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6 results for “3D Electron Diffraction”
Ionisation of Atoms Determined by Kappa Refinement against 3D Electron Diffraction Data
<p>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.</p> <p>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 (<em>1</em>) software and the dynamical refinements were performed using the JANA2020 (<em>2</em>) 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).</p> <p>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.</p> <p>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).</p> <p> </p> <p>References</p> <p>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. <em>Acta Cryst B</em> <strong>75</strong>, 512–522 (2019).</p> <p>2. V. Petříček, L. Palatinus, J. Plášil, M. Dušek, Jana2020 – a new version of the crystallographic computing system Jana. <em>Zeitschrift für Kristallographie - Crystalline Materials</em> <strong>238</strong>, 271–282 (2023).</p> <p> </p> <p>The following table summarises the crystallographic information and data collection parameters for the data sets.</p> <table> <tbody> <tr> <td> <p><strong>Crystal data</strong></p> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p>Sample</p> </td> <td> <p>Quartz</p> </td> <td> <p>Natrolite</p> </td> <td> <p>Natrolite</p> </td> <td> <p>Borane</p> </td> <td> <p>Caesium lead bromide</p> </td> <td> <p>Lutetium Aluminium Garnet</p> </td> </tr> <tr> <td> <p>Chemical formula</p> </td> <td> <p>SiO<sub>2</sub></p> </td> <td> <p>Na<sub>2</sub>Al<sub>2</sub>Si<sub>3</sub>O<sub>12</sub>H<sub>4</sub></p> </td> <td> <p>Na<sub>2</sub>Al<sub>2</sub>Si<sub>3</sub>O<sub>12</sub>H<sub>4</sub></p> </td> <td> <p>B<sub>18</sub>H<sub>22</sub></p> </td> <td> <p>CsPbBr<sub>3</sub></p> </td> <td> <p>Lu<sub>3</sub>Al<sub>5</sub>O<sub>12</sub></p> </td> </tr> <tr> <td> <p>M<sub>r</sub></p> </td> <td> <p>60.1</p> </td> <td>380.2</td> <td> <p>380.2</p> </td> <td> <p>108.4</p> </td> <td> <p>579.8</p> </td> <td> <p>851.8</p> </td> </tr> <tr> <td> <p>Crystal system, space group</p> </td> <td> <p>Trigonal, P3<sub>2</sub>21</p> </td> <td> <p>Orthorhombic, Fdd2</p> </td> <td> <p>Orthorhombic, Fdd2</p> </td> <td> <p>Orthorhombic, Pccn</p> </td> <td> <p>Orthorhombic, Pbnm</p> </td> <td> <p>Cubic, Ia3 ̅d</p> </td> </tr> <tr> <td> <p>a, b, c (Å)</p> </td> <td> <p>4.9012(24), 4.9012, 5.4068(26)</p> </td> <td> <p>18.3885(1), 18.7183(32), 6.6569(11)</p> </td> <td> <p>18.4125(9), 18.7073(7), 6.6306(2)</p> </td> <td> <p>10.7789(17), 11.9869(16), 10.7338(17)</p> </td> <td> <p>8.1189(4), 8.359(4), 11.7593(5)</p> </td> <td> <p>11.9105(4), 11.9105(4), 11.9105(4)</p> </td> </tr> <tr> <td> <p>α, β, γ (°)</p> </td> <td> <p>90, 90, 120</p> </td> <td>90, 90, 90</td> <td> <p>90, 90, 90</p> </td> <td> <p>90, 90, 90</p> </td> <td> <p>90, 90, 90</p> </td> <td> <p>90, 90, 90</p> </td> </tr> <tr> <td> <p>V (Å<sup>3</sup>)</p> </td> <td> <p>112.48(8)</p> </td> <td> <p>2291.31(54)</p> </td> <td> <p>2283.90(16)</p> </td> <td> <p>1386.87(36)</p> </td> <td> <p>798.1(1)</p> </td> <td> <p>1689.6(1)</p> </td> </tr> <tr> <td> <p>Z</p> </td> <td> <p>3</p> </td> <td> <p>8</p> </td> <td> <p>8</p> </td> <td> <p>4</p> </td> <td> <p>4</p> </td> <td> <p>8</p> </td> </tr> <tr> <td> <p>Crystal