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研究生:盧秀鳳
研究生(外文):Hsiu-feng Lu
論文名稱:理論探討氫化鑽石(111)表面之氣固異相反應與3-甲氨甲基-5-R-水楊醛(R=OCH3,Br)的分子內與alpha-氨基砒啶二聚物的分子間氫鍵與溶劑效應。
論文名稱(外文):Theoretical Study (1) the heterogenous reaction on hydrogen-covered diamond (111) surface. (2) the intra-hydrogen bond and solvent effect of 3-dimethylaminomethyl-5-R-salicylic aldehydes (R=OCH3, Br). (3) the inter-hydrogen bond and solvent effect of olig
指導教授:孫英傑孫英傑引用關係
指導教授(外文):Ying-Chieh Sun
學位類別:博士
校院名稱:國立臺灣師範大學
系所名稱:化學研究所
學門:自然科學學門
學類:化學學類
論文種類:學術論文
論文出版年:2002
畢業學年度:90
語文別:中文
論文頁數:175
中文關鍵詞:氫化的鑽石(111)表面氫鍵溶劑效應
外文關鍵詞:hydrogen-covered diamond (111) surfacehydrogen bondsolvent effect
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中文摘要
我們理論研究氫化之鑽石(111)表面之吸附氫拔取反應、吸附反應、蝕刻反應、與游移反應。我們所探討的吸附氫拔取反應用不同的自由基,諸如H、CH3、C2H、O、OH、NH2、CN、F、Cl、Br、CF3、與CCl3,我們的計算結果顯示,相較於原子氫,F、Cl、O、OH、CN、與C2H為強的拔氫劑,CH3、NH2、Br、CF3、與CCl3為弱的拔氫劑,這些自由基拔氫的能力約與其親電子性指標(electrophilicity index)相關,即親電子性指標值越大其拔氫能力越強。我們所探究的吸附反應,包括含碳核種與不含碳核種吸附基吸附在氫化之鑽石(111)表面之懸空鍵上,其吸附能的大小約與欲形成之鍵強(bond strength)相關,典型鍵強由強至弱為C-F>C-H>C-O>C-C>C-Cl>C-N,我們計算所得之吸附能大小由大至小為CN、F、H、OH、CH3、NH2、CF3、CH2F、Cl、CHF2、CH2Cl、CH2OH、CH2NH2、CCl3。由於氯原子吸附有大的立障,故不能反映出其天然鍵強較C-N強,同理甲基吸附基上之氫被取代,立障與取代基效應整體結果,可能不穩定化氫化之鑽石表面相較於甲基吸附基(adsorbate)。吸附基或吸附基上之原子或原子團被氫原子蝕刻的計算結果顯示CH3與CF3很難被原子氫拔取,吸附氯很容易被拔取,其拔取的難易次序由易至難約為Cl<H<NH2<OH<F<CH3<CF3,由吸附能與蝕刻難易的綜合結果暗示Cl、H、N、O、F物種應較難併入成長的鑽石薄膜中,在低的基材溫度下是有可能,但併入應是微量的,此與實驗的觀察是一致的。吸附原子或原子團在氫化的鑽石表面游移我們僅探究吸附氫、氟、氯在兩個懸空鍵游移,以及甲基吸附基上之氫在甲基懸空鍵與台地懸空鍵之間的轉移(標記為H/CH3),我們的計算結果顯示,受制於計算方法的選擇,但一致的結果為甲基吸附基上之氫在甲基懸空鍵與台地懸空鍵之間的轉移是容易的,僅需要吸附氫在台地上的游移所需的能障的一半,吸附氯較吸附氫在台地上的游移容易。由轉移能障與蝕刻能障及吸附氫被氫原子拔取的能障相比,鑽石(111)表面的游移反應在化學蒸鍍鑽石薄膜成長過程中,相對其他動力學過程是不重要的,此結果與其他的文獻的建議是一致的。
我們用密度泛函(density functional theory)之B3LYP方法,以及八種基底,分別為6-31+G(d,p)、6-31+G(2d,2p)、6-31+G(df,pd)、6-31+G(2df,2pd)、6-311+G(d,p)、6-311+G(2d,2p)、6-311+G(df,pd)、6-311+G(2df,2pd),探討3-dimethylaminomethyl-5-R-salicylic(R=OCH3, Br)aldehydes之分子內氫鍵異構物與用PCM(the Polarized Continuum model)方法探究這些異構物之溶劑效應。當R=OCH3時(compound 1)有八種分子內氫鍵異構物,R= Br時(compound 2)有四種分子內氫鍵異構物。我們的計算結果顯示其各各氫鍵異構物之相對能量用6-31+G(2d,2p)與6-311+G(2d,2p)基底和用6-311+G(2df,2pd)基底之計算結果接近,但考量溶劑效應用PCM方法,用6-31+G(df,pd)與6-311+G(df,pd)基底和用6-311+G(2df,2pd)基底之計算結果較接近。在真空中,我們的計算結果顯示compound 1與compound 2二者均以形成OH…O=C分子內氫鍵結構之異構物為主,但溶劑效應考量下,compound 1仍以OH…O=C分子內氫鍵結構之異構物為主,compound 2則變為以形成OH…N分子內氫鍵結構之異構物為主。由取代效應發現compound 2較compound 1此二氫鍵結構物的異同較大,但溶劑效應較能有效的穩定形成OH…N分子內氫鍵結構之異構物,此溶劑效應的不同穩定性的差異亦是compound 2較compound 1大,其競爭結果導致以形成OH…N分子內氫鍵結構之異構物為主要平衡物種。
我們用ab initio方法研究a-aminopyridine重複單元數與氫鍵二聚能的關係與溶劑效應。發現實驗觀察二聚焓與a-aminopyridine重複單元數有好的線性相關,我們的計算結果建議來自於氫鍵雙體累進之N-H…N氫鍵與單體最穩構形之累進的C-H…N氫鍵造成的。我們的計算結果顯示氯仿有足夠的能力扮演氫鍵給予者的角色,與a-aminopyridine形成氫鍵複合物,因此實驗觀察在氯仿溶劑所測之二聚焓較在環己烷中所測小許多,其原因可能來自氯仿分子與單體競爭砒啶之N,以形成氫鍵減低了二聚焓造成的。
Abstract
We examined four kinetics reactions on hydrogen-terminated diamond (111) surface using ab initio calculation: 1). The hydrogen abstraction reaction by atomic hydrogen and non-hydrogen radical(CH3, C2H, O, OH, NH2, CN, F, Cl, Br, CF3, and CCl3). 2). The adsorption reaction of the carbon-containing species(CN, CH3, CH2OH, CH2NH2, CH2F, CHF2, CF3, CH2Cl, and CCl3)and non-carbon-containing species(H, F, Cl, OH, and NH2). 