Allosteric release of cucurbit[6]uril from a rotaxane using a molecular signal.
Závodná, Aneta; Janovský, Petr; Kolařík, Václav; Ward, Jas S.; Prucková, Zdeňka; Rouchal, Michal; Rissanen, Kari; Vícha, Robert; Chemical science 16 (2024) 83–89; doi:10.1039/d4sc03970j

data_1573038
_publ_section_title
;
 Allosteric release of cucurbit[6]uril from a rotaxane using a molecular
 signal.
;
_journal_issue                   1
_journal_name_full               'Chemical science'
_journal_page_first              83
_journal_page_last               89
_journal_paper_doi               10.1039/d4sc03970j
_journal_volume                  16
_journal_year                    2024
_chemical_formula_moiety
'C23 H44 N2, C36 H36 N24 O12, 2(F6 P), 3(C2 H3 N), 0.5(C4 H10 O), 2(H2 O)'
_chemical_formula_sum            'C67 H98 F12 N29 O14.5 P2'
_chemical_formula_weight         1831.61
_space_group_crystal_system      cubic
_space_group_IT_number           205
_space_group_name_Hall           '-P 2ac 2ab 3'
_space_group_name_H-M_alt        'P a -3'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-08-13
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2024-08-14 deposited with the CCDC.	2024-11-01 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            24
_cell_length_a                   36.79372(9)
_cell_length_b                   36.79372(9)
_cell_length_c                   36.79372(9)
_cell_measurement_reflns_used    85733
_cell_measurement_temperature    120.00
_cell_measurement_theta_max      76.3970
_cell_measurement_theta_min      2.4060
_cell_volume                     49810.5(2)
_computing_cell_refinement       'CrysAlisPro 1.171.42.89a (Rigaku OD, 2023)'
_computing_data_collection       'CrysAlisPro 1.171.42.89a (Rigaku OD, 2023)'
_computing_data_reduction        'CrysAlisPro 1.171.42.89a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      120.0
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix-Arc 100'
_diffrn_measured_fraction_theta_full 1.000
_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     76.00 123.00   0.50    3.00    --   52.14 131.00 -74.00   94
  2  \w     71.00 173.00   0.50   20.00    --  102.12 139.00 100.00  204
  3  \w     -4.00  25.00   0.50    3.00    --  -51.89  19.00-150.00   58
  4  \w     28.00  79.00   0.50   20.00    --  102.12 -57.00-120.00  102
  5  \w     28.00  79.00   0.50   20.00    --  102.12 -57.00 150.00  102
  6  \w     25.00  52.00   0.50   20.00    --  102.12 -38.00   0.00   54
  7  \w   -119.00 -27.00   0.50    3.00    --  -51.89 -77.00-150.00  184
  8  \w   -126.00 -35.00   0.50    3.00    --  -51.89 -57.00  90.00  182
  9  \w   -164.00 -93.00   0.50   20.00    --  -87.58 -19.00 -30.00  142
 10  \w     25.00  52.00   0.50   20.00    --  102.12 -38.00  30.00   54
 11  \w     25.00  52.00   0.50   20.00    --  102.12 -38.00  60.00   54
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, HyPix-Arc 100'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0401064000
_diffrn_orient_matrix_UB_12      0.0112357000
_diffrn_orient_matrix_UB_13      -0.0043147000
_diffrn_orient_matrix_UB_21      0.0111422000
_diffrn_orient_matrix_UB_22      -0.0288431000
_diffrn_orient_matrix_UB_23      0.0282457000
_diffrn_orient_matrix_UB_31      0.0046285000
_diffrn_orient_matrix_UB_32      -0.0282086000
_diffrn_orient_matrix_UB_33      -0.0305769000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0855
_diffrn_reflns_av_unetI/netI     0.0269
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       40
_diffrn_reflns_limit_h_min       -43
_diffrn_reflns_limit_k_max       45
_diffrn_reflns_limit_k_min       -44
_diffrn_reflns_limit_l_max       45
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            226496
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.491
_diffrn_reflns_theta_min         2.080
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.409
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.753
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.89a (Rigaku Oxford Diffraction, 2023)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
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    1.465
_exptl_crystal_description       block
_exptl_crystal_F_000             22968
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: acetonitrile/diethylether'
_exptl_crystal_size_max          0.166
_exptl_crystal_size_mid          0.095
_exptl_crystal_size_min          0.087
_refine_diff_density_max         1.373
_refine_diff_density_min         -1.121
_refine_diff_density_rms         0.131
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.775
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1045
_refine_ls_number_reflns         16955
_refine_ls_number_restraints     289
_refine_ls_restrained_S_all      1.820
_refine_ls_R_factor_all          0.1234
_refine_ls_R_factor_gt           0.1167
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3824
_refine_ls_wR_factor_ref         0.3887
_reflns_Friedel_coverage         0.000
_reflns_number_gt                14778
_reflns_number_total             16955
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc03970j2.cif
_cod_data_source_block           6d
_cod_depositor_comments
'Adding full bibliography for 1573035--1573038.cif.'
