Structure determination of liquid molecules by encapsulation in an aromatic cavity with hydrogen bonding and enhanced C–H⋯π interactions
Qin, Shu-Qin; Xu, Wei; Ye, Wen-Cai; Jiang, Ren-Wang; CrystEngComm  (2022) –; doi:10.1039/D2CE01033J

data_7245791
_publ_section_title
;
 Structure determination of liquid molecules by encapsulation in an
 aromatic cavity with hydrogen bonding and enhanced C--H&#x22EF;\p
 interactions
;
_journal_name_full               CrystEngComm
_journal_paper_doi               10.1039/D2CE01033J
_journal_year                    2022
_chemical_formula_moiety         'C10 H6 O6 S2, 2(C6 H7.5 O), 2(C H6 N3)'
_chemical_formula_sum            'C24 H33 N6 O8 S2'
_chemical_formula_weight         597.68
_space_group_crystal_system      orthorhombic
_space_group_IT_number           61
_space_group_name_Hall           '-P 2ac 2ab'
_space_group_name_H-M_alt        'P b c a'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2021-12-27
_audit_creation_method
;
Olex2 1.3-alpha
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6408)
;
_audit_update_record
;
2022-05-23 deposited with the CCDC.	2022-11-09 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.0361(3)
_cell_length_b                   12.2207(2)
_cell_length_c                   19.6245(4)
_cell_measurement_reflns_used    3744
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      73.6880
_cell_measurement_theta_min      5.4290
_cell_volume                     3126.38(11)
_computing_cell_refinement       'CrysAlisPro 1.171.38.43f (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.43f (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.43f (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 1.3-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      150.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2684
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 0.991
_diffrn_measured_fraction_theta_max 0.991
_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      1.00  42.00   1.00    1.00    --   40.73 -99.00 -30.00   41
  2  \w     35.00 108.00   1.00    2.00    --  107.58 -94.00  30.00   73
  3  \w     34.00 122.00   1.00    2.00    --  107.58-125.00 -30.00   88
  4  \w     85.00 156.00   1.00    2.00    --  107.58  45.00 -30.00   71
  5  \w    130.00 165.00   1.00    2.00    --  107.58 120.00-134.00   35
  6  \w    109.00 158.00   1.00    2.00    --  107.58 125.00 -30.00   49
  7  \w     75.00 113.00   1.00    1.00    --   40.73  57.00-180.00   38
  8  \w    -95.00  -2.00   1.00    1.00    --  -40.73 125.00 150.00   93
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0017977000
_diffrn_orient_matrix_UB_12      -0.1249098000
_diffrn_orient_matrix_UB_13      0.0105443000
_diffrn_orient_matrix_UB_21      -0.0978768000
_diffrn_orient_matrix_UB_22      -0.0079507000
_diffrn_orient_matrix_UB_23      -0.0436517000
_diffrn_orient_matrix_UB_31      0.0661269000
_diffrn_orient_matrix_UB_32      -0.0150109000
_diffrn_orient_matrix_UB_33      -0.0644242000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0342
_diffrn_reflns_av_unetI/netI     0.0315
_diffrn_reflns_Laue_measured_fraction_full 0.991
_diffrn_reflns_Laue_measured_fraction_max 0.991
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            7703
_diffrn_reflns_point_group_measured_fraction_full 0.991
_diffrn_reflns_point_group_measured_fraction_max 0.991
_diffrn_reflns_theta_full        66.599
_diffrn_reflns_theta_max         66.599
_diffrn_reflns_theta_min         5.450
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.995
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.78426
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.43f (Rigaku Oxford Diffraction, 2015)
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    1.270
_exptl_crystal_description       block
_exptl_crystal_F_000             1260
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.11
_refine_diff_density_max         0.785
_refine_diff_density_min         -1.183
_refine_diff_density_rms         0.110
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.108
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     224
_refine_ls_number_reflns         2743
_refine_ls_number_restraints     148
_refine_ls_restrained_S_all      1.159
_refine_ls_R_factor_all          0.0869
_refine_ls_R_factor_gt           0.0793
_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^)+(0.1695P)^2^+4.2907P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2495
_refine_ls_wR_factor_ref         0.2628
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2347
_reflns_number_total             2743
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ce01033j2.cif
_cod_data_source_block           GNPS-5
_cod_database_code               7245791
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.810
_shelx_estimated_absorpt_t_min   0.782
_reflns_odcompleteness_completeness 100.00
_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 N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C7-C8
 1.35 with sigma of 0.02
 O5-C11 = O4-C10
 1.42 with sigma of 0.04
 O5-C2 = O4-C1
 1.42 with sigma of 0.04
 C8-C9
 1.52 with sigma of 0.02
 C7-C4
 1.52 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
Uanis(C7) \\sim Ueq, Uanis(C8) \\sim Ueq, Uanis(C9) \\sim Ueq, Uanis(C4) \\sim
Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C5) \\sim Ueq, Uanis(C6) \\sim Ueq, Uanis(C1) \\sim Ueq, Uanis(C2) \\sim
Ueq, Uanis(C3) \\sim Ueq, Uanis(C4) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 O4, O5, C4, C3, C2, C1, C6, C5, C7, C8, C9, C10, C11
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Fixed Sof: O4(0.5) O5(0.5) C4(0.5) C3(0.5) H3(0.5) C2(0.5) C1(0.5) C5(0.5)
 H5(0.5) C7(0.5) H7(0.5) C8(0.5) H8(0.5) C9(0.5) H9A(0.5) H9B(0.5) H9C(0.5)
 C10(0.5) H10A(0.5) H10B(0.5) H10C(0.5) C11(0.5) H11A(0.5) H11B(0.5) H11C(0.5)
6.a Riding coordinates:
 C9(H9A,H9B,H9C), C10(H10A,H10B,H10C)
6.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C6(H6), C5(H5), C7(H7), C8(H8), C12(H12), C15(H15), C16(H16)
6.c Fitted hexagon refined as free rotating group:
 C4(C3,C2,C1,C6,C5)
6.d X=CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B), N3(H3A,H3B)
6.e Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C)
;
_shelx_res_checksum              88591
_shelx_hkl_checksum              21924
_olex2_date_sample_data_collection 2020-09-26
_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 1.410
_oxdiff_exptl_absorpt_empirical_full_min 0.830