Precise heteroatom engineering for iodine capture promotion in porous organic cages.
Liu, Chao; Du, Ziwei; Ding, Xu; Wang, Zhixuan; Cao, Lili; Zhou, Ziwen; Chen, Jia; Zhang, Ning; Chemical communications (Cambridge, England) 61 (2025) 19076–19079; doi:10.1039/d5cc04036a

data_7135104
_publ_section_title
;
 Precise heteroatom engineering for iodine capture promotion in porous
 organic cages.
;
_journal_issue                   96
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              19076
_journal_page_last               19079
_journal_paper_doi               10.1039/d5cc04036a
_journal_volume                  61
_journal_year                    2025
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C102 H96 N18 Se3, 3[CH2Cl2]'
_chemical_formula_sum            'C105 H102 Cl6 N18 Se3'
_chemical_formula_weight         2065.62
_space_group_crystal_system      trigonal
_space_group_IT_number           144
_space_group_name_Hall           'P 31'
_space_group_name_H-M_alt        'P 31'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2025-10-17
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2025-10-17 deposited with the CCDC.	2025-10-23 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                120
_cell_formula_units_Z            3
_cell_length_a                   19.6339(10)
_cell_length_b                   19.6339(10)
_cell_length_c                   26.1675(12)
_cell_measurement_reflns_used    5386
_cell_measurement_temperature    298(2)
_cell_measurement_theta_max      18.69
_cell_measurement_theta_min      2.33
_cell_volume                     8735.9(7)
_computing_cell_refinement       'SAINT V8.40B (Bruker, 2016)'
_computing_data_collection       'Bruker D8 Venture diffractometer'
_computing_data_reduction        'SAINT V8.40B (Bruker, 2016)'
_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  (Sheldrick, 2015)'
_diffrn_ambient_temperature      298(2)
_diffrn_detector                 'Bruker PHOTON-II area detector'
_diffrn_detector_area_resol_mean 7.4
_diffrn_detector_type            'CMOS-PHOTONII area detector'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker PHOTON-II area detector'
_diffrn_measurement_method       'phi and omega scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0975
_diffrn_reflns_av_unetI/netI     0.1846
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -22
_diffrn_reflns_limit_l_max       29
_diffrn_reflns_limit_l_min       -31
_diffrn_reflns_number            44292
_diffrn_reflns_point_group_measured_fraction_full 0.965
_diffrn_reflns_point_group_measured_fraction_max 0.965
_diffrn_reflns_theta_full        24.995
_diffrn_reflns_theta_max         24.995
_diffrn_reflns_theta_min         2.075
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_target            Mo
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.134
_exptl_absorpt_correction_type   none
_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    1.178
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             3186
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.462
_refine_diff_density_min         -0.300
_refine_diff_density_rms         0.063
_refine_ls_abs_structure_details
;
 Flack x determined using 2645 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.059(10)
_refine_ls_extinction_coef       0.0017(5)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2025/1 (Sheldrick 2025)'
_refine_ls_goodness_of_fit_ref   0.987
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1438
_refine_ls_number_reflns         19779
_refine_ls_number_restraints     1781
_refine_ls_restrained_S_all      0.984
_refine_ls_R_factor_all          0.1996
_refine_ls_R_factor_gt           0.0866
_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^)+(0.1271P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2189
_refine_ls_wR_factor_ref         0.2805
_reflns_Friedel_coverage         0.932
_reflns_Friedel_fraction_full    0.931
_reflns_Friedel_fraction_max     0.931
_reflns_number_gt                8125
_reflns_number_total             19779
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cc04036a2.cif
_cod_data_source_block           a
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_diffrn_radiation_probe' value 'X-ray' was changed to
'x-ray' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 

 Adding full bibliography for 7135104.cif.
;
_cod_original_cell_volume        8735.9(10)
_cod_database_code               7135104
_shelx_shelxl_version_number     2025/1
_shelx_estimated_absorpt_t_max   0.895
_shelx_estimated_absorpt_t_min   0.867
_exptl_crystal_mounting_method
;
 Crystals were removed from the crystallisation vial and immediately coated
 with PDMS (polydimethylsiloxane/Dimethicone, CAS: 9006-65-9 on a glass slide.
 A suitable single crystal was selected and mounted on a glass fiber using
 vacuum silicone grease as adhesive. The glass fiber with single crystal was
 mounted on copper pin with solid paraffin. Operator: DJ_Tokyo.
