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#$Date: 2025-04-05 06:46:56 +0300 (Sat, 05 Apr 2025) $
#$Revision: 299024 $
#$URL: file:///home/coder/svn-repositories/cod/cif/7/06/36/7063658.cif $
#------------------------------------------------------------------------------
#
# This file is available in the Crystallography Open Database (COD),
# http://www.crystallography.net/
#
# All data on this site have been placed in the public domain by the
# contributors.
#
data_7063658
loop_
_publ_author_name
'Moreno-Narváez, María Esther'
'Arenaza-Corona, Antonino'
'González-Sebastián, Lucero'
'Ramírez, Teresa Apan'
'Ortega, Simón Hernández'
'Cruz-Navarro, J. Antonio'
'Alí-Torres, Jorge'
'Orjuela, Adrián L.'
'Reyes-Marquez, Viviana'
'Lomas-Romero, Leticia'
'Morales-Morales, David'
_publ_section_title
;
 Glycoconjugate Pd(ii) and Cu(ii) complexes of fluorinated N,O Schiff base
 ligands for targeted cancer therapy: synthesis, characterization and in
 vitro cytotoxic activity evaluation
;
_journal_issue                   13
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              5187
_journal_page_last               5199
_journal_paper_doi               10.1039/D4NJ05181E
_journal_volume                  49
_journal_year                    2025
_chemical_formula_moiety         'C28 H18 F6 N2 O4 Pd, 2(C2 H6 O S)'
_chemical_formula_sum            'C32 H30 F6 N2 O6 Pd S2'
_chemical_formula_weight         823.10
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-2019/3
_audit_update_record
;
2024-11-21 deposited with the CCDC.	2025-02-12 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 99.9390(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   17.7063(5)
_cell_length_b                   11.4094(3)
_cell_length_c                   8.6419(2)
_cell_measurement_reflns_used    9921
_cell_measurement_temperature    298(2)
_cell_measurement_theta_max      25.39
_cell_measurement_theta_min      2.34
_cell_volume                     1719.62(8)
_computing_cell_refinement       'APEX3 v2018.2 (Bruker, 2018)'
_computing_data_collection       'APEX3 v2018.2 (Bruker, 2018)'
_computing_data_reduction        'SAINT V8.37A  (Bruker, 2018)'
_computing_molecular_graphics
'Ortep-3 Ver 2.02 L.J. Farrugia (1997) J. Appl. Cryst. 30, 565'
_computing_publication_material  'SHELXL-2018/3 (Sheldrick, 2015)'
_computing_structure_refinement  'SHELXL-2019/2 (Sheldrick, 2019)'
_computing_structure_solution    'SHELXS-2018 (Bruker, 2015)'
_diffrn_ambient_temperature      298(2)
_diffrn_detector_area_resol_mean 52.0833
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device_type
'Bruker D8 Venture κ-geometry diffractometer 208039-01'
_diffrn_measurement_method       ω-scans
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0279
_diffrn_reflns_av_unetI/netI     0.0267
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       10
_diffrn_reflns_limit_l_min       -10
_diffrn_reflns_number            13051
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         25.389
_diffrn_reflns_theta_min         2.336
_diffrn_source                   'micro-focus X-ray source'
_exptl_absorpt_coefficient_mu    0.739
_exptl_absorpt_correction_T_max  0.7452
_exptl_absorpt_correction_T_min  0.6919
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
; 
 SADABS 2016/2: Krause, L., Herbst-Irmer, R., Sheldrick G.M. & Stalke D., 
 J. Appl. Cryst. 48 (2015) 3-10 
;
_exptl_crystal_colour            orange
_exptl_crystal_density_diffrn    1.590
_exptl_crystal_description       Prism
_exptl_crystal_F_000             832
_exptl_crystal_size_max          0.414
_exptl_crystal_size_mid          0.301
_exptl_crystal_size_min          0.264
_refine_diff_density_max         0.436
_refine_diff_density_min         -0.277
_refine_diff_density_rms         0.056
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.045
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     295
_refine_ls_number_reflns         3163
_refine_ls_number_restraints     199
_refine_ls_restrained_S_all      1.096
_refine_ls_R_factor_all          0.0482
_refine_ls_R_factor_gt           0.0337
_refine_ls_shift/su_max          0.008
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[σ²(Fo²)+(0.0318P)²+1.4543P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0723
_refine_ls_wR_factor_ref         0.0800
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2485
_reflns_number_total             3163
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            d4nj05181e2.cif
_cod_data_source_block           Pd(L3)2
_cod_depositor_comments
'Adding full bibliography for 7063651--7063658.cif.'
_cod_original_sg_symbol_H-M      'P 21/c'
_cod_database_code               7063658
_shelx_shelxl_version_number     2019/3
_shelx_space_group_comment
; 
The symmetry employed for this shelxl refinement is uniquely defined 
by the following loop, which should always be used as a source of 
symmetry information in preference to the above space-group names. 
