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Scanning Tunneling Microscopy (STM) has been used to study the physisorption and chemisorption behaviour for three simple organic haloalkanes; 1,5 Dichloropentane (DCP), Bromomethane (CH3Br) and Chloromethane (CH3Cl)) on Si(100) 2x1, at temperatures ranging from 270 K to room temperature. The results were interpreted by Density Functional Theory (DFT) performed by collaborators at McGill University and the University of Liverpool. Physisorbed molecules of DCP were found to self assemble into stable lines aligned predominantly perpendicular to the Si dimer pair rows on the surface. A novel mechanism for line formation of Dichloropentane, termed, Dipole Directed Assembly (DDA), was elucidated by DFT calculations. For CH3Br three different patterns of dissociative attachment of reaction products (CH3 and Br/Cl) were observed, and assigned to three reaction pathways. These experimentally determined relative yields were used to obtain differences in reaction activation energy, Delta Ea, between the reaction pathways. These, in turn, were compared with computed differences in reaction barriers, Delta Eb, obtained ab initio for the same pathways by DFT. For CH3Cl, two single-molecule patterns of attachment were found, and a new reaction pathway for attaching CH3Cl in long chains of alternating CH3 and Cl was discovered. The mechanisms for chain growth were determined experimentally by examination of single molecular steps. This mechanism was explained ab initio by DFT to be the result of relative barrier heights for the possible chain-growth pathways.

Scanning Tunneling Microscopy (STM) has been used to study the physisorption and chemisorption behaviour for three simple organic haloalkanes; 1,5 Dichloropentane (DCP), Bromomethane (CH3Br) and Chloromethane (CH3Cl)) on Si(100) 2x1, at temperatures ranging from 270 K to room temperature. The results were interpreted by Density Functional Theory (DFT) performed by collaborators at McGill University and the University of Liverpool. Physisorbed molecules of DCP were found to self assemble into stable lines aligned predominantly perpendicular to the Si dimer pair rows on the surface. A novel mechanism for line formation of Dichloropentane, termed, Dipole Directed Assembly (DDA), was elucidated by DFT calculations. For CH3Br three different patterns of dissociative attachment of reaction products (CH3 and Br/Cl) were observed, and assigned to three reaction pathways. These experimentally determined relative yields were used to obtain differences in reaction activation energy, Delta Ea, between the reaction pathways. These, in turn, were compared with computed differences in reaction barriers, Delta Eb, obtained ab initio for the same pathways by DFT. For CH3Cl, two single-molecule patterns of attachment were found, and a new reaction pathway for attaching CH3Cl in long chains of alternating CH3 and Cl was discovered. The mechanisms for chain growth were determined experimentally by examination of single molecular steps. This mechanism was explained ab initio by DFT to be the result of relative barrier heights for the possible chain-growth pathways.

The interaction and orbital energy levels of 3,4,9,10-perylene-tetracarboxylic dianhydride (PTCDA) molecules on a Pb/Si(111) 1x1 substrate have been investigated. A Si(111) sample was annealed to form the 7x7 configuration. 1.5 monolayer of Pb was evaporated onto the surface, which was then annealed. 0.5 monolayer of PTCDA was applied to the substrate through molecular beam epitaxy (MBE). The surface configuration of the substrate was monitored step by step by low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM). Scanning tunneling spectroscopy (STS) was used to pinpoint the energy levels of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the molecules. It was found that the PTCDA molecules formed a herringbone pattern on the substrate. The PTCDA electronic energy levels corresponding to the HOMO and the LUMO were obtained. From these values the energy gap between these orbitals, the molecular bandgap of PTCDA on Pb/Si(111) 1x1, was determined.

InN have individual property of electrnic and surface, our research is focused on the surface property. In this article, The surface property was studied by Auger Electron Spectroscopy (AES), Low Energy Electron Diffraction(LEED), Scanning Electron Microscope(SEM), and Scanning Tunneling Microscopy(STM). The method in this article for cleaning surface of InN are wet etching by HCl, Atomic Hydrogen Cleaning(AHC), and annealing. Wet etching by HCl was proceeding in air, and a lot of junk would be adsorbed in the surface of InN when it was taken from HCl to vacuum. Though wet etching was a simple method, it could not be a best method to clean surface of InN. AHC were a relative clean method in this article. Carbon and oxygen colud be removed effectively by AHC.The filament of AHC was heating the surface of InN when AHC was running, so the surface was annealing at that moment. After cleaning by AHC, LEED spot and AES signal were improved.

