Title

Manipulation and Self-Assembly of Molecules using Scanning Tunneling Microscopy

Alternative Title

주사 터널링 현미경을 이용한 분자의 조작과 자기조립 연구

DGIST Authors

Seo, Jungpil ; Jeong, Yongchan ; Kim, Hyunmin

Advisor

서정필

Co-Advisor(s)

Hyunmin Kim

Issued Date

2020

Awarded Date

2020-02

Citation

Yongchan Jeong. (2020). Manipulation and Self-Assembly of Molecules using Scanning Tunneling Microscopy. doi: 10.22677/Theses.200000281835

Type

Thesis

Description

Scanning tunneling microscopy, Manipulation of molecules, Molecular self-assembly, Ni-phthalocyanine, Essential amino acids

Table Of Contents

Ⅰ. Introduction 1
1.1 Manipulation of molecules at the atomic level using STM tip 1
1.1.1 Mechanisms of STM tip-induced manipulation 1
1.1.2 Paper reviews and motivations 5
1.2 Self-assembly of amino acids using STM 8
1.2.1 Molecular self-assembly 9
1.2.2 Amino acids 12
1.2.3 Paper reviews and motivations 14

II. Methods 17
2.1 Scanning tunneling microscopy (STM) 17
2.1.1 Basic theory for STM Principle 17
2.1.2 STM system 22
2.1.3 Experimental methods 23
2.2 Density functional theory (DFT) 24
2.2.1 Kohn-Sham equations 25
2.2.2 Exchange-correlation functionals 26
2.2.3 Calculation details 28

Section 1. Manipulation of molecules using STM tip on Au (111)
III. STM tip-induced chemical reaction of Ni-phthalocyanine 31
3.1 Molecular structure and properties of Ni-phthalocyanine 31
3.2 STM measurement 31
3.2.1 Diffusivity of Ni-phthalocyanine on Au (111) 32
3.2.2 Ni-phthalocyanine anchoring on Au (111) 34
3.2.3 dI/dV spectroscopy in anchored Ni-phthalocyanine 36
3.2.4 Observation of intact Ni-phthalocyanine 38
3.3 DFT calculation 39
3.4 Conclusion 43

IV. Franck-Condon-like excitation of Ni-phthalocyanine 45
4.1 STM measurement 45
4.1.1 Molecular anchoring by line-drawing mode of STM tip 45
4.1.2 Reaction rate according to bias voltage 47
4.2 DFT calculation 50
4.2.1 Anchoring mechanism of Ni-phthalocyanine on Au (111) 51
4.2.2 Vibrational mode of atoms in Ni-phthalocyanine 53
4.3 Conclusion 59

Section 2. Self-assembly of amino acids on Au (111)
V. Role of chirality in self-assembly of tryptophan 61
5.1 Molecular structure and properties of tryptophan 61
5.2 STM measurement 61
5.2.1 Deposition of tryptophan at a low substrate temperature 62
5.2.2 Deposition of tryptophan at a high substrate temperature 63
5.2.3 Self-assembled structure by single enantiomers 66
5.2.4 Self-assembled structure by two opposite enantiomers 67
5.3 DFT calculation 69
5.3.1 Adsorption of a L-tryptophan molecule on Au (111) 69
5.3.2 Interactions between two tryptophan molecules considering chirality 70
5.3.3 Configurations consisting of more than two tryptophan molecules 76
5.3.4 Understanding of self-assembled configurations of tryptophan 79
5.3.5 Heterochirality in tryptophan 80
5.4 Conclusion 81

VI. Dimensional crossing in self-assembly of leucine 83
6.1 Molecular structure and properties of leucine 83
6.2 STM measurement 83
6.2.1 Deposition of leucine at a high substrate temperature 84
6.2.2 Dependence of molecular coverage and annealing temperature 85
6.2.3 Configurations of self-assembled structures 87
6.2.4 Molecular chirality 90
6.3 DFT calculation 91
6.3.1 Interactions between two L-leucine molecules 92
6.3.2 Construction of continuous 1D structures 95
6.4 Conclusion 97

Reference 99
Summary in Korean 107

URI

http://dgist.dcollection.net/common/orgView/200000281835
http://hdl.handle.net/20.500.11750/11994

DOI

10.22677/Theses.200000281835

Degree

Doctor

Department

Emerging Materials Science

Publisher

DGIST

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