Structure of amorphous GeSe9 by neutron diffraction and first-principles molecular dynamics: Impact of trajectory sampling and size effects

The structure of glassy GeSe9 was investigated by combining neutron diffraction with density-functional-theory-based first-principles molecular dynamics. In the simulations, three different models of N = 260 atoms were prepared by sampling three independent temporal trajectories, and the glass structures were found to be substantially different from those obtained for models in which smaller numbers of atoms or more rapid quench rates were employed. In particular, the overall network structure is based on Se-n chains that are cross-linked by Ge(Se-4)(1/2) tetrahedra, where the latter are predominantly corner as opposed to edge sharing. The occurrence of a substantial proportion of Ge-Se-Se connections does not support a model in which the material is phase separated into Se-rich and GeSe2-rich domains. The appearance of a first-sharp diffraction peak in the Bhatia-Thornton concentration-concentration partial structure factor does, however, indicate a non-uniform distribution of the Ge-centered structural motifs on an intermediate length scale. Published by AIP Publishing.

Vibrational properties of vitreous GeSe2 with the Becke-Lee-Yang-Parr density functional

Luigi Giacomazzi, Carlo Massobrio, Alfredo Pasquarello

The vibrational properties of vitreous GeSe2 are studied within the Becke-Lee-Yang-Parr (BLYP) generalized gradient approximation to density functional theory. For this purpose, we consider two models. The first one is derived from a chemically ordered network, previously generated through classical molecular dynamics. The second one is generated through first-principles molecular dynamics simulations based on the BLYP functional and shows a larger variety of structural motifs. We describe the structural and electronic properties of our models, including bond lengths, first-neighbor coordinations, and the electronic density of states. The vibrational properties are addressed through the vibrational density of states, the infrared spectrum, and the Raman spectrum. For the chemically ordered model, the vibrational properties obtained with the BLYP functional are of comparable quality with respect to previous results obtained with the Perdew-Wang (PW) functional. However, a global consideration of our results indicates that the BLYP functional yields an overall improved description for the vibrational properties of vitreous GeSe2. The BLYP dielectric constants are closer to experimental values. Furthermore, we found that the Raman spectrum of the model generated through first-principles molecular dynamics within the BLYP scheme is largely improved with respect to an analogous model generated within the PW scheme.

2011

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

Low-energy Electron Holography Microscope for Imaging of Single Molecules

Sven Alexander Szilagyi

EPFL2022