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_4119850
_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, C6 H6'
_chemical_formula_sum            'C57 H48 O3 Pd2'
_chemical_formula_weight         993.75
_chemical_name_systematic
;
 ? 
;
_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'
_symmetry_space_group_name_Hall  '-P 2ybc'
_symmetry_space_group_name_H-M   'P 1 21/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_atom_sites_solution_secondary   difmap
_audit_creation_date             2013-02-07
_audit_creation_method
;
  Olex2 1.2
  (compiled Dec  5 2012 16:17:34, GUI svn.r4385)
;
_cell_angle_alpha                90.00
_cell_angle_beta                 114.397(3)
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   13.6130(3)
_cell_length_b                   23.3621(5)
_cell_length_c                   15.2236(4)
_cell_measurement_reflns_used    6142
_cell_measurement_temperature    109.95(10)
_cell_measurement_theta_max      25.2943
_cell_measurement_theta_min      2.8413
_cell_volume                     4409.2(2)
_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      109.95(10)
_diffrn_detector_area_resol_mean 16.1450
_diffrn_measured_fraction_theta_full 0.9980
_diffrn_measured_fraction_theta_max 0.9980
_diffrn_measurement_details
;
  1 omega  -89.00   29.00   1.0000  140.0000
omega____ theta____ kappa____ phi______ frames
    -      -15.5743    0.0000  -90.0000 118

  2 omega   -4.00   24.00   1.0000  140.0000
omega____ theta____ kappa____ phi______ frames
    -      -15.5743  -99.0000  -90.0000 28

  3 omega  -20.00   10.00   1.0000  140.0000
omega____ theta____ kappa____ phi______ frames
    -      -15.5743  -99.0000   60.0000 30

  4 omega   34.00   77.00   1.0000  140.0000
omega____ theta____ kappa____ phi______ frames
    -       16.9805 -178.0000 -180.0000 43
;
_diffrn_measurement_device_type  'SuperNova, Single source at offset), Eos'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      -0.0077156000
_diffrn_orient_matrix_UB_12      -0.0240432000
_diffrn_orient_matrix_UB_13      0.0248470000
_diffrn_orient_matrix_UB_21      0.0399521000
_diffrn_orient_matrix_UB_22      -0.0152595000
_diffrn_orient_matrix_UB_23      -0.0090561000
_diffrn_orient_matrix_UB_31      0.0402260000
_diffrn_orient_matrix_UB_32      0.0104975000
_diffrn_orient_matrix_UB_33      0.0438051000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.7107
_diffrn_reflns_av_R_equivalents  0.0377
_diffrn_reflns_av_unetI/netI     0.0582
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       28
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       12
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            17380
_diffrn_reflns_theta_full        25.35
_diffrn_reflns_theta_max         25.35
_diffrn_reflns_theta_min         2.85
_diffrn_source                   'SuperNova (Mo) x-ray Source'
_exptl_absorpt_coefficient_mu    0.862
_exptl_absorpt_correction_T_max  0.964
_exptl_absorpt_correction_T_min  0.945
_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            'clear dark black'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    black
_exptl_crystal_density_diffrn    1.497
_exptl_crystal_description       block
_exptl_crystal_F_000             2024
_exptl_crystal_size_max          0.0881
_exptl_crystal_size_mid          0.0626
_exptl_crystal_size_min          0.0492
_refine_diff_density_max         0.710
_refine_diff_density_min         -0.873
_refine_diff_density_rms         0.095
_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     662
_refine_ls_number_reflns         8075
