Construction of Pd-based coordination cages with three geometrically distinct ligands.
Li, Ru-Jin; de Montmollin, Jean; Fadaei-Tirani, Farzaneh; Scopelliti, Rosario; Severin, Kay; Dalton transactions (Cambridge, England : 2003)  (2023) –; doi:10.1039/d3dt00248a

data_7712854
_publ_section_title
;
 Construction of Pd-based coordination cages with three geometrically
 distinct ligands.
;
_journal_name_full
'Dalton transactions (Cambridge, England : 2003)'
_journal_paper_doi               10.1039/d3dt00248a
_journal_year                    2023
_chemical_formula_moiety         'C128 H80 N16 Pd4'
_chemical_formula_sum            'C128 H80 N16 Pd4'
_chemical_formula_weight         2267.68
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2023-01-13
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2023-01-13 deposited with the CCDC.	2023-04-14 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 99.765(6)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   25.5096(19)
_cell_length_b                   16.3107(10)
_cell_length_c                   41.832(3)
_cell_measurement_reflns_used    4727
_cell_measurement_temperature    140.00(10)
_cell_measurement_theta_max      46.6720
_cell_measurement_theta_min      3.4100
_cell_volume                     17153(2)
_computing_cell_refinement       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_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_environment      N~2~
_diffrn_ambient_temperature      140.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2817
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 0.990
_diffrn_measured_fraction_theta_max 0.990
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -72.00  16.00   1.00   15.00    --  -40.91  75.00 -23.00   88
  2  \w     15.00  42.00   1.00   15.00    --   40.91 -75.00-150.00   27
  3  \w     30.00 137.00   1.00   40.00    --  105.15 -75.00-150.00  107
  4  \w    102.00 162.00   1.00   40.00    --  105.15  75.00 -23.00   60
  5  \w   -115.00 -16.00   1.00   15.00    --  -40.91 -38.00  30.00   99
  6  \w    -21.00   5.00   1.00   15.00    --   40.91 -77.00   0.00   26
  7  \w    -33.00  64.00   1.00   15.00    --   40.91 -19.00-180.00   97
  8  \w     26.00  51.00   1.00   15.00    --   40.91 -77.00   0.00   25
  9  \w     29.00 131.00   1.00   40.00    --  105.15 -30.00-150.00  102
 10  \w    105.00 177.00   1.00   40.00    --  105.15 111.00 -60.00   72
 11  \w    109.00 155.00   1.00   40.00    --  105.15 111.00-180.00   46
 12  \w    106.00 134.00   1.00   40.00    --  105.15  77.00-150.00   28
 13  \w    113.00 167.00   1.00   40.00    --  105.15 111.00-150.00   54
 14  \w     42.00 104.00   1.00   40.00    --  105.15 -94.00  60.00   62
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0537399000
_diffrn_orient_matrix_UB_12      0.0039429000
_diffrn_orient_matrix_UB_13      -0.0231902000
_diffrn_orient_matrix_UB_21      0.0146499000
_diffrn_orient_matrix_UB_22      -0.0781072000
_diffrn_orient_matrix_UB_23      -0.0172319000
_diffrn_orient_matrix_UB_31      -0.0255449000
_diffrn_orient_matrix_UB_32      -0.0529590000
_diffrn_orient_matrix_UB_33      0.0236997000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.1072
_diffrn_reflns_av_unetI/netI     0.1293
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -25
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       41
_diffrn_reflns_limit_l_min       -36
_diffrn_reflns_number            54539
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        50.432
_diffrn_reflns_theta_max         50.432
_diffrn_reflns_theta_min         2.914
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.617
_exptl_absorpt_correction_T_max  0.708
_exptl_absorpt_correction_T_min  0.349
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.84a (Rigaku Oxford Diffraction, 2020)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_density_diffrn    0.878
_exptl_crystal_description       prism
_exptl_crystal_F_000             4576
_exptl_crystal_size_max          0.362
_exptl_crystal_size_mid          0.259
_exptl_crystal_size_min          0.082
