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abstract: This dissertation describes the work on two projects which involves measuring molecular conductance and studying their properties on the nanoscale using various Scanning Tunneling Microscopy (STM) techniques. The first molecule studied was a porphyrin-fullerene moiety known as a molecular Dyad for photovoltaic applications. This project is further divided into two section, the first one involving the characterization of the Dyad monolayers and conductance measurement in the dark. The Dyads are designed to form charge separated states on illumination. The lifetime of the charged states have been measured efficiently but the single-molecule conductance through the molecules have yet to be characterized. The second part of the project describes the set-up of a novel sample stage which enables the study of molecular conductance under illumination. This part also describes the subsequent study of the molecule under illumination and the observation of a unique charge-separated state. It also contains the verification of the presence of this charge-separated using other characterization techniques like transient absorption spectroscopy. The second project described in the dissertation was studying and comparing the predicted rectifying nature of two molecules, identical in every way except for one stereocenter. This project describes the formation of monolayers of the molecule on gold and then studying and analyzing the current-voltage characteristics of the molecules and looking for rectification. Both the molecules proved to be rectifying, one more than the other as predicted by theoretical calculations. / Dissertation/Thesis / Ph.D. Chemistry 2011

Organic electronics are becoming an increasingly important part of the semiconductor industry, with myriad applications enabled by their low cost, solution processability, and electrical conductivity. Charge transport in electronic applications involving organic semiconductor materials depends strongly on the electronic properties of nanoscale interfaces. Local variations in molecular environments can have a significant impact on the interfacial electronic properties, and subsequently the organic semiconductor electronic structure. Here, we use scanning tunneling microscopy and spectroscopy, supported by theoretical calculations, to investigate the impact of the local adsorption environment on the local density of states of oligothiophenes, carbon nanohoops, and carbon nanotubes. First, we present work showing that, for alkyl-substituted quaterthiophenes, molecular packing and electronic structure at interfaces differ substantially from the bulk, and a significant degree of structural and electronic variation occurs even in this relatively simple system. Then, we report on investigations of longer alkyl-substituted oligothiophenes, were we found a variety of planar molecular conformations that surprising exhibited similar, particle-in-a-box-like progressions of unoccupied molecular orbitals. Next, we share our research that found, for the first time, metal surface electrons confined within single adsorbed molecules. Finally, we study the impact of electrostatic defects in both metal and dielectric substrates on single-walled carbon nanotubes. The research presented in this dissertation increases our understanding of organic semiconductor interfaces and the impact of said interfaces on local molecular electronic structure, thereby aiding future organic semiconductor technological development. / 10000-01-01

This thesis explores structural and electronic properties of layered materials at the nanometre scale. Room temperature and low temperature ultrahigh vacuum scanning probe microscopy (scanning tunneling microscopy, scanning tunneling spectroscopy, atomic force microscopy) is used as the primary characterization method. The main findings in this thesis are: (a) observations of the atomic lattice and imaging local lattice defects of semiconducting ReS2 by scanning tunneling microscopy, (b) measurement of the electronic band gap of ReS2 by scanning tunneling spectroscopy, and (c) scanning tunneling microscopy study of 1T-TaS2 lattice and chemically functionalizing its defects with magnetic molecules.

