Azo-tagged C4N4 fluorophores: unusual overcrowded structures and their application to fluorescent imaging.
Kohei, Miki; Takizawa, Naoki; Tsutsumi, Ryosuke; Xu, Wei; Kumagai, Naoya; Organic & biomolecular chemistry 21 (2023) 2889–2893; doi:10.1039/d3ob00049d

data_7159128
_publ_section_title
;
 Azo-tagged C4N4 fluorophores: unusual overcrowded structures and their
 application to fluorescent imaging.
;
_journal_issue                   14
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              2889
_journal_page_last               2893
_journal_paper_doi               10.1039/d3ob00049d
_journal_volume                  21
_journal_year                    2023
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C40 H40 N8 O8, 2(C H4 O)'
_chemical_formula_sum            'C42 H48 N8 O10'
_chemical_formula_weight         824.88
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2022-02-25
_audit_creation_method
;
Olex2 1.5
(compiled 2021.12.09 svn.r5202d8cf for OlexSys, GUI svn.r6439)
;
_audit_update_record
;
2023-01-07 deposited with the CCDC.	2023-01-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 100.233(2)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   9.1606(2)
_cell_length_b                   24.5485(6)
_cell_length_c                   9.1691(2)
_cell_measurement_reflns_used    4888
_cell_measurement_temperature    93.15
_cell_measurement_theta_max      73.1810
_cell_measurement_theta_min      3.5790
_cell_volume                     2029.14(8)
_computing_cell_refinement       'CrysAlisPro 1.171.41.110a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.110a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.110a (Rigaku OD, 2021)'
_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    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      93.15
_diffrn_detector                 'Rigaku HyPix-6000 area detector'
_diffrn_detector_area_resol_mean 10.0
_diffrn_detector_type            'HPC area detector'
_diffrn_measured_fraction_theta_full 0.971
_diffrn_measured_fraction_theta_max 0.919
_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    -26.00  20.00   0.50    0.88    --   48.46 -19.00  30.00   92
  2  \w     43.00  73.00   0.50    1.37    --  107.23 -61.00-120.00   60
  3  \w     40.00  73.00   0.50    1.37    --  107.23 -61.00-150.00   66
  4  \w    -26.00  20.00   0.50    0.88    --   48.46 -19.00  60.00   92
  5  \w    -73.00 -27.00   0.50    1.37    -- -100.00  61.00  30.00   92
  6  \w    -73.00 -27.00   0.50    1.37    -- -100.00  61.00  90.00   92
  7  \w    -73.00 -27.00   0.50    1.37    -- -100.00  61.00 120.00   92
  8  \w    -73.00 -27.00   0.50    1.37    -- -100.00  61.00  60.00   92
  9  \w    -73.00 -27.00   0.50    1.37    -- -100.00  61.00   0.00   92
 10  \w    -73.00 -27.00   0.50    1.37    -- -100.00  61.00 -30.00   92
 11  \w   -173.00 -87.00   0.50    1.37    -- -100.00 -35.00-178.00  172
 12  \w   -173.00 -88.00   0.50    1.37    -- -100.00-115.00 -34.00  170
 13  \w   -172.00 -87.00   0.50    1.37    -- -100.00 -45.00 -30.00  170
 14  \w   -106.00 -27.00   0.50    1.37    -- -100.00  90.00 161.00  158
 15  \w    -20.00  27.00   0.50    0.88    --  -48.46  19.00-150.00   94
 16  \w    -20.00  27.00   0.50    0.88    --  -48.46  19.00-120.00   94
 17  \w    -20.00  27.00   0.50    0.88    --  -48.46  19.00  60.00   94
 18  \w     11.00  91.00   0.50    0.88    --   48.46-115.00 -34.00  160
 19  \w     36.00 104.00   0.50    1.37    --  107.23 -95.00-180.00  136
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Rigaku XtaLAB Synergy-Custom'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0384060000
_diffrn_orient_matrix_UB_12      -0.0608886000
_diffrn_orient_matrix_UB_13      -0.0221214000
_diffrn_orient_matrix_UB_21      0.0675388000
_diffrn_orient_matrix_UB_22      -0.0110979000
_diffrn_orient_matrix_UB_23      0.1634686000
