Multi-dimensional microenvironment engineering in heteroleptic coordination cages for programmable biomimetic recognition.
Xie, Xiao-Dan; Bai, Qixia; Zhang, Zhe; Wang, Pingshan; Zhang, Qi; Dalton transactions (Cambridge, England : 2003) 54 (2025) 13783–13788; doi:10.1039/d5dt01757b

data_7719329
_publ_section_title
;
 Multi-dimensional microenvironment engineering in heteroleptic
 coordination cages for programmable biomimetic recognition.
;
_journal_issue                   36
_journal_name_full
'Dalton transactions (Cambridge, England : 2003)'
_journal_page_first              13783
_journal_page_last               13788
_journal_paper_doi               10.1039/d5dt01757b
_journal_volume                  54
_journal_year                    2025
_chemical_formula_moiety         'C86 H63 N11 Pd2, 4(B F4)'
_chemical_formula_sum            'C86 H63 B4 F16 N11 Pd2'
_chemical_formula_weight         1810.51
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-06-21
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-05-23 deposited with the CCDC.	2025-08-08 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 105.463(2)
_cell_angle_gamma                90
_cell_formula_units_Z            12
_cell_length_a                   27.0908(9)
_cell_length_b                   31.4365(12)
_cell_length_c                   37.7374(14)
_cell_measurement_reflns_used    9052
_cell_measurement_temperature    170.00
_cell_measurement_theta_max      53.860
_cell_measurement_theta_min      2.545
_cell_volume                     30975(2)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      170.00
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.993
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           GaK\a
_diffrn_radiation_wavelength     1.34139
_diffrn_reflns_av_R_equivalents  0.1278
_diffrn_reflns_av_unetI/netI     0.0655
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       33
_diffrn_reflns_limit_h_min       -33
_diffrn_reflns_limit_k_max       38
_diffrn_reflns_limit_k_min       -38
_diffrn_reflns_limit_l_max       46
_diffrn_reflns_limit_l_min       -46
_diffrn_reflns_number            267533
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        53.594
_diffrn_reflns_theta_max         55.215
_diffrn_reflns_theta_min         2.446
_diffrn_source_current           2.86
_diffrn_source_power             0.1995708
_diffrn_source_voltage           69.78
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    2.296
_exptl_absorpt_correction_T_max  0.7508
_exptl_absorpt_correction_T_min  0.3301
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1939 before and 0.1158 after correction.
The Ratio of minimum to maximum transmission is 0.4397.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.165
_exptl_crystal_description       block
_exptl_crystal_F_000             10944
_exptl_crystal_size_max          0.17
_exptl_crystal_size_mid          0.17
_exptl_crystal_size_min          0.05
_refine_diff_density_max         1.259
_refine_diff_density_min         -2.122
_refine_diff_density_rms         0.115
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.027
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           fullcycle
_refine_ls_number_parameters     1804
_refine_ls_number_reflns         29606
_refine_ls_number_restraints     953
_refine_ls_restrained_S_all      1.044
_refine_ls_R_factor_all          0.1196
_refine_ls_R_factor_gt           0.0914
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1688P)^2^+128.7325P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2658
_refine_ls_wR_factor_ref         0.2895
_reflns_Friedel_coverage         0.000
_reflns_number_gt                20155
_reflns_number_total             29606
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5dt01757b2.cif
_cod_data_source_block           240621xxd_3
_cod_depositor_comments
'Adding full bibliography for 7719328--7719329.cif.'
