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_4119852
_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         'C63 H66 O15 Pd2, C H2 Cl2'
_chemical_formula_sum            'C64 H68 Cl2 O15 Pd2'
_chemical_formula_weight         1360.88
_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     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2013-04-29
_audit_creation_method
;
  Olex2 1.2
  (compiled Apr 23 2013 17:59:47, GUI svn.r4466)
;
_cell_angle_alpha                90.00
_cell_angle_beta                 94.240(2)
_cell_angle_gamma                90.00
_cell_formula_units_Z            4
_cell_length_a                   15.6423(12)
_cell_length_b                   23.0941(17)
_cell_length_c                   16.1426(12)
_cell_measurement_reflns_used    8972
_cell_measurement_temperature    115(2)
_cell_measurement_theta_max      27.31
_cell_measurement_theta_min      2.17
_cell_volume                     5815.5(8)
_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  0.0549
_diffrn_reflns_av_unetI/netI     0.0501
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -30
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            56062
_diffrn_reflns_theta_full        27.54
_diffrn_reflns_theta_max         27.54
_diffrn_reflns_theta_min         1.31
_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    0.780
_exptl_absorpt_correction_T_max  1
_exptl_absorpt_correction_T_min  0.862974
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS v.2.03 (Bruker,200?) was used for absorption correction.
R(int) was 0.0465 before and 0.0351 after correction.
The Ratio of minimum to maximum transmission is 0.8630.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            red
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.554
_exptl_crystal_description       cubes
_exptl_crystal_F_000             2792
_exptl_crystal_size_max          0.147
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.03
_refine_diff_density_max         1.634
_refine_diff_density_min         -1.123
_refine_diff_density_rms         0.203
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.066
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     880
_refine_ls_number_reflns         13381
_refine_ls_number_restraints     330
_refine_ls_restrained_S_all      1.059
_refine_ls_R_factor_all          0.0791
_refine_ls_R_factor_gt           0.0527
_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^)+(0.0581P)^2^+11.2942P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1201
_refine_ls_wR_factor_ref         0.1352
_reflns_number_gt                9949
_reflns_number_total             13381
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja403259c_si_002_5.cif
_cod_data_source_block           ijf0425m
_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               4119852
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Uiso/Uaniso restraints and constraints
Uanis(C54B) \\sim Ueq, Uanis(C54A) \\sim Ueq, Uanis(C55B) \\sim Ueq, 
Uanis(C55A) \\sim Ueq, Uanis(C58A) \\sim Ueq, Uanis(C58B) \\sim Ueq, 
Uanis(C59B) \\sim Ueq, Uanis(C59A) \\sim Ueq, Uanis(C63A) \\sim Ueq, 
Uanis(C63B) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(O14A) \\sim Ueq, Uanis(O14B) \\sim Ueq, Uanis(O15A) \\sim Ueq, 
Uanis(O15B) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C43A) \\sim Ueq, Uanis(C43B) \\sim Ueq, Uanis(C44A) \\sim Ueq, 
Uanis(C44B) \\sim Ueq, Uanis(C45A) \\sim Ueq, Uanis(C45B) \\sim Ueq, 
