Supramolecular assembly, chirality, and electronic properties of rubrene studied by STM and STS

This thesis presents the first experimental results of a scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) investigation of rubrene at the supramolecular, molecular and submolecular level. Based on its semiconducting and fluorescent properties, this molecule is of particular interest in view of the emerging fields of molecular electronics and optoelectronics which could one day replace the conventional technology relying on semiconductors such as silicon and gallium arsenide. The goal is the substitution of these inorganic materials by cheap and flexible layers of semiconducting organic molecules for a new class of diodes and transistors, as well as the realization of electronic switches based on individual molecules. One fundamental approach is to take advantage of the molecular self-assembly behavior which results in the creation of well-ordered supramolecular structures. The investigations of the self-assembly of rubrene adsorbed on metal surfaces (Au(111), Au(100), Ag(111), and Ag(100)), which were carried out within the framework of this thesis, show a surprising diversity of supramolecular structures. Amongst other shapes, the molecules organize themselves into geometries of perfect hexagonal and pentagonal symmetry and create multifaceted patterns on the surface. A fascinating peculiarity consists in the spontaneous construction of nested structures which are built up by a hierarchical self-assembly of individual molecules into pentagonal supermolecules which form in a second step perfect supramolecular decagons. The geometric shape of rubrene is characterized by a structural asymmetry leading to the existence of two mirror imaged versions of the molecule which are not superimposable to each other, such as for instance our left and right hand or the helical DNA. The aspect of chirality is crucial for basic processes in living systems and calls for a fundamental understanding of the interaction mechanisms occurring between chiral molecules. The experiments on rubrene reveal that the intermolecular bonding differentiates between the two chiral types of the molecule (chiral recognition), yielding the self-organization into homochiral structures. These assemblies exhibit a geometry which is again chiral, demonstrating a propagation of chirality throughout the three stages of the supramolecular hierarchy. The semiconducting behavior of rubrene is furthermore probed by STS measurements detecting the energetic positions of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO). The experimental data uncover that different adsorption conformations exhibit characteristic HOMO energies and reveal adsorption conformations of rubrene which preserve the intrinsic electronic structure of the free molecule. Furthermore, a switching of the molecular conformation and the electronic structure of one rubrene conformer is induced with the STM.

Investigation of low-dimensional supramolecular architectures by low-temperature scanning tunneling microscopy

Sylvain Clair

In this thesis we report investigations on supramolecular architectures assembled at well-defined metal surfaces. Supramolecular chemistry is dedicated to the study and use of non-covalent interactions to build highly organized molecular arrangements, aiming ultimately at creating systems with tailored properties and useful functions. The adaptation of its powerful principles to fabricate molecular systems at surfaces has already been proven to be very promising; the extended possibilities for the choice of on the one hand molecules with defined size, shape, symmetry and function, and on the other hand substrates with controlled composition, symmetry and patterning allow for a quasi-infinite tuning of the structure and properties of the respective assemblies. The Scanning Tunneling Microscope (STM) is a tool particularly efficient for the nanoscale elucidation of supramolecular systems at surfaces, simultaneously providing topographic and spectroscopic information at the single-atom level. In this regard, a new Low-Temperature STM (LT-STM) operational at temperatures in the range 5 to 400 K has been constructed. A detailed description of the instrument is provided and the demonstration of its exquisite performance represents a major achievement. In addition to local STM studies, complementary experiments were performed with a synchrotron radiation source using integral techniques, namely X-ray Absorption Spectroscopy (XAS) and X-ray Magnetic Circular Dichroism (XMCD). We present results obtained with the linear organic linker 1,4-benzenedicarboxylic acid (terephthalic acid - TPA) on the Au(111), Cu(111) and Cu(100) surfaces. The three-dimensional design principles of supramolecular chemistry could be successfully adapted to these low-dimensional systems. TPA molecules adsorbed on Au(111) organize in two-dimensional molecular sheets, wherein the typical one-dimensional hydrogen-bonded chain motif is found. We show that the inhomogeneities induced by the surface reconstruction can be used to examine the response of the supramolecular self-assembly. In particular, variations in the hydrogen bond length of up to 20% are encountered. On Cu(111), a strict commensurability of the supramolecular sheet to the substrate is not possible because of the reduced lattice spacing of the latter, and the creation of defects is analyzed. Due to their peculiar reactivity, the elbow sites of the reconstructed Au(111) surface act as nucleation centers in the epitaxial growth of transition metals (Fe, Co, Ni), leading to the formation of regular arrays of nanoscale metallic islands. We take advantage of this patterning to steer the formation of metallosupramolecular nano-architectures. Co-deposited TPA molecules attack both Fe and Co clusters and metal-carboxylate linkages evolve. Depending on the deposition parameters, nanoporous grids, mesoscopically organized stripes or truly one-dimensional linkages are obtained. Furthermore, the dynamics of the formation of the nanogrids are monitored in situ. Finally, we report investigations of the magnetic and electronic properties of surface-supported coordination architectures by means of XAS and XMCD. We studied Fe-terephthalate systems engineered on a Cu(100) substrate. Both mononuclear Fe(TPA)4 compounds and diiron centers structures in 2D Fe-TPA lattices exhibit a paramagnetic behavior. Moreover, we demonstrate the decisive influence of the ligand rather than the substrate on the electronic ground state of the metal centers, thus illustrating new vistas to effectively tailor the valence state and magnetic moment of transition metal atoms at surfaces.

