Structural variety in ytterbium dicarboxylate frameworks and in situ study diffraction of their solvothermal crystallisation
Breeze, Matthew I.; Chamberlain, Thomas W.; Clarkson, Guy J.; de Camargo, Raíssa Pires; Wu, Yue; de Lima, Juliana Fonseca; Millange, Franck; Serra, Osvaldo A.; O'Hare, Dermot; Walton, Richard I.; CrystEngComm 19 (2017) 2424–; doi:10.1039/C7CE00481H

data_7228055
_publ_section_title
;
 Structural variety in ytterbium dicarboxylate frameworks and in situ
 study diffraction of their solvothermal crystallisation
;
_journal_issue                   17
_journal_name_full               CrystEngComm
_journal_page_first              2424
_journal_paper_doi               10.1039/C7CE00481H
_journal_volume                  19
_journal_year                    2017
_chemical_formula_moiety         'C15 H13 N O7 Yb, 0.5(H2 O)'
_chemical_formula_sum            'C15 H14 N O7.5 Yb'
_chemical_formula_weight         501.31
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_symmetry_space_group_name_Hall  '-C 2yc'
_symmetry_space_group_name_H-M   'C 1 2/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_block_doi                 10.5517/ccdc.csd.cc14hcnn
_audit_creation_date             2015-07-28
_audit_creation_method
;
Olex2 1.2
(compiled 2015.01.26 svn.r3151 for OlexSys, GUI svn.r4998)
;
_audit_update_record
;
2015-12-16 deposited with the CCDC.
2017-04-11 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 101.395(2)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   18.2950(4)
_cell_length_b                   10.8482(2)
_cell_length_c                   17.3984(4)
_cell_measurement_reflns_used    6851
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      29.3060
_cell_measurement_theta_min      3.4070
_cell_volume                     3384.96(13)
_computing_cell_refinement
;
CrysAlisPro, Agilent Technologies,
Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET)
(compiled Aug 13 2014,18:06:01)
;
_computing_data_collection
;
CrysAlisPro, Agilent Technologies,
Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET)
(compiled Aug 13 2014,18:06:01)
;
_computing_data_reduction
;
CrysAlisPro, Agilent Technologies,
Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET)
(compiled Aug 13 2014,18:06:01)
;
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.2833
_diffrn_detector_type            Ruby
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.961
_diffrn_measurement_details
;
  1 omega   -6.00  108.00   0.5000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       23.1033   77.0000  150.0000 228

  2 omega  -22.00  118.00   0.5000   25.0000
omega____ theta____ kappa____ phi______ frames
    -       23.1033   77.0000  -60.0000 280

  3 omega   42.00   67.00   0.5000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -24.8220   77.0000 -120.0000 50

  4 omega   -9.00   19.00   0.5000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -24.8220   77.0000 -120.0000 56

  5 omega  -64.00   69.00   0.5000   25.0000
omega____ theta____ kappa____ phi______ frames
    -      -24.8220   77.0000   30.0000 266
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Xcalibur, Ruby, Gemini'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_UB_11      -0.0328388000
_diffrn_orient_matrix_UB_12      -0.0354829000
_diffrn_orient_matrix_UB_13      -0.0014490000
_diffrn_orient_matrix_UB_21      -0.0188485000
_diffrn_orient_matrix_UB_22      0.0530794000
_diffrn_orient_matrix_UB_23      0.0098677000
_diffrn_orient_matrix_UB_31      -0.0114857000
_diffrn_orient_matrix_UB_32      0.0142109000
_diffrn_orient_matrix_UB_33      -0.0404364000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_unetI/netI     0.0288
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.961
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -25
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            40716
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.961
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         29.419
_diffrn_reflns_theta_min         3.074
_diffrn_source                   'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    5.565
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.67856
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro, Agilent Technologies,
Version 1.171.37.35 (release 13-08-2014 CrysAlis171 .NET)
(compiled Aug 13 2014,18:06:01)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.967
_exptl_crystal_description       block
_exptl_crystal_F_000             1928
_exptl_crystal_size_max          0.30
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.08
_refine_diff_density_max         2.636
_refine_diff_density_min         -1.456
_refine_diff_density_rms         0.292
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.030
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     232
_refine_ls_number_reflns         8841
_refine_ls_number_restraints     32
_refine_ls_restrained_S_all      1.049
_refine_ls_R_factor_all          0.0478
_refine_ls_R_factor_gt           0.0358
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0782P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1042
_refine_ls_wR_factor_ref         0.1155
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7025
_reflns_number_total             8841
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c7ce00481h2.cif
_cod_data_source_block           mb2_twin1_hklf5
_cod_depositor_comments
'Adding full bibliography for 7228053--7228056.cif.'
_cod_original_formula_sum        'C15 H14 N O7.50 Yb'
_cod_database_code               7228055
_chemical_oxdiff_formula         'C15 H10N1 O8 Yb'
_diffrn_oxdiff_twin_integration_method simultaneous
_olex2_refinement_description
;

The crystal chosen had a twin component. The relationship between the UB matrix and the 
two twin orientations are 
Twin 1  1.0000  0.0000  0.0000  0.0000  1.0000  0.0000  0.0000  0.0000  1.0000
Twin 2 -0.9994 -0.0001 -0.4142  0.0001 -1.0001  0.0000 -0.0001  0.0001  0.9994

From the twin log generated by CrysalisPro
Twin analysis: Component 1 with component 2
TL  =UB[1]-1*UB[2]:  -0.9994  -0.0000  -0.4141    -0.0001  -1.0002  -0.0000    -0.0001  -0.0001   0.9994   det 0.999026
TL-1=UB[2]*UB[1]-1:  -1.0005   0.0001  -0.4146     0.0001  -0.9998   0.0000    -0.0001  -0.0001   1.0006   det 1.000975
the two orientations are related by a
rotation = -179.9892 deg around the following vectors: 
Reciprocal space (hkl): -0.2036 0.0002 0.9790
Direct space (uvw)    : -0.0001 -0.0000 1.0000

Twinned data refinement
The scale factors (twin ratios) were   0.8746(5) : 0.1254(5)

The integration of the data was conducted with the twinning suite in the Crysalis Pro software 
and refined with Olex2

The coordinated DMF had cigar shaped thermal ellipsoids and was refined with SIMU and DELU 
restraints to give it reasonable thermal parameters.

Electron density not close enough to be metal bound or part of the ligand was modeled as a 
partially occupied water (half occupancy). Hydrogens were placed at calculated positions on 
this water. The partially occupied water molecule was refined behind a PART -1 instruction 
as it is close to a symmetry related water but this is possible as it is only half occupied 
and lies in either one position or the other in the crystal lattice.

1. Twinned data refinement
 Scales: 0.8746(5) 0.1254(5)
2. 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
3. Rigid bond restraints
 O301, C302, N303, C304, C305
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
4. Uiso/Uaniso restraints and constraints
O301 \\sim C302 \\sim N303 \\sim C304 \\sim C305: within 1.7A with sigma of
0.002 and sigma for terminal atoms of 0.004
5. Others
 Fixed Sof: O1(0.5) H1A(0.5) H1B(0.5)
6.a Free rotating group:
 O1(H1A,H1B)
6.b Aromatic/amide H refined with riding coordinates:
 C205(H205), C302(H302), C104(H104), C108(H108), C107(H107), C105(H105),
 C204(H204)
6.c Idealised Me refined as rotating group:
 C305(H30A,H30B,H30C), C304(H30D,H30E,H30F)
;
_shelx_shelxl_version_number     2014/7
_olex2_submission_special_instructions 'No special instructions were received'