In or out? Adaptive metal binding by a diphosphine-based Zr metal-organic cage
Shin, Jiehye; Wade, Casey R.; Dalton Transactions  (2026) –; doi:10.1039/D6DT00536E

data_7720782
_publ_section_title
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 In or out? Adaptive metal binding by a diphosphine-based Zr metal-organic
 cage.
;
_journal_issue                   16
_journal_name_full
'Dalton transactions (Cambridge, England : 2003)'
_journal_page_first              6407
_journal_page_last               6414
_journal_paper_doi               10.1039/d6dt00536e
_journal_volume                  55
_journal_year                    2026
_chemical_formula_moiety
'C128 H140 Ag6 Cl2 N6 O24 P6 S4 Zr6, 5(F6 P), Cl, 31[C2H6SO]'
_chemical_formula_sum            'C190 H326 Ag6 Cl3 F30 N6 O55 P11 S35 Zr6'
_chemical_formula_weight         6908.21
_chemical_name_common            Zr-P2N2-Ag
_space_group_crystal_system      orthorhombic
_space_group_IT_number           57
_space_group_name_Hall           '-P 2c 2b'
_space_group_name_H-M_alt        'P b c m'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2026-01-13
_audit_creation_method
;
Olex2 1.5
(compiled 2025.07.13 svn.rb7424aed for OlexSys, GUI svn.r7314)
;
_audit_update_record
;
2026-03-03 deposited with the CCDC.	2026-03-31 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   21.0912(14)
_cell_length_b                   40.752(3)
_cell_length_c                   26.4875(19)
_cell_measurement_reflns_used    9707
_cell_measurement_temperature    100.00
_cell_measurement_theta_max      22.39
_cell_measurement_theta_min      2.22
_cell_volume                     22766(3)
_computing_cell_refinement       'SAINT v8.40B (Bruker, 2021)'
_computing_data_collection       'APEX5 v2023.9-RC115 (Bruker, 2023)'
_computing_data_reduction        'SAINT v8.40B (Bruker, 2021)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.00
_diffrn_detector                 'Bruker Photon III area detector'
_diffrn_detector_area_resol_mean 10.5
_diffrn_detector_type            'CMOS area detector'
_diffrn_measured_fraction_theta_full 0.993
_diffrn_measured_fraction_theta_max 0.993
_diffrn_measurement_device       'Kappa Four-Circle Diffractometer'
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'Double Bounce Multilayer Mirrors'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_radiation_xray_symbol    K-L~3~
_diffrn_reflns_av_R_equivalents  0.0665
_diffrn_reflns_av_unetI/netI     0.0252
_diffrn_reflns_Laue_measured_fraction_full 0.993
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       43
_diffrn_reflns_limit_k_min       -43
_diffrn_reflns_limit_l_max       28
_diffrn_reflns_limit_l_min       -28
_diffrn_reflns_number            303193
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        22.500
_diffrn_reflns_theta_max         22.500
_diffrn_reflns_theta_min         1.834
_diffrn_source                   'Micro Focus Rotating Anode'
_diffrn_source_type              'Bruker TXS'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.307
_exptl_absorpt_correction_T_max  0.0412
_exptl_absorpt_correction_T_min  0.0215
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1163 before and 0.0784 after correction.
The Ratio of minimum to maximum transmission is 0.5218.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    2.016
_exptl_crystal_description       block
_exptl_crystal_F_000             14064
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: dimethylsulfoxide/ethyl acetate'
_exptl_crystal_size_max          0.02
_exptl_crystal_size_mid          0.01
_exptl_crystal_size_min          0.01
_refine_diff_density_max         3.194
_refine_diff_density_min         -1.709
_refine_diff_density_rms         0.247
_refine_ls_extinction_coef       0.0022(4)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   2.667
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     952
_refine_ls_number_reflns         15176
_refine_ls_number_restraints     1222
_refine_ls_restrained_S_all      2.601
_refine_ls_R_factor_all          0.2128
_refine_ls_R_factor_gt           0.1705
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.5100
_refine_ls_wR_factor_ref         0.5723
_reflns_Friedel_coverage         0.000
_reflns_number_gt                10926
_reflns_number_total             15176
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d6dt00536e2.cif
_cod_data_source_block           Zr-P2N2-Ag
_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 7720780--7720784.cif.