EPFL2004

Single-molecule-level characterization of supramolecular systems at surfaces

Dietmar Payer

This thesis deals with the self-organization of individual building blocks, specifically organic molecules and metal atoms, into supramolecular structures on metal surfaces under ultra high vacuum conditions (UHV). Self-organization of supramolecular systems is a promising candidate for a bottom-up approach in the fabrication of complex structures with specific properties. This process is steered by interactions between functional groups of the individual building blocks and is of apparent interest to gain a detailed understanding of the influence and the behavior of these functional groups enabling intermolecular binding. In the first part of the thesis, we investigate hydrogen bonded structures on metal surfaces. Of especial interest is the possibility of the formation of ionic hydrogen bonds, a special class of hydrogen bond which connects a charged donor (acceptor) and a neutral acceptor (donor) and is important in biological systems. By combined Scanning Tunneling Microscopy (STM), X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) measurement we show the deprotonation of carboxylic functions in the molecules, forming carboxylate groups involved in intermolecular binding. With our complementary experimental and theoretical examinations we clearly show that the carboxylate groups are indeed still charged although adsorbed onto a conducting metal surface and that the observed structures can be computationally reproduced by using these charges in classical molecular dynamic calculations. Our investigations clearly reveal that all requirements for the formation of ionic hydrogen bonds in these samples at metal surfaces under solvent free conditions are fulfilled. In the second part, the confinement of surface state electrons in self-assembled hydrogen-bonded structures is investigated. The examined structure contains two-dimensional cavities, with different inner diameters in the periodic arrangement and in domain boundaries. Inside the cavities we detect a spatially localized modification in the local density of states (LDOS) of the Ag(111) surface state electrons. The energy of the peak correlates with the cavity area as predicted by a simple "particle in a box" model. This clearly shows that the surface state electrons form a confined state inside the cavities. Furthermore we examine self-assembled periodic structures as templates for binding single macrocyclic molecules. The macrocyclic molecules can be deposited by sublimation, as STM-topographs with submolecular resolution reflect the shape of the intact molecules and reveal a coverage dependent aggregation behavior. We show that it is possible to fabricate a structure in which at most one macrocyclic molecule per pore can be found in a defined binding position. In the last part of the thesis we investigate the influence of individual metal atoms on the chemical activity and the self-assembly process of molecules on metal surfaces. First, we demonstrate the high chemical reactivity of these metal atoms. In our experiments we address the chemical reactivity of static active sites, like kinks and step edges, and of dynamic active sites, like the metal atoms, separately. Doing this we show that a non-negligible amount of the chemical reactivity of a metal surface is due to this dynamic adatom gas. Furthermore the influence of metal atoms on the structure formation of organic molecules is investigated. We show that two-dimensional structures based on a complex formation between metal centers and ligands can be formed and that the coordination number is independent of the substrate symmetry. Furthermore, we show the possibility that on metal surfaces one can prepare three-fold coordinated Fe-centers, a coordination number which is rarely seen in three dimensional chemistry. In the last part we study catenanes, which consist of two interlocked macrocyclic molecules. Main interest is on the confirmation of a structural change of the catenanes adsorbed on a metal substrate. For our experiments we use the fact that the catenanes are designed to "trap" a Cu-atom by complex formation. As this reaction is associated with a structural change and a change in intermolecular interaction, we can verify a reaction of catenanes adsorbed onto a surface with Cu adatoms and therefore a structural alteration by simply imaging the formed structures. Our measurements show the possibility of depositing large molecules like catenanes by sublimation and of their potential for use as molecular machines adsorbed onto metal surfaces.

