Synthesis of a highly strained deep cavitand.
Mirzaei, M. Saeed; Mirzaei, Saber; Khosravi, Hormoz; Hernández Sánchez, Raúl; Chemical communications (Cambridge, England) 61 (2025) 14153–14156; doi:10.1039/d5cc04263a

data_1575452
_publ_section_title
;
 Synthesis of a highly strained deep cavitand.
;
_journal_issue                   74
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              14153
_journal_page_last               14156
_journal_paper_doi               10.1039/d5cc04263a
_journal_volume                  61
_journal_year                    2025
_chemical_formula_moiety         'C134 H124 O8, 7(C2 H3 N)'
_chemical_formula_sum            'C148 H145 N7 O8'
_chemical_formula_weight         2149.70
_space_group_crystal_system      tetragonal
_space_group_IT_number           88
_space_group_name_Hall           '-I 4ad'
_space_group_name_H-M_alt        'I 41/a :2'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-12-15
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2024-10-25 deposited with the CCDC.	2025-08-14 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            16
_cell_length_a                   37.6643(3)
_cell_length_b                   37.6643(3)
_cell_length_c                   56.4258(6)
_cell_measurement_reflns_used    26040
_cell_measurement_temperature    100
_cell_measurement_theta_max      48.8740
_cell_measurement_theta_min      2.2760
_cell_volume                     80045.6(12)
_computing_cell_refinement       'CrysAlisPro 1.171.42.79a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.79a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.79a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix-Arc 150'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.997
_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     34.00  90.00   0.50    6.00    --   63.28-125.00 -60.00  112
  2  \w     26.00 101.00   0.50    6.00    --   63.28   0.00 -60.00  150
  3  \w     25.00  72.00   0.50    6.00    --   63.28 -95.00  30.00   94
  4  \w     25.00  72.00   0.50    6.00    --   63.28 -95.00 -30.00   94
  5  \w     26.00 101.00   0.50    6.00    --   63.28   0.00 -60.00  150
  6  \w     38.00  84.00   0.50    6.00    --   75.91 -95.00   0.00   92
  7  \w     38.00  84.00   0.50    6.00    --   75.91 -95.00-150.00   92
  8  \w     38.00  84.00   0.50    6.00    --   75.91 -95.00-120.00   92
  9  \w     38.00  84.00   0.50    6.00    --   75.91 -95.00 -60.00   92
 10  \w     51.00  86.00   0.50    6.00    --   77.72 -95.00 -90.00   70
 11  \w     48.00 111.00   0.50    6.00    --   77.72  15.00 120.00  126
 12  \w     68.00 111.00   0.50    6.00    --   77.72   0.00   0.00   86
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix-Arc 150'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0328724000
_diffrn_orient_matrix_UB_12      -0.0227464000
_diffrn_orient_matrix_UB_13      0.0058131000
_diffrn_orient_matrix_UB_21      0.0166032000
_diffrn_orient_matrix_UB_22      -0.0102481000
_diffrn_orient_matrix_UB_23      0.0239984000
_diffrn_orient_matrix_UB_31      -0.0177955000
_diffrn_orient_matrix_UB_32      0.0323829000
_diffrn_orient_matrix_UB_33      0.0116879000
_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  0.0575
_diffrn_reflns_av_unetI/netI     0.0540
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       40
_diffrn_reflns_limit_h_min       -45
_diffrn_reflns_limit_k_max       45
_diffrn_reflns_limit_k_min       -35
_diffrn_reflns_limit_l_max       66
_diffrn_reflns_limit_l_min       -68
_diffrn_reflns_number            214975
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         70.066
_diffrn_reflns_theta_min         2.281
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.341
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.80541
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.79a (Rigaku Oxford Diffraction, 2022)
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    0.714
_exptl_crystal_description       octahedral
_exptl_crystal_F_000             18336
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.06
_exptl_crystal_size_min          0.05
_refine_diff_density_max         1.913
_refine_diff_density_min         -0.656
_refine_diff_density_rms         0.100
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.466
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1395
_refine_ls_number_reflns         37906
_refine_ls_number_restraints     303
_refine_ls_restrained_S_all      1.535
_refine_ls_R_factor_all          0.2008
_refine_ls_R_factor_gt           0.1662
_refine_ls_shift/su_max          1.557
_refine_ls_shift/su_mean         0.012
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4195
_refine_ls_wR_factor_ref         0.4440
_reflns_Friedel_coverage         0.000
_reflns_number_gt                23319
_reflns_number_total             37906
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cc04263a2.cif
_cod_data_source_block           pnet_rhs1
_cod_depositor_comments          'Adding full bibliography for 1575452.cif.'
