The scanning tunneling microscope-break junction (STM-BJ) technique is an ideal platform for single-molecule studies related to the design of molecular electronics. STM-BJ is particularly advantageous for molecular junctions for characterizing key properties of molecular conductance as well as many other related properties, which contribute to a growing understand of the mechanisms of electron transport on the single-molecular level. Prior STM-BJ studies have generally focused on simple systems with only one type of molecule forming one type of junction. However, some systems (such as those involve in-situ chemical reactions) are intrinsically complex with multiple molecules and junction structures that can be accessed in the experiment. The analysis of such complex systems requires more powerful analytical methods that can distinguish different junction types. Machine learning has been demonstrated as a powerful tool for the analysis of such large datasets. In this work, we develop tools to analyze, with a high-accuracy, individual junction characteristics using machine learning to classify the data and provide mechanistic understanding of the STM-BJ method.We start our work by investigating the imidazolyl linker. Imidazole is a five-member aromatic heterocycle with two nitrogen atoms, in which its pyridinic nitrogen can bind to gold electrodes. We study a series of alkanes of different lengths with two terminal 1-imidazolyl linker groups. While the intramolecular transmission across these molecules gives the pyridinic double peak, we find and prove that π-stacking between two imidazole rings is strong enough to form a third intermolecular conductance peak with higher conductance. This behavior is a good example where multiple types of junction are formed with just one molecule. Then, we focus on developing a trace-wise classification method using deep learning to resolve the data from such complicated systems of special molecules, mixture solutions, or in-situ¬ chemical reactions. Compared to existing methods, ours reduces the loss of information during the data preprocessing and demonstrates better performance by employing a convolutional neural network structure with larger capacity. Benchmarking with several commercially available molecules, we show that our model reaches up to 97% accuracy and outruns all the existing methods significantly. Nevertheless, we also demonstrate that our model can retain high accuracy when two essential parameters, the average conductance and the length of the molecular conductance plateau, are removed. Importantly, this capability has not been seen for the other algorithm designs. We then apply our method to an in-situ chemical reaction to realize the monitoring of the reaction process. This excellent performance of our model on the trace classification task demonstrates the capability of machine learning methods on STM-BJ data analysis. Finally, we also explore the feasibility of utilizing the machine learning toolkit in other types of analysis on molecular junctions. We study the relaxation of gold electrodes after junction rupture (termed “snapback”) and its relation to pre-rupture evolution of gold contact. With the assistance of machine learning tools, we reveal that while the snapback can be well explained by this evolution history, the length of molecular conductance plateau is not related to either the snapback or this history. We also discover that the junction formation probability for short molecules is negatively correlated to the extension of single-atomic gold contact. Based on these findings, we conclude that the major mechanism for a molecular junction formation involves a molecule bridging across the junction prior to the rupture of the gold contact, in contrast to the previously-accepted picture where the molecule is captured immediately following the rupture. As a conclusion, we apply machine learning/deep learning on STM-BJ data analysis by developing a model to efficiently classify STM-BJ traces with high accuracy, which is important for measuring complex systems containing multiple species. We also demonstrate the feasibility of analyzing junction formation mechanisms with the help of machine learning tools.

Complementing electronic components with molecular analogs is a promising alternative to further miniaturization of conventional silicon electronic devices in the quest to achieve functional molecular nanoscale circuit elements. To this end, molecular units have been widely investigated to evaluate their suitability for future nanoelectronic circuit applications. Previous work has typically either focused on tightly packed layers of dithiol molecule-encapsulated gold nanoparticles or small oligomeric structures comprised of nanoparticles linked by a few dithiol molecules. In this thesis, we study the electrical and electronic properties of metal-molecular networks having an intermediate number of dithiol molecules both theoretically and experimentally. Electronic transport through self-assembled networks with tunable thiol molecule: gold nanoparticle ratios (ranging from 1:1 to 50:1) is studied using two-terminal electrical characterization techniques. The tunability of the electrical properties (e.g., resistance, current etc.) of the molecular networks on modifying the thiol molecule: gold nanoparticle ratios and/or type of molecule used was observed. Specifically, the current in the molecular networks studied typically decreased with increasing molecule: AuNP. For example, in gold-benzenedithiol molecular networks with approximately the same length-to-width ratios, current at low bias, 0.3 V, was found to decrease from the μA range in 1:1 ratio samples to the nA range in 50:1 samples. Additionally, many gold-benzenedithiol molecular networks which had linear I-V characteristics at low biases displayed nonlinearities in their I-Vs at higher biases. In such cases, the nonlinearities in the I-Vs at higher biases became more pronounced with increasing molecule: AuNP ratio. For example, in a control sample, consisting of only gold nanoparticles, linear I-V behaviour was observed, while the 50:1 gold-benzenedithiol molecular network displayed NDR with a measured peak-to-valley ratio of approximately 1.52. A linear resistor circuit model provided accurate approximations of the low bias I-V behaviour of the molecular networks. Experimental studies were complemented with first principles density functional theory-based simulations of the molecular networks. Linear chains and branched networks of interconnected benzenedithiol molecules and Au6 clusters were the systems of interest in this study. Calculated current-voltage characteristics of the metal-molecular networks exhibited nonlinearities and rectification with negative differential resistance (NDR) peaks that became more pronounced with increasing chain length of the linear chains. Peak-to-valley current NDR ratios as large as ~ 500 and rectification ratios of ~ 10 (0.25 V) were shown for linear and branched circuit elements, respectively, illustrating how charge transport through molecular-scale devices could be controlled with precision by modifying the structure and geometry of molecule-nanoparticle networks. Observed nonlinearities (e.g., NDR, hysteresis, and rectification) in the I-Vs of the self-assembled metal-molecular networks studied highlight their potential for application as circuit elements in future nanoelectronic devices and circuits, including memory, logic, switching and sensing. Additionally, the device level physical randomness and imperfections induced during fabrication of the metal-molecular networks, as well as the variability of the resistance of the networks on modifying the molecule: gold nanoparticle ratios can be applied for generating random binary sequences. / Graduate

