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_1575069
_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
'C336 H264 Fe8 N72, 12.15(B F4), 2(H2 O), 13.2(C H4 O), 1.55(Cl), 12[CH4O], 11[CH4O], 0.6[BF4]'
_chemical_formula_sum            'C372.2 H412.8 B12.75 Cl1.55 F51 Fe8 N72 O38.2'
_chemical_formula_weight         8114.69
_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'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2025-05-23
_audit_creation_method
;
Olex2 1.5
(compiled 2025.04.05 svn.rf049d14d for OlexSys, GUI svn.r7224)
;
_audit_update_record
;
2025-05-29 deposited with the CCDC.	2025-07-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 96.4540(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   32.9811(2)
_cell_length_b                   30.0048(2)
_cell_length_c                   39.7967(3)
_cell_measurement_reflns_used    52661
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      72.3300
_cell_measurement_theta_min      2.7120
_cell_volume                     39132.9(5)
_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_temperature      100.15
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            'HyPix-Arc 100'
_diffrn_measured_fraction_theta_full 0.992
_diffrn_measured_fraction_theta_max 0.963
_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    -64.00 -39.00   0.50    0.50    --  -48.91  71.00  57.00   50
  2  \w   -115.00 -30.00   0.50    0.50    --  -48.91 -71.00 -72.00  170
  3  \w    -19.00  16.00   0.50    0.50    --  -48.91  71.00  57.00   70
  4  \w   -143.00 -61.00   0.50    2.50    --  -79.28 -71.00 -72.00  164
  5  \w    -53.00 -14.00   0.50    2.50    --  -79.28  71.00  57.00   78
  6  \w    -88.00 -62.00   0.50    2.50    --  -79.28  71.00  57.00   52
  7  \w     41.00  79.00   0.50    2.50    --   99.19 -71.00 -72.00   76
  8  \w    -24.00  24.00   0.50    0.50    --  -48.91  19.00  60.00   96
  9  \w    -75.00 -37.00   0.50    0.50    --  -48.91 -57.00  90.00   76
 10  \w      8.00  34.00   0.50    0.50    --   49.66 -71.00 -72.00   52
 11  \w    -49.00  -6.00   0.50    2.50    --  -79.28  45.00  30.00   86
 12  \w    -33.00  -4.00   0.50    2.50    --  -79.28  30.00-180.00   58
 13  \w    -33.00  -4.00   0.50    2.50    --  -79.28  30.00-120.00   58
 14  \w    -34.00  -6.00   0.50    2.50    --  -79.28  30.00   0.00   56
 15  \w    -35.00 -10.00   0.50    2.50    --  -79.28  30.00-150.00   50
 16  \w    -39.00 -13.00   0.50    2.50    --  -79.28  45.00-150.00   52
 17  \w    -35.00  -9.00   0.50    2.50    --  -79.28  30.00 -90.00   52
 18  \w     38.00  94.00   0.50    2.50    --   99.19 -94.00-150.00  112
 19  \w     85.00 144.00   0.50    2.50    --   99.19  30.00   0.00  118
 20  \w     30.00  70.00   0.50    2.50    --   99.19 -61.00   0.00   80
 21  \w     38.00  76.00   0.50    2.50    --   99.19 -94.00   0.00   76
 22  \w     30.00  55.00   0.50    2.50    --   99.19 -61.00 150.00   50
 23  \w     89.00 164.00   0.50    2.50    --   99.19  61.00  30.00  150
 24  \w     43.00  95.00   0.50    2.50    --   99.19 -94.00 150.00  104
 25  \w     34.00  65.00   0.50    2.50    --   99.19 -61.00-120.00   62
 26  \w     40.00  67.00   0.50    2.50    --   99.19 -61.00-150.00   54
 27  \w     37.00  62.00   0.50    2.50    --   99.19 -61.00  90.00   50
 28  \w    130.00 156.00   0.50    2.50    --   99.19  71.00  57.00   52
 29  \w     84.00 122.00   0.50    2.50    --   99.19  71.00  57.00   76
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix-Arc 100'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0436
_diffrn_reflns_av_unetI/netI     0.0371
_diffrn_reflns_Laue_measured_fraction_full 0.992
