An investigation into catalysed xanthene-based dye oxidation by a family of coordination cages.
Williams, James R.; Ward, Michael D.; Nanoscale 17 (2025) 17285–17293; doi:10.1039/d5nr02293b

data_1575068
_publ_section_title
;
 An investigation into catalysed xanthene-based dye oxidation by a family
 of coordination cages.
;
_journal_issue                   29
_journal_name_full               Nanoscale
_journal_page_first              17285
_journal_page_last               17293
_journal_paper_doi               10.1039/d5nr02293b
_journal_volume                  17
_journal_year                    2025
_chemical_formula_moiety         'C27 H27 Co N9, 2(B F4)'
_chemical_formula_sum            'C27 H27 B2 Co F8 N9'
_chemical_formula_weight         710.12
_chemical_name_systematic
tris(2-(1-methyl-1H-pyrazol-3-yl)pyridine)cobalt-di(tetrafluoroborate)
_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'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-03-21
_audit_creation_method
;
Olex2 1.5
(compiled 2025.03.04 svn.red2d20d0 for OlexSys, GUI svn.r7188)
;
_audit_update_record
;
2025-05-29 deposited with the CCDC.	2025-07-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 104.141(4)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   12.6814(4)
_cell_length_b                   12.1894(4)
_cell_length_c                   20.2334(8)
_cell_measurement_reflns_used    7056
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      67.7920
_cell_measurement_theta_min      3.7600
_cell_volume                     3032.88(19)
_computing_cell_refinement       'CrysAlisPro 1.171.43.90 (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 43.143a 64-bit (release 25-10-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.90 (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix-Arc 100'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.974
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w     39.00  70.00   0.50    1.00    --   99.19 -61.00 120.00   62
  2  \w     33.00  59.00   0.50    1.00    --   99.19 -61.00  30.00   52
  3  \w     32.00  59.00   0.50    1.00    --   99.19 -61.00 -30.00   54
  4  \w     44.00  69.00   0.50    1.00    --   99.19 -61.00  60.00   50
  5  \w     35.00  62.00   0.50    1.00    --   99.19 -61.00 -60.00   54
  6  \w    -18.00   7.00   0.50    1.00    --   49.66 -33.00-117.00   50
  7  \w     30.00  55.00   0.50    1.00    --   99.19 -61.00-180.00   50
  8  \w     33.00  68.00   0.50    1.00    --   99.19 -61.00-150.00   70
  9  \w     39.00  70.00   0.50    1.00    --   99.19 -61.00 -90.00   62
 10  \w    100.00 150.00   0.50    1.00    --   99.19  30.00 150.00  100
 11  \w     94.00 174.00   0.50    1.00    --   99.19  33.00  40.00  160
 12  \w    103.00 165.00   0.50    1.00    --   99.19 125.00 -60.00  124
 13  \w    115.00 167.00   0.50    1.00    --   99.19 125.00  30.00  104
 14  \w     54.00  80.00   0.50    1.00    --   49.66  33.00  40.00   52
 15  \w     47.00  90.00   0.50    1.00    --   99.19 -94.00 120.00   86
 16  \w    -52.00 -19.00   0.50    1.00    --  -34.00  71.00 109.23   66
 17  \w    -27.00  27.00   0.50    1.00    --  -48.73  33.00  40.00  108
 18  \w    -27.00  24.00   0.50    1.00    --  -48.73  19.00-180.00  102
 19  \w    -62.00 -28.00   0.50    1.00    --  -79.28  61.00-180.00   68
 20  \w    -35.00  -4.00   0.50    1.00    --  -79.28  30.00-120.00   62
 21  \w    -34.00  -5.00   0.50    1.00    --  -79.28  30.00   0.00   58
 22  \w    -35.00 -10.00   0.50    1.00    --  -79.28  30.00  60.00   50
 23  \w    -54.00 -24.00   0.50    1.00    --  -79.28  61.00 120.00   60
 24  \w    -30.00  -4.00   0.50    1.00    --  -79.28  30.00 150.00   52
 25  \w    -38.00 -13.00   0.50    1.00    --  -79.28  33.00  40.00   50
 26  \w    -34.00  -7.00   0.50    1.00    --  -79.28  30.00-150.00   54
 27  \w    -92.00 -46.00   0.50    1.00    --  -48.73 -33.00-117.00   92
 28  \w   -122.00 -97.00   0.50    1.00    --  -48.73 -33.00-117.00   50
 29  \w   -146.00 -63.00   0.50    1.00    --  -79.28 -33.00-117.00  166
 30  \w   -118.00 -92.00   0.50    1.00    --  -79.28 -94.00   0.00   52
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix-Arc 100'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0479828000
_diffrn_orient_matrix_UB_12      -0.0417007000
_diffrn_orient_matrix_UB_13      0.0583500000
_diffrn_orient_matrix_UB_21      0.1054055000
_diffrn_orient_matrix_UB_22      0.0331516000
_diffrn_orient_matrix_UB_23      0.0521722000
_diffrn_orient_matrix_UB_31      -0.0478649000
_diffrn_orient_matrix_UB_32      0.1145769000
_diffrn_orient_matrix_UB_33      0.0061664000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0392
_diffrn_reflns_av_unetI/netI     0.0359
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.974
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       15
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            23380
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.974
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.817
_diffrn_reflns_theta_min         3.747
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    5.205
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.53380
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.90 (Rigaku Oxford Diffraction, 2023)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear pinkish orange'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   pinkish
_exptl_crystal_colour_primary    orange
_exptl_crystal_density_diffrn    1.555
_exptl_crystal_description       block
_exptl_crystal_F_000             1444
_exptl_crystal_preparation
'2-(1-methyl-1H-pyrazol-3-yl)pyridine and Co(BF4)2 were refluexed in ethanol for 2 hours. cooling precipitated the product which was filtered and purified by recrystalisation from hot ethanol.'
