Orientational self-sorting in cuboctahedral Pd cages
Li, Ru-Jin; Tarzia, Andrew; Posligua, Victor; Jelfs, Kim E.; Sanchez, Nicolas; Marcus, Adam; Baksi, Ananya; Clever, Guido H.; Fadaei-Tirani, Farzaneh; Severin, Kay; Chemical Science  (2022) –; doi:10.1039/D2SC03856K

data_1567731
_publ_section_title
;
 Orientational self-sorting in cuboctahedral Pd cages
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/D2SC03856K
_journal_year                    2022
_chemical_formula_moiety
'C384 H288 N48 Pd12, 24(Cl), 200[C2H6SO], 15[C4H8O], 15[C4H10O]'
_chemical_formula_sum            'C904 H1758 Cl24 N48 O230 Pd12 S200'
_chemical_formula_weight         25521.08
_space_group_crystal_system      orthorhombic
_space_group_IT_number           67
_space_group_name_Hall           '-C 2a 2'
_space_group_name_H-M_alt        'C m m a'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_atom_sites_solution_secondary   difmap
_audit_creation_date             2022-09-01
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-09-26 deposited with the CCDC.	2022-09-30 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   54.9549(13)
_cell_length_b                   61.3516(13)
_cell_length_c                   56.7355(12)
_cell_measurement_reflns_used    25883
_cell_measurement_temperature    140.00(10)
_cell_measurement_theta_max      44.6830
_cell_measurement_theta_min      2.1360
_cell_volume                     191288(7)
_computing_cell_refinement       'CrysAlisPro 1.171.41.122a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.122a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.122a (Rigaku OD, 2021)'
_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, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      140.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix-Arc 150'
_diffrn_measured_fraction_theta_full 0.993
_diffrn_measured_fraction_theta_max 0.993
_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    -16.00  11.00   0.50   20.00    --   31.40 -19.00 -90.00   54
  2  \w     29.00  61.00   0.50   20.00    --   33.16-125.00  90.00   64
  3  \w     18.00  43.00   0.50   20.00    --   33.16-125.00 -60.00   50
  4  \w      6.00  47.00   0.50   20.00    --   33.16 -99.00 150.00   82
  5  \w    -14.00  13.00   0.50   20.00    --   33.16 -19.00   0.00   54
  6  \w    -24.00   9.00   0.50   20.00    --  -35.09  19.00 150.00   66
  7  \w    -66.00 -41.00   0.50   20.00    --  -35.09 125.00-120.00   50
  8  \w    -24.00  13.00   0.50   20.00    --  -35.09  19.00-150.00   74
  9  \w    -69.00  -9.00   0.50   20.00    --  -35.09   0.00 120.00  120
 10  \w    -18.00  10.00   0.50   20.00    --  -35.09  19.00 -60.00   56
 11  \w    -66.00 -35.00   0.50   20.00    --  -35.09 125.00-180.00   62
 12  \w    -22.00   3.00   0.50   20.00    --  -35.09  19.00-180.00   50
 13  \w    -18.00  12.00   0.50   20.00    --  -35.09  19.00 -30.00   60
 14  \w    -17.00   8.00   0.50   20.00    --  -35.09  19.00  60.00   50
 15  \w    -24.00   7.00   0.50   20.00    --  -35.09  19.00  90.00   62
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix-Arc 150'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0131409000
_diffrn_orient_matrix_UB_12      -0.0210889000
_diffrn_orient_matrix_UB_13      -0.0210572000
_diffrn_orient_matrix_UB_21      -0.0347681000
_diffrn_orient_matrix_UB_22      0.0018152000
_diffrn_orient_matrix_UB_23      -0.0102490000
_diffrn_orient_matrix_UB_31      0.0059447000
_diffrn_orient_matrix_UB_32      0.0311114000
_diffrn_orient_matrix_UB_33      -0.0137438000
_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  0.1401
_diffrn_reflns_av_unetI/netI     0.1604
_diffrn_reflns_Laue_measured_fraction_full 0.993
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       49
_diffrn_reflns_limit_h_min       -49
_diffrn_reflns_limit_k_max       51
_diffrn_reflns_limit_k_min       -55
_diffrn_reflns_limit_l_max       51
_diffrn_reflns_limit_l_min       -48
_diffrn_reflns_number            243338
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        44.573
_diffrn_reflns_theta_max         44.573
_diffrn_reflns_theta_min         2.121
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.286
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.626
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.122a (Rigaku Oxford Diffraction, 2021)
Numerical absorption correction based on Gaussian integration over
a multifaceted crystal model.