In the scope of this master thesis, a home-made brass scanning tunneling microscope (STM) was machined, assembled and tested for its functionality. For this microscope, a new approach-technique was used which follows the design suggested by Pan. The difference to Pan's design is the use of piezoplates, instead of piezostacks. Hence, the approach is still based on the stick and slip motion, but it allows the microscope to be more compact. A new and simple electronic circuit, in order to control the approach, is presented and was put together. This circuit is based on mechanical relays, which provide a sufficient long time gap between the single moving steps, due to their mechanical functional principle. Subsequently the approach-technique and the scanning was successfully tested. Finally, first images of HOPG were taken under ambient conditions. / text

In this thesis, the growth mechanism of graphene on a transition metal support is determined, and the epitaxial relationship investigated. The main technique used is low- temperature scanning tunnelling microscopy (STM), which is introduced in Chapter 2. Epitaxial graphene synthesised on copper (foil and (110) single crystal), from the dehydrogenation of ethene, is investigated by STM and low energy electron diffraction (LEED) in Chapter 4. Despite the weak epitaxial relationship that exists, LEED uncovers two preferred orientations of the graphene over the copper. Further investigation reveals restructuring of the copper foil from a predominantly (100) orientation to (n10) facets. Structural feedback is found to exist, with the graphene growth inducing and stabilising faceting of the copper surface, and the facets in-turn playing an important role in the graphene growth mechanism. The preferred orientations, which are also seen on the single crystal, are most likely determined during nucleation and early stage growth, where it is expected that the interaction is stronger. The growth mechanism for the formation of graphene from ethene is studied on a Rh(111) surface in Chapter 5. This is found to consist of two regimes, with the first revolving around the transformation from aliphatic hydrocarbons to aromatic intermediates. This occurs through the decomposition and condensation of ethene, resulting in the formation of one-dimensional polyaromatic hydrocarbons (1D-PAHs). The second regime is characterised by the transition from these 1D-PAHs, to the 2D graphene. The previously produced 1D-PAHs, decompose to form size-selective carbon clusters, with these clusters being the precursors to graphene condensation. In Chapter 6, the conclusions of Chapter 5 are built upon through investigation into the effect of different hydrocarbon feedstocks on the graphene growth pathway. Benzene, tetracene, and perylene are the feedstocks examined. In all cases 1D-PAHs are formed, which decompose to clusters that subsequently condense to form graphene.

Carbon nanotubes (CNTs) and graphene (G) are the two (semi-)conducting allotropes of carbon offering a very high surface to bulk ratio. When combined with electrochemistry and using the principles of molecular self-assembling, many new applications of CNTs and graphene have become feasible, e.g. in the field of molecular electronics, as energy storage materials and for drug delivery. In this work scanning probe microscopy techniques (STM, AFM and EC-AFM) are used to understand the structure of self-assembled organic and electroactive molecules, oligomers and polymers on the surface of CNTs and graphene, and to rationalize their function as supramolecular system in the macroscopic world. It was found that there is a strong tendency for self-assembling in solution of aromatic electrophores with HOMO/LUMO levels close to the semiconducting CNT frontier orbitals. The tunneling currents through the aromatic guest molecules on CNT are much higher than for the same molecule on highly oriented pyrolytic graphite (HOPG). In the 1st chapter of this thesis the different microscopic techniques used with special emphasis on the electrochemical atomic force microscopy (EC-AFM), a relatively new combination technique which plays an important role in this work, are presented. It is followed by the structural analysis of stiff, semi-flexible and flexible oligo-viologen on CNTs. Using a large set of molecules with well defined small structural differences allowed to study how the superstructure (guests@CNT) is determined by the tiny changes in the guest structure. Mostly helical super structures of guests around the CNT host were observed. The guest’s rod length, its side chain length and its flexibility translate unambiguously into the corresponding STM images. A non-linear, star shaped oligo-viologen cannot wrap CNT without overlapping star branches, as expected from model considerations. In collaboration with a Korean research group we were able to build an n-doped FET using a reduced rigid oligo-viologen@CNT. Along with the oligomer the formation of stiff poly-viologens@CNT and poy-imides@CNT are studied. As compared to the oligomers@CNT, the polymers@CNT have less conformational freedom when wrapping a CNT. Thus, exclusively double to multi stranded helical wrapping was observed. An interesting new phenomenon was discovered with stiff poly-viologen or poly-naphthaline tetracarboxylic acid diimide with purely sp2 configured atoms, i.e. an outer, large diameter helical structure of “the guest” polymer and a CNT “host” sitting inside the spiral. The spiral diameter was simulated using PM7 calculations. The CNT can be moved within the large spiral by voltage pulse application. Subsequently, the conformation of flexible poly-viologens and poly-TEMPO on host materials such as CNTs and vapor grown carbon fibers (VGCF) was studies. Again, helical wrapping is observed, but the diameter adapts here to the CNT diameter. Monomer subunit resolution was achieved in case of polyTEMPO. The practical importance in energy storage is discussed in the corresponding original paper. The next chapter of thesis focuses on AFM imaging of a new battery material, i.e. poly-ferrocene on graphene oxide (PVF@GO) and on reduced graphene oxide (PVF@rGO), as well as poly-viologen as PV@GO and PV@rGO. A highlight is definitely the visualization of the so-called ion-breathing, i.e. the reversible counter ion movement from solution into the battery material composite upon electrochemical reduction/oxidation. To the best of my knowledge, this phenomenon is for the first time visualized here by a combination of electrochemistry and AFM. STM analysis of electrically conductive rGO allows for subunit resolution of polyviologen@rGO sitting in partially 2D crystalline structure on rGO. In the last chapter, my publication on the drug delivery system doxorubicin at carbon nanotubes is described. Dox@CNT is already used as drug delivery system in animal tests, but little is known on the structure of the drug on the carrier, and a reductive release trigger has so far not been identified. Rich structural variations of the drug on the CNT (helical strands of monomers and dimers) were found. It is possible to get the drug loading efficiency from STM image analysis. Reductive release of Dox@CNT was also unknown so far. Electron injection into Dox@CNT from an electrode or from the biological reducing agent glutathione (GSH) leads to irreversible release of Dox. Experimental results are in excellent agreement with semi-empirical simulations.