_diffrn_reflns_Laue_measured_fraction_max 0.963
_diffrn_reflns_limit_h_max       40
_diffrn_reflns_limit_h_min       -41
_diffrn_reflns_limit_k_max       29
_diffrn_reflns_limit_k_min       -37
_diffrn_reflns_limit_l_max       48
_diffrn_reflns_limit_l_min       -49
_diffrn_reflns_number            159336
_diffrn_reflns_point_group_measured_fraction_full 0.992
_diffrn_reflns_point_group_measured_fraction_max 0.963
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.840
_diffrn_reflns_theta_min         2.361
_exptl_absorpt_coefficient_mu    3.244
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.75372
_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 dark yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.377
_exptl_crystal_description       block
_exptl_crystal_F_000             16851
_exptl_crystal_preparation       '2Fe(BF4)2 + 3L in methanol solvothermally'
_exptl_crystal_recrystallization_method
'x-ray quality crystals grown solverthermally'
_exptl_crystal_size_max          0.06
_exptl_crystal_size_mid          0.06
_exptl_crystal_size_min          0.06
_refine_diff_density_max         1.546
_refine_diff_density_min         -0.823
_refine_diff_density_rms         0.082
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.029
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2388
_refine_ls_number_reflns         38176
_refine_ls_number_restraints     722
_refine_ls_restrained_S_all      1.036
_refine_ls_R_factor_all          0.0863
_refine_ls_R_factor_gt           0.0698
_refine_ls_shift/su_max          0.005
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1192P)^2^+105.1069P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1965
_refine_ls_wR_factor_ref         0.2089
_reflns_Friedel_coverage         0.000
_reflns_number_gt                29780
_reflns_number_total             38176
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5nr02293b2.cif
_cod_data_source_block           fe8_1
_cod_depositor_comments
'Adding full bibliography for 1575067--1575070.cif.'
_cod_original_formula_sum
'C372.20 H412.80 B12.75 Cl1.55 F51 Fe8 N72 O38.20'
_cod_database_code               1575069
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_usercomment     'COBF1 in MA solution, no lights/air, orange'
_cell_oxdiff_angle_alpha         90.0131(6)
_cell_oxdiff_angle_beta          96.4494(6)
_cell_oxdiff_angle_gamma         90.0513(6)
_cell_oxdiff_length_a            32.9663(3)
_cell_oxdiff_length_b            30.0113(2)
_cell_oxdiff_length_c            39.8056(3)
_cell_oxdiff_measurement_reflns_used 52665
_cell_oxdiff_volume              39132.9(5)
_shelx_estimated_absorpt_t_max   0.829
_shelx_estimated_absorpt_t_min   0.829
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups, All O(H,H) groups
2. Restrained distances
 B46X-F50X = B46X-F48X = B46X-F49X = B46X-F47X
 1.42 with sigma of 0.02
 B11-F15X = B11-F14X = B11-F12X = B11-F13X
 1.42 with sigma of 0.02
 C81S-O82S
 1.42 with sigma of 0.01
 C71S-O72S = C11S-O12S = C21S-O22S = C31S-O32S = C41S-O42S = C51S-O52S = C61S-
 O62S = C91S-O92S
 1.42 with sigma of 0.02
 B16-F18X = B16-F19X = B16-F20X = B16-F17X
 1.42 with sigma of 0.01
 B31X-F34X = B31X-F33X = B31X-F32X = B31X-F35X
 1.42 with sigma of 0.02
 B26X-F28X = B26X-F30X = B26X-F29X = B26X-F27X
 1.42 with sigma of 0.02
 B36X-F40X = B36X-F39X = B36X-F37X = B36X-F38X
 1.42 with sigma of 0.02
 B21X-F24X = B21X-F23X = B21X-F22X = B21X-F25X
 1.42 with sigma of 0.02
 B41X-F45X = B41X-F43X = B41X-F42X = B41X-F44X
 1.42 with sigma of 0.02
 B11-F15X \\sim B11-F14X \\sim B11-F12X \\sim B11-F13X
 with sigma of 0.02
 F15X-F14X \\sim F14X-F12X \\sim F12X-F13X \\sim F13X-F15X \\sim F14X-F13X
