Mechanistic study of the formation of arbutin polymorphs and solvates
Taiwaikuli, Mukaidaisi; Wang, Ting; Chen, Kui; Feng, Yaoguang; Xing, Jiangna; Huang, Xin; Wang, Na; Zhou, Lina; Hao, Hongxun; CrystEngComm 25 (2023) 2075–2084; doi:10.1039/D2CE01670B

data_7246332
_publ_section_title
;
 Mechanistic study of the formation of arbutin polymorphs and solvates
;
_journal_issue                   14
_journal_name_full               CrystEngComm
_journal_page_first              2075
_journal_page_last               2084
_journal_paper_doi               10.1039/D2CE01670B
_journal_volume                  25
_journal_year                    2023
_chemical_absolute_configuration rm
_chemical_formula_moiety         '2(C12 H16 O7), C5 H9 N O'
_chemical_formula_sum            'C29 H41 N O15'
_chemical_formula_weight         643.63
_chemical_name_common            'Arbutin NMP solvent compound;solvate S5'
_chemical_name_systematic        'Arbutin NMP solvate'
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2022-09-14
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-12-06 deposited with the CCDC.	2023-02-23 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   6.3606(3)
_cell_length_b                   20.5593(9)
_cell_length_c                   23.4018(9)
_cell_measurement_reflns_used    11208
_cell_measurement_temperature    113.15
_cell_measurement_theta_max      31.7100
_cell_measurement_theta_min      2.6230
_cell_volume                     3060.2(2)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_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      113.15
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.956
_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   -120.00  60.00   1.00    3.00    --  -30.00  45.00   0.00  180
  2  \w   -120.00  30.00   1.00    3.00    --  -30.00  45.00  90.00  150
  3  \w   -120.00   0.00   1.00    3.00    --  -30.00  45.00 180.00  120
;
_diffrn_measurement_device       'abstract diffractometer'
_diffrn_measurement_device_type  'Rigaku Saturn 70 CCD'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0378577000
_diffrn_orient_matrix_UB_12      0.0054834000
_diffrn_orient_matrix_UB_13      -0.0280900000
_diffrn_orient_matrix_UB_21      -0.0094832000
_diffrn_orient_matrix_UB_22      -0.0336786000
_diffrn_orient_matrix_UB_23      -0.0060187000
_diffrn_orient_matrix_UB_31      -0.1044762000
_diffrn_orient_matrix_UB_32      0.0050627000
_diffrn_orient_matrix_UB_33      -0.0096650000
_diffrn_radiation_monochromator  confocal
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0782
_diffrn_reflns_av_unetI/netI     0.0849
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.956
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       31
_diffrn_reflns_limit_k_min       -31
_diffrn_reflns_limit_l_max       34
_diffrn_reflns_limit_l_min       -36
_diffrn_reflns_number            37615
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.928
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         33.555
_diffrn_reflns_theta_min         1.981
_diffrn_source                   'rotating anode'
_diffrn_source_type              'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.113
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.85754
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'CrysAlisPro 1.171.39.46 (Rigaku Oxford Diffraction, 2018)'
_exptl_crystal_density_diffrn    1.397
_exptl_crystal_F_000             1368
_exptl_crystal_size_max          0.24
_exptl_crystal_size_mid          0.22
_exptl_crystal_size_min          0.18
_refine_diff_density_max         0.248
_refine_diff_density_min         -0.249
_refine_diff_density_rms         0.057
_refine_ls_abs_structure_details
;
 Flack x determined using 2160 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.8(6)
_refine_ls_extinction_coef       0.0081(8)
_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   1.040
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     489
_refine_ls_number_reflns         11199
_refine_ls_number_restraints     324
_refine_ls_restrained_S_all      1.037
_refine_ls_R_factor_all          0.0991
_refine_ls_R_factor_gt           0.0615
_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^)+(0.0381P)^2^+0.2219P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1049
_refine_ls_wR_factor_ref         0.1239
_reflns_Friedel_coverage         0.740
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.893
_reflns_number_gt                7609
_reflns_number_total             11199
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ce01670b2.cif
_cod_data_source_block           r20220306a
_cod_depositor_comments
'Adding full bibliography for 7246329--7246332.cif.'