They are only intended as comments. 
;
_shelx_estimated_absorpt_t_min   0.750
_shelx_estimated_absorpt_t_max   0.829
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, y+1/2, -z+1/2'
'-x, -y, -z'
'x, -y-1/2, z-1/2'
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_occupancy
_atom_site_site_symmetry_order
_atom_site_calc_flag
_atom_site_refinement_flags_posn
_atom_site_refinement_flags_adp
_atom_site_refinement_flags_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
Pd1 Pd 0.500000 0.500000 1.000000 0.03933(12) Uani 1 2 d S . P . .
O1 O 0.38783(12) 0.49640(17) 0.9919(2) 0.0509(5) Uani 1 1 d . . . . .
O2 O 0.13307(13) 0.6174(2) 0.8876(3) 0.0671(6) Uani 1 1 d D . . . .
H2A H 0.1014(17) 0.659(3) 0.828(4) 0.081 Uiso 1 1 d D U . . .
N1 N 0.48797(14) 0.5871(2) 0.7931(3) 0.0435(6) Uani 1 1 d . . . . .
C1 C 0.35293(17) 0.6366(2) 0.7832(4) 0.0461(7) Uani 1 1 d . . . . .
C6 C 0.29246(19) 0.7026(3) 0.6991(4) 0.0585(9) Uani 1 1 d . . . . .
H6 H 0.302556 0.750796 0.618224 0.070 Uiso 1 1 calc R U . . .
C2 C 0.33665(17) 0.5624(2) 0.9057(3) 0.0427(7) Uani 1 1 d . . . . .
C3 C 0.26107(17) 0.5581(3) 0.9341(4) 0.0473(7) Uani 1 1 d . . . . .
H3 H 0.249319 0.508406 1.011908 0.057 Uiso 1 1 calc R U . . .
C4 C 0.20429(18) 0.6250(3) 0.8505(4) 0.0501(8) Uani 1 1 d . . . . .
C5 C 0.22001(19) 0.6993(3) 0.7304(4) 0.0608(9) Uani 1 1 d . . . . .
H5 H 0.181549 0.745355 0.673564 0.073 Uiso 1 1 calc R U . . .
C7 C 0.42494(17) 0.6400(3) 0.7330(4) 0.0480(7) Uani 1 1 d . . . . .
H7 H 0.427286 0.686176 0.645301 0.058 Uiso 1 1 calc R U . . .
C8 C 0.55302(17) 0.6023(3) 0.7155(3) 0.0451(7) Uani 1 1 d . . . . .
C9 C 0.57824(19) 0.7122(3) 0.6844(4) 0.0589(9) Uani 1 1 d . . . . .
H9 H 0.552001 0.778027 0.710134 0.071 Uiso 1 1 calc R U . . .
C10 C 0.6424(2) 0.7255(3) 0.6150(4) 0.0656(10) Uani 1 1 d . . . . .
H10 H 0.658384 0.800027 0.591346 0.079 Uiso 1 1 calc R U . . .
C11 C 0.68226(18) 0.6290(3) 0.5810(4) 0.0556(8) Uani 1 1 d . . . . .
C12 C 0.6569(2) 0.5182(3) 0.6102(4) 0.0587(9) Uani 1 1 d . . . . .
H12 H 0.683471 0.452648 0.584853 0.070 Uiso 1 1 calc R U . . .
C13 C 0.59215(19) 0.5049(3) 0.6770(4) 0.0540(8) Uani 1 1 d . . . . .
H13 H 0.574815 0.430232 0.696209 0.065 Uiso 1 1 calc R U . . .
C14 C 0.7556(2) 0.6429(3) 0.5183(5) 0.0777(10) Uani 1 1 d D U . . .
