High-resolution single-crystal 3D electron diffraction dataset and complementary data for urea crystal charge density analysis

This submission contains the charge density analysis data for urea crystal from:1. Experimental high-resolution single-crystal three-dimensional electron diffraction data (3DED)2. Theoretical electron static structure factors obtained from the periodic DFT calculations (DFT)3. Experimental high-resolution single-crystal X-ray diffraction data (XRD) 1. Experimental high-resolution single-crystal three-dimensional electron diffraction data (3DED)This submission contains raw experimental data, data reduction files, refinement files, and CIF files related to the experimental charge density analysis of urea crystal from high-resolution single-crystal three-dimensional electron diffraction (3DED). The dataset includes:a.     Raw experimental data from CrysAlis Pro (3DED_RAWExpData.zip)Crystals of urea were grown by slow evaporation of distilled water at room temperature. 3D ED measurements for urea was performed on Rigaku XtaLAB Synergy-ED diffractometers, equipped with a LaB6 source operating at 200 kV (λ= 0.0251 Å) and a Rigaku HyPix-ED detector. A small amount of sample was first gently crushed in a mortar and pestle to reduce the crystal size. Then, the crystalline powder was deposited on carbon coated copper TEM grids coated (holey carbon from Pelco). The sample was mounted on a Gatan ElsaTM 698 Cryo-transfer holder and cooled at 173 K prior to the insertion in the diffractometer, then cooled to 100 K in a vacuum (ca. 10-5 Pa). Diffraction patterns were collected on one single crystal of each compound using a selected area aperture (apparent diameter 2 μm) during continuous rotation of the crystals over ca. 120°, with a shutterless scan and frame width of 0.2 °. The program CrysAlisPro was used to control the data collection.b.     Data reduction files from PETS2 (3DED_DataReduction.zip)Data reduction was carried out in PETS2c.     Refinement files from JANA2020 (3DED_Refinements.zip)Dynamical IAM structure refinement was performed in Jana2020, starting from kinematical IAM. Next, the dynamical multipole model refinement was conducted in a stepwise fashion, beginning with transferred multipole parameters from the MATTS database and followed by iterative refinement of electron population, κ/κ′, and multipole parameters. Non-hydrogen and hydrogen atom positions and anisotropic displacement parameters were also refined freely.d.     CIF files documenting the whole process corresponding to each refinement. (3DED_CIFfiles.zip) 2. Theoretical electron static structure factors obtained from the periodic DFT calculations (DFT)This submission contains the results of multipole model refinement against theoretical electron static structure factors obtained from the periodic DFT calculation for urea crystal. The results were used to validate multipole model refinement from experimental high-resolution single-crystal three-dimensional electron diffraction data (3DED). The dataset includes:a.     Geometry optimization results from Crystal (DFT_GeomOptimization.zip)Periodic crystal geometry optimization was carried out in Crystalb.     Refinement files from JANA2020 (DFT_Refinement.zip)Multipole model refinement against theoretical electron static structure factor obtained from the periodic DFT calculation was conducted in a stepwise fashion, beginning with transferred multipole parameters from the MATTS database and followed by iterative refinement of electron population, κ/κ′, and multipole parameters. Atoms coordinates and ADPs were not refined. 3. Experimental high-resolution single-crystal X-ray diffraction data (XRD)This submission contains the results of multipole model refinement against experimental high-resolution single-crystal X-ray data (XRD) for urea crystal. The results were used to validate multipole model refinement from experimental high-resolution single-crystal three-dimensional electron diffraction data (3DED). The dataset includes:a.     Refinement files from JANA2020 (XRD_Refinement.zip)Multipole model refinement experimental high-resolution single-crystal X-ray data (XRD) was conducted in a stepwise fashion, beginning with transferred multipole parameters from the MATTS database and followed by iterative refinement of electron population, κ/κ′, and multipole parameters. Only non-hydrogen atom positions and anisotropic displacement parameters were also refined freely.