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_1573037
_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 H46 N2, C36 H36 N24 O12, 2(F6 P), 3(C2 H3 N), 0.5(C4 H10 O), 1.5(H2 O)'
_chemical_formula_sum            'C67 H99 F12 N29 O14 P2'
_chemical_formula_weight         1824.61
_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   mixed
_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                   36.76500(10)
_cell_length_b                   36.76500(10)
_cell_length_c                   36.76500(10)
_cell_measurement_reflns_used    238021
_cell_measurement_temperature    120.01(10)
_cell_measurement_theta_max      76.7300
_cell_measurement_theta_min      2.4010
_cell_volume                     49694.0(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_environment      N~2~
_diffrn_ambient_temperature      120.01(10)
_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 0.992
_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     -4.00  19.00   0.50    3.00    --  -51.89  19.00-180.00   46
  2  \w      1.00  21.00   0.50    3.00    --  -51.89  19.00-150.00   40
  3  \w     -4.00  25.00   0.50    3.00    --  -51.89  19.00  60.00   58
  4  \w     -4.00  20.00   0.50    3.00    --  -51.89  19.00  90.00   48
  5  \w     28.00  60.00   0.50    3.00    --   52.14  77.00  60.00   64
  6  \w     21.00 104.00   0.50    3.00    --   52.14-125.00 -30.00  166
  7  \w     38.00 117.00   0.50    3.00    --   52.14  77.00  90.00  158
  8  \w     67.00  99.00   0.50    3.00    --   52.14  77.00  60.00   64
  9  \w    -27.00 -10.00   0.50   15.50    --  -87.58  38.00-150.00   34
 10  \w   -122.00 -74.00   0.50   15.50    --  -87.58-125.00   0.00   96
 11  \w   -157.00-127.00   0.50   15.50    --  -87.58 -57.00-120.00   60
 12  \w    -53.00 -14.00   0.50   15.50    --  -87.58  57.00   0.00   78
 13  \w   -146.00-130.00   0.50   15.50    --  -87.58-125.00   0.00   32
 14  \w   -122.00 -73.00   0.50   15.50    --  -87.58 -57.00-120.00   98
 15  \w    -26.00 -10.00   0.50   15.50    --  -87.58  38.00  30.00   32
 16  \w    -49.00 -26.00   0.50   15.50    --  -87.58  57.00-120.00   46
 17  \w    -25.00 -10.00   0.50   15.50    --  -87.58  38.00 -60.00   30
 18  \w     29.00 108.00   0.50   15.50    --   94.00-107.00-177.03  158
 19  \w     62.00  79.00   0.50   15.50    --  102.12 -57.00-150.00   34
 20  \w     28.00  44.00   0.50   15.50    --  102.12 -57.00-150.00   32
 21  \w     25.00  47.00   0.50   15.50    --  102.12 -38.00  30.00   44
 22  \w     41.00 105.00   0.50   15.50    --  102.12 -99.00  60.00  128
 23  \w     79.00  95.00   0.50   15.50    --  102.12  77.00-180.00   32
 24  \w     25.00  41.00   0.50   15.50    --  102.12 -38.00 -30.00   32
 25  \w     46.00  62.00   0.50   15.50    --  102.12-125.00-180.00   32
 26  \w     80.00 111.00   0.50   15.50    --  102.12-125.00-180.00   62
 27  \w     89.00 104.00   0.50   15.50    --  102.12 -99.00  30.00   30
 28  \w     30.00  78.00   0.50   15.50    --  102.12 -57.00-180.00   96
 29  \w     34.00  76.00   0.50   15.50    --  102.12 -57.00  60.00   84
 30  \w     43.00  91.00   0.50   15.50    --  102.12 -99.00 -60.00   96
 31  \w     48.00  64.00   0.50   15.50    --  102.12 -57.00 -30.00   32
 32  \w     53.00  72.00   0.50   15.50    --  102.12 -99.00-180.00   38
 33  \w     28.00  43.00   0.50   15.50    --  102.12 -57.00 -30.00   30
 34  \w     87.00 106.00   0.50   15.50    --  102.12 -99.00-120.00   38
 35  \w     67.00  82.00   0.50   15.50    --  102.12 -99.00 -90.00   30
 36  \w     59.00  74.00   0.50   15.50    --  102.12 -99.00-120.00   30
 37  \w     71.00 106.00   0.50   15.50    --  102.12 -99.00 -30.00   70
 38  \w     35.00  60.00   0.50   15.50    --  102.12 -99.00 -90.00   50
 39  \w     30.00  52.00   0.50   15.50    --  102.12 -38.00 120.00   44
 40  \w     90.00 105.00   0.50   15.50    --  102.12 -99.00 -90.00   30
 41  \w     45.00  79.00   0.50   15.50    --  102.12 -57.00  90.00   68
 42  \w     65.00 172.00   0.50   15.50    --  102.12  19.00-120.00  214
 43  \w     32.00  96.00   0.50   15.50    --  102.12-125.00  60.00  128
 44  \w     78.00 104.00   0.50   15.50    --  102.12 -99.00-180.00   52
 45  \w     83.00  98.00   0.50   15.50    --  102.12 -77.00  60.00   30
 46  \w     29.00  52.00   0.50   15.50    --  102.12 -38.00 -90.00   46
 47  \w     41.00  66.00   0.50   15.50    --  102.12 -77.00  60.00   50
 48  \w    121.00 176.00   0.50   15.50    --  102.12  19.00 -30.00  110
 49  \w    110.00 148.00   0.50   15.50    --  102.12  38.00  90.00   76
 50  \w    131.00 158.00   0.50   15.50    --  102.12  77.00-180.00   54
 51  \w     91.00 106.00   0.50   15.50    --  102.12 -99.00  90.00   30
 52  \w     99.00 146.00   0.50   15.50    --  102.12  38.00 120.00   94
