Interplay between geometry, electron density, and polarizability of the controversial drug atoxyl in crystal and biological environments
Balmohammadi, Yaser; Metry, Eduardo; Malaspina, Lorraine A.; Cametti, Georgia; Nakamura, Yuiga; Grabowsky, Simon; RSC Advances 15 (2025) 46749–46760; doi:10.1039/D5RA05936D

data_7251380
_publ_section_title
;
 Interplay between geometry, electron density, and polarizability of the
 controversial drug atoxyl in crystal and biological environments
;
_journal_issue                   54
_journal_name_full               'RSC Advances'
_journal_page_first              46749
_journal_page_last               46760
_journal_paper_doi               10.1039/D5RA05936D
_journal_volume                  15
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C6 H8 As N O3'
_chemical_formula_sum            'C6 H8 As N O3'
_chemical_formula_weight         217.057
_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             2024-12-02
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-10-02 deposited with the CCDC.	2025-10-22 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 101.0696(9)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   7.24300(8)
_cell_length_b                   6.13597(7)
_cell_length_c                   8.70648(9)
_cell_measurement_reflns_used    19924
_cell_measurement_temperature    100.15
_cell_measurement_theta_max      21.2060
_cell_measurement_theta_min      1.6640
_cell_volume                     379.741(7)
_computing_cell_refinement       'CrysAlisPro 1.171.43.93a (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro 1.171.43.93a (Rigaku OD, 2023) (IMPORT)'
_computing_data_reduction        'CrysAlisPro 1.171.43.93a (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  'olex2.refine 1.5 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      100.15
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 5.8140
_diffrn_measured_fraction_theta_full 0.9908
_diffrn_measured_fraction_theta_max 0.9982
_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      0.00 180.00   0.20    0.05    --    0.00   0.00   0.00  900
  2  \w      0.00 180.00   0.20    0.05    --    0.00  15.00 -90.00  900
  3  \w      0.00 180.00   0.20    0.05    --    0.00  30.00-180.00  900
  4  \w      0.00 180.00   0.20    0.05    --    0.00  45.00-270.00  900
  5  \w      0.00 180.00   0.20    0.05    --    0.00  30.00   0.00  900
  6  \w      0.00 180.00   0.20    0.05    --    0.00   0.00-180.00  900
;
_diffrn_measurement_device       'abstract diffractometer'
_diffrn_measurement_device_type
'esperanto-CrysAlisPro-abstract goniometer imported esperanto images'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0037878000
_diffrn_orient_matrix_UB_12      -0.0021776000
_diffrn_orient_matrix_UB_13      0.0277043000
_diffrn_orient_matrix_UB_21      -0.0000692000
_diffrn_orient_matrix_UB_22      -0.0404064000
_diffrn_orient_matrix_UB_23      -0.0015601000
_diffrn_orient_matrix_UB_31      0.0347253000
_diffrn_orient_matrix_UB_32      -0.0003207000
_diffrn_orient_matrix_UB_33      0.0086315000
_diffrn_radiation_monochromator  synchrotron
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           synchrotron
_diffrn_radiation_wavelength     0.24830
_diffrn_reflns_av_R_equivalents  0.0595
_diffrn_reflns_av_unetI/netI     0.0194
_diffrn_reflns_Laue_measured_fraction_full 0.9908
_diffrn_reflns_Laue_measured_fraction_max 0.9982
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       0
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       0
_diffrn_reflns_number            71388
_diffrn_reflns_point_group_measured_fraction_full 0.9908
_diffrn_reflns_point_group_measured_fraction_max 0.9982
_diffrn_reflns_theta_full        8.5678
_diffrn_reflns_theta_max         15.18
_diffrn_reflns_theta_min         1.53
_diffrn_source                   synchrotron
_exptl_absorpt_coefficient_mu    0.264
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.88860
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.93a (Rigaku Oxford Diffraction, 2023)
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    1.898
_exptl_crystal_description       block
_exptl_crystal_F_000             216.256
_exptl_crystal_size_max          0.18
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.3229
_refine_diff_density_min         -0.2236
_refine_diff_density_rms         0.0613
_refine_ls_abs_structure_details
;
 Flack x determined using 3720 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.012(19)
_refine_ls_d_res_high            0.4740
_refine_ls_d_res_low             4.6449
_refine_ls_goodness_of_fit_ref   0.9947
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_constraints    0
_refine_ls_number_parameters     196
_refine_ls_number_reflns         7450
_refine_ls_number_restraints     27
_refine_ls_restrained_S_all      0.9912
_refine_ls_R_factor_all          0.0111
_refine_ls_R_factor_gt           0.0109
_refine_ls_shift/su_max          0.0009
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0035P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0232
_refine_ls_wR_factor_ref         0.0233
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              14
_reflns_limit_h_min              -15
_reflns_limit_k_max              12
_reflns_limit_k_min              0
_reflns_limit_l_max              18
_reflns_limit_l_min              0
_reflns_number_gt                3865
_reflns_number_total             7450
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d5ra05936d2.cif
_cod_data_source_block           P_Ars_Acid_quick_
_cod_original_sg_symbol_Hall     ' P 2yb'
_cod_database_code               7251380
_chemical_oxdiff_formula         C6H8AsNO3
_olex2_refinement_description
;
1. Rigid bond restraints
 As1, O1
 with sigma for 1-2 distances of 0.0001 and sigma for 1-3 distances of 0.0001
 As1, O2
 with sigma for 1-2 distances of 0.0001 and sigma for 1-3 distances of 0.0001
2. Uiso/Uaniso restraints and constraints
Uanis(H1a) \\sim Ueq, Uanis(H1c) \\sim Ueq: with sigma of 0.001 and sigma for
terminal atoms of 0.002
Uanis(H1b) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(H2) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
;
_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
   PARTITIONING:   NoSpherA2
   INT ACCURACY:   Normal
   METHOD:         B3LYP
   BASIS SET:      def2-TZVP
   CHARGE:         0
   MULTIPLICITY:   1
   DATE:           2024-12-02_10-53-51
;
_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
- Detector area scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.253
_oxdiff_exptl_absorpt_empirical_full_min 0.836