1. ABOUT THE DATASET
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Title: Molecular Crystals 4D-STEM Dataset for Microscopic Dislocation Analysis

Creator(s): Sang Pham[1], Natalia Koniuch[1], Emily Wynne[1], Andy Brown[1], Sean M. Collins[1]

Organisation(s): 1. University of Leeds

Publication Year: 2024

Description: This dataset contains original scanning electron diffraction data acquired on p-terphenyl, anthracene, theophylline, and leaf wax samples presented in the linked publication. The dataset also contains associated calibration data of Au-X grating and MoO3. The data is presented in HDF5 file format, consistent with the hyperspy Python package, an open-source package coded in Python.

Cite as: Pham, Sang; Koniuch, Natalia; Wynne, Emily; Brown, Andy; and Collins, Sean (2024): Molecular Crystals 4D-STEM Dataset for Microscopic Dislocation Analysis. University of Leeds. [Dataset] https://doi.org/10.5518/1589

Related publication: Sang Pham, Natalia Koniuch, Emily Wynne, Andy Brown, Sean M. Collins, Microscopic crystallographic analysis of dislocations in molecular crystals, Nature Materials, 2024 (Submitted)

Contact: t.s.pham@leeds.ac.uk; s.m.collins@leeds.ac.uk

2. TERMS OF USE
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Copyright [2024] [University of Leeds]. Unless otherwise stated, this dataset is licensed under a Creative Commons Attribution 4.0 International Licence: https://creativecommons.org/licenses/by/4.0/.

3. PROJECT AND FUNDING INFORMATION
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Title: Nanoscale photophysics at defects and interfaces in organic semiconductors

Dates: 1st February 2022 - 31st January 2025

Funding organisation: Engineering and Physical Sciences Research Council (EPSRC), EPSRC Centre for Doctoral Training in Molecules to Product in collaboration with Syngenta and AstraZeneca, iCASE studentship (AstraZeneca Ltd and the EPSRC), Diamond Light Source - Rutherford Appleton Laboratory (UK), and the University of Leeds

Grant no.: EP/V044907/1; EP/SO22473/1; 2182593; MG28500; MG30057; MG31258; MG30157; and MG31872

4. CONTENTS
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File listing

4D-STEM data for anthracene: 4D-STEM dataset of anthracene samples collected in mg30157 and mg31872.
4D-STEM data for p-terphenyl: 4D-STEM dataset of p-terphenyl samples collected in mg31258, mg30157 and mg30160.
4D-STEM data for theophylline: 4D-STEM dataset of theophylline samples.
4D-STEM data for wax: 4D-STEM dataset of wax samples.
Calibration data for anthracene and p-terphenyl: 4D-STEM calibration data of Au_X_grating and MoO3 collected in mg30157, mg30160, mg31258, mg31872.
Calibration data for theophylline and wax: 4D-STEM calibration data of Au_X_grating and MoO3 collected in the same sessions of theophylline and wax samples.

All above data are saved in HDF5 format, compatible with the hyperspy Python package, an open-source package coded in Python.

Dose series data: Diffraction data of anthracene and p-terphenyl collected at different electron fluences. The dose series data are saved in tif format, available for analysis with Fiji-ImageJ or hyperspy Python package.

5. METHODS
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Transmission electron microscopy (TEM): Electron diffraction pattern series as a function of cumulative electron fluence for p-terphenyl and anthracene were recorded using an FEI Titan3 Themis 300 (X-FEG high-brightness electron source, operated at 300 kV) microscope in a standard parallel beam TEM configuration (Supplementary Note 4).
For p-terphenyl an electron beam flux of 2.5 e- Å-2 s-1 was used whereas for anthracene an electron beam flux of 0.085 e- Å-2 s-1 was used. These values were determined from the current read out at the viewing screen, calibrated using a Faraday cup. A time-series of the selected area electron diffraction patterns were recorded for each compound across multiple crystals and multiple areas on the TEM grid.

Scanning electron diffraction (SED or 4D-STEM): SED data were acquired on the JEOL ARM300CF instrument (ePSIC, Diamond Light Source, UK) equipped with a high-resolution pole piece, a cold field emission gun, aberration-correctors in both the probe-forming and image-forming optics, and a 4-chip Merlin/Medipix pixelated electron counting STEM detector. The instrument was operated at 300 kV.
Selected samples were analysed at 200 kV, identified in the corresponding figure captions. The electron optics were configured for nanobeam diffraction by switching off the aberration corrector in the probe-forming optics and adjusting the condenser lens system to produce a convergence semiangle of 0.8 mrad using a 10 μm condenser aperture.
At 300 kV, this produces a 3-nm diffraction-limited probe diameter d_diff=1.22λ/α for electron de Broglie wavelength λ and convergence semiangle α. The probe current was measured using a Faraday cup as ~1 pA, and the exposure time at each probe position was set as 1 ms. The electron fluence was approximately 8.8 e- Å-2 at 300 kV or 5.4 e- Å-2 at 200 kV in a single scan, assuming a disk-like probe with a diameter equal to ddiff.
All SED measurements were conducted over a scan size of 256×256 probe positions. Image and diffraction calibration data, including reference calibration of residual elliptical distortion in the diffraction plane, were acquired using a gold diffraction cross-grating with a period of 500 nm (Ted Pella). These cross-gratings contain a small fraction of Pd (AuPd);
by comparison with an evaporated Au sample, we estimate ~1% error in Å-1/pixel calibrations at the camera lengths used in this work when calibrating with respect to the pure Au crystal structure (with no effect on elliptical distortion calibration). To minimise these effects on our analysis, we employed full pattern matching for indexation (see Data analysis).
The relative rotation between the diffraction pattern and the raster pattern was calibrated using standard MoO3 crystals (Agar Scientific). Calibration data were acquired under identical conditions to the molecular crystal samples. When accounting for this calibration, the diffraction patterns are rotated, resulting in a rotation of a ‘cross’ arising from a gap in the pixel readouts between the four quadrants of the Merlin/Medipix detector.