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_4119854
_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         'C57 H54 O9 Pd2, H2 O'
_chemical_formula_sum            'C57 H56 O10 Pd2'
_chemical_formula_weight         1113.82
_chemical_name_systematic
;
 ? 
;
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_symmetry_space_group_name_Hall  '-P 2yn'
_symmetry_space_group_name_H-M   'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2013-04-26
_audit_creation_method
;
  Olex2 1.2
  (compiled Apr 23 2013 17:59:47, GUI svn.r4466)
;
_cell_angle_alpha                90.00
_cell_angle_beta                 107.099(2)
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   13.2832(10)
_cell_length_b                   17.4986(13)
_cell_length_c                   21.4602(16)
_cell_measurement_reflns_used    5155
_cell_measurement_temperature    115(2)
_cell_measurement_theta_max      27.23
_cell_measurement_theta_min      2.42
_cell_volume                     4767.7(6)
_computing_cell_refinement       'SAINT v6.28A (Bruker, 2002)'
_computing_data_collection       'SMART v5.625 (Bruker, 2001)'
_computing_data_reduction        'SAINT v6.28A (Bruker, 2002)'
_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    'SHELXS-97 (Sheldrick, 1990)'
_diffrn_ambient_temperature      115
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_device_type  'CCD area detector'
_diffrn_measurement_method       'phi and omega scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0574
_diffrn_reflns_av_unetI/netI     0.0777
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -28
_diffrn_reflns_number            33757
_diffrn_reflns_theta_full        28.32
_diffrn_reflns_theta_max         28.32
_diffrn_reflns_theta_min         1.99
_diffrn_source                   'fine-focus sealed tube'
_diffrn_source_current           40.0
_diffrn_source_power             1.8
_diffrn_source_target            Mo
_diffrn_source_voltage           45.0
_exptl_absorpt_coefficient_mu    0.817
_exptl_absorpt_correction_T_max  1
_exptl_absorpt_correction_T_min  0.835704
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS v.2.03 (Bruker,200?) was used for absorption correction.
R(int) was 0.0440 before and 0.0347 after correction.
The Ratio of minimum to maximum transmission is 0.8357.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            red
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.552
_exptl_crystal_description       block
_exptl_crystal_F_000             2280
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.11
_exptl_crystal_size_min          0.07
_refine_diff_density_max         0.969
_refine_diff_density_min         -1.150
_refine_diff_density_rms         0.104
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.025
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     708
_refine_ls_number_reflns         11831
_refine_ls_number_restraints     30
_refine_ls_restrained_S_all      1.025
_refine_ls_R_factor_all          0.0944
_refine_ls_R_factor_gt           0.0497
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0517P)^2^+0.9243P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1032
_refine_ls_wR_factor_ref         0.1183
_reflns_number_gt                7595
_reflns_number_total             11831
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja403259c_si_002_7.cif
_cod_data_source_block           ijf0423m
_cod_depositor_comments
;
The following automatic conversions were performed:

'_diffrn_source_target' value 'MO' changed to 'Mo' according to the
built-in table from CIF Core dictionary named 'cif_core.dic' version
2.4.1 from 2010-06-29.

Automatic conversion script
Id: cif_fix_values 2281 2013-09-26 08:29:07Z andrius 
;
_cod_database_code               4119854