3). The etching reaction of the species CH3, CF3, F, Cl, OH, NH2, H from CH3, CH2F, CH2Cl, CH2OH adsorbates, respectively, F atom from CH2F, CF3 adsorbates, Cl atom from CH2Cl, CCl3 adsorbates, and NH2 from CH2NH2 adsorbate, abstracted by atomic H. 4). The migration reaction of various species(H, F, Cl)on diamond (111) surface. The calculated results of H-abstraction reaction abstracted by various radicals show that F, Cl, O, OH, CN, and C2H are much stronger abstractors while Br, NH2, CH3, CF3, and CCl3 radicals are weaker abstractors, compared with this abstraction reaction abstracted by H atoms, which is in excess in CVD environment. The energy barrier heights for these examined radicals are generally correlated well with an index of electrophilicity. The calculated adsorption energies of H, F, Cl, OH, NH2 and other carbon-containing species correlate well with typical C-H, C-F, C-Cl, C-O, C-N, and C-C bond strength. However, for fluorine or chlorine atoms, steric effect needs to be taken into consideration in rationalizing the calculated results. For OH and NH2 adsorbates, both steric and electron-donation effects make the adsorption of these two species harder, compared with CH3. The calculations gave that the order of adsorption energy in decreasing order is CN, F, H, OH, CH3, NH2, CF3, CH2F, Cl, CHF2, CH2Cl, CH2OH, CH2NH2, and CCl3. The calculation results for the abstraction of H, F, Cl, OH, and NH2 species of adsorbates abstracted by atomic H show that Cl is easier and F is harder to be removed than H. These calculated results correlate well with their bond strength with C atom. The energy barriers for this etching reaction in decreasing order is CF3, CH3, F, OH, NH2, H, Cl. These results suggest that the O, N, and F may be incorporated in diamond thin film in the diamond chemical vapor deposition growth process when non-carbon species involve in this process. For the migration of species between two neighbor dangling bond sites, the calculations for H, F, and Cl gave that the order for migration energy barriers is H>F>Cl when the HFB and B3LYP ab initio methods were used, and F>H>Cl when the MP2 method was used. All the calculated results show that chlorine atom and hydrogen atom of CH3 adsorbate transfer between chemisorbed moieties is easier than fluorine and hydrogen transfer.
In addition, we examined the intra-molecular hydrogen bond interaction and the solvent effect using the polarized continuum model(PCM)in two 3-dimethylaminomethyl-5-R-sailicylic(R=OCH3, Br)aldehydes using the density functional theory(B3LYP)with various basis sets, such as 6-31+G(d,p), 6-31+G(2d,2p), 6-31+G(df,pd), 6-31+G(2df,2pd), 6-311+G(d,p), 6-311+G(2d,2p), 6-311+G(df,pd), 6-311+G(2df,2pd). The relative energies of eight conformers for R=OCH3 and of four conformers for R=Br indicate that the structures with OH…O=C intra-molecular hydrogen bond is predominant equilibrium conformers in vacuum. In chloroform solution, the OH…O=C intra-molecular hydrogen bond in compound 1 (R=OCH3) is more favorable whereas OH…N intra-molecular hydrogen bond in compound 2 (R=Br) is more predominant. This is consistent with experimental study of intra-molecular hydrogen bonds in two 3-diethylaminomethyl-5-R-salicylic(R=OCH3, Br) aldehydes in chloroform solutions. Besides, it is noted that the difference of the OH…O=C and the OH…N intra-molecular hydrogen bond strength for the compound 1 is smaller than the compound 2. Also, the calculated results show that the solvation by chloroform stabilizes the conformer with OH…N intra-molecular hydrogen bond more for the compound 2 than compound 1.
