在這個博士研究論文中，我們的主要工作是開發一套IR光譜的模擬與解析工具，這套工具根據第一原理密度泛函理論(Density Functional Theory, DFT)分子動態模擬搭配虛位勢(pseudopotential)與LCAO基底函數來計算分子或半導體表面系統的分子動態軌跡與電荷分布動態，進而透過我們開發的電偶極矩自動相關函數(dipole moment auto-correlation function)與其傅立葉分析(Fourier analysis)成功地模擬分子與半導體Si(100)表面的紅外線振動光譜，最後搭配我們所設計的光譜解析技術來研究分子在半導體表面的振動動態與反應動態。這項技術首先成功地計算氣態有機分子的IR光譜，我們提出(I)結構座標自動相關函數(Structural Coordinate Autocorrelation Function, SCAF)，(II)部分電偶極矩自動相關函數解析(Partial Dipole-moment Autocorrelation Function, PaDAF)與(III)非等向性(Anisotropy) IR光譜解析方案使得模擬的IR光譜得以被解析成相關的振動模式。在成功確認光譜模擬工具與分子動態模擬的可行性之後，這套工具被應用到Si(100)表面、monohydride飽和的Si(100)表面、styrene吸附於Si(100)以及styrene一維分子線的IR光譜模擬上，光譜模擬結果與實驗間在定性上有相當好的一致性。此外，我們也分別針對(1)styrene在Si(100)表面上的[2+2] cycloaddition與(2)styrene在Si(100)表面上形成一維分子線的self-directed growth兩種重要表面反應進行在數個皮秒(picosecond)尺度下的反應動態與振動動態的研究，透過振動光譜與部分態密度(PDOS)的動態變化清楚地捕捉到吸附分子與表面的動態作用過程。此外，我們也計算了H-abstraction的反應能障、過渡態結構與PDOS變化，結果顯示styrene分子線的一維性質是導因於dimer row方向上具有兩種較低的H-abstraction反應能障途徑。最後我們也進行了電場對H-Si(100)系統的IR光譜影響以及電場於styrene-Si(100)-H系統所造成的電荷動態研究。結果顯示不同方向的垂直表面電場將導致H-Si振動頻率的紅位移與藍位移，另一方面我們也觀察到styrene-Si(100)-H系統在電場開啟後250飛秒(femtosecond)下的電荷重新分布動態與所伴隨的結構動態。

We successfully developed a series of IR spectrum simulation and corresponding spectrum analysis methods for studying the vibrational dynamics and the reaction dynamics of both molecular and surface systems. The time-correlation function theories were thoroughly studied to build 1) the Fourier trnsformed dipole-moment AutoCorrelation Function(dpACF) for IR spectrum simulation, 2) the Partial Dipole-moment AutoCorrelatoin Function(PaDAF) and the Structural Coordinate AutoCorrelation Function(SCAF) schemes for spectrum analysis, and 3) the Fourier transformed anisotropic dpACF for the IR spectrum simulations on surface systems. By utilizing Density Functional Theory in connection with accurate LCAO basis sets and norm-conserving pseudopotentials, efficient Born-Oppenheimer molecular dynamics(BOMD) simulations would thereby be performed to study the reaction dynamics of adsorbed molecules on surfaes at microscopic level. First of all, our IR spectrum simulation methods were validated by calculating the IR spectra of a series of organic molecules. Based on the success of IR spectrum simulations on gas-phase molecules, furthermore, we employed this IR spectrum simulation and analysis scheme to Si(100) clean surface, monohydride saturated Si(100) surface, i.e. H-Si(100)-2x1 surface, adsorbed styrenes on Si(100) surfaces, and adsorbed one dimensional(1-D) styrene molecular wire on Si(100) surface. Spectrum simulation results for these surface systems are also qualitatively consistent with experimental measurements. In addition, we also successfully studied the reaction dynamics, Partial Density of States(PDOS) evolutions, and the vibrational dynamics within several picoseconds for two kinds of surface reactions of adsorbed styrene on Si(100) surface, say, (1) the [2+2] cycloaddition of styrene on Si(100), and (2) the self-directed growth of 1-D styrene molecular wire on Si(100) via the H-abstraction reaction. On the other hand, we also calculated the transition state structures and their corresponding PDOS variations, however, our results show that the one dimensionality of styrene molecular wire is due to two possible lower energy barrier pathways of H-abstraction along dimer row direction. Finally, we also studied the effects on both IR spectrum of H-Si(100) and the charge dynamics of styrene-Si(100)-H under external electric field. The results show that the H-Si vibrational frequency could be red-shifted or blue-shifted under the presence of external electric field along surface normal, depending on the direction of the electric field. Charge redistribution dynamics of styrene-Si(100)-H accompanying the structure relaxation within 250 femtoseconds were also observed after turning on the external electric field.