A theoretical framework for calculating electron transport through molecular junctions is presented. It is based on scattering theory using a Green's function formalism. The model can take both elastic and inelastic scattering into account and treats chemical and physical bonds on equal footing. It is shown that it is quite reliable with respect to the choice of functional and basis set. Applications concerning both elastic and inelastic transport are presented, though the emphasis is on the inelastic transport properties. The elastic scattering application part is divided in two part. The first part demonstrates how the current magnitude is strongly related to the junction width, which provides an explanation why experimentalists get two orders of magnitude differences when performing measurements on the same type of system. The second part is devoted to a study of how hydrogenbonding affects the current-voltage (I-V) characteristics. It is shown that for a conjugated molecule with functional groups, the effects can be quite dramatic. This shows the importance of taking possible intermolecular interactions into account when evaluating and comparing experimental data. The inelastic scattering part is devoted to get accurate predictions of inelastic electron tunneling spectroscopy (IETS) experiments. The emphasis has been on elucidating the importance of various bonding conditions for the IETS. It is shown that the IETS is very sensitive to the shape of the electrodes and it can also be used to discriminate between different intramolecular conformations. Temperature dependence is nicely reproduced. The junction width is shown to be of importance and comparisons between experiment as well as other theoretical predictions are made. / QC 20101118

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Molecular electronics based on bottom-up electronic circuit design is a potential solution to meet the continuous need to miniaturize electronic devices. The development of highly conductive molecular wires, especially for long distance charge transfer, is a major milestone in the molecular electronics roadmap. A challenge presented by single molecule conductance is to define the relative influence of the molecular "core" and the molecular "interconnects" on the observed currents. Much focus has been placed on designing conductive, conjugated molecules. However, the electrode-molecule contacts can dominate the responses of metal-molecule-metal devices. We have experimentally and theoretically probed charge transfer through single phenyleneethynylene molecules terminated with thiol and carbodithioate linkers, using STM break-junction and non-equilibrium Green's function methods. The STM break-junction method utilizes repeatedly formed circuits where one or a few molecules are trapped between two electrodes, at least one of which has nanoscale dimensions. The statistical analysis of thousands of measurements yields the conductance of single molecules. Experimental data demonstrate that the carbodithioate linker not only augments electronic coupling to the metal electrode relative to thiol, but reduces the barrier to charge injection into the phenyleneethynylene bridge. The theoretical analysis shows that sulfur hybridization provides the genesis for the order-of-magnitude increased conductance in carbodithioate-terminated systems relative to those that feature the thiol linker. Collectively, these data emphasize the promising role for carbodithioate-based connectivity in molecular electronics applications involving metallic and semi-conducting electrodes. One of the strategies for building molecular wires that can transfer charge over long distance is to incorporate metal ions into the conductive molecular core. Peptide nucleic acid (PNA) is a great candidate for this purpose. Studying the conductivity of PNA can not only contribute to a better understanding of charge transfer through biomolecules, but can also help develop better molecular wires and other building blocks of molecular electronics. We study the charge transfer of PNA molecules using the STM break-junction technique and compare with traditional macroscopic voltammetric measurements. By measuring the resistance of different PNA molecules, we hope to develop a deep understanding of how charge transport though PNA is affected by factors such as the number and type of natural and artificial bases, embedded metal ions, pH, etc. Self-assembled monolayers (SAMs) of porphyrins are of great interest due to their diverse applications, including molecular devices, nano-templates, electrocatalysis, solar cells, and photosynthesis. We combined a molecular level study of the redox reactions using electrochemical scanning tunneling microscopy (EC-STM) with a macroscopic electrochemical technique, cyclic voltammetry (CV), to study two redox active porphyrin molecules, TPyP (5,10,15,20-Tetra(4-Pyridyl)-21H,23H-Porphine) and 5, 10, 15, 20-tetrakis (4-carboxylphenyl)-21H, 23H-porphine (TCPP). We showed that the adsorbed oxidized TPyP molecules slowly change to brighter contrast, consistent with the appearance of the reduced form of TPyP, under reduction condition (0.0VSCE). The time scale of the slow reduction is in the order of tens of minutes at 0.0VSCE, but accelerates at more negative potentials. We propose that protonation and deprotonation processes play an important role in the surface redox reaction due to geometric restriction of the molecules adsorbed on the surface. EC-STM and CV experiments were performed at various pH values to investigate the mechanism of this anomalously slow redox reaction. Our results show that the increased concentration of H+ hinders the reduction of porphyrins, a feature that has not been reported preciously. This provides insight into the details of the surface redox reaction. / Chemistry

