This thesis explores the mechanics of single molecule machines on a surface, aiming to understand the principles underlying synthetic single molecular machines. The study utilizes scanning tunneling microscopy (STM) at ultra-low temperatures and high vacuum conditions to investigate individual small molecules adsorbed on a substrate. In the first part, the transmission of rotation between single molecule-gears is examined, employing a star-shaped pentaphenylcyclopentadiene molecule manipulated by STM. The second part focuses on a zwitterionic and chiral molecule's dual functionality as a molecule-rotor or a molecule-vehicle (nanocar), with motion driven by tunneling electrons. The third part explores the origin of unidirectional rotation in a single molecule-rotor, analyzing the effects of thermal and electronic excitations on rotation dynamics. Overall, this work contributes to the fundamental understanding of nanoscale mechanical molecular devices and their potential applications.

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Radio frequency (RF) cavities are the foundational infrastructure which facilitates much of the fundamental research conducted in high energy particle physics. These RF cavities utilize their unique shape to produce resonant electromagnetic fields used to accelerate charged particles. Beside their core role in fundamental physics research, RF cavities have found application in other disciplines including material science, chemistry and biology which take advantage of their unique light sources. Industry has been keen on taking advantage of accelerator technology for a multitude of applications. Particle accelerators like the one found at Jefferson Lab’s Continuous Electron Beam Accelerator Facility must produce stable beams of high energy particles which is an incredibly costly endeavor to pursue. With the gargantuan size of these facilities, the cost of high-quality beam production is a matter of great importance. The quest to find highly efficient RF cavities has resulted in the widespread use of superconducting radio frequency (SRF) cavities which are the most efficient resonators that exploit a superconductor’s incredibly low AC surface resistance. While metals like Cu are up to the demanding job of RF cavity particle acceleration, their efficiency at transferring RF power to the particle beam is low when they are compared with SRF Nb cavities. Nb is the standard material for all SRF cavity technology particularly for its reproducibly low surface resistance, comparatively high transition temperature and thermodynamic critical field. Using superconducting Nb is not without its drawbacks. Keeping hundreds of Nb cavities in their superconducting state under extreme RF conditions is quite a daunting task. It requires the normal state not nucleate during operation. This is achieved by producing high-quality cavities with as few defects and impurities as possible while also keeping the cavities at low temperature, usually 2K. Again, due to the sheer scale of the facilities, hundred million-dollar cryogenic plants are required to handle the heat loads during SRF cavity operation. This means even small increases in maximum accelerating gradients or decrease in cavity surface resistance results in a sizably reduced operation cost. Considerable effort has been put forth to increase the efficiency of Nb cavities toward and even beyond the theoretical maximum accelerating gradients and quality factor for a clean superconductor. Recently, a new method to produce high quality factor cavities has emerged that involves nitrogen doping the cavity. The mechanism by which N doping causes the improvement is still not well understood, but the experimental research described in this dissertation shines some light into the mechanisms behind such a drastic improvement. These insights are universal for all superconductors and may prove useful for SRF cavities beyond Nb. With Nb approaching its fundamental limits, new materials are being proposed to increase the performance of future SRF cavities which MgB2 finds itself among. MgB2 is a two-band superconductor that possesses many properties that are very attractive for the next generation of SRF cavities. One of the most important properties is MgB2’s comparatively large critical temperature which in part predicts it will have a lower surface resistance than Nb at higher operating temperatures. Such behavior of MgB2 may unlock the possibility of using cryocoolers instead of costly liquid helium plants for large scale industrial use. This dissertation starts with an introduction to superconductivity, its theory, and application to SRF cavities as well as the open questions that can be addressed in Nb and the next generation of SRF materials. A description of the experimental techniques of scanning tunneling microscopy, X-ray photoelectron spectroscopy, and atomic force microscopy is presented. Our experimental investigation into Nb