DOI: 10.5281/zenodo.13359514
title: 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