Ionisation of Atoms Determined by Kappa Refinement against 3D Electron Diffraction Data

Description

The following submission contains the data reduction and processing files, dynamical refinement files, refinement files for theoretical structure factors, and CIF files of five inorganic compounds: quartz, natrolite, borane, caesium lead bromide, and lutetium aluminium garnet collected by 3D electron diffraction (3D ED) for studying ionisation of atoms by kappa refinement against 3D ED data. The data set for quartz was collected using the precession-assisted 3D ED method and for borane, caesium lead bromide, and lutetium aluminium garnet was collected using the continuous-rotation 3D ED method. Two data sets were collected from the same crystal for natrolite using continuous-rotation and precession-assisted 3D ED method. The data reduction and processing were done using PETS2 (1) software and the dynamical refinements were performed using the JANA2020 (2) software. The refinements were performed in two primary stages: IAM refinements (without taking into consideration the effects of charge transfer between the atoms) and kappa refinements (by taking into consideration the effects of charge transfer between the atoms). The submission also contains JANA2020 files of refinements against theoretical structure factors obtained using periodic DFT calculations and on the structure model obtained after IAM refinements of each of the experimental data sets. The folders are divided according to the compounds. Each folder contains the relevant data reduction and processing files (PETS2 files), dynamical refinement files (JANA2020 files for IAM and kappa refinements), refinement files for theoretical structure factors (JANA2020 files for IAM and kappa refinements) and final CIF files (for IAM and kappa refinements).   References 1.         L. Palatinus, P. Brázda, M. Jelínek, J. Hrdá, G. Steciuk, M. Klementová, Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0. Acta Cryst B 75, 512–522 (2019). 2.         V. Petříček, L. Palatinus, J. Plášil, M. Dušek, Jana2020 – a new version of the crystallographic computing system Jana. Zeitschrift für Kristallographie - Crystalline Materials 238, 271–282 (2023).   The following table summarises the crystallographic information and data collection parameters for the data sets. Crystal data             Sample Quartz Natrolite Natrolite Borane Caesium lead bromide Lutetium Aluminium Garnet Chemical formula SiO2 Na2Al2Si3O12H4 Na2Al2Si3O12H4   B18H22 CsPbBr3 Lu3Al5O12 Mr 60.1 380.2 380.2 108.4 579.8 851.8 Crystal system, space group Trigonal, P3221 Orthorhombic, Fdd2 Orthorhombic, Fdd2 Orthorhombic, Pccn Orthorhombic, Pbnm Cubic, Ia3 ̅d a, b, c (Å) 4.9012(24), 4.9012, 5.4068(26) 18.3885(1), 18.7183(32), 6.6569(11) 18.4125(9), 18.7073(7), 6.6306(2) 10.7789(17), 11.9869(16), 10.7338(17) 8.1189(4), 8.359(4), 11.7593(5) 11.9105(4), 11.9105(4), 11.9105(4) α, β, γ (°) 90, 90, 120 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 90, 90, 90 V (Å3) 112.48(8) 2291.31(54) 2283.90(16) 1386.87(36) 798.1(1) 1689.6(1) Z 3 8 8 4 4 8 Crystal size (mm) 0.0004 0.0005 0.0005 0.0015 0.0004 0.0003               Data collection             Diffractometer TEM FEI Technei G2 20 TEM FEI Technei G2 20 TEM FEI Technei G2 20 TEM FEI Technei G2 20 TEM FEI Technei G2 20 TEM FEI Technei G2 20 3D ED method Precession Precession Continuous Rotation Continuous Rotation Continuous Rotation Continuous Rotation Detector Medipix 3 ASI Cheetah Medipix 3 ASI Cheetah Medipix 3 ASI Cheetah Medipix 3 ASI Cheetah Medipix 3 ASI Cheetah Medipix 3 ASI Cheetah Radiation source LaB6 LaB6 LaB6 LaB6 LaB6 LaB6 Radiation type Electron, λ = 0.0251 Å Electron, λ = 0.0251 Å Electron, λ = 0.0251 Å Electron, λ = 0.0251 Å Electron, λ = 0.0251 Å Electron, λ = 0.0251 Å Temperature (K) 293 95 95 100 153 153 (sin θ/λ)max (Å−1) 1.25 1.1 1.00 0.85 1.00 1.4 No. of measured, independent andobserved [I > 3σ(I)] reflections 3631, 1076, 1004  15767, 6018, 4419  12368, 4546, 4422  30304, 13809, 4779 16736, 422, 363 23256, 1562, 1363               Software used             Data collection RATS software RATS software RATS software RATS software RATS software RATS software Data reduction and processing PETS2 PETS2 PETS2 PETS2 PETS2 PETS2 Refinement JANA2020 JANA2020 JANA2020 JANA2020 JANA2020 JANA2020 DFT calculation WIEN2k and Crystal23 WIEN2k Crystal23 Crystal23 WIEN2k WIEN2k              

Resources

Name Format Description Link
0 http://data.europa.eu/88u/dataset/oai-zenodo-org-13359514
0 http://data.europa.eu/88u/dataset/oai-zenodo-org-13359514
0 http://data.europa.eu/88u/dataset/oai-zenodo-org-13359514
0 http://data.europa.eu/88u/dataset/oai-zenodo-org-13359514
0 http://data.europa.eu/88u/dataset/oai-zenodo-org-13359514
0 http://data.europa.eu/88u/dataset/oai-zenodo-org-13359514

Tags

  • charge-density
  • kappa-refinement
  • quantum-crystallography
  • 3ded
  • electron-diffraction

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