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_1575653
_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         'C64 H42 N10 Pd2, 4(B F4), 4(C2 H3 N)'
_chemical_formula_sum            'C72 H54 B4 F16 N14 Pd2'
_chemical_formula_weight         1675.33
_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             2024-10-11
_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                63.129(2)
_cell_angle_beta                 85.660(2)
_cell_angle_gamma                82.854(2)
_cell_formula_units_Z            2
_cell_length_a                   11.4465(2)
_cell_length_b                   18.8695(4)
_cell_length_c                   20.7359(4)
_cell_measurement_reflns_used    24984
_cell_measurement_temperature    99.99(10)
_cell_measurement_theta_max      76.0250
_cell_measurement_theta_min      2.3730
_cell_volume                     3963.17(15)
_computing_cell_refinement       'CrysAlisPro 1.171.43.121a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.121a 64-bit (release 24-04-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.121a (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_temperature      100.15
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.996
_diffrn_measured_fraction_theta_max 0.919
_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    -80.00  18.00   0.50    2.50    --  -47.85 101.00 -34.00  196
  2  \w      4.00  80.00   0.50    2.50    --   47.85-101.00-138.00  152
  3  \w    -80.00 -20.00   0.50   10.00    --  -90.00 101.00 -34.00  120
  4  \w   -160.00 -85.00   0.50   10.00    --  -90.00-101.00-138.00  150
  5  \w    107.00 178.00   0.50   10.00    --  109.71 101.00 -34.00  142
  6  \w     40.00 106.00   0.50   10.00    --  109.71-101.00-138.00  132
  7  \w    -69.00  21.00   0.50    2.50    --  -47.85  77.00 120.00  180
  8  \w   -119.00 -36.00   0.50    2.50    --  -47.85 -48.00 -99.91  166
  9  \w    -69.00  21.00   0.50    2.50    --  -47.85  77.00 120.00  180
 10  \w    -48.00  24.00   0.50    2.50    --  -47.85  38.00 -30.00  144
 11  \w   -119.00 -36.00   0.50    2.50    --  -47.85 -51.00-173.69  166
 12  \w    -34.00  27.00   0.50    2.50    --  -47.85  19.00-120.00  122
 13  \w    -25.00  26.00   0.50    2.50    --   47.85 -19.00 -30.00  102
 14  \w   -160.00-102.00   0.50   10.00    --  -90.00 -99.00 -90.00  116
 15  \w    -48.00 -18.00   0.50   10.00    --  -90.00  38.00-120.00   60
 16  \w   -161.00 -85.00   0.50   10.00    --  -90.00 -53.00  91.83  152
 17  \w   -159.00 -90.00   0.50   10.00    --  -90.00-125.00  90.00  138
 18  \w    -48.00 -18.00   0.50   10.00    --  -90.00  38.00 -90.00   60
 19  \w    -48.00 -18.00   0.50   10.00    --  -90.00  38.00 150.00   60
 20  \w    -85.00 -21.00   0.50   10.00    --  -90.00 125.00 -60.00  128
 21  \w    -69.00 -18.00   0.50   10.00    --  -90.00  57.00  90.00  102
 22  \w   -160.00-102.00   0.50   10.00    --  -90.00 -99.00  60.00  116
 23  \w   -161.00 -88.00   0.50   10.00    --  -90.00 -54.00 -47.37  146
 24  \w    -69.00 -18.00   0.50   10.00    --  -90.00  57.00-180.00  102
 25  \w    -48.00 -18.00   0.50   10.00    --  -90.00  38.00  90.00   60
 26  \w   -105.00 -18.00   0.50   10.00    --  -90.00  77.00 -30.00  174
 27  \w   -161.00 -85.00   0.50   10.00    --  -90.00 -53.00  91.83  152
 28  \w   -149.00-123.00   0.50   10.00    --  -90.00-125.00  90.00   52
 29  \w    -44.00 -18.00   0.50   10.00    --  -90.00  38.00-180.00   52
 30  \w   -160.00-129.00   0.50   10.00    --  -90.00 -56.00 -67.50   62
 31  \w    -46.00 -19.00   0.50   10.00    --  -90.00  38.00 120.00   54
 32  \w   -120.00 -92.00   0.50   10.00    --  -90.00 -56.00 -67.50   56
 33  \w   -159.00-131.00   0.50   10.00    --  -90.00 -99.00 150.00   56
 34  \w    -55.00 -20.00   0.50   10.00    --  -90.00  57.00 -90.00   70
 35  \w     44.00 106.00   0.50   10.00    --  109.71 -99.00 150.00  124
 36  \w     49.00 103.00   0.50   10.00    --  109.71 -99.00-180.00  108
 37  \w     78.00 106.00   0.50   10.00    --  109.71 -99.00  30.00   56
 38  \w     51.00  77.00   0.50   10.00    --  109.71 -99.00  30.00   52
 39  \w     54.00 107.00   0.50   10.00    --  109.71-104.00 -85.13  106
 40  \w     41.00  94.00   0.50   10.00    --  109.71-125.00  60.00  106
 41  \w     78.00 105.00   0.50   10.00    --  109.71 -99.00 120.00   54
 42  \w     53.00  79.00   0.50   10.00    --  109.71 -77.00  30.00   52
 43  \w     51.00 106.00   0.50   10.00    --  109.71 -99.00 -60.00  110
 44  \w     61.00 105.00   0.50   10.00    --  109.71-125.00 150.00   88
