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研究生： 楊安正
Yang, An-Chang
論文名稱： 自組裝分子膜成分在奈米尺度下對親疏水性之影響研究
The Study of the Composition of Self-Assembled Monolayer on the Hydrophobicity or Hydrophilicity in Nanoscale
指導教授： 翁政義
Weng, Cheng-I
陳鐵城
Chen, Tei-Chen
學位類別： 博士
Doctor
系所名稱： 工學院 - 機械工程學系
Department of Mechanical Engineering
論文出版年： 2011
畢業學年度： 99
語文別： 英文
論文頁數： 128
中文關鍵詞： 分子動力學 、自組裝分子膜 、親水性 、疏水性
外文關鍵詞： Molecular Dynamics, Self-assembled Monolayers, Hydrophilicity, Hydrophobicity
相關次數： 點閱：147  下載：5 
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    • 本研究以分子動力學模擬研究自組裝分子膜組成成分對其親疏水性之影響，自組裝分子膜的親疏水性由週圍水分子的靜態與動態特性評估，水分子的靜態特性受自組裝分子的影響將由下列幾個指標反應：密度分佈、氫鍵數目分析以及水分子排列分析。而水分子的動態特性則是由擴散行為以及吸附行為進行探討。本研究探討的對象分為由自組裝分子膜修飾的平板以及奈米粒子兩種，自組裝分子的組成分分為官能基以及骨幹兩部分，採用的官能基有：甲基、羧基、羥基、胺基。而骨幹則是分為烷鏈以及寡乙二醇鏈。
    在官能基的討論中，未經修飾的平板、奈米粒子及非極性官能基的單分子層保護奈米粒子周圍，水分子會形成雙層的水殼層，並影響水分子的排列方式以及擴散行為，而在極性官能基修飾的平板和奈米粒子周圍，由於水分子和官能基介面間氫鍵的存在，削弱了水分子間形成氫鍵的能力。也因為介面間的氫鍵，使得水分子吸附在極性自組裝分子膜表面的時間較長。
    在骨幹的討論中，雖然骨幹的影響不像暴露在外的官能基那麼顯著，但是烷鏈和寡乙二醇鏈還是有不同。寡乙二醇鏈允許較多的水分子滲入自組裝分子膜，縱使寡乙二醇鏈會降低水分子間形成氫鍵的能力，但是整體的氫鍵網路還是比烷鏈週圍的完整。和官能基的影響相似，水分子和骨幹介面間氫鍵也影響到水分子的擴散及吸附行為。

    In this dissertation, molecular dynamics simulations are performed to investigate how the composition of self-assembled monolayer influences the hydrophobicity or hydrophilicity of itself. The hydrophobicity or hydrophilicity of self-assembled monolayer is evaluated by determining the static and dynamic properties of a water molecules lying closed to it. The effects of the composition on the static properties of water are quantified by the analysis of local structure such as the reduced density profiles, the average number of hydrogen bonds, and the water orientation distribution. Moreover, the dynamic properties of the water molecules are evaluated by means of diffusion and adsorption behavior. Two different scenarios are discussed in the present dissertation. One is a substrate modified with self-assembled monolayer. The other is a nanocluster with self-assembled monolayer coating. The self-assembled surfactant is consisted of functional group and the moiety. In this study, the methyl group is replaced with carboxyl group, hydroxyl group, and amine group. The alkanethiol chain is replaced partly with oligo-ethylene glycol chain.
    In the discussion of different tail groups of surfactant, the simulation results indicate that water molecules close to clean gold substrate or nanoclusters and non-polar methyl monolayer protected clusters form a two-shelled structure in which the molecules in the first shell prefer lying on the surface of the substrate or nanocluster or methyl monolayer protected clusters. The existence of interfacial hydrogen bonds between the water molecules and the tail group of surfactants results in a weakening of the water-water hydrogen bond network. Moreover, the presence of the two water shells constrains the motion of the water molecules close to the clean substrate or nanocluster and non-polar monolayer protected clusters. As a result, the residence time of the water molecules adjacent to the clean substrate or nanocluster and non-polar monolayer protected clusters are significantly longer than those of the molecules close to the three polar monolayer protected clusters.
    In the discussion of different moieties of surfactant, the results show that the hydrophilic oligo ethylene glycol segment increases the number of water molecules which penetrate the protective layer of monolayer protected clusters. As a result, the inter-water hydrogen bond network in the monolayer protected clusters with hydrophilic moieties is stronger than that with hydrophobic moieties. It is also shown that the presence of interfacial hydrogen bonds increases the adsorption of water molecules near the monolayer protected clusters. As a result, the residence time of the water molecules adjacent to the monolayer protected clusters with hydrophilic moieties is longer than that with hydrophobic moieties.

