title page

Abstract

Contents

Chapter 1. Introduction 17

References 24

Chapter 2. Study of the adsorption and decomposition of H20(이미지참조) on Ge(100) 29

2.1. Introduction 30

2.2. Experimental section 31

2.3. Results and discussion 32

2.4. Conclusion 41

References 42

Chapter 3. Cyclo-addition reaction of Lewis acidic molecule; AlCl3 44

3.1. Introduction 45

3.2. Experimental section 46

3.3. Results and discussion 48

3.4. Conclusions 59

References 60

Chapter 4. Adsorption structure and reaction mechanism of purine on Ge(100) studied by scanning tunneling microscopy in real time and by ab initio calculation 62

4.1. Introduction 63

4.2. Experimental section 66

4.3. Results and discussion 67

4.4. Conclusions 82

References 83

Chapter 5. Reaction of amino acids on the Ge(100) surface 90

5.1. Introduction 91

5.2. Experimental section 93

5.3. Results and discussion 97

5.3.1. Theoretical calculations of glycine on Ge(100) 97

5.3.2. IR study of glycine on Ge(100) 104

5.3.3. IR study of histidine on Ge(100) 113

5.3.4. STM study of histidine on Ge(100) 120

5.4. Conclusions 131

References 132

Summary 134

Acknowledgement 136

Curriculum vitae 140

Table 5.1. IR peak assignments for glycine on Ge(100). 105

Table 5.2. IR peak assignment imidazole on Ge(100) [21,22] 116

Figure 1.1. Bulk diamond structure of crystalline silicon and germanium. Each atom is tetrahedrally bonded to four nearest neighbors 18

Figure 1.2. Energy level diagram representing (a)four degenerate dangling-bonds (DB) from two bulk-like surface atoms, (b)dimer-bond formation depicted by a σ-bonding level and a σ*-bonding level, with two dangling-bonds remaining on each surface... 19

Figure 1.3. The filled state STM image (Vs = -2.0 V, It = 0.1 nA, 15 x 15 nm2 (이미지참조)) of room temperature clean Ge(100) surface. 22

Figure 2.1 Filled-state STM images (50 x 50 nm2, Vs = -1.6 V, It = 0.2 nA) of the Ge(100) surface after exposure to (a) 1.0 L, (b) 250 L, (c) 450 L and (d) 1100 L of H20. (SOD, singly occupied dimer; DOD, doubly occupied dimer)(이미지참조) 33

Figure 2.2. Filled-state STM images (12 x 12 nm2, Vs = -16 V, It = 0.2 nA) and structural diagrams showing (a) SODs and (b) DODs. 34

Figure 2.3. STM images of H2O on Ge(100) at bias voltages of (a) Vs = -1.6 V, and (b)-0.8 V(이미지참조). 35

Figure 2.4. Theoretically calculated filled-state (-1.6 V) STM images: (a) a water molecule adsorbed on a Ge(100) surface, and (b) dissociated H and OH on Ge(100). The top view of the surface is superimposed on each simulated image. 37

Figure 2.5. Sequential STM images of the same region showig the structure transformation of the H2O-adsorbed Ge(100) surface. SODs attributed to the adsorption of water are shown in (a), which are transformed to DODs in (b). The... 40

Figure 3.1. Filled-state STM images (Vs = -2.0 V, It = 0.1 nA, 20 x 20 nm2 ) of AICI3 adsorbed Ge(100) surface; (a) 0 ML, (b) 0.1 ML, (c) 0.3 ML and (d) 0.45 ML. The figures at the bottom are enlarged STM images of A and B feature. 49

Figure 3.2. STM images (7 x 7 nm2, It = 0.1 nA) of AICl3 on Ge(100) at bias voltages of (a) Vs = -2.0 V and (b) -1.2 V(이미지참조). 50

Figure 3.3. Sequential STM images (10 x 10 nm2, Vs = -2.0 V, It = 0.1 nA) of the same region showig the structure transformation of feature A. The AICl3 adsorbed surface dimer enclosed by white box is transformed to darker protrusion enclosed by yellow box. 51

Figure 3.4. Sequential STM images (5 x 5 nm2, vs = -2.0 V, It = 0.1 nA) of the same region showing the structure transformation of the AICI3 adsorbed Ge(100) surface. 52

Figure 3.5. Energy minimized adsorption configurations of AICI3 on Ge(100). 53

Figure 3.6. High resolution photoemission spectra of Ge 3d (upper panel) and CI 2p (lower panel) for adsorbed AICI3 on Ge(100) at room-temperature. (a) and (d) are the core level spectra of clean Ge(100) surface. (b) and (e) are the spectra of saturated... 55

