H/F replacement in secondary alcohols of sydnones as examples of isostructural OH⋯OC hydrogen bonded dimer structures
Dumitrascu, Florea; Popa, Marcel Mirel; Shova, Sergiu; Man, Isabela C.; Draghici, Constantin; Caira, Mino R.; CrystEngComm 27 (2025) 5162–5172; doi:10.1039/D5CE00492F

data_7250610
_publ_section_title
;
 H/F replacement in secondary alcohols of sydnones as examples of
 isostructural OH&#x22EF;O&#xE001;C hydrogen bonded dimer structures
;
_journal_issue                   30
_journal_name_full               CrystEngComm
_journal_page_first              5162
_journal_page_last               5172
_journal_paper_doi               10.1039/D5CE00492F
_journal_volume                  27
_journal_year                    2025
_chemical_formula_moiety         '2(C10 H8 N2 O3)'
_chemical_formula_sum            'C20 H16 N4 O6'
_chemical_formula_weight         408.37
_space_group_crystal_system      monoclinic
_space_group_IT_number           9
_space_group_name_Hall           'C -2yc'
_space_group_name_H-M_alt        'C 1 c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-03-09
_audit_creation_method
;
Olex2 1.5-ac6-020
(compiled 2024.02.14 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6966)
;
_audit_update_record
;
2025-03-11 deposited with the CCDC.	2025-06-27 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 96.462(7)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   19.8269(13)
_cell_length_b                   5.3804(4)
_cell_length_c                   9.1694(7)
_cell_measurement_reflns_used    1511
_cell_measurement_temperature    296.0(9)
_cell_measurement_theta_max      73.7680
_cell_measurement_theta_min      4.4730
_cell_volume                     971.95(12)
_computing_cell_refinement       'CrysAlisPro 1.171.43.137a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.137a 64-bit (release 10-09-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.137a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5-ac6-020 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-020 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXD  (Sheldrick, 2008)'
_diffrn_ambient_environment      air
_diffrn_ambient_temperature      296.0(9)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.995
_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    -72.00  -7.00   0.50    5.00    --  -46.76  94.00 -61.00  130
  2  \w     -4.00  24.00   0.50    5.00    --  -46.76  94.00 -61.00   56
  3  \w     32.00  57.00   0.50    5.00    --   46.76 -94.00-171.00   50
  4  \w    -65.00 -22.00   0.50   10.00    --  -91.75  94.00 -61.00   86
  5  \w     65.00 103.00   0.50   10.00    --  106.68 -94.00-171.00   76
  6  \w    106.00 178.00   0.50   10.00    --  106.68  94.00 -61.00  144
  7  \w   -115.00 -37.00   0.50    5.00    --  -46.76 -57.00-180.00  156
  8  \w    -28.00   0.00   0.50    5.00    --   46.76 -19.00 -90.00   56
  9  \w    -10.00  20.00   0.50    5.00    --   46.76 -19.00-180.00   60
 10  \w    -49.00 -20.00   0.50   10.00    --  -91.75  45.00 -90.00   58
 11  \w    -64.00 -37.00   0.50   10.00    --  -91.75  61.00  60.00   54
 12  \w   -157.00-101.00   0.50   10.00    --  -91.75 -95.00-120.00  112
 13  \w   -136.00-106.00   0.50   10.00    --  -91.75 -94.00-171.00   60
 14  \w    -49.00 -22.00   0.50   10.00    --  -91.75  45.00 150.00   54
 15  \w    -62.00 -37.00   0.50   10.00    --  -91.75  61.00 -60.00   50
 16  \w     35.00  62.00   0.50   10.00    --  106.68 -95.00 150.00   54
 17  \w     37.00  71.00   0.50   10.00    --  106.68 -61.00 -90.00   68
 18  \w     41.00  71.00   0.50   10.00    --  106.68 -61.00  60.00   60
 19  \w     43.00 103.00   0.50   10.00    --  106.68 -95.00-120.00  120
 20  \w     73.00 100.00   0.50   10.00    --  106.68 -95.00 150.00   54
 21  \w     37.00  71.00   0.50   10.00    --  106.68 -61.00  30.00   68
 22  \w     41.00 107.00   0.50   10.00    --  106.68-125.00  60.00  132
 23  \w     37.00  71.00   0.50   10.00    --  106.68 -61.00   0.00   68
 24  \w     40.00  70.00   0.50   10.00    --  106.68 -61.00-180.00   60
 25  \w     86.00 112.00   0.50    5.00    --   47.64  57.00-150.00   52
 26  \w    -14.00  24.00   0.50    5.00    --  -47.64  19.00 -30.00   76
 27  \w   -114.00 -88.00   0.50    5.00    --  -47.64 -38.00-150.00   52
 28  \w    -77.00 -51.00   0.50    5.00    --  -47.64 -38.00-150.00   52
