● Intrarow Adsorption Structure of Glycine on Ge(100)
The adsorption structure of glycine on Ge(100) was investigated using scanning tunneling microscopy (STM), density functional theory (DFT) calculations, and high-resolution photoemission spectroscopy (HRPES). We found a major adsorption feature of glycine on Ge(100) in the STM images. This feature appeared as a bright protrusion between two dimer rows with a dark adjacent dimer. The position of the bright protrusion located in the middle of the two dimer rows indicates a multibonding adsorption structure. The results of the theoretical calculations confirm that the adsorption structure of glycine on Ge(100) (between two possible multibonding adsorption structures) is an ‘intrarow O??H dissociated and N dative bonded structure’. In the HRPES experiments, we found an N 1s peak (at 399.5 eV) and two O 1s peaks (at 531.1 and 532.0 eV), which represent strong evidence that the adsorption configuration of glycine on Ge(100) is composed of both O-H dissociation and N dative bonding. All our STM, DFT, and HRPES results suggest that the adsorption structure of glycine molecules on Ge(100) is an ‘intrarow O??H dissociated and N dative bonded structure’.
● The Adsorption Configuration of Valine on Ge(100)
The adsorption geometry of valine molecules on Ge(100) surface were investigated by observing four core-level spectra (Ge 3d, C 1s, N 1s, and O 1s) using high-resolution photoemission spectroscopy (HRPES). In the HRPES spectrum, the binding energy of the single N 1s peak for valine adsorbed on a Ge(100) surface is similar to the energies of glycine, ammonia, or alanine adsorbed on the Ge(100) surface via N dative bonding. The O 1s signal is divided into two non-equivalent oxygen peaks, indicating that only one oxygen atom in the carboxyl group of valine participates in bonding with the Ge(100) surface. As a result, we conclude that both amine and carboxyl groups in valine molecules concurrently take part in the adsorption process on the Ge(100) surface with an ‘intrarow O??H dissociated and N dative bonded structure’. The adsorption geometry of valine is similar to that of glycine on the Ge(100) surface. This implies that the side chain effect, due to the isopropyl group in valine, does not influence the adsorption process of valine on the Ge(100) surface.
● Stereoselective Attachment via N dative bonding: S-Proline on Ge(100)
The adsorption configurations of S-proline on Ge(100) were studied using scanning tunneling microscopy (STM), density functional theory (DFT) calculations, and high-resolution photoemission spectroscopy (HRPES). We identified three adsorption structures of S-proline on Ge(100): (i) an ‘intrarow O??H dissociated and N dative bonded structure’, (ii) an ‘O??H dissociation structure’, and (iii) an ‘N dative bonded structure’. Moreover, because adsorption through the N atom of S-proline produces a new chiral center produced by N dative bonding with the surface, the adsorption configurations of S-proline on Ge(100) have either (R,S) or (S,S) chirality. Through DFT calculations, we clearly demonstrated that the adsorption configurations have (R,S) chirality with a preference for reaction at the Re face. This work presents a novel method for generating stereoselective attachment using S-proline molecules adsorbed on a Ge(100) surface.
● Nucleation of Two-dimensional Molecular Network: γ-Phenylalanine on Au(111)
The molecular self-assembly of γ-phenylalanine on a Au(111) surface was studied using scanning tunneling microscopy (STM). It is found that the self-assembly of γ-phenylalanine forms 1) the ring-shaped clusters at low coverage and 2) the 2D molecular network at one monolayer (ML) coverage. The ring-shaped clusters are mainly composed of six γ-phenylalanine molecules with flat configuration. Based on the line profile analysis, we have revealed that elliptical protrusions in both the ring-shaped clusters and the 2D molecular domain correspond to γ-phenylalanine molecules. A series of STM images obtained at submonolayer coverage show that 1) γ-phenylalanine molecules, before forming the ring-shaped clusters, continuously move on the Au(111) surface, 2) once they formed the ring-shaped clusters, they do not move on the surface, and 3) the moving γ-phenylalanine molecules play a role in extending the 2D molecular network. Moreover, we have found that the molecular linear chains in pairs are formed by the hydrogen bonding between γ-phenylalanine molecules, and then paired linear chains self-assemble to the 2D molecular network, which is governed by the hydrogen bonding in the parallel row and by combination of the hydrogen bonding and the substrate-mediated interaction in the perpendicular row.
● Direct Observation of Topographical Change due to Ultraviolet Irradiation on Collagen fibril
The morphological change of collagen fibril under UV irradiation was directly observed using atomic force microscopy (AFM). Based on the analysis of AFM images, we found that 1) The area at the gap region is more vulnerable to exposure of UV light than that at the overlap region, 2) The outer layer of the collagen fibril at the gap zone is gradually degraded during UV irradiation, and 3) The degradation level of the collagen fibril under direct UV light is a little. Even though the effect of direct UV irradiation on the collagen fibril is small, we have revealed, through the observation of topographical change using AFM, that the collagen fibril is directly degraded by UV irradiation.
