分子動力學模擬 (Molecular Dynamics Simulation) 是利用電腦模擬的方式，研究分子或原子在一段時間內的物理運動情形，現今已廣泛應用在材料、生化及藥物方面的研究。磷酸鋯類化合物是近年來發展起來的一類新型多功能介孔材料，其中晶形 α-磷酸鋯 (Zr(HPO4)2•H2O, 簡寫為 α-ZrP) 是一種陽離子型層狀化合物，具有規整層板結構和可設計性。十六烷基三甲基溴化銨 (CTAB) 是一種陽離子型表面活性劑，是一個具有長碳鏈疏水基團的銨鹽，可與其他可交換的陽離子發生離子交換。
本研究是將 CTAB 插入到 α-ZrP 層間，製備出插層複合材料 α-ZrP-CTAB，並將純水、苯酚 (phenol) 以及其混合溶液分別置入其中，接著利用分子動力學模擬來觀察溶液滲透與吸附情形。其結果可知，純水在 α-ZrP-CTAB 中可滲透過去，而苯酚則會被 α-ZrP-CTAB 所吸附而停留在其結構中，若是加入兩者的混合溶液，則水分子可通過但苯酚無法通過，故可達到分離混合溶液的效果。接著再將混合溶液中的苯酚離子化進行模擬，結果顯示離子化後的苯酚進入結構中的數量明顯減少，此也與文獻上所提到的實驗結果相符。

Molecular dynamics (MD) is a computer simulation of physical movements of atoms and molecules. MD has now been widely used in materials, biochemical and pharmaceutical research. In recent years, zirconium phosphate (ZrP) compounds developed a new type of multi-function mediated porous materials, which the crystalline α-zirconium phosphate (α-ZrP) is a cationic layered compounds, with a neat layer structure and easy to design. Cetyl trimethyl ammonium bromide (CTAB) is a cationic surfactant, it’s one kind of ammonium salt of a long carbon chain as hydrophobic groups. Ion exchange can occur with other exchangeable cations.
In this study, we first use CTAB inserted into α-ZrP interlayer to prepare α-ZrP-CTAB material. Second, we add phenol solution in the system, and use molecular dynamics simulations to observe the solution’s penetration and adsorption. The result shows that pure water can permeate through α-ZrP CTAB membrane, and pure phenol will be adsorbed by the α-ZrP-CTAB membrane. If we add phenol solution, the water molecules can pass through the α-ZrP-CTAB membrane but phenol molecule can’t. It can achieve the effect of separation of the mixed solution. Last we simulate phenolate solution system. The result shows that the number of phenolate molecule enter the membrane is less than phenol molecule in phenol solution. This result is also consistent with the experiments mentioned in the literature.

論文審定書....................................................................................................i
謝誌...............................................................................................................ii
論文提要......................................................................................................iii
中文摘要......................................................................................................iv
英文摘要.......................................................................................................v
目錄..............................................................................................................vi
圖目錄..........................................................................................................ix

第壹章 緒論.................................................................................................1
1-1 分子動力模擬................................................................................1
1-2 層狀化合物....................................................................................2
1-3 磷酸鋯 (Zirconium Phosphate).....................................................4
1-4 十六烷基三甲基溴化銨 (CTAB).................................................6
1-5 研究動機與方法............................................................................7
第貳章 原理及方法.....................................................................................8
2-1 分子動力模擬 (Molecular Dynamics Simulation).......................8
2-1-1 簡介....................................................................................8
2-1-2 分子動力學基本假設........................................................9
2-1-3 分子動力學基本架構........................................................9
2-2 系統作用力場..............................................................................11
2-3 數值方法…..................................................................................12
2-4 週期性邊界條件..........................................................................15
第參章 系統建構方法及參數設定...........................................................17
3-1 系統建構......................................................................................17
3-2 模擬參數......................................................................................19
3-2-1 結構最佳化參數設定......................................................19
3-2-2 分子動力模擬參數設定..................................................19
第肆章 結果與討論...................................................................................20
4-1 分子動力模擬初始結果..............................................................20
4-1-1 純水在 α-ZrP-CTAB 膜中的滲透情況探討.................20
4-1-2 純苯酚在 α-ZrP-CTAB 膜中的滲透情況探討.............22
4-1-3 20% 苯酚溶液在 α-ZrP-CTAB 膜中的滲透情況探..................................................................................................24
4-1-4 不同系統在氦板施加壓力為 9Å 時滲透情形比較.....26
4-2 利用分子動力模擬所得的軌跡圖進行分析..............................28
4-2-1 不同系統下 α-ZrP-CTAB 膜中 CTAB 上的碳鏈扭曲情形..............................................................................................28
4-2-2 不同系統下 α-ZrP-CTAB 膜中 CTAB 上的碳鏈在空間中的位向變化情形..................................................................33
4-2-3 不同系統下溶液中分子和 α-ZrP-CTAB 膜之間的關係..................................................................................................37
4-2-4 不同系統下溶液在環境中的動態分布..........................45
4-2-5 不同系統下溶液分子在 α-ZrP-CTAB 膜晶格中沿 a 軸及 c 軸的分布情形................................................................49
4-3 20% 苯酚系統中的苯酚離子化後的情形.................................53
4-3-1 20% 苯酚離子溶液系統在 α-ZrP-CTAB 膜中的滲透情況探討...........................................................................................53
4-3-2 20% 苯酚離子溶液系統 α-ZrP-CTAB 膜中 CTAB 上的碳鏈扭曲情形...............................................................................55
4-3-3 20% 苯酚離子溶液系統徑向分布函數結果....................57
4-3-4 20% 苯酚離子溶液系統下溶液分子在 α-ZrP-CTAB 膜晶格中沿 a 軸及 c 軸的分布情形............................................58
4-3-5 20% 苯酚離子溶液系統和實驗的比較............................60
第伍章 結論...............................................................................................62
第陸章 參考文獻.......................................................................................64

