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_1575652
_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         'C68 H46 N8 Pd2, 4(B F4), C4 H10 O, C2 H3 N'
_chemical_formula_sum            'C74 H59 B4 F16 N9 O Pd2'
_chemical_formula_weight         1650.34
_space_group_crystal_system      monoclinic
_space_group_IT_number           12
_space_group_name_Hall           '-C 2y'
_space_group_name_H-M_alt        'C 1 2/m 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-10-09
_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                90
_cell_angle_beta                 100.318(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   12.5045(4)
_cell_length_b                   42.5947(13)
_cell_length_c                   15.1704(5)
_cell_measurement_reflns_used    11489
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      76.1410
_cell_measurement_theta_min      5.0660
_cell_volume                     7949.5(4)
_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 0.999
_diffrn_measured_fraction_theta_max 0.980
_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    -69.00  34.00   1.00    1.44    --  -40.21  52.00 174.00  103
  2  \w    -34.00  69.00   1.00    1.44    --   40.21 -52.00  28.00  103
  3  \w     12.00 114.00   1.00    1.44    --   40.21  52.00 174.00  102
  4  \w     39.00 142.00   1.00    5.75    --  113.00 -52.00  28.00  103
  5  \w     39.00 142.00   1.00    5.75    --  113.00 -52.00  28.00  103
  6  \w     84.00 178.00   1.00    5.75    --  113.00  52.00 174.00   94
  7  \w   -114.00 -12.00   1.00    1.44    --  -40.21 -52.00  28.00  102
  8  \w     27.00  95.00   1.00    1.44    --   40.21-125.00  60.00   68
  9  \w     27.00  95.00   1.00    1.44    --   40.21-125.00 -90.00   68
 10  \w     38.00 109.00   1.00    5.75    --  113.00-111.00  60.00   71
 11  \w     85.00 178.00   1.00    5.75    --  113.00  45.00 120.00   93
 12  \w     35.00 144.00   1.00    5.75    --  113.00 -30.00 150.00  109
 13  \w    104.00 178.00   1.00    5.75    --  113.00 111.00-180.00   74
 14  \w     38.00 109.00   1.00    5.75    --  113.00-111.00 -30.00   71
 15  \w     38.00 109.00   1.00    5.75    --  113.00-111.00-150.00   71
 16  \w    104.00 178.00   1.00    5.75    --  113.00 111.00  90.00   74
 17  \w     11.00  72.00   1.00    1.44    --   40.21  57.00 -60.00   61
;
_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      0.0184810000
_diffrn_orient_matrix_UB_12      0.0073959000
_diffrn_orient_matrix_UB_13      -0.0955145000
_diffrn_orient_matrix_UB_21      -0.0922197000
_diffrn_orient_matrix_UB_22      -0.0227928000
_diffrn_orient_matrix_UB_23      -0.0386522000
_diffrn_orient_matrix_UB_31      -0.0826351000
_diffrn_orient_matrix_UB_32      0.0271025000
_diffrn_orient_matrix_UB_33      -0.0063157000
_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  0.0443
_diffrn_reflns_av_unetI/netI     0.0392
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.980
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       53
_diffrn_reflns_limit_k_min       -36
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            33019
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.980
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.253
_diffrn_reflns_theta_min         3.616
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.382
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.512
_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    1.379
_exptl_crystal_description       plate
_exptl_crystal_F_000             3320
_exptl_crystal_size_max          0.204
_exptl_crystal_size_mid          0.163
_exptl_crystal_size_min          0.078
_refine_diff_density_max         1.012
_refine_diff_density_min         -1.231
_refine_diff_density_rms         0.105
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.024
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     636
_refine_ls_number_reflns         8391
_refine_ls_number_restraints     577
_refine_ls_restrained_S_all      1.038
_refine_ls_R_factor_all          0.0776
_refine_ls_R_factor_gt           0.0658
_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^)+(0.1327P)^2^+9.4832P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1868
_refine_ls_wR_factor_ref         0.2019
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6806
_reflns_number_total             8391
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc04881h3.cif
_cod_data_source_block           anti-Pd2_1AC2_4AA2
_cod_depositor_comments
'Adding full bibliography for 1575651--1575653.cif.'
