Application of multiple small-wedge synchrotron crystallography for post-reaction structural characterization of a stimuli-responsive small-molecule crystal
Sasaki, Toshiyuki; Nakane, Takanori; Takimoto, Kazuyoshi; Ichiyanagi, Kouhei; Mori, Yuki; Baba, Seiki; Sakai, Naoki; Kurisu, Genji; Miyata, Mikiji; Uno, Takahiro; Itoh, Takahito; Bulletin of the Chemical Society of Japan 98 (2025) –; doi:10.1093/bulcsj/uoaf059

data_3000589
_publ_section_title
;
 Application of multiple small-wedge synchrotron crystallography for
 post-reaction structural characterization of a stimuli-responsive
 small-molecule crystal
;
_journal_name_full               'Bulletin of the Chemical Society of Japan'
_journal_paper_doi               10.1093/bulcsj/uoaf059
_journal_volume                  98
_journal_year                    2025
_chemical_formula_moiety         'C16 H16 O8'
_chemical_formula_sum            'C16 H16 O8'
_chemical_formula_weight         336.29
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   difmap
_atom_sites_solution_primary     dual
_audit_creation_date             2025-06-03
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_cell_angle_alpha                90
_cell_angle_beta                 101.692(6)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   8.7157(5)
_cell_length_b                   6.7991(3)
_cell_length_c                   12.3904(7)
_cell_measurement_reflns_used    2474
_cell_measurement_temperature    100
_cell_measurement_theta_max      70.6110
_cell_measurement_theta_min      5.1070
_cell_volume                     719.01(7)
_computing_cell_refinement       'CrysAlisPro 1.171.43.142a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.142a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.142a (Rigaku OD, 2024)'
_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 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100.00
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.990
_diffrn_measured_fraction_theta_max 0.990
_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   -100.00 -75.00   0.50    0.06    --    0.00   0.00 120.00   50
  2  \w    -99.00 -74.00   0.50    0.06    --    0.00   0.00  90.00   50
  3  \w   -100.00 -75.00   0.50    0.06    --    0.00   0.00 -60.00   50
  4  \w   -100.00 -75.00   0.50    0.06    --    0.00   0.00-120.00   50
  5  \w   -100.00 -75.00   0.50    0.06    --    0.00   0.00-180.00   50
  6  \w    -37.00  16.00   0.50    0.22    --   55.62 -19.00-150.00  106
  7  \w     27.00  58.00   0.50    0.22    --  111.23 -50.00-180.00   62
  8  \w     49.00  78.00   0.50    0.22    --  111.23 -63.00-180.00   58
  9  \w     29.00  58.00   0.50    0.22    --  111.23 -50.00 -90.00   58
 10  \w     27.00  54.00   0.50    0.22    --  111.23 -50.00  60.00   54
 11  \w     27.00  54.00   0.50    0.22    --  111.23 -50.00 -30.00   54
 12  \w     29.00  57.00   0.50    0.22    --  111.23 -50.00 -60.00   56
 13  \w     33.00  58.00   0.50    0.22    --  111.23 -50.00  90.00   50
 14  \w     46.00  71.00   0.50    0.22    --  111.23 -63.00 120.00   50
 15  \w     30.00  57.00   0.50    0.22    --  111.23 -50.00 150.00   54
 16  \w     65.00  90.00   0.50    0.22    --  111.23 -86.00 119.00   50
 17  \w     29.00 106.00   0.50    0.22    --  111.23-111.00  90.00  154
 18  \w     40.00  85.00   0.50    0.22    --   55.62-125.00   0.00   90
 19  \w     83.00 151.00   0.50    0.22    --  111.23-178.00  30.00  136
 20  \w     69.00 108.00   0.50    0.22    --  111.23-111.00  30.00   78
 21  \w     32.00  90.00   0.50    0.22    --  111.23-111.00   0.00  116
 22  \w     64.00 107.00   0.50    0.22    --  111.23-111.00-180.00   86
 23  \w     28.00  53.00   0.50    0.22    --  111.23-111.00-180.00   50
 24  \w      6.00 105.00   0.50    0.22    --   55.62 -99.00   0.00  198
 25  \w     13.00  43.00   0.50    0.06    --    0.00 -86.00 119.00   60
 26  \w    -17.00  59.00   0.50    0.22    --   55.62 -86.00 119.00  152
 27  \w    115.00 153.00   0.50    0.22    --  111.23   0.00  30.00   76
 28  \w    147.00 176.00   0.50    0.22    --  111.23   0.00  60.00   58
 29  \w    107.00 134.00   0.50    0.22    --   55.62   0.00 -30.00   54
 30  \w    111.00 136.00   0.50    0.22    --   55.62   0.00 -60.00   50
 31  \w    112.00 137.00   0.50    0.22    --   55.62   0.00 -90.00   50
 32  \w    108.00 133.00   0.50    0.22    --   55.62   0.00-150.00   50
