Coordination sphere interactions drive isomer selection in heteroleptic Pd(ii) cages with low-symmetry ligands.
Molinska, Paulina; Male, Louise; Lewis, James E. M.; Chemical science 16 (2025) 17939–17947; doi:10.1039/d5sc04881h

data_1575651
_publ_section_title
;
 Coordination sphere interactions drive isomer selection in heteroleptic
 Pd(ii) cages with low-symmetry ligands.
;
_journal_issue                   38
_journal_name_full               'Chemical science'
_journal_page_first              17939
_journal_page_last               17947
_journal_paper_doi               10.1039/d5sc04881h
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C72 H44 N8 Pd2, 4(B F4), 4(C2 H3 N)'
_chemical_formula_sum            'C80 H56 B4 F16 N12 Pd2'
_chemical_formula_weight         1745.40
_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             2024-10-10
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-05-15 deposited with the CCDC.	2025-08-22 downloaded from the CCDC.
;
_cell_angle_alpha                109.672(2)
_cell_angle_beta                 93.5810(10)
_cell_angle_gamma                105.223(2)
_cell_formula_units_Z            2
_cell_length_a                   12.9423(2)
_cell_length_b                   19.0119(4)
_cell_length_c                   20.2700(3)
_cell_measurement_reflns_used    39549
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      76.6650
_cell_measurement_theta_min      4.0370
_cell_volume                     4468.80(16)
_computing_cell_refinement       'CrysAlisPro 1.171.43.116a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.116a 64-bit (release 22-03-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.116a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.1768
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.985
_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    -82.00  41.00   1.00    1.42    --  -40.21  21.00  20.00  123
  2  \w    -82.00  41.00   1.00    1.42    --  -40.21  21.00  20.00  123
  3  \w   -121.00   2.00   1.00    1.42    --  -40.21 -21.00-145.00  123
  4  \w     -2.00 121.00   1.00    1.42    --   40.21  21.00  20.00  123
  5  \w     32.00 155.00   1.00    5.68    --  113.00 -21.00-145.00  123
  6  \w     71.00 178.00   1.00    5.68    --  113.00  21.00  20.00  107
  7  \w   -116.00 -14.00   1.00    1.42    --  -40.21 -38.00-150.00  102
  8  \w    -21.00  74.00   1.00    1.42    --   40.21 -77.00 120.00   95
  9  \w      3.00  30.00   1.00    1.42    --   40.21  88.00-110.88   27
 10  \w      3.00  30.00   1.00    1.42    --   40.21  89.00 -75.47   27
 11  \w      3.00  30.00   1.00    1.42    --   40.21  89.00 -19.17   27
 12  \w    -41.00  82.00   1.00    1.42    --   40.21 -21.00-145.00  123
 13  \w      6.00  81.00   1.00    1.42    --   40.21 -99.00  60.00   75
 14  \w      3.00  30.00   1.00    1.42    --   40.21  89.00  29.71   27
 15  \w    103.00 178.00   1.00    5.68    --  113.00  77.00-180.00   75
 16  \w     38.00 109.00   1.00    5.68    --  113.00-111.00-180.00   71
 17  \w    103.00 178.00   1.00    5.68    --  113.00  77.00 -60.00   75
 18  \w     38.00 109.00   1.00    5.68    --  113.00-111.00  60.00   71
 19  \w     34.00 147.00   1.00    5.68    --  113.00 -77.00 -30.00  113
 20  \w     29.00 107.00   1.00    5.68    --  113.00 -94.00-150.00   78
 21  \w     38.00 109.00   1.00    5.68    --  113.00-111.00 120.00   71
 22  \w     83.00 178.00   1.00    5.68    --  113.00  61.00-120.00   95
 23  \w     38.00 141.00   1.00    5.68    --  113.00 -45.00 -60.00  103
 24  \w     29.00 107.00   1.00    5.68    --  113.00 -94.00 -60.00   78
 25  \w     38.00 141.00   1.00    5.68    --  113.00 -45.00  60.00  103