Empirical absorption correction using spherical harmonics
as implemented in SCALE3 ABSPACK scaling algorithm
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    0.267
_exptl_crystal_description       irregular
_exptl_crystal_F_000             15552
_exptl_crystal_size_max          0.22
_exptl_crystal_size_mid          0.13
_exptl_crystal_size_min          0.072
_refine_diff_density_max         1.366
_refine_diff_density_min         -0.948
_refine_diff_density_rms         0.098
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.107
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     871
_refine_ls_number_reflns         38617
_refine_ls_number_restraints     1639
_refine_ls_restrained_S_all      1.103
_refine_ls_R_factor_all          0.1868
_refine_ls_R_factor_gt           0.1224
_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          0.3536
_refine_ls_wR_factor_ref         0.4058
_reflns_Friedel_coverage         0.000
_reflns_number_gt                14506
_reflns_number_total             38617
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2sc03856k2.cif
_cod_data_source_block           rj-30_final_pl
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_exptl_absorpt_correction_type' value 'Gaussian' was
changed to 'gaussian' 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 7556 2019-12-06 15:28:31Z antanas 
;
_cod_original_sg_symbol_Hall     '-C 2b 2'
_cod_original_sg_symbol_H-M      'C m m e'
_cod_database_code               1567731
_shelx_shelxl_version_number     2018/3
_audit_contact_author            'Farzaneh Fadaei Tirani'
_chemical_oxdiff_formula         'C904 H1758 Cl24 N48 O230 Pd12 S200'
_olex2_refinement_description
;
1. Restrained distances
 C173-C169 = C60-C142 = C57-C53 = C74-C71 = C68-C66 = C84-C81 = C90-C87 = C6-
 C3 = C17-C13 = C31-C28 = C97-C100
 1.5 with sigma of 0.01
 C174-C173 = C175-C173 = C176-C175 = C176-C100_$1 = C101-C100 = C174-C101_$1
 1.39 with sigma of 0.01
 C9-C47_$2
 1.5 with sigma of 0.005
 N12_$2-C92 = C94-C93 = C93-C92 = C94-C90 = C91-C90 = N12_$2-C91
 1.39 with sigma of 0.01
 C101-C100 = C174_$1-C101 = C176_$1-C100 = C176-C175 = C175-C173 = C174-C173
 1.39 with sigma of 0.01
 C8-C47_$2 \\sim C47_$2-C10
 with sigma of 0.01
 C48_$2-C9 \\sim C9-C51_$2
 with sigma of 0.01
2. Restrained planarity
 C100, C101, C173_$1, C174_$1, C175_$1, C176_$1
 with sigma of 0.01
 N12_$2, C90, C91, C92, C93, C94
 with sigma of 0.1
3. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.005 and sigma
for terminal atoms of 0.01 within 2A
N11 \\sim C47 \\sim C48 \\sim C49 \\sim C50 \\sim C51: within 2A with sigma of
0.001 and sigma for terminal atoms of 0.002 within 2A
4. 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
5.a Riding coordinates:
 C48(H48), C49(H49), C29(H29), C19(H19), C18(H18), C27(H27), C91(H91),
 C92(H92), C101(H101), C174(H174), C176(H176)
5.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C4(H4), C5(H5), C33(H33), C32(H32), C35(H35), C34(H34),
 C52(H52), C54(H54), C55(H55), C56(H56), C83(H83), C82(H82), C80(H80), C79(H79),
  C77(H77), C78(H78), C75(H75), C76(H76), C95(H95), C96(H96), C98(H98),
 C99(H99), C51(H51), C50(H50), C168(H168), C170(H170), C171(H171), C172(H172),
 C11(H11), C10(H10), C8(H8), C7(H7), C14(H14), C15(H15), C16(H16), C12(H12),
 C58(H58), C59(H59), C61(H61), C62(H62), C65(H65), C64(H64), C63(H63), C67(H67),
  C70(H70), C69(H69), C73(H73), C72(H72), C85(H85), C86(H86), C88(H88),
 C89(H89), C93(H93), C94(H94), C143(H143), C144(H144), C145(H145), C146(H146),
 C175(H175)
5.c Fitted hexagon refined as free rotating group:
 N1(C1,C2,C3,C4,C5), N5(C33,C32,C31,C35,C34), N6(C52,C53,C54,C55,C56), N8(C83,
 C82,C81,C80,C79), N9(C77,C78,C74,C75,C76), N10(C95,C96,C97,C98,C99), N11(C48,
 C47,C51,C50,C49), N19(C168,C169,C170,C171,C172), C6(C11,C10,C9,C8,C7), C13(C14,
 C15,C16,N2,C12), C28(C29,C19,C17,C18,C27), C57(C58,C59,C60,C61,C62), C66(C65,
 C64,C63,N7,C67), C71(C70,C69,C68,C73,C72), C84(C85,C86,C87,C88,C89), C142(C143,
 C144,N17,C145,C146)
;
_shelx_res_checksum              12257
_shelx_fab_checksum              68054
_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
- Detector area scaling
- B-factor correction
;
_oxdiff_exptl_absorpt_empirical_full_max 2.208
_oxdiff_exptl_absorpt_empirical_full_min 0.475