;
_cod_original_sg_symbol_H-M      Pbcm
_cod_database_code               7720782
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.987
_shelx_estimated_absorpt_t_min   0.974
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, H00Y of O00Y, H00X of O00X, H014 of O014, H015 of O015,
  All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, H00U of O00U, H010 of O010, All C(H,H,H,H,H,H) groups
2. Restrained distances
 F03U-F3
 2.27 with sigma of 0.02
 F03U-F5
 2.27 with sigma of 0.02
 F03U-F4
 2.27 with sigma of 0.02
 F03U-F02R
 2.27 with sigma of 0.02
 F2-F4
 2.27 with sigma of 0.02
 F2-F5
 2.27 with sigma of 0.02
 F2-F3
 2.27 with sigma of 0.02
 F2-F02R
 2.27 with sigma of 0.02
 F4-F5
 2.27 with sigma of 0.02
 F5-F3
 2.27 with sigma of 0.02
 F3-F02R
 2.27 with sigma of 0.02
 F02R-F4
 2.27 with sigma of 0.02
 S3-C02T = S3-C03T
 1.8 with sigma of 0.02
 C03N-C49
 1.4 with sigma of 0.02
 C49-C26
 1.4 with sigma of 0.02
 C03N-C26
 2.3 with sigma of 0.02
 C26-C26_$1
 1.4 with sigma of 0.02
 P3-F15 = P3-F1_$1 = P3-F1 = P3-F40 = P3-F8 = P3-F8_$1
 1.6 with sigma of 0.02
 F1-F15
 2.29132 with sigma of 0.02
 F40-F1
 2.10935 with sigma of 0.02
 F40-F8
 2.3491 with sigma of 0.02
 F40-F8_$1
 2.3491 with sigma of 0.02
 F8_$1-F8
 2.36868 with sigma of 0.02
 F8-F1
 2.29259 with sigma of 0.02
 F1_$1-F1
 2.05019 with sigma of 0.02
 Zr05-C03V
 2.5 with sigma of 0.02
 C03V_$1-C039_$1 = C03V-C03V_$1 = C03V-C039 = C03S-C039 = C03S-C039_$1
 1.42 with sigma of 0.02
 H039_$1-H03S
 2.537 with sigma of 0.02
 H039_$1-H03V_$1
 2.537 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(S3) = Uanis(S3A)
Uanis(O24A) = Uanis(O24)
Uanis(Cl3) = Uanis(P3)
4. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O24, S3, C02T, C03T
 with sigma for 1-2 distances of 0.0005 and sigma for 1-3 distances of 0.0005
 P3, F8, F40, F1, F15
 with sigma for 1-2 distances of 0.0005 and sigma for 1-3 distances of 0.0005
5. Same fragment restrains
{N028, C19, C64, C02K, C01L, C01J, O18, C02Y} sigma for 1-2: 0.02, 1-3: 0.04
as in
{N01Q, C01N, C61, C62, C01C, C63, O19, C038}
{P00F, F16, F7, F9, F100, F6, F38} sigma for 1-2: 0.02, 1-3: 0.04
as in
{P00E, F2, F3, F4, F5, F02R, F03U}
6. Others
 Fixed Sof: S3(0.5) H02M(0.5) H02N(0.5) H02P(0.5) H02I(0.5) H02J(0.5)
 H02L(0.5) O24(0.5) H03I(0.5) H03L(0.5) H03M(0.5) H03D(0.5) H03F(0.5) H03H(0.5)
 S3A(0.5) O24A(0.5)
7.a Ternary CH refined with riding coordinates:
 O00U(H00U), O010(H010), C039(H039), C03S(H03S), C03V(H03V)
7.b Secondary CH2 refined with riding coordinates:
 C038(H03A,H03B), C01U(H01A,H01B), C01W(H01C,H01D), C020(H02A,H02B), C02M(H02F,
 H02G), C02Y(H02Q,H02R)
7.c Me refined with riding coordinates:
 C02T(H02M,H02N,H02P), C02T(H02I,H02J,H02L), C03T(H03I,H03L,H03M), C03T(H03D,
 H03F,H03H)
7.d Aromatic/amide H refined with riding coordinates:
 C61(H61), C62(H62), C52(H52), C53(H53), C01O(H01O), C54(H54), O00X(H00X),
 O00Y(H00Y), O014(H014), O015(H015), C56(H56), C57(H57), C58(H58), C01T(H01T),
 C64(H64), C02K(H02K), C02X(H02X), C76(H76), C03G(H03G), C041(H041), C04A(H04A),
  C02O(H02O), C03E(H03E), C03Y(H03Y), C03K(H03K), C02F(H02H), C030(H030),
 C046(H046), C60(H60), C026(H026), C02C(H02S), C03J(H03J), C01X(H01X),
 C02P(H02T), C03B(H03C), C027(H027), C03N(H03N), C11(H11), C14(H14), C15(H15),
 C16(H16), C12(H12), C26(H26), C49(H49)
7.e Fitted pentagon refined as free rotating group:
 C030(C046,C60,C026,C02C), C03J(C01X,C02P,C03B,C027)
7.f Fitted hexagon refined as free rotating group:
 C51(C52,C53,C01Z,C01O,C54), C56(C57,C59,C58,C01T,C01V), C02N(C02X,C76,C03G,
 C041,C04A), C02O(C03E,C03Y,C03K,C01S,C02F), C13(C11,C14,C15,C16,C12)
7.g Idealised Me refined as rotating group:
 C65(H65A,H65B,H65C), C02J(H02C,H02D,H02E)
;
_smtbx_masks_special_details
'A solvent mask was calculated and 5297 electrons were found in a volume of 8900\%A^3^ in 1 void per unit cell. This is consistent with the presence of 32[C2H6SO], which account for 5376 electrons per unit cell.'
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_olex2_submission_special_instructions 'No special instructions were received'