_cod_database_code               1575652
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_formula         'C68 H48 Pd2 B4 F16 N8'
_shelx_estimated_absorpt_t_max   0.726
_shelx_estimated_absorpt_t_min   0.468
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 B2-F5 = B2-F6 = B2-F7 = B2-F8
 1.42 with sigma of 0.02
 B3-F9 = B3-F10 = B3-F11 = B3-F12
 1.42 with sigma of 0.02
 B4-F13 = B4-F14 = B4-F15 = B4-F16
 1.42 with sigma of 0.02
 O1-C35
 1.41 with sigma of 0.02
 O1-C37
 1.42 with sigma of 0.02
 C36-C35
 1.48 with sigma of 0.02
 C37-C38
 1.5 with sigma of 0.02
 O1A-C35A
 1.41 with sigma of 0.02
 O1A-C37A
 1.42 with sigma of 0.02
 C36A-C35A
 1.48 with sigma of 0.02
 C37A-C38A
 1.5 with sigma of 0.02
 C34-C32 = C34A-C23
 1.5 with sigma of 0.01
 O1-C36 = O1-C38
 2.37 with sigma of 0.04
 O1A-C36A = O1A-C38A
 2.37 with sigma of 0.04
 C37A-C35A
 2.47 with sigma of 0.04
 B2-F5 \\sim B2-F6 \\sim B2-F7 \\sim B2-F8
 with sigma of 0.02
 F7-F5 \\sim F5-F8 \\sim F8-F6 \\sim F6-F7 \\sim F5-F6 \\sim F7-F8
 with sigma of 0.04
 B3-F9 \\sim B3-F11 \\sim B3-F10 \\sim B3-F12
 with sigma of 0.02
 F9-F11 \\sim F11-F10 \\sim F10-F12 \\sim F12-F9 \\sim F11-F12 \\sim F9-F10
 with sigma of 0.04
 B4-F13 \\sim B4-F14 \\sim B4-F15 \\sim B4-F16
 with sigma of 0.02
 F15-F14 \\sim F14-F16 \\sim F16-F13 \\sim F13-F15 \\sim F14-F13 \\sim F15-F16
 with sigma of 0.04
 C36-C35 \\sim C37-C38
 with sigma of 0.02
 O1-C35 \\sim O1-C37
 with sigma of 0.02
 C36-O1 \\sim O1-C38
 with sigma of 0.04
 C36A-C35A \\sim C37A-C38A
 with sigma of 0.02
 O1A-C35A \\sim O1A-C37A
 with sigma of 0.02
 C36A-O1A \\sim O1A-C38A
 with sigma of 0.04
 C32-C34 \\sim C23-C34A
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
B2 \\sim F5 \\sim F6 \\sim F7 \\sim F8: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 2A
B3 \\sim F9 \\sim F10 \\sim F11 \\sim F12: 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: within 2A with sigma of 0.04 and
sigma for terminal atoms of 0.08 within 2A
C35 \\sim C36 \\sim C37 \\sim C38 \\sim O1: within 2A with sigma of 0.04 and
sigma for terminal atoms of 0.08 within 2A
C35A \\sim C36A \\sim C37A \\sim C38A \\sim O1A: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
C35 \\sim C36 \\sim C37 \\sim C38 \\sim O1 \\sim C35A \\sim C36A \\sim C37A
\\sim C38A \\sim O1A: within 16A with sigma of 0.04 and sigma for terminal
atoms of 0.04 within 16A
C36 \\sim C36A: within 16A with sigma of 0.01 and sigma for terminal atoms of
0.01 within 16A
4. Rigid body (RIGU) restrains
 B2, F5, F6, F7, F8
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B3, F9, F10, F11, F12
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B4, F13, F14, F15, F16
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C35, C36, C37, C38, O1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C35A, C36A, C37A, C38A, O1A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(H32)=Sof(C34A)=Sof(H34D)=Sof(H34E)=Sof(H34F)=1-FVAR(1)
 Sof(H23)=Sof(C34)=Sof(H34A)=Sof(H34B)=Sof(H34C)=FVAR(1)
 Fixed Sof: B2(0.5) F7(0.5) F5(0.5) F8(0.5) F6(0.5) B3(0.5) F9(0.5) F11(0.5)
 F10(0.5) F12(0.5) B4(0.5) F13(0.5) F14(0.5) F15(0.5) F16(0.5) C35(0.333333)
 H35A(0.333333) H35B(0.333333) C36(0.333333) H36A(0.333333) H36B(0.333333)
 H36C(0.333333) C37(0.333333) H37A(0.333333) H37B(0.333333) C38(0.333333)
 H38A(0.333333) H38B(0.333333) H38C(0.333333) O1(0.333333) C35A(0.166667)
 H35C(0.166667) H35D(0.166667) C36A(0.166667) H36D(0.166667) H36E(0.166667)
 H36F(0.166667) C37A(0.166667) H37C(0.166667) H37D(0.166667) C38A(0.166667)
 H38D(0.166667) H38E(0.166667) H38F(0.166667) O1A(0.166667) H39A(0.5) H39B(0.5)
 H39C(0.5)
6.a Secondary CH2 refined with riding coordinates:
 C35(H35A,H35B), C37(H37A,H37B), C35A(H35C,H35D), C37A(H37C,H37D)
6.b Me refined with riding coordinates:
 C36(H36A,H36B,H36C), C38(H38A,H38B,H38C), C36A(H36D,H36E,H36F), C38A(H38D,
 H38E,H38F)
6.c Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C4(H4), C9(H9), C10(H10), C11(H11), C18(H18),
 C19(H19), C20(H20), C21(H21), C22(H22), C23(H23), C24(H24), C25(H25), C30(H30),
  C32(H32), C33(H33)
6.d Idealised Me refined as rotating group:
 C14(H14A,H14B,H14C), C34(H34A,H34B,H34C), C34A(H34D,H34E,H34F), C39(H39A,H39B,
 H39C)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              5216
_shelx_fab_checksum              42260
_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 1.985
_oxdiff_exptl_absorpt_empirical_full_min 0.663