本篇論文透過第一原理分子動態模擬(DFT-based molecular dynamic simulation)來探討(1) 碳氫、碳鹵化合物透過金屬表面催化的碳鹵鍵解離及碳碳鍵偶合反應機制研究。並結合本實驗室所開發的表面反射式紅外光振動光譜(Reflected infrared adsorption spectroscopy)與時頻解析(time-frequency analysis)等光譜模擬工具來觀察分子在反應過程中的光譜變化。(2) 此外我們也透過局域態密度(Local density of state)來產生非彈性電子穿隧光譜(Inelastic electron tunneling spectroscopy)，研究STM-tip穿隧電子所誘導的CO脫附反應。

　　在論文第一部分，我們成功透過分子動態模擬進行 propargyl bromide (HC≡C(β)-C(α)H2Br(ads))與 propynyl iodide (CH3-C(β)≡C(α)-I(ads))在Ag(111)表面上的碳鹵鍵解離吸附反應，並觀察到銀表面與吸附分子在過渡態時可生成碳銀的鍵結，提升銀表面原子與吸附分子之間的電子非局域化性來誘發碳鹵鍵的解離。催化反應前後的光譜可透過短時間時頻解析(short-time Fourier transform analysis : STFT)的方式直接獲得催化反應前後的光譜訊號，並得到與實驗一致的結果。接著，我們更進一步探討不同混成軌域之吸附分子(methyl acetylide  (CH3-C(β)≡C(α)(ads)) and ethyl (H3C(β)-C(α)H2(ads)))在銀表面溫度增溫過程中的擴散能力，追蹤不同溫度下的反應動態。結果顯示，Cα為sp混成的methyl acetylide由於其與表面的鍵結較強(π-back donation效應)，因此相較於sp3混成的ethyl需要較高的表面溫度方可進行擴散(500K and 200K)導致較高的碳碳鍵偶合反應溫度。

　　在論文第二部分，我們藉由加入STM (Ag5 cluster tip)進行CO在銀表面上STM針尖誘導的分子動態研究。藉由分子動態模擬我們觀察到STM會誘導表面上CO分子進行分子旋轉運動並且形成CO-terminated Ag5 cluster tip。同時，我們搜集動態過程中的局域態密度(local density of state)變化來產生非彈性電子穿隧光譜　(Inelastic electron tunneling spectroscopy) ，並且搭配時頻解析工具成功觀察到CO分子在STM針尖誘導下frustrated rotation與CO stretching之間的非簡諧偶合效應(anharmonic coupling)。最後，我們進一步使用CO-terminated Ag5 cluster tip來模擬CoPz (Cobalt porphyrazin)分子在Ag(110)表面上的非彈性電子穿隧光譜，並成功觀察到與實驗相符合的CO frustrated translation位移訊號。

Density functional theory (DFT)-based molecular dynamic simulation in combination with time-resolved simulated reflected infrared adsorption spectroscopy is performed to study 1) the dynamic behavior of catalytic reaction for carbon-halogen dissociation and carbon-carbon self-coupling reaction on metal surface. 2) In addition, we performed our new methodology to generate the inelastic electron tunneling spectroscopy by collecting the dynamic trajectories of local density of state (LDOS) to investigate the STM-tip induced CO desorption reaction.  

In the part I of my thesis, firstly, we successfully investigate the adsorption behaviours of carbon-halogen rupture reaction for propargyl bromide (HC≡C(β)-C(α)H2Br(ads)) and propynyl iodide (CH3-C(β)≡C(α)-I(ads)) on Ag(111) surface by using DFT-based MD simulation. We found that the carbon-Ag interaction can induce the weakening of carbon-halogen bond due to the delocalization effect between the adsorbed molecule and Ag surface at transition state. In addition, the time-resolved spectra constructed by short-time Fourier transform (STFT) illustrate that the evolution of all the vibrational modes along the carbon-halogen dissociation reaction and have a good agreement with experimental RAIRS results. Secondly, we investigated the thermally induced diffusion processes of different hybridization state of Cα that is, methyl acetylide  (CH3-C(β)≡C(α)(ads) : sp hybridization of  Cα atom) and ethyl (H3C(β)-C(α)H2(ads) : sp3 hybridization of Cα atom), respectively. Our results indicate that the CH3-C(β)≡C(α)(ads) is very stable due to the strong π-back donation effect as methyl acetylide adsorbed on Ag(111) surface. Therefore the methyl acetylide will have higher diffusion temperature than that of ethyl on the same surface leading to the higher reaction temperature for the Cα-Cα self-coupling reaction.

