STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials

Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy on each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3D ED). The snapshot data acquisition in SerialED can be realized both in transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which brings challenges for its 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 (DM) scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL developed for serial X-ray crystallography. Our workflow for 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, and demonstrate, for the first time, ab initio structure determination through direct methods using the STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and SerialED data extend to 0.60 Å. We show that the structural model obtained using SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction (cRED) data from one crystal. This demonstrates that accurate structures can be obtained from SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that SerialED greatly improves data resolution of ZSM-25, compared to serial rotation electron diffraction (SerialRED), from 1.50 Å to 0.90 Å. This allows for the first time the use of standard phasing methods such as direct methods for ab initio structure determination of ZSM-25.