size (mm)</p> </td> <td> <p>0.0004</p> </td> <td> <p>0.0005</p> </td> <td> <p>0.0005</p> </td> <td> <p>0.0015</p> </td> <td> <p>0.0004</p> </td> <td> <p>0.0003</p> </td> </tr> <tr> <td> <p> </p> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p><strong>Data collection</strong></p> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p>Diffractometer</p> </td> <td> <p>TEM FEI Technei G2 20</p> </td> <td> <p>TEM FEI Technei G2 20</p> </td> <td> <p>TEM FEI Technei G2 20</p> </td> <td> <p>TEM FEI Technei G2 20</p> </td> <td> <p>TEM FEI Technei G2 20</p> </td> <td> <p>TEM FEI Technei G2 20</p> </td> </tr> <tr> <td> <p>3D ED method</p> </td> <td> <p>Precession</p> </td> <td> <p>Precession</p> </td> <td> <p>Continuous Rotation</p> </td> <td> <p>Continuous Rotation</p> </td> <td> <p>Continuous Rotation</p> </td> <td> <p>Continuous Rotation</p> </td> </tr> <tr> <td> <p>Detector</p> </td> <td> <p>Medipix 3 ASI Cheetah</p> </td> <td> <p>Medipix 3 ASI Cheetah</p> </td> <td> <p>Medipix 3 ASI Cheetah</p> </td> <td> <p>Medipix 3 ASI Cheetah</p> </td> <td> <p>Medipix 3 ASI Cheetah</p> </td> <td> <p>Medipix 3 ASI Cheetah</p> </td> </tr> <tr> <td> <p>Radiation source</p> </td> <td> <p>LaB<sub>6</sub></p> </td> <td> <p>LaB<sub>6</sub></p> </td> <td> <p>LaB<sub>6</sub></p> </td> <td> <p>LaB<sub>6</sub></p> </td> <td> <p>LaB<sub>6</sub></p> </td> <td> <p>LaB<sub>6</sub></p> </td> </tr> <tr> <td> <p>Radiation type</p> </td> <td> <p>Electron, λ = 0.0251 Å</p> </td> <td> <p>Electron, λ = 0.0251 Å</p> </td> <td> <p>Electron, λ = 0.0251 Å</p> </td> <td> <p>Electron, λ = 0.0251 Å</p> </td> <td> <p>Electron, λ = 0.0251 Å</p> </td> <td> <p>Electron, λ = 0.0251 Å</p> </td> </tr> <tr> <td> <p>Temperature (K)</p> </td> <td> <p>293</p> </td> <td> <p>95</p> </td> <td> <p>95</p> </td> <td> <p>100</p> </td> <td> <p>153</p> </td> <td> <p>153</p> </td> </tr> <tr> <td> <p>(sin θ/λ)<sub>max</sub> (Å<sup>−1</sup>)</p> </td> <td> <p>1.25</p> </td> <td> <p>1.1</p> </td> <td> <p>1.00</p> </td> <td> <p>0.85</p> </td> <td> <p>1.00</p> </td> <td> <p>1.4</p> </td> </tr> <tr> <td> <p>No. of measured, independent and<br>observed [I > 3σ(I)] reflections</p> </td> <td> <p>3631, 1076, 1004 </p> </td> <td> <p>15767, 6018, 4419 </p> </td> <td> <p>12368, 4546, 4422 </p> </td> <td> <p>30304, 13809, 4779</p> </td> <td> <p>16736, 422, 363</p> </td> <td> <p>23256, 1562, 1363</p> </td> </tr> <tr> <td> <p> </p> </td> <td> <p> </p> </td> <td> <p> </p> </td> <td> <p> </p> </td> <td> <p> </p> </td> <td> <p> </p> </td> <td> <p> </p> </td> </tr> <tr> <td> <p><strong>Software used</strong></p> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td> <p>Data collection</p> </td> <td> <p>RATS software</p> </td> <td> <p>RATS software</p> </td> <td> <p>RATS software</p> </td> <td> <p>RATS software</p> </td> <td> <p>RATS software</p> </td> <td> <p>RATS software</p> </td> </tr> <tr> <td> <p>Data reduction and