Configurational control of low-symmetry heteroleptic metal-organic cages with asymmetric ligands.
Yu, Hao; Guo, Ziteng; Tang, Jie; Han, Ningxu; Shi, Junjuan; Li, Meng; Zhang, Houyu; Wang, Ming; Chemical science 16 (2025) 6114–6120; doi:10.1039/d4sc08647c

data_1574092
_publ_section_title
;
 Configurational control of low-symmetry heteroleptic metal-organic cages
 with asymmetric ligands.
;
_journal_issue                   14
_journal_name_full               'Chemical science'
_journal_page_first              6114
_journal_page_last               6120
_journal_paper_doi               10.1039/d4sc08647c
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C138 H96 N12 Pd3'
_chemical_formula_sum            'C138 H96 N12 Pd3'
_chemical_formula_weight         2241.46
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-02-09
_audit_creation_method
;
Olex2 1.5-ac6-020
(compiled 2024.02.14 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6966)
;
_audit_update_record
;
2025-02-10 deposited with the CCDC.	2025-03-07 downloaded from the CCDC.
;
_cell_angle_alpha                69.586(2)
_cell_angle_beta                 75.581(2)
_cell_angle_gamma                63.458(2)
_cell_formula_units_Z            2
_cell_length_a                   24.626(2)
_cell_length_b                   24.7677(19)
_cell_length_c                   25.970(2)
_cell_measurement_reflns_used    9918
_cell_measurement_temperature    273.15
_cell_measurement_theta_max      20.09
_cell_measurement_theta_min      2.23
_cell_volume                     13198.3(18)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 1.5-ac6-020 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-020 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve 1.3 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      273.15
_diffrn_measured_fraction_theta_full 0.950
_diffrn_measured_fraction_theta_max 0.950
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           Synchrotron
_diffrn_radiation_wavelength     0.67016
_diffrn_reflns_av_R_equivalents  0.0551
_diffrn_reflns_av_unetI/netI     0.0587
_diffrn_reflns_Laue_measured_fraction_full 0.950
_diffrn_reflns_Laue_measured_fraction_max 0.950
_diffrn_reflns_limit_h_max       27
_diffrn_reflns_limit_h_min       -27
_diffrn_reflns_limit_k_max       27
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       28
_diffrn_reflns_limit_l_min       -28
_diffrn_reflns_number            124281
_diffrn_reflns_point_group_measured_fraction_full 0.950
_diffrn_reflns_point_group_measured_fraction_max 0.950
_diffrn_reflns_theta_full        21.837
_diffrn_reflns_theta_max         21.837
_diffrn_reflns_theta_min         0.977
_diffrn_source_current           0.0
_diffrn_source_power             0.0
_diffrn_source_voltage           0.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.195
_exptl_absorpt_correction_T_max  0.7447
_exptl_absorpt_correction_T_min  0.6526
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    0.564
_exptl_crystal_description       block
_exptl_crystal_F_000             2292
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.13
_exptl_crystal_size_min          0.11
_refine_diff_density_max         1.539
_refine_diff_density_min         -0.724
_refine_diff_density_rms         0.087
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.453
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1640
_refine_ls_number_reflns         35945
_refine_ls_number_restraints     14409
_refine_ls_restrained_S_all      1.270
_refine_ls_R_factor_all          0.1559
_refine_ls_R_factor_gt           0.1268
_refine_ls_shift/su_max          0.001
_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          0.3740
_refine_ls_wR_factor_ref         0.4083
_reflns_Friedel_coverage         0.000
_reflns_number_gt                20510
_reflns_number_total             35945
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc08647c2.cif
_cod_data_source_block           1
_cod_depositor_comments
'Adding full bibliography for 1574092--1574094.cif.'
