Construction of a low temperature STM and studies of large molecular systems

Several aspects in the field of molecular self assembly are addressed in this thesis. Thanks to the scanning tunnelling microscope (STM), structural, electronic and magnetic properties on surfaces can be studied down to the size of a single atom. In this thesis, I designed and built a STM operating in ultra high vacuum at liquid helium temperature. In Chapter 2 I highlight the design and key features of this system. I describe the development of UHF cabling under severe design constraints, intended to be used for a state of the art STM time resolved technique with nanosecond time resolution. The performance of the instrument is demonstrated by a few benchmark measurements. The arrangement of molecules on surfaces is sensitive to intermolecular interactions, but also to molecule-surface interactions. The surfaces used as support for molecules must therefore be well characterized from the structural, chemical and electronic points of view. Using STM, work function (WF) variations at the nanoscale on hexagonal boron nitride on rhodium (h-BN/Rh(111)) are investigated. These variations are the key to understanding the arrangement of molecules on this surface, yet their magnitude is disputed. Local WF is measured in two ways and compared with KPFM maps. The results provide insight about hot electronic states near surfaces, called image potential state, and their lifetimes. A new phase of h-BN/Rh(111) was discovered and a preliminary characterization of its origin is presented. STM can provide valuable information for understanding the arrangement and the electronic properties of molecules on surfaces. These capabilities are harnessed in Chapter 4 to study large molecules on metallic surfaces, and on thin dielectric surfaces. Angiotensin-II is a peptide, comprising 8 amino acids, small enough to fit in the nanometric cavities of h-BN/Rh(111). This peptide can be brought to the surface intact using electrospray ion-beam deposition. On a Cu surface, we observe that the peptides interact strongly with the substrate, and this interaction determines their arrangement and electronic properties. However, on a single layered sheet of h-BN/Rh(111), the peptides are sufficiently decoupled from the metal, and their electronic properties conserved. In a series of preliminary measurements, these electronic properties are studied in order to discriminate between the amino acids the peptide is made of. Additional strategies that may enable peptide sequencing by STM are discussed. Turning to still larger molecules, cytochrome-C is a protein made of 104 amino acids. On plain metal surfaces, its size and flexibility make the number of conformations available to it enormous. In Chapter 5 this protein is deposited on a nanopatterned surface, forcing it to adhere to a square grid. This makes the number of possible conformations manageable. A detailed look at these conformations reveals many details about how the proteins move on the surface and find their place on the grid. For example, it can inferred that short segments of the protein can diffuse on the surface at room temperature, while longer segments are immobilized. The critical length where diffusion begins is used to estimate the diffusion barrier energy. Furthermore, a simplified simulation of the landing process yields a good fit to the experimentally observed conformation distribution. This fit confirms the flexibility of the proteins and the negligible role of the amino acid side chains.