_refine_ls_number_restraints     15
_refine_ls_restrained_S_all      1.061
_refine_ls_R_factor_all          0.0613
_refine_ls_R_factor_gt           0.0440
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0384P)^2^+6.1280P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0953
_refine_ls_wR_factor_ref         0.1038
_reflns_number_gt                6507
_reflns_number_total             8075
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja403259c_si_002_3.cif
_cod_data_source_block           ijsf1302
_cod_original_cell_volume        4409.22(17)
_cod_database_code               4119850
_cod_database_fobs_code          4119850
_chemical_oxdiff_formula         'C57 H48 O3 Pd2'
_chemical_oxdiff_usercomment     'Alan AJR-1-5b-C6H6'
_reflns_odcompleteness_completeness 99.80
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     25.30
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  H39A of C39A, H38A of C38A, H37A of C37A, H36A of C36A, H35A of C35A, H41
  of C41, H41A of C41A, H42 of C42, H42A of C42A, H44 of C44, H44A of C44A, H45
  of C45, H45A of C45A, H46A of C46A, H48A of C48A, H49A of C49A, H50A of C50A,
  H51A of C51A, H47 of C47, H48 of C48, H49 of C49, H50 of C50, H51 of C51, H52
  of C52, H53 of C53, H54 of C54, H55 of C55, H56 of C56, H57 of C57, H52A of
  C52A, H53A of C53A, H54A of C54A, H55A of C55A, H56A of C56A, H57A of C57A,
  H34A of C34A, H33A of C33A, H32A of C32A, H31A of C31A, H30A of C30A, H30 of
  C30, H31 of C31, H32 of C32, H33 of C33, H34 of C34, H35 of C35, H36 of C36,
  H37 of C37, H38 of C38, H39 of C39, H15 of C15, H16 of C16, H17 of C17, H18
  of C18, H19 of C19, H20 of C20, H21 of C21, H22 of C22, H18A of C18A, H19A of
  C19A, H20A of C20A, H21A of C21A, H22A of C22A, H24 of C24, H24A of C24A, H25
  of C25, H25A of C25A, H27 of C27, H27A of C27A, H28 of C28, H28A of C28A, H2
  of C2, H1 of C1, H14 of C14, H13 of C13, H17A of C17A, H16A of C16A, H15A of
  C15A, H14A of C14A, H13A of C13A, H11A of C11A, H11 of C11, H10A of C10A, H10
  of C10, H8A of C8A, H8 of C8, H7A of C7A, H7 of C7, H1A of C1A, H2A of C2A,
  H3A of C3A, H4A of C4A, H5A of C5A, H5 of C5, H4 of C4, H3 of C3
2. Restrained distances
 O1A-C9 ~ C9-O1
 with sigma of 0.02
 O2-C26 ~ C26-O2A
 with sigma of 0.02
 O3A-C43 ~ C43-O3
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O3A) ~ Ueq, Uanis(O3) ~ Ueq: with sigma of 0.01 and sigma for terminal 
atoms of 0.02
Uanis(O2) = Uanis(O2A)
Uanis(C21) = Uanis(C21A)
Uanis(C22) = Uanis(C22A)
Uanis(C23) = Uanis(C23A)
Uanis(C18) = Uanis(C18A)
Uanis(C19) = Uanis(C19A)
Uanis(C20) = Uanis(C20A)
Uanis(C42) = Uanis(C42A)
Uanis(C41) = Uanis(C41A)
Uanis(C44) = Uanis(C44A)
Uanis(C45) = Uanis(C45A)
Uanis(C40) = Uanis(C40A)
Uanis(C39) = Uanis(C39A)
Uanis(C38) = Uanis(C38A)
Uanis(C37) = Uanis(C37A)
Uanis(C36) = Uanis(C36A)
Uanis(C35) = Uanis(C35A)
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(C46) = Uanis(C46A)
Uanis(C51) = Uanis(C51A)
Uanis(C50) = Uanis(C50A)
Uanis(C49) = Uanis(C49A)
Uanis(C48) = Uanis(C48A)
Uanis(C47) = Uanis(C47A)
Uanis(O3) = Uanis(O3A)
Uanis(O1) = Uanis(O1A)
Uanis(C52) = Uanis(C52A)
Uanis(C53) = Uanis(C53A)
Uanis(C54) = Uanis(C54A)
Uanis(C55) = Uanis(C55A)
Uanis(C56) = Uanis(C56A)
Uanis(C57) = Uanis(C57A)
Uanis(C17A) = Uanis(C17)
Uanis(C16) = Uanis(C16A)
Uanis(C15) = Uanis(C15A)
Uanis(C14) = Uanis(C14A)
Uanis(C13) = Uanis(C13A)
Uanis(C12A) = Uanis(C12)
Uanis(C6A) = Uanis(C6)
Uanis(C1A) = Uanis(C1)
Uanis(C2A) = Uanis(C2)
Uanis(C3) = Uanis(C3A)
Uanis(C4) = Uanis(C4A)
Uanis(C5A) = Uanis(C5)
Uanis(C27A) = Uanis(C27)
Uanis(C25A) = Uanis(C25)