;
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
2. Restrained distances
 C28-C27 = C28-C23 = C24-C23 = C25-C24 = C26-C25
 1.395 with sigma of 0.01
 C47-C46 = C46-C45 = C50-C45 = C50-C49 = C48-C47 = C49-C48
 1.395 with sigma of 0.01
 C81-C80 = C80-C79 = C84-C79 = C84-C83 = C83-C82 = C82-C81
 1.54 with sigma of 0.01
 C101-C100 = C102-C101 = C97-C102 = C98-C97 = C99-C98 = C99-C100
 1.54 with sigma of 0.01
 C94-C93 = C93-C92 = C95-C94 = C96-C95 = C96-C91 = C92-C91
 1.54 with sigma of 0.01
 C23-C25 \\sim C24-C26 \\sim C25-C27 \\sim C26-C28 \\sim C27-C23 \\sim C28-C24
 with sigma of 0.01
3. Restrained planarity
 C29, C37, Se2A, N3A, N4A, C23A, C24A, C25A, C26A, C27A, C28A
 with sigma of 0.01
 C29, C37, Se2, N3, N4, C23, C24, C25, C26, C27, C28
 with sigma of 0.01
 C29, C37, Se2B, N3B, N4B, C23B, C24B, C25B, C26B, C27B, C28B
 with sigma of 0.01
 C51, C59, Se3A, N5A, N6A, C45A, C46A, C47A, C48A, C49A, C50A
 with sigma of 0.01
 Se1A, N1A, N2A, C1A, C2A, C3A, C4A, C5A, C6A, C7, C15
 with sigma of 0.01
 Se1, N1, N2, C1, C2, C3, C4, C5, C6, C7, C15
 with sigma of 0.01
4. Uiso/Uaniso restraints and constraints
C29 \\sim C37 \\sim Se2 \\sim N3 \\sim N4 \\sim C23 \\sim C24 \\sim C25 \\sim
C26 \\sim C27 \\sim C28 \\sim Se2A \\sim N3A \\sim N4A \\sim C23A \\sim C24A
\\sim C25A \\sim C26A \\sim C27A \\sim C28A \\sim Se2B \\sim N3B \\sim N4B
\\sim C23B \\sim C24B \\sim C25B \\sim C26B \\sim C27B \\sim C28B: within 2A
with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
C51 \\sim C59 \\sim Se3 \\sim N5 \\sim N6 \\sim C45 \\sim C46 \\sim C47 \\sim
C48 \\sim C49 \\sim C50 \\sim Se3A \\sim N5A \\sim N6A \\sim C45A \\sim C46A
\\sim C47A \\sim C48A \\sim C49A \\sim C50A: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
N13 \\sim N14 \\sim C85 \\sim C86 \\sim C87 \\sim C88 \\sim C89 \\sim C90:
within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
N7 \\sim N8 \\sim C67 \\sim C68 \\sim C69 \\sim C70 \\sim C71 \\sim C72: within
2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
Se1 \\sim N1 \\sim N2 \\sim C1 \\sim C2 \\sim C3 \\sim C4 \\sim C5 \\sim C6
\\sim Se1A \\sim N1A \\sim N2A \\sim C1A \\sim C2A \\sim C3A \\sim C4A \\sim
C5A \\sim C6A \\sim C7 \\sim C15: within 2A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 2A
C101 \\sim C97 \\sim C98 \\sim C100 \\sim C102 \\sim C99 \\sim N18 \\sim N17
\\sim C22 \\sim C66: within 2A with sigma of 0.01 and sigma for terminal atoms
of 0.02 within 2A
C93 \\sim N16 \\sim C92 \\sim C91 \\sim N15 \\sim C96 \\sim C95 \\sim C94:
within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
5. Same fragment restrains
{C7, C15, Se1A, N1A, N2A, C1A, C2A, C3A, C4A, C5A, C6A} sigma for 1-2: 0.01,
1-3: 0.01
as in
{C7, C15, Se1, N1, N2, C1, C2, C3, C4, C5, C6}
{C29, C37, Se2A, N3A, N4A, C23A, C24A, C25A, C26A, C27A, C28A} sigma for 1-2:
0.01, 1-3: 0.01
{C29, C37, Se2B, N3B, N4B, C23B, C24B, C25B, C26B, C27B, C28B} sigma for 1-2:
