New Pd/Pt(ii) complexes as unsymmetrical ylide-based chemotherapeutic agents: synthesis, characterization, biological activity, electrochemical, and X-ray studies
Sabounchei, Seyyed Javad; Badpa, Khadijeh; Nematollahi, Davood; Sharafi-kolkeshvandi, Mahnaz; Hosseinzadeh, Leila; Karamian, Roya; Ghasemlou, Fatemeh; Gable, Robert W.; New Journal of Chemistry 42 (2018) 8968–; doi:10.1039/C8NJ00797G

data_7057369
_publ_section_title
;
 New Pd/Pt(ii) complexes as unsymmetrical ylide-based chemotherapeutic
 agents: synthesis, characterization, biological activity,
 electrochemical, and X-ray studies
;
_journal_issue                   11
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              8968
_journal_paper_doi               10.1039/C8NJ00797G
_journal_volume                  42
_journal_year                    2018
_chemical_formula_moiety         'C39 H32 Br2 O P2 Pd'
_chemical_formula_sum            'C39 H32 Br2 O P2 Pd'
_chemical_formula_weight         844.80
_space_group_crystal_system      orthorhombic
_space_group_IT_number           61
_space_group_name_Hall           '-P 2ac 2ab'
_space_group_name_H-M_alt        'P b c a'
_symmetry_space_group_name_Hall  '-P 2ac 2ab'
_symmetry_space_group_name_H-M   'P b c a'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2017-06-22
_audit_creation_method
;
Olex2 1.2
(compiled Mar 28 2017 19:26:29 for OlexSys, GUI svn.r5337)
;
_audit_update_record
;
2017-07-01 deposited with the CCDC.
2018-04-30 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   14.84001(10)
_cell_length_b                   16.55137(8)
_cell_length_c                   28.2482(2)
_cell_measurement_reflns_used    37896
_cell_measurement_temperature    130.00(10)
_cell_measurement_theta_max      77.0320
_cell_measurement_theta_min      3.3370
_cell_volume                     6938.39(8)
_computing_cell_refinement       'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      130.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.2273
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.998
_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    -48.00 -19.00   1.00    1.00    --  -40.81  38.00   0.00   29
  2  \w    -49.00  32.00   1.00    1.00    --  -40.81  38.00  30.00   81
  3  \w    -48.00  35.00   1.00    1.00    --  -40.81  38.00 -90.00   83
  4  \w     -1.00  74.00   1.00    1.00    --   40.81 -77.00  30.00   75
  5  \w     44.00  96.00   1.00    1.00    --   40.81-125.00 -60.00   52
  6  \w     30.00  61.00   1.00    1.96    --  113.00 -95.00  57.00   31
  7  \w     69.00 110.00   1.00    1.96    --  113.00-111.00  30.00   41
  8  \w     82.00 108.00   1.00    1.96    --  113.00 -95.00  57.00   26
  9  \w    114.00 146.00   1.00    1.96    --  113.00 -77.00 120.00   32
 10  \w    140.00 166.00   1.00    1.96    --  113.00 -15.00  60.00   26
 11  \w    122.00 177.00   1.00    1.96    --  113.00  45.00 -60.00   55
 12  \w    126.00 174.00   1.00    1.96    --  113.00 111.00 -90.00   48
 13  \w    135.00 175.00   1.00    1.96    --  113.00 111.00-180.00   40
 14  \w    120.00 176.00   1.00    1.96    --  113.00  30.00 -90.00   56
 15  \w    118.00 144.00   1.00    1.96    --  113.00 111.00 -30.00   26
 16  \w    107.00 148.00   1.00    1.96    --  113.00 178.00 -90.00   41
 17  \w    100.00 175.00   1.00    1.96    --  113.00 111.00-150.00   75
 18  \w     96.00 138.00   1.00    1.96    --  113.00 178.00   0.00   42
 19  \w     74.00 100.00   1.00    1.96    --  113.00 178.00 -90.00   26
 20  \w     57.00  82.00   1.00    1.96    --  113.00 178.00   0.00   25
 21  \w     83.00 113.00   1.00    1.96    --  113.00  30.00 -90.00   30
 22  \w     60.00  90.00   1.00    1.96    --  113.00 -30.00 -60.00   30
 23  \w     50.00  76.00   1.00    1.96    --  113.00 -61.00 -60.00   26
 24  \w     66.00  99.00   1.00    1.96    --  113.00 -94.00 -30.00   33
 25  \w     77.00 113.00   1.00    1.96    --  113.00-111.00 -60.00   36
 26  \w     70.00 116.00   1.00    1.96    --  113.00-111.00-120.00   46
 27  \w     74.00 116.00   1.00    1.96    --  113.00-111.00-150.00   42
 28  \w     57.00 113.00   1.00    1.96    --  113.00-111.00 -30.00   56
 29  \w     66.00 116.00   1.00    1.96    --  113.00-111.00  60.00   50
 30  \w     65.00  90.00   1.00    1.96    --  113.00 -30.00  90.00   25
 31  \w     82.00 107.00   1.00    1.96    --  113.00 -15.00  60.00   25
 32  \w     57.00 163.00   1.00    1.96    --  113.00  15.00  60.00  106
 33  \w     52.00  83.00   1.00    1.96    --  113.00 -45.00  90.00   31
 34  \w     42.00  97.00   1.00    1.96    --  113.00 -45.00 150.00   55
 35  \w     41.00  84.00   1.00    1.96    --  113.00 -77.00 120.00   43
 36  \w     38.00 119.00   1.00    1.96    --  113.00-119.00 149.76   81
 37  \w     37.00  62.00   1.00    1.96    --  113.00 -15.00  60.00   25
 38  \w     46.00  95.00   1.00    1.96    --  113.00 -45.00 -60.00   49
 39  \w     47.00  92.00   1.00    1.96    --  113.00 -45.00-150.00   45
 40  \w     36.00  90.00   1.00    1.96    --  113.00 -30.00-120.00   54
 41  \w     32.00  83.00   1.00    1.96    --  113.00 -94.00  90.00   51
 42  \w   -115.00 -12.00   1.00    1.00    --  -40.81 -57.00 120.00  103
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0961951000
_diffrn_orient_matrix_UB_12      -0.0095894000
_diffrn_orient_matrix_UB_13      0.0197578000
_diffrn_orient_matrix_UB_21      0.0388446000
_diffrn_orient_matrix_UB_22      0.0329826000
_diffrn_orient_matrix_UB_23      -0.0467522000
_diffrn_orient_matrix_UB_31      -0.0041657000
_diffrn_orient_matrix_UB_32      0.0864550000
_diffrn_orient_matrix_UB_33      0.0200110000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0517
_diffrn_reflns_av_unetI/netI     0.0212
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       35
_diffrn_reflns_limit_l_min       -35
_diffrn_reflns_number            77741
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.160
_diffrn_reflns_theta_min         4.297
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    8.116
_exptl_absorpt_correction_T_max  0.679
_exptl_absorpt_correction_T_min  0.211
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.46 (Rigaku Oxford Diffraction, 2015)
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            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.617
_exptl_crystal_description       block
_exptl_crystal_F_000             3360
_exptl_crystal_recrystallization_method
'grown by slow evaporation from dichloromethane'
_exptl_crystal_size_max          0.264
_exptl_crystal_size_mid          0.19
_exptl_crystal_size_min          0.156
_refine_diff_density_max         0.550
_refine_diff_density_min         -0.763
_refine_diff_density_rms         0.071
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.073
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     406
_refine_ls_number_reflns         7332
_refine_ls_number_restraints     6
_refine_ls_restrained_S_all      1.073
_refine_ls_R_factor_all          0.0285
_refine_ls_R_factor_gt           0.0269
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0324P)^2^+8.1246P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0686
_refine_ls_wR_factor_ref         0.0698
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6967
_reflns_number_total             7332
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c8nj00797g2.cif
_cod_data_source_block           rwg2017_15bgau
_cod_depositor_comments
'Adding full bibliography for 7057369--7057371.cif.'
_cod_original_cell_volume        6938.40(8)
_cod_database_code               7057369
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         'C39 H32 Br2 O P2 Pd'
_chemical_oxdiff_usercomment     PdYm
_reflns_odcompleteness_completeness 99.92
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     75.12
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
2. Uiso/Uaniso restraints and constraints
Uanis(C12) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
3.a Ternary CH refined with riding coordinates:
 C1(H1)
3.b Secondary CH2 refined with riding coordinates:
 C27(H27A,H27B)
3.c Aromatic/amide H refined with riding coordinates:
 C4(H4), C5(H5), C7(H7), C8(H8), C10(H10), C11(H11), C12(H12), C13(H13),
 C14(H14), C16(H16), C17(H17), C18(H18), C19(H19), C20(H20), C22(H22), C23(H23),
  C24(H24), C25(H25), C26(H26), C29(H29), C30(H30), C31(H31), C32(H32),
 C33(H33), C35(H35), C36(H36), C37(H37), C38(H38), C39(H39)
;
_shelx_res_checksum              52342
_olex2_exptl_crystal_mounting_method mounted
_olex2_submission_original_sample_id rwg2017_15
_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 1.189
_oxdiff_exptl_absorpt_empirical_full_min 0.785
_local_rwg_checkcif_report
;
PLAT911_ALERT_3_C Missing # FCF Refl Between THmin & STh/L= 0.600 2 Report 

