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_7720784
_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
'C120 H108 Cl6 N6 O20 P6 Pd3 Zr6, 2(C5 H11 N O), 2(Cl), 8[C5H11NO]'
_chemical_formula_sum            'C170 H218 Cl8 N16 O30 P6 Pd3 Zr6'
_chemical_formula_weight         4301.53
_chemical_name_common            Zr-P2N2-PdCl2
_space_group_crystal_system      orthorhombic
_space_group_IT_number           62
_space_group_name_Hall           '-P 2ac 2n'
_space_group_name_H-M_alt        'P n m a'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-12-19
_audit_creation_method
;
Olex2 1.5
(compiled 2025.07.13 svn.rb7424aed for OlexSys, GUI svn.r7314)
;
_audit_update_record
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2026-03-03 deposited with the CCDC.	2026-03-31 downloaded from the CCDC.
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_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   47.908(4)
_cell_length_b                   22.924(2)
_cell_length_c                   17.5652(18)
_cell_measurement_reflns_used    9056
_cell_measurement_temperature    100
_cell_measurement_theta_max      24.596
_cell_measurement_theta_min      2.164
_cell_volume                     19291(3)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_collection       'APEX5 v2023.9-RC115 (Bruker, 2023)'
_computing_data_reduction        'SAINT V8.40B (?, 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 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100
_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 0.995
_diffrn_measured_fraction_theta_max 0.995
_diffrn_measurement_device       'Kappa Four-Circle Diffractometer'
_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  0.0758
_diffrn_reflns_av_unetI/netI     0.0305
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       56
_diffrn_reflns_limit_h_min       -56
_diffrn_reflns_limit_k_max       27
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            364921
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        24.823
_diffrn_reflns_theta_max         24.823
_diffrn_reflns_theta_min         1.918
_diffrn_source                   'Micro Focus Rotating Anode'
_diffrn_source_current           50.0
_diffrn_source_power             2.5
_diffrn_source_type              'Bruker TXS'
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.812
_exptl_absorpt_correction_T_max  0.0613
_exptl_absorpt_correction_T_min  0.0395
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1050 before and 0.0636 after correction.
The Ratio of minimum to maximum transmission is 0.6444.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.481
_exptl_crystal_description       block
_exptl_crystal_F_000             8776
_exptl_crystal_recrystallization_method 'Solvothermal synthesis'
_exptl_crystal_size_max          0.8
_exptl_crystal_size_mid          0.7
_exptl_crystal_size_min          0.5
_refine_diff_density_max         2.431
_refine_diff_density_min         -1.292
_refine_diff_density_rms         0.199
_refine_ls_extinction_coef       0.00011(2)
_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   1.110
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     853
_refine_ls_number_reflns         17013
_refine_ls_number_restraints     970
_refine_ls_restrained_S_all      1.085
_refine_ls_R_factor_all          0.1412
_refine_ls_R_factor_gt           0.1026
_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^)+(0.0488P)^2^+520.4081P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2324
_refine_ls_wR_factor_ref         0.2679
_reflns_Friedel_coverage         0.000
_reflns_number_gt                12275
_reflns_number_total             17013
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d6dt00536e2.cif
_cod_data_source_block           Zr-P2N2-PdCl2
_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.
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_cod_original_sg_symbol_H-M      Pnma
_cod_database_code               7720784
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.687
_shelx_estimated_absorpt_t_min   0.563
_olex2_refinement_description
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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
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
3.a Ternary CH refined with riding coordinates:
 C02Q(H02Q), C02T(H02T), C02V(H02V), C02W(H02W), C02X(H02X), C034(H034)
3.b Secondary CH2 refined with riding coordinates:
 C01D(H01S,H01V), C01H(H01A,H01B), C01J(H01C,H01D), C01P(H01E,H01H), C01W(H01Z,
 H), C01Z(H01I,H01J), C022(H02A,H02B), C02L(H02M,H02N)
3.c Aromatic/amide H refined with riding coordinates:
 C00W(H00W), C010(H010), C012(H012), C013(H013), C016(H016), C01F(H01F),
 C01G(H01G), C01K(H01K), C01L(H01L), C01M(H01M), C01N(H01N), C01O(H01W),
 C01R(H01R), C01T(H01T), C01U(H01U), C01X(H01X), C01Y(H01Y), C021(H021),
 C023(H023), C025(H025), C026(H026), C027(H027), C028(H028), C029(H029),
 C02A(H02C), C02B(H02D), C02C(H02E), C02D(H02F), C02E(H02G), C02F(H02H),
 C02G(H02I), C02H(H02J), C02I(H02K), C02K(H02L), C02M(H02O), C02N(H02P),
 C02R(H02R), C02S(H02S)
3.d Idealised Me refined as rotating group:
 C01B(H01O,H01P,H01Q), C02O(H02U,H02Y,HA)
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_smtbx_masks_special_details
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A solvent mask was calculated and 1839 electrons were 
found in a volume of 7592\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
32[C5H11NO], which account for 1792 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'