 45  \w     70.00  97.00   0.50   10.00    --  109.71 -77.00-150.00   54
 46  \w     55.00 111.00   0.50   10.00    --  109.71-125.00 120.00  112
 47  \w     96.00 174.00   0.50   10.00    --  109.71  57.00 120.00  156
 48  \w     56.00 106.00   0.50   10.00    --  109.71 -99.00   0.00  100
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0797
_diffrn_reflns_av_unetI/netI     0.0558
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.919
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            68565
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.919
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         78.287
_diffrn_reflns_theta_min         2.389
_exptl_absorpt_coefficient_mu    4.414
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.559
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.121a (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    1.404
_exptl_crystal_description       plate
_exptl_crystal_F_000             1680
_exptl_crystal_size_max          0.148
_exptl_crystal_size_mid          0.075
_exptl_crystal_size_min          0.042
_refine_diff_density_max         2.001
_refine_diff_density_min         -1.511
_refine_diff_density_rms         0.132
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.028
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1008
_refine_ls_number_reflns         15631
_refine_ls_number_restraints     331
_refine_ls_restrained_S_all      1.027
_refine_ls_R_factor_all          0.0973
_refine_ls_R_factor_gt           0.0789
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1220P)^2^+18.4883P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2180
_refine_ls_wR_factor_ref         0.2323
_reflns_Friedel_coverage         0.000
_reflns_number_gt                12159
_reflns_number_total             15631
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc04881h3.cif
_cod_data_source_block           syn-Pd2_1AC2_3AA2
_cod_depositor_comments
'Adding full bibliography for 1575651--1575653.cif.'
_cod_database_code               1575653
_shelx_shelxl_version_number     2019/3
_shelx_estimated_absorpt_t_max   0.836
_shelx_estimated_absorpt_t_min   0.561
_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
 N13-C70
 1.14 with sigma of 0.02
 C70-N13
 1.137 with sigma of 0.01
 C70-C69
 1.456 with sigma of 0.01
 C69-N13
 2.593 with sigma of 0.02
 N14-C72
 1.14 with sigma of 0.02
 C72-N14
 1.137 with sigma of 0.01
 C72-C71
 1.456 with sigma of 0.01
 C71-N14
 2.593 with sigma of 0.02
 N14A-C72A
 1.14 with sigma of 0.02
 C72A-N14A
 1.137 with sigma of 0.01
 C72A-C71A
 1.456 with sigma of 0.01
 C71A-N14A
 2.593 with sigma of 0.02
 N11-C65
 2.59 with sigma of 0.02
 N13-C69
 2.59 with sigma of 0.04
 N14-C71
 2.59 with sigma of 0.04
 N14A-C71A
 2.59 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
B1 \\sim F1 \\sim F2 \\sim F3 \\sim F4 \\sim B2 \\sim F5 \\sim F6 \\sim F7
\\sim F8: within 10A with sigma of 0.04 and sigma for terminal atoms of 0.08
within 10A
C66 \\sim C65 \\sim N11: within 10A with sigma of 0.02 and sigma for terminal
atoms of 0.04 within 10A
C69 \\sim C70 \\sim N13: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
C71 \\sim C72 \\sim N14: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
C71A \\sim C72A \\sim N14A: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
C71 \\sim C72 \\sim N14 \\sim C71A \\sim C72A \\sim N14A: within 4A with sigma
of 0.02 and sigma for terminal atoms of 0.04 within 4A
4. Rigid body (RIGU) restrains
 C69, C70, N13
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C71, C72, N14
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C71A, C72A, N14A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(C71A)=Sof(H71D)=Sof(H71E)=Sof(H71F)=Sof(C72A)=Sof(N14A)=1-FVAR(1)
 Sof(C71)=Sof(H71A)=Sof(H71B)=Sof(H71C)=Sof(C72)=Sof(N14)=FVAR(1)
6.a Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C4(H4), C9(H9), C10(H10), C11(H11), C16(H16),
 C17(H17), C18(H18), C19(H19), C20(H20), C21(H21), C22(H22), C23(H23), C28(H28),
  C29(H29), C30(H30), C35(H35), C36(H36), C37(H37), C38(H38), C39(H39),
 C40(H40), C41(H41), C42(H42), C47(H47), C48(H48), C50(H50), C52(H52), C53(H53),
  C54(H54), C55(H55), C60(H60), C61(H61), C63(H63)
6.b Idealised Me refined as rotating group:
 C51(H51A,H51B,H51C), C64(H64A,H64B,H64C), C65(H65A,H65B,H65C), C67(H67A,H67B,
 H67C), C69(H69A,H69B,H69C), C71(H71A,H71B,H71C), C71A(H71D,H71E,H71F)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              40747
_shelx_fab_checksum              52882
_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
;