第一章  緒論	
	1-1 研究動機與目的	1
	1-2 分子電子元件背景	5
	1-3 self-directed growth過程在半導體表面的分子修飾	8
	1-4 研究方法概述	12
		
第二章  計算模擬方法簡介	
	2-1 電子結構理論應用在固態材料計算	16
		2-1-1 密度泛函理論(Density Functional Theory, DFT)	16
		2-1-2 週期性邊界條件	21
		2-1-3 虛位勢(pseudopotential)	28
	2-2 分子動態模擬(Molecular Dynamics, MD)	31
		2-2-1 力場(Force Field)分子動態模擬	31
		2-2-2 統計力學模擬系集(ensemble)	34
		2-2-3 第一原理分子動態模擬	40
		2-2-4  Born-Oppenheimer分子動態模擬(BO-MD)	41
	2-3 SIESTA計算程式介紹	44
		2-3-1  Norm-conserving虛位勢之處理	44
		2-3-2  基底函數(basis sets)	45
		2-3-3  Electron Hamiltonian與計算方式	46
	2-4 態密度(Density Of State)	49
		
第三章  時間相關函數與振動光譜模擬	
	3-1 振動光譜的理論計算模擬	52
	3-2 相關函數的定義與原理	56
	3-3 微擾(perturbation)理論與Fermi’s Golden Rule	62
	3-4 電磁波吸收光譜與時間相關函數	66
	3-5 利用BOMD與時間相關函數模擬紅外線吸收光譜	70
	3-6 紅外線光譜之振動模式解析	76
	3-7 電荷時間自動相關函數開發	82
		
第四章  分子系統的紅外線光譜模擬解析與其計算參數	
	4-1 虛位勢與基底函數之選用與驗證	85
	4-2 有機分子之分子動態與紅外線光譜模擬	90
		4-2-1 基底函數對光譜模擬的效應	90
		4-2-2  timestep對光譜模擬的效應	92
		4-2-3 有機分子的光譜模擬結果與光譜分析	94
	4-3 電荷震盪動態的解析結果	117
		
第五章  Styrene吸附於Si(100)表面的反應動態與振動動態	
	5-1 Si(100)表面模型與其振動動態	120
	5-2 monohydride飽和之Si(100)表面與其振動動態	132
	5-3 styrene於Si(100)表面之[2+2] cycloaddition	136
		5-3-1 [2+2] cycloaddition反應動態	138
		5-3-2 Styrene吸附後的模擬IR光譜	143
	5-4 Styrene在H-Si(100)表面的一維分子線	146
		5-4-1 Styrene一維分子線吸附結構	147
		5-4-2 H-abstraction能障與過渡態	150
		5-4-3 Styrene在H-Si(100)表面的反應動態	166
		5-4-4 Styrene一維分子線的動態與模擬IR光譜	177
	5-5 外加電場下H-Si(100)表面振動動態與STM去吸附實驗之探討	180
	5-6 styrene於Si(100)表面在外加電場下之動態	183
		
