Supramolecular assembly | EPFL Graph Search

In chemistry, a supramolecular assembly is a complex of molecules held together by noncovalent bonds. While a supramolecular assembly can be simply composed of two molecules (e.g., a DNA double helix or an inclusion compound), or a defined number of stoichiometrically interacting molecules within a quaternary complex, it is more often used to denote larger complexes composed of indefinite numbers of molecules that form sphere-, rod-, or sheet-like species. Colloids, liquid crystals, biomolecular condensates, micelles, liposomes and biological membranes are examples of supramolecular assemblies, and their realm of study is known as supramolecular chemistry. The dimensions of supramolecular assemblies can range from nanometers to micrometers. Thus they allow access to nanoscale objects using a bottom-up approach in far fewer steps than a single molecule of similar dimensions. The process by which a supramolecular assembly forms is called molecular self-assembly. Some try to distingui

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

Mechanistic Insight into Supramolecular Polymerization in Water Tunable by Molecular Geometry

Lukas Pfeifer, Fan Xu

Supramolecular self-assembly in water based on non-covalent bonding is attracting major attention due to the potential of hydrogels and aqueous polymers in biomedical applications. Although supramolecular polymerization in organic solvents is well established, the key design features, the assembly mechanisms in water and achieving control over the aggregate structures remain challenging. Here, we present the assembly and disassembly of geometrical isomers of a stiff-stilbene bis-urea amphiphile (SA) in pure water. A remarkable feature of this system is that the (E)-isomer forms supramolecular polymers in both pure water and organic solvents. Taking advantage of this unique property, the hydrophobic effect was studied by comparing the supramolecular assembly in both systems. The assembly process in water follows an enthalpy-driven nucleation-elongation (cooperative) supramolecular polymerization mechanism with a standard Gibbs free energy (Delta G degrees = -53 kJ mol(-1)) double the value of the one found in toluene. We attributed this distinctive feature to the hydrophobic effect in water. Furthermore, we discovered an isomer-dependent assembly process, which can be used to control aggregation in aqueous media. Due to the substantial geometric difference between (E)-SA and (Z)-SA, we compared their assembly in water to study the influence of different driving forces involved in the process. The supramolecular polymerization of (E)-SA was cooperatively influenced by hydrogen bonding, pi-stacking, and hydrophobic effects, whereas the assembly of (Z)-SA was mainly driven by hydrophobic effects. As a result, the fiber length of (E)-SA in water is much longer than that of (Z)-SA, presenting opportunities for geometrical control of aggregation in aqueous media. [GRAPHICS]

CHINESE CHEMICAL SOC2022

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