X-ray wavefunction refinement and comprehensive structural studies on bromo-substituted analogues of 2-deoxy-d-glucose in solid state and solution
Ziemniak, Marcin; Pawlędzio, Sylwia; Zawadzka-Kaźmierczuk, Anna; Dominiak, Paulina M.; Trzybiński, Damian; Koźmiński, Wiktor; Zieliński, Rafał; Fokt, Izabela; Priebe, Waldemar; Woźniak, Krzysztof; Pająk, Beata; RSC Advances 12 (2022) 8345–8360; doi:10.1039/D1RA08312K

data_7244613
_publ_section_title
;
 X-ray wavefunction refinement and comprehensive structural studies on
 bromo-substituted analogues of 2-deoxy-d-glucose in solid state and
 solution
;
_journal_issue                   14
_journal_name_full               'RSC Advances'
_journal_page_first              8345
_journal_page_last               8360
_journal_paper_doi               10.1039/D1RA08312K
_journal_volume                  12
_journal_year                    2022
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C6 H11 Br O5'
_chemical_formula_sum            'C6 H11 Br O5'
_chemical_formula_weight         243.055
_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             2021-04-26
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6272)
;
_audit_update_record
;
2021-11-09 deposited with the CCDC.	2022-03-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90.784(8)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   8.0544(8)
_cell_length_b                   10.3670(7)
_cell_length_c                   10.0444(8)
_cell_measurement_reflns_used    4989
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      67.0080
_cell_measurement_theta_min      4.1820
_cell_volume                     838.63(12)
_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 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.3 (Bourhis et al., 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2195
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.9981
_diffrn_measured_fraction_theta_max 0.9981
_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   -108.00 -13.00   1.00    2.50    --  -40.78 -57.00-180.00   95
  2  \w    -64.00  28.00   1.00    2.50    --  -40.78  37.00 150.00   92
  3  \w    -63.00  28.00   1.00    2.50    --  -40.78  77.00-150.00   91
  4  \w      6.00  31.00   1.00    2.50    --   40.78  85.00 138.38   25
  5  \w      5.00  30.00   1.00    2.50    --   40.78  87.00 160.17   25
  6  \w     60.00  87.00   1.00    2.50    --   40.78  37.00-150.00   27
  7  \w     23.00  66.00   1.00    2.50    --   40.78  37.00 -60.00   43
  8  \w     23.00  50.00   1.00    2.50    --   40.78  37.00-150.00   27
  9  \w      9.00  90.00   1.00    2.50    --   40.78  72.00  65.97   81
 10  \w     10.00 103.00   1.00    2.50    --   40.78  73.00 -28.52   93
 11  \w     19.00  76.00   1.00    2.50    --   40.78  37.00 150.00   57
 12  \w      7.00  77.00   1.00    2.50    --   40.78 -99.00  30.00   70
 13  \w      4.00  29.00   1.00    2.50    --   40.78  89.00-146.35   25
 14  \w    -20.00  44.00   1.00    2.50    --   40.78 -77.00 -60.00   64
 15  \w     75.00 137.00   1.00   12.50    --  103.66  59.00   8.31   62
 16  \w     78.00 137.00   1.00   12.50    --  103.66  51.00-140.82   59
 17  \w     75.00 158.00   1.00   12.50    --  103.66  58.00  82.46   83
 18  \w    144.00 171.00   1.00   12.50    --  103.66  64.00 158.14   27
 19  \w     22.00 102.00   1.00   12.50    --  103.66 -94.00  60.00   80
 20  \w     74.00 108.00   1.00   12.50    --  103.66  64.00 158.14   34
 21  \w     74.00  99.00   1.00   12.50    --  103.66  70.00-136.48   25
 22  \w     75.00 101.00   1.00   12.50    --  103.66  61.00 -90.00   26
 23  \w     22.00  91.00   1.00   12.50    --  103.66 -94.00 150.00   69
 24  \w     72.00 177.00   1.00   12.50    --  103.66  73.00 -46.88  105
 25  \w     75.00 101.00   1.00   12.50    --  103.66  61.00 120.00   26
 26  \w     74.00 123.00   1.00   12.50    --  103.66  65.00 -83.91   49
 27  \w    132.00 169.00   1.00   12.50    --  103.66  65.00 -83.91   37
 28  \w     79.00 170.00   1.00   12.50    --  103.66  45.00 150.00   91
 29  \w     27.00 109.00   1.00   12.50    --  103.66-111.00-120.00   82
 30  \w     36.00 133.00   1.00   12.50    --  103.66 -61.00-120.00   97
 31  \w    127.00 167.00   1.00   12.50    --  103.66  64.00  39.51   40
 32  \w    138.00 167.00   1.00   12.50    --  103.66  59.00-101.25   29
 33  \w     69.00 109.00   1.00   12.50    --  103.66-111.00   0.00   40
 34  \w     75.00 173.00   1.00   12.50    --  103.66  61.00  90.00   98
 35  \w     75.00 101.00   1.00   12.50    --  103.66  61.00  60.00   26
 36  \w     35.00  62.00   1.00   12.50    --  103.66-111.00   0.00   27