 29  \w    -22.00   4.00   0.50    5.00    --   47.64 -19.00-120.00   52
 30  \w   -157.00-130.00   0.50   10.00    --  -91.75 -30.00  60.00   54
 31  \w    -45.00 -20.00   0.50   10.00    --  -91.75  45.00 -60.00   50
 32  \w    -51.00 -26.00   0.50   10.00    --  -91.75  45.00-150.00   50
 33  \w   -164.00-134.00   0.50   10.00    --  -91.75 -30.00  90.00   60
 34  \w   -114.00 -73.00   0.50   10.00    --  -91.75 -77.00-120.00   82
 35  \w   -107.00 -75.00   0.50   10.00    --  -91.75 -61.00-120.00   64
 36  \w   -126.00 -79.00   0.50   10.00    --  -91.75 -30.00  60.00   94
 37  \w    -51.00 -25.00   0.50   10.00    --  -91.75  45.00-120.00   52
 38  \w   -131.00 -82.00   0.50   10.00    --  -91.75 -30.00  90.00   98
 39  \w   -158.00-120.00   0.50   10.00    --  -91.75 -45.00-150.00   76
 40  \w    -51.00 -26.00   0.50   10.00    --  -91.75  45.00 -30.00   50
 41  \w     66.00  91.00   0.50   10.00    --  106.68 -77.00 120.00   50
 42  \w    153.00 178.00   0.50   10.00    --  106.68  30.00   0.00   50
 43  \w     35.00  78.00   0.50   10.00    --  106.68 -95.00   0.00   86
 44  \w    119.00 145.00   0.50   10.00    --  106.68  30.00   0.00   52
 45  \w     65.00  91.00   0.50   10.00    --  106.68 -95.00 -90.00   52
 46  \w     85.00 111.00   0.50   10.00    --  106.68-125.00 -30.00   52
 47  \w     34.00  62.00   0.50   10.00    --  106.68 -95.00 -90.00   56
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0323905000
_diffrn_orient_matrix_UB_12      0.1167651000
_diffrn_orient_matrix_UB_13      -0.1445924000
_diffrn_orient_matrix_UB_21      -0.0154439000
_diffrn_orient_matrix_UB_22      0.2384568000
_diffrn_orient_matrix_UB_23      0.0833412000
_diffrn_orient_matrix_UB_31      0.0694325000
_diffrn_orient_matrix_UB_32      0.1073373000
_diffrn_orient_matrix_UB_33      -0.0274806000
_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  0.1039
_diffrn_reflns_av_unetI/netI     0.0474
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       6
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       10
_diffrn_reflns_limit_l_min       -10
_diffrn_reflns_number            4077
_diffrn_reflns_point_group_measured_fraction_full 0.731
_diffrn_reflns_point_group_measured_fraction_max 0.731
_diffrn_reflns_theta_full        66.562
_diffrn_reflns_theta_max         66.562
_diffrn_reflns_theta_min         4.489
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.890
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.46983
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.137a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_density_diffrn    1.395
_exptl_crystal_description       plate
_exptl_crystal_F_000             424
_exptl_crystal_size_max          0.06
_exptl_crystal_size_mid          0.04
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.326
_refine_diff_density_min         -0.250
_refine_diff_density_rms         0.073
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   -0.1(10)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.070
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     137
_refine_ls_number_reflns         1260
_refine_ls_number_restraints     2
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.0942
_refine_ls_R_factor_gt           0.0823
_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^)+(0.1817P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2312
_refine_ls_wR_factor_ref         0.2494
_reflns_Friedel_coverage         0.467
_reflns_Friedel_fraction_full    0.466
_reflns_Friedel_fraction_max     0.466
_reflns_number_gt                1026
_reflns_number_total             1260
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00492f2.cif
_cod_data_source_block           shs_956_fldu_autored
_cod_depositor_comments
'Adding full bibliography for 7250606--7250610.cif.'
_cod_database_code               7250610
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         CHNO
_chemical_oxdiff_usercomment     FA_5
_shelx_estimated_absorpt_t_max   0.982
_shelx_estimated_absorpt_t_min   0.949
_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.a Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C4(H4), C5(H5), C6(H6)
2.b Idealised Me refined as rotating group:
 C10(H10A,H10B,H10C)
;
_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 5.308
_oxdiff_exptl_absorpt_empirical_full_min 0.264