Capture and characterization of elusive cyclo-di-BADGE
Salami, Fatemeh; Lin, Jian-bin; Chen, Bing; Zhang, Baiyu; Zhao, Yuming; New Journal of Chemistry 47 (2023) 18302–18314; doi:10.1039/D3NJ03542E

data_7062702
_publ_section_title
;
 Capture and characterization of elusive cyclo-di-BADGE
;
_journal_issue                   39
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              18302
_journal_page_last               18314
_journal_paper_doi               10.1039/D3NJ03542E
_journal_volume                  47
_journal_year                    2023
_chemical_formula_moiety         'C36 H40 O6'
_chemical_formula_sum            'C36 H40 O6'
_chemical_formula_weight         568.68
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-10-27
_audit_creation_method
;
Olex2 1.5-ac5-023
(compiled 2022.04.12 svn.rca3783a0 for Rigaku Oxford Diffraction, GUI svn.r6498)
;
_audit_update_record
;
2022-12-08 deposited with the CCDC.	2023-09-11 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 101.0650(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   12.5112(2)
_cell_length_b                   24.0500(3)
_cell_length_c                   11.0199(2)
_cell_measurement_reflns_used    11327
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      79.0190
_cell_measurement_theta_min      4.4690
_cell_volume                     3254.18(9)
_computing_cell_refinement       'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5-ac5-023 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac5-023 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.977
_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    -43.00  24.00   0.50    8.08    --  -48.39  45.00  67.00  134
  2  \w   -120.00 -37.00   0.50    8.08    --  -48.39 -45.00 -83.00  166
  3  \w     38.00 121.00   0.50    8.08    --   48.39  45.00  67.00  166
  4  \w    -23.00  57.00   0.50    8.08    --   48.39 -45.00 -83.00  160
  5  \w   -161.00 -79.00   0.50   32.33    --  -90.00 -45.00 -83.00  164
  6  \w    101.00 178.00   0.50   32.33    --  111.50  45.00  67.00  154
  7  \w    -86.00 -13.00   0.50    8.08    --  -48.39 125.00-180.00  146
  8  \w    -65.00 -18.00   0.50   32.33    --  -90.00  61.00  90.00   94
  9  \w    -65.00 -18.00   0.50   32.33    --  -90.00  61.00-120.00   94
 10  \w     40.00 105.00   0.50   32.33    --  111.50 -94.00-150.00  130
 11  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00-120.00   78
 12  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00 -30.00   78
 13  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00  60.00   78
 14  \w    101.00 178.00   0.50   32.33    --  111.50  15.00-180.00  154
 15  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00 150.00   78
 16  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00 -90.00   78
 17  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00-150.00   78
 18  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00  30.00   78
 19  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00 -60.00   78
 20  \w     40.00 105.00   0.50   32.33    --  111.50 -94.00  60.00  130
 21  \w     40.00  79.00   0.50   32.33    --  111.50 -61.00  90.00   78
 22  \w    101.00 178.00   0.50   32.33    --  111.50  30.00 120.00  154
 23  \w     40.00 105.00   0.50   32.33    --  111.50 -94.00 150.00  130
 24  \w     95.00 178.00   0.50   32.33    --  111.50 125.00 -60.00  166
 25  \w     42.00  57.00   0.50   32.33    --  111.50-125.00 -90.00   30
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0962248000
_diffrn_orient_matrix_UB_12      -0.0356191000
_diffrn_orient_matrix_UB_13      -0.0240135000
_diffrn_orient_matrix_UB_21      -0.0422480000
_diffrn_orient_matrix_UB_22      0.0050164000
_diffrn_orient_matrix_UB_23      -0.1403663000
_diffrn_orient_matrix_UB_31      0.0685944000
_diffrn_orient_matrix_UB_32      0.0529891000
_diffrn_orient_matrix_UB_33      -0.0028039000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0454
_diffrn_reflns_av_unetI/netI     0.0344
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.977
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            33581
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.977
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.349
_diffrn_reflns_theta_min         3.676
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.625
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.65680
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.72a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            orange
_exptl_crystal_colour_primary    orange
_exptl_crystal_density_diffrn    1.161
_exptl_crystal_description       irregular
_exptl_crystal_F_000             1216
_exptl_crystal_size_max          0.094
_exptl_crystal_size_mid          0.086
_exptl_crystal_size_min          0.058
_refine_diff_density_max         0.345
_refine_diff_density_min         -0.305
_refine_diff_density_rms         0.049
_refine_ls_extinction_coef       0.00039(11)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.091
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     452
_refine_ls_number_reflns         6895
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.091
_refine_ls_R_factor_all          0.0802
_refine_ls_R_factor_gt           0.0700
_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^)+(0.0590P)^2^+2.7003P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1675
_refine_ls_wR_factor_ref         0.1734
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5856
_reflns_number_total             6895
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3nj03542e2.cif
_cod_data_source_block           t-a-cf3-y2
_cod_depositor_comments          'Adding full bibliography for 7062702.cif.'
_cod_database_code               7062702
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C36H40O6
_shelx_estimated_absorpt_t_max   0.965
_shelx_estimated_absorpt_t_min   0.944
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups, All O(H,H) groups
2. Others
 Sof(O4A)=Sof(H5B)=Sof(C19A)=Sof(H19C)=Sof(H19D)=Sof(C20A)=Sof(H20A)=Sof(C21A)=
 Sof(H21C)=Sof(H21D)=1-FVAR(1)
 Sof(O4)=Sof(H5A)=Sof(C19)=Sof(H19A)=Sof(H19B)=Sof(C20)=Sof(H20)=Sof(C21)=
 Sof(H21A)=Sof(H21B)=FVAR(1)
 Sof(O2A)=Sof(H2A)=Sof(H1BC)=Sof(H1BD)=Sof(C2A)=Sof(H2AA)=Sof(H3BC)=Sof(H3BD)=
 1-FVAR(2)
 Sof(O2)=Sof(H2)=Sof(H1AA)=Sof(H1AB)=Sof(C2)=Sof(H2B)=Sof(H3AA)=Sof(H3AB)=
 FVAR(2)
 Sof(O6A)=1-FVAR(3)
 Sof(O6)=FVAR(3)
3.a Ternary CH refined with riding coordinates:
 C2(H2B), C2A(H2AA), C20(H20), C20A(H20A)
3.b Secondary CH2 refined with riding coordinates:
 C1(H1AA,H1AB), C1(H1BC,H1BD), C3(H3AA,H3AB), C3(H3BC,H3BD), C19(H19A,H19B),
 C19A(H19C,H19D), C21(H21A,H21B), C21A(H21C,H21D)
3.c Aromatic/amide H refined with riding coordinates:
 C5(H5), C6(H6), C8(H8), C9(H9), C14(H14), C15(H15), C17(H17), C18(H18),
 C23(H23), C24(H24), C26(H26), C27(H27), C32(H32), C33(H33), C35(H35), C36(H36)
3.d Tetrahedral OH refined with riding coordinates:
 O5(H5A), O5(H5B)
3.e Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C), C12(H12A,H12B,H12C), C29(H29A,H29B,H29C), C30(H30A,H30B,
 H30C)
3.f Idealised tetrahedral OH refined as rotating group:
 O2(H2), O2A(H2A)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              90346
_shelx_fab_checksum              15594
_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 1.398
_oxdiff_exptl_absorpt_empirical_full_min 0.757