_cod_database_code               7246332
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C11 H10 N O'
_shelx_estimated_absorpt_t_max   0.980
_shelx_estimated_absorpt_t_min   0.973
_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, All O(H) groups
2. Restrained distances
 O7A-H7AA
 0.85 with sigma of 0.01
 O5A-H5AA
 0.85 with sigma of 0.01
 O8-C16 \\sim O8A-C16A
 with sigma of 0.02
 N1-C16 \\sim N1A-C16A
 with sigma of 0.02
 N1-C13 \\sim N1A-C13A
 with sigma of 0.02
 N1-C17 \\sim N1A-C17A
 with sigma of 0.02
 C16-C15 \\sim C16A-C15A
 with sigma of 0.02
 C15-C14 \\sim C15A-C14A
 with sigma of 0.02
 C14-C13 \\sim C14A-C13A
 with sigma of 0.02
 O8-N1 \\sim O8A-N1A
 with sigma of 0.04
 O8-C15 \\sim O8A-C15A
 with sigma of 0.04
 N1-C15 \\sim N1A-C15A
 with sigma of 0.04
 N1-C14 \\sim N1A-C14A
 with sigma of 0.04
 C16-C14 \\sim C16A-C14A
 with sigma of 0.04
 C16-C13 \\sim C16A-C13A
 with sigma of 0.04
 C16-C17 \\sim C16A-C17A
 with sigma of 0.04
 C15-C13 \\sim C15A-C13A
 with sigma of 0.04
 C13-C17 \\sim C13A-C17A
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
O8 \\sim N1 \\sim C13 \\sim C14 \\sim C15 \\sim C16 \\sim C17 \\sim O8A \\sim
N1A \\sim C13A \\sim C14A \\sim C15A \\sim C16A \\sim C17A: within 2A with
sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
Uanis(O8) \\sim Ueq, Uanis(N1) \\sim Ueq, Uanis(C13) \\sim Ueq, Uanis(C14)
\\sim Ueq, Uanis(C15) \\sim Ueq, Uanis(C16) \\sim Ueq, Uanis(C17) \\sim Ueq,
Uanis(O8A) \\sim Ueq, Uanis(N1A) \\sim Ueq, Uanis(C13A) \\sim Ueq, Uanis(C14A)
\\sim Ueq, Uanis(C15A) \\sim Ueq, Uanis(C16A) \\sim Ueq, Uanis(C17A) \\sim Ueq:
with sigma of 0.01 and sigma for terminal atoms of 0.02
4. Others
 Sof(O8A)=Sof(N1A)=Sof(C13A)=Sof(H13C)=Sof(H13D)=Sof(C14A)=Sof(H14C)=Sof(H14D)=
 Sof(C15A)=Sof(H15C)=Sof(H15D)=Sof(C16A)=Sof(C17A)=Sof(H17D)=Sof(H17E)=
 Sof(H17F)=1-FVAR(1)
 Sof(O8)=Sof(N1)=Sof(C13)=Sof(H13A)=Sof(H13B)=Sof(C14)=Sof(H14A)=Sof(H14B)=
 Sof(C15)=Sof(H15A)=Sof(H15B)=Sof(C16)=Sof(C17)=Sof(H17A)=Sof(H17B)=Sof(H17C)=
 FVAR(1)
5.a Ternary CH refined with riding coordinates:
 C7(H7A), C8(H8), C9(H9), C10(H10), C11(H11), C7A(H7AB), C8A(H8A), C9A(H9A),
 C10A(H10A), C11A(H11A)
5.b Secondary CH2 refined with riding coordinates:
 C12(H12A,H12B), C12A(H12C,H12D), C13(H13A,H13B), C14(H14A,H14B), C15(H15A,
 H15B), C13A(H13C,H13D), C14A(H14C,H14D), C15A(H15C,H15D)
5.c Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C5(H5A), C6(H6A), C2A(H2A), C3A(H3A), C5A(H5AB), C6A(H6AB)
5.d Idealised Me refined as rotating group:
 C17(H17A,H17B,H17C), C17A(H17D,H17E,H17F)
5.e Idealised tetrahedral OH refined as rotating group:
 O1(H1), O4(H4), O5(H5), O6(H6), O7(H7), O1A(H1A), O4A(H4A), O6A(H6AA)
;
_shelx_res_checksum              81614
_shelx_hkl_checksum              94559
_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
- Detector area scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.849
_oxdiff_exptl_absorpt_empirical_full_min 0.713