F1 F 0.8146(3) 0.6167(6) 0.6211(7) 0.134(2) Uani 0.726(6) 1 d D U P A 1
F2 F 0.7694(2) 0.7569(3) 0.4835(6) 0.1018(15) Uani 0.726(6) 1 d D U P A 1
F3 F 0.7549(3) 0.5901(5) 0.3883(7) 0.128(2) Uani 0.726(6) 1 d D U P A 1
F1A F 0.7481(7) 0.6867(15) 0.3818(15) 0.126(4) Uani 0.274(6) 1 d D U P A 2
F2A F 0.7882(6) 0.5332(7) 0.4945(16) 0.090(3) Uani 0.274(6) 1 d D U P A 2
F3A F 0.8094(8) 0.6889(13) 0.6139(16) 0.117(4) Uani 0.274(6) 1 d D U P A 2
S1 S -0.01115(7) 0.84661(10) 0.67091(14) 0.0690(4) Uani 0.878(3) 1 d D U P B 1
O3 O 0.0254(3) 0.7274(3) 0.6879(4) 0.0729(11) Uani 0.878(3) 1 d D U P B 1
C15 C 0.0617(3) 0.9480(5) 0.7442(8) 0.1062(18) Uani 0.878(3) 1 d D U P B 1
H15A H 0.085028 0.925841 0.848715 0.159 Uiso 0.878(3) 1 calc R U P B 1
H15B H 0.039894 1.024913 0.746141 0.159 Uiso 0.878(3) 1 calc R U P B 1
H15C H 0.099837 0.948395 0.677523 0.159 Uiso 0.878(3) 1 calc R U P B 1
C16 C -0.0669(3) 0.8591(5) 0.8180(8) 0.0952(19) Uani 0.878(3) 1 d D U P B 1
H16A H -0.107824 0.802955 0.800023 0.143 Uiso 0.878(3) 1 calc R U P B 1
H16B H -0.087929 0.936754 0.816620 0.143 Uiso 0.878(3) 1 calc R U P B 1
H16C H -0.035571 0.844596 0.918431 0.143 Uiso 0.878(3) 1 calc R U P B 1
S1A S 0.0292(5) 0.8672(8) 0.8125(11) 0.079(3) Uani 0.122(3) 1 d D U P B 2
O3A O 0.0268(19) 0.7428(12) 0.753(3) 0.070(5) Uani 0.122(3) 1 d D U P B 2
C15A C 0.027(2) 0.957(2) 0.646(3) 0.084(5) Uani 0.122(3) 1 d D U P B 2
H15D H 0.072167 0.943712 0.600799 0.126 Uiso 0.122(3) 1 calc R U P B 2
H15E H 0.025331 1.038123 0.676087 0.126 Uiso 0.122(3) 1 calc R U P B 2
H15F H -0.017672 0.939251 0.569578 0.126 Uiso 0.122(3) 1 calc R U P B 2
C16A C -0.0611(15) 0.899(3) 0.855(5) 0.087(6) Uani 0.122(3) 1 d D U P B 2
H16D H -0.098161 0.897869 0.759656 0.130 Uiso 0.122(3) 1 calc R U P B 2
H16E H -0.060429 0.975042 0.902336 0.130 Uiso 0.122(3) 1 calc R U P B 2
H16F H -0.074667 0.841158 0.926247 0.130 Uiso 0.122(3) 1 calc R U P B 2
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
S S 0.1246 0.1234 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
Pd Pd -0.9988 1.0072 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle_publ_flag
O1 Pd1 O1 180.00(11) . 3_667 ?
O1 Pd1 N1 88.45(9) . 3_667 ?
O1 Pd1 N1 91.55(9) 3_667 3_667 ?
O1 Pd1 N1 91.55(9) . . ?
O1 Pd1 N1 88.45(9) 3_667 . ?
N1 Pd1 N1 180.0 3_667 . ?
C2 O1 Pd1 126.99(18) . . ?
C4 O2 H2A 111(3) . . ?
C7 N1 C8 117.4(2) . . ?
C7 N1 Pd1 122.3(2) . . ?
C8 N1 Pd1 119.98(18) . . ?
C6 C1 C7 118.2(3) . . ?
C6 C1 C2 118.0(3) . . ?
C7 C1 C2 123.5(3) . . ?
C5 C6 C1 123.0(3) . . ?
C5 C6 H6 118.5 . . ?
C1 C6 H6 118.5 . . ?
O1 C2 C3 117.9(3) . . ?
O1 C2 C1 123.8(3) . . ?
C3 C2 C1 118.2(3) . . ?
C4 C3 C2 121.7(3) . . ?
C4 C3 H3 119.2 . . ?
C2 C3 H3 119.2 . . ?
O2 C4 C3 117.9(3) . . ?
O2 C4 C5 121.6(3) . . ?
C3 C4 C5 120.5(3) . . ?
C6 C5 C4 118.6(3) . . ?
C6 C5 H5 120.7 . . ?
C4 C5 H5 120.7 . . ?
N1 C7 C1 128.5(3) . . ?
N1 C7 H7 115.7 . . ?
C1 C7 H7 115.7 . . ?
C9 C8 C13 119.6(3) . . ?
C9 C8 N1 120.9(3) . . ?
C13 C8 N1 119.4(3) . . ?
C8 C9 C10 120.3(3) . . ?
C8 C9 H9 119.8 . . ?
C10 C9 H9 119.8 . . ?
C11 C10 C9 119.9(3) . . ?
C11 C10 H10 120.0 . . ?
C9 C10 H10 120.0 . . ?
C10 C11 C12 120.2(3) . . ?
C10 C11 C14 120.3(3) . . ?
C12 C11 C14 119.5(3) . . ?