Two-dimensional (2D) materials show novel electronic, optical and chemical properties and have great potential in devices such as field-effect transistors (FET), photodetectors and gas sensors. This thesis focuses on scanning tunneling microscopy and spectroscopy (STM/STS) investigation of interfaces and defects 2D transition metal dichalcogenides (TMDCs). The first part of the thesis focuses on the synthesis of 2D TiSe2 with chemical vapor transport (CVT). By properly choosing the growth condition, Sub-10 nm TiSe2 flakes were successfully obtained. A 2 × 2 charge density wave (CDW) was clearly observed on these ultrathin flakes by scanning tunneling microscopy (STM). Accurate CDW phase transition temperature was measured by transport measurements. This work opens up a new approach to synthesize TMDCs. The second part of the thesis focuses on monolayer vacancy islands growing on TiSe2 surface under electrical stressing. We have observed nonlinear area evolution and growth from triangular to hexagonal driven by STM subjected electrical stressing. Our simulations of monolayer island evolution using phase-field modeling and first-principles calculations are in good agreement with our experimental observations. The results could be potentially important for device reliability in systems containing ultrathin TMDCs and related 2D materials subject to electrical stressing. The third part of the thesis focuses on point defects in 2D PtSe2. We observed five types of distinct defects from STM topography images and measured the local density of states (LDOS) of those defects from scanning tunneling spectroscopy (STS). We identified the types and characteristics of these defects with the first-principles calculations. Our findings would provide critical insight into tuning of carrier mobility, charge carrier relaxation, and electron-hole recombination rates by defect engineering or varying growth condition in few-layer 1T-PtSe2 and other related 2D materials. / Doctor of Philosophy / Since the discovery of graphene in 2004, two-dimensional (2D) materials have attracted more and more attentions. When the thickness of a layered material thinned to one or few atoms, it shows interesting properties different from its bulk phase. Due to the reduced dimensionality, interfaces and defects in 2D materials will significantly affect the electronic property and chemical activity. However, such nanometer scale features are several orders of magnitude smaller than the wavelength of visible light, which is the limit of resolution for optical microscope. Scanning tunneling microscope (STM) is widely used in study of 2D materials not only because it can provide the topography and local electronic information at atomic scale, but also because of the possibility of directly fabricate atomic scale structure on the surface. The first part of the thesis focuses on the synthesis of 2D TiSe2 with chemical vapor transport (CVT). TiSe2 belongs to the transition metal dichalcogenides (TMDCs) family, showing a sandwiched layered structure. When the temperature goes down to 200K, a 2 × 2 superlattice called charge density wave (CDW) will show up, which is clearly observed in our STM images. The second part of the thesis focuses on monolayer vacancy islands growing on TiSe2 surface controlled by electrical stressing. During continuous STM scanning, we have observed nonlinear area growth of the vacancy islands. The shape of those islands transfers from triangular to hexagonal. We successfully simulated such growth using phase-field modeling and first-principles calculations. The results could be potentially important for device reliability in systems containing ultrathin TMDCs and related 2D materials subject to electrical stressing. The third part of the thesis focuses on defects in 2D PtSe2. We observed five types of distinct defects in our STM topography images. By comparing them with DFT-calculated simulation images, we identified the types and characteristics of these defects. Our findings would provide critical insight into tuning of carrier mobility, charge carrier relaxation, and electron-hole recombination rates by defect engineering in few-layer 1T-PtSe2 and other related 2D materials.