In the part II of my thesis, the DFT-based MD simulation with a Fourier transform of the derivative of local density of states autocorrelation function is introduced to generate the inelastic electron tunnelling spectra for evaluating he effect of STM-tip on adsorption dynamics for CO(ads) on the Ag(110) surface. Based on dynamic results, the STM-tip can induce the desorption process of CO on Ag(110) to produce a functionalized STM-tip (CO-terminated Ag5 cluster tip). By using the STFT, the anharmonic coupling between the frustrated rotation and CO stretching mode can be investigated. Finally, the CO-terminated Ag5 cluster tip can be further used to scan the CoPz (Cobalt porphyrazin) on Ag(110) to generate the local IETS spectrum. Our new methodology successfully observe the frustrated translation of CO vibration  senses the spatially varying potential energy landscape of the molecule and its surroundings and have a good agreement with experimental IETS results.

Contents
Chapter 1. Introduction 1
1-1 Temperature induced carbon-halogen dissociated reaction and Cα-Cα self-coupling reactions ………………………………………………………………………………………………4
1-2 STM-tip induced CO desorption reaction and inelastic electron tunneling spectra 9
Chapter 2. Theoretical background 17
2-1. Electronic structure calculation 17
2-1-1. Born-Oppenheimer approximation 18
2-1-2. Hartree Fock theory 18
2-1-3. Density functional theory 22
2-1-4. Exchange-correlation functions 24
2-1-5. Pseudopotential 26
2-2. Molecular dynamics simulations 29
2-2-1. Equations of motions 31
2-2-2. Ensemble 35
2-2-3. Thermostat 38
2-3. Siesta program 42
2-3-1. Electron Hamiltonian 43
2-3-2. Basis set 43
2-3-3. Electron Density 46
2-3-4. VDW-functional 46
References 48
Chapter 3. Simulated time-resolved vibrational spectra 49
3-1. Fermi-Golden rule 49
3-2. Fermi–Golden rule on absorption of radiation 54
3-3. Simulated inelastic electron tunneling spectrum (IETS) 57
3-3-1. Fermi-Golden rule on tunneling process 59
3-3-2. Simulated IETS spectrum 68
3-4. Short-time Fourier transform (STFT) 73
References 77
Chapter 4. Temperature induced carbon-halogen dissociated reaction and Cα-Cα self-coupling reactions 78
4-1. Introduction 78
4-2. Computational method 82
4-3. C-X rupture of C3H3X groups adsorbed on Ag(111) surface 88
4-3-1. Adsorption geometries and reaction dynamics of C3H3X adsorption onto Ag(111) 88
4-3-2. Calculated infrared spectra and the spectrogram of C3H3X on Ag(111) 96
4-4. C-C self-coupling of adsorbed on Ag(111) surface 99
4-4-1. Reaction dynamics of C2H5I and C3H3I adsorbed on Ag(111) 99
4-4-2. Temperature induced diffusion dynamics of the adsorbed on the Ag(111) surface 111
4-4-3. C-C self-coupling reactions of the adsorbed on Ag(111) surface 113
4-5. Conclusion 119
References 121
Chapter 5. STM induced CO desorption reaction and inelastic electron tunneling spectra 123
5-1. Introduction 123
5-2. Computational method 125
5-3. Tunneling electron induced desorption of CO adsorbed on Ag(110) surface 127
5-3-1. Geometrical and electronic properties for Ag5-CO(ads) -Ag(110) by STFT analysis 127
5-3-2. Simulated IETS for Ag5-CO(ads)-Ag(110) by STFT analysis 130
5-3-3.Anharmonic coupling for Ag5-CO(ads)-Ag(110) by STFT analysis 133
5.4. The simulated point spectrum of CoPz adsorbed on Ag(110) by CO-terminated tip 136
5-5. Conclusion 142
References 143
Curriculum Vitae 145
Publications 147