_cod_database_code               7719329
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.894
_shelx_estimated_absorpt_t_min   0.696
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 B2-F3 = B2-F4 = B2-F5 = B2-F6
 1.42 with sigma of 0.02
 B7-F19 = B7-F1G = B7-F1H = B7-F1I
 1.42 with sigma of 0.02
 B1-F1 = B1-F2 = B1-F7 = B1-F8
 1.42 with sigma of 0.02
 B3-F9 = B3-F10 = B3-F11 = B3-F12
 1.42 with sigma of 0.02
 B4-F13 = B4-F14 = B4-F15 = B4-F16
 1.42 with sigma of 0.02
 B5-F17 = B5-F18 = B5-F1A = B5-F1B
 1.42 with sigma of 0.02
 B6-F1C = B6-F1D = B6-F1E = B6-F1F
 1.42 with sigma of 0.02
 C34-C29 = C34-C33
 1.39 with sigma of 0.01
 B7-F19 \\sim B7-F1G \\sim B7-F1H \\sim B7-F1I
 with sigma of 0.02
 F19-F1G \\sim F1G-F1H \\sim F1H-F1I \\sim F1I-F19 \\sim F1G-F1I \\sim F19-F1H
 with sigma of 0.04
 B2-F3 \\sim B2-F4 \\sim B2-F5 \\sim B2-F6
 with sigma of 0.02
 F3-F4 \\sim F4-F5 \\sim F5-F6 \\sim F6-F3 \\sim F4-F6 \\sim F3-F5
 with sigma of 0.04
 B1-F1 \\sim B1-F2 \\sim B1-F7 \\sim B1-F8
 with sigma of 0.02
 F1-F2 \\sim F2-F7 \\sim F7-F8 \\sim F8-F1 \\sim F2-F8 \\sim F1-F7
 with sigma of 0.04
 B3-F9 \\sim B3-F10 \\sim B3-F11 \\sim B3-F12
 with sigma of 0.02
 F9-F10 \\sim F10-F11 \\sim F11-F12 \\sim F12-F9 \\sim F10-F12 \\sim F9-F11
 with sigma of 0.04
 B4-F13 \\sim B4-F14 \\sim B4-F15 \\sim B4-F16
 with sigma of 0.02
 F13-F14 \\sim F14-F15 \\sim F15-F16 \\sim F16-F13 \\sim F14-F16 \\sim F13-F15
 with sigma of 0.04
 B5-F17 \\sim B5-F18 \\sim B5-F1A \\sim B5-F1B
 with sigma of 0.02
 F17-F18 \\sim F18-F1A \\sim F1A-F1B \\sim F1B-F17 \\sim F18-F1B \\sim F17-F1A
 with sigma of 0.04
 B6-F1C \\sim B6-F1D \\sim B6-F1E \\sim B6-F1F
 with sigma of 0.02
 F1C-F1D \\sim F1D-F1E \\sim F1E-F1F \\sim F1F-F1C \\sim F1D-F1F \\sim F1C-F1E
 with sigma of 0.04
 B1-F1 \\sim B1A-F20
 with sigma of 0.02
 B1-F2 \\sim B1A-F2A
 with sigma of 0.02
 B1-F7 \\sim B1A-F7A
 with sigma of 0.02
 B1-F8 \\sim B1A-F8A
 with sigma of 0.02
 F1-F2 \\sim F20-F2A
 with sigma of 0.04
 F1-F7 \\sim F20-F7A
 with sigma of 0.04
 F1-F8 \\sim F20-F8A
 with sigma of 0.04
 F2-F7 \\sim F2A-F7A
 with sigma of 0.04
 F2-F8 \\sim F2A-F8A
 with sigma of 0.04
 F7-F8 \\sim F7A-F8A
 with sigma of 0.04
 B2-F3 \\sim B2A-F3A
 with sigma of 0.02
 B2-F4 \\sim B2A-F4A
 with sigma of 0.02
 B2-F5 \\sim B2A-F5A
 with sigma of 0.02
 B2-F6 \\sim B2A-F6A
 with sigma of 0.02
 F3-F4 \\sim F3A-F4A
 with sigma of 0.04
 F3-F5 \\sim F3A-F5A
 with sigma of 0.04
 F3-F6 \\sim F3A-F6A
 with sigma of 0.04
 F4-F5 \\sim F4A-F5A
 with sigma of 0.04
 F4-F6 \\sim F4A-F6A
 with sigma of 0.04
 F5-F6 \\sim F5A-F6A
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
F1G \\sim F1H \\sim F1I \\sim F19 \\sim B7: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
B7 \\sim F1G \\sim F1H \\sim F1I \\sim F19: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
F1A \\sim F1B \\sim F17 \\sim F18 \\sim B5: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
F3 \\sim F4 \\sim F5 \\sim F6 \\sim B2: within 2A with sigma of 0.01 and sigma
for terminal atoms of 0.02 within 2A
F13 \\sim F14 \\sim F15 \\sim F16 \\sim B4: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
F9 \\sim F10 \\sim F11 \\sim F12 \\sim B3: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
