本論文係利用分子動力學方法探究兩個表面科學相關之研究，分別為奈米水液滴在聚甲基丙烯酸甲酯基板及單一三羧酸衍生物分子吸附在(100)及(110)平面之金基板平面上的運動行為研究，期望藉由此研究讓研究者們能更深入了解分子的物理吸附特徵與現象，更在領域上有所貢獻，本論文的兩大主題分別如下。

液滴尺寸對於液滴吸附於聚甲基丙烯酸甲酯(PMMA)表面上之結構與運動行為的影響：由於近十年的模擬研究中，水液滴在高分子基板上的濕潤行為研究皆考慮高分子基板為固定基板模型，但由模擬結果發現，固定模型不適合於PMMA基板的模擬，因為固定模型影響了PMMA分子的擴散及吸附在PMMA表面上水分子的穿透行為。我們選取了不同尺寸的液滴來探究尺寸對吸附之水分子以及PMMA分子的特性影響，小尺寸的液滴吸附在PMMA基板上時，會有較多的水分子穿透基板，且液滴所覆蓋的局部粗糙度會明顯較高。小液滴的水分子容易因擴散而滲入基板，使得液滴的接觸角減小，而對於較大的液滴(1000個水分子以上的奈米液滴)，接觸角會越接近巨觀實驗所觀察的結果；在水分子的結構方面，結果顯示穿透水的平均氫鍵數與液滴的尺寸成反比；在動態行為的研究上，藉由速度場的分析發現了水液滴在基板上的特殊的律動行為；自我擴散速率分析上發現，穿透水分子的擴散速率明顯較低，而越接近液滴與真空表面的水分子，擴散速率則明顯的上昇；最後在水分子的頻譜、氫鍵生存時間、氫鍵的鬆弛時間及氫鍵角度分佈等分析上，發現氫鍵角度改變與氫鍵生存時間行為息息相關。

表面結構對於三羧酸衍生物分子在金基板表面之動態及靜態行為的研究: 本研究係利用分子動力學法觀察三羧酸衍生物分子(tricarboxylic acid derivative, 1, 3, 5-tri (carboxymethoxy) benzene (TCMB, C6H3(OCH2COOH)3 ))在金基板上的遷移行為，從結構上來看，我們發現因為TCMB分子因為烷鏈上-CH2-基面向基板並接觸的數量不同，TCMB分子會有四種不同構形，此接觸的數量及TCMB分子與表面間的幾何互補性皆是影響TCMB分子在金表面上遷移運動、旋轉運動、交互作用能、及TCMB分子與金表面鎖與鑰匙 (Lock- and-Key) 等行為的重要因素。最後我們總結，吸附分子與表面結構間的互補性越差，將導致分子的不穩定遷移，此結果將對於單分子膜的設計上有所幫助。

This dissertation, studies two specific topics related to the research of surface science by employing the molecular dynamics (MD) approach, that of a water droplet deposited on a poly (methyl methacrylate) (PMMA) substrate and that of a single tricarboxylic acid derivative, 1, 3, 5-tri(carboxymethoxy) benzene (TCMB, C6H3(OCH2COOH)3 ) adsorbed on gold (100) and (110) surfaces. These can help engineers clarify the characteristics and phenomena of physical adsorption of the molecule, as well as contributing to the application of surface science. This work is divided into two parts.

Effect of droplet size on the structural and dynamical behavior of a water droplet spreading on a PMMA amorphous surface: note that most experts prefer to consider a rigid model as the substrate in research of surface wetting because it is more efficient to run the MD simulation such that a long simulation can be accomplished in a short time. The results verify that the rigid model is not suitable to act as the PMMA substrate in simulation because it prevents the diffusion of PMMA molecules, which then affects the penetration behavior of water molecules in the droplet upon impact with the PMMA surface. Several sizes of water droplets are considered in order to understand the size influence of the droplet on the properties of water molecules and on the PMMA surface. The penetrated water molecules and the local roughness increase with a decrease in the size of the droplet, which also leads to a smaller contact angle of the water droplet on the PMMA substrate. When the droplet is composed of more than 1000 water molecules, the contact angle shows agreement with experimental results. As regarding the structure of the water molecule in the droplet on PMMA substrate, the average number of hydrogen-bonded penetrating water molecules is in inverse proportion to the size of the droplet By examining the velocity field, the regular motion of the water droplet is found during the equilibrium process and after the droplet reaches the equilibrium state. The diffusion of the water molecules shows a significant decrease for the penetrated water molecules and an increase as it gradually approaches the vapor/liquid interface. Finally, calculations at different regions are made for the vibration spectrum of the oxygen atom, life time, and the relaxation time of the hydrogen bond. The changes of the hydrogen-bond dynamics of the hydrogen bond are consistent with the change of the distribution of the hydrogen bond angle.

