DOI: 10.5281/zenodo.15594027
title: Crystal Structures of XeF2∙2PtF4 and XeF2∙2PdF4 Determined by 3D Electron Diffraction and Structural Models of XePtF6

description: 3D Electron diffraction

3D ED data were collected on a Tecnai G2 transmission electron microscope (TEM). Data sets were collected at a temperature of 100 K using a continuous rotation electron diffraction (cRED) method with a tilt step of 0.30° per diffraction frame. The electron beam was generated using a LaB6 source at 200 kV (λ = 0.02508 Å), and a Medipix 3 hybrid pixel detector ASI CheeTah (512 × 512 pixels, 24-bit dynamic range) was used to collect the diffraction patterns. The data reduction and processing were done in PETS2 (1), and the structure solution and refinements were done in JANA2020 (2) software. For the 3D ED measurement of XeF2·2PdF4, a single dataset was used, while for XeF2·2PtF4, two datasets from two different crystals were merged. The processed merged data can be found in the folder “Merged”.

3D_ED-data folder:

The submitted 3D ED data contains raw diffraction images in .tiff format for each crystal. It also contains the relevant data reduction and processing files (PETS2 files), the final refined file (JANA2020 files), final CIF, and structure factor (.fcf) files. Measurement conditions for a crystal and PETS parameters can be found in .pts file. 

 

Periodic DFT calculations

Calculations performed using the r2SCAN functional (3, 4) with the van der Waals D3 correction (5, 6). Calculation parameters: 700 eV cutoff of the plane-wave basis set; PAW pseudopotentials; SCF convergence: 10–6 eV per cell; k-point mesh with a 2π × 0.03 Å−1 spacing.

DFT-data folder:

Input files and results of Density Functional Theory (DFT) modelling (geometry optimization) performed in VASP 6.3.4 code for XeMF6 (M = Cr, Mn, Pd, Pt) and XeM2F10 (M = Mn, Pd, Pt) compounds (each stoichiometry in a separate folder). For XeMF6 compounds three structure types were considered: cis-chain, tetramers, trans-chains. Files for each polymorph are included in a subfolder of the parent stoichiometry folder.

Description of files (ASCII format):

Geom_r2SCAN_D3.sh – submission script

KPOINTS – k-point sampling

POTCAR – PAW pseudopotential file

POSCAR_next – input geometry 

[stoichiometry]-[symmetry tag or structure description]-[pressure in kbar]-r2SCAN_D3.vasp – structure optimized at a given pressure given in VASP format.

 

Powder X-ray Diffraction

Powder X-ray diffraction patterns were obtained on a Rigaku OD XtaLAB Synergy-S diffractometer equipped with a Dectris EIGER2 R CdTe 1M detector using microfocused Ag Kα radiation (λ = 0.56087 Å). In each measurement, 6 frames were recorded with an exposure time of 300 s per frame with the detector positioned 90 mm away from the sample. The measurements were conducted at a temperature of 100 K, achieved using an Oxford Cryosystems 800 Series Cryostream. PXRD profiles were extracted and processed using CrysAlisPro software. Prior to analysis, the samples were pulverized in an agate mortar within a glovebox and loaded into F2-passivated quartz capillaries (500 µm diameter), which were subsequently flame-sealed in a hydrogen–oxygen flame.

PXRD-data folder:

The supplied dataset consist of extracted powder diffractograms for XeF2·2PtF4 and XeF2·2PdF4 in the .dat file format together with the raw diffraction images in the .odeiger file format.

 

Raman Spectroscopy

Ambient and low-temperature Raman spectra were measured on a Bruker Senterra II confocal Raman microscope using a 785-nm emission line. The spectra were measured in the 50–1410 cm−1 range with a resolution of 1.5 cm−1. Low-temperature spectra were measured at 100 K employing a Linkam LTS420 low-temperature stage. Complete set of measurement parameters for each submitted spectrum is given below:

nXeF2·PtF4 (labelled as XeF2_Pt_aHF) – 50 × 1000 µm aperture, 25 mW laser power, 50x objective, recorded at room temperature.

XeF2·PtF4 – 50 × 1000 µm aperture, 25 mW laser power, 50x objective, recorded at room temperature.

XeF2·2PtF4 – 15 × 1000 µm aperture, 100 mW laser power, 20x objective, recorded at 100 K.

XeF2·PdF4 + XeF2 – 50 × 1000 µm aperture, 10 mW laser power, 20x objective, recorded at room temperature.

XeF2·PdF4 – 50 × 1000 µm aperture, 10 mW laser power, 20x objective, recorded at room temperature.

XeF2·2PdF4 – 15 × 1000 µm aperture, 25 mW laser power, 20x objective, recorded at 100 K.

Sample preparation involved loading the materials into quartz capillaries, as described above in the powder X-ray diffraction section. Background subtraction on the spectra was performed in Bruker Opus 8.7 software suite using 3 iterations of concave rubber band correction with 64 baseline points.

Raman-data folder:

The subfolders labeled "processed" and "raw" contain the Raman spectra of the aforementioned compounds, with and without background subtraction, respectively. All spectra are provided in the comma-delimited .dpt file format. Note: the broad features observed in the 1100–1300 cm−1 region in some of the spectra are measurement artefacts, most likely originating from the use of the quartz capillaries, and not a component of the Raman spectra of the compounds.

 

ATR-IR Spectroscopy

Infrared spectra were measured inside an N2 atmosphere glovebox on a Bruker Alpha II FT-IR spectrometer equipped with a Platinum Diamond-ATR sampling module. Prior to analysis, the compounds were finely ground in an agate mortar. Spectra were recorded in the range of 400–4000 cm−1 with a resolution of 4 cm−1 and 24 scans taken per measurement.

ATR-IR-data folder:

The submitted data consists of unprocessed ATR-IR spectra, given in the comma-delimited .dpt file format.

 

References:

(1) Palatinus, L.; Brázda, P.; Jelínek, M.; Hrdá, J.; Steciuk, G.; Klementová, M. Specifics of the Data Processing of Precession Electron Diffraction Tomography Data and Their Implementation in the Program PETS2.0. Acta Crystallogr. B 2019, 75 (4), 512–522. https://doi.org/10.1107/S2052520619007534.

(2) Petříček, V.; Dušek, M.; Palatinus, L. Crystallographic Computing System JANA2006: General features. Z. Kristallogr. Cryst. Mater. 2014, 229 (5), 345–352. https://doi.org/10.1515/zkri-2014-1737.

(3) Sun, J.; Ruzsinszky, A.; Perdew, J. P. Strongly Constrained and Appropriately Normed Semilocal Density Functional. Phys. Rev. Lett. 2015, 115 (3), 036402. https://doi.org/10.1103/PhysRevLett.115.036402.

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(5) Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. J. Chem. Phys. 2010, 132 (15), 154104. https://doi.org/10.1063/1.3382344.

(6) Ehlert, S.; Huniar, U.; Ning, J.; Furness, J. W.; Sun, J.; Kaplan, A. D.; Perdew, J. P.; Brandenburg, J. G. r2SCAN-D4: Dispersion Corrected Meta-Generalized Gradient Approximation for General Chemical Applications. J. Chem. Phys. 2021, 154 (6), 061101. https://doi.org/10.1063/5.0041008.

(7) Rigaku OD. CrysAlisPro. Rigaku Corporation, Wroclaw, Poland, 2024.