Conformational Adaptability Enabled Higher-Order Self-Sorting Processes in Coordination Cages
Parbin, Minaz; Sivalingam, Vellaiyadevan; Venkatachalam, Ramkumar; Chand, Dillip Kumar; Chemical Science  (2026) –; doi:10.1039/D5SC05568G

data_1576413
_publ_section_title
;
 Conformational Adaptability Enabled Higher-Order Self-Sorting Processes
 in Coordination Cages
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/D5SC05568G
_journal_year                    2026
_chemical_formula_moiety
'C84 H60 N12 O4 Pd2, 0.5(C4 H6 N2), 4(N O3), 0.5(H4 O2), 5[C2H3N], 5[H2O]'
_chemical_formula_sum            'C96 H90 N22 O22 Pd2'
_chemical_formula_weight         2116.750
_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'
_symmetry_Int_Tables_number      62
_audit_creation_date             2025-11-11
_audit_creation_method
;
Olex2 1.5-dev
(compiled 2025.11.07 svn.reb371d55 for OlexSys, GUI svn.r7346)
;
_audit_update_record
;
2025-11-27 deposited with the CCDC.	2025-12-11 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   35.3355(18)
_cell_length_b                   21.0797(10)
_cell_length_c                   12.7746(7)
_cell_measurement_reflns_used    8901
_cell_measurement_temperature    110(2)
_cell_measurement_theta_max      17.66
_cell_measurement_theta_min      2.19
_cell_volume                     9515.3(8)
_computing_cell_refinement       'Bruker D8 QUEST'
_computing_data_collection       'Bruker D8 QUEST'
_computing_data_reduction        'Bruker D8 QUEST'
_computing_molecular_graphics    'Olex2 1.5-dev (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-dev (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5-dev (Bourhis et al., 2015)'
_computing_structure_solution    'Bruker D8 QUEST'
_diffrn_ambient_temperature      110.00
_diffrn_measured_fraction_theta_full 0.9941
_diffrn_measured_fraction_theta_max 0.9941
_diffrn_measurement_device_type  'Bruker D8 QUEST'
_diffrn_measurement_method       'Bruker D8 QUEST'
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0884
_diffrn_reflns_av_unetI/netI     0.0245
_diffrn_reflns_Laue_measured_fraction_full 0.9941
_diffrn_reflns_Laue_measured_fraction_max 0.9941
_diffrn_reflns_limit_h_max       27
_diffrn_reflns_limit_h_min       -27
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       9
_diffrn_reflns_limit_l_min       -9
_diffrn_reflns_number            59812
_diffrn_reflns_point_group_measured_fraction_full 0.9941
_diffrn_reflns_point_group_measured_fraction_max 0.9941
_diffrn_reflns_theta_full        15.8631
_diffrn_reflns_theta_max         15.86
_diffrn_reflns_theta_min         1.97
_exptl_absorpt_coefficient_mu    0.464
_exptl_absorpt_correction_T_max  0.924
_exptl_absorpt_correction_T_min  0.897
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'SADABS, BRUKER 2018'
_exptl_crystal_colour            Yellow
_exptl_crystal_density_diffrn    1.478
_exptl_crystal_description       Block
_exptl_crystal_F_000             4347.100
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.22
_exptl_crystal_size_min          0.18
_refine_diff_density_max         0.8634
_refine_diff_density_min         -0.5319
_refine_diff_density_rms         0.0903
_refine_ls_d_res_high            1.3001
_refine_ls_d_res_low             10.3521
_refine_ls_goodness_of_fit_ref   1.1689
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    77
_refine_ls_number_parameters     603
_refine_ls_number_reflns         2354
_refine_ls_number_restraints     454
_refine_ls_restrained_S_all      1.0417
_refine_ls_R_factor_all          0.0818
_refine_ls_R_factor_gt           0.0778
_refine_ls_shift/su_max          -0.0007
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0927P)^2^+119.8544P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2019
_refine_ls_wR_factor_ref         0.2052
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              27
_reflns_limit_h_min              0
_reflns_limit_k_max              16
_reflns_limit_k_min              0
_reflns_limit_l_max              9
