The Elusive Structure of Pd2(dba)3. Examination by Isotopic Labeling, NMR Spectroscopy, and X-ray Diffraction Analysis: Synthesis and Characterization of Pd2(dba-Z)3 Complexes
Anant R. Kapdi; Adrian C. Whitwood; David C. Williamson; Jason M. Lynam; Michael J. Burns; Thomas J. Williams; Alan J. Reay; Jordan Holmes; Ian J. S. Fairlamb; Journal of the American Chemical Society 135 (2013) 8388–8399; doi:10.1021/ja403259c

data_4119849
_publ_section_title
;
 The Elusive Structure of Pd2(dba)3. Examination by Isotopic Labeling, NMR
 Spectroscopy, and X-ray Diffraction Analysis: Synthesis and
 Characterization of Pd2(dba-Z)3 Complexes
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              8388
_journal_page_last               8399
_journal_paper_doi               10.1021/ja403259c
_journal_volume                  135
_journal_year                    2013
_chemical_formula_moiety         'C51 H42 O3 Pd2, C1 H2 Cl2'
_chemical_formula_sum            'C52 H44 Cl2 O3 Pd2'
_chemical_formula_weight         1000.57
_chemical_name_systematic
;
 ? 
;
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_symmetry_space_group_name_Hall  '-P 1'
_symmetry_space_group_name_H-M   'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_atom_sites_solution_secondary   difmap
_audit_creation_date             2013-03-07
_audit_creation_method
;
  Olex2 1.2
  (compiled Dec  5 2012 16:17:34, GUI svn.r4385)
;
_cell_angle_alpha                114.651(2)
_cell_angle_beta                 96.795(2)
_cell_angle_gamma                95.356(2)
_cell_formula_units_Z            2
_cell_length_a                   12.2214(4)
_cell_length_b                   12.8052(3)
_cell_length_c                   15.0153(3)
_cell_measurement_reflns_used    15325
_cell_measurement_temperature    110.00(10)
_cell_measurement_theta_max      32.0635
_cell_measurement_theta_min      2.9618
_cell_volume                     2094.03(10)
_computing_cell_refinement
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
;
_computing_data_collection
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
;
_computing_data_reduction
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
;
_computing_molecular_graphics
;
O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.
;
_computing_publication_material
;
O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.
;
_computing_structure_refinement
;
SHELXL, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122
;
_computing_structure_solution
'SUPERFLIP, J. Appl. Cryst. (2007) 40, 786-790'
_diffrn_ambient_temperature      110.00(10)
_diffrn_detector_area_resol_mean 16.1450
_diffrn_measured_fraction_theta_full 0.9980
_diffrn_measured_fraction_theta_max 0.9902
_diffrn_measurement_details
;
  1 omega  -69.00   44.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -25.1672   19.0000  -90.0000 113

  2 omega  -44.00   40.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -25.1672   57.0000  -30.0000 84

  3 omega   45.00   73.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172 -178.0000  120.0000 28

  4 omega   -4.00   96.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172   77.0000   90.0000 100

  5 omega   38.00   68.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172  -99.0000  -30.0000 30

  6 omega   -3.00   43.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172   77.0000 -180.0000 46

  7 omega   19.00   57.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172  -99.0000 -120.0000 38

  8 omega -102.00  -34.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -25.1672  178.0000    0.0000 68

  9 omega  -94.00   -4.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -25.1672  -57.0000 -180.0000 90

 10 omega    5.00   75.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172   57.0000    0.0000 70