  RESPONSE:  Inside Detector rejection region or otherwise not measured

PLAT934_ALERT_3_C Number of (Iobs-Icalc)/SigmaW > 10 Outliers .... 1 Check 

  RESPONSE:  There did not seem to be anything wrong with this peak, so it was
             retained in the refinement data

PLAT972_ALERT_2_C Check Calcd Residual Density 0.77A From Pt1 -1.66 eA-3 
PLAT972_ALERT_2_C Check Calcd Residual Density 0.76A From Pt1 -1.65 eA-3 

  RESPONSE:  Some inaccuracy in the absorption correction or possibly slight
             disorder

PLAT083_ALERT_2_G SHELXL Second Parameter in WGHT Unusually Large 6.47 Why ? 

  RESPONSE:  Possibly due to some disorder or effects of the absorption
             corrections

PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X) Pt1 --Br1 .. 7.1 s.u. 
PLAT232_ALERT_2_G Hirshfeld Test Diff (M-X) Pt1 --Br2 .. 12.0 s.u. 

  RESPONSE:  All atoms are correctly assigned

PLAT793_ALERT_4_G The Model has Chirality at C1 (Centro SPGR) S Verify 

  RESPONSE:  True

PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L= 0.600 54 Note 

  RESPONSE:  Not all reflections between theta 75 deg and theta(max) are
             able to be measured by the detector

PLAT913_ALERT_3_G Missing # of Very Strong Reflections in FCF .... 1 Note 

  RESPONSE:  Inside Detector rejection region or otherwise not measured

PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density. 3 Note 

  RESPONSE:  Noted

;