_refine_diff_density_max         0.696
_refine_diff_density_min         -0.636
_refine_diff_density_rms         0.095
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.936
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1093
_refine_ls_number_reflns         17792
_refine_ls_number_restraints     1698
_refine_ls_restrained_S_all      0.927
_refine_ls_R_factor_all          0.1757
_refine_ls_R_factor_gt           0.1176
_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          0.3319
_refine_ls_wR_factor_ref         0.3568
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6785
_reflns_number_total             17792
_reflns_threshold_expression     'I > 2\s(I)'
_twin_special_details
;
Component 2 rotated by -172.7010\% 
around [0.01 0.99 -0.14] (reciprocal) or [-0.00 1.00 -0.02] (direct)
;
_cod_data_source_file            d3dt00248a2.cif
_cod_data_source_block           rj09
_cod_database_code               7712854
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C128 H80 N16 Pd4'
_shelx_estimated_absorpt_t_max   0.756
_shelx_estimated_absorpt_t_min   0.354
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
2. Restrained distances
 C6-C4 \\sim C8-C7 \\sim C18-C16 \\sim C20-C19 \\sim C47-C50 \\sim C51-C52
\\sim C58-C56 \\sim C59-C60 ~
 C67-C70 \\sim C71-C72 \\sim C78-C76 \\sim C79-C80 \\sim C30-C27 \\sim C32-C31
\\sim C36-C38 \\sim C39-C40
 \\sim C87-C90 \\sim C91-C92 \\sim C98-C94 \\sim C100-C99 \\sim C108-C110 \\sim
C111-C112 \\sim C122-C120 ~
 C124-C123
 with sigma of 0.02
 C111-C110 \\sim C122-C123 \\sim C70-C71 \\sim C78-C79 \\sim C39-C38 \\sim
C31-C30 \\sim C50-C51 \\sim C58-
 C59 \\sim C91-C90 \\sim C99-C98 \\sim C19-C18 \\sim C6-C7
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(C29) \\sim Ueq, Uanis(C48) \\sim Ueq, Uanis(C49) \\sim Ueq, Uanis(N7)
\\sim Ueq, Uanis(C69) \\sim Ueq, Uanis(C68) \\sim Ueq, Uanis(C65) \\sim Ueq,
Uanis(C32) \\sim Ueq, Uanis(C34) \\sim Ueq, Uanis(C35) \\sim Ueq, Uanis(C36)
\\sim Ueq, Uanis(C37) \\sim Ueq, Uanis(C38) \\sim Ueq, Uanis(C87) \\sim Ueq,
Uanis(C86) \\sim Ueq, Uanis(C85) \\sim Ueq, Uanis(N8) \\sim Ueq, Uanis(C89)
\\sim Ueq, Uanis(C90) \\sim Ueq, Uanis(C91) \\sim Ueq, Uanis(C93) \\sim Ueq,
Uanis(C92) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C33) \\sim Ueq, Uanis(C125) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5.a Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C5(H5), C17(H17), C15(H15), C14(H14), C13(H13),
 C25(H25), C26(H26), C28(H28), C29(H29), C45(H45), C46(H46), C48(H48), C49(H49),
  C12(H12), C9(H9), C10(H10), C11(H11), C23(H23), C22(H22), C21(H21), C24(H24),
 C69(H69), C68(H68), C66(H66), C65(H65), C62(H62), C61(H61), C64(H64), C63(H63),
  C109(H109), C107(H107), C106(H106), C105(H105), C117(H117), C118(H118),
 C119(H119), C121(H121), C82(H82), C81(H81), C84(H84), C83(H83), C115(H115),
 C114(H114), C113(H113), C116(H116), C127(H127), C126(H126), C125(H125),
 C128(H128), C102(H102), C101(H101), C104(H104), C103(H103), C42(H42), C41(H41),
  C44(H44), C43(H43), C33(H33), C34(H34), C35(H35), C37(H37), C53(H53),
 C54(H54), C55(H55), C57(H57), C77(H77), C75(H75), C74(H74), C73(H73), C86(H86),
  C85(H85), C89(H89), C88(H88), C93(H93), C97(H97), C96(H96), C95(H95)
5.b Fitted hexagon refined as free rotating group:
 N1(C1,C2,C3,C4,C5), N2(C17,C16,C15,C14,C13), N3(C25,C26,C27,C28,C29), N4(C45,
 C46,C47,C48,C49), N5(C12,C8,C9,C10,C11), N6(C23,C22,C21,C20,C24), N7(C69,C68,
 C67,C66,C65), N9(C62,C61,C60,C64,C63), N10(C109,C108,C107,C106,C105), N11(C117,
 C118,C119,C120,C121), N12(C82,C81,C80,C84,C83), N13(C115,C114,C113,C112,C116),
 N14(C127,C126,C125,C124,C128), N15(C102,C101,C100,C104,C103), N16(C42,C41,C40,
 C44,C43), C32(C33,C34,C35,C36,C37), C52(C53,C54,C55,C56,C57), C72(C77,C76,C75,
 C74,C73), C87(C86,C85,N8,C89,C88), C94(C93,C92,C97,C96,C95)
;
_shelx_res_checksum              72760
_shelx_hkl_checksum              82088
_shelx_fab_checksum              69347
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 2.635
_oxdiff_exptl_absorpt_empirical_full_min 0.387
_oxdiff_twin_integration_method  simultaneous
_oxdiff_twin_items               2