Crystal structure and polymorphic forms of auranofin revisited.
Ziemniak, Marcin; Trzybiński, Damian; Pawlędzio, Sylwia; Filipowicz, Gabriela; Pająk-Tarnacka, Beata; Priebe, Waldemar; Woźniak, Krzysztof; RSC advances 15 (2025) 10378–10389; doi:10.1039/d5ra00196j

data_7250226
_publ_section_title
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 Crystal structure and polymorphic forms of auranofin revisited.
;
_journal_issue                   13
_journal_name_full               'RSC advances'
_journal_page_first              10378
_journal_page_last               10389
_journal_paper_doi               10.1039/d5ra00196j
_journal_volume                  15
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C20 H34 Au O9 P S'
_chemical_formula_sum            'C20 H34 Au O9 P S'
_chemical_formula_weight         678.494
_chemical_name_systematic        auranofin
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_symmetry_Int_Tables_number      4
_audit_creation_date             2025-01-31
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2025.01.22 svn.rc7346086 for OlexSys, GUI svn.r7128)
;
_audit_update_record
;
2025-02-27 deposited with the CCDC.	2025-03-18 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 106.247(4)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   10.0684(4)
_cell_length_b                   8.1314(3)
_cell_length_c                   16.1310(6)
_cell_measurement_reflns_used    6706
_cell_measurement_temperature    100.01(10)
_cell_measurement_theta_max      67.1400
_cell_measurement_theta_min      2.8210
_cell_volume                     1267.91(9)
_computing_cell_refinement       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5-alpha (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_temperature      100
_diffrn_detector_area_resol_mean 5.2195
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 1.0000
_diffrn_measured_fraction_theta_max 1.0000
_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    -85.00 -11.00   1.00    1.00    --  -40.48 125.00   0.00   74
  2  \w    -65.00 -32.00   1.00    1.00    --  -40.48 -57.00 150.00   33
  3  \w   -113.00 -14.00   1.00    1.00    --  -40.48 -38.00-150.00   99
  4  \w   -114.00 -87.00   1.00    1.00    --  -40.48 -57.00 150.00   27
  5  \w   -114.00 -11.00   1.00    1.00    --  -40.48 -57.00  30.00  103
  6  \w     17.00  53.00   1.00    1.00    --   40.48 -77.00-150.00   36
  7  \w     44.00 109.00   1.00    1.00    --  104.09-111.00 -60.00   65
  8  \w     30.00 101.00   1.00    1.00    --  104.09-111.00-150.00   71
  9  \w     33.00 151.00   1.00    1.00    --  104.09 -15.00-120.00  118
 10  \w     30.00 128.00   1.00    1.00    --  104.09 -45.00 -30.00   98
 11  \w     32.00  70.00   1.00    1.00    --  104.09 -94.00 -30.00   38
 12  \w    114.00 149.00   1.00    1.00    --  104.09  77.00 -90.00   35
 13  \w    103.00 138.00   1.00    1.00    --  104.09  77.00  90.00   35
 14  \w     35.00 126.00   1.00    1.00    --  104.09 -45.00  60.00   91
 15  \w     41.00 103.00   1.00    1.00    --  104.09 -94.00   0.00   62
 16  \w     28.00 127.00   1.00    1.00    --  104.09 -30.00 150.00   99
 17  \w    114.00 141.00   1.00    1.00    --  104.09 111.00   0.00   27
 18  \w     56.00 106.00   1.00    1.00    --  104.09 -94.00  90.00   50
 19  \w     74.00 101.00   1.00    1.00    --  104.09 -61.00 150.00   27
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0332
_diffrn_reflns_av_unetI/netI     0.0421
_diffrn_reflns_Laue_measured_fraction_full 1.0000
_diffrn_reflns_Laue_measured_fraction_max 1.0000
_diffrn_reflns_limit_h_max       7
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            8687
_diffrn_reflns_point_group_measured_fraction_full 0.9993
_diffrn_reflns_point_group_measured_fraction_max 0.9993
_diffrn_reflns_theta_full        67.0146
_diffrn_reflns_theta_max         67.01
_diffrn_reflns_theta_min         2.85
_exptl_absorpt_coefficient_mu    12.487
_exptl_absorpt_correction_T_max  0.675
_exptl_absorpt_correction_T_min  0.267
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.84a (Rigaku Oxford Diffraction, 2020)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
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    1.777
_exptl_crystal_description       needle
_exptl_crystal_F_000             667.793
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: ethanol'
_exptl_crystal_size_max          0.248
_exptl_crystal_size_mid          0.059
_exptl_crystal_size_min          0.035
_refine_diff_density_max         0.9458
_refine_diff_density_min         -1.2283
_refine_diff_density_rms         0.1174
_refine_ls_abs_structure_details
'Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668.'
_refine_ls_abs_structure_Flack   -0.049(6)
_refine_ls_d_res_high            0.8374
_refine_ls_d_res_low             15.4869
_refine_ls_goodness_of_fit_ref   1.0317
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    50
_refine_ls_number_parameters     296
_refine_ls_number_reflns         4525
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.0317
_refine_ls_R_factor_all          0.0283
_refine_ls_R_factor_gt           0.0273
_refine_ls_shift/su_max          -0.0007
_refine_ls_shift/su_mean         0.0001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0444P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0694
_refine_ls_wR_factor_ref         0.0704
_reflns_Friedel_coverage         0.999
_reflns_limit_h_max              11
_reflns_limit_h_min              -12
_reflns_limit_k_max              9
_reflns_limit_k_min              -9
_reflns_limit_l_max              19
_reflns_limit_l_min              -19
_reflns_number_gt                4411
_reflns_number_total             4525
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d5ra00196j2.cif
_cod_data_source_block           2021_05_20_DT_MZ-AUR_N
_cod_original_cell_volume        1267.91(8)
_cod_original_sg_symbol_Hall     ' P 2yb'
_cod_database_code               7250226
_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
2.a Ternary CH refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C4(H4), C5(H5)
2.b Secondary CH2 refined with riding coordinates:
 C10(H10a,H10b), C12(H12a,H12b), C14(H14a,H14b), C28(H28a,H28b)
2.c Idealised Me refined as rotating group:
 C11(H11a,H11b,H11c), C13(H13a,H13b,H13c), C15(H15a,H15b,H15c), C18(H18a,H18b,
 H18c), C22(H22a,H22b,H22c), C26(H26a,H26b,H26c), C31(H31a,H31b,H31c)
;
_olex2_refine_details
;
Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors.

The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
- for a fragment of the crystal.
This fragment can be embedded in an electrostatic crystal field by employing cluster charges
or modelled using implicit solvation models, depending on the software used.
The following options were used:
   SOFTWARE:       ORCA 5.0
   PARTITIONING:   NoSpherA2
   INT ACCURACY:   Normal
   METHOD:         PBE
   BASIS SET:      x2c-TZVP
   CHARGE:         0
   MULTIPLICITY:   1
   RELATIVISTIC:   ZORA
   DATE:           2025-01-31_15-02-12
;
_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
;