The benefits of Cu Kβ radiation for the single-crystal X-ray structure determination of crystalline sponges
Meurer, Florian; von Essen, Carolina; Kühn, Clemens; Puschmann, Horst; Bodensteiner, Michael; IUCrJ 9 (2022) –; doi:10.1107/S2052252522002147

data_1566583
_publ_section_title
;
 The benefits of Cu K\b radiation for the single-crystal X-ray structure
 determination of crystalline sponges
;
_journal_issue                   3
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252522002147
_journal_volume                  9
_journal_year                    2022
_chemical_formula_moiety
'C36 H26 I6 N12 Zn3, C17 H14 O4, 0.25(C6 H12)'
_chemical_formula_sum            'C54.5 H43 I6 N12 O4 Zn3'
_chemical_formula_weight         1887.52
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2021-06-23
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2021.06.18 svn.r64d69d6c for OlexSys, GUI svn.r6354)
;
_cell_angle_alpha                90
_cell_angle_beta                 101.933(4)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   34.4866(13)
_cell_length_b                   14.9746(6)
_cell_length_c                   31.0009(12)
_cell_measurement_reflns_used    8812
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      72.7200
_cell_measurement_theta_min      4.1430
_cell_volume                     15663.6(11)
_computing_cell_refinement       'CrysAlisPro 1.171.41.47a (Rigaku OD, 2019)'
_computing_data_collection       'CrysAlisPro 1.171.41.47a (Rigaku OD, 2019)'
_computing_data_reduction        'CrysAlisPro 1.171.41.47a (Rigaku OD, 2019)'
_computing_molecular_graphics    'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      100.15
_diffrn_detector_area_resol_mean 4.2047
_diffrn_detector_type            TitanS2
_diffrn_measured_fraction_theta_full 0.977
_diffrn_measured_fraction_theta_max 0.939
_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    -44.00  25.00   1.00   20.00    --  -44.42  57.00-120.00   69
  2  \w     27.00  80.00   1.00   20.00    --   44.42-125.00   0.00   53
  3  \w     24.00 110.00   1.00   20.00    --   44.42  57.00  60.00   86
  4  \w     37.00  72.00   1.00  100.00    --  104.50 -45.00   0.00   35
  5  \w    104.00 173.00   1.00  100.00    --  104.50 125.00 -60.00   69
  6  \w     81.00 170.00   1.00  100.00    --  104.50  30.00 150.00   89
  7  \w     44.00 112.00   1.00  100.00    --  104.50-125.00  60.00   68
  8  \w     33.00 112.00   1.00  100.00    --  104.50-125.00 -60.00   79
  9  \w     36.00  72.00   1.00  100.00    --  104.50 -45.00  30.00   36
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, TitanS2'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0577
_diffrn_reflns_av_unetI/netI     0.0696
_diffrn_reflns_Laue_measured_fraction_full 0.977
_diffrn_reflns_Laue_measured_fraction_max 0.939
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -40
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -18
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -35
_diffrn_reflns_number            28426
_diffrn_reflns_point_group_measured_fraction_full 0.977
_diffrn_reflns_point_group_measured_fraction_max 0.939
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.991
_diffrn_reflns_theta_min         3.653
_diffrn_source                   'micro-focus sealed X-ray tube'
_exptl_absorpt_coefficient_mu    19.985
_exptl_absorpt_correction_T_max  0.402
_exptl_absorpt_correction_T_min  0.205
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.47a (Rigaku Oxford Diffraction, 2019)
Numerical absorption correction based on gaussian integration over
   a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_density_diffrn    1.601
_exptl_crystal_description       block
_exptl_crystal_F_000             7152
_exptl_crystal_size_max          0.16
_exptl_crystal_size_mid          0.13
_exptl_crystal_size_min          0.09
_refine_diff_density_max         1.727
_refine_diff_density_min         -2.174
_refine_diff_density_rms         0.261
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.066
