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_1573035
_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
'C36 H36 N24 O12, C21 H42 N2, 2(F6 P), C7 H8, 3(C2 H3 N), 7(C7 H8)'
_chemical_formula_sum            'C119 H167 F12 N29 O12 P2'
_chemical_formula_weight         2485.71
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-12-04
_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                 91.6470(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   16.05160(10)
_cell_length_b                   25.7006(2)
_cell_length_c                   27.3571(2)
_cell_measurement_reflns_used    72719
_cell_measurement_temperature    120.0(1)
_cell_measurement_theta_max      76.2770
_cell_measurement_theta_min      2.4310
_cell_volume                     11281.12(14)
_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(1)
_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 0.999
_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    -20.00   6.00   0.50    0.50    --  -51.89  48.00  27.00   52
  2  \w   -111.00 -80.00   0.50    0.50    --  -51.89 -48.00-121.00   62
  3  \w    -23.00  67.00   0.50    0.50    --   51.89 -48.00-121.00  180
  4  \w     39.00 127.00   0.50    0.50    --   51.89  48.00  27.00  176
  5  \w   -150.00-116.00   0.50    3.00    --  -87.58 -48.00-121.00   68
  6  \w    -40.00 -15.00   0.50    3.00    --  -87.58  48.00  27.00   50
  7  \w     87.00 176.00   0.50    3.00    --  102.12  48.00  27.00  178
  8  \w     26.00  51.00   0.50    3.00    --  102.12 -48.00-121.00   50
  9  \w     -3.00  25.00   0.50    0.50    --  -51.89  19.00  90.00   56
 10  \w     -4.00  24.00   0.50    0.50    --  -51.89  19.00 120.00   56
 11  \w     22.00 102.00   0.50    0.50    --   51.89-125.00 -90.00  160
 12  \w   -100.00 -19.00   0.50    3.00    --  -87.58 125.00  30.00  162
 13  \w   -100.00 -46.00   0.50    3.00    --  -87.58  77.00  30.00  108
 14  \w    -49.00 -14.00   0.50    3.00    --  -87.58  57.00 -30.00   70
 15  \w    -53.00 -16.00   0.50    3.00    --  -87.58  57.00-150.00   74
 16  \w    -53.00 -14.00   0.50    3.00    --  -87.58  57.00  60.00   78
 17  \w   -155.00 -90.00   0.50    3.00    --  -87.58 -99.00   0.00  130
 18  \w   -121.00 -95.00   0.50    3.00    --  -87.58-125.00  30.00   52
 19  \w   -158.00-130.00   0.50    3.00    --  -87.58-125.00  30.00   56
 20  \w     36.00  79.00   0.50    3.00    --  102.12 -99.00 -60.00   86
 21  \w     40.00 106.00   0.50    3.00    --  102.12 -99.00-120.00  132
 22  \w     32.00  80.00   0.50    3.00    --  102.12-125.00-180.00   96
 23  \w    138.00 168.00   0.50    3.00    --  102.12  77.00-120.00   60
 24  \w     88.00 129.00   0.50    3.00    --  102.12  38.00  90.00   82
 25  \w     41.00 106.00   0.50    3.00    --  102.12 -99.00-180.00  130
 26  \w     36.00  74.00   0.50    3.00    --  102.12 -77.00  30.00   76
 27  \w     40.00  75.00   0.50    3.00    --  102.12 -57.00-150.00   70
 28  \w     43.00  69.00   0.50    3.00    --  102.12-125.00-150.00   52
 29  \w     76.00 106.00   0.50    3.00    --  102.12 -99.00 150.00   60
 30  \w    144.00 170.00   0.50    3.00    --  102.12  57.00   0.00   52
 31  \w     80.00 136.00   0.50    3.00    --  102.12 125.00  60.00  112
 32  \w     41.00 106.00   0.50    3.00    --  102.12 -99.00 -30.00  130
 33  \w    147.00 175.00   0.50    3.00    --  102.12  38.00  90.00   56
 34  \w     54.00 106.00   0.50    3.00    --  102.12 -99.00  90.00  104
 35  \w    109.00 175.00   0.50    3.00    --  102.12  38.00  60.00  132
 36  \w     78.00 103.00   0.50    3.00    --  102.12  77.00 120.00   50
 37  \w    123.00 149.00   0.50    3.00    --  102.12  77.00 120.00   52
 38  \w     35.00  60.00   0.50    3.00    --  102.12 -57.00-120.00   50
 39  \w     73.00 106.00   0.50    3.00    --  102.12 -99.00 120.00   66
 40  \w     70.00 105.00   0.50    3.00    --  102.12 -99.00 -90.00   70
 41  \w     81.00 106.00   0.50    3.00    --  102.12 -99.00-150.00   50
 42  \w     38.00  76.00   0.50    3.00    --  102.12 -99.00-150.00   76
 43  \w     62.00 106.00   0.50    3.00    --  102.12 -99.00  30.00   88
 44  \w    111.00 176.00   0.50    3.00    --  102.12  38.00 -30.00  130
 45  \w     51.00 106.00   0.50    3.00    --  102.12 -99.00   0.00  110
 46  \w     79.00 105.00   0.50    3.00    --  102.12 -99.00  60.00   52
 47  \w     35.00  71.00   0.50    3.00    --  102.12-125.00-120.00   72
 48  \w     91.00 117.00   0.50    3.00    --  102.12  38.00   0.00   52
 49  \w    129.00 155.00   0.50    3.00    --  102.12  38.00   0.00   52