 26  \w     38.00 141.00   1.00    5.68    --  113.00 -45.00  60.00  103
 27  \w     38.00 109.00   1.00    5.68    --  113.00-111.00 -60.00   71
 28  \w    103.00 178.00   1.00    5.68    --  113.00  77.00  30.00   75
 29  \w    103.00 178.00   1.00    5.68    --  113.00  77.00  90.00   75
 30  \w    104.00 178.00   1.00    5.68    --  113.00 111.00 -60.00   74
 31  \w     38.00 109.00   1.00    5.68    --  113.00-111.00   0.00   71
 32  \w    104.00 178.00   1.00    5.68    --  113.00 111.00-150.00   74
 33  \w     29.00 107.00   1.00    5.68    --  113.00 -94.00-120.00   78
 34  \w     29.00 107.00   1.00    5.68    --  113.00 -94.00 150.00   78
 35  \w      3.00  30.00   1.00    1.42    --   40.21  89.00  85.88   27
 36  \w      4.00  31.00   1.00    1.42    --   40.21  86.00-174.04   27
 37  \w     11.00 114.00   1.00    1.42    --   40.21  57.00  90.00  103
 38  \w      4.00  31.00   1.00    1.42    --   40.21  86.00 140.48   27
 39  \w     27.00  95.00   1.00    1.42    --   40.21-125.00 -60.00   68
 40  \w     11.00 114.00   1.00    1.42    --   40.21  57.00-180.00  103
 41  \w      4.00  31.00   1.00    1.42    --   40.21  86.00  61.64   27
 42  \w      6.00  81.00   1.00    1.42    --   40.21 -99.00-150.00   75
 43  \w      4.00  31.00   1.00    1.42    --   40.21  86.00-141.30   27
 44  \w     52.00 178.00   1.00    5.68    --  113.00  15.00 150.00  126
 45  \w     85.00 178.00   1.00    5.68    --  113.00  45.00 -60.00   93
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0375554000
_diffrn_orient_matrix_UB_12      -0.0867956000
_diffrn_orient_matrix_UB_13      -0.0080569000
_diffrn_orient_matrix_UB_21      0.1187243000
_diffrn_orient_matrix_UB_22      0.0037186000
_diffrn_orient_matrix_UB_23      0.0197485000
_diffrn_orient_matrix_UB_31      -0.0119858000
_diffrn_orient_matrix_UB_32      0.0244944000
_diffrn_orient_matrix_UB_33      0.0790209000
_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  0.0448
_diffrn_reflns_av_unetI/netI     0.0331
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.985
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       24
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       25
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            90234
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.985
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.340
_diffrn_reflns_theta_min         3.589
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.931
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.568
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.116a (Rigaku Oxford Diffraction, 2024)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.297
_exptl_crystal_description       plate
_exptl_crystal_F_000             1752
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.1
_refine_diff_density_max         1.645
_refine_diff_density_min         -1.246
_refine_diff_density_rms         0.117
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.045
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1134
_refine_ls_number_reflns         18676
_refine_ls_number_restraints     513
_refine_ls_restrained_S_all      1.063
_refine_ls_R_factor_all          0.0701
_refine_ls_R_factor_gt           0.0613
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1178P)^2^+7.7566P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1758
_refine_ls_wR_factor_ref         0.1862
_reflns_Friedel_coverage         0.000
_reflns_number_gt                15921
_reflns_number_total             18676
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc04881h3.cif
_cod_data_source_block           anti-Pd2_1AA2_2AB2
_cod_depositor_comments
'Adding full bibliography for 1575651--1575653.cif.'