SRF cavity cutouts starts with a discussion of the material’s limitations for SRF applications with an emphasis on the proximity effect which arises at the surface of this material due to its myriad of naturally forming oxides. The results of our scanning tunneling microscopy measurements for typically prepared Nb and nitrogen doped Nb follows and comparisons are made which show that the surface oxides are fundamentally different between these samples likely resulting in the profound enhancement of the cavity’s quality factor. Experimental investigation into the native oxide of hot spot nitrogen doped Nb shows a degraded oxide and superconducting properties as compared with the cold spot. The dissertation continues with a brief introduction to MgB2, followed by our scanning tunneling and electron tunneling insights into MgB2. The dissertation is concluded with a summary of our investigations and broader impact of our research on the SRF community. / Physics

Two dimensional (2D) materials, including graphene, hexagonal boron nitride and layered transition metal dichalcogenides (TMDs), have been a revolution in condensed matter physics and they are at the forefront of recent scientific research. They are being explored for their unusual electronic, optical and magnetic properties with special interest in their potential uses for sensing, information processing and memory. Molybdenum disulfide (MoS2) has been the flagship semiconducting TMD over the past ten years due to its unique electronic, optical and mechanical properties. In this thesis, we grow mono- to few layer MoS2 films using ambient pressure chemical vapor depositions (AP-CVD) to obtain high quality samples. We employ low temperature scanning tunneling microscopy and spectroscopy (LT-STM/STS) to study the effect of layer number on the electronic density of states (DOS) of MoS¬2. We find a reduction of the magnitude of the quasiparticle band gap from one to two monolayers (MLs) thick. This reduction is found to be due mainly to a shift of the valence band maxima (VBM) where the conduction band minimum (CBM) does not change dramatically. Density functional theory (DFT) modeling of this system shows that the overlap of the interfacial S-pz orbitals is responsible for shifting the valence band edge at the Γ-point toward the Fermi level (EF), reducing the magnitude of the band gap. Additionally, we show that the crystallographic orientation of monolayer MoS2 with respect to the HOPG substrate can also affect the electronic DOS. This is demonstrated with five different monolayer regions having each with a unique relative crystallographic orientation to the underlying substrate. We find that the quasiparticle band gap is closely related to the moiré pattern periodicity, specifically the larger the moiré periodicity the larger the band gap. Using DFT, we find that artificially increasing the interaction between the film and the substrate means that the magnitude of the band gap reduces. This indicates that the moiré pattern period acts like a barometer for interlayer coupling. We investigate the effect of defects, both point and extended defects, on the electronic properties of mono- to few layer MoS¬2 films. Atomic point defects such including Mo interstitials, S vacancies and O substitutions are identified by STM topography. Two adjacent defects were investigated spectroscopically and found to greatly reduce the quasiparticle band gap and arguments were made to suggest that they are Mo-Sx complex vacancies. Similarly, grain boundaries were found to reduce the band gap to approximately ¼ of the gap found on the pristine film. We use Kelvin probe force microscopy (KPFM) to investigate the affect of annealing the films in UHV. The work function measurements show metastable states are created after the annealing that relax over time to equilibrium values of the work function. Scanning transmission electron microscopy (STEM) is used to show that S vacancies can recombine over time offering a feasible mechanism for the work function changes observed in KPFM. Lastly, we report how strain affects the quasiparticle band gap of monolayer MoS2 by bending the substrate using a custom built STM sample holder. We find that the local, atomic-scale strain can be determined by a careful calibration procedure and a modified, real-space Lawler Fujita algorithm. We find that the band gap of MoS2 reduces with strain at a rate of approximately 400 meV/% up to a maximum strain of 3.1%, after which the film can slip with respect to the substrate. We find evidence of this slipping as nanoscale ripples and wrinkling whose local strain fields alter the local electronic DOS. / Physics