Effect of surface structure on the structural and dynamical behavior of a tricarboxylic acid derivative molecule on Au surfaces: the dynamical behavior of the single tricarboxylic acid derivative, 1, 3, 5-tri(carboxymethoxy) benzene (TCMB, C6H3(OCH2COOH)3 ) on Au (100) and (110) surfaces by molecular dynamics simulation approach is studied to provide better understanding of surface diffusion. Four possible conformations of the adsorbed TCMB molecule on the Au surface are found, with differences arising from different numbers of CH2 groups adsorbed on the Au substrate. Both the number of CH2 groups in the TCMB molecule that interact with Au surface and the different geometric relationship between the TCMB molecule and the Au surface strongly affect the translational motion, rotational motion, interaction energy and the Lock-and-Key behaviors of the TCMB molecule. A poor complementarity between the TCMB molecule shape and atomic structure of the surface results in significant migration of the molecule and is therefore an unstable adsorption. These results will be useful for the design of a molecular monolayer.

Contents I
List of Figures IV
List of Tables VII
List of Symbols VIII
List of Abbreviations XIII
Abstract XIV
Chapter 1 Introduction 1
1-1 Introduction to Surface Wetting Technology 1
1-1-1 Application and Theory 1
1-1-2 Reviewing of Molecular Modeling for Surface Wetting 2
1-2 Introduction to Surface adsorption behavior of molecules on solid surfaces 5
1-2-1 Application and Experiment Studies 5
1-2-2 Reviewing of Molecular Modeling for Surface Adsorption 6
1-3 Hydrogen-Bonding Dynamics and Diffusion 8
1-4 Outline of the Dissertation 8
Chapter 2 Molecular Dynamics Modeling 10
2-1 Introduction 10
2-2 Equations of Motion 10
2-3 Empirical Force Field Model 12
2-3-1 Development and Outline of Force Field for Bio-molecule and polymer system 12
2-3-2 Energy Calculation and Dynamics Force Field 13
2-3-3 Tight-Binding Potential 14
2-3-4 Dreiding Force Field 15
2-4 Thermodynamic Ensembles 15
2-5 Constant temperature dynamics 16
2-5-1 Rescaling of Velocity 16
2-5-2 Heat Bath: weak coupling method 17
2-5-3 Heat Bath: Stochastic collision method 18
2-5-4 Heat Bath: extended system coupling method 19
2-6 Constant Pressure dynamics 20
Chapter 3 Numerical methodology of Molecular Dynamics 22
3-1 Periodic boundary conditions and minimum image convention 22
3-2 Treatment of non-bonded interaction 24
3-3 Non-bonded neighbor lists 28
3-4 Flow chart of Molecular Dynamics 30
Chapter 4 Results and Discussion 31
4-1 Droplet size effect on the structural and dynamical behavior of water droplet spreading on a PMMA Amorphous surface 31
4-1-1 Poly (methyl methacrylate) (PMMA) 31
4-1-1 Simulation Model 32
4-1-2 Surface Topology of PMMA substrate 36
4-1-3 Comparison of Adsorption Process between Rigid model and Flexible model 37
4-1-4 Adsorption Process and Snapshot 41
4-1-5 Topology of PMMA Surface after the Adsorption of Water Droplet 45
4-1-6 Analysis of Contact Angle 47
4-1-7 Structure of Hydrogen Bond 49
4-1-8 Analysis of Velocity Field 53
4-1-9 Self-Diffusion coefficient of water molecule 55
4-1-10 Vibration spectrum of water molecule 59
4-1-11 Hydrogen Bond Angle and Strength 61
4-1-12 Hydrogen Bond Dynamics 63
4-2 Effect of Surface Structure on the Structural and Dynamical Behavior of an Aromatic Carboxylic Acid Molecule on Au Surfaces 67
4-2-1 Tricarboxylic acid derivatives of 1,3,5-tris (carboxymethoxy) benzene ( C6H3(OCH2COOH) 3) molecule 67
4-2-2 Simulation Model 67
4-2-3 Migration Trajectory 71
4-2-4 Geometric Relationship between TCMB Molecule and Au Surface 74
4-2-5 Translational Motion and Rotational Motion 78
4-2-6 Adsorption Energy 84
4-2-7 Dynamical Behaviors 86
Chapter 5 Conclusion and Future Works 88
5-1 Conclusion of the study of water droplet spreading on a PMMA Amorphous surface 88
5-1-1 Structural Characteristic 88
5-1-2 Dynamical behavior 88
5-2 Conclusion of the study of an Aromatic Carboxylic Acid Molecule on Au Surfaces 89
5-3 Future Works 92
Appendix A Parameters in force field 96
References 101

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