EPFL2007

Growth and characterization of specific self-assembled supramolecular architectures at crystal surfaces

Marta Canas Ventura

In the framework of this thesis self-assembled supramolecular architectures of several molecular species on crystal metal surfaces are characterized. These investigations combine results obtained by means of scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), X-Ray Photoelectron Spectroscopy (XPS), and Near-Edge X-Ray Absorption Fine Structure Spectroscopy (NEXAFS). The interest in controlling the formation of specific arrangements of supramolecular ensembles at surfaces is motivated to a great extent by the prospect to design molecular devices and nanomaterials with customized properties. The goal is a "spontaneous" creation of targeted, well-ordered molecular architectures, which shall be achieved by taking advantage of the molecule's propensity to self-assemble. Control means, in this context, predictability. This term address the accuracy of the prediction of the structures resulting from molecular self-assembly for systems exhibiting different characteristics. Here, system stands for a particular combination of a single-crystal surface and adsorbed molecular species. In a first part, the focus is given to the impact of a Pd(111) surface exhibiting high chemical activity. Due to surface induced deprotonation two resulting chemical states are found for the adsorbed terephthalic acid species. Deprotonation of the carboxyl moieties is observed to affect the topology of the molecular assemblies even though hydrogen bonds (H-bonds) are responsible for the stabilization of assemblies of both, intact and deprotonated molecular species. Therefore, the selective fabrication of a single specific molecular structure becomes a challenge when the surface is prone to induce chemical reactions. Secondly, a molecular species exhibiting conformational flexibility is studied on a largely inert Au(111) surface. It is observed that the characteristic conformational flexibility is also active on the surface, and the molecule is found to adopt different conformations depending on the locally most favorable bonding motif. In particular, phenyl groups may undergo a rotation such that one-dimensional chains can be stabilized by means of intermolecular H-bonds. This phenomenon is very interesting from an adsorbate-substrate interaction point of view, but it limits the predictability of supramolecular structures formed upon self-assembly. In a third step, a comparative study of the self-assembly of three closely related molecular species highlights the impact of concurrent competing intermolecular interactions. Molecules exhibiting an increasing number of possible interaction channels are found to assemble into an increasing number of distinct supramolecular architectures. The most flexible molecular species allowing for different hydrogen-bonding patterns as well as dipolar coupling self-assembles into various structurally complex architectures. Structural predictability, however, is low since the formation of one or the other assembly appears to depend on small variations in sample preparation conditions and on poorly controllable local surface properties. Finally, a system where the resulting structures fully agree with predictions evidences the possibility to control the formation of targeted specific supramolecular architectures. The formation of well ordered bimolecular ribbons and wires over extended length scales is accomplished by the rational choice of both, complementary building blocks for the selective formation of three-fold H-bonds and a nanostructured surface to guide the molecular self-assembly. Furthermore, the impact of H-bond formation on the electronic structure of self-assembled molecular building blocks is probed by STS measurements. The experimental data reveal shifts in the electronic levels depending on the H-bond configuration and on the local characteristics of the underlying surface. In order to improve the precision of such a study, single molecules, homo- and heteromolecular dimers as well as trimers are successfully isolated and assembled by molecular manipulation with the STM tip. Further STS studies on such artificially assembled structures are suggested.

EPFL2008