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_3000588
_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                 104.401(3)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   8.4689(3)
_cell_length_b                   7.6011(2)
_cell_length_c                   12.5302(4)
_cell_measurement_reflns_used    2130
_cell_measurement_temperature    100
_cell_measurement_theta_max      70.6420
_cell_measurement_theta_min      5.7620
_cell_volume                     781.26(4)
_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 0.996
_diffrn_measured_fraction_theta_max 0.992
_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    0.05    --    0.00   0.00-180.00   50
  2  \w   -100.00 -75.00   0.50    0.05    --    0.00   0.00-150.00   50
  3  \w   -100.00 -75.00   0.50    0.05    --    0.00   0.00-120.00   50
  4  \w   -100.00 -75.00   0.50    0.05    --    0.00   0.00 -60.00   50
  5  \w     27.00  78.00   0.50    0.05    --  111.23 -63.00  60.00  102
  6  \w     27.00  54.00   0.50    0.05    --  111.23 -50.00  60.00   54
  7  \w     33.00  58.00   0.50    0.05    --  111.23 -50.00 150.00   50
  8  \w     61.00 114.00   0.50    0.05    --  111.23-128.00  99.00  106
  9  \w     44.00 116.00   0.50    0.05    --   55.62-142.00 -71.00  144
 10  \w     92.00 122.00   0.50    0.05    --  111.23-142.00 -71.00   60
 11  \w     72.00 100.00   0.50    0.05    --  111.23-111.00-180.00   56
 12  \w    111.00 136.00   0.50    0.05    --   55.62   0.00-120.00   50
 13  \w    118.00 159.00   0.50    0.05    --  111.23   0.00 -90.00   82
 14  \w    132.00 164.00   0.50    0.05    --  111.23   0.00 -60.00   64
 15  \w    115.00 178.00   0.50    0.05    --  111.23   0.00   0.00  126
 16  \w    106.00 138.00   0.50    0.05    --  111.23 178.00-120.00   64
 17  \w     68.00  95.00   0.50    0.05    --  111.23 178.00-120.00   54
 18  \w     86.00 147.00   0.50    0.05    --  111.23 142.00 -15.00  122
 19  \w    -58.00 -32.00   0.50    0.05    --    0.00 142.00 -15.00   52
 20  \w    -64.00 -38.00   0.50    0.05    --    0.00 128.00 174.00   52
 21  \w     -7.00  24.00   0.50    0.05    --  -55.62  19.00 -60.00   62
 22  \w     -5.00  23.00   0.50    0.05    --  -55.62  19.00 -90.00   56
 23  \w    -50.00 -23.00   0.50    0.05    -- -106.00  63.00-150.00   54
 24  \w    -54.00 -25.00   0.50    0.05    -- -106.00  50.00   0.00   58
 25  \w    -52.00 -27.00   0.50    0.05    -- -106.00  50.00  60.00   50
 26  \w    -14.00  27.00   0.50    0.05    --  -55.62  19.00  30.00   82
 27  \w   -140.00-114.00   0.50    0.05    --  -55.62 -99.00-150.00   52
 28  \w   -139.00 -79.00   0.50    0.05    --  -55.62-142.00 -71.00  120
 29  \w   -123.00 -62.00   0.50    0.05    -- -106.00-142.00 -71.00  122
 30  \w   -147.00 -90.00   0.50    0.05    --  -55.62 -99.00  30.00  114
 31  \w   -104.00 -72.00   0.50    0.05    --  -55.62-128.00  99.00   64
 32  \w   -147.00-121.00   0.50    0.05    --  -55.62 -99.00-180.00   52
 33  \w   -118.00 -86.00   0.50    0.05    --  -55.62 -99.00-180.00   64
 34  \w    -67.00 -27.00   0.50    0.05    -- -106.00 111.00 120.00   80
 35  \w    -80.00 -43.00   0.50    0.05    -- -106.00 111.00 150.00   74
;
_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  0.0195
_diffrn_reflns_av_unetI/netI     0.0213
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.992
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            3402
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.191
_diffrn_reflns_theta_min         5.710
_exptl_absorpt_coefficient_mu    0.993
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.80141
_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    1.430
_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         0.295
_refine_diff_density_min         -0.189
_refine_diff_density_rms         0.040
_refine_ls_extinction_coef       0.0071(10)
_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   1.159
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_parameters     142
_refine_ls_number_reflns         1415
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.159
_refine_ls_R_factor_all          0.0366
_refine_ls_R_factor_gt           0.0352
_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^)+(0.0426P)^2^+0.1890P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0898
_refine_ls_wR_factor_ref         0.0907
_reflns_Friedel_coverage         0.000
_reflns_Friedel_fraction_full    .
_reflns_Friedel_fraction_max     .
_reflns_number_gt                1365
_reflns_number_total             1415
_reflns_threshold_expression     'I > 2\s(I)'
_journal_article_reference       uoaf059
_cod_data_source_file            Lab-Monomer1.cif
_cod_data_source_block           monomer1
_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 3000588 into public domain as published material.
;
_cod_database_code               3000588
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.907
_shelx_estimated_absorpt_t_min   0.742
_olex2_refinement_description
;
;
_shelx_res_checksum              26738
_shelx_hkl_checksum              64547
_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
;