由於全氟磺酸聚合物不易結晶，再加上其晶體與離子區域的複雜性，導致全氟磺酸的結構已經有很長的一段時間具有爭議性。Gierke團隊，根據小角度x-ray散射之研究進一步假設全氟磺酸有似反微胞之構型。這些微胞彼此藉由一個又窄又短的通道互相連結，運輸水分子。而此一假設為目前最廣泛引用的模型。但到目前為止，全氟磺酸聚合物並沒有公認的形態結構，這也使得我們想進一步去探討其真正的結構。
在本研究中，我們利用分子動力學模擬短鏈的全氟磺酸單體在不同水合數下的運動情形，並將其單體彼此互相接近下產生新的鍵結，而這些鍵結促使全氟磺酸單體聯結成一個不規則的網狀構形。為了比較修改鍵結前後兩系統的差異，我們分析平衡後的兩系統的體積﹑密度﹑徑向分布函數﹑擴散係數……等。而這些分析結果也明確顯示兩系統有所差異。

A widely accepted model for the solid-state structure of Nafion has not been given due to the low crystallinity and complexity of co-organized crystalline and ionic domains. This complex phase-separated morphology has been the target of several investigations which led to different models. The cluster-network model of Gierke et al. can be considered as the most widely referenced model. Based on small-angle X-ray scattering (SAXS) studies and several further assumptions, the model proposes that there are clusters of sulfonate terminated side chains that are organized as inverted micelles. These micelles are interconnected by a network of short and narrow channels which allow water and ion transport. So far, Nafion polymer morphology is has not be recognized. It makes us go further to explore its true structure.
In this study, we use molecular dynamics simulation to investigate the movement situations of short chain Nafion monomers at various levels of hydration. When the distance between two Nafion monomers is enough close, we generate the new Netted of them. These new Netted makes Nafion into an irregular net configuration. In order to compare the difference between netted and free system, we analyze the RDF volume, density, diffusion coefficient and radial distribution function of the two systems. These analysis results also clearly show the difference of two systems.

論文審定書 i
謝誌 ii
論文提要 iii
中文摘要 iv
Abstract v
目錄 vi
圖次 viii
表次 x
第壹章 緒論 1
1-1分子動力模擬 1
1-2 質子交換膜介紹 1
1-3 全氟磺酸形態(NAFION MORPHOLOGY) 4
1-4 質子傳遞機制(PROTON TRANSPORT MECHANISM) 7
1-5 NAFION膜內的兩種擴散係數 8
1-6 研究動機 9
第貳章 原理即方法 10
2-1 分子動力模擬 (MOLECULAR DYNAMICS SIMULATION) 10
2-1-1簡介 10
2-1-2 分子動力學基本假設 10
2-2 分子力場 13
2-3 牛頓運動方程式的數值方法 14
2-4 週期性邊界條件 16
第參章 系統建構方法及參數設定 17
3-1 系統建構 17
3-2 模擬軟體 20
3-3 模擬參數設定 21
3-3-1結構最佳化參數設定 21
3-3-2分子動力模擬參數設定 21
第肆章 結果與討論 23
4-1 分子動力模擬初始結果 23
4-1-1 Nafion膜內的分子在低水合數(λ=2)時的聚集情形 23
4-1-1 Nafion膜內的分子在高水合數(λ=16)時的聚集情形 24
4-2不同水合數下NAFION薄膜的膨脹趨勢 25
4-2-1體積膨脹趨勢 25
4-2-2 密度 27
4-3兩系統在不同水合數下水分子和NAFION薄膜之間的關係 31
4-3-1 徑向分布函數 31
4-3-2 Nafion膜與水分子的徑向分佈函數圖 32
4-3-3 比較兩系統在同水合數下徑向分布函數圖之差異 35
4-4兩系統內水分子及質子之擴散係數比較及探討 42
4-4-1 利用均方位移分析膜內水分子及質子的流動情形 42
4-4-2 比較兩系統內水分子的擴散係數 45
第伍章 結論 50
第陸章 參考文獻 52