_cod_original_cell_volume        49810.5(4)
_cod_database_code               1573038
_shelxl_version_number           2014/6
_shelx_estimated_absorpt_t_max   0.893
_shelx_estimated_absorpt_t_min   0.809
_diffrn_oxdiff_digest_frames
;
0179d1901d318868f577e3ac327b65dfb4012303d54
;
_diffrn_oxdiff_digest_hkl
;
010735840833a51ac66c2a552d3e8ca7919e4e
;
_reflns_odcompleteness_completeness 99.76
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     74.33
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 H23A_$1-H23B
 -2.12 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
P221 \\sim F222 \\sim F223 \\sim F224 \\sim F225 \\sim F226 \\sim F227: within
1.7A with sigma of 0.02 and sigma for terminal atoms of 0.04
4. Rigid body (RIGU) restrains
 P201, F202, F203, F204, F205, F206, F207
 with sigma for 1-2 distances of 0.003 and sigma for 1-3 distances of 0.003
 P231, F232, F233, F234, F235, F236, F237
 with sigma for 1-2 distances of 0.003 and sigma for 1-3 distances of 0.003
 C1, C2, C3, C4
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C14, C15, C16, C17, C18, C19, C20, C21, C22, C23, C24, C25
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Fixed Sof: P221(0.33333) F222(0.33333) F223(0.33333) F224(0.33333)
 F225(0.33333) F226(0.33333) F227(0.33333) P231(0.33333) F232(0.33333)
 F233(0.33333) F234(0.33333) F235(0.33333) F236(0.33333) F237(0.33333)
6.a Free rotating group:
 C24(C16,C17,C18,C19,C20,C21,C22,C23,C25), P201(F202,F203,F204,F205,F206,F207),
  P221(F222,F223,F224,F225,F226,F227), P231(F232,F233,F234,F235,F236,F237)
6.b Ternary CH refined with riding coordinates:
 C2(H2), C24(H24), C20(H20), C22(H22), C54(H54), C58(H58), C66(H66), C70(H70),
 C78(H78), C82(H82), C90(H90), C94(H94), C102(H102), C106(H106), C114(H114),
 C118(H118)
6.c Secondary CH2 refined with riding coordinates:
 C4(H4A,H4B), N5(H5A,H5B), C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B),
 C10(H10C,H10D), C11(H11C,H11D), N12(H12E,H12F), C13(H13A,H13B), C17(H17A,H17B),
  C18(H18A,H18B), C19(H19A,H19B), C21(H21A,H21B), C23(H23A,H23B), C25(H25A,
 H25B), C61(H61A,H61B), C62(H62A,H62B), C73(H73A,H73B), C74(H74A,H74B),
 C85(H85A,H85B), C86(H86A,H86B), C97(H97A,H97B), C98(H98A,H98B), C109(H10A,
 H10B), C110(H11A,H11B), C121(H12A,H12B), C122(H12C,H12D)
6.d Aromatic/amide H refined with riding coordinates:
 C14(H14), C15(H15)
6.e Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C3(H3A,H3B,H3C), C303(H30A,H30B,H30C)
;
_shelx_res_checksum              85644
_shelx_hkl_checksum              74072
_shelx_fab_checksum              6582
_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
- B-factor correction
;
_oxdiff_exptl_absorpt_empirical_full_max 1.637
_oxdiff_exptl_absorpt_empirical_full_min 0.759