Practical Crystallography with a Transmission Electron Microscope

Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.

Ceramic of ZrB2 and its composite of the ceramics with SiC are used for ultrahigh temperature protection coatings in re-entry space vehicles because of high melting temperature of ZrB2 (3245°C). Chemical composition and microstructure of the ceramics are critical to thennal shock properties of the ceramics. Especially oxidation of boron and formation of boron oxide will degrade property of thermal resistance. Conventional TEM with Energy dispersive X-ray spectroscopy (EDS) is unable to study light elements like boron. However, parallel-recorded electron energy-loss spectroscopy (EELS) and energy-filtering GIF system associated with field-emission gun (FEG) TEM are able to carry out chemical imaging and chemical information of light elements. Bonding structure and oxidation states of an element (such as B) can be obtained by using EELS. Figure A is a zero-loss bright-field TEM image showing an interface between ZrB2 and SiC. Figure B is a Plasmon-loss filtered TEM image of the same area. A plasmon peak at about 20 eV was used for this image.

The structure of disordered SiC nanowires was studied by using the three-dimensional rotation electron diffraction (RED) technique. The streaks shown in the RED images indicated the stacking faults of the nanowire. High-resolution transmission electron microscopy imaging was employed to support the results from the RED data. It suggested that a 2H polytype is most possible for the nanowires.

Optimization of three-dimensional electron diffuse scattering data acquisition

Grain boundary (GB) electrical activity is increased by heat treatment in silicon; the origin of the phenomenon is a subject of controversy and is often attributed to oxide precipitation. This letter presents microanalytical results (conventional and scanning transmission electron microscopy, energy dispersive x-ray spectroscopy, and electron energy loss spectroscopy), obtained on a Σ=25 bicrystal before and after annealing in sealed ampoules at 900 °C. The enhancement of the electrical activity, confirmed by electron beam induced current and deep level transient spectroscopy, is shown to appear at the boundary simultaneously with precipitates containing copper and nickel. The major role of the fast diffusing 3d metals on the GB electrical properties is demonstrated.

The paper reports structural and microchemical investigations of low-dimensional semiconducting materials by combined imaging and spectroscopical techniques of transmission electron microscopy (TEM). The materials systems under investigation comprise graded (Al,Ga)As layers, (In,Ga)As quantum wires in V-grooved (001)InP, and (In,Ga)As quantum dots in GaAs. In order to elucidate structural peculiarities of these objects conventional and high-resolution TEM (CTEM/HRTEM) were performed, whereas information about the chemical composition and element distribution was obtained through electron energy loss spectroscopy (EELS), energy-filtered TEM (EFTEM), and energy-dispersive X-ray spectroscopy (EDXS). Particularly, the application possibilities of EFTEM are here demonstrated for revealing the local element content at high lateral resolution in a semi-quantitative manner.

Thin films of BaTiO3 deposited on (100)LaAlO3 substrate by metal-organic chemical vapor deposition (MOCVD) are investigated using several electron-optical techniques. Combined high resolution transmission electron microscopy (HRTEM), electron energy loss spectrometry (EELS), and convergent beam electron diffraction (CBED) indicate a substantial influence of lattice strain on the structural and optical characteristics of BaTiO3 films. Spatially resolved EELS and CBED studies indicate that the substrate influence persists up to about 40 nm away from the interface. The changes in the dielectric function of the films, as inferred from spatially resolved EELS, appear to correlate well with internal lattice strain in the films as deduced from convergent beam electron diffraction (CBED).

Metal-organic frameworks (MOFs) have attracted considerable interest due to their well-defined pore architecture and structural tunability on molecular dimensions. While single-crystal X-ray diffraction (SCXRD) has been widely used to elucidate the structures of MOFs at the atomic scale, the formation of large and well-ordered crystals is still a crucial bottleneck for structure determination. To alleviate this challenge, three-dimensional electron diffraction (3D ED) has been developed for structure determination of nano- (submicron-)sized crystals. Such 3D ED data are collected from each single crystal using transmission electron microscopy. In this protocol, we introduce the entire workflow for structural analysis of MOFs by 3D ED, from sample preparation, data acquisition and data processing to structure determination. We describe methods for crystal screening and handling of crystal agglomerates, which are crucial steps in sample preparation for single-crystal 3D ED data collection. We further present how to set up a transmission electron microscope for 3D ED data acquisition and, more importantly, offer suggestions for the optimization of data acquisition conditions. For data processing, including unit cell and space group determination, and intensity integration, we provide guidelines on how to use electron and X-ray crystallography software to process 3D ED data. Finally, we present structure determination from 3D ED data and discuss the important features associated with 3D ED data that need to be considered. We believe that this protocol provides critical details for implementing and utilizing 3D ED as a structure determination platform for nano- (submicron-)sized MOFs as well as other crystalline materials.

