Self-assembly of organometallic macrocycles and cages

Neutral metallamacrocycles with four or ten metal centers were obtained by reaction of [(R3P)PdCl2]2 with 2,3-dihydroxypyridine and derivatives or 2-hydroxynicotinic acid in the presence of base. In all these assemblies, the two O-donor atoms of the ligand bind to one metal center to form a chelate ring, while the N-donor atom binds to another metal center, linking the subunits together. The tetrameric complexes showed a low affinity for small aromatic diols. The procedure was adapted for the synthesis of water-soluble macrocycles: ligands which contain both the 2,3-dihydroxypyridine motive and a tertiary amine function that can be protonated were reacted in water with the acetato-bridged complex [(Et3P)Pd(CH3COO)2]2 to give tetrameric macrocycles in over 90% yields. Scrambling experiments showed that the Pd(II) macrocycles are highly inert. The reaction of ReBr3(CO)32 with 3-hydroxy-1,2,3-benzotriazine-4(3H)-one in the presence of base gave the ionic rhenium complex [ReBr(C7H4N3O2)(CO)3][NEt4], from which a neutral metallamacrocycle was obtained upon abstraction of (NEt4)Br. Its connectivity is comparable to that of the Pd(II) macrocycles. In coordinating solvents, this macrocycle disrupts and the monomeric solvent adducts are formed. In the presence of BF4-, it undergoes an anion-templated rearrangement to give a new, trimeric macrocycle which cocrystallizes with an unusual C3-symmetric [Ag(η2-benzene)3(OH2)][BF4] complex, the tetrafluoroborate anion being encapsulated in the cavity of the macrocycle. By reacting [(cymene)RuCl2]2 with 3,5-pyridinedicarboxylic acid, a trifunctional ligand in which the three donor atoms are unable to coordinate to the same metal center, an hexameric coordination cage was obtained. This complex has a trigonal antiprism geometry. Half of the carbonyl O-atoms of the bridging ligands are positioned in close proximity to each other, forming two binding sites on the surface. The cage can thus act as an exo-receptor for alkali metal cations (Na+, K+, Cs+). 1H and 13C NMR investigations as well as a single crystal X-ray analysis revealed that upon addition of alkali metal salts, the hexanuclear assembly partly rearranges to form a dodecameric coordination cage with icosahedral geometry. Although entropically disfavored, this process takes place because in this new complex all carbonyl O-atoms are part of a binding site (eight metal cations can be accommodated on the surface of the cage). Furthermore, due to the reduced surface curvature of the dodecanuclear assembly, these O-atoms are closer together, forming more suited binding sites for the alkali guest cations. To best of our knowledge, a coordination cage with an icosahedral geometry has not been reported so far.

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

Functional Nanostructures Based on Organometallic Half-Sandwich Complexes

Hexanuclear coordination cages of the formula [(C5Me4R)M(C7H3NO 4)]6 (M = Rh, Ir; R = Me, H) were obtained by stepwise reaction of [(C5Me4R)M(μ-Cl)Cl]2 with, first AgOAc and then pyridine-3,5-dicarboxylic acid. Crystallographic analyses show that the cages adopt a distorted octahedral geometry with the pyridine-3,5-dicarboxylates functioning as dianionic bridging ligands, each of which connects three different (C5Me4R)M fragments. The cages act as exoreceptors for large alkali metal cations K+ and Cs+, as well as NH4+, but show low affinity for Na+. Crystallographic and NMR spectroscopic analyses indicate that two metal ions can be coordinated to the surface of the cages. The respective binding sites comprise three carbonyl O-atoms from the bridging pyridine-3,5-dicarboxylate ligands. Novel supramolecular architectures were obtained by reacting the dinuclear macrocycle [(cymene)Ru(μ-C12H12O4)(H 2O)]2 with different N-donor ligands. A tetranuclear assembly was obtained with 1,2-di(4-pyridyl)ethylene, whereas hexanuclear complexes were formed with 2,4,6-tris(4-pyridyl)triazine and 1,3,5-tris(4-pyridylethynyl)benzene. The reaction with 5,10,15,20-tetra(4-pyridyl)porphyrine, on the other hand gave tetra- or octanuclear complexes, depending on the stoichiometry that was employed. The 2,4,6-tris(4-pyridyl)triazine complex was shown to act as a host for polycyclic aromatic compounds such as pyrene, triphenylene and coronene. A hexanuclear coordination cage has been formed by self-assembly of three elongated [(cymene)Ru(μ-C14H10O6)] 2 dinuclear macrocycles and two equivalents of 2,4,6-tris(4-pyridyl)triazine. The twisted coordination prism with a height of 3.5 Å (bottom to top) could be untwined by addition of coronene to – for half-sandwich complex-based cages – unprecedented size of 10.8 Å (bottom to top). Crystallographic and NMR spectroscopic analyses indicate that two coronene molecules can be encapsulated inside this cage.