Les isolants topologiques 3D sont un nouvel état de la matière décrit par un volume iso-lant électriquement et recouvert par des états de surface métalliques. Une jonction Joseph-son topologique (TJJ) formée autour de ces états de surface peut théoriquement contenirun mode lié d’Andreev ayant une périodicité doublée par rapport aux modes liés d’An-dreev conventionnels 2p périodiques. Le mode d’Andreev 4p périodique serait la briqueélémentaire de l’ordinateur quantique topologique. Ainsi, nous étudions la dynamique dece mode particulier lors de mesures de Shapiro sur des jonctions Josephson fabriquées surdes isolants topologiques à base de bismuth.A?n d’identi?er les e?ets d’un mode 4p-périodique dans une mesure de Shapiro, nousutilisons un model phénoménologique permettant de simuler la caractéristique courant-tension d’une TJJ lors de telles mesures. Nous prédisons deux signatures du mode 4p-périodique et estimons leur robustesse face aux e?ets de chau?age par e?et Joule et face àun modèle d’empoisonnement thermiquement activé du mode 4p-périodique.Par des mesures de Shapiro, nous étudions la dynamique des TJJ basées sur le matériausimple qu’est le Bi2Se3. L’observation des deux mêmes signatures précédemment anticipéespar nos simulations, à savoir un ordre d’apparition non conventionnel des pas de Shapiroainsi que la persistance d’un supercourant à la fermeture du plateau de Shapiro n = 0prouve la présence d’un mode 4p-périodique.Notre étude s’est également portée sur un autre isolant topologique le BiSbTeSe2. Nousavons e?ectué sa croissance par cristallisation liquide-solide et avons mis en évidence,par des mesures d’interférométrie supraconductrice une supraconductivité de surface sanstransport électronique par le volume. / Three dimensional topological insulators (3D TI) are a new state of matter composedof an electrically insulating bulk covered by metallic surface states. Theoretically, a topo-logical Josephson junction composed of these surface states can host an Andreev Boundstate (ABS) that has twice the periodicity of the conventional 2p periodic ABSs. The4p periodic ABS is expected to be the building block of topological quantum computing.Therefore, we study the dynamic of this particular ABS by performing Shapiro measure-ment on Josephson junctions built with bismuth based 3D TI.To identify the e?ects of a 4p periodic ABS in a Shapiro measurement, we use a phe-nomenological model that simulates the voltage-current characteristics of a TJJ. We predicttwo signatures of the 4p periodic ABS and estimate their robustness against Joule heatingand thermally activated quasiparticle poisoning of the 4p periodic mode.We study the Josephson junctions dynamics by performing Shapiro measurements onjunctions built on Bi2Se3. We observe the two previously anticipated signatures, whichare the non-conventional appearance order of the Shapiro steps and the remaining of asupercurrent at the closing of the Shapiro step n = 0. They prove the presence of a 4pperiodic ABS.We also study the topological insulator BiSbTeSe2 that we have grown by using themelting growth method. By superconducting interferometric measurements, we show asuperconducting surface transport without bulk electronic conduction.

This dissertation provides a brief introduction into scanning tunneling microscopy, and then Chapter III reports on the design and operation of a cryogenic ultra-high vacuum scanning tunneling microscope (STM) coupled to a closed-cycle cryostat (CCC). The STM is thermally linked to the CCC through helium exchange gas confined inside a volume enclosed by highly flexible rubber bellows. The STM is thus mechanically decoupled from the CCC, which results in a significant reduction of the mechanical noise transferred from the CCC to the STM. Noise analysis of the tunneling current shows current fluctuations up to 4% of the total current, which translates into tip-sample distance variations of up to 1.5 picometers. This noise level is sufficiently low for atomic-resolution imaging of a wide variety of surfaces. To demonstrate this, atomic-resolution images of Au(111) and NaCl(100)/Au(111) surfaces, as well as of carbon nanotubes deposited on Au(111), were obtained. Other performance characteristics such as thermal drift analysis and a cool-down analysis are reported. Scanning tunneling spectroscopy (STS) measurements based on the lock-in technique were also carried out and showed no detectable presence of noise from the CCC. These results demonstrate that the constructed CCC-coupled STM is a highly stable instrument capable of highly detailed spectroscopic investigations of materials and surfaces at the atomic-scale. A study of electron transport in single-walled carbon nanotubes (SWCNTs) was also conducted. In Chapter IV, STS is used to study the quantum-confined electronic states in SWCNTs deposited on the Au(111) surface. The STS spectra show the vibrational overtones which suggest rippling distortion and dimerization of carbon atoms on the SWCNT surface. This study experimentally connects the properties of well-defined localized electronic states to the properties of their associated vibronic states. In Chapter V, a study of PbS nanocrystals was conducted to study the effect of localized sub-bandgap states associated with surface imperfections. A correlation between their properties and the atomic-scale structure of chemical imperfections responsible for their appearance was established to understand the nature of such surface states. This dissertation includes both previously published/unpublished and co-authored material.