Besides, we examined the inter-molecular hydrogen bond interaction of a-aminopyridine dimer and the solvent effect using ab initio calculation. According to experimental measurements, the dimerization enthalpy is linearly correlated with number of a-aminopyridine repeated units. Our calculated results suggest that this is because of formation of NH…N hydrogen bonds of dimers and CH…N hydrogen bonds of the monomers. The calculated results also suggest that the C-H bond of chloroform can be a proton donor, and is able to form hydrogen bond with the N on the pyridine ring. This may be why there is less dimerization enthalpy in chloroform than in cyclohexane observed in an experiment.
目錄
中文摘要 i
英文摘要iii
表目錄vi
圖目錄viii
第一部份:理論研究氫化鑽石(111)表面之氣固異相反應1
第一章:簡介 1
第二章:方法 8
2-1:表面氫被拔取反應所用的模板 ( cluster ) 與方法的選擇 9
2-2:吸附反應所用的模版 ( cluster ) 與方法的選擇 17
2-3:蝕刻反應所用的模版 ( cluster ) 與方法的選擇 18
2-4:游移反應所用的模版 ( cluster ) 與方法的選擇 21
第三章:結果與討論 23
3-1:表面氫被數種拔氫劑拔取的反應 23
3-2:鄰接基效應32
3-3:階梯上的氫被氫原子拔取41
3-4:吸附反應 43
3-5:蝕刻反應48
3-6:游移反應57
第四章:總結60
第五章:參考文獻63
第二部分:理論探討3-二甲氨甲基-5-R-水楊醛的分子內氫鍵與溶劑效應69
第一章:簡介69
第二章:方法71
第三章:結果與討論76
3-1:基底效應76
3-1-1:在真空下77
3-1-2:在氯仿溶劑下,用PCM(polarizable continuum method)方法模擬溶劑效應86
3-1-3:基底效應總結96
3-2:比較3-DMAM-5-OCH3-SA時,a-type與b-type的異同98
3-3:比較各種氫鍵異構物的穩定性101
3-3-1:3-dimethylaminomethyl-5-Br-salicylic aldehydes(3-DMAM-5-Br-SAs)102
3-3-2:3-dimethylaminomethyl-5-OCH3-salicylic aldehydes106
3-3-3:3-dimethylaminomethyl-5-H-salicylic aldehydes(3-DMAM-5-H-SAs)110
3-3-4:取代效應,3-DMAM-5-R-SAs,比較R=H、Br 與OCH3113
3-3-5:溶劑效應124
3-3-6:零點能量修正126
3-3-7:溫度效應127
第四章:總結128
第五章:參考資料130
附錄2-1:B3LYP/6-311+G(2df,2pd)//B3LYP/6-31+G(d,p)方法所計算在氯仿介質下之溶解自由能組成,利用PCM方法.132
第三部份:理論探討a-氨基口比啶二聚物之分子間氫鍵與溶劑效應133
第一章:簡介133
第二章:方法:136
第三章:結果與討論:139
3-3-1:比較HF/6-31G*與HF/LanL2DZ方法作結構優選的結構與能量異同。139
3-3-2:探討重複單元數與二聚化焓值的關係。148
3-3-3:尋找適當的密度泛函(DFT)的理論方法。156
3-3-4:尾端苯甲基的考量對結構與二聚能的影響。158
3-3-5:氯仿溶劑分子作為氫鍵質子供給者的能力。161
第四章:總結161
第五章:參考資料163
附錄3-1:Geometrical parameters for N-H×××N hydrogen bonds observed in the crystal lattices of n=1, 2, and 3.164
附錄3-2:實驗的晶體構造165
附錄3-3:The values of , and upon dimerization as a function of the repeating unit of a-aminopyridine at 298 K (in kJmol-1)166
附錄3-4:Plot of (kJmol-1) versus n, the number of repeating 2-aminopyridine units: (a) in CDCl3 (303 K), (b) in cyclohexane (298 K).166
附錄3-5:n=1, 氫鍵二聚物之結構參數分別用HF/6-31G*與HF/LanL2DZ結構優選化後之結構。167
附錄3-6:為附錄3-5所對應之原子序號圖。173
附錄3-7:n=1,三種可能的單體結構,其中(a)為global minimum。174
附錄3-8:n=2,五種可能的單體結構,其中(a)為類似雙體結構之單體結構之單體結構,(b)為global minimum。174
附錄3-9:n=3,五種可能的單體結構,其中(a)為類似雙體結構之單體結構之單體結構,(c)為global minimum。175
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