_cod_original_cell_volume        13197.9(18)
_cod_database_code               1574092
_shelx_shelxl_version_number     2019/3
_shelx_estimated_absorpt_t_max   0.979
_shelx_estimated_absorpt_t_min   0.971
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
2. Restrained distances
 C43-C6
 1.45 with sigma of 0.01
 C96-C83
 1.45 with sigma of 0.01
 C89-C92
 1.45 with sigma of 0.01
 C153-C192
 1.45 with sigma of 0.01
 C160-C181
 1.45 with sigma of 0.01
 C159-C180
 1.45 with sigma of 0.01
 C144-C141
 1.55 with sigma of 0.01
 C201-C170
 1.55 with sigma of 0.01
 C186-C176
 1.55 with sigma of 0.01
 C99-C97
 1.45 with sigma of 0.01
 C115-C107
 1.45 with sigma of 0.01
 C111-C51
 1.45 with sigma of 0.01
 C196-C177
 1.52 with sigma of 0.01
 C156-C167
 1.5 with sigma of 0.01
 C203-C148
 1.52 with sigma of 0.01
 C133-C15
 1.45 with sigma of 0.01
 C123-C65
 1.53 with sigma of 0.01
 C63-C29
 1.53 with sigma of 0.01
 Pd4-N17 \\sim Pd4-N4
 with sigma of 0.02
 N17-C187 \\sim N4-C1
 with sigma of 0.02
 N17-C185 \\sim N4-C10
 with sigma of 0.02
 C189-C160 \\sim C4-C160
 with sigma of 0.04
 C187-C189 \\sim C1-C4
 with sigma of 0.02
 C187-C181 \\sim C1-C6
 with sigma of 0.04
 C183-C160 \\sim C8-C160
 with sigma of 0.04
 C181-C183 \\sim C6-C8
 with sigma of 0.02
 C181-C160 \\sim C6-C160
 with sigma of 0.02
 C189-C181 \\sim C4-C6
 with sigma of 0.02
 C187-C185 \\sim C1-C10
 with sigma of 0.04
 C183-C185 \\sim C8-C10
 with sigma of 0.02
 C189-C183 \\sim C4-C8
 with sigma of 0.04
 C181-C185 \\sim C6-C10
 with sigma of 0.04
 Pd4-C187 \\sim Pd4-C1
 with sigma of 0.04
 Pd4-C185 \\sim Pd4-C10
 with sigma of 0.04
 N17-C189 \\sim N4-C4
 with sigma of 0.04
 N17-C183 \\sim N4-C8
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
C1 \\sim C4 \\sim C6 \\sim C8 \\sim C10 \\sim C2 \\sim C129 \\sim C65 \\sim
C131 \\sim C33 \\sim C12 \\sim C14 \\sim C16 \\sim C18 \\sim C20 \\sim C22
\\sim C24 \\sim C26 \\sim C28 \\sim C30 \\sim C11 \\sim C89 \\sim C45 \\sim C91
\\sim C23 \\sim C29 \\sim C117 \\sim C59 \\sim C119 \\sim C15 \\sim C121 \\sim
C34 \\sim C36 \\sim C37 \\sim C38 \\sim C40 \\sim C42 \\sim C44 \\sim C46 \\sim
C48 \\sim C50 \\sim C41 \\sim C83 \\sim C21 \\sim C85 \\sim C43 \\sim C87 \\sim
C47 \\sim C95 \\sim C3 \\sim C97 \\sim C49 \\sim C52 \\sim C54 \\sim C56 \\sim
C58 \\sim C60 \\sim C62 \\sim C55 \\sim C111 \\sim C7 \\sim C113 \\sim C57
\\sim C115 \\sim C61 \\sim C123 \\sim C31 \\sim C125 \\sim C63 \\sim C127 \\sim
C64 \\sim C66 \\sim C68 \\sim C70 \\sim C72 \\sim C74 \\sim C76 \\sim C75 \\sim
C19 \\sim C77 \\sim C39 \\sim C79 \\sim C5 \\sim C80 \\sim C81 \\sim C82 \\sim
C84 \\sim C86 \\sim C88 \\sim C90 \\sim C92 \\sim C94 \\sim C96 \\sim C98 \\sim
C93 \\sim C99 \\sim C25 \\sim C101 \\sim C51 \\sim C103 \\sim C13 \\sim C100
\\sim C102 \\sim C104 \\sim C106 \\sim C108 \\sim C110 \\sim C105 \\sim C53
\\sim C107 \\sim C27 \\sim C109 \\sim C118 \\sim C120 \\sim C122 \\sim C124
\\sim C126 \\sim C128 \\sim C130 \\sim C132 \\sim C133 \\sim C67 \\sim C135
\\sim C17 \\sim C137 \\sim C134 \\sim C136 \\sim C138 \\sim C69 \\sim C35 \\sim
C71 \\sim C9 \\sim C73 \\sim C173 \\sim C175 \\sim C177 \\sim C178 \\sim C179
