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_7134393
_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         'C19 H28 N, C6 H6, I'
_chemical_formula_sum            'C25 H34 I N'
_chemical_formula_weight         475.43
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-10-20
_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                 97.198(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   17.4227(6)
_cell_length_b                   9.8519(3)
_cell_length_c                   13.1335(3)
_cell_measurement_reflns_used    7982
_cell_measurement_temperature    120.00(10)
_cell_measurement_theta_max      76.4330
_cell_measurement_theta_min      2.6510
_cell_volume                     2236.56(12)
_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      120.00(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 0.996
_diffrn_measured_fraction_theta_max 0.994
_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    -11.00  14.00   0.50    0.20    --   51.64 -85.00 113.00   50
  2  \w   -105.00 -80.00   0.50    0.80    --  -87.58 -85.00 113.00   50
  3  \w   -152.00-125.00   0.50    0.80    --  -87.58 -85.00 113.00   54
  4  \w    -69.00 -44.00   0.50    0.80    --  -87.58  85.00-126.00   50
  5  \w     37.00 127.00   0.50    0.80    --  102.12 -85.00 113.00  180
  6  \w     86.00 127.00   0.50    0.80    --  102.12  85.00-126.00   82
  7  \w    -80.00 -37.00   0.50    0.20    --  -51.51  85.00-126.00   86
  8  \w   -122.00 -75.00   0.50    0.20    --  -51.51-125.00 -90.00   94
  9  \w     -2.00  25.00   0.50    0.20    --  -51.51  19.00-180.00   54
 10  \w    -27.00  15.00   0.50    0.20    --  -51.51  85.00-126.00   84
 11  \w    -21.00  29.00   0.50    0.20    --   51.64 -19.00-180.00  100
 12  \w     22.00  76.00   0.50    0.20    --   51.64 -85.00 113.00  108
 13  \w    -53.00 -23.00   0.50    0.80    --  -87.58  57.00-180.00   60
 14  \w    -47.00 -16.00   0.50    0.80    --  -87.58  57.00-150.00   62
 15  \w   -106.00 -21.00   0.50    0.80    --  -87.58  77.00  60.00  170
 16  \w     25.00  50.00   0.50    0.80    --  102.12 -38.00 150.00   50
 17  \w     31.00  67.00   0.50    0.80    --  102.12 -57.00 -60.00   72
 18  \w     37.00  63.00   0.50    0.80    --  102.12 -57.00 150.00   52
 19  \w     25.00  52.00   0.50    0.80    --  102.12 -38.00  30.00   54
 20  \w     36.00  64.00   0.50    0.80    --  102.12 -77.00 -90.00   56
 21  \w     25.00  50.00   0.50    0.80    --  102.12 -38.00 120.00   50
 22  \w     58.00  93.00   0.50    0.80    --  102.12-125.00 -90.00   70
 23  \w     71.00 169.00   0.50    0.80    --  102.12  19.00 150.00  196
 24  \w     26.00  51.00   0.50    0.80    --  102.12 -38.00-180.00   50
 25  \w     47.00  74.00   0.50    0.80    --  102.12 -57.00   0.00   54
 26  \w     29.00  62.00   0.50    0.80    --  102.12 -57.00 120.00   66
 27  \w     31.00  73.00   0.50    0.80    --  102.12 -57.00-180.00   84
 28  \w     74.00 114.00   0.50    0.80    --  102.12 -77.00 -90.00   80
 29  \w     26.00  51.00   0.50    0.80    --  102.12 -38.00 -30.00   50
 30  \w     36.00  80.00   0.50    0.80    --  102.12 -99.00-180.00   88
 31  \w     29.00  61.00   0.50    0.80    --  102.12 -57.00 -90.00   64
;
_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      -0.0026841000
_diffrn_orient_matrix_UB_12      -0.1370738000
_diffrn_orient_matrix_UB_13      0.0559904000
_diffrn_orient_matrix_UB_21      -0.0878288000
_diffrn_orient_matrix_UB_22      0.0165328000
_diffrn_orient_matrix_UB_23      0.0008663000
_diffrn_orient_matrix_UB_31      -0.0148192000
_diffrn_orient_matrix_UB_32      -0.0734336000
_diffrn_orient_matrix_UB_33      -0.1041390000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0588
_diffrn_reflns_av_unetI/netI     0.0538
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.994
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            18421
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.994
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.429
_diffrn_reflns_theta_min         2.556
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    11.293
_exptl_absorpt_correction_T_max  0.935
_exptl_absorpt_correction_T_min  0.464
_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    1.412
_exptl_crystal_description       plate
_exptl_crystal_F_000             976
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: pyridine/benzene'
_exptl_crystal_size_max          0.148
_exptl_crystal_size_mid          0.043
_exptl_crystal_size_min          0.006
_refine_diff_density_max         2.097
_refine_diff_density_min         -1.897
_refine_diff_density_rms         0.131
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.077
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     329
_refine_ls_number_reflns         4543
_refine_ls_number_restraints     126
_refine_ls_restrained_S_all      1.065
_refine_ls_R_factor_all          0.0664
_refine_ls_R_factor_gt           0.0522
_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^)+(0.0843P)^2^+3.4224P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1389
_refine_ls_wR_factor_ref         0.1468
_reflns_Friedel_coverage         0.000
_reflns_number_gt                3608
_reflns_number_total             4543
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cc00868a2.cif
_cod_data_source_block           1
_cod_depositor_comments
'Adding full bibliography for 7134393--7134395.cif.'
