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_1573036
_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, C22 H44 N2, 2(F6 P), 5.75(H2 O)'
_chemical_formula_sum            'C58 H91.5 F12 N26 O17.75 P2'
_chemical_formula_weight         1727.01
_space_group_crystal_system      orthorhombic
_space_group_IT_number           40
_space_group_name_Hall           'A 2 -2a'
_space_group_name_H-M_alt        'A m a 2'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-09-18
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2024-09-18 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            4
_cell_length_a                   17.47878(10)
_cell_length_b                   27.72924(12)
_cell_length_c                   15.22975(7)
_cell_measurement_reflns_used    57423
_cell_measurement_temperature    298(2)
_cell_measurement_theta_max      76.4810
_cell_measurement_theta_min      3.1720
_cell_volume                     7381.45(6)
_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      air
_diffrn_ambient_temperature      298(2)
_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 1.000
_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     14.00  41.00   0.50    0.40    --   46.00  91.00 -92.06   54
  2  \w   -119.00 -27.00   0.50    0.40    --  -51.89 -77.00-150.00  184
  3  \w     -4.00  25.00   0.50    0.40    --  -51.89  19.00-120.00   58
  4  \w     -4.00  25.00   0.50    0.40    --  -51.89  19.00   0.00   58
  5  \w     19.00 104.00   0.50    0.40    --   51.89-125.00   0.00  170
  6  \w   -129.00 -37.00   0.50    0.40    --  -62.00 -77.00 136.44  184
  7  \w   -148.00 -58.00   0.50    0.40    --  -78.00 -69.00  34.84  180
  8  \w   -155.00 -86.00   0.50    1.50    --  -87.58 -99.00 120.00  138
  9  \w   -112.00 -20.00   0.50    1.50    --  -87.58  77.00  90.00  184
 10  \w   -112.00 -20.00   0.50    1.50    --  -87.58  77.00-150.00  184
 11  \w    -54.00 -13.00   0.50    1.50    --  -87.58  57.00   0.00   82
 12  \w   -168.00 -77.00   0.50    1.50    --  -95.50 -62.00-174.58  182
 13  \w     88.00 176.00   0.50    1.50    --  102.12  38.00 120.00  176
 14  \w     80.00 173.00   0.50    1.50    --  102.12 125.00-120.00  186
 15  \w     25.00  52.00   0.50    1.50    --  102.12 -38.00-120.00   54
 16  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00-120.00  142
 17  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00 150.00  142
 18  \w     88.00 176.00   0.50    1.50    --  102.12  38.00 150.00  176
 19  \w     25.00  52.00   0.50    1.50    --  102.12 -38.00 -60.00   54
 20  \w     63.00 176.00   0.50    1.50    --  102.12  19.00  60.00  226
 21  \w     28.00  79.00   0.50    1.50    --  102.12 -57.00 150.00  102
 22  \w     32.00 111.00   0.50    1.50    --  102.12-125.00   0.00  158
 23  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00  90.00  142
 24  \w     32.00 111.00   0.50    1.50    --  102.12-125.00  30.00  158
 25  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00  30.00  142
 26  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00  60.00  142
 27  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00 -90.00  142
 28  \w     28.00  79.00   0.50    1.50    --  102.12 -57.00   0.00  102
 29  \w     32.00 111.00   0.50    1.50    --  102.12-125.00-120.00  158
 30  \w     25.00  52.00   0.50    1.50    --  102.12 -38.00-150.00   54
 31  \w     35.00 106.00   0.50    1.50    --  102.12 -99.00 -60.00  142
 32  \w     25.00  52.00   0.50    1.50    --  102.12 -38.00 150.00   54
 33  \w     28.00  79.00   0.50    1.50    --  102.12 -57.00 -90.00  102
 34  \w     28.00  79.00   0.50    1.50    --  102.12 -57.00-150.00  102
 35  \w     88.00 176.00   0.50    1.50    --  102.12  38.00  90.00  176
 36  \w     35.00 127.00   0.50    1.50    --  102.12 -77.00 150.00  184
 37  \w     88.00 176.00   0.50    1.50    --  102.12  38.00-150.00  176
 38  \w     14.00  41.00   0.50    0.40    --   46.00  91.00 -12.23   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      -0.0009372000
_diffrn_orient_matrix_UB_12      -0.0182524000
_diffrn_orient_matrix_UB_13      0.0955312000
_diffrn_orient_matrix_UB_21      -0.0881454000
_diffrn_orient_matrix_UB_22      0.0009593000
_diffrn_orient_matrix_UB_23      -0.0005575000
_diffrn_orient_matrix_UB_31      -0.0012609000
_diffrn_orient_matrix_UB_32      -0.0524575000
_diffrn_orient_matrix_UB_33      -0.0332202000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0249
_diffrn_reflns_av_unetI/netI     0.0111
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       29
_diffrn_reflns_limit_k_min       -34
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            74539
_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         74.502
_diffrn_reflns_theta_min         3.187
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.566
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.91582
_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    1.554
_exptl_crystal_description       block
_exptl_crystal_F_000             3606
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: Acetonitrile/water'
_exptl_crystal_size_max          0.163
_exptl_crystal_size_mid          0.086
_exptl_crystal_size_min          0.051
_refine_diff_density_max         0.655
_refine_diff_density_min         -0.324
_refine_diff_density_rms         0.057
_refine_ls_abs_structure_details
;
 Flack x determined using 3643 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.002(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.040
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     689
_refine_ls_number_reflns         7788
_refine_ls_number_restraints     38
_refine_ls_restrained_S_all      1.046
_refine_ls_R_factor_all          0.0387
_refine_ls_R_factor_gt           0.0383
_refine_ls_shift/su_max          0.004
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0766P)^2^+4.5628P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1092
_refine_ls_wR_factor_ref         0.1096
_reflns_Friedel_coverage         0.922
_reflns_Friedel_fraction_full    0.999
_reflns_Friedel_fraction_max     0.996
_reflns_number_gt                7679
_reflns_number_total             7788
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc03970j2.cif
_cod_data_source_block           6b
_cod_depositor_comments
'Adding full bibliography for 1573035--1573038.cif.'