\\sim F15X-F12X
 with sigma of 0.04
 B16-F18X \\sim B16-F19X \\sim B16-F20X \\sim B16-F17X
 with sigma of 0.02
 B46X-F50X \\sim B46X-F48X \\sim B46X-F49X \\sim B46X-F47X
 with sigma of 0.02
 F18X-F19X \\sim F19X-F20X \\sim F20X-F17X \\sim F17X-F18X \\sim F19X-F17X
\\sim F18X-F20X
 with sigma of 0.04
 F50X-F48X \\sim F48X-F49X \\sim F49X-F47X \\sim F47X-F50X \\sim F48X-F47X
\\sim F50X-F49X
 with sigma of 0.04
 B31X-F34X \\sim B31X-F33X \\sim B31X-F32X \\sim B31X-F35X
 with sigma of 0.02
 F34X-F33X \\sim F33X-F32X \\sim F32X-F35X \\sim F35X-F34X \\sim F33X-F35X
\\sim F34X-F32X
 with sigma of 0.04
 B26X-F28X \\sim B26X-F30X \\sim B26X-F29X \\sim B26X-F27X
 with sigma of 0.02
 F28X-F30X \\sim F30X-F29X \\sim F29X-F27X \\sim F27X-F28X \\sim F30X-F27X
\\sim F28X-F29X
 with sigma of 0.04
 B36X-F40X \\sim B36X-F39X \\sim B36X-F37X \\sim B36X-F38X
 with sigma of 0.02
 F40X-F39X \\sim F39X-F37X \\sim F37X-F38X \\sim F38X-F40X \\sim F39X-F38X
\\sim F40X-F37X
 with sigma of 0.04
 B21X-F24X \\sim B21X-F23X \\sim B21X-F22X \\sim B21X-F25X
 with sigma of 0.02
 F24X-F23X \\sim F23X-F22X \\sim F22X-F25X \\sim F25X-F24X \\sim F23X-F25X
\\sim F24X-F22X
 with sigma of 0.04
 B41X-F45X \\sim B41X-F43X \\sim B41X-F42X \\sim B41X-F44X
 with sigma of 0.02
 F45X-F43X \\sim F43X-F42X \\sim F42X-F44X \\sim F44X-F45X \\sim F43X-F44X
\\sim F45X-F42X
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
B11 \\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
C81S \\sim O82S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C51S \\sim O52S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
B16 \\sim F17X \\sim F18X \\sim F19X \\sim F20X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
B46X \\sim F47X \\sim F48X \\sim F49X \\sim F50X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
B31X \\sim F32X \\sim F33X \\sim F34X \\sim F35X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
B26X \\sim F27X \\sim F28X \\sim F29X \\sim F30X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
B36X \\sim F37X \\sim F38X \\sim F39X \\sim F40X: 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
B41X \\sim F42X \\sim F43X \\sim F44X \\sim F45X: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
C11S \\sim O12S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C21S \\sim O22S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C31S \\sim O32S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C41S \\sim O42S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C61S \\sim O62S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C71S \\sim O72S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C91S \\sim O92S: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
Uanis(C41S) = Uanis(O42S)
Uanis(F20X) = Uanis(B16) = Uanis(F17X) = Uanis(F18X) = Uanis(F19X)
Uanis(F12X) = Uanis(B11) = Uanis(F13X) = Uanis(F14X) = Uanis(F15X)
4. Rigid body (RIGU) restrains
 B11, F12X, F13X, F14X, F15X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C81S, O82S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C51S, O52S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B16, F17X, F18X, F19X, F20X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B46X, F47X, F48X, F49X, F50X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B31X, F32X, F33X, F34X, F35X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B26X, F27X, F28X, F29X, F30X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 B36X, F37X, F38X, F39X, F40X
 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
 B41X, F42X, F43X, F44X, F45X