This dissertation presents results of a project bringing Scanning Tunneling Microscope (STM) into a regime of unlimited operational time at cryogenic conditions. Freedom from liquid helium consumption was achieved and technical characteristics of the instrument are reported, including record low noise for a scanning probe instrument coupled to a close-cycle cryostat, which allows for atomically resolved imaging, and record low thermal drift. Subsequent studies showed that the new STM opened new prospects in nanoscience research by enabling Scanning Tunneling Spectroscopic (STS) spatial mapping to reveal details of the electronic structure in real space for molecules and low-dimensional nanomaterials, for which this depth of investigation was previously prohibitively expensive. Quantum-confined electronic states were studied in single-walled carbon nanotubes (SWCNTs) deposited on the Au(111) surface. Localization on the nanometer-scale was discovered to produce a local vibronic manifold resulting from the localization-enhanced electron-vibrational coupling. STS showed the vibrational overtones, identified as D-band Kekulé vibrational modes and K-point transverse out-of plane phonons. This study experimentally connected the properties of well-defined localized electronic states to the properties of associated vibronic states. Electronic structures of alkyl-substituted oligothiophenes with different backbone lengths were studied and correlated with torsional conformations assumed on the Au(111) surface. The molecules adopted distinct planar conformations with alkyl ligands forming cis- or trans- mutual orientations and at higher coverage self-assembled into ordered structures, binding to each other via interdigitated alkyl ligands. STS maps visualized, in real space, particle-in-a-box-like molecular orbitals. Shorter quaterthiophenes have substantially varying orbital energies because of local variations in surface reactivity. Different conformers of longer oligothiophenes with significant geometrical distortions of the oligothiophene backbones surprisingly exhibited similar electronic structures, indicating insensitivity of interaction with the surface to molecular conformation. Electronic states for annealed ligand-free lead sulfide nanocrystals were investigated, as well as hydrogen-passivated silicon nanocrystals, supported on the Au(111) surface. Delocalized quantum-confined states and localized defect-related states were identified, for the first time, via STS spatial mapping. Physical mechanisms, involving surface reconstruction or single-atom defects, were proposed for surface state formation to explain the observed spatial behavior of the electronic density of states. This dissertation includes previously published co-authored material.

abstract: Charge transport in molecular systems, including DNA (Deoxyribonucleic acid), is involved in many basic chemical and biological processes. Studying their charge transport properties can help developing DNA based electronic devices with many tunable functionalities. This thesis investigates the electric properties of double-stranded DNA, DNA G-quadruplex and dsDNA with modified base. First, double-stranded DNA with alternating GC sequence and stacked GC sequence were measured with respect to length. The resistance of DNA sequences increases linearly with length, indicating a hopping transport mechanism. However, for DNA sequences with stacked GC, a periodic oscillation is superimposed on the linear length dependence, indicating a partial coherent transport. The result is supported by the finding of delocalization of the highest occupied molecular orbitals of Guanines from theoretical simulation and by fitting based on the Büttiker’s theory. Then, a DNA G4-duplex structures with a G-quadruplex as the core and DNA duplexes as the arms were studied. Similar conductance values were observed by varying the linker positions, thus a charge splitter is developed. The conductance of the DNA G-tetrads structures was found to be sensitive to the π-stacking at the interface between the G-quadruplex and DNA duplexes by observing a higher conductance value when one duplex was removed and a polyethylene glycol (PEG) linker was added into the interface. This was further supported by molecular dynamic simulations. Finally, a double-stranded DNA with one of the bases replaced by an anthraquinone group was studied via electrochemical STM break junction technique. Anthraquinone can be reversibly switched into the oxidized state or reduced state, to give a low conductance or high conductance respectively. Furthermore, the thermodynamics and kinetics properties of the switching were systematically studied. Theoretical simulation shows that the difference between the two states is due to a difference in the energy alignment with neighboring Guanine bases. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

