本研究利用電腦模擬研究含二茂鐵小分子導電凝膠劑 ferrocenyl-dicholesteryl N-formamidoformamide (Fc-LS2) 及 ferrocenyl cholesteryl N-formanidoformamide (Fc-LS) 在溶液中的相行為及電子轉移性質。利用分子動力模擬將 Fc-LS2 及 Fc-LS 分別放入甲醇與丙醇及甲醇與戊醇中，模擬凝膠劑分子在溶液中的的構象變化及相轉變情形。結果顯示，Fc-LS2 分子在丙醇溶液中及 Fc-LS 分子在戊醇溶液中均會形成凝膠，而 Fc-LS2 及Fc-LS 在甲醇溶液中則會形成聚集沉澱。溶劑的擴散係數說明了 Fc-LS2/1-propanol 及 Fc-LS/1-pentanol 具有凝膠的行為，而在Fc-LS2/methanol 及 Fc-LS/methanol 中則是像液體。此外，結合分子動力學及量子力學來計算凝膠系統的電子轉移性質。結果指出形成凝膠的體系有較大的電子轉移性質，凝膠分子間與溶液之間的氫鍵均會改善電子轉移特性。最後，此模擬方法有助於改善小分子導電凝膠劑發展，並對於模擬凝膠體系提供一個新的方向。

Molecular dynamics (MD) simulations were carried out to investigate the conformations of ferrocenyl-dicholesteryl N-formamidoformamide (Fc-LS2) and ferrocenyl cholesteryl N-formanidoformamide (Fc-LS) gelator in solvent of methanol 1-propanol, and 1-pentanol. Fc-LS2 and Fc-LS comprises ferrocene and cholesteryl units linked by a biocompatible N-formamidoformamide peptide unit. Our results showed that Fc-LS2 and Fc-LS formed a gel with 1-propanol and 1-pentanol respectively but not with methanol. Calculation of diffusion coefficients showed that the Fc-LS2/1-propanol and Fc-LS/1-pentanol system behave like a gel over a wide range of temperatures, while the Fc-LS2/methanol and Fc-LS/methanol system behaves more like a liquid.
Electron transfer properties of the Fc-LS2/methanol, Fc-LS2/1-propanol, Fc-LS/methanol and Fc-LS/1-pentanol systems were also investigated by quantum mechanical (QM) calculations. The results indicated that the electron transfer integrals of the Fc-LS2/1-propanol and Fc-LS/1-pentanol system are larger than those of the Fc-LS2/methanol and Fc-LS/methanol system. The amino acid linkages contribute to improved charge-transport properties. This suggests that the former is a favorable system for electron transport. Finally, our study demonstrated that the combination of MD and QM represents an effective approach to investigate conductive-gel systems.

Table of Contents
論文審定書 i
誌謝 ii
摘要 iii
Abstract iv
Table of Contents vi
List of Figures ix
List of Tables xiii

Chapter 1. Introduction 1
1.1 Low Molecular-Mass Organic Gelators 2
1.2 Conductive Gels 4
1.3 Cholesteryl-Ferrocenyl-Amino Acid Gelators 6
Chapter 2. Computer Simulation Methods 8
2.1 Molecular Dynamics Simulation 9
2.1.1 Equations of Motion and Verlet Leapfrog Integration 9
2.1.2 Force Field 10
2.1.3 Thermodynamic Ensembles 12
2.1.4 Periodic Boundary Condition 13
2.1.5 Mean Square Displacement, Diffusion Coefficient, and Radial Distribution Function 15
2.2 Quantum Mechanics Calculation 17
2.2.1 Density Functional Theory 18
2.2.2 Semi-Empirical Methods 19
Chapter 3. Conformational Properties of Gelators in Solvents 21
3.1 Introduction 21
3.2 Simulation Method 23
3.3 The Initial Structures of Fc-LS2 and Fc-LS Gelators 26
3.4 Molecular Dynamics Simulation for Fc-LS2 Gelator Systems 27
3.4.1 The End-to-End Distance and Angle Distribution of Fc-LS2 Molecules 30
3.4.2 The Intermolecular Relationship of Fc-LS2 Gelators 32
3.4.3 The Intermolecular Relationship of Fc-LS2 Gelators and Solvents 34
3.5 Molecular Dynamics Simulation for Fc-LS Gelator Systems 37
3.5.1 The Intermolecular Relationship of Fc-LS Gelators 40
3.5.2 The Intermolecular Relationship of Fc-LS Gelators and solvents 42
3.6 Conclusion 44
Chapter 4. Gel Behavior in the Gelator/Solvent System 46
4.1 Introduction 46
4.2 Simulation Method 47
4.3 Percentage of Solvent in Gelator System 48
4.4 Mobility of Solvent in Different Systems 50
4.5 Phase Behavior of Fc-LS2 and Fc-LS Systems 52
4.6 Conclusion 58
Chapter 5. Electron Transfer Properties of Fc-LS2 and Fc-LS systems 59
5.1 Introduction 59
5.2 Simulation Method 60
5.3 Electron Transfer Theory 61
5.3.1 Einstein Relation 61
5.3.2 Marcus Theory 62
5.3.3 Transfer Integral 64
5.4 Charge Transfer Properties of Fc-LS2 and Fc-LS systems 67
5.4.1 Electron Transfer Integral of Fc-LS2 System 69
5.4.2 Electron Transfer Integral of Fc-LS System 72
5.5 Conclusion 74
Chapter 6. Summary 76
References 78

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