Scanning tunneling microscopy on large bio-molecular systems on surfaces

Sebastian Koslowski

The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of intriguing functionalities. A key question in mimicking their assembly and function is the precise understanding of the specific interactions between the contained amino acids on the level of a sub-molecular length scale. An excellent tool to probe samples at these length scales is available with scanning tunneling microscopy (STM) and its operation under the controlled conditions of ultra-high vacuum (UHV) and low temperature. Within this thesis it is demonstrated how high-resolution studies by STMin combination with a controlled sample preparation by electrospray ion beam deposition (ES-IBD) under UHV conditions allows for the structural determination of peptides on surfaces. Furthermore the results presented here contribute to the development of a method capable of directly identifying individual amino acids within a peptide sequence. The structural and electronic properties of molecules on surfaces crucially depend on their interaction with the underlying substrate. Implementing a thin dielectric layer on the metallic surface, electronically decouples molecules from the substrate and enables an unperturbed observation of the molecular electronic structure. In Chapter 2 the properties of hexagonal boron nitride (h-BN) on Rh(111) as decoupling layer are assessed on behalf of the structural and electronic properties of the molecular model system pentacene adsorbed on it. In a second part of this chapter the discovery and the characterization of a new phase of h-BN/Rh(111) is described. In Chapter 3, we gained insight into the properties of amino acids on metal surfaces by utilizing the capability of the STM to probe the structure and the electronic characteristics in high resolution imaging and scanning tunneling spectroscopy (STS). As a second important aspect of this chapter, the modification of STM tips with amino acids is investigated as a method to enhance the structural and electronic resolution. An experimental protocol allowing to adhere amino acids on the STM tip be could developed. Using functional STM tips in STS experiments on amino acids enabled the observation of specific molecular resonances. An obstacle in investigating large bio-polymers, such as natural peptides, is their high structural complexity and conformational freedom. Therefore the utilization of custom designed synthetic sequences tailored towards a specific property is a good approach. In Chapter 4 studies performed on two synthetic peptide sequences deposited by ES-IBD on an Au(111) surface are discussed. The first sequence assembled in ordered two-dimensional networks. A folded gas-phase conformation could be utilized to rationalize the observed structures in the networks. Subsequently it was shown that the self-assembly behavior of the peptide could be steered towards chain-like assemblies by modifying the sequence at the peptide C-terminal. Using specific amino acid functionalized STM tips a sensitivity towards an amino acid of the same type in the peptide sequence could be observed. Thereby a partial sequencing of the synthetic peptide was enabled.

EPFL2017

On-Surface Assembly and Reactions of Organic Molecules in Ultra-High Vacuum

Claudius Morchutt

This thesis comprises the study of two types of 2D materials, those stabilized by non-covalent and those by covalent interactions. They are synthesized and studied on well-defined metallic surfaces in ultra-high vacuum (UHV). The self-assembly of terephthalic acid (TPA) on Ag(100) is explored. TPA stays intact upon deposition at room temperature (RT) and forms islands stabilized by hydrogen bonds. TPA islands influence the homoepitaxial growth of silver and reduce the sticking coefficient of Ag atoms. At RT Ag atoms intercalate TPA islands which are not disrupted. In contrast, TPA molecules in conjunction with Mg atoms on Ag(100) results in tip-induced altering of the surface. The electric field between tip and sample interacts with Mg atoms and TPA, which leads to a restructuring of the step-edges during scanning. Moreover, the self-assembly of the organic semiconductor 2,7-dicyano[1]benzothiene[3,2-b]benzothiophene (cBTBT) on Ag(111) at RT is presented. The pro-chiral molecules form compact islands with a chevron-like structure containing both enantiomers. Deposition of Fe atoms leads to an amorphous metal-organic coordination network (MOCN). Statistical analysis reveals that conformational entropy plays a critical part in its stabilization. Phase segregation into spatially homogeneously crystalline domains of molecules and metal atoms upon annealing suggests that the amorphous network is kinetically trapped at RT during the preparation process. The second part presents the on-surface synthesis of 2D polymers via different coupling schemes. First, the Ullmann coupling on Au(111) is explored. The molecule 1,3,5-tris(4-bromophenyl)benzene (TBPB) debrominates upon annealing and polyphenylene is formed. To investigate the influence of metal substrates on the dehalogenation, a single layer of hexagonal boron nitride as well as graphene grown on Ni(111) is introduced. On both surfaces TBPB forms self-assembly islands stabilized by halogen bonds, while on bare Ni(111) the substrate-molecule interaction dominates resulting in structures without long-range order. Upon annealing on both surfaces dehalogenation is induced and 2D nanostructures are formed. On bare Ni(111) the precursor molecules merely decompose. The experimental annealing temperatures are consistent with debromination barriers calculated by DFT. An example of the synthesis of tailor-made 2D structures by using particularly designed precursor molecules is also given. A terminal alkyne with a triazine core undergoes on-surface Glaser coupling and cyclotrimerization on Au(111) resulting in nitrogen doped 2D polymers. Finally, a comprehensive study of the on-surface decarboxylation reaction of 1,3,5-tris(4-carboxyphenyl)benzene (TCPB) on Cu(111) is presented. TCPB deprotonates upon deposition on Cu(111) at RT and self-assembles in compact islands. The self-assembly is stabilized by ionic hydrogen bonds between deprotonated and negatively charged oxygen atoms and hydrogen atoms of neighboring molecules. Annealing leads to decarboxylation and formation of 2D nanostructures. The reaction occurs in a clean fashion because CO2 leaves the surface. In addition, STS reveals that the lowest unoccupied molecular orbital (LUMO) of the 2D polymer is destabilized compared to the LUMO of the monomer although the pi-electron system is more extended in the polymer. The decarboxylation impacts the energy position of the LUMO to a greater extend which is corroborated by DFT calculations.

