My main research interest for my graduated studies was to develop new ways to control the attachment of organic molecules on the semiconductor surfaces and to understand their interfacial architecture at the atomic level. For my Ph. D thesis work, I have interested the adsorption structure and mechanism of simple gas phase molecules: $H_2$, liquid phase molecules: pyrimidine $(C_4H_4N_2)$, water $(H_2O)$, thiophene $(C_4H_4S)$ and the complex solid phase molecules: purine $(C_5H_4N_4)$, histidine $(C_6H_9N_3O_2)$. The thesis consists of five chapters. Summaries of each chapters are as follows.
Study of the adsorption and decomposition of $H_2O$ on Ge(100)
The adsorption and decomposition of water on Ge(100) have been investigated using real-time scanning tunneling microscopy (STM) and density-functional theory (DFT) calculations. The STM results revealed two distinct adsorption features of $H_2O$ on Ge(100) corresponding to molecular adsorption and H-OH dissociative adsorption. In the molecular adsorption geometry, $H_2O$ molecules are bound to the surface via Ge-O dative bonds between the O atom of $H_2O$ and the electrophillic down atom of the Ge dimer. In the dissociative adsorption geometry, the $H_2O$ molecule dissociates into H and OH, which bind covalently to a Ge-Ge dimer on Ge(100) in a H-Ge-Ge-OH configuration. The DFT calculations showed that the dissociative adsorption geometry is more stable than the molecular adsorption geometry. This finding is consistent with the STM results, which showed that the dissociative product becomes dominant as the $H_2O$ coverage is increased. The simulated STM images agreed very well with the experimental images. In the real-time STM experiments, we also observed a structural transformation of the $H_2O$ molecule from the molecular adsorption to the dissociative adsorption geometry.
Cyclo-addition reaction of Lewis acidic molecule: $AlCl_3$
The adsorption and decomposition of $AlCl_3$ on Ge(100) was studied using scanning tunneling microscopy (STM), high-resolution core-level photoemission spectroscopy (HRPES), and density functional theory (DFT) calculation. Through the analysis of STM image and Ge 3d and Cl 2p core-level spectra of $AlCl_3$on Ge(100), we found that $AlCl_3$ molecule reacts with two Ge-atoms via cyclo-addition reaction, which formed Cl-Ge and $AlCl_2$ -Ge without breaking $AlCl_3$. In addition, we used DFT calculation to confirm the proposed adsorption structure and to explain the structural transformation. To our knowledge this is the first result to elucidate the adsorption structure of acid molecule on Ge(100).
Adsorption structure and reaction mechanism of purine on Ge(100) studied by scanning tunneling microscopy in real time and by ab initio calculation
The adsorption of purine molecule onto the Ge(100) surface was investigated using both scanning tunneling microscopy (STM) and the density functional calculation. Filled-state STM image ($V_s$ = -2.0 V) of Ge(100) surface after adsorption of purine at room temperature shows the round shape protrusions between the buckled dimer rows. The STM image shows that the adsorption of purine molecule induces a local rearrangement of the Ge(100) surface from a c(4 x 2) to p(2 X 2) structure. This STM result indicates that the adsorption of purine on the Ge(100) surface proceeds preferentially via multi Ge-N dative bonding with three N atoms. We also investigated the adsorption structure using density functional calculation. We find that making three dative bonds between N-atoms of purine and down Ge-atoms is the energetically most favored adsorption structure. In this work, we find that purine molecules form a highly oriented layers on the Ge(100) surface through a Lewis acid-base type reaction. A closely packed monolayer of purine molecules having multifunctional groups (three N atoms) bonded to the surface by the Ge-N bonding may be used for the further subsequent reaction.
