Analysis of COF-300 synthesis: probing degradation processes and 3D electron diffraction structure.
Bourda, Laurens; Bhandary, Subhrajyoti; Ito, Sho; Göb, Christian R; Van Der Voort, Pascal; Van Hecke, Kristof; IUCrJ 11 (2024) –; doi:10.1107/S2052252524003713

data_1571596
_publ_section_title
;
 Analysis of COF-300 synthesis: probing degradation processes and 3D
 electron diffraction structure.
;
_journal_coeditor_code           VQ5005
_journal_issue                   4
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252524003713
_journal_volume                  11
_journal_year                    2024
_chemical_formula_moiety         'C41 H28 N4, 1[H2O]'
_chemical_formula_sum            'C41 H30 N4 O'
_chemical_formula_weight         594.72
_space_group_crystal_system      tetragonal
_space_group_IT_number           88
_space_group_name_Hall           '-I 4ad'
_space_group_name_H-M_alt        'I 41/a :2'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2023-12-22
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   20.7(3)
_cell_length_b                   20.7(3)
_cell_length_c                   8.8(2)
_cell_measurement_reflns_used    554
_cell_measurement_temperature    298(1)
_cell_measurement_theta_max      0.8670
_cell_measurement_theta_min      0.0880
_cell_volume                     3771(12)
_computing_cell_refinement       'CrysAlisPro 1.171.42.46a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.46a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.46a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_temperature      298(1)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix3000 fast'
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
--------------------------------------------------------------------------
  1  \w    -45.00  45.00   0.50    1.00    --    0.00   0.00   0.00  180
  2  \w    -50.00  50.00   0.50    1.00    --    0.00   0.00   0.00  200
;
_diffrn_measurement_device       'electron diffractometer'
_diffrn_measurement_device_type
'XtaLAB Synergy-ED, HyPix3000 fast, electron source at 200keV'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0000654000
_diffrn_orient_matrix_UB_12      0.0012081000
_diffrn_orient_matrix_UB_13      0.0000407000
_diffrn_orient_matrix_UB_21      -0.0011654000
_diffrn_orient_matrix_UB_22      -0.0000629000
_diffrn_orient_matrix_UB_23      -0.0008110000
_diffrn_orient_matrix_UB_31      -0.0003435000
_diffrn_orient_matrix_UB_32      -0.0000501000
_diffrn_orient_matrix_UB_33      0.0027412000
_diffrn_radiation_monochromator  'transmission electron microscope'
_diffrn_radiation_probe          electron
_diffrn_radiation_type           'transmission electron microscope'
_diffrn_radiation_wavelength     0.0251
_diffrn_reflns_av_R_equivalents  0.2204
_diffrn_reflns_av_unetI/netI     0.0916
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -8
_diffrn_reflns_number            7656
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        0.719
_diffrn_reflns_theta_max         0.719
_diffrn_reflns_theta_min         0.089
_diffrn_source                   'transmission electron microscope'
_exptl_absorpt_coefficient_mu    0.000
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.32693
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.46a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.052
_exptl_crystal_description       hexagonal
_exptl_crystal_F_000             507
_refine_diff_density_max         0.138
_refine_diff_density_min         -0.154
_refine_diff_density_rms         0.039
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.316
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     103
_refine_ls_number_reflns         983
_refine_ls_number_restraints     81
_refine_ls_restrained_S_all      1.271
_refine_ls_R_factor_all          0.1808
_refine_ls_R_factor_gt           0.1372
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3425
_refine_ls_wR_factor_ref         0.3793
_reflns_Friedel_coverage         0.000
_reflns_number_gt                633
_reflns_number_total             983
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            vq5005.cif
_cod_data_source_block           1
_cod_original_cell_volume        3755(157)
_cod_original_sg_symbol_H-M      'I 41/a'
_cod_database_code               1571596
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C164  H128  N16  '
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.883(8)
 0.117(8)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
3. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4.a Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C6(H6), C7(H7), C8(H8), C10(H10), C11(H11)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 40 electrons were 
found in a volume of 1056\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
4[H2O] per Unit Cell 
which account for 40 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              37745
_shelx_hkl_checksum              6920
_shelx_fab_checksum              99374
_olex2_exptl_crystal_mounting_method 'Mounted on a TEM grid'
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.554
_oxdiff_exptl_absorpt_empirical_full_min 0.473