Uanis(C46A) \\sim Ueq, Uanis(C46B) \\sim Ueq, Uanis(C47A) \\sim Ueq, 
Uanis(C47B) \\sim Ueq, Uanis(C48A) \\sim Ueq, Uanis(C48B) \\sim Ueq, 
Uanis(C49A) \\sim Ueq, Uanis(C49B) \\sim Ueq, Uanis(C50A) \\sim Ueq, 
Uanis(C50B) \\sim Ueq, Uanis(C51) \\sim Ueq, Uanis(C52A) \\sim Ueq, 
Uanis(C52B) \\sim Ueq, Uanis(C53A) \\sim Ueq, Uanis(C53B) \\sim Ueq, 
Uanis(C54A) \\sim Ueq, Uanis(C54B) \\sim Ueq, Uanis(C55A) \\sim Ueq, 
Uanis(C55B) \\sim Ueq, Uanis(C56A) \\sim Ueq, Uanis(C56B) \\sim Ueq, 
Uanis(C57A) \\sim Ueq, Uanis(C57B) \\sim Ueq, Uanis(C58A) \\sim Ueq, 
Uanis(C58B) \\sim Ueq, Uanis(C59A) \\sim Ueq, Uanis(C59B) \\sim Ueq, 
Uanis(C60A) \\sim Ueq, Uanis(C60B) \\sim Ueq, Uanis(C61A) \\sim Ueq, 
Uanis(C61B) \\sim Ueq, Uanis(C62A) \\sim Ueq, Uanis(C62B) \\sim Ueq, 
Uanis(C63A) \\sim Ueq, Uanis(C63B) \\sim Ueq: with sigma of 0.01 and sigma for 
terminal atoms of 0.02
Uanis(O12A) = Uanis(O12B)
Uanis(C48B) = Uanis(C48A)
Uanis(C43B) = Uanis(C43A)
Uanis(C44A) = Uanis(C44B)
Uanis(C46B) = Uanis(C46A)
Uanis(C47B) = Uanis(C47A)
Uanis(C56B) = Uanis(C56A)
Uanis(C60A) = Uanis(C60B)
Uanis(C61B) = Uanis(C61A)
Uanis(C52A) = Uanis(C52B)
Uanis(C53B) = Uanis(C53A)
Uanis(C50B) = Uanis(C50A)
Uanis(C49A) = Uanis(C49B)
Uanis(C58B) = Uanis(C58A)
Uanis(C59B) = Uanis(C59A)
Uanis(C54A) = Uanis(C54B)
Uanis(C55B) = Uanis(C55A)
Uanis(C63A) = Uanis(C63B)
Uanis(O13A) = Uanis(O13B)
Uanis(C62B) = Uanis(C62A)
3. others
 Sof(C43B)=Sof(H43B)=Sof(C44B)=Sof(C45B)=Sof(H45B)=Sof(C46B)=Sof(C47B)=
 Sof(H47B)=Sof(C48B)=Sof(C49B)=Sof(H49B)=Sof(C50B)=Sof(H50B)=Sof(C52B)=
 Sof(H52B)=Sof(C53B)=Sof(H53B)=Sof(C54B)=Sof(C55B)=Sof(H55B)=Sof(C56B)=
 Sof(C57B)=Sof(H57B)=Sof(C58B)=Sof(C59B)=Sof(H59B)=Sof(C60B)=Sof(H60D)=
 Sof(H60E)=Sof(H60F)=Sof(C61B)=Sof(H61D)=Sof(H61E)=Sof(H61F)=Sof(C62B)=
 Sof(H62D)=Sof(H62E)=Sof(H62F)=Sof(C63B)=Sof(H63D)=Sof(H63E)=Sof(H63F)=
 Sof(O12B)=Sof(O13B)=Sof(O14B)=Sof(O15B)=1-FVAR(1)
 Sof(C43A)=Sof(H43A)=Sof(C44A)=Sof(C45A)=Sof(H45A)=Sof(C46A)=Sof(C47A)=
 Sof(H47A)=Sof(C48A)=Sof(C49A)=Sof(H49A)=Sof(C50A)=Sof(H50A)=Sof(C52A)=
 Sof(H52A)=Sof(C53A)=Sof(H53A)=Sof(C54A)=Sof(C55A)=Sof(H55A)=Sof(C56A)=
 Sof(C57A)=Sof(H57A)=Sof(C58A)=Sof(C59A)=Sof(H59A)=Sof(C60A)=Sof(H60A)=
 Sof(H60B)=Sof(H60C)=Sof(C61A)=Sof(H61A)=Sof(H61B)=Sof(H61C)=Sof(C62A)=
 Sof(H62A)=Sof(H62B)=Sof(H62C)=Sof(C63A)=Sof(H63A)=Sof(H63B)=Sof(H63C)=
 Sof(O12A)=Sof(O13A)=Sof(O14A)=Sof(O15A)=FVAR(1)
 Sof(H64C)=Sof(H64D)=Sof(Cl1B)=Sof(Cl2B)=1-FVAR(2)
 Sof(H64A)=Sof(H64B)=Sof(Cl1A)=Sof(Cl2A)=FVAR(2)
4.a Secondary CH2 refined with riding coordinates:
 C64(H64A,H64B), C64(H64C,H64D)
4.b Aromatic/amide H refined with riding coordinates:
 C1(H1), C3(H3), C5(H5), C7(H7), C8(H8), C10(H10), C11(H11), C13(H13),
 C15(H15), C17(H17), C22(H22), C24(H24), C26(H26), C28(H28), C29(H29), C31(H31),
  C32(H32), C34(H34), C36(H36), C38(H38), C43A(H43A), C43B(H43B), C45A(H45A),
 C45B(H45B), C47A(H47A), C47B(H47B), C49A(H49A), C49B(H49B), C50A(H50A),
 C50B(H50B), C52A(H52A), C52B(H52B), C53A(H53A), C53B(H53B), C55A(H55A),
 C55B(H55B), C57A(H57A), C57B(H57B), C59A(H59A), C59B(H59B)
4.c Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C19(H19A,H19B,H19C), C20(H20A,H20B,H20C), C21(H21A,H21B,
 H21C), C39(H39A,H39B,H39C), C40(H40A,H40B,H40C), C41(H41A,H41B,H41C), C42(H42A,
 H42B,H42C), C60A(H60A,H60B,H60C), C60B(H60D,H60E,H60F), C61A(H61A,H61B,H61C),
 C61B(H61D,H61E,H61F), C62A(H62A,H62B,H62C), C62B(H62D,H62E,H62F), C63A(H63A,
 H63B,H63C), C63B(H63D,H63E,H63F)
;