Nos últimos 30 anos o crescimento paralelo das Ciências de Superfície tradicionais, em ambiente de ultra-alto vácuo (UHV), com a Eletroquímica levou ao nascimento de um novo campo interdisciplinar: Física de Superfície e Eletroquímica. Técnicas de ambas as áreas dão informações complementares e assim, quando realizadas em conjunto podem fornecer muitas respostas em nível atômico, estrutural e eletrônico quando o eletrodo está em contato com a solução eletrolítica. A intenção primordial dessa Dissertação foi o estudo fundamental das fases ricas em oxigênio presentes na superfície de Ru(0001) através de caracterizações eletroquímicas e morfológicas utilizando um sistema que permitiu o acoplamento de uma célula eletroquímica miniatura de fluxo a câmaras de UHV. Inicialmente exibi-se a modificação e a construção de equipamentos necessários para a preparação do sistema binário Au-Pt(111) e do óxido monocristalino Ru2O(110). Imagens de STM em escala morfológica mostraram o crescimento anisotrópico do filme de RuO2(110) sobre um substrato monocristalino de Ru(0001). Resultados obtidos através da técnica de Voltametria Cíclica na eletrooxidação de CO em RuO2(110) corroboraram cálculos teóricos sobre a estrutura da superfície quando esta em ambiente úmido. Superfícies modelos baseadas em ouro, crescido epitaxialmente sobre um substrato de Pt(111), foram preparadas no sistema de UHV. Dados eletroquímicos foram correlacionados às composições superficiais destas, mostrando o efeito do substrato prevalecendo sobre o efeito eletrônico. / In the last 30 years the parallel growth of the traditional Surface Science, under UHV environment, and Electrochemistry gave rise to a new interdisciplinary field: Surface Science and Electrochemistry. Techniques from both sciences give complementary information. Thus, in tandem, they are able to elucidate many atomic, structural and electronic phenomena, of an electrode in contact with a solution. The main goal of this Dissertation was the fundamental study of the Oxygen-rich Ru(0001) surface through electrochemical and morphologic characterizations using a coupled system which allowed the attachment of a miniature flow cell to UVH-chambers. Initially it is shown the construction and modifications of required equipments for the preparation of the binary system Au-Pt(111) and single crystal RuO2(110) oxide. Attainable morphological STM images demonstrated the anisotropic growth of the RuO2(110) over a Ru(0001) substrate. Results of the electrooxidation of CO on RuO2(110), obtained by means of Cyclic Voltammetry, corroborated theoretical calculations concerning the oxide superficial structure in a humid environment. Model surfaces based on Au, epitaxialy grown on a Pt(111) substrate, were prepared under UHV conditions. Electrochemical data and superficial composition were correlated, confirming that the substrate effect overcomes electronic strain effects.

The ability to isolate single atomic layers of van der Waals materials has led to renewed interest in the electronic and optical properties of these materials as they can be fundamentally different at the monolayer limit. Moreover, these 2D crystals can be assembled together layer by layer, with controllable sequence and orientation, to form artificial materials that exhibit new features that are not found in monolayers nor bulk. Twisted bilayer graphene is one such prototype system formed by two monolayer graphene layers placed on top of each other with a twist angle between their lattices, whose electronic band structure depends on the twist angle. This thesis presents the efforts to explore the electronic and optical properties of twisted bilayer graphene by Raman spectroscopy and scanning tunneling microscopy measurements. We first synthesize twisted bilayer graphene with various twist angles via chemical vapor deposition. Using a combination of scanning tunneling microscopy and Raman spectroscopy, the twist angles are determined. The strength of the Raman G peak is sensitive to the electronic band structure of twisted bilayer graphene and therefore we use this peak to monitor changes upon doping. Our results demonstrate the ability to modify the electronic and optical properties of twisted bilayer graphene with doping. We also fabricate twisted bilayer graphene by controllable stacking of two graphene monolayers with a dry transfer technique. For twist angles smaller than one degree, many body interactions play an important role. It requires eight electrons per moire unit cell to fill up each band instead of four electrons in the case of a larger twist angle. For twist angles smaller than 0.4 degree, a network of domain walls separating AB and BA stacking regions forms, which are predicted to host topologically protected helical states. Using scanning tunneling microscopy and spectroscopy, these states are confirmed to appear on the domain walls when inversion symmetry is broken with an external electric field. We observe a double-line profile of these states on the domain walls, only occurring when the AB and BA regions are gaped. These states give rise to channels that could transport charge in a dissipationless manner making twisted bilayer graphene a promising platform to realize controllable topological networks for future applications.