0.01, 1-3: 0.01
as in
{C29, C37, Se2, N3, N4, C23, C24, C25, C26, C27, C28}
{C51, C59, Se3A, N5A, N6A, C45A, C46A, C47A, C48A, C49A, C50A} sigma for 1-2:
0.01, 1-3: 0.01
as in
{C51, C59, Se3, N5, N6, C45, C46, C47, C48, C49, C50}
6. Others
 1*[Sof(Se2)+Sof(N3)+Sof(N4)+Sof(C23)+Sof(C24)+Sof(C25)+Sof(C26)+Sof(H26)+
 Sof(C27)+Sof(H27)+Sof(C28)]+1*[Sof(Se2A)+Sof(N3A)+Sof(N4A)+Sof(C23A)+Sof(C24A)+
 Sof(C25A)+Sof(C26A)+Sof(H26A)+Sof(C27A)+Sof(H27A)+Sof(C28A)]+1*[Sof(Se2B)+
 Sof(N3B)+Sof(N4B)+Sof(C23B)+Sof(C24B)+Sof(C25B)+Sof(C26B)+Sof(H26B)+Sof(C27B)+
 Sof(H27B)+Sof(C28B)]=1 with esd of 0
 Sof(Se2)=Sof(N3)=Sof(N4)=Sof(C23)=Sof(C24)=Sof(C25)=Sof(C26)=Sof(H26)=
 Sof(C27)=Sof(H27)=Sof(C28)=FVAR(1)
 Sof(Se2A)=Sof(N3A)=Sof(N4A)=Sof(C23A)=Sof(C24A)=Sof(C25A)=Sof(C26A)=Sof(H26A)=
 Sof(C27A)=Sof(H27A)=Sof(C28A)=FVAR(2)
 Sof(Se2B)=Sof(N3B)=Sof(N4B)=Sof(C23B)=Sof(C24B)=Sof(C25B)=Sof(C26B)=Sof(H26B)=
 Sof(C27B)=Sof(H27B)=Sof(C28B)=FVAR(3)
 Sof(Se3A)=Sof(N5A)=Sof(N6A)=Sof(C45A)=Sof(C46A)=Sof(C47A)=Sof(C48A)=Sof(H48A)=
 Sof(C49A)=Sof(H49A)=Sof(C50A)=1-FVAR(4)
 Sof(Se3)=Sof(N5)=Sof(N6)=Sof(C45)=Sof(C46)=Sof(C47)=Sof(C48)=Sof(H48)=
 Sof(C49)=Sof(H49)=Sof(C50)=FVAR(4)
 Sof(Se1A)=Sof(N1A)=Sof(N2A)=Sof(C1A)=Sof(C2A)=Sof(C3A)=Sof(C4A)=Sof(H4A)=
 Sof(C5A)=Sof(H5A)=Sof(C6A)=1-FVAR(5)
 Sof(Se1)=Sof(N1)=Sof(N2)=Sof(C1)=Sof(C2)=Sof(C3)=Sof(C4)=Sof(H4)=Sof(C5)=
 Sof(H5)=Sof(C6)=FVAR(5)
7.a Ternary CH refined with riding coordinates:
 C67(H67), C68(H68), C73(H73), C74(H74), C79(H79), C80(H80), C85(H85),
 C86(H86), C91(H91), C92(H92), C97(H97), C98(H98)
7.b Secondary CH2 refined with riding coordinates:
 C69(H69A,H69B), C70(H70A,H70B), C71(H71A,H71B), C72(H72A,H72B), C75(H75A,
 H75B), C76(H76A,H76B), C77(H77A,H77B), C78(H78A,H78B), C81(H81A,H81B),
 C82(H82A,H82B), C83(H83A,H83B), C84(H84A,H84B), C87(H87A,H87B), C88(H88A,H88B),
  C89(H89A,H89B), C90(H90A,H90B), C93(H93A,H93B), C94(H94A,H94B), C95(H95A,
 H95B), C96(H96A,H96B), C99(H99A,H99B), C100(H10A,H10B), C101(H10C,H10D),
 C102(H10E,H10F)
7.c Aromatic/amide H refined with riding coordinates:
 C4(H4), C5(H5), C8(H8), C10(H10), C12(H12), C13(H13), C14(H14), C16(H16),
 C18(H18), C20(H20), C21(H21), C22(H22), C26(H26), C27(H27), C30(H30), C32(H32),
  C34(H34), C35(H35), C36(H36), C38(H38), C40(H40), C42(H42), C43(H43),
 C44(H44), C48(H48), C49(H49), C52(H52), C54(H54), C56(H56), C57(H57), C58(H58),
  C60(H60), C62(H62), C64(H64), C65(H65), C66(H66), C4A(H4A), C5A(H5A),
 C26A(H26A), C27A(H27A), C48A(H48A), C49A(H49A), C26B(H26B), C27B(H27B)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 362 electrons were 
found in a volume of 2644\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of 
3[CH2Cl2] per Asymmetric Unit 
which account for 378 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              49420
_shelx_fab_checksum              17960
_olex2_submission_special_instructions 'No special instructions were received'