<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)

This thesis investigates the mechanically controlled break junctions, with a particular emphasis on elucidating the behaviour of molecular currents at room temperature. The core of this experimental investigation involves a detailed analysis of conductance, examining how it varies over time and with changes in the gap between electrodes. Additionally, this study thoroughly evaluates transmission properties, coupling effects, and current characteristics. A pivotal aspect of the research was the meticulous current measurement, followed by carefully selecting optimal data sets. This process set the stage for an in-depth analysis of resonant tunnelling phenomena observed through a single channel. Notably, these experiments were conducted under open atmospheric conditions at room temperature. A significant finding from this study is the recognition that our current model requires refinement. This adjustment is necessary to more accurately encapsulate a broader spectrum of molecular transport mechanisms. Furthermore, this work significantly advances our comprehension of quantum effects in single-molecule junctions, particularly concerning similar molecules to Corannulene extending to some organometallics. One of the essential disclosures is the identification of deviations in the transport model, primarily attributable to electron-electron interactions. This insight is crucial as it paves the way for developing a more comprehensive and precise model, enhancing our understanding of molecular-scale electronic transport.:List of Figures xi List of Tables xiii Acronyms xiii Terminology xv Symbols xvi Abstract xvii 1 Introduction 1 1.1 Motivation and Objectives . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.2 Molecular Electronics Background . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 RelatedWork, the State of Art . . . . . . . . . . . . . . . . . . . . . . . . . 4 1.4 Structure of the work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2 Methods and Implementations 7 2.1 Mechanically Controlled Break Junctions Principle . . . . . . . . . . . . . . 8 2.1.1 Setups forMCBJ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.1.2 Measurement Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.1.3 Electrical Diagramof theMeasurement . . . . . . . . . . . . . . . . . 15 2.1.4 Criteria to Select the Data . . . . . . . . . . . . . . . . . . . . . . . . 15 2.2 Experiment Realisation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 3 Molecules and Transport 20 3.1 Molecules in the Scope of this Thesis . . . . . . . . . . . . . . . . . . . . . . 20 3.1.1 Fixation of pi-Conjugated Molecules on Gold Surfaces via Thiol Bond 20 i 3.2 Ballistic Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 3.2.1 Tunnelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 3.3 Single Level Model (SLM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 3.3.1 Chemical Nature of theMolecular Channels . . . . . . . . . . . . . . 24 3.4 TransportMechanisms inMolecules attached toMCBJ . . . . . . . . . . . . 25 4 Results and Discussions 28 4.1 Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 4.1.1 Opening Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 4.1.2 HistogramfromtheMeasurements . . . . . . . . . . . . . . . . . . . 30 4.2 Current . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 4.2.1 Current in Toluene . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 4.2.2 Current in Corannulene . . . . . . . . . . . . . . . . . . . . . . . . . 44 4.2.3 Current in Fe+3 Salen . . . . . . . . . . . . . . . . . . . . . . . . . . 49 4.2.4 Current Measurement after Consecutive Opening - Case Study: Fe+3 Salen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 4.2.5 Single LevelModel - Case Study: Corannulene . . . . . . . . . . . . . 53 4.2.6 Lorentzian Distribution and Fitting in Salen organometallics and Corannulene . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.2.7 Single Level Model - Study of the case: Fe+3 Salen . . . . . . . . . . 66 4.3 Transmission and Coupling . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 4.3.1 Transmission and Coupling - Case Study: Fe+3 Salen . . . . . . . . . 70 4.4 Conclusive Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 4.4.1 Hypothesis of Scattering . . . . . . . . . . . . . . . . . . . . . . . . . 76 5 Conclusion and Further Work 78 5.1 The CurrentMeasurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79 5.2 Further Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80 A Current with Mean Normalization i A.1 Categories ofMeasurements . . . . . . . . . . . . . . . . . . . . . . . . . . . ii A.1.1 Measurements without hysteresis or very small . . . . . . . . . . . . . ii A.1.2 Measurements with hysteresis . . . . . . . . . . . . . . . . . . . . . . vi A.2 Measurements without Fitting . . . . . . . . . . . . . . . . . . . . . . . . . . xii B Our best fits where the SLM fails xi