_cod_original_formula_sum        'C58 H91.50 F12 N26 O17.75 P2'
_cod_database_code               1573036
_shelxl_version_number           2014/6
_shelx_estimated_absorpt_t_max   0.924
_shelx_estimated_absorpt_t_min   0.784
_diffrn_oxdiff_digest_frames
;
01de2715c855156fc377cccee391bee22105104eec3
;
_diffrn_oxdiff_digest_hkl
;
01659cb8d32a4ddcde798744813a382b6fe36a
;
_reflns_odcompleteness_completeness 100.00
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     74.33
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, {H5A,H5B} of O231, All C(H,H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, {H27A,H27B} of O271, {H22C,H22D} of O221, {H21A,H21B}
  of O211, {H25A,H25B} of O251, {H28A,H28B} of O281, {H23A,H23B} of O231, {H24C,
  H24D} of O241, {H20C,H20D} of O201, {H26A,H26B} of O261
2. Restrained distances
 H20C-O211_$1
 1.97 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C2) = Uanis(C3)
Uanis(O281) = Uanis(O261)
Uanis(O251) = Uanis(O271)
4. Rigid body (RIGU) restrains
5. Others
 Fixed Sof: C1(0.5) H1A(0.5) H1B(0.5) H1C(0.5) C2(0.5) H2(0.5) C3(0.5)
 H3A(0.5) H3B(0.5) H3C(0.5) C4(0.5) H4A(0.5) H4B(0.5) N5(0.5) C6(0.5) H6A(0.5)
 H6B(0.5) C7(0.5) H7A(0.5) H7B(0.5) C8(0.5) H8A(0.5) H8B(0.5) C9(0.5) H9A(0.5)
 H9B(0.5) C10(0.5) H10A(0.5) H10B(0.5) C11(0.5) H11A(0.5) H11B(0.5) N12(0.5)
 H12A(0.5) H12B(0.5) H13A(0.5) H13B(0.5) C14(0.5) H14A(0.5) H14B(0.5) C16(0.5)
 H16A(0.5) H16B(0.5) C17(0.5) H17A(0.5) H17B(0.5) C18(0.5) H18A(0.5) H18B(0.5)
 C19(0.5) H19(0.5) C20(0.5) H20A(0.5) H20B(0.5) C21(0.5) H21(0.5) C22(0.5)
 H22A(0.5) H22B(0.5) C23(0.5) H23(0.5) C24(0.5) H24A(0.5) H24B(0.5) O201(0.5)
 H20C(0.5) H20D(0.5) O211(0.5) H21A(0.5) H21B(0.5) O221(0.25) H22C(0.25)
 H22D(0.25) O231(0.25) H5A(0.5) H5B(0.5) H23A(0.25) H23B(0.25) O241(0.5)
 H24C(0.5) H24D(0.5) O251(0.25) H25A(0.25) H25B(0.25) O261(0.25) H26A(0.25)
 H26B(0.25) O271(0.125) H27A(0.125) H27B(0.125) O281(0.25) H28A(0.25) H28B(0.25)
 Fixed X: H22C(0.46586) H22D(0.50364) H5A(0.25177) H5B(0.310881) H23A(0.4042)
 H23B(0.327361) H25A(0.667741) H25B(0.64345) H26A(0.54614) H26B(0.603741)
 H27A(0.504709) H27B(0.46098) H28A(0.599509) H28B(0.5303)
 Fixed Y: H22C(0.59084) H22D(0.60171) H5A(0.87596) H5B(0.86683) H23A(0.57038)
 H23B(0.556789) H25A(0.68209) H25B(0.64666) H26A(0.5402) H26B(0.55254)
 H27A(0.476159) H27B(0.515321) H28A(0.542729) H28B(0.55248)
 Fixed Z: H22C(0.39735) H22D(0.317141) H5A(0.87464) H5B(0.80297)
 H23A(0.409619) H23B(0.42699) H25A(0.55282) H25B(0.49599) H26A(0.509419)
 H26B(0.571321) H27A(0.40821) H27B(0.43188) H28A(0.617701) H28B(0.65696)
6.a Free rotating group:
 O201(H20C,H20D), O211(H21A,H21B), O241(H24C,H24D)
6.b Ternary CH refined with riding coordinates:
 C2(H2), C19(H19), C21(H21), C23(H23), C54(H54), C66(H66), C70(H70), C78(H78),
 C82(H82), C94(H94)
6.c Secondary CH2 refined with riding coordinates:
 C4(H4A,H4B), C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B), C10(H10A,
 H10B), C11(H11A,H11B), N12(H12A,H12B), C13(H13A,H13B), C14(H14A,H14B),
 C16(H16A,H16B), C17(H17A,H17B), C18(H18A,H18B), C20(H20A,H20B), C22(H22A,H22B),
  C24(H24A,H24B), C61(H61A,H61B), C62(H62A,H62B), C73(H73A,H73B), C74(H74A,
 H74B), C85(H85A,H85B), C86(H86A,H86B)
6.d Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C3(H3A,H3B,H3C)
;
_shelx_res_checksum              85705
_shelx_hkl_checksum              13484
_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 1.362
_oxdiff_exptl_absorpt_empirical_full_min 0.798