    摘要 I Abstract II Acknowledgment IV Contents V List of Figures X Acronyms XIV Nomenclature XV Chapter 1 Introduction 1 1.1 Motivation 1 1.2 Literature Review 4 1.2.1 Hydrophobicity and Hydrophilicity of Material 4 1.2.2 Applications of Surface Modification 5 1.2.3 Molecular Dynamics Simulation of Interfacial Phenomenon 6 1.3 Objectives 9 1.4 Dissertation Organization 10 Chapter 2 Theoretical Approach 11 2.1 Molecular Dynamics 11 2.2 Equations of Motion 13 2.2.1 Lagrangian Mechanics 13 2.2.2 Hamiltonian Mechanics 14 2.3 Force Fields 16 2.3.1 Interaction of Surfactant-Surfactant, Surfactant-Water, Water-Water 16 2.3.2 Interaction of Substrate-Substrate (Cluster-Cluster) 19 2.3.3 Interaction of Surfactant-Substrate (Surfactant-Cluster) 20 2.3.4 Interaction of Surfactant-Water 20 2.4 Molecular Dynamics in Various Ensembles 21 2.4.1 NVE Scaling Method 22 2.4.2 NVT Ensemble 23 2.5 Determination of Properties 23 2.6 Physical Model 24 2.7 Static and Dynamic Properties 25 2.7.1 Reduced Density 25 2.7.2 Water Orientation 28 2.7.3 Hydrogen Bonding 31 2.7.4 Diffusion of Water 33 2.7.5 Adsorption of Water 33 Chapter 3 Implement of Molecular Dynamics 35 3.1 Integration the Equation of Motion 35 3.1.1 Verlet Algorithm 35 3.1.2 Velocity Verlet Algorithm 36 3.2 Boundary Conditions 38 3.2.1 Vacuum Boundary Condition 38 3.2.2 Stochastic Boundary Condition 38 3.2.3 Periodic Boundary Condition 39 3.3 Neighbor List 45 3.3.1 Verlet List 48 3.3.2 Cell List Method 49 3.3.3 Combine Method 49 3.4 Parallel Computing 50 3.4.1 Atomic Decomposition 51 3.4.2 Spatial Decomposition 53 Chapter 4 Results and Discussion 55 4.1 Water Molecules on the SAMs 55 4.1.1 Simulation Model 55 4.1.2 Reduced Density Profile of Water 58 4.1.3 Water Orientation 62 4.1.4 Hydrogen Bonding Network 66 4.1.5 Diffusion coefficient of Water 69 4.2 Water Molecules near the MPCs with Different Tail 71 4.2.1 Simulation Model 71 4.2.2 Reduced Density Profile of Water 75 4.2.3 Water Orientation 78 4.2.4 Hydrogen Bonding Network 86 4.2.5 Diffusion of Water 90 4.2.6 Adsorption of Water 91 4.3 Water Molecules near the MPCs with Different Backbone 94 4.3.1 Simulation Model 94 4.3.2 Reduced Density Profile of Water 97 4.3.3 Hydrogen Bonding Network 100 4.3.4 Adsorption of Water 102 Chapter 5 Conclusions and Suggestions 105 5.1 Conclusions 105 5.2 Suggestions 106 Appendix A: Introduction to several MD packages 109 Appendix B: CAM Cluster System 115 References 118 Vita 127

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