<p> This thesis consists of two projects: alignment of copper phthalocyanine compounds on Au(111) and sidewall functionalization of single-walled carbon nanotubes on graphite. Both of these projects are performed with scanning tunneling microscopy (STM), which is used to study the structure of modified surfaces that are of interest in molecular electronics.</p> <p> In the first project, copper phthalocyanine compounds are made into a thin film with different methods, such as solution deposition, self-assembly and Langmuir-Blodgett film deposition. Those films are important materials in photoelectric devices such as organic light emitting diodes (OLED's). Molecules in these films are aligned on the solid surface with face-on orientation or edge-on orientation. However, the films of molecules with face-on orientation are preferentially used in LED's. In this project, we focus on finding a method to force molecules with face-on orientation in the film. The structure of copper octakisalkylthiophthalocyanine films on Au(111) was investigated with STM under ambient conditions. Columns of molecules are commonly observed due to the π-π interaction between molecules. The presence and length of alkyl chains in the molecules affects the alignment of molecules on the gold surface. The weak interaction between molecules and substrate caused the structure to be easily modified by an STM tip.</p> <p> In addition, chemical sidewall functionalization of SWCNTs was also explored with STM under ambient conditions. It was found that the spatial distribution of functional groups on nanotube sidewall is not random. Understanding the rules behind the distribution of functional groups will allow scientists to better control carbon nanotube functionalization and improve the properties of nanotubes. High resolution STM images provide direct evidence of the distribution and the effects of functional groups on nanotubes. Possible mechanisms are proposed to elucidate the process of SWCNT functionalization by free radicals and via the Bingel reaction.</p> / Thesis / Master of Science (MSc)

In recent years, two-dimensional (2D) van der Waals (vdW) materials have aroused much interest for their unique structural, thermal, optical, and electronic properties and have become a hot topic in condensed matter physics and material science. Many research methods, including scanning tunneling microscopy (STM), transmission electron microscopy (TEM), optical and transport measurements, have been used to investigate these unique properties. Among them, STM stands out as a powerful characterization tool with atomic resolution and is capable of simultaneously revealing both atomic structures and local electronic properties. This dissertation focuses on scanning tunneling microscopy and spectroscopy (STM/S) investigation of 2D metal chalcogenides and heterostructures. The first part of the dissertation focuses on the continuous interface in WS2/MoS2 heterostructures grown by the chemical vapor deposition (CVD) method. We observed a closed interface between the MoS2 monolayer and the heterobilayer with atomic resolution. Furthermore, our scanning tunneling spectroscopy (STS) results and density functional theory (DFT) calculations revealed band gaps of the heterobilayer and the MoS2 monolayer agree with previously reported values for MoS2 monolayer and MoS2/WS2 heterobilayer on SiO2 fabricated through the mechanical exfoliation method. The results could deepen our understanding of the growth mechanism, interlayer interactions and electronic structures of 2D transition metal dichalcogenides (TMD) heterostructures synthesized via CVD. The second part of the dissertation focuses on phase transformation in 2D In2Se3. We observed that 2D In2Se3 layers with thickness ranging from single to ~20 layers stabilized at the beta phase with a superstructure at room temperature. After cooling down to around 180 K, the beta phase converted to a more stable beta' phase that was distinct from previously reported phases in 2D In2Se3. The kinetics of the reversible thermally driven beta-to-beta' phase transformation was investigated by temperature dependent transmission electron microscopy and Raman spectroscopy, combined with the expected minimum-energy pathways obtained from our first-principles calculations. Furthermore, DFT calculations reveal in-plane ferroelectricity in the beta' phase. STS measurements show that the indirect bandgap of monolayer beta' In2Se3 is 2.50 eV, which is larger than that of the multilayer form with a measured value of 2.05 eV. Our results on the reversible thermally driven phase transformation in 2D In2Se3 will provide insights to tune the functionalities of 2D In2Se3 and other emerging 2D ferroelectric materials and shed light on their numerous potential applications like non-volatile memory devices. The third part of the dissertation focuses on domain boundaries in 2D ferroelectric In2Se3. The atomic structure of domain boundaries in two-dimensional (2D) ferroelectric beta' In2Se3 is visualized with scanning tunneling microscopy and spectroscopy (STM/S) combined with DFT calculations. A double-barrier energy potential across the 60° tail to tail domain boundaries in monolayer beta' In2Se3 is also