List of Figures

1 1. Experiment RAIRS spectrum of (a) propargyl bromide (HC≡C(β)-C(α)H2Br(ads)) adsorption at 110K and 200K, and (b) propynyl iodide (CH3-C(β)≡C(α)-I(ads)) adsorption at 110K and 200K. 5
1 2. Schematic diagrams showing the different steps in the formation of a single bond with the STM. A tip-induced desorption reaction of CO(ads) adsorbed on Ag(110) surface. 9
1 3. The scheme diagram show that the low-frequency modes (the frustrated-translation and frustrated rotation) will couple with the high-frequency modes (C-O stretching) and to induce the desorption and diffusion of CO adsorbed on Ag(110) surface by STM experiments. 10
1 4. Point spectroscopy revealing variation of CO frustrated translation vibration over different parts of the molecule. 11
1 5. Calculated IETS curves under the NEGF method for the Cu surface + CO adsorbed system. Tip-sample distances are indicated in the insets. 12
2 1. Comparison of a wavefunction in the Coulomb and potential. The real wavefunction (red solid line) and the pseudo wavefunction (blue dashed line) match above a certain cutoff radius rc. 28
2 2. The flow chart of the molecular dynamics simulation. 31
2 3. Schematic illustration of closed system. 38
3 1. A plot of sin2(wkmt/2)/wkm2 versus wkm, show how the central peak increases as t2 and narrows as 1/t. 53
3 2. (a) The Scheme of a STM instrument. (b) Energy band diagram of a tunneling process from the tip state into the sample state with a positive bias voltage. 58
3 3. (a) Energy band structure of a tunneling process with a vibrational mode of frequency localized inside: “a” is an elastic tunneling process; “b” is an inelastic tunneling process. (b) Their corresponding I(V) curve and the second-derivative of I(V) curve (d2I/dV2). 59
3 4. Schematic representation of the tip, barrier, and sample regions with graphs of the sample potential (red line) and the tip potential (blue line). 61
3 5. The Fermi-Dirac distribution for 0K, 293K and 2000K 65
3 6. Schematic picture of tip and sample geometry, tip center r0 and the distant from the center of tip to the surface (r) defined by Tersoff and Hamann. 67
3 7. The rectangular function is shown at moving time τ=0. 75
3 8. There are four cosine functions of this signal, cos(2π10t), cos(2π25t), cos(2π50t), cos(2π100t) at different time. 75
3 9. There are four frequencies – 10, 25, 50 and 100 (1/time) – in the spectrogram. It shows the variations of frequencies over time-evolution. 76
4 1. The probable initial structural models for the carbon-halogen dissociation reaction of propynyl iodide and propagyl bromide. 89
4 2. Some possible optimized structures of HC≡C(β)-C(α)H2Br(ads) adsorbed on the Ag(111) surface 89
4 3. Some possible optimized structures of CH3-C(β)≡C(α)-I(ads) adsorbed on the Ag(111) surface 90
4 4.  The total energy trajectories of HC≡C(β)-C(α)H2Br(ads) and CH3-C(β)≡C(α)-I(ads) along the dissociative adsorption reaction process 91
4 5. The time-evolutions of (a) the C-Br and Ag-Cγ bond length along the C-Br dissociative reaction and (b) the C-I and Ag-Cβ bond length along the C-I dissociative reaction. 93
4 6. The time-evolutions of (a) the Cα-Cβ and Cβ-Cγ bond length of HC≡C(β)-C(α)H2Br(ads) along the C-Br dissociative reaction and (b) the Cα-Cβ and Cβ-Cγ bond length of CH3-C(β)≡C(α)-I(ads) along the C-I dissociative reaction. 94
4 7. DOS projected onto the Cγ atom (light blue line), Br atom (red line) and surface Ag atom (black line). From top to button: the PDOS of HC≡C(β)-C(α)H2Br(ads) for the reactant and transition state along the C-Br dissociation reaction. 95
4 8. DOS projected onto the Cβ atom (light blue line), I atom (red line) and surface Ag atom (black line). From top to button: the PDOS of CH3-C(β)≡C(α)-I(ads) for the reactant and transition state along the C-Br dissociation reaction. 95
4 9. The spectrogram obtained STFT-DMAF of HC≡C(β)-C(α)H2Br(ads) adsorbed on the Ag(111) surface along C-Br dissociation reaction on the Ag(111) surface 98
4 10. The spectrogram obtained STFT-DMAF of CH3-C(β)≡C(α)-I(ads) adsorbed on the Ag(111) surface along C-I dissociation reaction on the Ag(111) surface 99
4 11. Some possible optimized structures of H3C-C()≡C()(ads) and I coadsorbed on the Ag(111) surface 100
4 12. Some possible optimized structures of H3C(β)-C(α)H2(ads) and I coadsorbed on the Ag(111) surface 102