_cod_original_cell_volume        2236.54(11)
_cod_original_sg_symbol_H-M      P21/c
_cod_database_code               7134393
_shelxl_version_number           2014/6
_shelx_estimated_absorpt_t_max   0.935
_shelx_estimated_absorpt_t_min   0.286
_diffrn_oxdiff_digest_frames
;
017b048c49c7c6198a0398e9a4895a7fec024202c6d
;
_diffrn_oxdiff_digest_hkl
;
01cf682ee28a7068b93845f84eb6973df1fa12
;
_reflns_odcompleteness_completeness 99.26
_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
2. Rigid body (RIGU) restrains
 C12, C12A, C13, C13A, C14, C14A, C15, C15A, C16, C16A, C17, C17A, C18, C18A,
 C19, C19A, C20, C20A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
3. Others
 Sof(C12A)=Sof(H12C)=Sof(H12D)=Sof(C13A)=Sof(H13C)=Sof(H13D)=Sof(C14A)=
 Sof(H14C)=Sof(H14D)=Sof(C15A)=Sof(H15A)=Sof(C16A)=Sof(H16C)=Sof(H16D)=
 Sof(C17A)=Sof(H17A)=Sof(C18A)=Sof(H18C)=Sof(H18D)=Sof(C19A)=Sof(H19A)=
 Sof(C20A)=Sof(H20C)=Sof(H20D)=1-FVAR(1)
 Sof(C12)=Sof(H12A)=Sof(H12B)=Sof(C13)=Sof(H13A)=Sof(H13B)=Sof(C14)=Sof(H14A)=
 Sof(H14B)=Sof(C15)=Sof(H15)=Sof(C16)=Sof(H16A)=Sof(H16B)=Sof(C17)=Sof(H17)=
 Sof(C18)=Sof(H18A)=Sof(H18B)=Sof(C19)=Sof(H19)=Sof(C20)=Sof(H20A)=Sof(H20B)=
 FVAR(1)
4.a Ternary CH refined with riding coordinates:
 C15(H15), C15A(H15A), C17(H17), C17A(H17A), C19(H19), C19A(H19A)
4.b Secondary CH2 refined with riding coordinates:
 C12(H12A,H12B), C12A(H12C,H12D), C13(H13A,H13B), C13A(H13C,H13D), C14(H14A,
 H14B), C14A(H14C,H14D), C16(H16A,H16B), C16A(H16C,H16D), C18(H18A,H18B),
 C18A(H18C,H18D), C20(H20A,H20B), C20A(H20C,H20D)
4.c Aromatic/amide H refined with riding coordinates:
 C6(H6), C7(H7), C9(H9), C10(H10), C101(H101), C102(H102), C103(H103),
 C104(H104), C105(H105), C106(H106)
4.d Idealised Me refined as rotating group:
 C2(H2A,H2B,H2C), C3(H3A,H3B,H3C), C4(H4A,H4B,H4C)
;
_shelx_res_checksum              74683
_shelx_hkl_checksum              19579
_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 1.716
_oxdiff_exptl_absorpt_empirical_full_min 0.754