_diffrn_orient_matrix_UB_31      -0.1521697000
_diffrn_orient_matrix_UB_32      0.0104264000
_diffrn_orient_matrix_UB_33      0.0440655000
_diffrn_radiation_monochromator  'multi-layer mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.1504
_diffrn_reflns_av_unetI/netI     0.0971
_diffrn_reflns_Laue_measured_fraction_full 0.971
_diffrn_reflns_Laue_measured_fraction_max 0.919
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -30
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -8
_diffrn_reflns_number            14720
_diffrn_reflns_point_group_measured_fraction_full 0.897
_diffrn_reflns_point_group_measured_fraction_max 0.831
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.309
_diffrn_reflns_theta_min         3.601
_diffrn_source                   'rotating anode X-ray generator'
_diffrn_source_type              micromax007
_exptl_absorpt_coefficient_mu    0.811
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.89312
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.110a (Rigaku Oxford Diffraction, 2021)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light orange'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    orange
_exptl_crystal_density_diffrn    1.350
_exptl_crystal_description       plate
_exptl_crystal_F_000             872
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.02
_refine_diff_density_max         1.233
_refine_diff_density_min         -0.642
_refine_diff_density_rms         0.175
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   0.5(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.289
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     555
_refine_ls_number_reflns         7086
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.289
_refine_ls_R_factor_all          0.1611
_refine_ls_R_factor_gt           0.1315
_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          0.3082
_refine_ls_wR_factor_ref         0.3433
_reflns_Friedel_coverage         0.765
_reflns_Friedel_fraction_full    0.818
_reflns_Friedel_fraction_max     0.738
_reflns_number_gt                5128
_reflns_number_total             7086
_reflns_threshold_expression     'I > 2\s(I)'
_twin_special_details
;
Component 2 rotated by 179.4701\% 
around [0.71 0.02 0.71] (reciprocal) or [0.71 0.00 0.71] (direct)
;
_cod_data_source_file            d3ob00049d2.cif
_cod_data_source_block           exp_720_twin1_hklf4
_cod_depositor_comments
;
Adding full bibliography for 7159126--7159129.cif.

2025-04-01
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C84 H96 N16 O20'
_cod_original_formula_weight         1649.76
_cod_original_formula_moiety         '2(C40 H40 N8 O8), 4(C H4 O)'
_cod_original_formula_units_Z            1
_cod_database_code               7159128
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N O'
_chemical_oxdiff_usercomment     '220224_MK_2, 6-OMe'
_shelx_estimated_absorpt_t_max   0.984
_shelx_estimated_absorpt_t_min   0.923
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2.a Rotating group:
 N00D(H00A,H00B), N00J(H00C,H00D)
2.b Aromatic/amide H refined with riding coordinates:
 C00P(H00P), C00V(H00V), C011(H011), C013(H013), C016(H016), C017(H017),
 C019(H019), C01C(H01D), C01D(H01E), C01E(H01F), C01G(H01J), C01I(H01N)
2.c Idealised Me refined as rotating group:
 C00Y(H00E,H00F,H00G), C01B(H01A,H01B,H01C), C01F(H01G,H01H,H01I), C01H(H01K,
 H01L,H01M), C01J(H01Z,H,HA), C01K(H01O,H01P,H01Q), C01L(H01,HB,HC), C01M(H01R,
 H01S,H01T), C01N(H01U,H01V,H01W), C01O(H01X,H01Y,HD)
2.d Idealised tetrahedral OH refined as rotating group:
 O008(H008), O00L(H00L)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              73665
_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 1.816
_oxdiff_exptl_absorpt_empirical_full_min 0.802
_oxdiff_twin_integration_method  simultaneous
_oxdiff_twin_items               2