Reaction of Amino Acids on the Ge(100) Surface
The adsorption of amino acids on the Ge(100) surface was investigated using scanning tunneling microscopy (STM), multiple internal reflection Fourier transform infrared (MIR-FTIR) spectroscopy, and density functional theory. All amino acids consist of a carboxylic acid (-COOH) and an amino $(-NH_2)$ functional group attached to the same tetrahedral α-carbon atom. Amino acids are distinguished by the different R-groups attached to the α-carbon. The simplest amino acid is glycine, with an H as the R-group. Our MIR-FTIR results indicate that for glycine, the principal surface product is formed by OH dissociation of the carboxylic acid group. This result is consistent with calculations, which indicate that the OH dissociation product is the most thermodynamically stable. More than one surface product is evident in the spectra, however, with the results suggesting products containing nitrogen dative bonds. Based on the understanding of glycine, the effect of the side chain can be probed in more complex amino acids. Histidine $(C_6H_9N_3O_2)$, a basic amino acid, has an imidazole group as the R-group. STM results reveal the ordering of histidine molecules on the Ge(100) surface. At saturation coverage, the STM images show globally ordered arrays consisting of dumbbell shape features that are independent of the direction of the underlying dimer rows of the Ge (100) surface.
\underline{Ge(100) 표면 위에서 $H_2O$ 의 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 $H_2O$의 구조를 분석한 결과 분자 상태로 흡착한 $H_2O$ 와 H-OH의 결합이 끊어진 채 흡착한 형태를 관찰하였다. 분자 상태로 흡착한 구조에 있어서는 $H_2O$ 의 O atom 이 상대적으로 전자가 작은 아래 Ge 원자에 전자를 주어 결합을 형성하게 된다. 분해 흡착 구조에 있어서는 $H_2O$ 분자가 O 와 OH 로 분해되어 흡착 한 뒤 H-Ge-Ge-OH 구조를 형성하게 된다. 실시간 STM 관찰을 통해서 분자 흡착 된 H_2O 가 분해되는 것을 확인하였다. DFT 계산 결과에서는 분해 흡착된 구조가 분자 흡착된 구조보다 더 안정하게 나타난다. 시물레이션 된 STM image 는 실험결과와 아주 잘 일치한다.
\underline{Ge(100) 표면위에 Lewis acid 원자인 $AlCl_3$ 의 cyclo addition 반응}
Ge(100) 표면 위에서 $AlCl_3$ 의 흡착과 분해를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM) 과 전자 밀도 이론 (Density-functional theory, DFT) 그리고 광전자분광분석 (High-Resolution Photoemission Spectroscopy, HRPES) 를 통하여 연구 했다. STM 과 Ge 3d 그리고 Cl 2p core-level 스펙트럼 분석을 통해서 $AlCl_3$ 가 Ge 표면 위에 흡착할 때 cyclo-addition 반응으로 흡착하며 Cl-Ge 결합과 $AlCl_2-Ge$ 결합을 형성하는 것을 밝혔다. 그리고 DFT 계산을 통해서 $AlCl_3$ 의 흡착구조가 변화하는 것을 설명하였다.
\underline{Ge(100) 표면위에 purine 의 흡착 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. N 이 전자를 주게 됨으로써 발생하는 양전하를 안정화 하기 위해서 α위치에 있는 C 원자가 활성화 되서 H 원자가 떨어져 나가게 된다. 이 흡착 과정은 흡식 화학에서 이종 고리식 분자의 “동위원소교환” 반응과 아주 유사하다. 흡식 화학에서 C(8) 원소의 활성화하기 위한 물의 역할을 진공에서는 Ge 원자의 dangling bond 가 대신 해주게 된다.
\underline{Ge(100) 표면위에 amino acid 의 흡착 구조와 흡착 과정에 관한 연구}
Ge(100) 표면 위에서 amino acid 의 흡착과 분해를 주사 터널링 현미경 (Scanning Tunneling Microscopy, STM) 과 퓨리에 변환 적외선 분광기 (Multiple Internal Reflection Fourier Transform infrared, MIR-FTIR) 그리고 전자 밀도 이론 (Density-functional theory, DFT) 을 통하여 연구 했다. 가장 간단한 amino acid 인 glycine 을 연구한 결과 -COOH 작용기의 OH 가 분해 흡착 함으로써 표면에 흡착 한다는 것이 밝혀졌다. IR 스펙트럼 들을 분석한 결과 한가지 이상의 흡착구조가 있다는 것이 밝혀졌는데, 가장 대표적인 것이 $-NH_2$ 작용기의 N 이 전자를 주거 결합을 하는 것이다. 보다 복잡한 결과인 histidine 에 관해서 연구해 본 결과 histidine 은 side group 의 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.