1. B. J. Alder, T. E. Wainwright J. Chem. Phys. 1957, 27, 1208-1209.
2. A. Rahman Phys. Rev. 1964, 136, A405-A411.
3. K. Kremer, G. S. Grest J. Chem. Phys. 1990, 92, 5057-5086.
4. A. D. MacKerell, D. Bashford, et al. J. Phys. Chem. B 1998, 102, 3586-3616.
5. K. David, Y. Masato, et al. J. Clin. Invest. 2002, 109, 1395-1399.
6. D. Wolf, V. Yamakov, et al. Acta Materialia 2005, 53, 1-40.
7. W. F. Gunsteren, H. J. C. Berendsen Angew. Chem. Int. Ed. Engl. 1990, 29, 992-1023.
8. M. C. Payne, M. P. Teter, et al. Rev. Mod. Phys. 1992, 64, 1045-1097
9. S. B. Fowler, R. B. Best, et al. J. Mol. Biol. 2002, 322, 841-849.
10. G. D. Harp, B. J. Berne J. Chem. Phys. 1968, 49, 1249-1254.
11. A. Rahman, F. H. Stillinger J. Chem. Phys. 1971, 55, 3336-3359.
12. S. Plimpton J. Comput. Phys. 1995, 117, 1-19.
13. S. Plimpton, B. Hendrickson J. Comput. Chem. 1996, 17, 326-337.
14. H. J. C. Berendsen, D. Spoel, et al. Comput. Phys. Commun. 1995, 91, 43-56.
15. M. F. Crowley, T. A. Darden, et al. Journal of Supercomputing 1997, 11, 255-278.
16. L. Kalé, R. Skeel, et al. J. Comput. Phys. 1999, 151, 283-312.

17. G. Alberti, U. Costantino, et al. Comprehensive Supramolecular Chemistry. Oxford, UK: Elsevier, 1996.
18. L. N. Geng, M. H. Xiang, et al. Progress in Chemistry 2004, 16, 717-727.
19. T. E. Mallouk, J. A. Gavin Acc. Chem. Res. 1998, 31, 209-217.
20. J. W. Johnson, A. J. Jacobsen, et al. J. Am. Chem. Soc. 1989, 111, 381-383.
21. G. Gao, T. E. Mallouk Inorg. Chem. 1991, 30, 1434-1438.
22. M. Curini, F. Epifino, et al. Synthetic Communications 2002, 32, 355-362.
23. A. Clearfield, D. S. Thakur J. Catal. 1981, 69, 230-233.
24. G. Busca, V. Lorenzelli, et al. J. Chem. Soc., Faraday Trans. 1 1987, 83, 853-864.
25. Y. J. Feng, W. He, et al. Materials Review 2007, 2, 46-48.
26. F. A. Mumpton PNAS 1999, 96, 3463-3470.
27. B. E. Scheetz, D. K. Agrawal, et al. Waste Management 1994, 14, 489-505.
28. U. Costantino, F. Marmottini, et al. Catal. Lett. 1993, 22, 333-336.
29. A. Díaz, A. David, et al. Biomacromolecules 2010, 11, 2465-2470.
30. H. Wu, C. Liu, et al. Polym. Int. 2010, 59, 923-930.
31. G. Alberti, R. Vivani, et al. J. Por. Mater. 1998, 5, 205-220.
32. J. M. Troup, A. Clearfield Inorg. Chem. 1977, 16, 3311-3314.
33. A. Clearfield, J. A. Stynes J. Inorg. Nucl. Chem. 1964, 26, 117-129.
34. D. M. Poojary, B. Shpeizer, et al. J. Chem. Soc. Dalton. Trans. 1995, 1, 111-113.
35. S. F. Wang, Y. X. Sun, et al. Microchimica Acta 2005, 149, 185-191.
36. J. H. Choy, S. Y. Kwak, et al. Mater. Lett. 1997, 33, 143-147.
37. L. P. Meier, R. Nueesch, et al. J. Colloid Interface Sci. 2001, 238, 24-32.
38. W. Yao, H. N. Wang, et al. Acta Phys. –Chim. Sin. 2011, 27, 1763-1771.
39. Y. Hasegawa, R. Matsuda, et al. J. Inclusion Phenom. Macrocyclic Chem. 2002, 42, 33-38.
40. L. Beneš, K. Melánová, et al. Eur. J. Inorg. Chem. 2003, 8, 1577-1580.
41. D. M. Kaschak, S. A. Johnson, et al. J. Am. Chem. Soc. 1998, 120, 10887-10894.
42. N. Metropolis, A. W. Rosenbluth, et al. J. Chem. Phys. 1953, 21, 1087-1092.
43. B. J. Alder, T. E. Wainwright J. Chem. Phys. 1959, 31, 459-466.
44. J. H. Irving, J. G. Kirkwood J. Chem. Phys. 1950, 18, 817-829.
45. A. K. Rappé, C. J. Casewit, et al. J. Am. Chem. Soc. 1992, 114, 10024-10035.
46. M. P. Allen, D. J. Tildesley Computer Simulation of Liquids. Clarendon Press : Oxford, 1987.