Design of a new palladium(ii) halide complex as a bio-active material: synthesis, physico-chemical studies, DFT-computations and evaluation of anti-inflammatory, antioxidant and anti-gastric damage activities
Bougossa, Sarra; Mhadhbi, Noureddine; Ben Ahmed, Ali; Hamdi, Mohamed; Elghniji, Kais; Erwann, Jeanneau; Hamden, Khaled; Oueslati, Abderrazek; Naïli, Houcine; RSC Advances 14 (2024) 17413–17433; doi:10.1039/D4RA02984D

data_7248758
_publ_section_title
;
 Design of a new palladium(ii) halide complex as a bio-active material:
 synthesis, physico-chemical studies, DFT-computations and evaluation of
 anti-inflammatory, antioxidant and anti-gastric damage activities
;
_journal_issue                   25
_journal_name_full               'RSC Advances'
_journal_page_first              17413
_journal_page_last               17433
_journal_paper_doi               10.1039/D4RA02984D
_journal_volume                  14
_journal_year                    2024
_chemical_formula_moiety         'Cl6 Pd, 2(H2 O), 2(C6 H10 N2)'
_chemical_formula_sum            'C12 H24 Cl6 N4 O2 Pd'
_chemical_formula_weight         575.45
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2021-09-17
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6272)
;
_audit_update_record
;
2024-02-07 deposited with the CCDC.	2024-05-19 downloaded from the CCDC.
;
_cell_angle_alpha                81.799(8)
_cell_angle_beta                 83.134(8)
_cell_angle_gamma                66.739(10)
_cell_formula_units_Z            1
_cell_length_a                   7.7207(8)
_cell_length_b                   7.7941(8)
_cell_length_c                   9.5977(9)
_cell_measurement_reflns_used    7068
_cell_measurement_temperature    150.01(10)
_cell_measurement_theta_max      29.2550
_cell_measurement_theta_min      3.4110
_cell_volume                     523.91(10)
_computing_cell_refinement       'CrysAlisPro 1.171.40.82a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.82a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.82a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      150.01(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.4685
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.920
_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    -85.00  14.00   1.00    1.00    --  -10.24 -37.00  30.00   99
  2  \w    -38.00  63.00   1.00    1.00    --  -10.24  57.00 150.00  101
  3  \w    -43.00  39.00   1.00    1.00    --  -10.24  77.00-150.00   82
  4  \w    -21.00  39.00   1.00    1.00    --   11.34  77.00  60.00   60
  5  \w      1.00  52.00   1.00    1.00    --   11.34 -99.00 -60.00   51
  6  \w    -37.00  66.00   1.00    1.00    --  -10.24  31.00  45.00  103
  7  \w    -21.00  39.00   1.00    1.00    --   11.34  77.00-150.00   60
  8  \w      1.00  52.00   1.00    1.00    --   11.34 -99.00  60.00   51
  9  \w    -13.00  86.00   1.00    1.00    --   11.34  37.00 -30.00   99
 10  \w    -21.00  39.00   1.00    1.00    --   11.34  77.00 -30.00   60
 11  \w    -43.00  39.00   1.00    1.00    --  -10.24  77.00 -60.00   82
 12  \w    -43.00 -18.00   1.00    1.00    --  -10.24  77.00 -30.00   25
 13  \w      1.00  52.00   1.00    1.00    --   11.34 -99.00-120.00   51
 14  \w      1.00  52.00   1.00    1.00    --   11.34 -99.00 150.00   51
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Xcalibur, Atlas, Gemini ultra'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0237053000
_diffrn_orient_matrix_UB_12      0.0960443000
_diffrn_orient_matrix_UB_13      -0.0252074000
_diffrn_orient_matrix_UB_21      -0.0971307000
_diffrn_orient_matrix_UB_22      0.0175473000
_diffrn_orient_matrix_UB_23      0.0165989000
_diffrn_orient_matrix_UB_31      0.0072005000
_diffrn_orient_matrix_UB_32      0.0197067000
_diffrn_orient_matrix_UB_33      0.0684925000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0686
_diffrn_reflns_av_unetI/netI     0.0601
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.920
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            13853
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.920
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         29.507
_diffrn_reflns_theta_min         2.860
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    1.665
_exptl_absorpt_correction_T_max  0.813
_exptl_absorpt_correction_T_min  0.645
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.82a (Rigaku Oxford Diffraction, 2020)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
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    1.824
_exptl_crystal_description       block
_exptl_crystal_F_000             288
_exptl_crystal_size_max          0.35
_exptl_crystal_size_mid          0.342
_exptl_crystal_size_min          0.157
_refine_diff_density_max         1.712
_refine_diff_density_min         -1.690
_refine_diff_density_rms         0.250
_refine_ls_extinction_coef       0.068(6)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.191
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     120
_refine_ls_number_reflns         2682
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.191
_refine_ls_R_factor_all          0.0780
_refine_ls_R_factor_gt           0.0558
_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^)+(0.0538P)^2^+3.4193P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1286
_refine_ls_wR_factor_ref         0.1587
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2179
_reflns_number_total             2682
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ra02984d1.cif
_cod_data_source_block           3pcdcl
_cod_database_code               7248758
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C12 H24 Cl6 N4 O2 Pd1'
_reflns_odcompleteness_completeness 99.95
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     26.32
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H,H) groups
 At 1.5 times of:
  All O(H,H) groups
2.a Free rotating group:
 O1(H1B,H1C)
2.b Secondary CH2 refined with riding coordinates:
 C6(H6A,H6B)
2.c Aromatic/amide H refined with riding coordinates:
 N1(H1), C1(H1A), C2(H2), C3(H3), C5(H5)
2.d Idealised Me refined as rotating group:
 N2(H2A,H2B,H2C)
;
_shelx_res_checksum              28703
_shelx_hkl_checksum              7895
_olex2_date_sample_data_collection 2021-09-15
_olex2_diffrn_ambient_temperature_device 'Oxford Cryosystems'
_olex2_exptl_crystal_mounting_method
'The crystal was mounted on a nylon loop in perfluoroether oil'
_olex2_submission_original_sample_id 3PCdCl
_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 1.664
_oxdiff_exptl_absorpt_empirical_full_min 0.759