 37  \w     76.00 101.00   1.00   12.50    --  103.66  61.00 150.00   25
 38  \w     74.00 100.00   1.00   12.50    --  103.66  64.00  39.51   26
 39  \w     76.00 103.00   1.00   12.50    --  103.66  61.00  -5.97   27
 40  \w     74.00 106.00   1.00   12.50    --  103.66  66.00 170.05   32
 41  \w     75.00 119.00   1.00   12.50    --  103.66  61.00 -60.00   44
 42  \w     77.00 134.00   1.00   12.50    --  103.66  51.00-151.99   57
 43  \w    124.00 169.00   1.00   12.50    --  103.66 111.00-150.00   45
 44  \w     78.00 169.00   1.00   12.50    --  103.66  45.00-120.00   91
 45  \w     74.00 175.00   1.00   12.50    --  103.66  63.00  21.44  101
 46  \w     81.00 106.00   1.00   12.50    --  103.66  45.00   0.00   25
 47  \w     75.00 102.00   1.00   12.50    --  103.66  59.00-101.25   27
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0055159000
_diffrn_orient_matrix_UB_12      0.0666791000
_diffrn_orient_matrix_UB_13      0.1371595000
_diffrn_orient_matrix_UB_21      -0.0208052000
_diffrn_orient_matrix_UB_22      0.1322292000
_diffrn_orient_matrix_UB_23      -0.0679888000
_diffrn_orient_matrix_UB_31      -0.1900332000
_diffrn_orient_matrix_UB_32      -0.0127866000
_diffrn_orient_matrix_UB_33      0.0094881000
_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  0.0626
_diffrn_reflns_av_unetI/netI     0.0502
_diffrn_reflns_Laue_measured_fraction_full 0.9981
_diffrn_reflns_Laue_measured_fraction_max 0.9981
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            11095
_diffrn_reflns_point_group_measured_fraction_full 0.9967
_diffrn_reflns_point_group_measured_fraction_max 0.9967
_diffrn_reflns_theta_full        67.0745
_diffrn_reflns_theta_max         67.07
_diffrn_reflns_theta_min         4.40
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    6.614
_exptl_absorpt_correction_T_max  0.838
_exptl_absorpt_correction_T_min  0.550
_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    1.925
_exptl_crystal_description       needle
_exptl_crystal_F_000             486.856
_exptl_crystal_size_max          0.16
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.04
_refine_diff_density_max         2.6002
_refine_diff_density_min         -1.6072
_refine_diff_density_rms         0.3009
_refine_ls_abs_structure_details
'Flack, H. D. (1983). Acta Cryst. A39, 876-881.'
_refine_ls_abs_structure_Flack   -0.01(5)
_refine_ls_d_res_high            0.8370
_refine_ls_d_res_low             10.0435
_refine_ls_goodness_of_fit_ref   1.0500
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_constraints    28
_refine_ls_number_parameters     267
_refine_ls_number_reflns         2982
_refine_ls_number_restraints     21
_refine_ls_restrained_S_all      1.0461
_refine_ls_R_factor_all          0.0811
_refine_ls_R_factor_gt           0.0790
_refine_ls_shift/su_max          0.0001
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1492P)^2^+12.4186P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2258
_refine_ls_wR_factor_ref         0.2285
_reflns_Friedel_coverage         0.995
_reflns_limit_h_max              9
_reflns_limit_h_min              -9
_reflns_limit_k_max              12
_reflns_limit_k_min              -12
_reflns_limit_l_max              11
_reflns_limit_l_min              -11
_reflns_number_gt                2845
_reflns_number_total             2982
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d1ra08312k2.cif
_cod_data_source_block           2020_12_08_2BM-2_N
_cod_original_sg_symbol_Hall     ' P 2yb'
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               7244613
_reflns_odcompleteness_completeness 99.81
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1. Restrained distances
 C4B-H4B
 1.09 with sigma of 0.01
 C6B-H6BB
 1.09 with sigma of 0.01
 H1AA-O1A
 0.97 with sigma of 0.02
 H4AA-O4A
 0.97 with sigma of 0.01
 C4A-H4A
 0.97 with sigma of 0.02
 H6AA-C6A
 1.09 with sigma of 0.01
 H3BA-O3B
 0.97 with sigma of 0.01
 H6AB-C6A
 1.09 with sigma of 0.01
 C6B-H6BA
 1.09 with sigma of 0.01
 C1B-H1B
 1.09 with sigma of 0.01
 C2B-H2B
 1.09 with sigma of 0.01
 C1A-H1A
 1.09 with sigma of 0.01
 C2A-H2A
 1.09 with sigma of 0.01
 C3A-H3A
 1.09 with sigma of 0.01
2. Uiso/Uaniso restraints and constraints
Uanis(O3A) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.005
3.a Ternary CH refined with riding coordinates:
 C5A(H5A), C3B(H3B), C4B(H4B), C5B(H5B)
3.b Idealised tetrahedral OH refined as rotating group:
 O1B(H1BA), O6B(H6B)
;
_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 2.003
_oxdiff_exptl_absorpt_empirical_full_min 0.623