Uanis(C24A) = Uanis(C24)
Uanis(C28A) = Uanis(C28)
Uanis(C10) = Uanis(C10A)
Uanis(C8A) = Uanis(C8)
4. others
 Sof(C1)=Sof(H1)=Sof(C2)=Sof(H2)=Sof(C3)=Sof(H3)=Sof(C4)=Sof(H4)=Sof(C5)=
 Sof(H5)=Sof(C6)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-
 Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=Sof(C7)=Sof(H7)=1-Sof(H1)=1-
 Sof(H1)=Sof(C8)=Sof(H8)=1-Sof(H1)=1-Sof(H1)=Sof(C10)=Sof(H10)=1-Sof(H1)=1-
 Sof(H1)=Sof(C11)=Sof(H11)=1-Sof(H1)=1-Sof(H1)=Sof(C12)=1-Sof(H1)=1-Sof(H1)=1-
 Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=1-Sof(H1)=
 1-Sof(H1)=Sof(C13)=Sof(H13)=Sof(C14)=Sof(H14)=Sof(C15)=Sof(H15)=Sof(C16)=
 Sof(H16)=Sof(C17)=Sof(H17)=Sof(O1)=1-Sof(H1)
 Sof(C18)=Sof(H18)=Sof(C19)=Sof(H19)=Sof(C20)=Sof(H20)=Sof(C21)=Sof(H21)=
 Sof(C22)=Sof(H22)=Sof(C23)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-
 Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=
 Sof(C24)=Sof(H24)=1-Sof(H18)=1-Sof(H18)=Sof(C25)=Sof(H25)=1-Sof(H18)=1-
 Sof(H18)=Sof(C27)=Sof(H27)=1-Sof(H18)=1-Sof(H18)=Sof(C28)=Sof(H28)=1-Sof(H18)=
 1-Sof(H18)=Sof(C29)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-
 Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=1-Sof(H18)=Sof(C30)=
 Sof(H30)=Sof(C31)=Sof(H31)=Sof(C32)=Sof(H32)=Sof(C33)=Sof(H33)=Sof(C34)=
 Sof(H34)=Sof(O2)=1-Sof(H18)
 Sof(C35)=Sof(H35)=Sof(C36)=Sof(H36)=Sof(C37)=Sof(H37)=Sof(C38)=Sof(H38)=
 Sof(C39)=Sof(H39)=Sof(C40)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-
 Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=
 Sof(C41)=Sof(H41)=1-Sof(H35)=1-Sof(H35)=Sof(C42)=Sof(H42)=1-Sof(H35)=1-
 Sof(H35)=Sof(C44)=Sof(H44)=1-Sof(H35)=1-Sof(H35)=Sof(C45)=Sof(H45)=1-Sof(H35)=
 1-Sof(H35)=Sof(C46)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-
 Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=1-Sof(H35)=Sof(C47)=
 Sof(H47)=Sof(C48)=Sof(H48)=Sof(C49)=Sof(H49)=Sof(C50)=Sof(H50)=Sof(C51)=
 Sof(H51)=Sof(O3)=1-Sof(H35)
 Sof(C52)=Sof(H52)=Sof(C53)=Sof(H53)=Sof(C54)=Sof(H54)=Sof(C55)=Sof(H55)=
 Sof(C56)=Sof(H56)=Sof(C57)=Sof(H57)=1-Sof(H52)=1-Sof(H52)=1-Sof(H52)=1-
 Sof(H52)=1-Sof(H52)=1-Sof(H52)=1-Sof(H52)=1-Sof(H52)=1-Sof(H52)=1-Sof(H52)=1-
 Sof(H52)=1-Sof(H52)
5.a Ternary CH refined with riding coordinates:
 C7(H7), C7A(H7A), C8(H8), C8A(H8A), C10(H10), C10A(H10A), C11(H11),
 C11A(H11A), C24(H24), C24A(H24A), C25(H25), C25A(H25A), C27(H27), C27A(H27A),
 C28(H28), C28A(H28A), C41(H41), C41A(H41A), C42(H42), C42A(H42A), C44(H44),
 C44A(H44A), C45(H45), C45A(H45A)
5.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C4(H4), C5(H5), C5A(H5A), C4A(H4A), C3A(H3A),
 C2A(H2A), C1A(H1A), C13A(H13A), C14A(H14A), C15A(H15A), C16A(H16A), C17A(H17A),
  C13(H13), C14(H14), C15(H15), C16(H16), C17(H17), C18(H18), C19(H19),
 C20(H20), C21(H21), C22(H22), C18A(H18A), C19A(H19A), C20A(H20A), C21A(H21A),
 C22A(H22A), C34A(H34A), C33A(H33A), C32A(H32A), C31A(H31A), C30A(H30A),
 C30(H30), C31(H31), C32(H32), C33(H33), C34(H34), C35(H35), C36(H36), C37(H37),
  C38(H38), C39(H39), C39A(H39A), C38A(H38A), C37A(H37A), C36A(H36A),
 C35A(H35A), C46A(H46A), C48A(H48A), C49A(H49A), C50A(H50A), C51A(H51A),
 C47(H47), C48(H48), C49(H49), C50(H50), C51(H51), C52(H52), C53(H53), C54(H54),
  C55(H55), C56(H56), C57(H57), C52A(H52A), C53A(H53A), C54A(H54A), C55A(H55A),
 C56A(H56A), C57A(H57A)
5.c Fitted hexagon refined as free rotating group:
 C6A(C5A,C4A,C3A,C2A,C1A), C12A(C13A,C14A,C15A,C16A,C17A), C23A(C18A,C19A,C20A,
 C21A,C22A), C29A(C34A,C33A,C32A,C31A,C30A), C40A(C39A,C38A,C37A,C36A,C35A),
 C46A(C47A,C48A,C49A,C50A,C51A), C52A(C53A,C54A,C55A,C56A,C57A)
;