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_7245790
_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, C12 H19 N, 2(C H6 N3)'
_chemical_formula_sum            'C24 H37 N7 O6 S2'
_chemical_formula_weight         583.72
_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                   13.0691(9)
_cell_length_b                   12.2502(9)
_cell_length_c                   19.5115(18)
_cell_measurement_reflns_used    3462
_cell_measurement_temperature    150.0(10)
_cell_measurement_theta_max      27.8120
_cell_measurement_theta_min      3.3160
_cell_volume                     3123.8(4)
_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 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      150.0(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2684
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.879
_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    -62.00  -2.00   1.00    3.25    --  -11.59 -37.00  90.00   60
  2  \w    -13.00  29.00   1.00    3.25    --  -11.59 -99.00  30.00   42
  3  \w     34.00  77.00   1.00    3.25    --   11.74-178.00 -30.00   43
;
_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      -0.0405154000
_diffrn_orient_matrix_UB_12      0.0251169000
_diffrn_orient_matrix_UB_13      0.0184162000
_diffrn_orient_matrix_UB_21      0.0357476000
_diffrn_orient_matrix_UB_22      0.0211162000
_diffrn_orient_matrix_UB_23      0.0239820000
_diffrn_orient_matrix_UB_31      0.0053793000
_diffrn_orient_matrix_UB_32      0.0477561000
_diffrn_orient_matrix_UB_33      -0.0201072000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0423
_diffrn_reflns_av_unetI/netI     0.0467
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.879
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -24
_diffrn_reflns_number            11388
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.879
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         29.557
_diffrn_reflns_theta_min         2.088
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.217
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.67944
_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    1.241
_exptl_crystal_description       block
_exptl_crystal_F_000             1240
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.566
_refine_diff_density_min         -0.433
_refine_diff_density_rms         0.060
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.056
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     228
_refine_ls_number_reflns         3843
_refine_ls_number_restraints     118
_refine_ls_restrained_S_all      1.088
_refine_ls_R_factor_all          0.0853
_refine_ls_R_factor_gt           0.0577
_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^)+(0.0758P)^2^+1.2044P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1445
_refine_ls_wR_factor_ref         0.1674
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2688
_reflns_number_total             3843
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ce01033j2.cif
_cod_data_source_block           GNPS-6
_cod_database_code               7245790
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.979
_shelx_estimated_absorpt_t_min   0.972
_reflns_odcompleteness_completeness 99.92
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     26.32
_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
 C11-C10 = C10-C12 = C9-C7 = C8-C7
 1.52 with sigma of 0.02
 N4-C1
 1.48 with sigma of 0.02
 C10-C6 = C7-C2
 1.52 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C9) \\sim Ueq, Uanis(C7) \\sim Ueq, Uanis(C8) \\sim Ueq: with sigma of
0.01 and sigma for terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 C1, C2, C3, C4, C5, C6, C7, C8, C9, C10, C11, C12, N4
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Fixed Sof: C1(0.5) C2(0.5) C3(0.5) H3(0.5) C4(0.5) H4(0.5) C5(0.5) H5(0.5)
 C6(0.5) C7(0.5) H7(0.5) C8(0.5) H8A(0.5) H8B(0.5) H8C(0.5) C9(0.5) H9A(0.5)
 H9B(0.5) H9C(0.5) C10(0.5) H10(0.5) C11(0.5) H11A(0.5) H11B(0.5) H11C(0.5)
 C12(0.5) H12A(0.5) H12B(0.5) H12C(0.5) N4(0.5) H4A(0.5) H4B(0.5)
6.a Rotating group:
 N4(H4A,H4B)
6.b Ternary CH refined with riding coordinates:
 C7(H7), C10(H10)
6.c Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5), C13(H13), C14(H14), C15(H15)
6.d Fitted hexagon refined as free rotating group:
 C1(C2,C3,C4,C5,C6)
6.e X=CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B), N3(H3A,H3B)
6.f Idealised Me refined as rotating group:
 C8(H8A,H8B,H8C), C9(H9A,H9B,H9C), C11(H11A,H11B,H11C), C12(H12A,H12B,H12C)
;
_shelx_res_checksum              60057
_shelx_hkl_checksum              4982
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 1.542
_oxdiff_exptl_absorpt_empirical_full_min 0.661