Chemical species | EPFL Graph Search

A chemical species is a chemical substance or ensemble composed of chemically identical molecular entities that can explore the same set of molecular energy levels on a characteristic or delineated time scale. These energy levels determine the way the chemical species will interact with others (engaging in chemical bonds, etc.). The species can be an atom, molecule, ion, or radical, and it has a specific chemical name and chemical formula. The term is also applied to a set of chemically identical atomic or molecular structural units in a solid array. In supramolecular chemistry, chemical species are those supramolecular structures whose interactions and associations are brought about via intermolecular bonding and debonding actions, and function to form the basis of this branch of chemistry. For instance:

The chemical species argon is an atomic species of formula Ar;
dioxygen and ozone are different molecular species, of respective formulas O2 and O3;
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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

Design, characterisation and modelling of a high current DC arc plasma source for silicon and silicon carbide processing at low pressure

Lukas Derendinger

In the frame of this thesis, two similar high current DC arc (HCDCA) plasma sources were investigated in a low gas pressure regime (10-3-10-2 mbar). One of them was initially designed for the epitaxial growth of silicon and silicon germanium (LEP), the other for the industrial deposition of diamond (BAI). The LEP source was analysed using pure argon plasmas. Measurements of the ion saturation current were performed with a custom-built multi-Langmuir probe to analyse plasma density homogeneity. Plasma instabilities at 50 Hz were observed and studied by different means. One source of the instability is the AC current used for the filament heating, whereas lower frequency instabilities are due to the use of a ring shaped anode. A sensitive Hall sensor was used to measure the magnetic field induced by the discharge current. It was found that depending on the plasma parameters gas pressure and external magnetic field the current tends to attach at different points on the anode, leading to a complete loss of reactor symmetry. The installation of an additional cusp field around the reactor chamber lead to an increase of the overall homogeneity of the plasma density, but it could not resolve the problems of current attachment. In the following the ring anode was replaced by a point anode and the maximum external magnetic field strength was increased by a factor of ten. With a novel multi-Hall probe the current density of the now columnar shaped plasma was measured, showing a strongly peaked current density profile, when an external magnetic field is applied. Together with ion saturation current measurements made with a Langmuir probe, the electron temperature inside the plasma column was estimated to be about 4 eV. In earlier works made on the BAI reactor the high dissociation efficiency of the HCDCA plasma source has already been shown. Optical emission spectra were compared between RF plasmas, low pressure (1.5mbar) HCDCA plasmas and our very low pressure (10-3-10-2 mbar) HCDCA plasmas. The dominating species found in RF plasma spectra are molecular, the spectra of low pressure HCDCA plasmas are dominated by atomic species and the spectra of very low pressure HCDCA plasmas are dominated by ions, emphasising the high dissociation efficiency of this system. Silane and Methane was used as precursor gases in the BAI reactor for the deposition of silicon carbide films. Promising high deposition rates up to 9 nm/s were found, but FTIR spectroscopy showed high hydrogen and oxygen concentrations in the porous films, making the not optimised deposited material useless for the application of wear-resistant coatings. Microcrystalline hydrogenated silicon (µc-Si:H) is viewed as a cost- and energy-effective alternative to crystalline silicon for the production of solar cells. A detailed analysis of the deposition rate and the Raman crystallinity of µc-Si:H films deposited in the BAI reactor showed deposition rates up to 6.5 nm/s and a wide range of crystallinity from 0-80%. Film thickness inhomogeneity in silicon solar cells has to be less than 5%. To meet this standard a first substantial improvement was achieved with the installation of a linear gas injection along the plasma column. Tests on large surface glasses (47 × 37 cm2) revealed strong diffusive effects, which could be reproduced with a simple gas diffusion model. The model showed the necessity to reduce the dead volume around the plasma and to set the substrates as close as possible to the plasma column in order to minimise film thickness inhomogeneity due to diffusion. Deposition rate measurements made in these conditions assured the results of the model. The development of a method to estimate the dissociation efficiency of the plasma by simple pressure measurements showed also an important increase of the silane dissociation from 75-92% when the plasma is confined in a smaller volume. Therefore, compared to the reactor with a large dead volume, only a third of the initial silane is lost to the pumps.

EPFL2008

Model evaluation of short-lived climate forcers for the Arctic Monitoring and Assessment Programme: a multi-species, multi-model study

Luca Pozzoli, Julia Schmale

While carbon dioxide is the main cause for global warming, modeling short-lived climate forcers (SLCFs) such as methane, ozone, and particles in the Arctic allows us to simulate near-term climate and health impacts for a sensitive, pristine region that is warming at 3 times the global rate. Atmospheric modeling is critical for understanding the long-range transport of pollutants to the Arctic, as well as the abundance and distribution of SLCFs throughout the Arctic atmosphere. Modeling is also used as a tool to determine SLCF impacts on climate and health in the present and in future emissions scenarios. In this study, we evaluate 18 state-of-the-art atmospheric and Earth system models by assessing their representation of Arctic and Northern Hemisphere atmospheric SLCF distributions, considering a wide range of different chemical species (methane, tropospheric ozone and its precursors, black carbon, sulfate, organic aerosol, and particulate matter) and multiple observational datasets. Model simulations over 4 years (2008–2009 and 2014–2015) conducted for the 2022 Arctic Monitoring and Assessment Programme (AMAP) SLCF assessment report are thoroughly evaluated against satellite, ground, ship, and aircraft-based observations. The annual means, seasonal cycles, and 3-D distributions of SLCFs were evaluated using several metrics, such as absolute and percent model biases and correlation coefficients. The results show a large range in model performance, with no one particular model or model type performing well for all regions and all SLCF species. The multi-model mean (mmm) was able to represent the general features of SLCFs in the Arctic and had the best overall performance. For the SLCFs with the greatest radiative impact (CH4, O3, BC, and SO ), the mmm was within ±25 % of the measurements across the Northern Hemisphere. Therefore, we recommend a multi-model ensemble be used for simulating climate and health impacts of SLCFs. Of the SLCFs in our study, model biases were smallest for CH4 and greatest for OA. For most SLCFs, model biases skewed from positive to negative with increasing latitude. Our analysis suggests that vertical mixing, long-range transport, deposition, and wildfires remain highly uncertain processes. These processes need better representation within atmospheric models to improve their simulation of SLCFs in the Arctic environment. As model development proceeds in these areas, we highly recommend that the vertical and 3-D distribution of SLCFs be evaluated, as that information is critical to improving the uncertain processes in models.

2022