Enhancing iodine capture through a zirconium-based metal-organic cage featuring functionalized indole units.
Yang, Shungang; Wu, Zhengyang; Wang, Kang; Wei, Nan; Feng, Yanyan; Cui, Peng; Jiang, Yao; Chemical communications (Cambridge, England) 62 (2026) 1927–1931; doi:10.1039/d5cc05987a

data_7135506
_publ_section_title
;
 Enhancing iodine capture through a zirconium-based metal-organic cage
 featuring functionalized indole units.
;
_journal_issue                   6
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              1927
_journal_page_last               1931
_journal_paper_doi               10.1039/d5cc05987a
_journal_volume                  62
_journal_year                    2026
_chemical_formula_moiety
'C60 H51 N3 O20 Zr6, 2(Cl), 9.85[C4H8O2], 1[CH3CN], 1[H2O]'
_chemical_formula_sum            'C101.4 H134.8 Cl2 N4 O40.7 Zr6'
_chemical_formula_weight         2679.14
_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   mixed
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2025-12-15
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2025-12-16 deposited with the CCDC.	2025-12-17 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 92.428(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   23.1003(6)
_cell_length_b                   14.9053(3)
_cell_length_c                   27.9120(6)
_cell_measurement_reflns_used    26860
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      57.0460
_cell_measurement_theta_min      1.8660
_cell_volume                     9601.9(4)
_computing_cell_refinement       'CrysAlisPro 1.171.43.141a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.141a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.141a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2025/1 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix-Arc 150'
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.990
_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      6.00  33.00   0.50    0.89    --   38.00 -77.00 -96.44   54
  2  \w    -11.00  15.00   0.50    0.89    --   30.00 -39.00  51.62   52
  3  \w      9.00  35.00   0.50    0.89    --   42.00 -88.00 100.94   52
  4  \w    -22.00   7.00   0.50    0.89    --   22.00 -30.00 152.01   58
  5  \w     -7.00  18.00   0.50    0.89    --   -0.32  97.00  36.99   50
  6  \w     15.00  41.00   0.50    0.89    --   -0.32  34.00 165.44   52
  7  \w    -75.00 -50.00   0.50    0.89    --  -42.00 140.00  75.06   50
  8  \w     -7.00  19.00   0.50    0.89    --   -0.32  97.00  58.39   52
  9  \w     13.00  38.00   0.50    0.89    --   -0.32  54.00  12.31   50
 10  \w     18.00  31.00   0.50    0.89    --  -14.00  26.00 -76.91   26
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'ROD, Synergy Custom DW system, HyPix-Arc 150'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0227538000
_diffrn_orient_matrix_UB_12      0.0163193000
_diffrn_orient_matrix_UB_13      0.0154765000
_diffrn_orient_matrix_UB_21      0.0109172000
_diffrn_orient_matrix_UB_22      -0.0442178000
_diffrn_orient_matrix_UB_23      0.0028613000
_diffrn_orient_matrix_UB_31      0.0175389000
_diffrn_orient_matrix_UB_32      0.0063153000
_diffrn_orient_matrix_UB_33      -0.0200009000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0397
_diffrn_reflns_av_unetI/netI     0.0461
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       31
_diffrn_reflns_limit_h_min       -31
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            84017
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         28.700
_diffrn_reflns_theta_min         2.000
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Mo) X-ray Source'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.784
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.82799
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.141a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.853
_exptl_crystal_description       block
_exptl_crystal_F_000             5483
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.1
_refine_diff_density_max         1.351
_refine_diff_density_min         -0.586
_refine_diff_density_rms         0.103
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.034
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1067
_refine_ls_number_reflns         24541
_refine_ls_number_restraints     986