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     753
_refine_ls_number_reflns         14938
_refine_ls_number_restraints     200
_refine_ls_restrained_S_all      1.059
_refine_ls_R_factor_all          0.1393
_refine_ls_R_factor_gt           0.1227
_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^)+(0.1889P)^2^+504.6206P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3415
_refine_ls_wR_factor_ref         0.3555
_reflns_Friedel_coverage         0.000
_reflns_number_gt                11396
_reflns_number_total             14938
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5046.cif
_cod_data_source_block           alpha_me-daid_zni2
_cod_original_formula_sum        'C54.50 H43 I6 N12 O4 Zn3'
_cod_database_code               1566583
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.266
_shelx_estimated_absorpt_t_min   0.142
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C2-C1 = C2-C7 = C1-C4 = C4-C5 = C5-C6 = C6-C7
 1.54 with sigma of 0.02
 C2-C4 = C2-C6 = C1-C5 = C4-C6 = C5-C7
 2.54 with sigma of 0.04
 C2-C1 \\sim C1-C4 \\sim C4-C5 \\sim C5-C6 \\sim C6-C7 \\sim C7-C2
 with sigma of 0.02
 C2-C6 \\sim C4-C6 \\sim C1-C7 \\sim C1-C5 \\sim C5-C7 \\sim C2-C4
 with sigma of 0.04
 Zn09-N00T \\sim Zn-N00T
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
C2 \\sim C4 \\sim C2 \\sim C6 \\sim C1 \\sim C5 \\sim C4 \\sim C6 \\sim C5
\\sim C7: within 2A with sigma of 0.01 and sigma for terminal atoms of 0.01
within 2A
C01Z \\sim C020: within 2A with sigma of 0.001 and sigma for terminal atoms of
0.001 within 2A
C020 \\sim C01Z: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.01 within 2A
C024 \\sim C022 \\sim C01Y \\sim C01I \\sim C01L \\sim C01P: within 2A with
sigma of 0.001 and sigma for terminal atoms of 0.001 within 2A
C01W \\sim C01X \\sim C00L \\sim C016 \\sim C014: within 2A with sigma of 0.001
and sigma for terminal atoms of 0.001 within 2A
Uanis(O01U) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.04
Uanis(C7) \\sim Ueq, Uanis(C2) \\sim Ueq, Uanis(C1) \\sim Ueq, Uanis(C4) \\sim
Ueq, Uanis(C6) \\sim Ueq, Uanis(C5) \\sim Ueq: with sigma of 0.1 and sigma for
terminal atoms of 0.1
Uanis(C020) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C3) = Uanis(C017)
Uanis(I03) = Uanis(I03A)
Uanis(I06A) = Uanis(I06)
Uanis(Zn) = Uanis(Zn09)
Uanis(C025) = Uanis(C01E)
4. Rigid body (RIGU) restrains
 I06A, Zn, I03A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 I06, Zn09, I03
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(Zn)=Sof(I06A)=Sof(I03A)=1-FVAR(1)
 Sof(I03)=Sof(I06)=Sof(Zn09)=FVAR(1)
 Fixed Sof: C2(0.25) H2A(0.25) H2B(0.25) C1(0.25) H1A(0.25) H1B(0.25) C4(0.25)
 H4A(0.25) H4B(0.25) C5(0.25) H5A(0.25) H5B(0.25) C6(0.25) H6A(0.25) H6B(0.25)
 C7(0.25) H7A(0.25) H7B(0.25)
 Fixed X: C01Z(0.274199)
 Fixed Y: C01Z(-0.16917)
 Fixed Z: C01Z(0.53323)
6.a Secondary CH2 refined with riding coordinates:
 C2(H2A,H2B), C1(H1A,H1B), C4(H4A,H4B), C5(H5A,H5B), C6(H6A,H6B), C7(H7A,H7B)
6.b Me refined with riding coordinates:
 C01Z(H01C,H01I,H01K)
6.c Aromatic/amide H refined with riding coordinates:
 N00D(H00D), N00H(H00H), C00U(H00U), C00X(H00X), C00Z(H00Z), C010(H010),
 C014(H014), C015(H015), C016(H016), C017(H017), C018(H018), C019(H019),
 C01A(H01A), C01B(H01B), C01D(H01D), C01E(H01E), C01F(H01F), C01G(H01G),
 C01H(H01H), C01J(H01J), C01O(H01O), C01P(H01P), C01Q(H01Q), C01R(H01R),
 C01T(H01T), C01V(H01V), C01W(H01W), C01X(H01X), C01Y(H01Y), C021(H021),
 C023(H023), C024(H024), C025(H025), C3(H3)
6.d Idealised Me refined as rotating group:
 C020(H02A,H02B,H02C)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 552 electrons were 
found in a volume of 3260\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of 
1.5[C6H12] per Asymmetric Unit 
which account for 576 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              54290
_shelx_hkl_checksum              52495
_shelx_fab_checksum              7835
_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
- B-factor correction
;