第六章  論文總結	187
		
參考文獻	192
	
英文索引	196

[1] Lin, J. S.; Kuo, Y. T. Thin Solid Films 2000, 370, 192. 
[2] Lin, J. S.; Lee, L. F. Int. J. Quantum Chem. 2004, 97, 736.
[3] Lin, J. S.; Lee, L. F.; Chou, W. C. J. Chin. Chem. Soc. 2003, 50, 611-620.
[4] Lin, J. S.; Chou, W. C. Surf. Sci. 2004, 560, 79-87.
[5] Lin, J. S.; Chou, W. C. Theochem 2003, 635, 115-124.
[6] Lin, J. S.; Chou, W. C. Surf. Rev. Lett. 2004, 11, 229-234.
[7] Lin, J. S.; Chou, W. C. Int. J. Quantum Chem. 2005, 102, 858-865.
[8] Lin, J. S.; Chou, W. C.; Lu, S. Y.; Jang, G. J.; Tseng, B. R.; Li, Y. T. J. Phys. 
Chem. B 2006, 110, 23460-23466. 
[9] Lopinski, G. P.; Wayner, D. D. M.; Wolkow, R. A. Nature 2000, 406, 48-51.
[10] Kang, J. K.; Musgrave, C. B. J. Chem. Phys. 2002, 116, 9907-9913.
[11] Cho, J. H.; Oh, D. H.; Kleinman, L. Phys. Rev. B 2002, 65, 081310-1-4.
[12] Pei, Y.; Ma, J. Langmuir 2006, 22, 3040-3048.
[13] Moore, G. E. Electronics 1965, 38, 114-117.
[14] Aviram, A.; Ratner, M. A. Chem. Phys. Lett. 1974, 29, 277-283.
[15] Carroll, R. L.; Gorman C. B. Angew. Chem. Int. Ed. 2002, 41, 4378-4400.
[16] Joachim, C.; Gimzewski, J. K.; Aviram A. Nature 2000, 408, 541-547.
[17] Health, J. R.; Ratner, M. A. Physics Today 2003, 56, 43-49.
[18] Reed, M. A. Proc. IEEE 1999, 87, 652-658.
[19] Guisinger, N. P.; Yoder, N. L.; Hersam, M. C. PNAS 2005, 102, 8838-8843.
[20] Machida, S.; Hamaguchi, K.; Nagao, M.; Yasui, F.; Mukai K.; Yamashita,
 Y.; Yoshinobu J. J. Phys. Chem. B 2002, 106, 1691-1696.
[21] Hamers, R. J.; Coulter, S. K.; Ellison, M. D.; Hovis, J. S.; Schwartz, M. P. 
Acc. Chem. Res. 2000, 33, 617-624.
[22] Guisinger, N. P.; Greene, M. E.; Basu, R.; Baluch, A. S.; Hersam, M. C.
Nano Lett. 2004, 4, 55-59.
[23] Rakshit, T.; Liang, G.-C.; Ghosh, A. W.; Datta, S. J. Comp. Elec. 2005, 4, 
83-86.
[24] Negative resistance. (2007, May 19). In Wikipedia, The Free Encyclopedia., from http://en.wikipedia.org/wiki/Negative_Resistance
[25] Chen, J; Reed, M. A.; Rawlett, A. M.; Tour, J. M. Science 1999, 286, 
1550-1552.
[26] Linford, M. R.; Fenter, P.; Eisenberger, P. M.; Chidsey, C. E. D. J. Am. 
Chem. Soc. 1995, 117, 3145-3155.
[27] Linford, M. R.; Chidsey, C. E. D. J. Am. Chem. Soc. 1993, 115, 
12631-12632.
[28] Tong, X.; DiLabio, G. A.; Wolkow, R. A. Nano Lett. 2004, 4, 979-983.
[29] Tong, X.; DiLabio, G. A.; Clarkin, O. J.; Wolkow, R. A. Nano Lett. 2004, 4, 
357-360. 
[30] Soler, J. M.; Artacho, E; Gale, J. D.; García, A; Junquera, J.; Ordejón, P.; 
Sánchez-Portal, D. J. Phys.: Condens. Matter 2002, 14, 2745-2779.
[31] Hohenberg, P.; Kohn. W. Phys. Rev. 1964, 136, 864-871.
