Metal cations switch geometry of β-cyclodextrin complexes
Kolařík, Václav; Hromádková, Aneta; Knirsch, Adam; Prucková, Zdeňka; Janovský, Petr; Rouchal, Michal; Ward, Jas S.; Rissanen, Kari; Vícha, Robert; Chemical Communications 61 (2025) 7077–7080; doi:10.1039/D5CC00868A

data_7134395
_publ_section_title
;
 Metal cations switch geometry of \b-cyclodextrin complexes
;
_journal_issue                   39
_journal_name_full               'Chemical Communications'
_journal_page_first              7077
_journal_page_last               7080
_journal_paper_doi               10.1039/D5CC00868A
_journal_volume                  61
_journal_year                    2025
_chemical_formula_moiety         'C22 H26 N, C2 H6 O, I'
_chemical_formula_sum            'C24 H32 I N O'
_chemical_formula_weight         477.40
_space_group_crystal_system      orthorhombic
_space_group_IT_number           61
_space_group_name_Hall           '-P 2ac 2ab'
_space_group_name_H-M_alt        'P b c a'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-11-22
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2025-02-06 deposited with the CCDC.	2025-04-10 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   12.4980(3)
_cell_length_b                   11.2458(2)
_cell_length_c                   31.4625(7)
_cell_measurement_reflns_used    12481
_cell_measurement_temperature    120.01(10)
_cell_measurement_theta_max      76.4180
_cell_measurement_theta_min      2.8080
_cell_volume                     4422.05(16)
_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)'
_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 0.999
_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   -119.00 -78.00   0.50    0.05    --  -51.51-145.00-115.00   82
  2  \w     -2.00  24.00   0.50    0.05    --  -51.51  19.00  69.00   52
  3  \w   -154.00-101.00   0.50    0.15    --  -87.61-107.00 132.00  106
  4  \w     66.00 153.00   0.50    0.15    --  102.08  19.00  69.00  174
  5  \w     33.00 106.00   0.50    0.15    --  102.08-107.00 132.00  146
  6  \w     47.00  72.00   0.50    0.15    --  102.08-126.00  52.00   50
  7  \w   -118.00 -41.00   0.50    0.05    --  -51.51 -77.00-180.00  154
  8  \w     -4.00  21.00   0.50    0.05    --  -51.51  19.00 150.00   50
  9  \w    -76.00  14.00   0.50    0.05    --  -51.51  77.00 120.00  180
 10  \w    -47.00 -21.00   0.50    0.15    --  -87.61  57.00   0.00   52
 11  \w    -44.00 -14.00   0.50    0.15    --  -87.61  57.00-120.00   60
 12  \w     38.00  64.00   0.50    0.15    --  102.08 -57.00 -30.00   52
 13  \w     36.00  73.00   0.50    0.15    --  102.08 -57.00 120.00   74
 14  \w     71.00 127.00   0.50    0.15    --  102.08 -77.00 120.00  112
 15  \w     38.00  68.00   0.50    0.15    --  102.08 -57.00  30.00   60
 16  \w     41.00  67.00   0.50    0.15    --  102.08 -77.00 120.00   52
 17  \w     28.00  74.00   0.50    0.15    --  102.08 -57.00-180.00   92
 18  \w     25.00  52.00   0.50    0.15    --  102.08 -38.00 -90.00   54
 19  \w     39.00  78.00   0.50    0.15    --  102.08 -57.00 -60.00   78
 20  \w     43.00  71.00   0.50    0.15    --  102.08 -57.00   0.00   56
 21  \w     26.00  52.00   0.50    0.15    --  102.08 -38.00 120.00   52
 22  \w     39.00  75.00   0.50    0.15    --  102.08 -57.00 150.00   72
 23  \w     93.00 162.00   0.50    0.15    --  102.08 125.00-150.00  138
 24  \w     26.00  51.00   0.50    0.15    --  102.08 -38.00  30.00   50
 25  \w     25.00  52.00   0.50    0.15    --  102.08 -38.00  90.00   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      -0.1192055000
_diffrn_orient_matrix_UB_12      0.0347045000
_diffrn_orient_matrix_UB_13      0.0006453000
_diffrn_orient_matrix_UB_21      -0.0017668000
_diffrn_orient_matrix_UB_22      -0.0009572000
_diffrn_orient_matrix_UB_23      -0.0489448000
_diffrn_orient_matrix_UB_31      -0.0312566000
_diffrn_orient_matrix_UB_32      -0.1325707000
_diffrn_orient_matrix_UB_33      0.0005292000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0665
_diffrn_reflns_av_unetI/netI     0.0433
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -39
_diffrn_reflns_number            32744
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.499
_diffrn_reflns_theta_min         2.809
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    11.462
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.114
_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    1.434
_exptl_crystal_description       plate
_exptl_crystal_F_000             1952
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: ethanol/pentane'
_exptl_crystal_size_max          0.215
_exptl_crystal_size_mid          0.094
_exptl_crystal_size_min          0.011
_refine_diff_density_max         1.199
_refine_diff_density_min         -1.592
_refine_diff_density_rms         0.143
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.209
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     308
_refine_ls_number_reflns         4505
_refine_ls_number_restraints     258
_refine_ls_restrained_S_all      1.176
_refine_ls_R_factor_all          0.0817
_refine_ls_R_factor_gt           0.0731
_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^)+66.0290P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1536
_refine_ls_wR_factor_ref         0.1569
_reflns_Friedel_coverage         0.000
_reflns_number_gt                3921
_reflns_number_total             4505
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cc00868a2.cif
_cod_data_source_block           6
_cod_depositor_comments
'Adding full bibliography for 7134393--7134395.cif.'
