Insights Into the Properties of Amygdalin Solvatomorphs: X-ray Structures, Intermolecular Interactions, and Transformations.
Zhang, Tingting; Yang, Shiying; Zhang, Baoxi; Yang, Dezhi; Lu, Yang; Du, Guanhua; ACS omega 7 (2022) 8906–8918; doi:10.1021/acsomega.1c07314

data_4519402
_publ_section_title
;
 Insights Into the Properties of Amygdalin Solvatomorphs: X-ray
 Structures, Intermolecular Interactions, and Transformations.
;
_journal_issue                   10
_journal_name_full               'ACS omega'
_journal_page_first              8906
_journal_page_last               8918
_journal_paper_doi               10.1021/acsomega.1c07314
_journal_volume                  7
_journal_year                    2022
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C20 H27 N O11, C6 H14 O, 2(H2 O)'
_chemical_formula_sum            'C26 H45 N O14'
_chemical_formula_weight         595.63
_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     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2021-11-28
_audit_creation_method
;
Olex2 1.2-beta
(compiled 2015.11.10 svn.r3248 for OlexSys, GUI svn.r5133)
;
_cell_angle_alpha                90.00
_cell_angle_beta                 100.2992(17)
_cell_angle_gamma                90.00
_cell_formula_units_Z            2
_cell_length_a                   9.41164(19)
_cell_length_b                   7.95651(14)
_cell_length_c                   20.6510(4)
_cell_measurement_reflns_used    15207
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      72.1620
_cell_measurement_theta_min      4.3510
_cell_volume                     1521.51(5)
_computing_cell_refinement       'CrysAlisPro 1.171.41.80a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.41.80a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.41.80a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.976
_diffrn_measured_fraction_theta_max 0.976
_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    -71.00  46.00   1.00    5.00    --  -44.00  70.00 225.00  117
  2  \w    -71.00  46.00   1.00    5.00    --  -44.00  70.00  90.00  117
  3  \w    -71.00  46.00   1.00    5.00    --  -44.00  70.00 135.00  117
  4  \w    -71.00   2.00   1.00    5.00    --  -44.00  70.00 325.00   73
  5  \w    -71.00  -2.00   1.00    5.00    --  -44.00  70.00   0.00   69
  6  \w   -134.00 -87.00   1.00    5.00    --  -44.00   0.00 180.00   47
  7  \w    -24.00   6.00   1.00    5.00    --  -44.00   0.00 225.00   30
  8  \w    -71.00 -43.00   1.00    5.00    --  -44.00  70.00 270.00   28
  9  \w   -127.00 -10.00   1.00    5.00    -- -100.00  70.00   0.00  117
 10  \w   -127.00 -10.00   1.00    5.00    -- -100.00  70.00 325.00  117
 11  \w   -127.00 -10.00   1.00    5.00    -- -100.00  70.00  90.00  117
 12  \w   -127.00 -10.00   1.00    5.00    -- -100.00  70.00 180.00  117
 13  \w   -127.00 -13.00   1.00    5.00    -- -100.00  70.00 225.00  114
 14  \w   -119.00 -10.00   1.00    5.00    -- -100.00  45.00 225.00  109
 15  \w   -119.00 -10.00   1.00    5.00    -- -100.00  45.00 135.00  109
 16  \w   -127.00 -18.00   1.00    5.00    -- -100.00  70.00 135.00  109
 17  \w   -119.00 -10.00   1.00    5.00    -- -100.00  45.00   0.00  109
 18  \w   -119.00 -10.00   1.00    5.00    -- -100.00  45.00 325.00  109
 19  \w   -117.00 -10.00   1.00    5.00    -- -100.00  30.00  90.00  107
 20  \w   -117.00 -10.00   1.00    5.00    -- -100.00  30.00 325.00  107
 21  \w   -119.00 -25.00   1.00    5.00    -- -100.00  45.00  90.00   94
 22  \w   -145.00 -55.00   1.00    5.00    -- -100.00   0.00  90.00   90
 23  \w   -145.00 -55.00   1.00    5.00    -- -100.00   0.00   0.00   90
 24  \w   -127.00 -70.00   1.00    5.00    -- -100.00  70.00 270.00   57
;
_diffrn_measurement_device       'abstract diffractometer'
_diffrn_measurement_device_type
'dtrek-CrysAlisPro-abstract goniometer imported rigaku-d*trek images'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0384581000
_diffrn_orient_matrix_UB_12      0.0275973000
_diffrn_orient_matrix_UB_13      -0.0749361000
_diffrn_orient_matrix_UB_21      0.0127488000
_diffrn_orient_matrix_UB_22      -0.1904410000
_diffrn_orient_matrix_UB_23      -0.0112050000
_diffrn_orient_matrix_UB_31      -0.1613197000
_diffrn_orient_matrix_UB_32      -0.0216828000
_diffrn_orient_matrix_UB_33      0.0030019000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0876
_diffrn_reflns_av_unetI/netI     0.0465
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            24749
_diffrn_reflns_theta_full        72.28
_diffrn_reflns_theta_max         72.28
_diffrn_reflns_theta_min         4.35
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.893
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.36391
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.80a (Rigaku Oxford Diffraction, 2020)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_density_diffrn    1.300
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             640
_refine_diff_density_max         0.221
_refine_diff_density_min         -0.233
_refine_diff_density_rms         0.046
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   0.21(17)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.132
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     524
_refine_ls_number_reflns         5725
_refine_ls_number_restraints     4
_refine_ls_restrained_S_all      1.131
_refine_ls_R_factor_all          0.0558
_refine_ls_R_factor_gt           0.0541
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0971P)^2^+0.1374P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1541
_refine_ls_wR_factor_ref         0.1574
_reflns_number_gt                5437
_reflns_number_total             5725
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ao1c07314_si_004.cif
_cod_data_source_block           6354-20210918
_cod_database_code               4519402
_reflns_odcompleteness_completeness 97.59
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     72.13
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 O1W-H1WB
 1 with sigma of 0.02
 O1W-H1WA
 1 with sigma of 0.02
 H1H-H11
 2.3 with sigma of 0.02
3. Others
 Sof(H1HA)=Sof(H1HB)=Sof(H5HA)=Sof(H5HB)=Sof(C4HA)=Sof(H4HA)=Sof(H4HB)=
 Sof(C3HA)=Sof(H3HA)=Sof(H3HB)=Sof(C2HA)=Sof(H2HA)=Sof(H2HB)=1-FVAR(1)
 Sof(H1HC)=Sof(H1HD)=Sof(H5HC)=Sof(H5HD)=Sof(C4HB)=Sof(H4HC)=Sof(H4HD)=
 Sof(C3HB)=Sof(H3HC)=Sof(H3HD)=Sof(C2HB)=Sof(H2HC)=Sof(H2HD)=FVAR(1)
4.a Secondary CH2 refined with riding coordinates:
 C1H(H1HA,H1HB), C1H(H1HC,H1HD), C5H(H5HA,H5HB), C5H(H5HC,H5HD), C4HA(H4HA,
 H4HB), C3HA(H3HA,H3HB), C2HA(H2HA,H2HB), C4HB(H4HC,H4HD), C3HB(H3HC,H3HD),
 C2HB(H2HC,H2HD)
4.b Idealised Me refined as rotating group:
 C6H(H6HA,H6HB,H6HC)
4.c Idealised tetrahedral OH refined as rotating group:
 O1H(H1H)
;
_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 8.431
_oxdiff_exptl_absorpt_empirical_full_min 0.397