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_7057370
_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         'C40 H34 Br2 O P2 Pd'
_chemical_formula_sum            'C40 H34 Br2 O P2 Pd'
_chemical_formula_weight         858.83
_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             2017-09-25
_audit_creation_method
;
Olex2 1.2
(compiled Aug 10 2017 17:28:52 for OlexSys, GUI svn.r5381)
;
_audit_update_record
;
2017-09-26 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                   15.459(2)
_cell_length_b                   16.811(2)
_cell_length_c                   27.327(4)
_cell_measurement_reflns_used    3028
_cell_measurement_temperature    130.01(10)
_cell_measurement_theta_max      75.6320
_cell_measurement_theta_min      4.1190
_cell_volume                     7101.8(16)
_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      130.01(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.2273
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.998
_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    -41.00  27.00   1.00   12.50    --  -40.68  38.00 120.00   68
  2  \w    -45.00  35.00   1.00   12.50    --  -40.68  38.00-180.00   80
  3  \w     48.00  98.00   1.00   12.50    --   40.68-125.00 120.00   50
  4  \w     11.00  80.00   1.00   12.50    --   40.68 -99.00 -90.00   69
  5  \w     39.00 143.00   1.00   45.00    --  113.00 -61.00 -60.00  104
  6  \w     35.00  91.00   1.00   45.00    --  113.00 -30.00 120.00   56
  7  \w     38.00  98.00   1.00   45.00    --  113.00 -45.00-180.00   60
  8  \w     35.00  91.00   1.00   45.00    --  113.00 -30.00-120.00   56
  9  \w     52.00 174.00   1.00   45.00    --  113.00  15.00  60.00  122
;
_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      0.0288101000
_diffrn_orient_matrix_UB_12      -0.0810881000
_diffrn_orient_matrix_UB_13      0.0207410000
_diffrn_orient_matrix_UB_21      0.0859271000
_diffrn_orient_matrix_UB_22      0.0070894000
_diffrn_orient_matrix_UB_23      -0.0274897000
_diffrn_orient_matrix_UB_31      0.0413389000
_diffrn_orient_matrix_UB_32      0.0421088000
_diffrn_orient_matrix_UB_33      0.0446726000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.1035
_diffrn_reflns_av_unetI/netI     0.1181
_diffrn_reflns_Laue_measured_fraction_full 0.998
_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       -15
_diffrn_reflns_limit_l_max       32
_diffrn_reflns_limit_l_min       -29
_diffrn_reflns_number            23200
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.236
_diffrn_reflns_theta_min         4.209
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    7.940
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.432
_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    1.606
_exptl_crystal_description       needle
_exptl_crystal_F_000             3424
_exptl_crystal_size_max          0.22
_exptl_crystal_size_mid          0.026
_exptl_crystal_size_min          0.026
_refine_diff_density_max         3.037
_refine_diff_density_min         -1.825
_refine_diff_density_rms         0.179
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.062
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     432