Figure 4.1. Lewis structure of purine. 65

Figure 4.2. STM images (25 x 25 nm2, Vs = -2.0 V, It = 0.2 na) of the Ge(100) surface after exposure to (a) 0.01 ML, (b) 0.08 ML, (c) 0.18 ML and (d) 0.25 ML of purine(이미지참조). 68

Figure 4.3. Filled-state STM images (20 x 16 nm2, Vs = -2.0 V, It = 0.2 nA) of 0.01 ML purine on Ge(100). Three types of bright features attribute to different adsorption structures of purine molecules are enlarged and shown in the right hand... 70

Figure 4.4. Possible adsorption structures of purine on Ge(100) and their adsorption energies; (a) GeN(1) dative bonding, (b) Ge-N(3) dative bonding, (c) Ge-N(7) dative bonding, (d) double dative bondimg through atoms N(1) and N(3), (e) double... 71

Figure 4.5. (a) Experimental and (b) theoretically calculated STM images of purine on Ge(100). 72

Figure 4.6. Filled-state STM images (14 x 14 nm2, Vs = -2.0 V, It = 0.2 nA) of 0.01 ML purine on Ge(100)(이미지참조). 73

Figure 4.7. Configurational changes of adsorbed molecules on Ge(100): (a) from feature A to feature B, (b) from feature B to feature C. 75

Figure 4.8. Filled-state STM images (20 x 20 nm2, Vs = -2.0 V, It = 0.2 nA) of the Ge(100) surface with purine coverage of 0.15 ML (a). The enlarged STM image of the white circle is shown in (b). The STM image after annealing the purine... 76

Figure 4.9. Isotopic hydrogen exchange reaction mechanism of purine in aqueous solution [74-81]. 78

Figure 4.10. Suggested adsorption mechanism of purine on Ge(100). 81

Figure 5.1. Lewis structure of glycine. 97

Figure 5.2. Possible adsorption structures of glycine on Ge(100) using a single-dimer cluster: (a) Ge-O dative bonding through carbonyl oxygen, (b) Ge-O dative bonding through hydoxyl oxygen, (c) O-H dissociation, (d) Ge-N dative bonding... 98

Figure 5.3. Critical points on the potential energy surfaces for NH- and OH- dissociation pathways. 99

Figure 5.4. Critical points on the potential energy surface for interdimer, intrarow NH- and OH-dissociation of glycine on Ge(100). 101

Figure 5.5. Cumulative infrared spectra of glycine on Ge(100) at 310 K after dosing at torr continuously for (a) 29 minutes, (b) 36 minutes, (c) 42 minutes, (d) 48 minutes, (e) 54 minutes, (f) 60 minutes, (g) 67 minutes, and (h) 74 minutes at... 104

Figure 5.6. Characteristic infrared peak areas plotted as a function of exposure at 310 K for (a) the N-dative-bonded NH2(이미지참조) bending mode and (b) v(Ge-H), v(C=O) and v(C-O) modes. 110

Figure 5.7. Lewis structures of histidine and its pirmary constituents. 113

Figure 5.8. Expected dative bonded adsorption structure for imidazole on Ge(100). 115

Figure 5.9. Infrared spectrum of saturation coverage of imidazole on Ge(100) at room temperature. 116

Figure 5.10. Infrared spectrum of saturation coverage of (a) glycine, (b) imidazole and (c) histidine on Ge(100) at room temperature. 118

Figure 5.11. Filled-state STM images (30 x 30 nm2, Vs = -2.0 V, It = 0.1 nA) of the clean Ge(100) surface(이미지참조). 120

Figure 5.12. (a) Filled-state STM images (8.5 x 8. nm2, Vs = -2.0 V, It = 0.1 nA) of Ge(100) after adsorption of 0.01 monolayers (ML) of histidine at 380 K and (b) structural diagrams of histidine on Ge(100)(이미지참조). 121

Figure 5.13. Filled-state STM images (8.5 x 8.5 nm2, Vs = -2.0 V, It = 0.1 nA) of Ge(100) after adsorption of 0.01 monolayers (ML) of histidine at 380 K and structural diagrams of histidine on Ge(100). 122

Figure 5.14. Filled-state STM images (Vs = -2.0 V, It = 0.1 nA) of the Ge(100) surfaces with histidine coverages of (a) 0.01 ML, (b) 0.1 ML, and (c) 0.2 ML. (d) Here, the area enclosed by the blue box in (c) is enlarged. L-Histidine is exposed... 124

Figure 5.15. STM images of histidine on Ge(100) at bias voltages of (a) Vs =-2.0 V, (c) +1.0 V, and (d) +2.0 V. (b) Cross-section line profile along [110](이미지참조) in (a). L-Histidine is exposed at 380 K. And all STM images are taken at room temperature. 125