_refine_ls_restrained_S_all      1.020
_refine_ls_R_factor_all          0.0815
_refine_ls_R_factor_gt           0.0553
_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^)+(0.0801P)^2^+15.1385P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1500
_refine_ls_wR_factor_ref         0.1687
_reflns_Friedel_coverage         0.000
_reflns_number_gt                16424
_reflns_number_total             24541
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cc05987a2.cif
_cod_data_source_block           9769-a2
_cod_original_formula_sum        'C101.40 H134.80 Cl2 N4 O40.70 Zr6'
_cod_database_code               7135506
_shelx_shelxl_version_number     2025/1
_shelx_estimated_absorpt_t_max   0.926
_shelx_estimated_absorpt_t_min   0.905
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All O(H) groups
2. Rigid bond restraints
 N2, C15
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.002
3. Uiso/Uaniso restraints and constraints
Zr4 \\sim Zr5 \\sim C1 \\sim O3 \\sim O4 \\sim N1 \\sim C2 \\sim C3 \\sim C4
\\sim C5 \\sim C6 \\sim C7 \\sim C8 \\sim C9 \\sim C10 \\sim O3A \\sim O4A
\\sim N1A \\sim C2A \\sim C3A \\sim C4A \\sim C5A \\sim C6A \\sim C7A \\sim C8A
\\sim C9A \\sim C10A: within 2A with sigma of 0.01 and sigma for terminal atoms
of 0.02 within 2A
Zr5 \\sim C51 \\sim C52 \\sim C53 \\sim C54 \\sim C55 \\sim C51A \\sim C52A
\\sim C53A \\sim C54A \\sim C55A: within 2A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 2A
C21 \\sim C30 \\sim N3 \\sim C22 \\sim C23 \\sim C24 \\sim C25 \\sim C26 \\sim
C27 \\sim C28 \\sim C29 \\sim N3A \\sim C22A \\sim C23A \\sim C24A \\sim C25A
\\sim C26A \\sim C27A \\sim C28A \\sim C29A: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
Cl1 \\sim Cl1A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
Uanis(Cl1A) \\sim Ueq, Uanis(Cl1) \\sim Ueq: with sigma of 0.02 and sigma for
terminal atoms of 0.04
4. Same fragment restrains
{Zr5, C51A, C52A, C53A, C54A, C55A} sigma for 1-2: 0.01, 1-3: 0.01
as in
{Zr5, C51, C52, C53, C54, C55}
{N1A, C2A, C3A, C4A, C5A, C6A, C7A, C8A, C9A} sigma for 1-2: 0.01, 1-3: 0.01
as in
{N1, C2, C3, C4, C5, C6, C7, C8, C9}
{N3A, C22A, C23A, C24A, C25A, C26A, C27A, C28A, C29A} sigma for 1-2: 0.01, 1-3:
0.01
as in
{N3, C22, C23, C24, C25, C26, C27, C28, C29}
5. Others
 Sof(O3A)=Sof(O4A)=Sof(N1A)=Sof(H1A)=Sof(C2A)=Sof(C3A)=Sof(H3AA)=Sof(C4A)=
 Sof(C5A)=Sof(C6A)=Sof(H6A)=Sof(C7A)=Sof(H7A)=Sof(C8A)=Sof(C9A)=Sof(H9A)=
 Sof(C10A)=1-FVAR(1)
 Sof(O3)=Sof(O4)=Sof(N1)=Sof(H1)=Sof(C2)=Sof(C3)=Sof(H3)=Sof(C4)=Sof(C5)=
 Sof(C6)=Sof(H6)=Sof(C7)=Sof(H7)=Sof(C8)=Sof(C9)=Sof(H9)=Sof(C10)=FVAR(1)
 Sof(N3A)=Sof(H3AB)=Sof(C22A)=Sof(C23A)=Sof(H23A)=Sof(C24A)=Sof(C25A)=
 Sof(C26A)=Sof(H26A)=Sof(C27A)=Sof(H27A)=Sof(C28A)=Sof(C29A)=Sof(H29A)=1-FVAR(2)
 Sof(N3)=Sof(H3A)=Sof(C22)=Sof(C23)=Sof(H23)=Sof(C24)=Sof(C25)=Sof(C26)=
 Sof(H26)=Sof(C27)=Sof(H27)=Sof(C28)=Sof(C29)=Sof(H29)=FVAR(2)
 Sof(Cl1A)=1-FVAR(3)
 Sof(Cl1)=FVAR(3)
 Sof(C51A)=Sof(H51A)=Sof(C52A)=Sof(H52A)=Sof(C53A)=Sof(H53A)=Sof(C54A)=
 Sof(H54A)=Sof(C55A)=Sof(H55A)=1-FVAR(4)
 Sof(C51)=Sof(H51)=Sof(C52)=Sof(H52)=Sof(C53)=Sof(H53)=Sof(C54)=Sof(H54)=
 Sof(C55)=Sof(H55)=FVAR(4)
6.a Riding coordinates:
 O14(H14), O15(H15), O16(H16), O18(H18), O19(H19), O20(H20)
6.b Aromatic/amide H refined with riding coordinates:
 C51(H51), C52(H52), C53(H53), C54(H54), C55(H55), N2(H2), C13(H13), C16(H16A),
  C17(H17), C19(H19A), C31(H31), C32(H32), C33(H33), C34(H34), C35(H35),
 C36(H36), C37(H37), C38(H38), C39(H39), C40(H40), C41(H41), C42(H42), C43(H43),
  C44(H44), C45(H45), C46(H46), C47(H47), C48(H48), C49(H49), C50(H50),
 C56(H56), C57(H57), C58(H58), C59(H59), C60(H60), N1(H1), C3(H3), C6(H6),
 C7(H7), C9(H9), N3(H3A), C23(H23), C26(H26), C27(H27), C29(H29), N1A(H1A),
 C3A(H3AA), C6A(H6A), C7A(H7A), C9A(H9A), N3A(H3AB), C23A(H23A), C26A(H26A),
 C27A(H27A), C29A(H29A), C51A(H51A), C52A(H52A), C53A(H53A), C54A(H54A),
 C55A(H55A)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 2011 electrons were 
found in a volume of 4154\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
19.7[C4H8O2], 2[CH3CN], 2[H2O] per Asymmetric Unit 
which account for 2019 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              95799
_shelx_fab_checksum              41698
_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 1.544
_oxdiff_exptl_absorpt_empirical_full_min 0.683