 11 omega    1.00   99.00   1.0000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       26.4172   37.0000  -60.0000 98
;
_diffrn_measurement_device_type  'SuperNova, Single source at offset), Eos'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      0.0321011000
_diffrn_orient_matrix_UB_12      0.0559417000
_diffrn_orient_matrix_UB_13      0.0171452000
_diffrn_orient_matrix_UB_21      0.0458578000
_diffrn_orient_matrix_UB_22      -0.0260503000
_diffrn_orient_matrix_UB_23      -0.0194511000
_diffrn_orient_matrix_UB_31      -0.0192424000
_diffrn_orient_matrix_UB_32      0.0012124000
_diffrn_orient_matrix_UB_33      -0.0459689000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.7107
_diffrn_reflns_av_R_equivalents  0.0487
_diffrn_reflns_av_unetI/netI     0.0483
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -18
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -21
_diffrn_reflns_number            37706
_diffrn_reflns_theta_full        25.00
_diffrn_reflns_theta_max         32.14
_diffrn_reflns_theta_min         2.97
_diffrn_source                   'SuperNova (Mo) x-ray Source'
_exptl_absorpt_coefficient_mu    1.031
_exptl_absorpt_correction_T_max  0.938
_exptl_absorpt_correction_T_min  0.780
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.21 (release 14-08-2012 CrysAlis171 .NET)
(compiled Sep 14 2012,17:21:16)
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)
;
_exptl_crystal_colour            'dark red'
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.587
_exptl_crystal_description       block
_exptl_crystal_F_000             1012
_exptl_crystal_recrystallization_method DCM
_exptl_crystal_size_max          0.3172
_exptl_crystal_size_mid          0.1571
_exptl_crystal_size_min          0.0798
_refine_diff_density_max         1.063
_refine_diff_density_min         -1.338
_refine_diff_density_rms         0.104
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.086
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     635
_refine_ls_number_reflns         13493
_refine_ls_number_restraints     21
_refine_ls_restrained_S_all      1.087
_refine_ls_R_factor_all          0.0531
_refine_ls_R_factor_gt           0.0395
_refine_ls_shift/su_max          0.005
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0358P)^2^+1.6073P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0907
_refine_ls_wR_factor_ref         0.1009
_reflns_number_gt                11017
_reflns_number_total             13493
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja403259c_si_002_2.cif
_cod_data_source_block           ijsf1232
_cod_original_cell_volume        2094.03(9)
_cod_database_code               4119849
_chemical_oxdiff_formula         'C52 H44 Cl2 O3 Pd2'
_chemical_oxdiff_usercomment     'Alan's AJR-1-5b-DCM'
_reflns_odcompleteness_completeness 99.80
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     30.01
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  H22A of C22A, H21A of C21A, H20A of C20A, H28 of C28, H5 of C5, H39 of C39,