4 13. DOS projected onto the Cα atom (blue line) and Ag d states (green line). From left to right: the PDOS of I(hcpH) and H3C-C(β) ≡C(α)(ads) (hcpH-tilted) coadsorbed on the Ag(111) surface, and I(hcpH) and H3C-C(β)≡C(α)(ads) (hcpH-stand up) coadsorbed on the Ag(111) surface. For each system, the top panel shows the PDOS of the isolated subsystems, while the bottom panel refers to the H3C-C(β) ≡C(α)(ads)after adsorption. 103
4 14. DOS projected onto the Cα atom (blue line) and Ag d states (green line). From left to right: the PDOS of I(hcpH) and H3C(β)-C(α)H2(ads)(top) coadsorbed on the Ag(111) surface, and I(hcpH) and H3C(β)-C(α)H2(ads) (hcpH) coadsorbed on the Ag(111) surface. For each system, the top panel shows the PDOS of the isolated subsystems, while the bottom panel refesr to the H3C(β)-C(α)H2(ads) after adsorption. 104
4 15. a) Calculated IR spectra of H3C-C(β)≡C(α)(ads) and I(ads) coadsorbed on the Ag(111) surface at the temperature of 200K and 400K, respectively. Experimental and normal mode calculations are included for comparison. b) The populations of Ang:[ -C-C(β)≡C(α)- axis] of H3C-C(β)≡C(α)(ads) adsorbed on the Ag(111) surface during DFTMD simulation at 200K and 400K, respectively. c) The temperature difference spectrum of H3C-C(β)≡C(α)(ads) and I(ads) coadsorbed on the Ag(111) surface. 107
4 16. a) Calculated IR spectra of H3C(β)-C(α)H2(ads) and I(ads) coadsorbed on the Ag(111) surface at the temperature of 100K and 150K. Experimental and normal mode calculations are included for comparison. b) The populations of Ang:[-C()-C()- axis] of H3C(β)-C(α)H2(ads) adsorbed on the Ag(111) surface during DFTMD simulation at 100K and 150K, respectively. c) The temperature difference spectrum of H3C(β)-C(α)H2(ads)  and  I(ads)  coadsorbed on the Ag(111) surface. 109
4 17. a) The population of both H3C-C(β)≡C(α)(ads) and I(ads) projected onto the Ag(111) surface during the DFTMD simulations at 200K, 400K, 500K. b) The population of both H3C(β)-C(α)H2(ads) and I(ads) projected on the Ag(111) surface during the DFTMD simulations at 100K, 150K, 200K. 113
4 18. The proposed reaction pathways for self-coupling reaction of (a) H3C-C(β) ≡C(α)(ads) and (b) H3C(β)-C(α)H2(ads) coadsorbed on the Ag(111) surface. 115
4 19. The possible energetic profile for self-coupling reaction of H3C-C(β)≡C(α)(ads) coadsorbed on the Ag(111) surface along the hollow-bridge-hollow reaction pathway. 115
4 20. Two possible energetic profiles for self-coupling reaction of H3C(β)-C(α)H2(ads) coadsorbed on the Ag(111) surface along the top-bridge-top reaction pathway (green line) and the hollow-bridge-hollow reaction pathway (black line). 116
5 1. (a) The optimized structure for CO(ads)-Ag(110), Ag5(trigonal-tip)-CO(ads) -Ag(110), and Ag5(planar-tip)-CO(ads)-Ag(110) and corresponding electronic structures of the LDOS at the Fermi energy. (b) The simulated STM image of CO(ads)-Ag(110), (c) Ag5(trigonal-tip)-CO(ads)-Ag(110), (d) Ag5(planar-tip)-CO(ads)-Ag(110), (d) and the experimental STM result. 128
5 2.  DOS projected onto the CO molecule (green line) and their neighboring Ag surface atom (blue line) and Ag tip atom (red line). From the top to bottom: the PDOS of CO(ads) adsorbed on Ag(110), Ag5(trigonal-tip)-CO(ads) adsorbed on Ag(110) and Ag5(planar-tip)-CO(ads) adsorbed on Ag(110) 129
5 5. The spectrogram obtained by STFT analysis for the IETS spectrum for the Ag5(planar-tip)-CO(ads) adsorbed on the Ag(110) surface and corresponding structural changed during 6ps MD simulation. The two kind of frustrated rotation motions are shown in inserted Figure by SFPF analysis. 135
5 6. (a) The structure of Cobalt phthalocyaine (CoPc) and Cobalt porphyrazin (CoPz). (b) the top view for the CoPz adsorbed on the Ag(110) surface, (c) The dynamic process for the CO-terminated STM-tip scanning over the CoPz adsorbed molecule. 137
5 7. DOS projected onto the cobalt (red line), CO (green line) and Pyrrole ring (blue line) 138
5 8. The dynamic trajectories of tunneling conductance during 50K MD simulation as the CO-terminated STM-tip scanning over the CoPz adsorbed on Ag(110) surface. 139
5 9. The calculated IETS spectrum for the CO-terminated STM-tip above the cobalt (red line) and pyrrole ring (purple line). The experiment IETS are include for the comparison. 140
5 10. The time-evolutions of the C-O bond length of the CO-terminated STM-tip above the cobalt and pyrrole ring and their corresponding vibrational spectrum. 141






