Géométrie moléculaire | EPFL Graph Search

La géométrie moléculaire ou structure moléculaire désigne l'arrangement 3D des atomes dans une molécule. . Détermination La géométrie moléculaire peut être établie à l'aide de différents outils, dont la spectroscopie et la diffraction. Les spectroscopies infrarouge, rotationnelle et Raman peuvent donner des informations relativement à la géométrie d'une molécule grâce aux absorbances vibrationnelles et rotationnelles. Les diffractométries de rayons X, de neutrons et des électrons peuvent donner des informations à propos des solides cristallins. La diffraction de gaz d'électrons peut être utilisée pour de petites molécules à l'état gazeux. La RMN et le FRET peuvent servir à obtenir d'autres informations, telles la distance relative, les angles dihédraux, les angles et la connectivité. La géométrie des molécules est plus facile à obtenir lorsqu'elles sont à basse température. Les plus grosses molécules existent souvent sous plusieurs formes géométriques stables (conformérie

Rational Design of Pd-Based Catalysts for Selective Alkyne Hydrogenations

Rocio Micaela Crespo Quesada

Traditionally, the search for active and selective catalysts involved a rather tedious "hit-and-miss" approach in which hundreds, if not thousands catalysts were tested until the optimal substance was identified. With the advancing theoretical understanding of catalysis and the development of computational power, a new era of rational catalyst design is dawning. This approach, grounded on first principles, is based on new advances in synthesis, characterization and modeling with the ultimate aim of predicting the expected behavior of a catalyst based on chemical composition, molecular structure and morphology. The rational design of a catalyst is a complex process which spans across several levels of scale. In this thesis, the pursuit of a rational design for Pd-based catalysts effective in alkyne hydrogenations is presented. A multi-level integrated approach was thus applied ranging from the nano-scale design of the active sites for a specific reaction, taking into account its structure sensitivity, to the micro-scale design of the supported Pd nanoparticles including metal-additive and metal-support interactions as well as mass and heat transfer phenomena. In order to rationally design a catalyst at a nano-scale, i.e. a catalyst's active site, several methodologies have been hitherto applied, such as the study on single crystals or model catalysts. Here we present the use of metal nanoparticles with tuned sizes (5-30 nm) and shapes (cubes, octahedra and cube-octahedra) prepared via colloidal techniques. These nanoparticles can be tested per se and represent a new generation of model catalysts, complementing single crystal studies, which inherently lack the complexity of industrial catalysis. However, metal nanoparticles, especially those prepared in a controlled manner in order to tailor their shape and size, require the use of stabilizing and/or capping agents capable of directing their growth. These substances can mask the true catalytic behavior of the nanoparticles. Thus, it is of great importance to study the interactions of the active phase with the substances that are in close contact with it, in the so-called meso-scaled level of rational catalyst design. Therefore, the effect of the nature of the stabilizing agent on the catalytic response was studied, as well as the promoting effect of some of these substances. Finally, a methodology was developed capable of eliminating organic stabilizing agents from the surface of nanoparticles without compromising their morphological stability. The knowledge gathered in the first two levels can be applied further to reach the microscale rational catalyst design. In this thesis, a final catalyst consisting on well-defined stabilizer-free supported Pd nanoparticles was used in the hydrogenation of acetylene. This deep study of the catalytic behavior of well-defined Pd catalysts throughout several levels of scale and complexity have given us the tools needed to perform a rational catalyst design for alkyne hydrogenations. Depending on the specific reaction, the active phase can be optimized in terms of the desired activity and selectivity and can be tuned even further with the use of specific additives. Finally, the appropriate support also exerts a promoting effect on the nanoparticles and ensures their anchoring in addition to avoiding heat and mass transfer artifacts.

EPFL2011

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

Low-energy Electron Holography Microscope for Imaging of Single Molecules

Sven Alexander Szilagyi

Structure determination techniques are an essential tool to investigate and understand molecules, especially in biology, where functionality crucially depends on structure. The dominant high-resolution methods, such as transmission electron microscopy and X-ray diffraction, rely on ensemble averaging, making them unsuitable for evidencing structural variations of flexible molecules. Common single-molecule imaging techniques like scanning probe microscopy achieve high resolution but lack access to 3D objects. A possible way to overcome these limitations is offered by low-energy electron holography (LEEH). So far, LEEH achieved molecular imaging at resolutions in the range of 7-8 Å on the single-molecule level. A resolution in the range of a few Å, which would give access to atomic details of molecular structures, is in theory attainable. Obtaining a resolution near the theoretical limit requires a fully optimized LEEH setup and workflow, for which in particular sample and emitter preparation are crucial. Here, I present a novel LEEH microscope with a unique experimental workflow, which is capable of resolving molecular substructures with an unprecedented resolution for LEEH experiments. The newly constructed LEEH microscope takes advantage of an efficient vibration isolation system and is remote-controlled to minimize external perturbations. The setup is capable of low-temperature (50 K) measurements, which enhances the stability of the system. A reliable way for preparing highly coherent electron emitters constituted by sharp tungsten tips is presented along with different methods for improving their performance via functionalization and UHV treatments. I show an optimized and reliable substrate preparation protocol resulting in ultra-clean free-standing single-layer graphene (SLG) samples. Native electrospray ion beam deposition (ES-IBD) allows for the transfer of non-volatile molecules from solution into gas phase and onto the substrate. By employing a quadrupole mass selection, highly pure molecular ion beams are obtained, which are soft-landed onto the SLG substrate in a controlled and reproducible manner while retaining an intact structure. This versatile preparation method allows us to study a great variety of molecules by LEEH. Data on proteins with masses ranging from 12-820 kDa reveal molecular shapes consistent with model structures. Locally, structural details as small as 5 Å were identified, thus we are approaching our goal of a resolution in the range of a few Å. The application of our methodology to flexible proteins, exemplified by antibodies, allowed for the imaging of their conformational variability and for determining the influence of the sample preparation on their structure. This gave us the possibility to directly image gas-phase related conformations. Data of compact molecular systems with masses below 3 kDa reveal that our LEEH microscope is able to investigate small molecules, such as porphyrines, at high imaging contrast. The presented results indicate that an optimized LEEH setup and workflow in combination with ES-IBD is a versatile microscopy method, which is filling the gap between high-resolution and single-molecule techniques by elucidating structural details of various molecular species.

EPFL2022