processing</p> </td> <td> <p>PETS2</p> </td> <td> <p>PETS2</p> </td> <td> <p>PETS2</p> </td> <td> <p>PETS2</p> </td> <td> <p>PETS2</p> </td> <td> <p>PETS2</p> </td> </tr> <tr> <td> <p>Refinement</p> </td> <td> <p>JANA2020</p> </td> <td> <p>JANA2020</p> </td> <td> <p>JANA2020</p> </td> <td> <p>JANA2020</p> </td> <td> <p>JANA2020</p> </td> <td> <p>JANA2020</p> </td> </tr> <tr> <td> <p>DFT calculation</p> </td> <td> <p>WIEN2k and Crystal23</p> </td> <td> <p>WIEN2k</p> </td> <td> <p>Crystal23</p> </td> <td> <p>Crystal23</p> </td> <td> <p>WIEN2k</p> </td> <td> <p>WIEN2k</p> </td> </tr> <tr> <td> <p> </p> </td> <td> <p> </p> </td> <td> </td> <td> <p> </p> </td> <td> <p> </p> </td> <td> <p> </p> </td> <td> </td> </tr> </tbody> </table>
Accurate lattice parameters from 3D electron diffraction data I: Optical distortions
<p>3D ED data were measured with an FEI Tecnai G2 20 transmission electron microscope equipped with an Olympus SIS Veleta camera (CCD, 14 bit, 2048 x 2048 px) and a NanoMEGAS Digistar precession unit.</p> <p>Supporting information for article submitted to a scientific journal. Examples 1 and 2 including manuals and command files for optical distortions refinement in 3D ED data using PETS2 software.</p> <p>Manuals for the examples are available as the supporting information of the submitted article.</p>
Crystal structure of natural product Argyrin-D determined by 3D electron diffraction
<p>360° rotation of the Argyrin D model (stick mode with carbon, yellow; nitrogen, blue; oxygen, red; sulfur, gold and hydrogen, white) defined by a 2Fo-Fc map contoured at 1.2 sigma (grey mesh). The model was refined at a resolution of 1.1Å in Phenix using implemented electron scattering factors and restraints to R and Rfree values of 17.3 and 18.6%, respectively.</p>
3D Electron Diffraction Dataset of CAU-55-Cl
<p>3D electron diffraction dataset in XDS format and a video (AVI) showing the diffraction frames (sped up approximately 50 times). The material studied is CAU-55-Cl.</p> <p> </p> <p>Data were collected on a JEOL JEM-2100 LaB<sub>6</sub> microscope with an Amsterdam Scientific Instruments TimePix detector, using the software <a href="https://zenodo.org/record/3470096">Instamatic</a>.</p>
3D electron diffraction dataset of natural product Beauveriolide Q
<p><span>3D ED data was recorded using EPU-D, with the original dataset saved in MRC format. The PETS2 processing file contains all the dataset’s metadata. Structure analysis and refinement data are also included.</span></p>
Indomethacin Polymorph δ Revealed to be Two Plastically Bendable Crystal Forms by 3D Electron Diffraction: Correcting a 47-Year-Old Misunderstanding
<p>Raw electron diffraction data of indomethacin polymorphs <span class="math-tex">\(δ\)</span> and <span class="math-tex">\(θ\)</span> obtained via solution and melt crystallization, respectively. Single crystals were grown using microdroplet melt crystallization and crushed to give microcrystals suitable for electron diffraction. Data were collected using a JEOL JEM-2100 LaB6 TEM operated at 200 kV and equipped with a Timepix hybrid pixel detector.</p> <p> </p>
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