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C11S, O12S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C21S, O22S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C31S, O32S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C41S, O42S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C61S, O62S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C71S, O72S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C91S, O92S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Fixed Sof: B11(0.65) F12X(0.65) F13X(0.65) F14X(0.65) F15X(0.65) B16(0.575)
 F17X(0.575) F18X(0.575) F19X(0.575) F20X(0.575) C11S(0.9) H11A(0.9) H11B(0.9)
 H11C(0.9) O12S(0.9) H12S(0.9) C21S(0.85) H21A(0.85) H21B(0.85) H21C(0.85)
 O22S(0.85) H22S(0.85) C31S(0.85) H31A(0.85) H31B(0.85) H31C(0.85) O32S(0.85)
 H32S(0.85) C41S(0.85) H41A(0.85) H41B(0.85) H41C(0.85) O42S(0.85) H42S(0.85)
 C51S(0.5) H51A(0.5) H51B(0.5) H51C(0.5) O52S(0.5) H52S(0.5) C61S(0.5)
 H61A(0.5) H61B(0.5) H61C(0.5) O62S(0.5) H62S(0.5) C71S(0.8) H71A(0.8)
 H71B(0.8) H71C(0.8) O72S(0.8) H72S(0.8) C81S(0.6) H81A(0.6) H81B(0.6)
 H81C(0.6) O82S(0.6) H82S(0.6) C91S(0.75) H91A(0.75) H91B(0.75) H91C(0.75)
 O92S(0.75) H92S(0.75) B21X(0.9) F22X(0.9) F23X(0.9) F24X(0.9) F25X(0.9)
 B36X(0.6) F37X(0.6) F38X(0.6) F39X(0.6) F40X(0.6) B41X(0.5) F42X(0.5)
 F43X(0.5) F44X(0.5) F45X(0.5) B46X(0.85) F47X(0.85) F48X(0.85) F49X(0.85)
 F50X(0.85) Cl15(0.425) Cl40(0.35)
6.a Free rotating group:
 O13(H13G,H13H)
6.b Secondary CH2 refined with riding coordinates:
 C26A(H26A,H26B), C26B(H26C,H26D), C46B(H46B,H46C), C25C(H25A,H25B), C46C(H46D,
 H46E), C26D(H26E,H26F), C46D(H46F,H46G), C26E(H26G,H26H), C46E(H46H,H46I),
 C26F(H26I,H26J), C44F(H44F,H44G), C46F(H46J,H46K)
6.c Aromatic/amide H refined with riding coordinates:
 C13A(H13A), C14A(H14A), C15A(H15A), C16A(H16A), C23A(H23A), C24A(H24A),
 C33A(H33A), C34A(H34A), C35A(H35A), C36A(H36A), C43A(H43A), C44A(H44A),
 C46A(H46A), C52A(H52A), C53A(H53A), C54A(H54A), C62A(H62A), C63A(H63A),
 C64A(H64A), C13B(H13B), C14B(H14B), C15B(H15B), C16B(H16B), C23B(H23B),
 C24B(H24B), C33B(H33B), C34B(H34B), C35B(H35B), C36B(H36B), C43B(H43B),
 C44B(H44B), C52B(H52B), C53B(H53B), C54B(H54B), C62B(H62B), C63B(H63B),
 C64B(H64B), C13C(H13C), C14C(H14C), C15C(H15C), C16C(H16C), C23C(H23C),
 C24C(H24C), C33C(H33C), C34C(H34C), C35C(H35C), C36C(H36C), C43C(H43C),
 C44C(H44C), C52C(H52C), C53C(H53C), C54C(H54C), C62C(H62C), C63C(H63C),
 C64C(H64C), C13D(H13D), C14D(H14D), C15D(H15D), C16D(H16D), C23D(H23D),
 C24D(H24D), C33D(H33D), C34D(H34D), C35D(H35D), C36D(H36D), C43D(H43D),
 C44D(H44D), C52D(H52D), C53D(H53D), C54D(H54D), C62D(H62D), C63D(H63D),
 C64D(H64D), C13E(H13E), C14E(H14E), C15E(H15E), C16E(H16E), C23E(H23E),
 C24E(H24E), C33E(H33E), C34E(H34E), C35E(H35E), C36E(H36E), C43E(H43E),
 C44E(H44E), C52E(H52E), C53E(H53E), C54E(H54E), C62E(H62E), C63E(H63E),
 C64E(H64E), C13F(H13F), C14F(H14F), C15F(H15F), C16F(H16F), C23F(H23F),
 C24F(H24F), C33F(H33F), C34F(H34F), C35F(H35F), C36F(H36F), C43F(H43F),
 C52F(H52F), C53F(H53F), C54F(H54F), C62F(H62F), C63F(H63F), C64F(H64F)
6.d Tetrahedral OH refined with riding coordinates:
 O52S(H52S)
6.e Idealised Me refined as rotating group:
 C11S(H11A,H11B,H11C), C21S(H21A,H21B,H21C), C31S(H31A,H31B,H31C), C41S(H41A,
 H41B,H41C), C51S(H51A,H51B,H51C), C61S(H61A,H61B,H61C), C71S(H71A,H71B,H71C),
 C81S(H81A,H81B,H81C), C91S(H91A,H91B,H91C)
6.f Idealised tetrahedral OH refined as rotating group:
 O12S(H12S), O22S(H22S), O32S(H32S), O42S(H42S), O62S(H62S), O72S(H72S),
 O82S(H82S), O92S(H92S)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              12766
_shelx_fab_checksum              79262
_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 1.238
_oxdiff_exptl_absorpt_empirical_full_min 0.832