_cod_original_cell_volume        4468.80(15)
_cod_database_code               1575651
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_formula         'C72 H44 Pd2 B4 F16 N8'
_shelx_estimated_absorpt_t_max   0.695
_shelx_estimated_absorpt_t_min   0.507
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 B4-F13 = B4-F14 = B4-F16 = B4-F15
 1.42 with sigma of 0.02
 B4A-F13A = B4A-F14A = B4A-F15A = B4A-F16A
 1.42 with sigma of 0.02
 C80-N12
 1.137 with sigma of 0.01
 C80-C79
 1.456 with sigma of 0.01
 C80A-N12A
 1.137 with sigma of 0.01
 C80A-C79A
 1.456 with sigma of 0.01
 N12-C79
 2.59 with sigma of 0.04
 N12A-C79A
 2.59 with sigma of 0.04
 B3-F10 \\sim B3-F10A
 with sigma of 0.02
 B3-F11 \\sim B3-F11A
 with sigma of 0.02
 B3-F12 \\sim B3-F12A
 with sigma of 0.02
 B4-F13 \\sim B4-F14 \\sim B4-F16 \\sim B4-F15
 with sigma of 0.02
 F13-F14 \\sim F14-F16 \\sim F16-F15 \\sim F15-F13 \\sim F14-F15 \\sim F13-F16
 with sigma of 0.04
 B4A-F13A \\sim B4A-F14A \\sim B4A-F15A \\sim B4A-F16A
 with sigma of 0.02
 F13A-F14A \\sim F14A-F15A \\sim F15A-F16A \\sim F16A-F13A \\sim F14A-F16A
\\sim F13A-F15A
 with sigma of 0.04
3. Rigid bond restraints
 B4A, F13A, F14A, F15A, F16A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C80A, C79A, N12A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C79, C80, N12
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
B4 \\sim F13 \\sim F15 \\sim F14 \\sim F16: within 2A with sigma of 0.04 and
sigma for terminal atoms of 0.08 within 2A
B4A \\sim F13A \\sim F14A \\sim F15A \\sim F16A: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
B4 \\sim F13 \\sim F14 \\sim F15 \\sim F16 \\sim B4A \\sim F13A \\sim F14A
\\sim F15A \\sim F16A: within 16A with sigma of 0.02 and sigma for terminal
atoms of 0.05 within 16A
C79 \\sim C80 \\sim N12 \\sim C79A \\sim C80A \\sim N12A: within 16A with sigma
of 0.02 and sigma for terminal atoms of 0.04 within 16A
5. Rigid body (RIGU) restrains
 B4, F13, F14, F15, F16
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B4A, F13A, F14A, F15A, F16A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C79, C80, N12
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C80A, C79A, N12A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(B4A)=Sof(F13A)=Sof(F14A)=Sof(F15A)=Sof(F16A)=1-FVAR(1)
 Sof(B4)=Sof(F13)=Sof(F14)=Sof(F15)=Sof(F16)=FVAR(1)
 Sof(F10A)=Sof(F11A)=Sof(F12A)=1-FVAR(2)
 Sof(F10)=Sof(F11)=Sof(F12)=FVAR(2)
 Sof(C79A)=Sof(H79D)=Sof(H79E)=Sof(H79F)=Sof(C80A)=Sof(N12A)=1-FVAR(3)
 Sof(C79)=Sof(H79A)=Sof(H79B)=Sof(H79C)=Sof(C80)=Sof(N12)=FVAR(3)
7.a Aromatic/amide H refined with riding coordinates:
 C1(H1), C4(H4), C6(H6), C7(H7), C8(H8), C9(H9), C13(H13), C14(H14), C15(H15),
 C17(H17), C21(H21), C22(H22), C23(H23), C24(H24), C25(H25), C26(H26), C27(H27),
  C28(H28), C33(H33), C34(H34), C35(H35), C37(H37), C41(H41), C44(H44),
 C45(H45), C46(H46), C47(H47), C48(H48), C49(H49), C50(H50), C51(H51), C52(H52),
  C57(H57), C58(H58), C59(H59), C60(H60), C61(H61), C62(H62), C63(H63),
 C64(H64), C69(H69), C70(H70), C71(H71), C72(H72)
7.b Idealised Me refined as rotating group:
 C73(H73A,H73B,H73C), C75(H75A,H75B,H75C), C77(H77A,H77B,H77C), C79(H79A,H79B,
 H79C), C79A(H79D,H79E,H79F)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              77049
_shelx_fab_checksum              44347
_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 1.326
_oxdiff_exptl_absorpt_empirical_full_min 0.778