Research Article: Automated electron diffraction tomography – development and applications

Date Published: August 01, 2019

Publisher: International Union of Crystallography

Author(s): Ute Kolb, Yaşar Krysiak, Sergi Plana-Ruiz.


Electron diffraction tomography, a potential method for structure analysis of nanocrystals, and, in more detail, the strategies to use automated diffraction tomography (ADT) technique are described. Examples of ADT application are discussed according to the material class.

Partial Text

Crystalline nanomaterials from industrial as well as natural sources are present in nearly every aspect of our live. Their structural characterization over several length scales down to atomic resolution is crucial in order to understand and optimize physical properties and to invent new applications. Diffraction methods using X-ray or neutron sources, are commonly applied for crystal structure analysis of crystalline materials. X-ray powder diffraction (XRPD), a widespread technique for which well consolidated structure analysis routines exist, provides the three-dimensional diffraction space in only one dimension. For large unit cells, low symmetry, phase mixtures and impure samples may cause problems in indexing and correct intensity extraction. Additionally, peak profiles may be broadened and asymmetric due to crystal size, strain effects or disorder. The investigation of single crystals is necessary in order to gain information from the full three-dimensional diffraction space. In contrast to X-rays, which can be used only for structure analysis on single crystals down to about one micron, electrons undergo 103 times stronger interaction with matter but they can be used to obtain individual access to crystals down to few nanometres, so-called nanocrystals. For the investigation of such crystals this is realized in a transmission electron microscope (TEM), providing electron diffraction (ED), atomic-resolved imaging in the conventional mode [high-resolution TEM (HRTEM)] or scanning mode [high-resolution STEM (HR-STEM)] as well as spectroscopic information [energy-dispersive spectroscopy (EDS) or electron energy-loss spectroscopy (EELS)] (Hirsch, 1977 ▸; Reimer & Kohl, 2008 ▸; Williams & Carter, 2008 ▸). One of the main advantages of ED is that data can be obtained with high resolution but smaller electron doses compared to HRTEM or HR-STEM, which means that less radiation damage is produced on the crystal at similar resolution.

In order to gain a robust, reliable and easy applicable method for the acquisition of more complete and kinematic ED data from single nanocrystals, automated diffraction tomography (ADT) was developed (Kolb et al., 2007 ▸). In contrast to the above-mentioned traditional ED methods, ADT utilizes non-oriented (off-zone) ED patterns. The inclination of the electron beam from the zone axis reduces systematic dynamical effects arising from the interaction of systematic reflection classes (such as 00l), thus providing diffraction data closer to the kinematical behaviour. As a second benefit, the orientation of a crystal axis along the goniometer axis becomes obsolete and only the adjustment of the eucentric height remains. ED patterns are collected while the crystal is tilted sequentially in fixed tilt steps in the range of 0.2–1° dependent on the goal of the investigation. For diffraction data acquisition, the illumination is set to a nano-sized and semi-parallel beam using a small condenser aperture [nanoelectron diffraction (NED) or nanobeam diffraction (NBD) method according to the TEM manufacturer, but referred hereafter as nanobeam electron diffraction (NBED)] or to a parallel beam that illuminates a larger area of the sample by means of a selected area aperture (SAED method). In respect to data acquisition, this strategy demands the tracking of the crystal during tilt series acquisition by imaging techniques. In general, TEM and STEM imaging can be used equally, but STEM imaging was used for ADT in the first instance due to the lower electron dose applied to the sample. For full integration of the diffraction space wedges, electron beam precession can be applied (Vincent & Midgley, 1994 ▸; Midgley & Eggeman, 2015 ▸). An additional effect of precession electron diffraction (PED) application is the reduction of remaining dynamical effects originating from non-systematic reflections (Oleynikov et al., 2007 ▸). A more detailed description is provided in Section 2.1. In respect to data processing, the first step involves the determination of unit-cell parameters and space groups and, after indexing, in a second step, the extraction of reflection intensities. Off-zone diffraction implies the need for three-dimensional reconstruction of the diffraction space. For this purpose the ADT3D program was developed; thus guiding through the different steps in an easy and systematic way (Kolb et al., 2008 ▸; Schlitt et al., 2012 ▸). A more detailed explanation of the ADT3D program and its newer version is provided in Section 2.2 (both programs distributed by NanoMEGAS SPRL, Belgium). The logical approach is similarly implemented in other programs (Oleynikov, 2011 ▸; Palatinus, 2011 ▸; Clabbers et al., 2018 ▸). Visual inspection of the total scattering information in three dimensions is particularly important for the detection of additional crystalline individuals inside the investigated volume, as well as special crystallographic features such as superstructures, incoherent modulation, twinning or disorder. Recently, the ADT method proved to be suitable for two-dimensionally disordered samples, which enables ab initio structure analysis of the average crystal structure and, subsequently, description of the stacking sequence by means of quantitative comparison of simulated ED patterns with cuts from the measured reciprocal volume (see Section 3).

