Therefore, in order to understand the dynamical behaviors of TCMB monolayer on gold surface. In this work, the temperature effect on the adsorption behavior and the dynamic behavior of TCMB monolayer structure on the Au(111) substrate are investigated. From the calculation of the cohesive energy between molecules and the interaction energy between the molecule and the Au(111) substrate, we found that there are significant changes in cohesive energy and interaction energy at specific temperatures, which can be attributed to the deformation of the monolayer structure. Finally, the mean square displacement (MSD), diffusion coefficient(D) and distance between the molecule and the Au(111) substrate are calculated to investigate the diffusion property and motion behavior of TCMB monolayer at specific temperatures.

目錄
目錄 I
圖目錄 IV
表目錄 VII
中文摘要 VIII
英文摘要 IX
符號說明 XI

第一章 緒論 1
1.1 研究動機與目的 2
1.2 有序薄膜之製程方法 5
1.3 文獻回顧 9
1.4 本文架構 10
第二章 分子動力學理論方法 11
2.1 運動方程式 12
2.2 積分法則 13
2.3 勢能函數 14
2.3.1. 三羧酸衍生物分子之作用勢能 14
2.3.2. 金原子間作用勢能 17
2.3.3. 三羧酸衍生物與金原子間之作用勢能 19
2.4 時間步階選取 20
2.5 溫度修正 21
2.5.1. 反正規化法(Rescaling method) 21
2.5.2. 諾斯-胡佛恆溫法(Nos&eacute;-Hoover thermostat) 22
2.6 週期性邊界的處理 24
第三章 分子動力學數值方法 25
3.1 節省模擬時間之方法 25
3.1.1. 截斷半徑法(Cut-off method) 25
3.1.2. 維理表列法(Verlet List) 26
3.1.3. 巢室表列法(Cell Link) 28
3.1.4. 維理表列結合巢室表列法 30
3.2 物理參數與無因次化 32
3.3 數值統計方法 34
3.3.1. 平方位移(Square Displacement) 34
3.3.2. 平均平方位移(Mean Square Displacement) 34
3.3.3. 擴散係數(Diffusion Coefficients) 35
3.4 模擬流程圖 36
3.4.1. 單一的三羧酸衍生物於金表面系統之流程圖 36
3.4.2. 三羧酸衍生物單層膜於金表面系統之流程圖 37
第四章 結果分析與討論 38
4.1 分子於Au(111)表面的結構與性質 38
4.1.1. 物理模型之建構 38
4.1.2. 結構特性 41
4.1.3. 吸附性質 41
4.1.4. 運動行為 43
4.2 分子於不同排列基板之影響 54
4.2.1. 結構特性 54
4.2.2. 運動行為 55
4.2.3. 吸附性質 57
4.3 三羧酸衍生物單層膜受不同溫度之影響 64
4.3.1. 三羧酸衍生物單層膜構形改變 64
4.3.2. 單層膜移動行為及擴散性質 65
4.3.3. 單層膜之吸附性質 67
第五章 結論與建議 74
5.1 結論 74
5.2 建議與未來展望 77

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