  H37 of C37, H30 of C30, H25 of C25, H19 of C19, H24 of C24, H14 of C14, H4 of
  C4, H8 of C8, H2 of C2, H33 of C33, H16 of C16, H51 of C51, H18 of C18, H34A
  of C34A, H18A of C18A, H19A of C19A, H39A of C39A, H44 of C44, H7A of C7A,
  H8A of C8A, H11A of C11A, H10A of C10A, H25A of C25A, H24A of C24A, H42A of
  C42A, H41A of C41A, H45A of C45A, H17A of C17A, H13A of C13A, H14A of C14A,
  H15A of C15A, H16A of C16A, H35A of C35A, H36A of C36A, H38A of C38A, H37A of
  C37A, H31A of C31A, H30A of C30A, H33A of C33A, H32A of C32A, H51A of C51A,
  H50A of C50A, H49A of C49A, H48A of C48A, H47A of C47A, {H52A,H52B} of C52A,
  H45 of C45, H38 of C38, H42 of C42, H41 of C41, H11 of C11, H10 of C10, H20
  of C20, H21 of C21, H7 of C7, H22 of C22, H44A of C44A, H27A of C27A, H28A of
  C28A, H5A of C5A, H4A of C4A, H1A of C1A, H2A of C2A, H3A of C3A, H17 of C17,
  {H52C,H52D} of C52, H13 of C13, H47 of C47, H32 of C32, H31 of C31, H15 of
  C15, H48 of C48, H27 of C27, H34 of C34, H49 of C49, H3 of C3, H35 of C35,
  H50 of C50, H1 of C1, H36 of C36
2. Restrained distances
 C52-Cl1 = C52-Cl2
 1.745 with sigma of 0.005
 C25A-C26A = C26A-C27A
 1.476 with sigma of 0.02
 C52A-Cl1A = C52A-Cl2A
 1.745 with sigma of 0.005
 C9A-O1A
 1.233 with sigma of 0.02
 Cl1-Cl2
 2.9 with sigma of 0.01
 Cl1A-Cl2A
 2.9 with sigma of 0.01
3. Uiso/Uaniso restraints and constraints
Uanis(C43) ~ Ueq, Uanis(C43A) ~ Ueq: with sigma of 0.005 and sigma for 
terminal atoms of 0.01
Uanis(C28) = Uanis(C28A)
Uanis(C24) = Uanis(C24A)
Uanis(C23) = Uanis(C23A)
Uanis(C18) = Uanis(C18A)
Uanis(C19) = Uanis(C19A)
Uanis(C20) = Uanis(C20A)
Uanis(C21) = Uanis(C21A)
Uanis(C22) = Uanis(C22A)
Uanis(C29) = Uanis(C29A)
Uanis(C30) = Uanis(C30A)
Uanis(C31) = Uanis(C31A)
Uanis(C32) = Uanis(C32A)
Uanis(C33) = Uanis(C33A)
Uanis(C34) = Uanis(C34A)
Uanis(C8) = Uanis(C8A)
Uanis(C10) = Uanis(C10A)
Uanis(C7) = Uanis(C7A)
Uanis(C6) = Uanis(C6A)
Uanis(C5) = Uanis(C5A)
Uanis(C4) = Uanis(C4A)
Uanis(C3) = Uanis(C3A)
Uanis(C2) = Uanis(C2A)
Uanis(C1) = Uanis(C1A)
Uanis(C11) = Uanis(C11A)
Uanis(C12) = Uanis(C12A)
Uanis(C13) = Uanis(C13A)
Uanis(C14) = Uanis(C14A)
Uanis(C15) = Uanis(C15A)
Uanis(C16) = Uanis(C16A)
Uanis(C17) = Uanis(C17A)
Uanis(C42) = Uanis(C42A)
Uanis(C41) = Uanis(C41A)
Uanis(C45) = Uanis(C45A)
Uanis(C44) = Uanis(C44A)
Uanis(C40) = Uanis(C40A)
Uanis(C35) = Uanis(C35A)
Uanis(C36) = Uanis(C36A)
Uanis(C37) = Uanis(C37A)
Uanis(C38) = Uanis(C38A)
Uanis(C39) = Uanis(C39A)
Uanis(C48) = Uanis(C48A)
Uanis(C49) = Uanis(C49A)
Uanis(C50) = Uanis(C50A)
Uanis(C51) = Uanis(C51A)
Uanis(C46) = Uanis(C46A)
Uanis(C47) = Uanis(C47A)
Uanis(O3A) = Uanis(O3)
Uanis(C43) = Uanis(C43A)
Uanis(C26) = Uanis(C26A)
Uanis(C25) = Uanis(C25A)
Uanis(C27) = Uanis(C27A)
Uanis(O2) = Uanis(O2A)
Uanis(Cl1) = Uanis(Cl1A)
Uanis(C52) = Uanis(C52A)
Uanis(Cl2) = Uanis(Cl2A)
Uanis(C9) = Uanis(C9A)
Uanis(O1) = Uanis(O1A)
4. others
 Sof(O1)=Sof(C9)=Sof(C5)=Sof(H5)=Sof(C6)=Sof(C17)=Sof(H17)=Sof(C12)=Sof(C13)=
 Sof(H13)=Sof(C15)=Sof(H15)=Sof(C3)=Sof(H3)=Sof(C1)=Sof(H1)=Sof(C16)=Sof(H16)=