revealed. The results will deepen our understanding of domain boundaries in 2D ferroelectric materials and stimulate innovative applications of these materials. / Doctor of Philosophy / Two-dimensional (2D) materials are materials consisting of a single layer or a few layers of atoms. They exhibit unique and interesting properties distinct from their bulk counterparts. Over the past decade, much effort has been devoted to a large family of 2D materials — 2D metal chalcogenides that exhibit fascinating structural and electronic properties. These 2D metal chalcogenides can also be stacked together to form various heterostructures. The scanning tunneling microscope (STM) is a powerful tool to study these materials with atomic resolution and is capable of simultaneously revealing both atomic structures and local electronic properties. It can also be used to manipulate nanometer-scale structures on the material surface. In this dissertation, we use scanning tunneling microscopy and spectroscopy (STM/S) to investigate 2D metal chalcogenides and heterostructures. The first part of the dissertation focuses on WS2/MoS2 heterostructures grown by the chemical vapor deposition (CVD) method. We observed a closed interface between the MoS2 monolayer and the heterobilayer with atomic resolution. Furthermore, our scanning tunneling spectroscopy (STS) results and density functional theory (DFT) calculations revealed band gaps of the heterobilayer and the MoS2 monolayer. The results could deepen our understanding of the growth mechanism, interlayer interactions and electronic structures of 2D transition metal dichalcogenides (TMD) heterostructures synthesized via CVD. The second part of the dissertation focuses on phase transformation in 2D In2Se3. We observed that 2D In2Se3 layers transform from beta phase to a more stable beta' phase when the sample is cooled down from room temperature to 77 K. This thermally driven beta-to-beta' phase transformation was found to be reversible by temperature dependent transmission electron microscopy and Raman spectroscopy, corroborated with the expected minimum-energy pathways obtained from our first-principles calculations. Furthermore, DFT calculations reveal in-plane ferroelectricity in the beta' phase. Our results on the reversible thermally driven phase transformation in 2D In2Se3 will provide insights to tune the functionalities of 2D In2Se3 and other emerging 2D ferroelectric materials. The third part of the dissertation focuses on domain boundaries in 2D ferroelectric In2Se3. The atomic structure of domain boundaries in 2D ferroelectric beta' In2Se3 is visualized by using STM/S combined with DFT calculations. A double-barrier energy potential across the 60° tail to tail domain boundaries in monolayer beta' In2Se3 is also revealed. The results will deepen our understanding of domain boundaries in 2D ferroelectric materials and stimulate innovative applications of these materials.

The term “electroluminescence” refers to light emission resulting from the application of an electrical bias. Electron tunneling across a biased, nanoscale junction can serve as the excitation source for photon emission. This effect is also mediated by the plasmonic environment of the junction, where a strong local field can enhance light emission by orders of magnitude. This dissertation presents measurements of electroluminescence from nanoscale gaps and single-molecule junctions. These measurements are made possible by a custom light emission detection system coupled to a scanning tunneling microscope break junction (STM-BJ) instrument. Conductance and light emission data are obtained simultaneously for thousands of junctions. Chapter 1 discusses molecular optoelectronics, a field at the intersection of plasmonic phenomena and molecular electronics, and introduces the STM-BJ technique for measuring molecular junctions. Chapter 2 describes the light emission detection setup that is operated in tandem with the STM-BJ instrument. Chapter 3 presents a study of Au tunnel junctions. This lays the groundwork for the plasmonics at play in these electroluminescent systems, detangling how gap size, electrical bias, and emission wavelength affect plasmonic enhancement. In Chapters 4 and 5, Au-molecule-Au junctions are investigated in some of the first experimental studies of single-molecule electroluminescence at ambient conditions. Chapter 4 uses light emission data from molecular junctions to estimate finite-frequency shot noise and uncover critical information about transmission characteristics. Chapter 5 presents one of the first examples of single-molecule strong light-matter coupling in an electroluminescent system, substantiated by spectroscopy data. This dissertation greatly expands on existing knowledge of plasmonic phenomena, particularly in relation to electroluminescent devices. Furthermore, it lays a strong foundation for single-molecule spectroscopy studies using the STM-BJ technique.