_refine_ls_number_reflns         6498
_refine_ls_number_restraints     96
_refine_ls_restrained_S_all      1.057
_refine_ls_R_factor_all          0.1547
_refine_ls_R_factor_gt           0.1180
_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^)+(0.0433P)^2^+191.1501P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2507
_refine_ls_wR_factor_ref         0.2757
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4269
_reflns_number_total             6498
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c8nj00797g2.cif
_cod_data_source_block           rwg2017_29agau
_cod_depositor_comments
'Adding full bibliography for 7057369--7057371.cif.'
_cod_database_code               7057370
_shelx_shelxl_version_number     2017/1
_chemical_oxdiff_formula         'C40 H34 Br2 O P2 Pd'
_reflns_odcompleteness_completeness 99.31
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     69.95
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
2. Shared sites
{C15, C15A}
{C18, C18A}
3. Restrained distances
 P1-C28 = P1-C28A = P2-C27 = P2-C27A
 1.82 with sigma of 0.001
 C27-C28 = C27A-C28A
 1.45 with sigma of 0.001
 P1-C27 = P1-C27A = P2-C28 = P2-C28A
 2.78278 with sigma of 0.001
 C15-C16 = C16-C17 = C17-C18 = C18-C19 = C19-C20 = C20-C15
 1.38715 with sigma of 0.001
 C15-C17 = C16-C18 = C17-C19 = C18-C20 = C19-C15 = C20-C16
 2.40243 with sigma of 0.001
4. Restrained planarity
 C15, C16, C17, C18, C19, C20
 with sigma of 0.1
 C15A, C16A, C17A, C18A, C19A, C20A
 with sigma of 0.1
5. Uiso/Uaniso restraints and constraints
Uanis(C17) \\sim Ueq, Uanis(C17A) \\sim Ueq, Uanis(C18) \\sim Ueq, Uanis(C18A)
\\sim Ueq, Uanis(C19) \\sim Ueq, Uanis(C19A) \\sim Ueq, Uanis(C20) \\sim Ueq,
Uanis(C20A) \\sim Ueq: with sigma of 0.025 and sigma for terminal atoms of 0.05
Uanis(C16) \\sim Ueq, Uanis(C16A) \\sim Ueq: with sigma of 0.015 and sigma for
terminal atoms of 0.03
Uanis(C27) = Uanis(C27A) = Uanis(C28) = Uanis(C28A)
Uanis(C15) = Uanis(C15A)
Uanis(C16) = Uanis(C16A)
Uanis(C17) = Uanis(C17A)
Uanis(C18) = Uanis(C18A)
Uanis(C19) = Uanis(C19A)
Uanis(C20) = Uanis(C20A)
6. Same fragment restrains
{C16, C17, C18, C19, C20} sigma for 1-2: 0.005, 1-3: 0.01
as
{C15A, C16A, C17A, C18A, C19A}
7. Others
 Sof(C27A)=Sof(H27C)=Sof(H27D)=Sof(C28A)=Sof(H28C)=Sof(H28D)=1-FVAR(1)
 Sof(C27)=Sof(H27A)=Sof(H27B)=Sof(C28)=Sof(H28A)=Sof(H28B)=FVAR(1)
 Sof(C15A)=Sof(C16A)=Sof(H16A)=Sof(C17A)=Sof(H17A)=Sof(C18A)=Sof(H18A)=
 Sof(C19A)=Sof(H19A)=Sof(C20A)=Sof(H20A)=1-FVAR(3)
 Sof(C15)=Sof(C16)=Sof(H16)=Sof(C17)=Sof(H17)=Sof(C18)=Sof(H18)=Sof(C19)=
 Sof(H19)=Sof(C20)=Sof(H20)=FVAR(3)
8.a Ternary CH refined with riding coordinates:
 C1(H1)
8.b Secondary CH2 refined with riding coordinates:
 C27(H27A,H27B), C27A(H27C,H27D), C28(H28A,H28B), C28A(H28C,H28D)
8.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), C16A(H16A),
 C17A(H17A), C18A(H18A), C19A(H19A), C20A(H20A), C22(H22), C23(H23), C24(H24),
 C25(H25), C26(H26), C30(H30), C31(H31), C32(H32), C33(H33), C34(H34), C36(H36),
  C37(H37), C38(H38), C39(H39), C40(H40)
;
_shelx_res_checksum              39682
_local_rwg_checkcif_response
;
PLAT342_ALERT_3_B Low Bond Precision on C-C Bonds ............... 0.03242 Ang.