\\sim C190 \\sim C191 \\sim C192 \\sim C193 \\sim C194 \\sim C139 \\sim C203
\\sim C172 \\sim C204 \\sim C168 \\sim C140 \\sim C142 \\sim C144 \\sim C146
\\sim C149 \\sim C147 \\sim C196 \\sim C171 \\sim C198 \\sim C167 \\sim C200
\\sim C148 \\sim C150 \\sim C152 \\sim C154 \\sim C156 \\sim C158 \\sim C169
\\sim C157 \\sim C184 \\sim C159 \\sim C166 \\sim C160 \\sim C174 \\sim C141
\\sim C161 \\sim C143 \\sim C176 \\sim C145 \\sim C180 \\sim C151 \\sim C165
\\sim C153 \\sim C182 \\sim C155 \\sim C181 \\sim C183 \\sim C185 \\sim C187
\\sim C189 \\sim C186 \\sim C162 \\sim C170 \\sim C163 \\sim C188 \\sim C164
\\sim C195 \\sim C197 \\sim C199 \\sim C201 \\sim C202 \\sim C32 \\sim C78
\\sim C116 \\sim C112 \\sim C114 \\sim N1 \\sim N3 \\sim N4 \\sim N5 \\sim N6
\\sim N8 \\sim N12 \\sim N7 \\sim N2 \\sim N9 \\sim N11 \\sim N14 \\sim N15
\\sim N13 \\sim N16 \\sim N17 \\sim N18 \\sim N205: within 5A with sigma of
0.01 and sigma for terminal atoms of 0.02 within 5A
4. Others
 Sof(Pd3)=1-FVAR(1)
 Sof(Pd1)=FVAR(1)
 Fixed Sof: N4(0.5) C1(0.5) H1(0.5) C4(0.5) H4(0.5) C6(0.5) C8(0.5) H8(0.5)
 C10(0.5) H10(0.5) N5(0.5) C2(0.5) H2(0.5) C129(0.5) H129(0.5) C65(0.5)
 C131(0.5) H131(0.5) C33(0.5) H33(0.5) C11(0.5) H11(0.5) C89(0.5) C45(0.5)
 H45(0.5) C91(0.5) H91(0.5) N7(0.5) C23(0.5) H23(0.5) C29(0.5) C117(0.5)
 H117(0.5) C59(0.5) H59(0.5) C119(0.5) H119(0.5) C15(0.5) C121(0.5) H121(0.5)
 C41(0.5) H41(0.5) C83(0.5) C21(0.5) H21(0.5) C85(0.5) H85(0.5) C43(0.5)
 C87(0.5) H87(0.5) C47(0.5) H47(0.5) N2(0.5) C95(0.5) H95(0.5) C3(0.5) H3(0.5)
 C97(0.5) C49(0.5) H49(0.5) C55(0.5) H55(0.5) C111(0.5) C7(0.5) H7(0.5)
 C113(0.5) H113(0.5) C57(0.5) H57(0.5) C115(0.5) C61(0.5) H61(0.5) C123(0.5)
 C31(0.5) H31(0.5) C125(0.5) H125(0.5) C63(0.5) C127(0.5) H127(0.5) C88(0.5)
 H88(0.5) C90(0.5) H90(0.5) C92(0.5) C94(0.5) H94(0.5) C96(0.5) C98(0.5)
 H98(0.5) C99(0.5) C25(0.5) H25(0.5) C101(0.5) H101(0.5) C51(0.5) C103(0.5)
 H103(0.5) C13(0.5) H13(0.5) C105(0.5) H105(0.5) C53(0.5) H53(0.5) C107(0.5)
 C27(0.5) H27(0.5) C109(0.5) H109(0.5) N9(0.5) C133(0.5) C67(0.5) H67(0.5)
 C135(0.5) H135(0.5) N11(0.5) C17(0.5) H17(0.5) C137(0.5) H137(0.5) N14(0.5)
 C173(0.5) H173(0.5) C175(0.5) H175(0.5) C177(0.5) C178(0.5) H178(0.5)
 C179(0.5) H179(0.5) N15(0.5) C190(0.5) H190(0.5) C191(0.5) H191(0.5) C192(0.5)
 C193(0.5) H193(0.5) C194(0.5) H194(0.5) C139(0.5) H139(0.5) C203(0.5)
 C172(0.5) H172(0.5) C204(0.5) H204(0.5) N13(0.5) C168(0.5) H168(0.5) C140(0.5)
 H140(0.5) C142(0.5) H142(0.5) C144(0.5) C146(0.5) H146(0.5) C149(0.5)
 H149(0.5) N16(0.5) C147(0.5) H147(0.5) C196(0.5) C171(0.5) H171(0.5) C198(0.5)
 H198(0.5) C167(0.5) C200(0.5) H200(0.5) C148(0.5) C150(0.5) H150(0.5)
 C152(0.5) H152(0.5) C154(0.5) H154(0.5) C156(0.5) C158(0.5) H158(0.5)
 C169(0.5) H169(0.5) C157(0.5) H157(0.5) C184(0.5) H184(0.5) C159(0.5)
 C166(0.5) H166(0.5) C160(0.5) C174(0.5) H174(0.5) C141(0.5) C161(0.5)
 H161(0.5) C143(0.5) H143(0.5) C176(0.5) C145(0.5) H145(0.5) C180(0.5)
 C151(0.5) H151(0.5) C165(0.5) H165(0.5) C153(0.5) C182(0.5) H182(0.5)
 C155(0.5) H155(0.5) C181(0.5) C183(0.5) H183(0.5) C185(0.5) H185(0.5) N17(0.5)