[32] Martin, R. M. Electronic Structure, basic theory and practical methods 
2004 (Cambridge).
[33] Kohn, W.; Sham, L. J. Phys. Rev. 1965, 140, 1133-1138.
[34] Leach, A. R. Molecular Modelling: principles and applications 2001 (Prentice Hall).
[35] Perdew, J. P.; Zunder, Phys. Rev. B 1981, 23, 5075.
[36] Perdew, J. P.; Wang, Y. Phys. Rev. B 1992, 45, 13244.
[37] Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
[38] Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Let. 1996, 77, 3865.
[39] Perdew, J. P.; Wang, Y. Phys. Rev. B 1991, 44, 13298-13307.
[40] Monkhorst, H. J.; Pack, J. D. Phys. Rev. B 1976, 13, 5188.
[41] Segall, M. D.; Lindan, P. L. D.; Probert, M. J.; Pickard, C. J.; Hasnip, P. J.; Clark, S. J.; Payne, M. C. J. Phys.: Condens. Matter 2002, 14, 2717.
[42] Grosso, G.; Parravicini, G. P. Solid State Physics 2000 (ACADEMIC PRESS).
[43] Kittel, C. Introduction to Solid State Physics 1996 (New York: Wiley).
[44] Goringe, C. M.; Bowler, D. R.; Hernandez, E. Rep. Prog. Phys. 1997, 60, 1447.
[45] Ordejon, P. Comput. Mater. Sci. 1998, 12, 157.
[46] Ordejon, P.; Drabold, D. A.;Grumbach, M. P.; Martin, R. M. Phys. Rev. B 1993, 48, 14 646.
[47] Sankey, O. F.; Niklewski, D. J. Phys. Rev. B 1989, 40, 3979.
[48] Rappe, A. M.; Rabe, K. M.; Kaxiras, K.; Joannopoulos, J. D. Phys. Rev. B 1990, 41, 1227.
[49] Lin, J. S.; Qteish, A.; Payne, M. C.; Heine, V. Phys. Rev. B 1993, 47, 4174.
[50] Lin, J. S.; Payne, M. C.; Heine, V.; McConnell, J. D. G. Phys. Chem. Minerals 1994, 21, 150.
[51] Lee, M. H. Advanced Pseudopotentials, Ph.D. Thesis 1995 (Cambridge University, U.K.).
[52] Papaport, D. C. The Art of Molecular Dynamics Simulation 2004 (Cambridge).
[53] Molecular dynamics. (2007, June 22). In Wikipedia, The Free Encyclopedia., from http://en.wikipedia.org/wiki/Molecular_dynamics
[54] Woodcock, L. V. Chem. Phys. Lett. 1971, 10, 257-261.
[55] Nose, S. J. Chem. Phys. 1984, 81, 511.
[56] Nose, S. Mol. Phys. 1984, 52, 255.
[57] Hoover, W. G. Phys. Rev. A 1985, 31, 1695.
[58] Car, R.; Parrinello, M. Phys. Rev. Lett. 1985, 55, 2471.
[59] http://www.uam.es/departamentos/ciencias/fismateriac/siesta/
[60] Troullier, N.; Martins, J. L. Phys. Rev. B. 1991, 43, 1993.
[61] Kleinman, L.; Bylander, D. M. Phys. Rev. Lett. 1982, 48, 1425.
[62] Huzinaga, S.; et. al. Gaussian Basis Sets for Molecular Calculations 1984 (Berlin: Elsevier).
[63] Hoffmann, R. Solid and Surface: A Chemist’s View of Bonding in Extended Structure 1988 (New York: VCH).
[64] Burdett, J. K. Chemical Bonding in Solids 1995 (New York: OXFORD UNIVERSITY PRESS).
[65] 周文祺 碳氟化物在Ag(111)表面與其在Si(100)表面吸附反應之理論研究 2003 (淡江大學化學系碩士論文).