_exptl_crystal_recrystallization_method
'slow vapour diffusition of pentane into DCM.'
_exptl_crystal_size_max          0.04
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.01
_refine_diff_density_max         1.101
_refine_diff_density_min         -0.605
_refine_diff_density_rms         0.076
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.040
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     569
_refine_ls_number_reflns         5984
_refine_ls_number_restraints     496
_refine_ls_restrained_S_all      1.043
_refine_ls_R_factor_all          0.1073
_refine_ls_R_factor_gt           0.0813
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1348P)^2^+3.9853P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2266
_refine_ls_wR_factor_ref         0.2477
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4227
_reflns_number_total             5984
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5nr02293b2.cif
_cod_data_source_block           co(pypzme)3_1
_cod_depositor_comments
'Adding full bibliography for 1575067--1575070.cif.'
_cod_database_code               1575068
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_formula         'Co C27 N9 B2 F6 H27'
_cell_oxdiff_angle_alpha         90.007(2)
_cell_oxdiff_angle_beta          104.144(2)
_cell_oxdiff_angle_gamma         90.0371(19)
_cell_oxdiff_length_a            12.6779(3)
_cell_oxdiff_length_b            12.1922(3)
_cell_oxdiff_length_c            20.2345(6)
_cell_oxdiff_measurement_reflns_used 7056
_cell_oxdiff_volume              3032.87(13)
_shelx_estimated_absorpt_t_max   0.950
_shelx_estimated_absorpt_t_min   0.819
_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
2. Restrained distances
 B11X-F13X = B11X-F14X = B11X-F15X = B11X-F12X
 1.42 with sigma of 0.02
 B21X-F25X = B21X-F24X = B21X-F22X = B21X-F23X
 1.42 with sigma of 0.02
 Co1-N21A \\sim Co1-N21D
 with sigma of 0.02
 Co1-N11A \\sim Co1-N11D
 with sigma of 0.02
 N21A-N22A \\sim N21D-N22D
 with sigma of 0.02
 N21A-C25A \\sim N21D-C25D
 with sigma of 0.02
 N11A-C12A \\sim N11D-C12D
 with sigma of 0.02
 N11A-C16A \\sim N11D-C16D
 with sigma of 0.02
 N22A-C23A \\sim N22D-C23D
 with sigma of 0.02
 N22A-C26A \\sim N22D-C26D
 with sigma of 0.02
 C12A-C25A \\sim C12D-C25D
 with sigma of 0.02
 C12A-C13A \\sim C12D-C13D
 with sigma of 0.02
 C25A-C24A \\sim C25D-C24D
 with sigma of 0.02
 C16A-C15A \\sim C16D-C15D
 with sigma of 0.02
 C24A-C23A \\sim C24D-C23D
 with sigma of 0.02
 C13A-C14A \\sim C13D-C14D
 with sigma of 0.02
 C14A-C15A \\sim C14D-C15D
 with sigma of 0.02
 Co1-N22A \\sim Co1-N22D
 with sigma of 0.04
 Co1-C12A \\sim Co1-C12D
 with sigma of 0.04
 Co1-C25A \\sim Co1-C25D
 with sigma of 0.04
 Co1-C16A \\sim Co1-C16D
 with sigma of 0.04
 N21A-C12A \\sim N21D-C12D
 with sigma of 0.04
 N21A-C24A \\sim N21D-C24D
 with sigma of 0.04
 N21A-C23A \\sim N21D-C23D
 with sigma of 0.04
 N21A-C26A \\sim N21D-C26D
 with sigma of 0.04
 N11A-C25A \\sim N11D-C25D
 with sigma of 0.04
 N11A-C13A \\sim N11D-C13D
 with sigma of 0.04
 N11A-C15A \\sim N11D-C15D
 with sigma of 0.04
 N22A-C25A \\sim N22D-C25D
 with sigma of 0.04
 N22A-C24A \\sim N22D-C24D
 with sigma of 0.04
 C12A-C16A \\sim C12D-C16D
 with sigma of 0.04
 C12A-C24A \\sim C12D-C24D
 with sigma of 0.04
 C12A-C14A \\sim C12D-C14D
 with sigma of 0.04
 C25A-C13A \\sim C25D-C13D