 C187(0.5) H187(0.5) C189(0.5) H189(0.5) C186(0.5) C162(0.5) H162(0.5)
 C170(0.5) C163(0.5) H163(0.5) C188(0.5) H188(0.5) C164(0.5) H164(0.5)
 C195(0.5) H195(0.5) N18(0.5) C197(0.5) H197(0.5) C199(0.5) H199(0.5) C201(0.5)
 C202(0.5) H202(0.5)
5.a Aromatic/amide H refined with riding coordinates:
 C1(H1), C4(H4), C8(H8), C10(H10), C2(H2), C129(H129), C131(H131), C33(H33),
 C12(H12), C16(H16), C18(H18), C20(H20), C22(H22), C24(H24), C26(H26), C30(H30),
  C11(H11), C45(H45), C91(H91), C23(H23), C117(H117), C59(H59), C119(H119),
 C121(H121), C34(H34), C37(H37), C42(H42), C44(H44), C48(H48), C50(H50),
 C41(H41), C21(H21), C85(H85), C87(H87), C47(H47), C95(H95), C3(H3), C49(H49),
 C54(H54), C56(H56), C60(H60), C62(H62), C55(H55), C7(H7), C113(H113), C57(H57),
  C61(H61), C31(H31), C125(H125), C127(H127), C68(H68), C70(H70), C74(H74),
 C76(H76), C19(H19), C77(H77), C79(H79), C5(H5), C80(H80), C82(H82), C84(H84),
 C86(H86), C88(H88), C90(H90), C94(H94), C98(H98), C93(H93), C25(H25),
 C101(H101), C103(H103), C13(H13), C102(H102), C104(H104), C108(H108),
 C110(H110), C105(H105), C53(H53), C27(H27), C109(H109), C120(H120), C124(H124),
  C130(H130), C132(H132), C67(H67), C135(H135), C17(H17), C137(H137),
 C136(H136), C69(H69), C35(H35), C9(H9), C73(H73), C173(H173), C175(H175),
 C178(H178), C179(H179), C190(H190), C191(H191), C193(H193), C194(H194),
 C139(H139), C172(H172), C204(H204), C168(H168), C140(H140), C142(H142),
 C146(H146), C149(H149), C147(H147), C171(H171), C198(H198), C200(H200),
 C150(H150), C152(H152), C154(H154), C158(H158), C169(H169), C157(H157),
 C184(H184), C166(H166), C174(H174), C161(H161), C143(H143), C145(H145),
 C151(H151), C165(H165), C182(H182), C155(H155), C183(H183), C185(H185),
 C187(H187), C189(H189), C162(H162), C163(H163), C188(H188), C164(H164),
 C195(H195), C197(H197), C199(H199), C202(H202), C32(H32), C78(H78), C116(H116),
  C114(H114)
5.b Fitted hexagon refined as free rotating group:
 N4(C1,C4,C6,C8,C10), N5(C2,C129,C65,C131,C33), N8(C12,C14,C16,C18,C20),
 N12(C22,C24,C26,C28,C30), C11(C89,C45,C91,N7,C23), C29(C117,C59,C119,C15,C121),
  C40(C42,C44,C46,C48,C50), C41(C83,C21,C85,C43,C87), C47(N2,C95,C3,C97,C49),
 C52(C54,C56,C58,C60,C62), C55(C111,C7,C113,C57,C115), C61(C123,C31,C125,C63,
 C127), C66(C68,C70,C72,C74,C76), C75(C19,C77,C39,C79,C5), C88(C90,C92,C94,C96,
 C98), C99(C25,C101,C51,C103,C13), C100(C102,C104,C106,C108,C110), C105(C53,
 C107,C27,C109,N9), C133(C67,C135,N11,C17,C137), C138(C69,C35,C71,C9,C73),
 N14(C173,C175,C177,C178,C179), N15(C190,C191,C192,C193,C194), C139(C203,C172,
 C204,N13,C168), C140(C142,C144,C146,C149,N16), C147(C196,C171,C198,C167,C200),
 C148(C150,C152,C154,C156,C158), C169(C157,C184,C159,C166,C160), C174(C141,C161,
 C143,C176,C145), C180(C151,C165,C153,C182,C155), C181(C183,C185,N17,C187,C189),
  C186(C162,C170,C163,C188,C164), C195(N18,C197,C199,C201,C202), N205(C32,C78,
 C116,C112,C114)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              69663
_shelx_fab_checksum              86553
_olex2_submission_special_instructions 'No special instructions were received'