 53  \w     59.00  79.00   0.50   15.50    --  102.12 -57.00 -90.00   40
 54  \w     67.00 103.00   0.50   15.50    --  102.12 -99.00-150.00   72
 55  \w     35.00 106.00   0.50   15.50    --  102.12 -99.00   0.00  142
 56  \w     67.00 118.00   0.50   15.50    --  102.12  19.00 -30.00  102
;
_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      -0.0193892000
_diffrn_orient_matrix_UB_12      0.0246517000
_diffrn_orient_matrix_UB_13      0.0277929000
_diffrn_orient_matrix_UB_21      0.0348219000
_diffrn_orient_matrix_UB_22      0.0010619000
_diffrn_orient_matrix_UB_23      0.0232910000
_diffrn_orient_matrix_UB_31      0.0130097000
_diffrn_orient_matrix_UB_32      0.0339015000
_diffrn_orient_matrix_UB_33      -0.0209406000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0725
_diffrn_reflns_av_unetI/netI     0.0217
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.992
_diffrn_reflns_limit_h_max       42
_diffrn_reflns_limit_h_min       -44
_diffrn_reflns_limit_k_max       37
_diffrn_reflns_limit_k_min       -43
_diffrn_reflns_limit_l_max       43
_diffrn_reflns_limit_l_min       -45
_diffrn_reflns_number            284279
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.408
_diffrn_reflns_theta_min         2.081
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.405
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.89344
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.89a (Rigaku Oxford Diffraction, 2023)
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    1.463
_exptl_crystal_description       block
_exptl_crystal_F_000             22896
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: acetonitrile/diethylether'
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.08
_refine_diff_density_max         1.150
_refine_diff_density_min         -0.811
_refine_diff_density_rms         0.128
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.803
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1072
_refine_ls_number_reflns         16806
_refine_ls_number_restraints     278
_refine_ls_restrained_S_all      1.845
_refine_ls_R_factor_all          0.1189
_refine_ls_R_factor_gt           0.1130
_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          0.3818
_refine_ls_wR_factor_ref         0.3864
_reflns_Friedel_coverage         0.000
_reflns_number_gt                14899
_reflns_number_total             16806
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc03970j2.cif
_cod_data_source_block           6c
_cod_depositor_comments
'Adding full bibliography for 1573035--1573038.cif.'
_cod_original_cell_volume        49694.0(4)
_cod_database_code               1573037
_shelxl_version_number           2014/6
_shelx_estimated_absorpt_t_max   0.900
_shelx_estimated_absorpt_t_min   0.856
_diffrn_oxdiff_digest_frames
;
01a206585c215af221ecca40cce66f12ac0002729d4
;
_diffrn_oxdiff_digest_hkl
;
01999bde01cc3910f4c7b8ea1fbee1dfe021df
;
_reflns_odcompleteness_completeness 99.99
_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, All O(H,H) groups
2. Restrained distances
 C15-C14
 1.5 with sigma of 0.02
 C3-C2 = C1-C2
 1.5 with sigma of 0.02
 C2-C4
 1.5 with sigma of 0.01
 H40B-O83_$1
 1.95 with sigma of 0.01
 H40A-F223_$2
 2.02 with sigma of 0.01
 H15B-H17A
 -2.1 with sigma of 0.01
 C13-C15
 2.45 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
P231 \\sim F232 \\sim F233 \\sim F234 \\sim F235 \\sim F236 \\sim F237: within
1.7A with sigma of 0.02 and sigma for terminal atoms of 0.04
C13 \\sim C14 \\sim C15 \\sim C16 \\sim C17 \\sim C18 \\sim C19 \\sim C20 \\sim
C21 \\sim C22 \\sim C23 \\sim C24 \\sim C25: within 1.7A with sigma of 0.02 and
sigma for terminal atoms of 0.04
C13 \\sim C14 \\sim C15: 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 0.004 and sigma for 1-3 distances of 0.004
 C1, C2, C3, C4
 with sigma for 1-2 distances of 0.003 and sigma for 1-3 distances of 0.003
 P221, F222, F223, F224, F225, F226, F227
 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)
 O401(0.5) H40A(0.5) H40B(0.5)
6.a Free rotating group:
 C16(C17,C18,C19,C20,C21,C22,C23,C24,C25), P221(F222,F223,F224,F225,F226,F227),
  P231(F232,F233,F234,F235,F236,F237), O401(H40A,H40B)
6.b Ternary CH refined with riding coordinates:
 C2(H2), C20(H20), C22(H22), C24(H24), 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), C14(H14A,H14B),
  C15(H15A,H15B), 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 Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C3(H3A,H3B,H3C), C303(H30A,H30B,H30C)
;
_shelx_res_checksum              62048
_shelx_hkl_checksum              48377
_shelx_fab_checksum              55013
_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 1.565
_oxdiff_exptl_absorpt_empirical_full_min 0.641