Single-molecule-level characterization of supramolecular systems at surfaces

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.

Design of Surface-Supported Bio-inspired Networks for CO2 and O2 Activation at Room Temperature

Daniel Eduardo Hurtado Salinas

The structure of a biological system defines its function. Therefore, nature has developed sophisticated systems that catalyze chemical reactions that are vital for life on earth. For instance, the photosynthesis is a biological process that is partially regulated by the metallo-enzyme RuBisCO (Ribulose-1,5-bisphosphate carboxylase/oxygenase), whose function is to catalyze the capture and transfer of CO2 into organic molecules. This carboxylation reaction occurs at the active site, where a magnesium ion (Mg2+) is bound to organic molecules with carboxylate (COO-) and amine (NH2) functional groups. In the last decades, supramolecular chemistry has proven to be a valid approach to replicate the structural characteristics of these natural metal-organic systems. Metal atoms and organic molecules are used as building blocks to form two-dimensional (2D) metal-organic networks (MONs) on metal surfaces, through a self-assembly process that occurs spontaneously. In these systems the molecules bind to the metal centers and control their oxidation states that, as found in metallo-enzymes, is crucial to perform a catalytic task. Therefore, these supramolecular assemblies show promising features to be explored for heterogeneous catalysis. The main objective of this thesis is to reverse the structure-function equation, that is: instead of finding specific functions of well-known 2D structures for future applications, 2D structures are designed to reproduce the specific functions of well-known bio-systems. Thus, inspired in the structure of the active site of RuBisCO, 2D Mg-based supramolecular assemblies are rationally designed on Cu(100) or Mg(0001) surfaces at room temperature (RT) as a platform for CO2 adsorption. This work is the first study of self-assembly of alkaline earth metal atoms (Mg) with organic molecules ((1,4-benzenedicarboxylic acid (TPA) and 2,4,6-tris(4-aminophenyl)-1,3,5-triazine (TAPT)) on metal surfaces. The first part of this thesis investigates the self-assembly of TAPT molecules. Scanning Tunneling Microscopy (STM) and High Resolution X-ray Photoemission Spectroscopy (HR-XPS) demonstrate that the molecules typically semi-deprotonate to form MONs with the adatoms from the host substrates. The exposure of these structures to CO2 results in the carboxylation of the amino groups. The second part proves that the COOH moieties of TPA molecules fully-deprotonate to form homo-molecular structures. The incorporation of Mg adatoms result in ionic MONs, which reproduce the carboxylate environment of the active site of RuBiSCO. STM, XPS and Density Functional Theory (DFT) analyze the structural changes, the chemical reactions and charge transfer during either the CO2 or O2 adsorption on the Mg2+ centers. The last part focusses on the co-deposition of both molecules to form 2D metallic-hetero-molecular networks with Mg2+ centers. The role of the Mg2+ centers as active sites for molecular adsorption and model systems for gas storage is studied. STM reveals that CO2 partially modifies the network towards a configuration that resembles the active site of RuBisCO. The formation of 3D structures to enhance CO2 adsorption is also evaluated.

EPFL2018

Self-assembly of multiligand supramolecular architectures at metal surfaces

Alexander Langner

Self-assembly of organic molecules represents an efficient and convenient bottom-up approach for the structural functionalization of surfaces at the nanometer scale. The great potential of assembling supramolecular architectures from organic molecules lies in the vast choice of building blocks that are accessible. This allows to predefine and to direct the molecular organization through the steric and electronic information stored in the molecules. A large variety of homotopic supramolecular structures can be achieved, however limited in complexity. The full realization of highly developed surface architectures for designable chemical functions and physical properties may depend critically on a higher level of complexity, which could be satisfied by utilizing a mixture of different molecular building blocks. Within this thesis, the self-organization of multi-component systems at well-defined metal surfaces is investigated by scanning tunneling microscopy. The mixtures consist of different representatives of linear polyaromatic ligands with carboxylate or pyridyl derived functional groups. The assembly is directed by hydrogen bonding, metal-organic complex formation or a combination of both, i.e. a hierarchical interaction scheme. The aim of this thesis is threefold: First, the homotopic self-assembly of different pyridyl ligands is investigated as a basis for the multi-component systems. One-dimensional chains as well as two dimensional (2D) networks can be formed by copper-pyridyl coordination motifs. The influence of the substrate on these structures will be discussed in detail. Moreover, the self-organization process of multi-components is investigated at the fundamental level. Since functional groups primarily discriminate the different molecular species during the assembly and with that assure a distinguished arrangement, selective bonding schemes are essential for the design of highly ordered supramolecular architectures. Two suitable selective coordination motifs are identified, an iron-carboxylate and a copper-pyridyl complex node. In ligand mixtures, strong preference of one metal species is observed at surfaces, which would not be expected in solution. In addition, redundant mixtures (i.e. ligands of different size but same functional group) serve as model systems to investigate the dynamic self-organization process of modular multicomponent systems, e.g. self-selection or error tolerance, directly with nanometer accuracy. Self-selection is observed if the molecular recognition is steered by a highly reversible coordination bond, while a more robust bonding fosters structural adaption and tolerance to the introduced error (i.e. redundant mixture). These experiments underline the importance of reversibility of the interactions steering the self-assembly process into highly ordered structures. Finally, the extended possibilities due to the multi-component approach for the construction of advanced architectures and structural control are explored: Complex and sophisticated supramolecular networks can be directly synthesized out of simple molecules at the surface. A hierarchical assembly is presented, where a coordination motif defines a primary unit, while hydrogen bonding steers the 2D organization. The secondary level of interaction (hydrogen bonding) can be exclusively addressed, leading to distinct 2D arrangement of the undisturbed primary coordination units. A concept of structural control by rational design is presented, where geometric network parameters can be modified by the replacement of the appropriate molecular species. Due the multi-component nature of the systems, a finer tuning of the structure is enabled (independent substitution of each component) compared to homotopic assemblies. Moreover, a continuation of the multi-component concept is demonstrated, where organizational control is imposed to a homotopic system by adding an additional molecular species. It is demonstrated that a long range order and thermal stability is imposed onto meta-stable Cu-pyridyl coordination chains by cooperative assembly with a carboxylate species.

EPFL2009

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