Does the Surface Matter? Hydrogen-Bonded Chain Formation of an Oxalic Amide Derivative in a Two- and Three-Dimensional Environment

We report on a multi-technique investigation of the supramolecular organisation of N,N-diphenyl oxalic amide under differently dimensioned environments, namely three-dimensional (3D) in the bulk crystal, and in two dimensions on the Ag(111) surface as well as on the reconstructed Au(111) surface. With the help of Xray structure analysis and scanning tunneling microscopy (STM) we find that the molecules organize in hydrogen-bonded chains with the bonding motif qualitatively changed by the surface confinement. In two dimensions, the chains exhibit enantiomorphic order even though they consist of a racemic mixture of chiral entities. By a combination of the STM data with near-edge X-ray absorption fine-structure spectroscopy, we show that the conformation of the molecule adapts such that the local registry of the functional group with the substrate is optimized while avoiding steric hindrance of the phenyl groups. In the low coverage case, the length of the chains is limited by the Au(111) reconstruction lines restricting the molecules into fcc stacked areas. A kinetic Monte Carlo simulated annealing is used to explain the selective assembly in the fcc stacked regions.

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

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

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