List of Tables

Table 4 1. Calculated adsorption energies (Eads) and corresponding structural parameters of both of the H3C-C(β)≡C(α)(ads) and H3C(β)-C(α)H2(ads) with I(ads) bonded to the 3-fold hollow site on the Ag(111) surface. 101
Table 4 2. Calculated major IR active peaks of both of the H3C-C(β)≡C(α)(ads) and H3C(β)-C(α)H2(ads) with I(ads) coadsorbed on the Ag(111) surface at various temperatures upon adsorption. Experimental RAIRS and calculated normal mode IR peaks (without scaling factor of 0.9612) are also included for comparison. 106
Table 4 3. Calculated bond lengths (Å) of the reactant, transition state and product a) along a) the hollow-bridge-hollow reaction pathway for self-coupling reaction of H3C-C(β)≡C(α)(ads) coadsorbed on the Ag(111) surface and b) the hollow-bridge-hollow reaction pathway for self-coupling reaction of H3C(β)-C(α)H2(ads) coadsorbed on the Ag(111) surface. 117
Table 5 1. Calculated major IETS active peaks for Ag5(trigonal-tip)-CO(ads) and Ag5(planar-tip)-CO(ads) adsorbed on the Ag(111) surface at 50K. Experimental IETS is also included for comparison. 133

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