An amidato divalent ytterbium cluster: synthesis and molecular structure, its reactivity to carbodiimides and application in the guanylation reaction
Gong, Chao; Ding, Hao; Lu, Chengrong; Zhao, Bei; Yao, Yingming; Dalton Trans.  (2017) –; doi:10.1039/C7DT00871F

data_7042733
_publ_section_title
;
 An amidato divalent ytterbium cluster: synthesis and molecular structure,
 its reactivity to carbodiimides and application in the guanylation
 reaction
;
_journal_name_full               'Dalton Trans.'
_journal_paper_doi               10.1039/C7DT00871F
_journal_year                    2017
_chemical_formula_moiety         'C114 H132 N6 O6 Yb2, 2(C7 H8)'
_chemical_formula_sum            'C128 H148 N6 O6 Yb2'
_chemical_formula_weight         2212.60
_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     heavy
_atom_sites_solution_secondary   difmap
_audit_creation_date             2013-01-29
_audit_creation_method
;
  Olex2 1.2
  (compiled Dec  5 2012 16:20:19, GUI svn.r4385)
;
_audit_update_record
;
2017-02-25 deposited with the CCDC.
2017-03-30 downloaded from the CCDC.
;
_cell_angle_alpha                68.116(3)
_cell_angle_beta                 67.267(3)
_cell_angle_gamma                85.184(2)
_cell_formula_units_Z            1
_cell_length_a                   13.8319(4)
_cell_length_b                   14.3956(4)
_cell_length_c                   16.1575(5)
_cell_measurement_reflns_used    8981
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      29.4433
_cell_measurement_theta_min      3.2926
_cell_volume                     2746.71(17)
_computing_cell_refinement
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.20 (release 27-06-2012 CrysAlis171 .NET)
(compiled Jul 11 2012,15:38:31)
;
_computing_data_collection
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CrysAlisPro, Agilent Technologies,
Version 1.171.36.20 (release 27-06-2012 CrysAlis171 .NET)
(compiled Jul 11 2012,15:38:31)
;
_computing_data_reduction
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.20 (release 27-06-2012 CrysAlis171 .NET)
(compiled Jul 11 2012,15:38:31)
;
_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
;
XL, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122
;
_computing_structure_solution
;
XS, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122
;
_diffrn_ambient_temperature      293(2)
_diffrn_detector_area_resol_mean 10.4692
_diffrn_measured_fraction_theta_full 0.9979
_diffrn_measured_fraction_theta_max 0.9979
_diffrn_measurement_details
;
  1 omega  -25.00    0.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -12.4985  -99.0000   60.0000 25

  2 omega  -79.00   12.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -12.4985  -57.0000   60.0000 91

  3 omega  -78.00   19.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -12.4985  -77.0000  -60.0000 97

  4 omega  -40.00   61.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -12.4985   57.0000 -150.0000 101

  5 omega   32.00  101.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -       12.1079 -178.0000 -180.0000 69