● Ge(100) 표면 위에서 glycine의 intrarow 흡착 구조
Ge(100) 표면 위에서 glycine 의 흡착 구조를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM), 밀도 범함수 이론 (Density Functional Theory, DFT) 계산과 고분해능 광전자 분광법 (High-Resolution Photoemission Spectroscopy, HRPES)을 이용하여 연구하였다. 주사 터널링 현미경을 이용하여 흡착된 glycine구조를 분석한 결과 glycine은 Ge(100) 표면 위에 다중결합을 통해 흡착 한다는 것을 확인하였다. 밀도 범함수 이론계산 방법을 이용하여 glycine이 Ge(100) 표면 위에서 흡착될 수 있는 두 가지 가능한 다중 결합 중 “intrarow O-H dissociated and N dative bonded structure”가 더 안정한 흡착 구조임을 밝히었다. 또한 고분해능 광전자 분광법을 이용하여 Ge(100) 표면 위에서 glycine 의 흡착 구조가 “intrarow O-H dissociated and N dative bonded structure”임을 다시 한번 규명하였다.
● Ge(100) 표면 위에서 valine 의 흡착 구조
Ge(100) 표면 위에서 valine 의 흡착 구조를 고분해능 광전자 분광법 (High-Resolution Photoemission Spectroscopy, HRPES)을 통하여 연구하였다. valine 은 Ge(100) 표면에 glycine 과 동일한 구조인 “intrarow O-H dissociated and N dative bonded structure”로 흡착한다는 것을 밝히므로서, valine 분자의 비활성 isopropyl 겉사슬은 Ge(100) 표면과 어떠한 상호작용도 하지 않음을 규명하였다.
● N dative bonding을 통한 입체선택적 흡착: Ge(100) 표면 위에서 S-proline
Ge(100) 표면 위에서 S-proline의 흡착 구조를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM), 밀도 범함수 이론 (Density Functional Theory, DFT) 계산과 고분해능 광전자 분광법 (High-Resolution Photoemission Spectroscopy, HRPES)을 이용하여 연구하였다. 주사 터널링 현미경을 이용하여 흡착된 S-proline구조를 분석한 결과 다음과 같이 총 3가지 흡착 구조를 확인하였다: (i) ‘intrarow O??H dissociated and N dative bonded structure’, (ii) ‘O??H dissociation structure’과 (iii) ‘N dative bonded structure’. 또한, S-proline의 N 원자를 통한 흡착은 새로운 chiral center를 만드므로, Ge(100) 표면 위에서 S-proline의 흡착구조는 (R.S) 또는 (S,S) chirality를 갖게 된다. 밀도 범함수 이론 계산 방법을 이용하여, S-proline이 Ge(100) 표면에 흡착 할 때는 (R,S) chirality 갖고 흡착한다는 것을 규명하였다.
● 2차원 분자 네트워크 형성: Au(111) 표면 위에서 γ-phenylalanine
Au(111) 표면 위에서 γ-phenylalanine의 분자 자기조립을 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM)을 이용하여 연구하였다. 주사 터널링 현미경을 이용하여 γ-phenylalanine의 분자 자기조립은 1) 낮은 coverage에서는 반지모양의 cluster들을 형성하고, 2) 1 monolayer coverage에서는 2차원 분자 네트워크를 형성한다는 것을 확인하였다. line pro-file 분석을 통해 반지모양의 cluster와 2차원 분자 네트워크를 구성하고 있는 타원형 protru-sion들이 γ-phenylalanine 분자들과 일지 한다는 것을 밝히었다. 또한 submonolayer coverage에서 연속적인 STM 이미지를 관찰할 결과, 1) cluster를 형성하지 않은 γ-phenylalanine 분자는 계속적으로 움직이고 있고, 2) 형성된 반지모양의 cluster는 표면위에 고정되어 있으며, 3) 움직이는 γ-phenylalanine 분자들은 2차원 분자 네트워크를 성장시키는 역할을 한다는 것을 규명하였다. 또한 분자 선형 체인은 γ-phenylalanine 분자들의 수소결합에 의해 쌍으로 생성되고, 쌍을 이룬 선형 체인은 2차원 분자 네트워크로 자기조립한다. 이러한 2차원 분자 네트워크의 평행한 열은 수소결합에 의해 생성되고, 수직한 열은 수소결합과 기질에 의해 중재된 상호작용(substrate-mediated interaction)의 조합에 의해 형성된다는 것을 확인하였다.
● Collagen fibril에 자외선 조사 의한 구조적 변화의 직접적인 관찰
자외선 조사에 의한 collagen의 구조적 변화를 atomic force microscopy (AFM)을 이용하여 직접적으로 관찰하였다. AFM 이미지 분석을 통해, 다음과 같은 현상을 발견하였다. 1) gap지역이 overlap지역보다 자외선에 의해 영향을 받기 쉽고, 2) 자외선 조사 동안 gap 지역에 있는 collagen fibril의 최외각 막은 점차적으로 분해되고, 3) 자외선 조사에 의한 collagen fibril의 분해정도는 적다는 것을 확인하였다. 비록 직접적인 자외선에 의한 영향은 적지만, AFM을 이용한 구조적 변화의 관찰을 통해서 우리는 collagen fibril이 자외선 조사에 의해 직접적으로 분해된다는 것을 밝히었다.
