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Scanning Tunneling Microscopy and Atomic Force Microscopy Investigation of Organic Molecules

Scanning Tunneling Microscopy and Atomic Force Microscopy Investigation of Organic Molecules

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MICHNOWICZ, Tomasz, 2019. Scanning Tunneling Microscopy and Atomic Force Microscopy Investigation of Organic Molecules [Dissertation]. Konstanz: University of Konstanz

@phdthesis{Michnowicz2019Scann-46705, title={Scanning Tunneling Microscopy and Atomic Force Microscopy Investigation of Organic Molecules}, year={2019}, author={Michnowicz, Tomasz}, address={Konstanz}, school={Universität Konstanz} }

<rdf:RDF xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bibo="http://purl.org/ontology/bibo/" xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:void="http://rdfs.org/ns/void#" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > <rdf:Description rdf:about="https://kops.uni-konstanz.de/rdf/resource/123456789/46705"> <dc:rights>terms-of-use</dc:rights> <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/41"/> <dcterms:abstract xml:lang="eng">The importance of organic chemistry in modern science and industry has lead to an emergence of a variety of advanced techniques for the identification of organic molecules. The most common of them are vibrational spectroscopies, diffraction techniques and nuclear magnetic resonance spectroscopy (NMR). Resolving the molecular structures with thesemethods relies on the unique responses and interactions of the ensemble of the molecules to the applied stimuli, such as electromagnetic radiation or particle beams. Another approach to the structural determination relies on the real-space investigation and is offered by microscopy techniques. One of them, scanning tunneling microscopy (STM) is capable of identification of the organic structures by imaging explicitly single molecules at the nanoscale. Further integration of non-contact atomic force microscopy (nc-AFM) with STM allows direct observation of the molecular structures with atomic resolution. This unique possibility can be utilized to study chemistry with extraordinary precision at the scale of individual molecules. In this thesis, a homebuilt combined STM/nc-AFM instrument is used to investigate three distinct organic systems, focusing on the structure elucidation and chemical reactivity of single organic molecules. The first research project concerns the structural and electronic properties of a tetracenothiophene (TCT), adsorbed on the Cu(111) surface. The TCT molecule is a pentacene derivative with a sulfur-containing thiophene group. The two pathways of an electric-field-driven desulfurization reaction of this thiophene group are demonstrated: a two-step pathway and a direct transition from the intact to the desulfurized state. The reaction is triggered by positioning the STM tip above the thiophene moiety and ramping the bias voltage. In the two-step pathway, the first step is induced only by the presence of the electric field. The second step can be induced by applying the electric field and simultaneously injecting the electrons into the system. With both high-resolution STM and nc-AFM imaging, we identify the two steps as the subsequent splitting of the two C-S bonds of the thiophene group. As a result, the two carbon atoms of the former thiophene group form covalent bonds to Cu surface atoms. After the reaction, the desulfurized molecule is anchored to the substratemechanically. The conductance measured through the molecule suspended between the tip and the sample electrodes increases by »50 % after the reaction. Due to the properties of the facile thiophene-copper bonding, it is of interest as an anchoring technique in single-molecule electronics. In the second project, the chemical reactions induced by hyperthermal collisions of Reichardt’s Dye molecules with a metal surface are investigated. Collisions with hyperthermal kinetic energies lead to a non-equilibrium process where the high energy of themolecules is dispersed in a very short time. By controlling the kinetic energy of the incident organic molecules with Electrospray Ionization-Beam Deposition (ES-IBD), we accessed new, thermally inaccessible states. We identified both thermally and kinetically created species of Reichardt’s Dye with the STM/nc-AFMimaging and compared the results. Hyperthermal deposition of Reichardt’s Dye indeed leads to the creation of new states that are inaccessible by thermal activation. This approach to reaction kinetics can be applied to different systems to yield new molecular species. In the last chapter, we test the ability of STM/nc-AFM to identify the branched structures of small carbohydrates. This class of molecules is representative of many biologically active molecules that are difficult to analyze with traditional methods such as mass spectrometry and nuclearmagnetic resonance spectroscopy. The carbohydrates can exhibit a polymerized and branched structure, often consisting of monosaccharideswith identical mass and composition. Therefore, the full identification of their structure, if possible at all, requires a series of precise experiments, significantly increasing the material consumption. Carbohydrates, as well as proteins and peptides, are often not available in required amounts. The real space approach to investigating carbohydrates, including STM and nc-AFM, may provide information about the branching aspect of carbohydrate structure at low material cost, thanks to the possibility of structural identification performed on a single organic molecule. We analyzed a model system consisting of linear pentamers and branched hexamers of mannose. The studies of these linear carbohydrates lead to the identification of single monosaccharide units on Cu(100) and Cu(111). We also identified and assigned folded structures encountered during the experiments to single and double pentamers ofmannose. Moreover, the imaging allowed us to approximately localize the branching points in the branched hexamers of mannose. This effort demonstrates the potential of using STM/nc-AFMas a complementary technique for the structural identification of carbohydrates.</dcterms:abstract> <dcterms:issued>2019</dcterms:issued> <dcterms:title>Scanning Tunneling Microscopy and Atomic Force Microscopy Investigation of Organic Molecules</dcterms:title> <dc:creator>Michnowicz, Tomasz</dc:creator> <foaf:homepage rdf:resource="http://localhost:8080/jspui"/> <dcterms:rights rdf:resource="https://kops.uni-konstanz.de/page/termsofuse"/> <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/> <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/46705/3/Michnowicz_2-biulkpo29zf25.pdf"/> <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-08-21T08:05:19Z</dcterms:available> <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-08-21T08:05:19Z</dc:date> <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/rdf/resource/123456789/41"/> <dc:language>eng</dc:language> <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/46705"/> <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/46705/3/Michnowicz_2-biulkpo29zf25.pdf"/> <dc:contributor>Michnowicz, Tomasz</dc:contributor> </rdf:Description> </rdf:RDF>

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