Accurate EELS background subtraction – an adaptable method in MATLAB

Electron energy-loss spectroscopy (EELS) is a technique that can give useful information on elemental composition and bonding environments. However in practice, the complexity of the background contributions, which can arise from multiple sources, can hamper the interpretation of the spectra. As a result, background removal is both an essential and difficult part of EELS analysis, especially during quantification of elemental composition. Typically, a power law is used to fit the background but this is often not suitable for many spectra such as in the low-loss region (< 50 eV) and when there are overlapping EELS edges. In this article, we present a series of scripts written in MATLAB v. R2019b that aims to provide statistical information on the model used to fit the background, allowing the user to determine the accuracy of background subtraction. The scripts were written for background subtraction of vibrational EELS in the ultralow-loss region near the zero-loss peak but can also be applied to other kinds of EEL spectra. The scripts can use a range of models for fitting, provided by the Curve Fitting Toolbox of MATLAB, and the user is able to precisely define the window for fitting as well as for edge integration. We demonstrate the advantages of using these scripts by comparing their background subtraction of example spectra to the most commonly used software, Gatan Microscopy Suite 3. The example spectra include those containing multiple scattering, multiple overlapping peaks, as well as vibrational EELS. Additionally, a comprehensive guide to using the scripts has been included in the Supplementary Information

Reactions of polyaromatic molecules in crystals under electron beam of the transmission electron microscope

Reactivity of a series of related molecules under the 80keV electron beam have been investigated and correlated with their structures and chemical composition. Hydrogenated and halogenated derivatives of hexaazatrinaphthylene, coronene, and phthalocyanine were prepared by sublimation in vacuum to form solventless crystals then deposited onto transmission electron microscopy (TEM) grids. The transformation of the molecules in the microcrystals were triggered by an 80keV electron beam in the TEM and studied using correlated selected area electron diffraction, conventional bright field imaging, and energy dispersive X-ray spectroscopy. The critical fluence (ē nm-2) required to cause a disappearance of the diffraction pattern was recorded and used as a measure of the reactivity of the molecules. The same electron flux (102 ē nm-2 s-1) was used throughout. Fully halogenated molecules were found to be the most stable and did not change significantly under our experimental conditions, followed by fully hydrogenated molecules with critical fluences of 104 ē nm-2. Surprisingly, semi-halogenated molecules that contained an equal number of hydrogen and halogen atoms were found to be the least stable, with critical fluences an order of magnitude lower at 103 ē nm-2. This is attributed to elimination of H-X (where X = F or Cl), followed by polymerisation of aryne / aryl radicals within the crystal. The critical fluence for the semi-fluorinated hexaazatrinaphthylene is the lowest as the presence of water molecules in its crystal lattice significantly decreased the stability of the organic molecules under the electron beam. Semi-halogenation reduces the beam stability of organic molecules compared to the parent hydrogenated molecule, thus providing the chemical guidance for design of electron beam stable materials. Understanding of molecular reactivity in the electron beam is necessary for advancement of molecular imaging and analysis methods by the TEM, molecular materials processing, and electron beam-driven synthesis of novel materials