F1 \\sim F2 \\sim F7 \\sim F8 \\sim B1: within 2A with sigma of 0.01 and sigma
for terminal atoms of 0.02 within 2A
F1C \\sim F1D \\sim F1E \\sim F1F \\sim B6: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
F1 \\sim F2 \\sim F7 \\sim F8 \\sim B1 \\sim F2A \\sim F7A \\sim F8A \\sim F20
\\sim B1A: within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02
within 2A
F3 \\sim F4 \\sim F5 \\sim F6 \\sim B2 \\sim F3A \\sim F4A \\sim F5A \\sim F6A
\\sim B2A: within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02
within 2A
4. Rigid body (RIGU) restrains
 F1G, F1H, F1I, F19, B7
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F3, F4, F5, F6, B2
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F1, F2, F7, F8, B1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F9, F10, F11, F12, B3
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F13, F14, F15, F16, B4
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F1A, F1B, F17, F18, B5
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 F1C, F1D, F1E, F1F, B6
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(F2A)=Sof(F7A)=Sof(F8A)=Sof(F20)=Sof(B1A)=1-FVAR(1)
 Sof(F1)=Sof(F2)=Sof(F7)=Sof(F8)=Sof(B1)=FVAR(1)
 Sof(F3A)=Sof(F4A)=Sof(F5A)=Sof(F6A)=Sof(B2A)=1-FVAR(2)
 Sof(F3)=Sof(F4)=Sof(F5)=Sof(F6)=Sof(B2)=FVAR(2)
 Fixed Sof: N7(0.25) H7A(0.25) H7B(0.25) N8(0.75) H8A(0.75) H8B(0.75) H1(0.75)
 H13(0.75) H20(0.75) C21(0.25) H21A(0.25) H21B(0.25) H21C(0.25) H22(0.25)
 H34(0.25) H41(0.25) C42(0.25) H42A(0.25) H42B(0.25) H42C(0.25) C43(0.75)
 H43A(0.75) H43B(0.75) H43C(0.75) C44(0.75) H44A(0.75) H44B(0.75) H44C(0.75)
 N16(0.5) H16A(0.5) H16B(0.5) C111(0.5) H11D(0.5) H11E(0.5) H11F(0.5) H112(0.5)
 H124(0.5) H131(0.5) C132(0.5) H13A(0.5) H13B(0.5) H13C(0.5) F1A(0.5) F1B(0.5)
 F17(0.5) F18(0.5) B5(0.5) F1C(0.5) F1D(0.5) F1E(0.5) F1F(0.5) B6(0.5)
6.a Rotating group:
 N5(H5A,H5B), N6(H6A,H6B), N7(H7A,H7B), N8(H8A,H8B), N15(H15A,H15B), N16(H16A,
 H16B)
6.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C5(H5), C9(H9), C10(H10), C11(H11), C13(H13),
 C17(H17), C18(H18), C19(H19), C20(H20), C22(H22), C23(H23), C24(H24), C26(H26),
  C30(H30), C31(H31), C32(H32), C34(H34), C38(H38), C39(H39), C40(H40),
 C41(H41), C47(H47), C48(H48), C50(H50), C54(H54), C55(H55), C56(H56), C62(H62),
  C63(H63), C64(H64), C69(H69), C70(H70), C72(H72), C76(H76), C77(H77),
 C78(H78), C84(H84), C85(H85), C86(H86), C91(H91), C92(H92), C94(H94), C98(H98),
  C99(H99), C100(H100), C106(H106), C107(H107), C108(H108), C112(H112),
 C113(H113), C114(H114), C116(H116), C120(H120), C121(H121), C122(H122),
 C124(H124), C128(H128), C129(H129), C130(H130), C131(H131)
6.c Idealised Me refined as rotating group:
 C21(H21A,H21B,H21C), C42(H42A,H42B,H42C), C43(H43A,H43B,H43C), C44(H44A,H44B,
 H44C), C45(H45A,H45B,H45C), C66(H66A,H66B,H66C), C67(H67A,H67B,H67C), C88(H88A,
 H88B,H88C), C89(H89A,H89B,H89C), C110(H11A,H11B,H11C), C111(H11D,H11E,H11F),
 C132(H13A,H13B,H13C)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              27309
_shelx_hkl_checksum              21676
_shelx_fab_checksum              14719
_olex2_submission_special_instructions 'No special instructions were received'