EPFL2016

Scanning Tunneling Luminescence of Pentacene Nanocrystals

Alexander Kabakchiev

Organic semiconductors are promising materials for future electronic and electroluminescence applications. A detailed understanding of organic layers and nano-sized crystals down to single molecules can address fundamental questions of contacting organic semiconductors at the nanometer limit and obtaining luminescence from them. In this thesis, electroluminescence spectra from pentacene, a policyclic hydrocarbon (acene), are discussed. The luminescence is induced by the current from the tip of a scanning tunneling microscope (STM). Pentacene is an organic semiconductor which gained a lot of attention in technology because of its electronic properties suitable for applications in thin film devices. Moreover, recent fundamental studies employed pentacene as a standard to demonstrate sub-molecular resolution by scanning probe techniques. This work reports the first observation of light emission from nanometer-sized pentacene crystals grown on an ultrathin insulating layer on noble metal surfaces. Different STM-techniques are combined to characterize the individual systems studied with respect to topography, crystal structure, electronic properties and work function changes. The initial step of the project was the implementation of an optical system for light collection from the tunnel-junction of a low-temperature STM. In the set-up, a novel approach based on the use of in situ adjustable lenses has been realized. Three lenses placed in the vicinity of the tip-apex allow light collection into three independent channels which can be used for versatile optical analysis. An important part in the characterization of the organic system was to clarify the interaction between adsorbed molecules and substrates. We investigated individual pentacene molecules on different ultrathin insulator-metal systems. With the STM tip in tunnel contact, the molecules are situated in a double barrier junction formed by the insulating layer on one side and the vacuum gap on the other side. The metal surface and the STM-tip form the electrodes. The electronic properties of pentacene in this configuration have been characterized. Insulator-metal-systems, which provide a good electronic decoupling for pentacene from the metal, have been chosen as substrates for the growth of pentacene nanocrystals. Using the sub-molecular resolution of the STM we resolved the structure of the top-layer of the pentacene nanocrystals and found that the crystal phase agrees with the pentacene bulk structure. Moreover, the comparison of charge injection barriers between individual molecules and nanocrystals of pentacene indicates a significant change of electronic properties after the formation of ordered structure from the individual building blocks. Optical spectroscopy of the emitted light reveals an excitonic emission from the nanocrystals, which is in very good agreement with photoemission spectra of macroscopic crystals. Although a highly localized current-injection by the STM tip is used for excitation, it can be concluded that the source of light emission is delocalized. In contrast to luminescence measurements reported for other organic materials in STM, the excitation is not localized on the individual molecule, into which a charge is injected by the STM-tip. Our study indicates the importance of inter-molecular coupling leading to a high mobility of the excited state which has to be considered in the framework of STM-induced luminescence. A further result is the observation of the Stark shift of pentacene luminescence, that has so far not been measured at large electric fields of the order of 1V/nm. The evaluation of the Stark shift provides information on dipole and polarizability change during the decay of an exciton. The measured large dipole change of the lowest singlet exciton in pentacene indicates a mixing of the Frenkel exciton (FE) with a small contribution of charge-transfer (CT). Finally, we developed a set-up for photon correlation measurements in the STM. The properties of photon statistics is a means which can unambiguously prove that the luminescence is due to a single-photon source, i.e. a light source which emits no more than one photon at a time. A typical example of such a source is the emission from a single molecule. We performed photon correlations measurements of the luminescence from pentacene and C60 nanocrystals. While the excitonic bulk emission of pentacene is not expected to represent a single photon emitter, we also did not observe anticorrelations in the case of C60 indicating the importance of the local environment in the STM-junction, e.g. the short distance to the metal electrodes.

EPFL2010