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Uiso/Uaniso restraints and constraints
Uanis(C22B) \\sim Ueq, Uanis(C22A) \\sim Ueq, Uanis(C23B) \\sim Ueq, 
Uanis(C23A) \\sim Ueq, Uanis(O9) \\sim Ueq: with sigma of 0.01 and sigma for 
terminal atoms of 0.02
Uanis(O7A) = Uanis(O7B)
Uanis(C56A) = Uanis(C56B)
Uanis(C40A) = Uanis(C40B)
Uanis(C41B) = Uanis(C41A)
Uanis(C39B) = Uanis(C39A)
Uanis(C44B) = Uanis(C44A)
Uanis(C43B) = Uanis(C43A)
Uanis(C42A) = Uanis(C42B)
Uanis(C26B) = Uanis(C26A)
Uanis(C27A) = Uanis(C27B)
Uanis(C29A) = Uanis(C29B)
Uanis(C30A) = Uanis(C30B)
Uanis(C31B) = Uanis(C31A)
Uanis(C35B) = Uanis(C35A)
Uanis(C34A) = Uanis(C34B)
Uanis(C33B) = Uanis(C33A)
Uanis(C32B) = Uanis(C32A)
Uanis(O6A) = Uanis(O6B)
Uanis(C38A) = Uanis(C38B)
Uanis(C25B) = Uanis(C25A)
Uanis(C20A) = Uanis(C20B)
Uanis(C21B) = Uanis(C21A)
Uanis(C22B) = Uanis(C22A)
Uanis(C24B) = Uanis(C24A)
Uanis(C23B) = Uanis(C23A)
Uanis(C55A) = Uanis(C55B)
Uanis(C50B) = Uanis(C50A)
Uanis(C54A) = Uanis(C54B)
Uanis(C53B) = Uanis(C53A)
Uanis(C52A) = Uanis(C52B)
Uanis(C51B) = Uanis(C51A)
3. others
 Sof(C20B)=Sof(C21B)=Sof(H21B)=Sof(C22B)=Sof(H22B)=Sof(C23B)=Sof(C24B)=
 Sof(H24B)=Sof(C25B)=Sof(H25B)=Sof(C26B)=Sof(H26B)=Sof(C27B)=Sof(H27B)=
 Sof(C29B)=Sof(H29B)=Sof(C30B)=Sof(H30B)=Sof(C31B)=Sof(C32B)=Sof(H32B)=
 Sof(C33B)=Sof(H33B)=Sof(C34B)=Sof(C35B)=Sof(H35B)=Sof(C36B)=Sof(H36B)=Sof(O5B)=
 1-FVAR(1)
 Sof(C20A)=Sof(C21A)=Sof(H21A)=Sof(C22A)=Sof(H22A)=Sof(C23A)=Sof(C24A)=
 Sof(H24A)=Sof(C25A)=Sof(H25A)=Sof(C26A)=Sof(H26A)=Sof(C27A)=Sof(H27A)=
 Sof(C29A)=Sof(H29A)=Sof(C30A)=Sof(H30A)=Sof(C31A)=Sof(C32A)=Sof(H32A)=
 Sof(C33A)=Sof(H33A)=Sof(C34A)=Sof(C35A)=Sof(H35A)=Sof(C36A)=Sof(H36A)=Sof(O5A)=
 FVAR(1)
 Sof(C39B)=Sof(C40B)=Sof(H40B)=Sof(C41B)=Sof(H41B)=Sof(C42B)=Sof(C43B)=
 Sof(H43B)=Sof(C44B)=Sof(H44B)=Sof(C45B)=Sof(H45B)=Sof(C46B)=Sof(H46B)=
 Sof(C48B)=Sof(H48B)=Sof(C49B)=Sof(H49B)=Sof(C50B)=Sof(C51B)=Sof(H51B)=
 Sof(C52B)=Sof(H52B)=Sof(C53B)=Sof(C54B)=Sof(H54B)=Sof(C55B)=Sof(H55B)=Sof(O8B)=
 Sof(O7B)=Sof(C56B)=Sof(H56D)=Sof(H56E)=Sof(H56F)=1-FVAR(2)
 Sof(C39A)=Sof(C40A)=Sof(H40A)=Sof(C41A)=Sof(H41A)=Sof(C42A)=Sof(C43A)=
 Sof(H43A)=Sof(C44A)=Sof(H44A)=Sof(C45A)=Sof(H45A)=Sof(C46A)=Sof(H46A)=
 Sof(C48A)=Sof(H48A)=Sof(C49A)=Sof(H49A)=Sof(C50A)=Sof(C51A)=Sof(H51A)=
 Sof(C52A)=Sof(H52A)=Sof(C53A)=Sof(C54A)=Sof(H54A)=Sof(C55A)=Sof(H55A)=
 Sof(C56A)=Sof(H56A)=Sof(H56B)=Sof(H56C)=Sof(O7A)=Sof(O8A)=FVAR(2)
 Sof(O6B)=Sof(C38B)=Sof(H38D)=Sof(H38E)=Sof(H38F)=1-FVAR(3)
 Sof(C38A)=Sof(H38A)=Sof(H38B)=Sof(H38C)=Sof(O6A)=FVAR(3)
4.a Free rotating group:
 O10(H10A,H10B)
4.b Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C5(H5), C6(H6), C7(H7), C8(H8), C10(H10), C11(H11), C13(H13),
 C14(H14), C16(H16), C17(H17), C21A(H21A), C22A(H22A), C24A(H24A), C25A(H25A),
 C26A(H26A), C27A(H27A), C29A(H29A), C30A(H30A), C32A(H32A), C33A(H33A),
 C35A(H35A), C36A(H36A), C21B(H21B), C22B(H22B), C24B(H24B), C25B(H25B),
 C26B(H26B), C27B(H27B), C29B(H29B), C30B(H30B), C32B(H32B), C33B(H33B),
 C35B(H35B), C36B(H36B), C40A(H40A), C41A(H41A), C43A(H43A), C44A(H44A),
 C45A(H45A), C46A(H46A), C48A(H48A), C49A(H49A), C40B(H40B), C41B(H41B),
 C43B(H43B), C44B(H44B), C45B(H45B), C46B(H46B), C48B(H48B), C49B(H49B),
 C51A(H51A), C52A(H52A), C54A(H54A), C55A(H55A), C51B(H51B), C52B(H52B),
 C54B(H54B), C55B(H55B)
4.c Fitted hexagon refined as free rotating group:
 C20A(C21A,C22A,C23A,C24A,C25A), C31A(C32A,C33A,C34A,C35A,C36A), C31B(C32B,
 C33B,C34B,C35B,C36B), C39A(C40A,C41A,C42A,C43A,C44A), C39B(C40B,C41B,C42B,C43B,
 C44B), C50A(C51A,C52A,C53A,C54A,C55A), C50B(C51B,C52B,C53B,C54B,C55B)
4.d Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C19(H19A,H19B,H19C), C37(H37A,H37B,H37C), C38A(H38A,H38B,
 H38C), C56A(H56A,H56B,H56C), C57(H57A,H57B,H57C), C56B(H56D,H56E,H56F),
 C38B(H38D,H38E,H38F)
;