  RESPONSE:  Due to the disorder of the crystal and the presence of Pd and
             Br atoms
  
PLAT971_ALERT_2_B Check Calcd Residual Density 0.99A From Pd1 2.95 eA-3 
PLAT971_ALERT_2_B Check Calcd Residual Density 1.00A From Pd1 2.85 eA-3 
PLAT971_ALERT_2_B Check Calcd Residual Density 1.17A From Pd1 2.59 eA-3 

  RESPONSE:  Due to the disorder of the crystal
  
PLAT082_ALERT_2_C High R1 Value .................................. 0.12 Report
PLAT084_ALERT_3_C High wR2 Value (i.e. > 0.25) ................... 0.28 Report

  RESPONSE:  Due to the disorder of the crystal and poor quality data
  
PLAT220_ALERT_2_C Non-Solvent Resd 1 C Ueq(max)/Ueq(min) Range 3.6 Ratio 

  RESPONSE:  Due to the disorder of the crystal and poor quality data

PLAT234_ALERT_4_C Large Hirshfeld Difference C1 --C2 .. 0.21 Ang. 

  RESPONSE:  These atoms were correctly assigned. Due to the disorder of
             the crystal and poor quality data
  
PLAT241_ALERT_2_C High MainMol Ueq as Compared to Neighbors of C11 Check 
PLAT241_ALERT_2_C High MainMol Ueq as Compared to Neighbors of C13 Check 
PLAT241_ALERT_2_C High MainMol Ueq as Compared to Neighbors of C24 Check 
PLAT241_ALERT_2_C High MainMol Ueq as Compared to Neighbors of C33 Check 
PLAT241_ALERT_2_C High MainMol Ueq as Compared to Neighbors of C37 Check 
PLAT242_ALERT_2_C Low  MainMol Ueq as Compared to Neighbors of P1 Check 

  RESPONSE:  Due to the disorder of the crystal and poor quality data

PLAT906_ALERT_3_C Large K value in the Analysis of Variance ...... 12.013 Check
PLAT906_ALERT_3_C Large K value in the Analysis of Variance ...... 3.253 Check 

  RESPONSE:  Due to the weak and poor quality data, errors in measuring the
             intensity of data by CCD detectors is largest for low intensity
             data

PLAT911_ALERT_3_C Missing num FCF Refl Between THmin & STh/L= 0.600 13 Report 

  RESPONSE:  Inside Detector rejection region
  
PLAT971_ALERT_2_C Check Calcd Residual Density 0.97A From Pd1 2.46 eA-3 
PLAT971_ALERT_2_C Check Calcd Residual Density 0.94A From Br2 2.22 eA-3 
PLAT971_ALERT_2_C Check Calcd Residual Density 1.08A From Br2 2.21 eA-3 
PLAT971_ALERT_2_C Check Calcd Residual Density 1.21A From Br1 1.91 eA-3 
PLAT971_ALERT_2_C Check Calcd Residual Density 1.08A From Br2 1.68 eA-3 
PLAT971_ALERT_2_C Check Calcd Residual Density 0.99A From Br1 1.64 eA-3 
PLAT972_ALERT_2_C Check Calcd Residual Density 0.97A From Pd1 -2.11 eA-3 
PLAT972_ALERT_2_C Check Calcd Residual Density 0.95A From Pd1 -1.89 eA-3 
PLAT972_ALERT_2_C Check Calcd Residual Density 0.99A From Pd1 -1.80 eA-3 
PLAT972_ALERT_2_C Check Calcd Residual Density 0.98A From Pd1 -1.62 eA-3 

  RESPONSE:  Due to the disorder of the crystal and poor quality data
  
PLAT002_ALERT_2_G Number of Distance or Angle Restraints on AtSite 17 Note 
PLAT003_ALERT_2_G Number of Uiso or Uij Restrained non-H Atoms ... 10 Report 
PLAT083_ALERT_2_G SHELXL Second Parameter in WGHT Unusually Large 191.30 Why ? 
PLAT171_ALERT_4_G The CIF-Embedded .res File Contains EADP Records 7 Report 
PLAT172_ALERT_4_G The CIF-Embedded .res File Contains DFIX Records 5 Report 
PLAT174_ALERT_4_G The CIF-Embedded .res File Contains FLAT Records 2 Report 
PLAT175_ALERT_4_G The CIF-Embedded .res File Contains SAME Records 1 Report 
PLAT186_ALERT_4_G The CIF-Embedded .res File Contains ISOR Records 2 Report 

  RESPONSE:  Due to the disorder of the crystal and poor quality data
  
PLAT301_ALERT_3_G Main Residue Disorder ..............(Resd 1).. 17% Note 

  RESPONSE:  Noted
  
PLAT432_ALERT_2_G Short Inter X...Y Contact C19 .. C37 .. 3.16 Ang. 

  RESPONSE:  Due to the disorder of the crystal
  
PLAT793_ALERT_4_G The Model has Chirality at C1 (Centro SPGR) S Verify 

  RESPONSE:  Noted
  
PLAT860_ALERT_3_G Number of Least-Squares Restraints ............. 96 Note 

  RESPONSE:  Due to the disorder of the crystal 
  
PLAT910_ALERT_3_G Missing num of FCF Reflection(s) Below Theta(Min). 1 Note

  RESPONSE: Behind beamstop
  
PLAT912_ALERT_4_G Missing num of FCF Reflections Above STh/L= 0.600 2 Note 

  RESPONSE:  The detector does not measure all data at high angle
  
PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density. 2 Info 

  RESPONSE:  Noted
;
_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 1.534
_oxdiff_exptl_absorpt_empirical_full_min 0.743