Analysis of surface contaminants on beryllium and aluminum windows

Energy dispersive X-ray spectroscopy (EDXS) has limited application to microanalysis of radioactive materials because of degraded detector performance and the “intrinsic” spectrum associated with the radioactive decay. Electron energy loss spectroscopy (EELS) is not affected by specimen radioactivity and also offers the possibility of improved spatial resolution. Measurements of radiation-induced segregation (RIS) in irradiated stainless steels have been made by both techniques. Analytical electron microscopy was performed at 100 kV in a Philips EM400T/FEG, equipped with an EDAX 9100/70 EDXS system and a Gatan 666 parallel detection EELS (PEELS). Microanalysis was performed in the STEM mode (<2-nm-diam probe with >0.5 nA) with the same acquisition time (50 s) used for both techniques.Initial measurements were performed on an ion-irradiated modified type 316 stainless steel (designated LS1A), which had moderate-width (∼20 nm) RIS profiles at grain boundaries. Profiles measured by EDXS and PEELS match well and show chromium depletion and nickel enrichment (Fig. 1).

Fifty years old, and still going strong: Transmission electron optical studies of materials

Li-ion batteries have yet to reach their full application potential due to their inherent cycling performance issues, such as voltage instability and capacity fading, while fundamental questions remain unanswered regarding the mechanisms responsible. However, Mn-based layered oxides continue to be promising candidates for cathodes in high-energy-density Li batteries given their high voltage and high discharge capacities. A significant impediment to gaining insight into these layered oxides lies in their complexity and inhomogeneity. Thus, the focus of the present contribution will be on the parent material, Li2MnO3, which shows cycling characteristics similar to its more complex offspring. Scanning transmission electron microscopy (STEM) and spectroscopy are used to characterize structural and electronic properties of both pristine and cycled material. STEM-based methods are quickly becoming the most promising characterization tools for these and similar materials, owed largely to the wide-range of techniques available on advanced STEM instruments, including the direct imaging of both heavy and light elements, and both energy-dispersive X-ray (EDX) and electron energy loss (EEL) spectroscopies. Imaging modes such as high/low angle annular dark field (H/LAADF) and annular bright field (ABF) are exploited to image heavy atomic columns, strain contrast, and light atomic columns, respectively. Additionally, electron energy loss spectroscopy along with calculations based on density functional theory are used to probe the local electronic structure by monitoring the O K- and Mn L-edges, which can be used to track changes to both the O content and the Mn valence. Thus, the focus will remain on the structural and electronic evolution of the pristine layered oxide explored by combining spectroscopy and atomic-scale imaging with various in situ microscopy techniques and ex situ electrochemical cycling. Specifically, features such as the atomic ordering of Mn/Li atoms, O vacancy evolution, and Mn valence will be of particular interest.

Conventional X-ray powder diffraction analyses of aluminum-substituted lithium nickel oxides showed pronounced broadening of the (11l) type peaks with increasing aluminum concentrations. It was postulated that a segregation tendency of nickel and aluminum in the layered lithium nickel oxide structure could lead to anisotropic strains and size effects for the (110) type planes and thus pronounced broadening. Variation in the distribution of aluminum and nickel was detected among different crystals by energy-dispersive X-ray spectroscopy (EDX) and within individual crystals at the nanometer-scale by electron energy loss spectroscopy (EELS). Synchrotron X-ray powder diffraction analyses of the “LiNi1−yAlyO2” (0.10 ≤ y ≤ 0.50) samples revealed that strains in the (110) planes continuously increased with the aluminum concentration, which was then confirmed by convergent beam and selected area electron diffraction studies. Therefore, a combination of synchrotron X-ray powder diffraction, electron diffraction, E...

Among lithium battery cathode materials, Li1.2Ni0.13Mn0.54Co0.13O2 (LR-NMC) has a high theoretical capacity, but suffers from voltage and capacity fade during cycling. This is partially ascribed to transition metal cation migration, which involves the local transformation of the honeycomb layered structure to spinel-like nano-domains. Determination of the honeycomb layered/spinel phase ratio from powder X-ray diffraction data is hindered by the nanoscale of the functional material and the domains, diverse types of twinning, stacking faults, and the possible presence of the rock salt phase. Determining the phase ratio from transmission electron microscopy imaging can only be done for thin regions near the surfaces of the crystals, and the intense beam that is needed for imaging induces the same transformation to spinel as cycling does. In this article, it is demonstrated that the low electron dose sufficient for electron diffraction allows the collection of data without inducing a phase transformation. Using calculated electron diffraction patterns, we demonstrate that it is possible to determine the volume ratio of the different phases in the particles using a pair-wise comparison of the intensities of the reflections. Using this method, the volume ratio of spinel structure to honeycomb layered structure is determined for a submicron sized crystal from experimental three-dimensional electron diffraction (3D ED) and precession electron diffraction (PED) data. Both twinning and the possible presence of the rock salt phase are taken into account. After 150 charge–discharge cycles, 4% of the volume in LR-NMC particles was transformed irreversibly from the honeycomb layered structure to the spinel structure. The proposed method would be applicable to other multi-phase materials as well.

