The crystal structure of benzyl 3β-acetylglycyrrhetate, C39H54O5
Zhao, Ruo-Lin; Wang, Hui-Yun; Wang, Xiao-Hui; Liu, Li; Meng, Qing-Guo; Zeitschrift für Kristallographie - New Crystal Structures 235 (2020) 1319–1321; doi:10.1515/ncrs-2020-0296

data_8105455
_publ_section_title
;
 The crystal structure of benzyl 3\b-acetylglycyrrhetate, C39H54O5
;
_journal_issue                   6
_journal_name_full
'Zeitschrift f\"ur Kristallographie - New Crystal Structures'
_journal_page_first              1319
_journal_page_last               1321
_journal_paper_doi               10.1515/ncrs-2020-0296
_journal_volume                  235
_journal_year                    2020
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C39 H54 O5'
_chemical_formula_sum            'C39 H54 O5'
_chemical_formula_weight         602.82
_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   geom
_atom_sites_solution_primary     iterative
_cell_angle_alpha                90
_cell_angle_beta                 117.789(3)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   6.98138(17)
_cell_length_b                   37.9050(6)
_cell_length_c                   7.28644(16)
_cell_measurement_reflns_used    9020
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      66.9040
_cell_measurement_theta_min      6.8400
_cell_volume                     1705.83(8)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution
;
Superflip (Palatinus & Chapuis, 2007;Palatinus & van der Lee, 2008;
Palatinus et al., 2012)
;
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.4674
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.991
_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    -32.00  30.00   1.00    1.00    --   42.08 -38.00  60.00   62
  2  \w     -3.00  91.00   1.00    1.00    --   42.08-125.00-150.00   94
  3  \w     40.00  66.00   1.00    1.00    --   42.08 -38.00  60.00   26
  4  \w    119.00 147.00   1.00    3.12    --   92.50  61.00  60.00   28
  5  \w     63.00 120.00   1.00    3.12    --   92.50 -77.00 -90.00   57
  6  \w     64.00 124.00   1.00    3.12    --   92.50 -91.00  83.90   60
  7  \w     76.00 123.00   1.00    3.12    --   92.50 125.00-180.00   47
  8  \w     19.00  79.00   1.00    3.12    --   92.50-125.00-120.00   60
  9  \w    140.00 165.00   1.00    3.12    --   92.50 125.00  30.00   25
 10  \w     17.00  42.00   1.00    3.12    --   92.50 -77.00 -90.00   25
 11  \w     11.00  83.00   1.00    3.12    --   92.50 -95.00  90.00   72
 12  \w     32.00  58.00   1.00    3.12    --   92.50 -91.00  83.90   26
 13  \w     90.00 116.00   1.00    3.12    --   92.50  77.00-180.00   26
 14  \w     42.00  68.00   1.00    3.12    --   92.50 -30.00 -90.00   26
 15  \w     85.00 112.00   1.00    3.12    --   92.50 -30.00 -90.00   27
 16  \w     73.00 155.00   1.00    3.12    --   92.50 125.00-120.00   82
 17  \w    103.00 161.00   1.00    3.12    --   92.50 125.00 -30.00   58
 18  \w     74.00 122.00   1.00    3.12    --   92.50  61.00  30.00   48
 19  \w     23.00  72.00   1.00    3.12    --   92.50-125.00 -30.00   49
 20  \w     19.00  44.00   1.00    3.12    --   92.50-125.00 120.00   25
 21  \w     68.00  93.00   1.00    3.12    --   92.50-125.00 120.00   25
 22  \w     42.00  69.00   1.00    3.12    --   92.50 -95.00-120.00   27
 23  \w     80.00 113.00   1.00    3.12    --   92.50  61.00  60.00   33
 24  \w     88.00 162.00   1.00    3.12    --   92.50  30.00-180.00   74
 25  \w     31.00  60.00   1.00    1.00    --   42.20  38.00 -60.00   29
 26  \w     87.00 113.00   1.00    3.12    --   92.50  30.00  90.00   26
 27  \w     36.00  90.00   1.00    3.12    --   92.50 -45.00  90.00   54
 28  \w     31.00  69.00   1.00    3.12    --   92.50-125.00   0.00   38
 29  \w     87.00 124.00   1.00    3.12    --   92.50 -90.00 173.00   37
 30  \w    139.00 166.00   1.00    3.12    --   92.50  30.00  90.00   27