C13 C12 C11 119.9(3) . . ?
C13 C12 H12 120.1 . . ?
C11 C12 H12 120.1 . . ?
C12 C13 C8 120.0(3) . . ?
C12 C13 H13 120.0 . . ?
C8 C13 H13 120.0 . . ?
F3A C14 F1A 113.0(7) . . ?
F3 C14 F1 112.4(4) . . ?
F3 C14 F2 103.3(4) . . ?
F1 C14 F2 102.6(4) . . ?
F3A C14 F2A 100.5(6) . . ?
F1A C14 F2A 101.2(6) . . ?
F3A C14 C11 114.2(7) . . ?
F1A C14 C11 114.9(6) . . ?
F3 C14 C11 113.1(4) . . ?
F1 C14 C11 112.2(4) . . ?
F2 C14 C11 112.3(3) . . ?
F2A C14 C11 111.2(5) . . ?
O3 S1 C16 106.9(2) . . ?
O3 S1 C15 106.4(3) . . ?
C16 S1 C15 98.9(3) . . ?
S1 C15 H15A 109.5 . . ?
S1 C15 H15B 109.5 . . ?
H15A C15 H15B 109.5 . . ?
S1 C15 H15C 109.5 . . ?
H15A C15 H15C 109.5 . . ?
H15B C15 H15C 109.5 . . ?
S1 C16 H16A 109.5 . . ?
S1 C16 H16B 109.5 . . ?
H16A C16 H16B 109.5 . . ?
S1 C16 H16C 109.5 . . ?
H16A C16 H16C 109.5 . . ?
H16B C16 H16C 109.5 . . ?
O3A S1A C16A 107.2(9) . . ?
O3A S1A C15A 105.9(8) . . ?
C16A S1A C15A 99.2(8) . . ?
S1A C15A H15D 109.5 . . ?
S1A C15A H15E 109.5 . . ?
H15D C15A H15E 109.5 . . ?
S1A C15A H15F 109.5 . . ?
H15D C15A H15F 109.5 . . ?
H15E C15A H15F 109.5 . . ?
S1A C16A H16D 109.5 . . ?
S1A C16A H16E 109.5 . . ?
H16D C16A H16E 109.5 . . ?
S1A C16A H16F 109.5 . . ?
H16D C16A H16F 109.5 . . ?
H16E C16A H16F 109.5 . . ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
_geom_bond_publ_flag
Pd1 O1 1.976(2) . ?
Pd1 O1 1.976(2) 3_667 ?
Pd1 N1 2.024(2) 3_667 ?
Pd1 N1 2.024(2) . ?
O1 C2 1.308(3) . ?
O2 C4 1.357(4) . ?
O2 H2A 0.841(10) . ?
N1 C7 1.296(4) . ?
N1 C8 1.440(4) . ?
C1 C6 1.405(4) . ?
C1 C7 1.416(4) . ?
C1 C2 1.423(4) . ?
C6 C5 1.356(4) . ?
C6 H6 0.9300 . ?
C2 C3 1.403(4) . ?
C3 C4 1.366(4) . ?
C3 H3 0.9300 . ?
C4 C5 1.405(5) . ?
C5 H5 0.9300 . ?
C7 H7 0.9300 . ?
C8 C9 1.374(4) . ?
C8 C13 1.380(4) . ?
C9 C10 1.381(4) . ?
C9 H9 0.9300 . ?
C10 C11 1.367(5) . ?
C10 H10 0.9300 . ?
C11 C12 1.379(5) . ?
C11 C14 1.499(5) . ?
C12 C13 1.379(4) . ?
C12 H12 0.9300 . ?
C13 H13 0.9300 . ?
C14 F3A 1.263(9) . ?
C14 F1A 1.267(8) . ?
C14 F3 1.273(5) . ?
C14 F1 1.285(6) . ?
C14 F2 1.366(5) . ?
C14 F2A 1.409(7) . ?
S1 O3 1.502(3) . ?
S1 C16 1.745(5) . ?
S1 C15 1.767(5) . ?
C15 H15A 0.9600 . ?
C15 H15B 0.9600 . ?
C15 H15C 0.9600 . ?
C16 H16A 0.9600 . ?
C16 H16B 0.9600 . ?
C16 H16C 0.9600 . ?
S1A O3A 1.508(10) . ?
S1A C16A 1.739(11) . ?
S1A C15A 1.766(11) . ?
C15A H15D 0.9600 . ?
C15A H15E 0.9600 . ?
C15A H15F 0.9600 . ?
C16A H16D 0.9600 . ?
C16A H16E 0.9600 . ?
C16A H16F 0.9600 . ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
_geom_hbond_publ_flag
O2 H2A O3^a 0.841(10) 1.822(13) 2.656(5) 171(4) . yes