EDT is nowadays used by a growing number of scientific groups. The broad applicability of EDT covers inorganic materials such as alloys (Bowden et al., 2018 ▸), natural minerals (Gemmi et al., 2012 ▸; Rozhdestvenskaya et al., 2017 ▸; Németh et al., 2018 ▸), archaeological materials (Zacharias et al., 2018 ▸; Nicolopoulos et al., 2018 ▸), a large number of zeolites (Jiang et al., 2011 ▸; Willhammar et al., 2012 ▸; Mugnaioli & Kolb, 2014 ▸; Bereciartua et al., 2017 ▸), phosphates (Mugnaioli, Sedlmaier et al., 2012 ▸), perovskites (Klein, 2011 ▸; Gorelik et al., 2011 ▸), samples with organic ligands (Förster et al., 2015 ▸), zeolite with incorporated templates (Rius et al., 2013 ▸) or hybrid materials (Bellussi et al., 2012 ▸), as well as more electron beam-sensitive samples such as metal–organic frameworks (MOFs) (Denysenko et al., 2011 ▸; Rhauderwiek et al., 2018 ▸; Wang et al., 2018 ▸), small organic molecules (Gorelik et al., 2012 ▸) such as pigments (Teteruk et al., 2014 ▸) or pharmaceuticals (van Genderen et al., 2016 ▸; Wang et al., 2017 ▸; Palatinus et al., 2017 ▸; Das et al., 2018 ▸; Gruene et al., 2018 ▸; Jones et al., 2018 ▸) as well as proteins (Nederlof et al., 2013 ▸; Nannenga & Gonen, 2014 ▸; Lanza et al., 2019 ▸). Furthermore, the method was proven to be even suitable for in situ investigations (Karakulina et al., 2018 ▸). The crystal sizes shown here in these examples are in the regime of several hundred down to one hundred nanometres.

The high potential of EDT for crystal structure analysis of nanocrystals, where other diffraction methods such as X-ray single crystal or powder diffraction fail, has been demonstrated many times since 2007, when the development of the first method was described. Here we provide a description of the different approaches and propose to reference all the different acquisition techniques in the general name of EDT. Apart from this survey, we focus on the ADT method developed in our group, which is so far the only method combining STEM imaging for tracking purposes with tomographic diffraction data acquisition. The benefit of this approach is discussed from a technical point of view as well as demonstrated in the case of applications to several classes of materials. This includes the accessibility of crystals down to a size of 20 nm and the possibility of accessing the average structure of the disordered material with a subsequent description of the disorder. In addition, it was demonstrated that ADT is capable of acquiring EDT data from beam-sensitive materials with only weak scattering atoms by using a CCD camera. Especially for phase mixtures, it is important to be able to derive information from all phases, which may not only differ in terms of crystal size but as well by properties such as crystallinity, solubility, stability and bioavailability. As an example, a structure analysis of carbamazepine was successfully performed based on a single ADT data set. The structure, which was refined without any constraint, is in good agreement with those solved by EDT on the basis of significantly larger crystals.