_cod_original_cell_volume        4422.06(18)
_cod_original_sg_symbol_H-M      Pbca
_cod_database_code               7134395
_shelxl_version_number           2014/6
_diffrn_oxdiff_digest_frames
;
018531e0cd0e6e5a000dda1c913afd550c02102f503
;
_diffrn_oxdiff_digest_hkl
;
01484905900d26b7b0f3b41019b1c92e20318f
;
_reflns_odcompleteness_completeness 99.55
_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
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Uiso/Uaniso restraints and constraints
C14 \\sim C15 \\sim C15A \\sim C16 \\sim C16A \\sim C17 \\sim C17A \\sim C18
\\sim C18A \\sim C19 \\sim C19A \\sim C20 \\sim C20A \\sim C21 \\sim C21A \\sim
C22 \\sim C22A \\sim C23 \\sim C23A: within 1.7A with sigma of 0.02 and sigma
for terminal atoms of 0.04
3. Others
 Sof(C20A)=Sof(H20A)=Sof(C15A)=Sof(H15C)=Sof(H15D)=Sof(C16A)=Sof(H16C)=
 Sof(H16D)=Sof(C17A)=Sof(H17C)=Sof(H17D)=Sof(C18A)=Sof(H18A)=Sof(C19A)=
 Sof(H19C)=Sof(H19D)=Sof(C21A)=Sof(H21A)=Sof(H21B)=Sof(C22A)=Sof(H22A)=
 Sof(C23A)=Sof(H23A)=Sof(H23B)=1-FVAR(1)
 Sof(C15)=Sof(H15A)=Sof(H15B)=Sof(C16)=Sof(H16A)=Sof(H16B)=Sof(C17)=Sof(H17A)=
 Sof(H17B)=Sof(C18)=Sof(H18)=Sof(C19)=Sof(H19A)=Sof(H19B)=Sof(C20)=Sof(H20)=
 Sof(C21)=Sof(H21C)=Sof(H21D)=Sof(C22)=Sof(H22)=Sof(C23)=Sof(H23C)=Sof(H23D)=
 FVAR(1)
4.a Free rotating group:
 C20A(C15A,C16A,C17A,C18A,C19A,C21A,C22A,C23A)
4.b Ternary CH refined with riding coordinates:
 C18(H18), C20(H20), C20A(H20A), C18A(H18A), C22A(H22A), C22(H22)
4.c Secondary CH2 refined with riding coordinates:
 C15(H15A,H15B), C16(H16A,H16B), C17(H17A,H17B), C19(H19A,H19B), C15A(H15C,
 H15D), C16A(H16C,H16D), C17A(H17C,H17D), C19A(H19C,H19D), C21A(H21A,H21B),
 C23A(H23A,H23B), C21(H21C,H21D), C23(H23C,H23D), C102(H10A,H10B)
4.d Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C5(H5), C6(H6), C9(H9), C10(H10), C12(H12), C13(H13)
4.e Idealised Me refined as rotating group:
 C7(H7A,H7B,H7C), C103(H10C,H10D,H10E)
4.f Idealised tetrahedral OH refined as rotating group:
 O101(H101)
;
_shelx_res_checksum              4057
_shelx_hkl_checksum              68064
_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 1.360
_oxdiff_exptl_absorpt_empirical_full_min 0.860