  6 omega -103.00  -60.00   1.0000    2.0000
omega____ theta____ kappa____ phi______ frames
    -      -12.4985 -178.0000 -150.0000 43
;
_diffrn_measurement_device_type  'Xcalibur, Atlas, Gemini'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      0.0138896000
_diffrn_orient_matrix_UB_12      -0.0385325000
_diffrn_orient_matrix_UB_13      -0.0190561000
_diffrn_orient_matrix_UB_21      0.0135258000
_diffrn_orient_matrix_UB_22      -0.0295054000
_diffrn_orient_matrix_UB_23      0.0396959000
_diffrn_orient_matrix_UB_31      -0.0522562000
_diffrn_orient_matrix_UB_32      -0.0218649000
_diffrn_orient_matrix_UB_33      0.0262002000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.7107
_diffrn_reflns_av_R_equivalents  0.0612
_diffrn_reflns_av_unetI/netI     0.0643
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            28571
_diffrn_reflns_theta_full        26.37
_diffrn_reflns_theta_max         26.37
_diffrn_reflns_theta_min         3.30
_diffrn_source                   'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    1.750
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.64609
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro, Agilent Technologies,
Version 1.171.36.20 (release 27-06-2012 CrysAlis171 .NET)
(compiled Jul 11 2012,15:38:31)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            prism
_exptl_crystal_density_diffrn    1.338
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             1146
_exptl_crystal_size_max          0.7
_exptl_crystal_size_mid          0.65
_exptl_crystal_size_min          0.3
_refine_diff_density_max         2.149
_refine_diff_density_min         -1.076
_refine_diff_density_rms         0.107
_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     706
_refine_ls_number_reflns         11189
_refine_ls_number_restraints     116
_refine_ls_restrained_S_all      1.062
_refine_ls_R_factor_all          0.0448
_refine_ls_R_factor_gt           0.0357
_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^)+(0.0296P)^2^+1.7438P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0791
_refine_ls_wR_factor_ref         0.0861
_reflns_number_gt                9861
_reflns_number_total             11189
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            c7dt00871f2.cif
_cod_data_source_block           g121010d
_cod_original_cell_volume        2746.71(13)
_cod_database_code               7042733
_reflns_odcompleteness_completeness 99.79
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     26.32
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  H6 of C6, H5 of C5, H4 of C4, H14 of C14, H17 of C17, H3 of C3, H12 of C12,
  H11 of C11, H10 of C10, H7 of C7, H24 of C24, H31 of C31, H23 of C23, H26 of
  C26, H22 of C22, H25 of C25, H29 of C29, H30 of C30, H33 of C33, H63B of C63B,
   H62B of C62B, H61B of C61B, H60B of C60B, H59B of C59B, H63A of C63A, H62A
  of C62A, H61A of C61A, H60A of C60A, H59A of C59A, H55 of C55, H52 of C52,
  H50 of C50, H49 of C49, H48 of C48, H45 of C45, H44 of C44, H43 of C43, H42
  of C42, H41 of C41, H36 of C36
 At 1.5 times of:
  {H15A,H15B,H15C} of C15, {H16A,H16B,H16C} of C16, {H18A,H18B,H18C} of C18,
  {H19A,H19B,H19C} of C19, {H34A,H34B,H34C} of C34, {H64A,H64B,H64C} of C64B,
  {H64D,H64E,H64F} of C64A, {H57A,H57B,H57C} of C57, {H56A,H56B,H56C} of C56,
  {H54A,H54B,H54C} of C54, {H53A,H53B,H53C} of C53, {H38A,H38B,H38C} of C38,
  {H37A,H37B,H37C} of C37, {H35A,H35B,H35C} of C35
2. Restrained distances
 C58A-C64A = C58B-C64B
 1.5 with sigma of 0.02
3. Rigid bond restraints
 C58A, C59A, C60A, C61A, C62A, C63A, C64A
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C58B, C59B, C60B, C61B, C62B, C63B, C64B
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
4. Uiso/Uaniso restraints and constraints
C58A ~ C59A ~ C60A ~ C61A ~ C62A ~ C63A ~ C64A: within 1.7A with sigma of 0.005 and sigma for terminal atoms of 0.01
C58B ~ C59B ~ C60B ~ C61B ~ C62B ~ C63B ~ C64B: within 1.7A with sigma of 0.005 and sigma for terminal atoms of 0.01
5. Others
 Sof(C58A)=Sof(C59A)=Sof(H59A)=Sof(C60A)=Sof(H60A)=Sof(C61A)=Sof(H61A)=
 Sof(C62A)=Sof(H62A)=Sof(C63A)=Sof(H63A)=Sof(C64A)=Sof(H64D)=Sof(H64E)=
 Sof(H64F)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-
 Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-
 Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)=1-Sof(C59A)
6.a Ternary CH refined with riding coordinates:
 C14(H14), C17(H17), C33(H33), C36(H36), C52(H52), C55(H55)
6.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5), C6(H6), C7(H7), C10(H10), C11(H11), C12(H12),
 C22(H22), C23(H23), C24(H24), C25(H25), C26(H26), C29(H29), C30(H30), C31(H31),
  C41(H41), C42(H42), C43(H43), C44(H44), C45(H45), C48(H48), C49(H49),
 C50(H50), C59A(H59A), C60A(H60A), C61A(H61A), C62A(H62A), C63A(H63A),
 C59B(H59B), C60B(H60B), C61B(H61B), C62B(H62B), C63B(H63B)
6.c Fitted hexagon refined as free rotating group:
 C58B(C59B,C60B,C61B,C62B,C63B)
6.d Idealised Me refined as rotating group:
 C15(H15A,H15B,H15C), C16(H16A,H16B,H16C), C18(H18A,H18B,H18C), C19(H19A,H19B,
 H19C), C34(H34A,H34B,H34C), C35(H35A,H35B,H35C), C37(H37A,H37B,H37C), C38(H38A,
 H38B,H38C), C53(H53A,H53B,H53C), C54(H54A,H54B,H54C), C56(H56A,H56B,H56C),
 C57(H57A,H57B,H57C), C64A(H64D,H64E,H64F), C64B(H64A,H64B,H64C)
;