 31  \w     91.00 156.00   1.00    3.12    --   92.50 125.00 120.00   65
 32  \w     88.00 116.00   1.00    3.12    --   92.50 -45.00-180.00   28
 33  \w     68.00 118.00   1.00    3.12    --   92.50 -61.00 -30.00   50
 34  \w    109.00 142.00   1.00    3.12    --   92.50 -15.00   0.00   33
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Xcalibur, Atlas, Gemini ultra'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0407414000
_diffrn_orient_matrix_UB_12      -0.0385877000
_diffrn_orient_matrix_UB_13      0.0748608000
_diffrn_orient_matrix_UB_21      0.2399757000
_diffrn_orient_matrix_UB_22      0.0086659000
_diffrn_orient_matrix_UB_23      0.1432316000
_diffrn_orient_matrix_UB_31      -0.0546899000
_diffrn_orient_matrix_UB_32      0.0093517000
_diffrn_orient_matrix_UB_33      0.1760282000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0238
_diffrn_reflns_av_unetI/netI     0.0206
_diffrn_reflns_Laue_measured_fraction_full 0.991
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       43
_diffrn_reflns_limit_k_min       -45
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            17341
_diffrn_reflns_point_group_measured_fraction_full 0.931
_diffrn_reflns_point_group_measured_fraction_max 0.931
_diffrn_reflns_theta_full        66.876
_diffrn_reflns_theta_max         66.876
_diffrn_reflns_theta_min         4.666
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance Ultra (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.593
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.87754
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46e (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.174
_exptl_crystal_description       block
_exptl_crystal_F_000             656
_exptl_crystal_size_max          0.24
_exptl_crystal_size_mid          0.22
_exptl_crystal_size_min          0.15
_refine_diff_density_max         0.178
_refine_diff_density_min         -0.112
_refine_diff_density_rms         0.029
_refine_ls_abs_structure_details
;
 Flack x determined using 2361 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.07(7)
_refine_ls_extinction_coef       0.0105(8)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2014/7 (Sheldrick 2014'
_refine_ls_goodness_of_fit_ref   1.040
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     406
_refine_ls_number_reflns         5669
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.040
_refine_ls_R_factor_all          0.0345
_refine_ls_R_factor_gt           0.0326
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0498P)^2^+0.1323P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0852
_refine_ls_wR_factor_ref         0.0872
_reflns_Friedel_coverage         0.849
_reflns_Friedel_fraction_full    0.869
_reflns_Friedel_fraction_max     0.869
_reflns_number_gt                5431
_reflns_number_total             5669
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            suppl_ncrs-2020-0296_suppl.cif
_cod_data_source_block           a
_cod_original_cell_volume        1705.82(8)
_cod_database_code               8105455
_chemical_oxdiff_formula         'C1 H1 O1'
_reflns_odcompleteness_completeness 98.56
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2.a Ternary CH refined with riding coordinates:
 C3(H3), C5(H5), C9(H9), C18(H18)
2.b Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C2(H2A,H2B), C6(H6A,H6B), C7(H7A,H7B), C15(H15A,H15B), C16(H16A,
 H16B), C19(H19A,H19B), C21(H21A,H21B), C22(H22A,H22B), C31(H31A,H31B)
2.c Aromatic/amide H refined with riding coordinates:
 C12(H12), C33(H33), C34(H34), C35(H35), C36(H36), C37(H37)
2.d Idealised Me refined as rotating group:
 C23(H23A,H23B,H23C), C24(H24A,H24B,H24C), C25(H25A,H25B,H25C), C26(H26A,H26B,
 H26C), C27(H27A,H27B,H27C), C28(H28A,H28B,H28C), C30(H30A,H30B,H30C), C39(H39A,
 H39B,H39C)
;