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_7245789
_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         '2(C10 H6 O6 S2), 4(C H6 N3), 2(C10 H11 O2)'
_chemical_formula_sum            'C44 H58 N12 O16 S4'
_chemical_formula_weight         1139.26
_space_group_crystal_system      orthorhombic
_space_group_IT_number           34
_space_group_name_Hall           'P 2 -2n'
_space_group_name_H-M_alt        'P n n 2'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2022-05-13
_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            1
_cell_length_a                   8.0559(3)
_cell_length_b                   21.6299(6)
_cell_length_c                   7.2362(2)
_cell_measurement_reflns_used    1821
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      73.4760
_cell_measurement_theta_min      4.0720
_cell_volume                     1260.90(7)
_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    'SHELXS  (Sheldrick, 2008)'
_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 0.998
_diffrn_measured_fraction_theta_max 0.998
_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    -48.00  28.00   1.00    1.00    --  -40.73  37.00  30.00   76
  2  \w     10.00  57.00   1.00    1.00    --   40.73 -99.00-120.00   47
  3  \w     25.00  52.00   1.00    2.00    --  107.58 -94.00-180.00   27
  4  \w     79.00 174.00   1.00    2.00    --  107.58  30.00 -60.00   95
  5  \w     96.00 162.00   1.00    2.00    --  107.58 125.00-150.00   66
  6  \w     97.00 174.00   1.00    2.00    --  107.58  45.00  30.00   77
  7  \w     52.00  89.00   1.00    1.00    --   40.73-125.00  30.00   37
;
_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      0.0040345000
_diffrn_orient_matrix_UB_12      -0.1839617000
_diffrn_orient_matrix_UB_13      0.0572625000
_diffrn_orient_matrix_UB_21      0.0586818000
_diffrn_orient_matrix_UB_22      0.0376492000
_diffrn_orient_matrix_UB_23      0.1129411000
_diffrn_orient_matrix_UB_31      -0.0401180000
_diffrn_orient_matrix_UB_32      0.0363444000
_diffrn_orient_matrix_UB_33      0.1711982000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0188
_diffrn_reflns_av_unetI/netI     0.0239
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       24
_diffrn_reflns_limit_k_min       -25
_diffrn_reflns_limit_l_max       7
_diffrn_reflns_limit_l_min       -8
_diffrn_reflns_number            2776
_diffrn_reflns_point_group_measured_fraction_full 0.787
_diffrn_reflns_point_group_measured_fraction_max 0.787
_diffrn_reflns_theta_full        66.572
_diffrn_reflns_theta_max         66.572
_diffrn_reflns_theta_min         5.861
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    2.444
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.81058
_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    1.500
_exptl_crystal_description       block
_exptl_crystal_F_000             598
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.900
_refine_diff_density_min         -0.740
_refine_diff_density_rms         0.105
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.64(12)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.137
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     217
_refine_ls_number_reflns         1760
_refine_ls_number_restraints     116
_refine_ls_restrained_S_all      1.367
_refine_ls_R_factor_all          0.0779
_refine_ls_R_factor_gt           0.0718
_refine_ls_shift/su_max          0.036
_refine_ls_shift/su_mean         0.003
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1417P)^2^+1.4126P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2083
_refine_ls_wR_factor_ref         0.2208
_reflns_Friedel_coverage         0.451
_reflns_Friedel_fraction_full    0.535
_reflns_Friedel_fraction_max     0.535
_reflns_number_gt                1594
_reflns_number_total             1760
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ce01033j2.cif
_cod_data_source_block           GNPS-3
_cod_original_cell_volume        1260.89(7)
_cod_database_code               7245789
_shelx_shelxl_version_number     2018/3
_reflns_odcompleteness_completeness 100.00
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.36(12)
 0.64(12)
2. 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
3. Restrained distances
 C4-O4
 1.45 with sigma of 0.02
 C9-C8
 1.55 with sigma of 0.02
 C5-O5 = O5-C10
 1.45 with sigma of 0.02
 C7-C8
 1.49 with sigma of 0.02
 C1-C7
 1.32 with sigma of 0.02
 C2-C1
 1.39 with sigma of 0.02
 C5-C10
 2.511 with sigma of 0.04
 C1-C7
 2.503 with sigma of 0.04
 C2-C7
 2.521 with sigma of 0.04
4. Uiso/Uaniso restraints and constraints
C9 \\sim C3 \\sim C2 \\sim C4: within 2A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 2A
C9 \\sim C8 \\sim C7: within 2A with sigma of 0.01 and sigma for terminal atoms
of 0.02 within 2A
5. Rigid body (RIGU) restrains
 O4, O5, C9, C8, C7, C5, C3, C6, C10, C1, C2, C4
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
6. Others
 Fixed Sof: O4(0.5) O5(0.5) C9(0.5) H9A(0.5) H9B(0.5) H9C(0.5) C8(0.5) H8(0.5)
 C7(0.5) H7(0.5) C10(0.5) H10A(0.5) H10B(0.5) H10C(0.5) C2(0.5) H2(0.5) C3(0.5)
 H3(0.5) C4(0.5) C5(0.5) C6(0.5) H6(0.5) C1(0.5)
7.a Riding coordinates:
 C9(H9A,H9B,H9C)
7.b Rotating group:
 N3(H3A,H3B)
7.c Aromatic/amide H refined with riding coordinates:
 C11(H11), C12(H12), C15(H15), C8(H8), C7(H7), C2(H2), C3(H3), C6(H6)
7.d Fitted hexagon refined as free rotating group:
 C2(C3,C4,C5,C6,C1)
7.e X=CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B)
7.f Idealised Me refined as rotating group:
 C10(H10A,H10B,H10C)
;
_shelx_res_checksum              44752
_shelx_hkl_checksum              38560
_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 1.315
_oxdiff_exptl_absorpt_empirical_full_min 0.653