 33  \w    112.00 174.00   0.50    0.22    --  111.23   0.00 -30.00  124
 34  \w    140.00 172.00   0.50    0.22    --  111.23  86.00-122.00   64
 35  \w    115.00 144.00   0.50    0.22    --  111.23 178.00   0.00   58
 36  \w     64.00 108.00   0.50    0.22    --  111.23 178.00   0.00   88
 37  \w     65.00 127.00   0.50    0.22    --  111.23 178.00 120.00  124
 38  \w     18.00  43.00   0.50    0.06    --    0.00  86.00-122.00   50
 39  \w    -21.00   6.00   0.50    0.06    --    0.00  86.00-122.00   54
 40  \w    -52.00 -25.00   0.50    0.22    -- -106.00  50.00-180.00   54
 41  \w    -51.00 -24.00   0.50    0.22    -- -106.00  50.00-150.00   54
 42  \w    -52.00 -23.00   0.50    0.22    -- -106.00  50.00-120.00   58
 43  \w    -11.00  23.00   0.50    0.22    --  -55.62  19.00-150.00   68
 44  \w    -17.00   8.00   0.50    0.22    --  -55.62  19.00 -30.00   50
 45  \w    -52.00 -27.00   0.50    0.22    -- -106.00  50.00  90.00   50
 46  \w    -15.00  16.00   0.50    0.22    --  -55.62  19.00 150.00   62
 47  \w    -35.00  25.00   0.50    0.22    --  -55.62  37.00  60.00  120
 48  \w    -11.00  16.00   0.50    0.22    --  -55.62  19.00   0.00   54
 49  \w   -131.00 -74.00   0.50    0.22    -- -106.00   0.00-180.00  114
 50  \w   -165.00-134.00   0.50    0.22    -- -106.00   0.00-180.00   62
 51  \w   -100.00 -61.00   0.50    0.22    -- -106.00  86.00-122.00   78
 52  \w    -69.00  -7.00   0.50    0.22    --  -55.62  86.00-122.00  124
 53  \w   -146.00-119.00   0.50    0.22    -- -106.00  86.00-122.00   54
 54  \w   -172.00 -83.00   0.50    0.22    -- -106.00-111.00 150.00  178
 55  \w    -92.00 -41.00   0.50    0.22    -- -106.00-178.00 -30.00  102
 56  \w   -126.00 -98.00   0.50    0.22    -- -106.00-178.00 -30.00   56
 57  \w   -117.00 -90.00   0.50    0.22    -- -106.00-111.00-180.00   54
 58  \w   -131.00-104.00   0.50    0.22    --  -55.62 -99.00 -90.00   54
 59  \w   -145.00 -88.00   0.50    0.22    --  -55.62 -99.00  30.00  114
 60  \w   -127.00 -97.00   0.50    0.22    --  -55.62 -86.00 119.00   60
 61  \w   -123.00 -80.00   0.50    0.22    -- -106.00 -86.00 119.00   86
 62  \w   -165.00-131.00   0.50    0.22    -- -106.00 -86.00 119.00   68
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0362
_diffrn_reflns_av_unetI/netI     0.0249
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            4755
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.250
_diffrn_reflns_theta_min         5.702
_exptl_absorpt_coefficient_mu    1.080
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.72007
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.142a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.553
_exptl_crystal_description       plate
_exptl_crystal_F_000             352
_exptl_crystal_size_max          0.32
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.296
_refine_diff_density_min         -0.202
_refine_diff_density_rms         0.069
_refine_ls_extinction_coef       .
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.077
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_parameters     141
_refine_ls_number_reflns         1307
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.077
_refine_ls_R_factor_all          0.0541
_refine_ls_R_factor_gt           0.0477
_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^)+(0.0971P)^2^+0.1225P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1378
_refine_ls_wR_factor_ref         0.1472
_reflns_Friedel_coverage         0.000
_reflns_Friedel_fraction_full    .
_reflns_Friedel_fraction_max     .
_reflns_number_gt                1157
_reflns_number_total             1307
_reflns_threshold_expression     'I > 2\s(I)'
_journal_article_reference       uoaf059
_cod_data_source_file            Lab-Poly-1.cif
_cod_data_source_block           poly1
_cod_depositor_comments
;Re-refinement of the structure. Hydrogen atoms were located from
 difference Fourier maps and refined, replacing the previous riding
 model (AFIX) treatment.

 Releasing structure 3000589 into public domain as published material.
;
_cod_database_code               3000589
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.900
_shelx_estimated_absorpt_t_min   0.724
_olex2_refinement_description
;
;
_shelx_res_checksum              90718
_shelx_hkl_checksum              86028
_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
;