Caténane | EPFL Graph Search

Un caténane est une architecture moléculaire formée d'au moins deux macrocycles imbriqués l'un dans l'autre, formant une sorte de chaine (en latin catena). Deux cycles imbriqués ne peuvent pas être séparés sans casser au moins une liaison covalente d'un des deux cycles. Le concept des caténanes est proche de celui d'autre molécules imbriquées telles les rotaxanes, les nœuds moléculaires ou les nœuds borroméens moléculaires. Une nouvelle terminologie est utilisée pour décrire la connexion entre les cycles d'un caténane : on parle de liaison mécanique. Synthèse thumb|250px|Exemple de synthèse de caténane Il y a deux approches de la synthèse d'un caténane. La première consiste à faire une réaction de cyclisation, avec l'espoir qu'un certain nombre de cycles se forment autour d'autres cycles, produisant ainsi le caténane escompté. Cette approche dite statistique a amené à la première synthèse d'un caténane, mais la méthode est très inefficace. De plus, elle nécessite de diluer

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

Toward mechanical switching of surface-adsorbed [2]catenane by in situ copper complexation

Klaus Kern, Dietmar Payer, Stephan Rauschenbach

Using scanning tunneling microscopy (STM), electrospray ionization mass spectrometry (ESI-MS), and X-ray photoelectron spectroscopy (XPS), we demonstrate that a free (2]catenane consisting of two interlocking 30-membered rings (cat-30) can be deposited on a Ag(111) surface by vacuum sublimation without decomposition. The deposited cat-30 molecules self-organize as ordered dimer chain structures at the surface, presumably via intermolecular pi-pi stacking. An in situ addition of Cu atoms to the surface-adsorbed catenanes induces a drastic change in the molecular organization, i.e., from the dimer chain structure to isolated species. The nitrogen core level spectra suggest that the cat-30 phenanthroline units coordinate with Cu, indicating that the free catenane has been transformed into a Cu-complexed [2]catenane. Since it is known that the two interlocked macrocyclic rings of the free ligand cat-30 completely rearrange, i.e., circumrotate, upon complexation to copper, our results reveal that when adsorbed on the silver surface, the two macrocyclic rings of the free [2]catenane can glide within one another so as to generate the corresponding copper complex by in situ Cu complexation.

2007

DNA Topology

Guillaume Witz

This thesis explores different aspects of DNA topology through experimental and numerical techniques. Topology is a vast mathematical field, that deals with the spatial properties of objects undergoing continuous deformations, but here it is restricted to the description of closed space curves such as rings, knots and catenanes. Topology is connected to practical problems in different domains including polymer physics, because a polymer chain is a type of space curve, whose statistical properties are affected by the closure of its ends; and biology, because the double-helical interwinding of the two strands formingDNA is described by topological concepts, and also because a closed DNA molecule can adopt complex topologies like knotted or catenated conformations in vivo. Both physical and biological aspects of topology are investigated in the three chapters of this thesis. Chapter 1 introduces on a general level the experimental techniques, numerical methods and topology concepts that are at the core of the presented research. Chapter 2 is an experimental study of the statistical properties of DNA rings adsorbed on surfaces, and imaged by atomic force microscopy (AFM). DNA rings of different sizes are first studied in a dilute state, allowing us to investigate the consequences of the circular topology on polymer physics of two-dimensional chains. We confirm certain theoretical results, e.g. the topological invariance of the scaling exponent in two dimensions; but we also propose new models taking into account the specificities of the problem, in particular the interplay between excluded volume effects and topology, for the description of standard polymer physics measures like the asphericity or the bond correlation function. In addition to isolated DNA rings, we study DNA rings in a semi-dilute state. Comparing the statistical properties of the DNA rings imaged by AFM with a numerical model, we formulate a simplified description of this system in terms of two dimensional pressurized vesicles. Finally, we study a last case, in which DNA rings are confined within circular boundaries in two dimensions. We show how confinement strongly affects the statistical properties of the DNA chains, and verify that our experimental system is a good model for polymer confinement by comparing the data with numerical simulations. In chapter 3, we use numerical simulations to study two other topological forms taken by closed DNA in vivo: catenanes and knots. In both cases, we analyze the conformations of these objects, in particular as a function of their torsional state, and find complex behaviors proper to these topologies: for example, the large scale supercoiling of toroidal catenanes, or the different response of left- and right-handed knots to torsion. We then focus on the activity of a class of enzymes called topoisomerases, that are able to change the topology of DNA molecules (e.g. by unknotting a DNA knot). In particular, we try to deduce how the structural properties of DNA knots and catenanes affect the activity of one of these enzymes called topo IV, and also simulate its activity. We show that our numerical model provides results that compare well with experimental data, and could therefore provide a basis for the design of new experiments. Finally, we present a new model for the simulation of the activity of another topoisomerase called gyrase, that is responsible for introducing supercoiling into DNA. This model includes a few essential features of the interaction between gyrase and DNA, which permit to efficiently reproduce experimental measurements.