 Sof(C2)=Sof(H2)=Sof(C14)=Sof(H14)=Sof(C8)=Sof(H8)=Sof(C4)=Sof(H4)=Sof(C7)=
 Sof(H7)=Sof(C10)=Sof(H10)=Sof(C11)=Sof(H11)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-
 Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=
 1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-
 Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=
 1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)=1-Sof(C9)
 Sof(O2)=Sof(C30)=Sof(H30)=Sof(C26)=Sof(C28)=Sof(H28)=Sof(C29)=Sof(C23)=
 Sof(C32)=Sof(H32)=Sof(C31)=Sof(H31)=Sof(C27)=Sof(H27)=Sof(C34)=Sof(H34)=
 Sof(C33)=Sof(H33)=Sof(C18)=Sof(H18)=Sof(C19)=Sof(H19)=Sof(C24)=Sof(H24)=
 Sof(C25)=Sof(H25)=Sof(C22)=Sof(H22)=Sof(C21)=Sof(H21)=Sof(C20)=Sof(H20)=1-
 Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-
 Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-
 Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-
 Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-
 Sof(C30)=1-Sof(C30)=1-Sof(C30)=1-Sof(C30)
 1-Sof(C37)=Sof(C37)=Sof(H37)=Sof(C39)=Sof(H39)=Sof(C43)=Sof(C46)=Sof(C40)=
 Sof(C47)=Sof(H47)=Sof(C48)=Sof(H48)=Sof(C49)=Sof(H49)=Sof(C35)=Sof(H35)=
 Sof(C50)=Sof(H50)=Sof(C36)=Sof(H36)=Sof(C51)=Sof(H51)=Sof(C41)=Sof(H41)=
 Sof(C42)=Sof(H42)=Sof(C38)=Sof(H38)=Sof(C45)=Sof(H45)=Sof(C44)=Sof(H44)=1-
 Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-
 Sof(C37)=1-Sof(C37)=Sof(O3)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-
 Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-
 Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-
 Sof(C37)=1-Sof(C37)=1-Sof(C37)=1-Sof(C37)
 Sof(Cl1)=Sof(Cl2)=Sof(C52)=Sof(H52C)=Sof(H52D)=1-Sof(Cl2)=1-Sof(Cl2)=1-
 Sof(Cl2)=1-Sof(Cl2)=1-Sof(Cl2)
5.a Ternary CH refined with riding coordinates:
 C28(H28), C27(H27), C24(H24), C25(H25), C8(H8), C7(H7), C10(H10), C11(H11),
 C41(H41), C42(H42), C45(H45), C44(H44), C7A(H7A), C8A(H8A), C11A(H11A),
 C10A(H10A), C25A(H25A), C24A(H24A), C42A(H42A), C41A(H41A), C45A(H45A),
 C44A(H44A), C28A(H28A), C27A(H27A)
5.b Secondary CH2 refined with riding coordinates:
 C52(H52C,H52D), C52A(H52A,H52B)
5.c Aromatic/amide H refined with riding coordinates:
 C30(H30), C37(H37), C39(H39), C5(H5), C17(H17), C13(H13), C47(H47), C32(H32),
 C31(H31), C15(H15), C48(H48), C34(H34), C49(H49), C3(H3), C35(H35), C50(H50),
 C1(H1), C36(H36), C33(H33), C16(H16), C2(H2), C51(H51), C18(H18), C14(H14),
 C19(H19), C4(H4), C22(H22), C21(H21), C20(H20), C38(H38), C5A(H5A), C4A(H4A),
 C3A(H3A), C2A(H2A), C1A(H1A), C13A(H13A), C14A(H14A), C15A(H15A), C16A(H16A),
 C17A(H17A), C30A(H30A), C31A(H31A), C32A(H32A), C33A(H33A), C34A(H34A),
 C18A(H18A), C19A(H19A), C20A(H20A), C21A(H21A), C22A(H22A), C35A(H35A),
 C36A(H36A), C37A(H37A), C38A(H38A), C39A(H39A), C51A(H51A), C50A(H50A),
 C49A(H49A), C48A(H48A), C47A(H47A)
5.d Fitted hexagon refined as free rotating group:
 C6A(C5A,C4A,C3A,C2A,C1A), C12A(C13A,C14A,C15A,C16A,C17A), C29A(C30A,C31A,C32A,
 C33A,C34A), C23A(C18A,C19A,C20A,C21A,C22A), C40A(C35A,C36A,C37A,C38A,C39A),
 C46A(C51A,C50A,C49A,C48A,C47A)
;