EPFL2010

Low-dimensional supramolecular architectures at metal surfaces

Sebastian Stepanow

This thesis is concerned with supramolecular architectures assembled at metal surfaces. The investigations pursued two objectives. On the one hand, the focus was placed on the fabrication of low-dimensional surface-supported network structures by applying the concepts of conventional three-dimensional supramolecular chemistry at surfaces. Three main driving forces were explored for the construction of low-dimensional assemblies: hydrogen bonding, metal coordination and ionic interactions. The realized structures were characterized by scanning tunneling microscopy (STM) under ultra-high vacuum conditions. In particular, the interplay between the adsorbate-substrate coupling and lateral adsorbate interactions was addressed in the experiments. Further, the electronic and magnetic properties of the fabricated coordination structures were investigated. This characterization was done by x-ray absorption experiments at the synchrotron facility in Grenoble. Moreover, the response of the metal units and open cavity structures to the adsorption of large organic and small gas molecules was studied by temperature controlled STM experiments. The first part of the thesis deals with hydrogen bonded supramolecular assemblies. Simple aromatic carboxylic acids were employed to study the assembly principles and in particular effects arising from the substrate and molecular structure. The investigation of TPA (1,4-benzenedicarboxylic acid) adlayers on Cu(100) at different substrate temperatures revealed how the protonation status of the carboxyl moieties affects the topology of the assemblies. Further, the influence of the molecular backbone functionality and symmetry is addressed in comparative investigations on TPA and PDA (2,5-pyrazinedicarboxylic acid) as well as BDA (4,4'-biphenyldicarboxylic acid) and SDA (4',4" trans-ethene-l,2-diyl-bisbenzoic acid) adlayers on Cu(100). In the second part of the thesis, metal-ligand interactions were employed for the construction of supramolecular architectures at a Cu(100) surface. The concepts of conventional coordination chemistry were successfully applied at the surface. Iron atoms in conjunction with rod-like aromatic molecular linkers comprising carboxyl, pyridyl and hydroxyl functional groups assemble into a rich variety of open network structures with distinctly arranged mono- and diiron coordination centers and well-defined cavities. The results show that the adsorbate-substrate coupling considerably affects the local coordination environment of the iron units when the molecular backbone length is varied. The occurrence of structural isomerism in open network structures is addressed in a comparative study of heterofunctional and homofunctional linker molecules. It is shown that the former ligand allows only one topologically pure structure while the other linker forms two phases with different topology. The hydroxyl ligand has been used to construct distorted hexagonal coordination networks containing threefold coordinated single iron atoms. The comparison between the networks on Cu(100) and Ag(111) surfaces shows marked differences, which are attributed to adsorbate-substrate interactions. Finally, a novel design strategy for the fabrication of two-dimensional coordination structures at surfaces is introduced by using alkali metal ions in conjunction with carboxylate ligands. The interaction between the components is dominated by electrostatic forces and is of intermediate bond strength as in the case of hydrogen bonding and transition metal coordination. It is expected, that substrate symmetry and registry plays a larger role in the network formation, because the ionic interaction is not directional. The chemical as well as magnetic properties of the fabricated coordination networks are examined in the last part of the thesis. The adsorption of C60 molecules on open network structures reveals how cavity size and chemical functionality affect the bond strength to the guest molecules as well as the number of accommodated C60 molecules. Since transition metal clusters, and in particular diiron units, are the catalytic active centers in various proteins, the reactivity of various mono- and diiron coordination structures to molecular oxygen was investigated in temperature controlled STM experiments. In particular, the focus was placed on the structural relaxation upon gas adsorption and chemical reaction. At last, the magnetic properties of the metal coordination centers are addressed in XMCD experiments. The iron units are found to be paramagnetic at temperatures down to 5 K and show distinct magnetic anisotropy and magnetization loops. These experiments demonstrate that surface-supported metal coordination structures are a promising class of materials for applications in the field of heterogenous catalysis and surface magnetism.

EPFL2005