Half-clathrochelate Complexes as Versatile Links in Supramolecular Chemistry

Clathrochelate complexes have been widely investigated with different size and shape and used as building blocks for the obtainment of discrete supramolecular architectures. These clathrochelate complexes are very stable and kinetically inert complexes. A new link, described as a 'half-clathrochelate complex' with one boronate ester-cap and one 'open' side can be used as novel structural motifs in supramolecular chemistry. Since the metal ion is not completely encapsulated, these complexes are more labile than standard clathrochelate complexes with two boronate ester caps. The half-clathrochelate complexes are obtained by metal-templated condensation reactions of 2-pyridylaldoximes with boronic acids. For applications in supramolecular chemistry, half-clathrochelate complexes are very intriguing compounds for several reasons: the central metal ion can be varied to obtain diamagnetic or paramagnetic complexes and substituents at the pyridyl group of the oxime ligand can be used to fuse half-clathrochelate complexes into defined supramolecular assemblies such as dinuclear triple-stranded helicates or tetrahedral cages.

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

Mimicking Enzymatic Active Sites on Surfaces for Energy Conversion Chemistry

Klaus Kern, Magalí Alejandra Lingenfelder, Sebastian Stepanow

Metal organic supramolecular chemistry on surfaces has matured to a point where its underlying growth mechanisms are well understood and structures of defined coordination environments of metal atoms can be synthesized in a controlled and reproducible procedure. With surface-confined molecular self-assembly, scientists have a tool box at hand which can be used to prepare structures with desired properties, as for example a defined oxidation number and spin state of the transition metal atoms within the organic matrix. From a structural point of view, these coordination sites in the supramolecular structure resemble the catalytically active sites of metallo-enzymes, both characterized by metal centers coordinated to organic ligands. Several chemical reactions take place at these embedded metal ions in enzymes and the question arises whether these reactions also take place using metal organic networks as catalysts. Mimicking the active site of metal atoms and organic ligands of enzymes in artificial systems is the key to understanding the selectivity and efficiency of enzymatic reactions. Their catalytic activity depends on various parameters including the charge and spin configuration in the metal ion, but also on the organic environment, which can stabilize intermediate reaction products, inhibits catalytic deactivation, and serves products and therefore ensures the selectivity of the enzyme. Charge and spin on the transition metal in enzymes depend on the one hand on the specific metal element, and on the other hand on its organic coordination environment. These two parameters can carefully be adjusted in surface confined metal organic networks, which can be synthesized by virtue of combinatorial mixing of building synthons. Different organic ligands with varying functional groups can be combined with several transition metals and spontaneously assemble into ordered networks. The catalytically active metal centers are adequately separated by the linking molecules and constitute promising candiates for heterogeneous catalysts. Recent advances in synthesis, characterization, and catalytic performance of metal organic networks are highlighted in this Account. Experimental results like structure determination of the networks, charge and spin distribution in the metal centers, and catalytic mechanisms for electrochemical reactions are presented. In particular, we describe the activity of two networks for the oxygen reduction reaction in a combined scanning tunneling microscopy and electrochemical study. The similarities and differences of the networks compared to metallo-enzymes will be discussed, such as the metal surface that operates as a geometric template and concomitantly functions as an electron reservoir, and how this leads to a new class of bioinspired catalysts. The possibility to create functional two-dimensional coordination complexes at surfaces taking inspiration from nature opens up a new route for the design of potent nanocatalyst materials for energy conversion.

Amer Chemical Soc2015

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