 with sigma of 0.04
 C25A-C23A \\sim C25D-C23D
 with sigma of 0.04
 C16A-C14A \\sim C16D-C14D
 with sigma of 0.04
 C13A-C15A \\sim C13D-C15D
 with sigma of 0.04
 C23A-C26A \\sim C23D-C26D
 with sigma of 0.04
 B11X-F13X \\sim B11X-F14X \\sim B11X-F15X \\sim B11X-F12X
 with sigma of 0.02
 F13X-F14X \\sim F14X-F15X \\sim F15X-F12X \\sim F12X-F13X \\sim F14X-F12X
\\sim F13X-F15X
 with sigma of 0.04
 B21X-F25X \\sim B21X-F24X \\sim B21X-F22X \\sim B21X-F23X
 with sigma of 0.02
 F25X-F24X \\sim F24X-F22X \\sim F22X-F23X \\sim F23X-F25X \\sim F24X-F23X
\\sim F25X-F22X
 with sigma of 0.04
 B21X-F25X \\sim B21X-F25Y
 with sigma of 0.02
 B21X-F24X \\sim B21X-F22Y
 with sigma of 0.02
 B21X-F22X \\sim B21X-F24Y
 with sigma of 0.02
 B21X-F23X \\sim B21X-F23Y
 with sigma of 0.02
 B11X-F13X \\sim B11X-F12Y
 with sigma of 0.02
 B11X-F14X \\sim B11X-F15Y
 with sigma of 0.02
 B11X-F15X \\sim B11X-F14Y
 with sigma of 0.02
 B11X-F12X \\sim B11X-F13Y
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
B11X \\sim F12X \\sim F13X \\sim F14X \\sim F15X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
B21X \\sim F22X \\sim F23X \\sim F24X \\sim F25X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
N11D \\sim C12D \\sim C13D \\sim C14D \\sim C15D \\sim C16D \\sim N21D \\sim
N22D \\sim C23D \\sim C24D \\sim C25D \\sim C26D: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
Uanis(F23Y) = Uanis(F24Y) = Uanis(F22Y) = Uanis(F25Y)
Uanis(F13Y) = Uanis(F12Y) = Uanis(F14Y) = Uanis(F15Y)
Uanis(C24B) = Uanis(C23B)
4. Rigid body (RIGU) restrains
 B11X, F12X, F13X, F14X, F15X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B21X, F22X, F23X, F24X, F25X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N11D, C12D, C13D, C14D, C15D, C16D, N21D, N22D, C23D, C24D, C25D, C26D
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C24B, C23B, N22B, N21B, C25B, C26B, C12B, N11B, C16B, C15B, C14B, C13B
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(N11D)=Sof(C12D)=Sof(C13D)=Sof(H13D)=Sof(C14D)=Sof(H14D)=Sof(C15D)=
 Sof(H15D)=Sof(C16D)=Sof(H16D)=Sof(N21D)=Sof(N22D)=Sof(C23D)=Sof(H23D)=
 Sof(C24D)=Sof(H24D)=Sof(C25D)=Sof(C26D)=Sof(H26J)=Sof(H26K)=Sof(H26L)=1-FVAR(1)
 Sof(N11A)=Sof(C12A)=Sof(C13A)=Sof(H13A)=Sof(C14A)=Sof(H14A)=Sof(C15A)=
 Sof(H15A)=Sof(C16A)=Sof(H16A)=Sof(N21A)=Sof(N22A)=Sof(C23A)=Sof(H23A)=
 Sof(C24A)=Sof(H24A)=Sof(C25A)=Sof(C26A)=Sof(H26A)=Sof(H26B)=Sof(H26C)=FVAR(1)
 Sof(F22Y)=Sof(F23Y)=Sof(F24Y)=Sof(F25Y)=1-FVAR(2)
 Sof(F22X)=Sof(F23X)=Sof(F24X)=Sof(F25X)=FVAR(2)
 Sof(F12Y)=Sof(F13Y)=Sof(F14Y)=Sof(F15Y)=1-FVAR(3)
 Sof(F12X)=Sof(F13X)=Sof(F14X)=Sof(F15X)=FVAR(3)
6.a Aromatic/amide H refined with riding coordinates:
 C13A(H13A), C14A(H14A), C15A(H15A), C16A(H16A), C23A(H23A), C24A(H24A),
 C13B(H13B), C14B(H14B), C15B(H15B), C16B(H16B), C23B(H23B), C24B(H24B),
 C13C(H13C), C14C(H14C), C15C(H15C), C16C(H16C), C23C(H23C), C24C(H24C),
 C13D(H13D), C14D(H14D), C15D(H15D), C16D(H16D), C23D(H23D), C24D(H24D)
6.b Idealised Me refined as rotating group:
 C26A(H26A,H26B,H26C), C26B(H26D,H26E,H26F), C26C(H26G,H26H,H26I), C26D(H26J,
 H26K,H26L)
;
_shelx_res_checksum              32345
_olex2_exptl_crystal_mounting_method 'nylon loop magnetic mount - fomblin oil'
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.785
_oxdiff_exptl_absorpt_empirical_full_min 0.736