_reflns_limit_l_min              0
_reflns_number_gt                2169
_reflns_number_total             2354
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d5sc05568g2.cif
_cod_data_source_block           MINAZ-1
_cod_database_code               1576413
_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 C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 N7-C43
 1.18 with sigma of 0.01
 C43-C44
 1.48 with sigma of 0.01
 O3-O5 = O5-O4 = O4-O3
 2.15 with sigma of 0.01
 O6-O7 = O7-O8 = O8-O6
 2.15 with sigma of 0.01
3. Rigid bond restraints
 C1, C2, C3, C4, C5, C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, C17,
 C18, C19, C20, C21, C22, C23, C24, C25, C26, C27, C28, C29, C30, C31, C32, C33,
  C34, C35, C36, C37, Pd1, C32A, C33A, C34A, C35A, C36A, C37A, C38, C39, C40,
 C41, C42, C43
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C32A, C33A, C34A, C35A, C36A, C37A, N9, O6, O7, O3, O4, O5, N8
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
C32A \\sim C33A \\sim C34A \\sim C35A \\sim C36A \\sim C37A \\sim N9 \\sim O6
\\sim O7 \\sim O3 \\sim O4 \\sim O5 \\sim N8: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
C1 \\sim C2 \\sim C3 \\sim C4 \\sim C5 \\sim C6 \\sim C7 \\sim C8 \\sim C9
\\sim C10 \\sim C11 \\sim C12 \\sim C13 \\sim C14 \\sim C15 \\sim C16 \\sim C17
\\sim C18 \\sim C19 \\sim C20 \\sim C21 \\sim C22 \\sim C23 \\sim C24 \\sim C25
\\sim C26 \\sim C27 \\sim C28 \\sim C29 \\sim C30 \\sim C31 \\sim C32 \\sim C33
\\sim C34 \\sim C35 \\sim C36 \\sim C37 \\sim Pd1 \\sim C32A \\sim C33A \\sim
C34A \\sim C35A \\sim C36A \\sim C37A \\sim C38 \\sim C39 \\sim C40 \\sim C41
\\sim C42 \\sim C43: within 2A with sigma of 0.01 and sigma for terminal atoms
of 0.02 within 2A
Uanis(C43) \\sim Ueq, Uanis(C35A) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
5. Others
 Sof(C32A)=Sof(C33A)=Sof(H33A)=Sof(C34A)=Sof(H34A)=Sof(C35A)=Sof(C36A)=
 Sof(H36A)=Sof(C37A)=Sof(H37A)=1-FVAR(1)
 Sof(C32)=Sof(C33)=Sof(H33)=Sof(C34)=Sof(H34)=Sof(C35)=Sof(C36)=Sof(H36)=
 Sof(C37)=Sof(H37)=FVAR(1)
 Fixed Sof: H44a(0.5) H44b(0.5) H44c(0.5) H9a(0.5) H9b(0.5)
6.a Riding coordinates:
 O9(H9a,H9b)
6.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C5(H5), C8(H8), C9(H9), C10(H10), C12(H12), C16(H16),
 C17(H17), C18(H18), C20(H20), C23(H23), C24(H24), C25(H25), C26(H26), C27(H27),
  C28(H28), C29(H29), C31(H31), C33(H33), C34(H34), C36(H36), C37(H37),
 C33A(H33A), C34A(H34A), C36A(H36A), C37A(H37A), C39(H39), C40(H40), C41(H41),
 C42(H42), N2(H2a), N3(H3a)
6.c Fitted hexagon refined as free rotating group:
 C32(C33,C34,C35,C36,C37)
6.d Idealised Me refined as rotating group:
 C44(H44a,H44b,H44c)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 658 electrons were 
found in a volume of 2084\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 5 MeCN and 5 water per Formula Unit 
which account for 640 electrons per unit cell.

Diffuse solvent was treated with the SQUEEZE routine (PLATON).
SQUEEZE identified solvent-accessible voids of 2084 \%A*3 per unit cell
containing a total of 658 electrons per unit cell. These contributions
were removed from the structure-factor file (HKLF 5), and the model
was refined against the masked data. 

Based on the electron count, this corresponds approximately to 
five molecules of C~2~H~3~N , five molecules of H~2~O per formula unit, 
which is consistent with the crystallization conditions. 
These solvent molecules were not included in the final atomistic model.

The chemical formula, formula weight, F(000), and density values have been 
updated to include the squeezed solvent contribution, whereas the atomic 
coordinates and displacement parameters exclude the solvent atoms.

The reported chemical formula,formula weight, F(000), and derived quantities
refer only to the ordered portion of the structure. 
Attempts to model the solvent explicitly were unsuccessful.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_olex2_submission_special_instructions 'No special instructions were received'