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.