 50  \w     44.00  75.00   0.50    3.00    --  102.12 -57.00  60.00   62
;
_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      0.0828070000
_diffrn_orient_matrix_UB_12      0.0169041000
_diffrn_orient_matrix_UB_13      -0.0222988000
_diffrn_orient_matrix_UB_21      -0.0072526000
_diffrn_orient_matrix_UB_22      0.0535294000
_diffrn_orient_matrix_UB_23      0.0248491000
_diffrn_orient_matrix_UB_31      0.0480700000
_diffrn_orient_matrix_UB_32      -0.0210435000
_diffrn_orient_matrix_UB_33      0.0453639000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0301
_diffrn_reflns_av_unetI/netI     0.0184
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -32
_diffrn_reflns_limit_l_max       34
_diffrn_reflns_limit_l_min       -33
_diffrn_reflns_number            187105
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.504
_diffrn_reflns_theta_min         2.359
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.177
_exptl_absorpt_correction_T_max  0.953
_exptl_absorpt_correction_T_min  0.844
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.89a (Rigaku Oxford Diffraction, 2023)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
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       plate
_exptl_crystal_F_000             5272
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: acetonitrile/toluene'
_exptl_crystal_size_max          0.239
_exptl_crystal_size_mid          0.121
_exptl_crystal_size_min          0.065
_refine_diff_density_max         0.874
_refine_diff_density_min         -0.512
_refine_diff_density_rms         0.068
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1172
_refine_ls_number_reflns         23051
_refine_ls_number_restraints     128
_refine_ls_restrained_S_all      1.068
_refine_ls_R_factor_all          0.0861
_refine_ls_R_factor_gt           0.0800
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1245P)^2^+13.0507P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2415
_refine_ls_wR_factor_ref         0.2465
_reflns_Friedel_coverage         0.000
_reflns_number_gt                20122
_reflns_number_total             23051
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc03970j2.cif
_cod_data_source_block           6a
_cod_depositor_comments
'Adding full bibliography for 1573035--1573038.cif.'
_cod_database_code               1573035
_shelxl_version_number           2014/6
_shelx_estimated_absorpt_t_max   0.937
_shelx_estimated_absorpt_t_min   0.795
_diffrn_oxdiff_digest_frames
;
012912599bc415933981b4d9977f54906e0428071f5
;
_diffrn_oxdiff_digest_hkl
;
01f9b084014b59ba8ffd03502598f48da86f49
;
_reflns_odcompleteness_completeness 99.92
_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 C(H,H,H,H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C7A-C6
 1.55 with sigma of 0.02
 C8A-C9
 1.5 with sigma of 0.015
3. Rigid body (RIGU) restrains
 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
 P211, F212, F213, F214, F215, F216, F217
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4. Others
 Sof(H6BC)=Sof(H6BD)=Sof(C7A)=Sof(H7AA)=Sof(H7AB)=Sof(C8A)=Sof(H8AA)=Sof(H8AB)=
 Sof(H9BC)=Sof(H9BD)=1-FVAR(1)
 Sof(H6AA)=Sof(H6AB)=Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(C8)=Sof(H8A)=Sof(H8B)=
 Sof(H9AA)=Sof(H9AB)=FVAR(1)
 Sof(P221)=Sof(F222)=Sof(F223)=Sof(F224)=Sof(F225)=Sof(F226)=Sof(F227)=1-FVAR(2)
 Sof(P211)=Sof(F212)=Sof(F213)=Sof(F214)=Sof(F215)=Sof(F216)=Sof(F217)=FVAR(2)
5.a Free rotating group:
 P221(F222,F223,F224,F225,F226,F227)
5.b Ternary CH refined with riding coordinates:
 C2(H2), C18(H18), 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)
5.c Secondary CH2 refined with riding coordinates:
 C4(H4A,H4B), N5(H5A,H5B), C6(H6AA,H6AB), C6(H6BC,H6BD), C7(H7A,H7B), C7A(H7AA,
 H7AB), C8(H8A,H8B), C8A(H8AA,H8AB), C9(H9AA,H9AB), C9(H9BC,H9BD), C10(H10C,
 H10D), C11(H11C,H11D), N12(H12E,H12F), C13(H13A,H13B), C15(H15A,H15B),
 C16(H16A,H16B), C17(H17A,H17B), C19(H19A,H19B), C21(H21A,H21B), C23(H23A,H23B),
  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)
5.d Aromatic/amide H refined with riding coordinates:
 C322(H322), C323(H323), C324(H324), C325(H325), C326(H326)
5.e Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C3(H3A,H3B,H3C), C303(H30A,H30B,H30C), C313(H31A,H31B,H31C),
 C327(H32A,H32B,H32C)
;
_shelx_res_checksum              97589
_shelx_hkl_checksum              65286
_shelx_fab_checksum              53757
_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 1.452
_oxdiff_exptl_absorpt_empirical_full_min 0.646