_cod_original_cell_volume        80045.6(15)
_cod_original_sg_symbol_H-M      'I 41/a'
_cod_database_code               1575452
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_formula         'C O '
_shelx_estimated_absorpt_t_max   0.983
_shelx_estimated_absorpt_t_min   0.967
_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
2. Restrained distances
 C26A-C27A = C27A-C28A = C28A-C29A = C29A-C30A = C30A-C31A = C31A-C32A = C32A-
 C33A = C33A-C34A
 1.5 with sigma of 0.02
 C26B-C27B = C27B-C28B = C28B-C29B = C29B-C30B
 1.5 with sigma of 0.02
 C26C-C27C = C27C-C28C = C28C-C29C = C29C-C30C = C30C-C31C = C31C-C32C = C32C-
 C33C = C33C-C34C
 1.5 with sigma of 0.02
 N60S-C60S
 1.2 with sigma of 0.02
 C34A-C32A
 2.5 with sigma of 0.02
 C60S-C61S
 1.5 with sigma of 0.02
 C29A-C30A
 1.5 with sigma of 0.02
 C30S-C31S
 1.5 with sigma of 0.02
3. Rigid bond restraints
 C26A, C27A, C28A, C29A, C30A, C31A, C32A, C33A, C34A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C26D, C27D, C28D, C29D, C30D, C31D, C32D, C33D, C34D, C35D, C36D
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C26B, C27B, C28B, C29B, C30B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C26C, C27C, C28C, C29C, C30C, C31C, C32C, C33C, C34C
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
C26A \\sim C27A \\sim C28A \\sim C29A \\sim C30A \\sim C31A \\sim C32A \\sim
C33A \\sim C34A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C26D \\sim C27D \\sim C28D \\sim C29D \\sim C30D \\sim C31D \\sim C32D \\sim
C33D \\sim C34D \\sim C35D \\sim C36D: within 2A with sigma of 0.01 and sigma
for terminal atoms of 0.02 within 2A
C26B \\sim C27B \\sim C28B \\sim C29B \\sim C30B: within 2A with sigma of 0.01
and sigma for terminal atoms of 0.02 within 2A
C26C \\sim C27C \\sim C28C \\sim C29C \\sim C30C \\sim C31C \\sim C32C \\sim
C33C \\sim C34C: within 2A with sigma of 0.005 and sigma for terminal atoms of
0.01 within 2A
Uanis(C27B) \\sim Ueq, Uanis(C28B) \\sim Ueq, Uanis(C29B) \\sim Ueq: with sigma
of 0.03 and sigma for terminal atoms of 0.06
Uanis(C27C) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
Uanis(N20S) \\sim Ueq, Uanis(C20S) \\sim Ueq, Uanis(C21S) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(C41S) = Uanis(C40S) = Uanis(N40S)
Uanis(N50S) = Uanis(C50S) = Uanis(C51S)
Uanis(N30S) = Uanis(C30S) = Uanis(C31S)
Uanis(C10S) = Uanis(C11S) = Uanis(N10S)
Uanis(N1S) = Uanis(C1S) = Uanis(C2S)
Uanis(N20S) = Uanis(C20S) = Uanis(C21S)
Uanis(C60S) = Uanis(N60S) = Uanis(C61S)
5.a Ternary CH refined with riding coordinates:
 C19A(H19A), C19B(H19B), C19C(H19C), C19D(H19D), C26A(H26A), C26B(H26B),
 C26C(H26C), C26D(H26D)
5.b Secondary CH2 refined with riding coordinates:
 C27A(H27A,H27B), C27B(H27C,H27D), C27C(H27E,H27F), C27D(H27G,H27H), C28A(H28A,
 H28B), C28B(H28C,H28D), C28C(H28E,H28F), C28D(H28G,H28H), C29A(H29A,H29B),
 C29B(H29C,H29D), C29C(H29E,H29F), C29D(H29G,H29H), C30A(H30A,H30B), C30C(H30F,
 H30G), C30D(H30H,H30I), C31A(H31A,H31B), C31C(H31C,H31D), C31D(H31E,H31F),
 C32A(H32A,H32B), C32C(H32C,H32D), C32D(H32E,H32F), C33A(H33A,H33B), C33C(H33C,
 H33D), C33D(H33E,H33F), C34D(H34G,H34H), C35D(H35A,H35B)
5.c Aromatic/amide H refined with riding coordinates:
 C1A(H1A), C1B(H1B), C1C(H1C), C1D(H1D), C2A(H2A), C2B(H2B), C2C(H2C),
 C2D(H2D), C4A(H4A), C4B(H4B), C4C(H4C), C4D(H4D), C5A(H5A), C5B(H5B), C5C(H5C),
  C5D(H5D), C8A(H8A), C8B(H8B), C8C(H8C), C8D(H8D), C9A(H9A), C9B(H9B),
 C9C(H9C), C9D(H9D), C11A(H11A), C11B(H11B), C11C(H11C), C11D(H11D), C12A(H12A),
  C12B(H12B), C12C(H12C), C12D(H12D), C14A(H14A), C14B(H14B), C14C(H14C),
 C14D(H14D), C16A(H16A), C16B(H16B), C16C(H16C), C16D(H16D), C18A(H18A),
 C18B(H18B), C18C(H18C), C18D(H18D), C21A(H21A), C21B(H21B), C21C(H21C),
 C21D(H21D), C24A(H24A), C24B(H24B), C24C(H24C), C24D(H24D)
5.d Idealised Me refined as rotating group:
 C30B(H30C,H30D,H30E), C34A(H34A,H34B,H34C), C34C(H34D,H34E,H34F), C36D(H36A,
 H36B,H36C), C2S(H2SA,H2SB,H2SC), C11S(H11E,H11F,H11G), C21S(H21E,H21F,H21G),
 C31S(H31G,H31H,H31I), C41S(H41A,H41B,H41C), C51S(H51A,H51B,H51C), C61S(H61A,
 H61B,H61C)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              21573
_shelx_hkl_checksum              13288
_shelx_fab_checksum              39337
_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 1.242
_oxdiff_exptl_absorpt_empirical_full_min 0.867