本篇論文以密度泛函理論與LCAO基底函數並搭配Troullier-Martins方案的non-conserving虛位勢(pseudopotential)來討論兩個議題，(1)重氮分子依奈米碳管導電性質的選擇性吸附反應(2) IC3H3解離吸附後在Ag(111)表面上的分子動態模擬IR光譜。

　　第一部分模擬的結果顯示，在半導體性質(8,0) [zigzag類型]和金屬性質(9,0) [zigzag類型]、(5,5) [armchair類型]奈米碳管上，硝基苯自由基(NO2C6H4)的直接加成(direct addition)反應於不同導電性質的奈米碳管間不具有選擇性，而硝基苯重氮化合物自由基(NO2C6H4N2)的解離吸附(dissociative addition)反應會選擇性的與金屬性質奈米碳管發生反應，因為在金屬性質的系統中，奈米碳管於過渡態時會藉由電荷的轉移(由奈米碳管至反應物)來穩定過渡態的結構，進而幫助反應更快的進行。在此我們證明了，可能發生選擇性反應的兩個分子中，只有硝基苯重氮化合物自由基(NO2C6H4N2)確實會選擇性的與金屬性質奈米碳管發生反應。

    第二部分中，藉由執行BOMD並搭配本實驗室開發的傅立葉轉換電偶極矩時間自動相關函數工具，我們成功的以週期性系統的分子動態模擬IR光譜取得與實驗上RAIRS光譜的一致性，並以PaDAF和SCAF解析工具確認出C3H3在Ag(111)表面上其CCC骨幹的兩種運動動態(L型與直線型運動)與2000cm-1 doublet訊號的關聯。此外分析表面振動態與C-Ag鍵結振動態在X、Y和Z三個方向上的偶合訊號，反應出I與C3H3間的距離夠近時，C3H3會集中在X方向上運動。最後比較叢聚型模型與週期性模型的分子動態模擬IR光譜，我們證明了表面運動對模擬IR光譜有著關鍵的影響。總而言之，藉由解析週期性系統的分子動態模擬IR光譜，我們可以很仔細的確認出C3H3與I在Ag(111)表面上的運動與其IR光譜的關係，以提供此類實驗更多的微觀角度做為分析IR光譜的參考。

Density Functional Theory in connection with accurate LCAO basis sets and norm-conserving pseudopotentials were used to study two issues which are (1) The Selective Functionalization of Single-Walled Carbon Nanotubes with Diazonium Radical and (2) The Molecular Dynamic Simulated IR Spectrum of Adsorbed C3H3(ads) and I(ads) on the Ag(111) Surface.

   For the first, we investigated (1) NO2C6H4 direct addition (2) NO2C6H4N2 dissociative addition reaction on semiconductor (8,0)[zigzag type], metallic (9,0)[zigzag type]and(5,5)[armchair type] carbon nanotubes. The calculated results indicated that only NO2C6H4N2 dissociative addition will selectively react with metallic carbon nanotubes which provide electrons to stabilize the transition state structure, lower the activation energy barrier and accelerate the reaction. 

   For the second, BOMD(Born-Oppenheimer molecular dynamics) in connection with the Fourier transformed dipole-moment AutoCorrelation Function tool were used to generate IR spectrum. IR spectrum simulated by periodic model (C3H3(ads) and I(ads) adsorbed on Ag(111)-(3x3) surface) is in good agreement with RAIRS experimental result and the results from PaDAF and SCAF analysis(two tools for spectrum analysis) further confirm that the two backbone(C-C≡C) motions (L-sha pe and line- shape) of C3H3(ads) were related to the doublet signals around 2000 cm-1. In addition, the coupling signals from motions of surface and C-Ag bond on X,Y and Z directions could reflect the fact that when I(ads) and C3H3(ads) are close enough, C3H3(ads) will move along X direction. Finally, by comparing our calculated results of both cluster model and periodic model, we proved that surface motion is crucial for simulating IR spectrum.

第一章 緒論
1-1 重氮分子選擇性反應的發現及重要性                       1
1-2 IC3H3在Ag(111)表面上的反應與紅外線光譜                 4

第二章 計算方法
2-1 固態材料的電子結構計算                                 7
 2-1-1 密度泛函理論                                        7
 2-1-2 週期性邊界條件                                     12
 2-1-3 虛位勢                                             13
2-2 第一原理分子動態模擬                                  16
 2-2-1 統計力學模擬系集                                   17
 2-2-2 Born-Oppenheimer分子動態模擬                       21
2-3 第一原理分子動態模擬紅外線光譜                        24
 2-3-1 時間相關函數與紅外線光譜的模擬                     25
 2-3-2 紅外線光譜振動模式的解析方法                       28
2-4 態密度(DOS)                                           32

第三章 重氮分子與奈米碳管的選擇性吸附反應
3-1 RC6H4與RC6H4N2在反應中扮演的角色                      34
3-2 奈米碳管簡介                                          37
 3-2-1 命名原則與電子結構                                 37
 3-2-2 結構產生-由石墨到奈米碳管                          40
3-3 計算系統及參數的選擇                                  41
 3-3-1 計算系統的選擇及模型的建立                         41
 3-3-2 計算參數的使用與測試                               45
3-4 NO2C6H4在奈米碳管上的吸附反應                         47
 3-4-1 NO2C6H4與(8,0)、(9,0)和(5,5)反應的分析與比較       47
3-5 NO2C6H4N2在奈米碳管上的解離吸附反應                   49
 3-5-1 反應途徑的設計原則                                 49
 3-5-2 解離吸附起始點及終點結構的建立                     50
 3-5-3 失敗的過渡態搜尋法                                 56
 3-5-4 NO2C6H4N2中N2解離及C6H4翻轉的能量資訊              61
 3-5-5 NO2C6H4N2與(8,0)、(9,0)和(5,5)反應的過渡態搜尋     62
 3-5-6 NO2C6H4N2與(8,0)、(9,0)和(5,5)反應的分析與比較     67
3-6 總結                                                  77

第四章IC3H3在Ag(111)表面上的分子動態模擬IR光譜
4-1 反射式紅外光吸收光譜(RAIRS)的實驗結果                 78
4-2 Ag金屬表面簡介                                        80
4-3 計算參數的選擇                                        82
4-4 IC3H3的紅外線光譜分析                                 86
4-5 C3H3與I吸附在Ag(111)的模擬IR光譜—叢聚型系統          92
4-6 C3H3與I吸附在Ag(111)的模擬IR光譜—週期性系統          97
 4-6-1 計算系統的選擇                                     97
 4-6-2 週期性系統的紅外線光譜分析                         99
4-7 綜合結果討論                                         111
 4-7-1 表面模型對模擬紅外線光譜的影響                    111
 4-7-2 IC3H3解離吸附前後模擬紅外線光譜的比較             115
 4-7-3總結                                               117
          
參考資料                                                 119

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