[66] Atkins, P. W. Molecular Quantum Mechanics 1997 (New York: OXFORD UNIVERSITY PRESS).
[67] Noid, D. W.; Koszykowski, M. L.; Marcus, R. A. J. Chem. Phys. 1977, 67, 404-408.
[68] Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1981, 74, 4872-1981.
[69] Berendsen, H. J.; Postma, J. P. M.; Gunsteren, W. F. Van; Hermans, J. in Intermolecular Forces, edited by B. Pullman 1981, 331-342 (Reidel, Dordrecht).
[70] Guilot, B. J. Chem. Phys. 1991, 95, 1543-1551.
[71] Unger, L. W.; Scherer, N. F.; Voth, G. A. Biophysical Journal 1997, 72, 5-17.
[72] Chelli, R; Carkini, Gianni; Procacci, P.; Righini, R.; Califano, S. J. Chem. Phys. 2000, 113, 6851-6863.
[73] Meng, S.; Xu, L. F.; Wang, E. G.; Gao, Shiwu Phys. Rev. Lett. 2002, 89, 176104-1.
[74] Lekka, C. E.; Mehl, M. J.; Bernstein, N.; Papaconstantopoulos, D. A. Phys. Rev. B 2003, 68, 035422.
[75] Suzuki, S.; Kawamura, K. J. Phys. Chem. B 2004, 108, 13468-13474.
[76] Gaigeot, M. P.; Sprik, M. J. Phys. Chem. B 2003, 107, 10344-10358.
[77] Gaigeot, M. P.; Vuilleumier, R.; Sprik, M.; Borgis, D. J. Chem. Theory Comput. 2005, 1, 772-789.
[78] Ramires, R. W. The FFT Fundamentals and Concepts 1985 (New Jersey: Tektronix Inc.).
[79] McQuarrie, D. A. Statistical Mechanics 1976 (Mei Ya Publications Inc.).
[80] Lide, B. R. CRC Handbook of Chemistry and Physics, 81st ed. 2000 (CRC, Boca Raton, FL).
[81] Scott, A. P.; Radom, L. J. Phys. Chem. 1996, 100, 16502-16513.
[82] NIST(National Institute of Standards and Technology) chemistry webbook,   
Number 69, June 2005., from http://webbook.nist.gov/chemistry/ 
[83] Ciraci, S.; Butz, R.; Oellig, E. M.; Wagner, H. Phys. Rev. B 1984, 30, 711-720.
[84] Kobayashi, H.; Edamoto, K.; Onchi, M.; Nishijima, M J. Chem. Phys. 1983, 78, 7429.
[85] Chanbal, Y. J.; Raghavachari, K. Phys. Rev. Lett. 1984, 53, 282-285.
[86] Tully, J. C.; Chanbal, Y. J.; Raghavachari, K.; Bowman, J. M.; Lucchese, R. R. Phys. Rev. B 1985, 31, 1184-1186.
[87] Niwano, M.; Shinohara, M.; Neo, Yoichiro; Yokoo, K. Appl. Surf. Sci. 2000, 162, 111-115.
[88] Hofer, W. A.; Fisher, A. J.; Lopinski, G. P.; Wolkow, R. A. Chem. Phys. Lett. 2002, 365, 129-134.
[89] Avouris, Ph.; Walkup, R. E.; Rossi, A. R.; Akpati, H. C.; Nordlander, P.; Shen, T.-C.; Abeln, G. C.; Lyding, J. W. Surf. Sci. 1996, 363, 368-377.
[90] Pitters, J. L.; Piva, P. G.; Tong, X.; Wolkow, R. A. Nano Lett. 2003, 3, 1431-1435.
[91] Patitsas, S. N.; Lopinski, G. P.; Hul’ko, O.; Moffatt, D. J.; Wolkow, R. A. Surf. Sci. 2000, 457, L425-L431.
[92] Alavi, S.; Rousseau, R.; Lopinski, G. P.; Wolkow, R. A.; Seideman, T. Faraday Discuss 2000, 117, 213-229.