The first section of this chapter concerns scattering factors for the diffraction of electrons by crystalline solids. An explanation of the theory of scattering by a perfect crystal is followed by a discussion of the kinematical, two-beam and phase-grating approximations. Relativistic and absorption effects are considered. Extensive tables of atomic scattering amplitudes for electrons for neutral and ionized atoms are presented. The second section of the chapter briefly discusses the parameterization of electron atomic scattering factors. Tables of useful parameters as a function of accelerating voltage and elastic atomic scattering factors for neutral atoms are given. Complex scattering factors for the diffraction of electrons by gases are discussed in the third section of the chapter. This section includes tables of scattering factors of interest for gas-phase electron diffraction from atoms and molecules in the keV energy region. In addition to the tables and a description of their uses, a discussion of the theoretical uncertainties related to the material in the tables is also provided. The tables give scattering factors for elastic and inelastic scattering from free atoms. The theory of molecular scattering based on these atomic quantities is also discussed. Electron energy-loss spectroscopy on solids is discussed in the fourth section of the chapter. Topics covered include: the use of electron beams; single and multiple scattering; the classification of the different excitations in a spectrum; instrumentation; and the excitation spectra of valence and core electrons. The fifth section of the chapter describes oriented texture patterns. Lamellar and fibre texture patterns are discussed and applications to metals and organic materials are mentioned. The computation of dynamic wave amplitudes in then described in the sixth section of the chapter. This section deals first with the multislice method. The numerical procedure is outlined and factors that influence the choice of thickness of the slice are discussed. Two checks that can be performed during a multislice calculation are noted. The Bloch-wave method is then described. The use of Bloch waves to describe electron diffraction and electron imaging in thin crystals is outlined together with the concept of the dispersion surface. These emerge as natural solutions of the Schrodinger equation with a periodic optical potential to generate the elastic scattering and also the loss of intensity from the coherent wave field due to thermal diffuse and inelastic scattering. The Bloch-wave approach is a useful complement to the multislice method and provides a clear picture of wave propagation in perfect and imperfect crystals. In the seventh section of the chapter, the measurement of structure factors and the determination of crystal thickness by electron diffraction are described. The use of convergent-beam electron diffraction to obtain integrated intensities is discussed and the relationship between intensity features and the dispersion surface is explained. The last section of the chapter concerns crystal-structure determination by high-resolution microscopy. This technique allows the arrangement of atomic columns in thin crystals to be observed directly. The resolution of the best instruments is now slightly below 0.1 nm. The images usually show a projection through a slice of crystal about 20 nm thick, however tomographic (three-dimensional) reconstruction is now possible at nanometre resolution. The images show the host of microphases, grain boundaries, twins, line and planar defects which broad-beam methods, such as X-ray diffraction, provide the average scattering from. These defects often control the properties of crystals, engineering materials and electronic devices. Individual nanostructures, such as carbon nanotubes and catalyst particles, may be imaged at atomic resolution. Fine twinning, polytypes, intergrowth of oxide phases etc. can be identified, and increasingly the detailed atomic structure of defects (such as oxide, superconductor and semiconductor interfaces) is being determined. Substitutional dopant atoms have recently been imaged for the first time. In biology the method is limited by radiation damage; however by summing many images of identical randomly oriented macromolecules, tomographic density maps can be reconstructed at subnanometre resolution from hydrated proteins which cannot be crystallized (e.g. membrane proteins). This section reviews the theoretical principles of high-resolution electron microscopy, including few-beam and structure image formation, effects of electron-optical lens aberrations, partial coherence, resolution-limiting factors, image-simulation methods, dynamical effects, and a summary of super-resolution schemes. Keywords: absorption; atomic scattering amplitudes; atomic scattering factors; Bethe theory; Bloch-wave method; core-electron spectroscopy; core-loss spectroscopy; crystal thickness; crystalline solids; dielectric description; dynamical diffraction; dynamical wave amplitudes; EELS; elastic scattering; electron diffraction; electron energy-loss spectroscopy; electron microscopy; electrons; free-electron gas; high-resolution electron microscopy; HREM; hyper-resolution; inelastic scattering; lamellar textures; lattice-fringe images; molecular scattering factors; multiple scattering; multislice method; oriented texture patterns; plasmons; real solids; relativistic effects; STEM; scanning transmission electron microscopes; scattering factors; solid-state effects; spectrometers; structure factors; surface plasmons; texture; wave amplitudes; X-ray diffraction