(1) Alder, B. J.; Wainwright, T. E. Journal of Chemical Physics 1957, 27, 1208.
(2) Rahman, A. Physical Review 1964, 136, A405.
(3) Harp, G. D.; Berne, B. J. Journal of Chemical Physics 1968, 49, 1249.
(4) Rahman, A.; Stilling.Fh Journal of Chemical Physics 1971, 55, 3336.
(5) Kremer, K.; Grest, G. S. Journal of Chemical Physics 1990, 92, 5057.
(6) Vangunsteren, W. F.; Berendsen, H. J. C. Angewandte Chemie-International Edition in English 1990, 29, 992.
(7) Payne, M. C.; Teter, M. P.; Allan, D. C.; Arias, T. A.; Joannopoulos, J. D. Reviews of Modern Physics 1992, 64, 1045.
(8) Fowler, S. B.; Best, R. B.; Toca Herrera, J. L.; Rutherford, T. J.; Steward, A.; Paci, E.; Karplus, M.; Clarke, J. Journal of Molecular Biology 2002, 322, 841.
(9) Kozono, D.; Yasui, M.; King, L. S.; Agre, P. The Journal of Clinical Investigation 2002, 109, 1395.
(10) Jang, S. S.; Molinero, V.; Cagın, T.; Goddard, W. A. The Journal of Physical Chemistry B 2004, 108, 3149.
(11) Wolf, D.; Yamakov, V.; Phillpot, S. R.; Mukherjee, A.; Gleiter, H. Acta Materialia 2005, 53, 1.
(12) MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. The Journal of Physical Chemistry B 1998, 102, 3586.
(13) Hogarth, W. H. J.; da Costa, J. C. D.; Lu, G. Q. Journal of Power Sources 2005, 142, 223.
(14) Eikerling, M.; Kornyshev, A. A.; Kucernak, A. R. Physics Today 2006, 59, 38.
(15) Paddison, S. J.; BCH, S.; A, H. Annual Review of Materials Research 2003, 33, 289.
(16) Mauritz, K. A.; Moore, R. B. Chemical Reviews 2004, 104, 4535.
(17) Heitner-Wirguin, C. Journal of Membrane Science 1996, 120, 1.
(18) Gierke, T. D.; Munn, G. E.; Wilson, F. C. Journal of Polymer Science: Polymer Physics Edition 1981, 19, 1687.
(19) Haubold, H. G.; Vad, T.; Jungbluth, H.; Hiller, P. Electrochimica Acta 2001, 46, 1559.
(20) Yeager, H. L.; Steck, A. Journal of the Electrochemical Society 1981, 128, 1880.
(21) Yeo, S. C.; Eisenberg, A. Journal of Applied Polymer Science 1977, 21, 875.
(22) Fujimura, M.; Hashimoto, T.; Kawai, H. Macromolecules 1981, 14, 1309.
(23) Fujimura, M.; Hashimoto, T.; Kawai, H. Macromolecules 1982, 15, 136.
(24) Rubatat, L.; Gebel, G.; Diat, O. Macromolecules 2004, 37, 7772.
(25) Rubatat, L.; Rollet, A. L.; Gebel, G.; Diat, O. Macromolecules 2002, 35, 4050.
(26) Haubold, H. G.; Vad, T.; Jungbluth, H.; Hiller, P. Electrochimica Acta 2001, 46, 1559.
(27) Schmidt-Rohr, K.; Chen, Q. Nat Mater 2008, 7, 75.
(28) Gierke, T. D. Bulletin of the American Physical Society 1981, 26, 462.
(29) Smitha, B.; Sridhar, S.; Khan, A. A. Journal of Membrane Science 2005, 259, 10.
(30) Kreuer, K.-D.; Paddison, S. J.; Spohr, E.; Schuster, M. Chemical Reviews 2004, 104, 4637.
(31) Kreuer, K. D.; Rabenau, A.; Weppner, W. Angewandte Chemie-International Edition in English 1982, 21, 208.
(32) Gao, H.; Lian, K. RSC Advances 2014, 4, 33091.
(33) Evans, C. M.; Singh, M. R.; Lynd, N. A.; Segalman, R. A. Macromolecules 2015, 48, 3303.
(34) Arsenault, R. J.; Beeler, J. R. Computer Simulation in Material Science; ASM.INTERNATIONAL: USA, 1988.
(35) Smith, R.; Jakas, M. O. Atomic and Ion Collisions in Solids and at Surfaces: Theory,Simulation and Applications; Cambridge University Press: USA, 1997.
(36) Berendsen, H. J. C.; Postma, J. P. M.; Vangunsteren, W. F.; Dinola, A.; Haak, J. R. Journal of Chemical Physics 1984, 81, 3684.
(37) Mayo, S. L.; Olafson, B. D.; Goddard, W. A. The Journal of Physical Chemistry 1990, 94, 8897.
(38) Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. Journal of the American Chemical Society 1992, 114, 10024.
(39) Bunte, S. W.; Sun, H. The Journal of Physical Chemistry B 2000, 104, 2477.
(40) Rapaport, D. C. The Art of Molecular Dynamics Simulation, 2004.
(41) Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford Science: London, 1991.
(42) Frenkel, D.; Smit, B. Understanding Molecular Simulation Academic Press: San Diego, 2004.
(43) Haile, J. M. Molecular Dynamics Simulation: Elementary Methods, 1992.
(44) Venkatnathan, A.; Devanathan, R.; Dupuis, M. Journal of Physical Chemistry B 2007, 111, 7234.
(45) Morris, D. R.; Sun, X. Journal of Applied Polymer Science 1993, 50, 1445.
(46) Perrin, J.-C.; Lyonnard, S.; Volino, F. The Journal of Physical Chemistry C 2007, 111, 3393.
(47) Zawodzinski, T. A.; Neeman, M.; Sillerud, L. O.; Gottesfeld, S. The Journal of Physical Chemistry 1991, 95, 6040.