Figure 5.16. STM images (12 x 12 nm2, It = 0.1 nA) at bias voltages of (a) Vs = -2.0 V and (b) +1.0 V and theoretically calcurated STM images at (c) Vs = -2.0 V and (d) + 1.0 V(이미지참조). 130

Ge(100) 표면 위에서 H₂0의 흡착과 분해에 관한 연구

Ge(100) 표면 위에서 물의 흡착과 분해를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM)과 전자 밀도 이론 (Density-functional theory, DFT)을 통하여 연구 했다. 주사 터널링 현미경으로 Ge(100) 위에 흡착된 H₂O의 구조를 분석한 결과 분자 상태로 흡착한 H₂O와 H-OH의 결합이 끊어진 채 흡착한 형태를 관찰하였다. 분자 상태로 흡착한 구조에 있어서는 H₂O의 O atom이 상대적으로 전자가 작은 아래 Gc 원자에 전자를 주어 결합을 형성하게 된다. 분해 흡착 구조에 있어서는 H20 분자가 O와 OH로 분해되어 흡착 한 뒤 H-Ge-Ge-OH 구조를 형성하게 된다. 실시간 STM 관찰을 통해서 분자 흡착 된 H₂O가 분해되는 것을 확인하였다. DR 계산 결과에서는 분해 흡착된 구조가 분자 흡착 된 구조보다 더 안정하게 나타난다. 시뮬레이션 된 SIM image는 실험결과와 아주 잘 일치한다.

Ge(100) 표면위에 Lewis acid 원자인 AlCl₃의 cvclo addition 반응

Ge(100) 표면 위에서 AlCI₃의 흡착과 분해를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM)과 전자 밀도 이론 (Density-functional theory, DFT) 그리고 광전자분광분석 (Hi호-Resolution Photoemission Spectroscopy, HRPES)를 통하여 연구 했다. STM 과 Ge 3d 그리고 Cl 2p core-level 스펙트럼 분석을 통해서 AlCl₃가 Ge 표면 위에 흡착할 때 cyclo-addition 반응으로 흡착하며 Cl-Ge 결합과 AlCl₂-Gc 결합을 형성하는 것을 밝혔다. 그리고 DFT 계산을 통해서 AlCl₃의 흡착구조가 변화하는 것을 설명하였다.

Ge(100) 표면위에 purine의 홉착 구조와 흡착 과정에 관한 연구

Ge(100) 표면 위에서 purine의 흡착과 분해를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM) 과 전자 밀도 이론 (Density-functional theory, DFT) 을 통하여 연구 했다. 우리는 상온에서 purine 에 있는 두 개의 N 원자가 전자 친화적인 아래 Ge 원자에 전자를 주어서 결합을 형성하는 것을 관찰하였다. N이 전자를 주게 됨으로써 발생하는 양전하를 안정화 하기 위해서 a위치에 있는 C 원자가 활성화 되서 H원자가 떨어져 나가게 된다. 이 흡착 과정은 흡식 화학에서 이종 고리식 분자의 "동위원소교환" 반응과 아주 유사하다. 흡식 화학에서 C(8) 원소의 활성화하기 위한 물의 역할을 진공에서 는 Ge 원자의 dangling bond가 대신 해주게 된다.

Ge(100) 표면위에 amino acid의 흡착 구조와 흡착 과정에 관한 연구

G(100) 표면 위에서 amino acid의 흡착과 분해를 주사 터널링 현미경(Scanning Tunneling Microscopy, STM)과 퓨리에 변환 적외선 분광기(Mu1tiple Internal Re리ection Fourier Transform infrared, MIR-FTIR) 그리고 전자 밀도 이론 (Density-functional theory, DFT)을 통하여 연구 했다. 가장 간단한 amino acid인 glycine을 연구한 결과 -COOH 작용기의 OH가 분해 흡착 함으로써 표면에 흡착 한다는 것이 밝혀졌다. IR 스펙트럼 틀을 분석한 결과 한가지 이상의 흡착구조가 있다는 것이 밝혀졌는데, 가장 대표적인 것이 -MH2 작용기의 N이 전자를 주거 결합을 하는 것이다. 보다 복잡한 결과인 histidine에 관해서 연구해 본 결과 histidine은 side goup의 imidazole 의 N 원자가 아래 Ge 원자에 전자를 주는 결합과 OH 분해 결합으로 표면에 흡착하는 것을 확인하였다. 또한, STM 실험으로 특정한 조건에서 histidine 분자들은 넓은 영역에서 균일한 배열을 한다는 것을 밝혔다.