Recurrent Supramolecular Patterns in a Series of Salts of Heterocyclic Polyamines and Heterocyclic Dicarboxylic Acids: Synthesis, Single-Crystal X-ray Structure, Hirshfeld Surface Analysis, Energy Framework, and Quantum Chemical Calculations
Bojarska, Joanna; Łyczko, Krzysztof; Breza, Martin; Mieczkowski, Adam; Crystals 14 (2024) 733–; doi:10.3390/cryst14080733

data_1572516
_publ_section_title
;
 Recurrent Supramolecular Patterns in a Series of Salts of Heterocyclic
 Polyamines and Heterocyclic Dicarboxylic Acids: Synthesis, Single-Crystal
 X-ray Structure, Hirshfeld Surface Analysis, Energy Framework, and
 Quantum Chemical Calculations
;
_journal_issue                   8
_journal_name_full               Crystals
_journal_page_first              733
_journal_paper_doi               10.3390/cryst14080733
_journal_volume                  14
_journal_year                    2024
_chemical_formula_moiety         'C6 H3 O4 S, C4 H7 N4 S'
_chemical_formula_sum            'C10 H10 N4 O4 S2'
_chemical_formula_weight         314.34
_chemical_name_systematic
'4,6-diamino-2-thiopyrimidin-1,3-dium 4-carboxythiophene-3-carboxylate'
_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   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2024-06-11
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_cell_angle_alpha                90
_cell_angle_beta                 91.394(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   4.20086(14)
_cell_length_b                   21.3241(7)
_cell_length_c                   13.9944(4)
_cell_measurement_reflns_used    2659
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      70.2810
_cell_measurement_theta_min      4.1310
_cell_volume                     1253.24(7)
_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 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2017/1 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.0(1)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 16.0131
_diffrn_detector_type            Eos
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.983
_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    -20.00  26.00   1.00    1.00    --    0.00 -77.00  60.00   46
  2  \w      6.00  31.00   1.00    1.72    --   54.00 -37.00  60.00   25
  3  \w     39.00  65.00   1.00    1.72    --   54.00  57.00   0.00   26
  4  \w    -13.00  14.00   1.00    1.72    --   54.00 -57.00-180.00   27
  5  \w     67.00 118.00   1.00    1.72    --   54.00  57.00  60.00   51
  6  \w     54.00 124.00   1.00    1.72    --   54.00  37.00  30.00   70
  7  \w      6.00  58.00   1.00    1.72    --   54.00 -99.00-120.00   52
  8  \w     59.00  92.00   1.00    1.72    --   54.00 -99.00-120.00   33
  9  \w     26.00  96.00   1.00    1.72    --   54.00 -99.00  30.00   70
 10  \w     41.00  75.00   1.00    1.72    --   54.00  57.00 -60.00   34
 11  \w     35.00  79.00   1.00    1.72    --   54.00 -37.00  60.00   44
 12  \w     46.00  97.00   1.00    1.72    --   54.00  57.00 -30.00   51
 13  \w    151.00 178.00   1.00    1.72    --  108.00  37.00 -30.00   27
 14  \w     84.00 109.00   1.00    1.72    --  108.00  37.00 -30.00   25
 15  \w     87.00 112.00   1.00    1.72    --  108.00  50.00 -90.00   25
 16  \w     86.00 113.00   1.00    1.72    --  108.00  50.00   0.00   27
 17  \w     90.00 120.00   1.00    1.72    --  108.00  50.00 -60.00   30
 18  \w     96.00 157.00   1.00    1.72    --  108.00  63.00   0.00   61
 19  \w    105.00 174.00   1.00    1.72    --  108.00  77.00  90.00   69
 20  \w    121.00 171.00   1.00    1.72    --  108.00  63.00-120.00   50
 21  \w     88.00 120.00   1.00    1.72    --  108.00  63.00-120.00   32
 22  \w     36.00  68.00   1.00    1.72    --  108.00 -91.00   0.00   32
 23  \w     39.00 103.00   1.00    1.72    --  108.00 -91.00 120.00   64
 24  \w     88.00 119.00   1.00    1.72    --  108.00  50.00 -30.00   31
 25  \w     87.00 112.00   1.00    1.72    --  108.00  63.00 -30.00   25
 26  \w    122.00 174.00   1.00    1.72    --  108.00 111.00  60.00   52
 27  \w    132.00 176.00   1.00    1.72    --  108.00  63.00 -90.00   44
 28  \w     87.00 112.00   1.00    1.72    --  108.00  63.00 -90.00   25
 29  \w     82.00 109.00   1.00    1.72    --  108.00  25.00  30.00   27
 30  \w     86.00 113.00   1.00    1.72    --  108.00  63.00 -60.00   27
 31  \w     83.00 108.00   1.00    1.72    --  108.00  37.00 -60.00   25
 32  \w    113.00 170.00   1.00    1.72    --  108.00  50.00 150.00   57
 33  \w    147.00 174.00   1.00    1.72    --  108.00  25.00  30.00   27
 34  \w    120.00 178.00   1.00    1.72    --  108.00  77.00 -60.00   58
 35  \w     39.00 111.00   1.00    1.72    --  108.00 -37.00 -30.00   72
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Eos'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.3116525000
_diffrn_orient_matrix_UB_12      -0.0319266000
_diffrn_orient_matrix_UB_13      0.0294600000
_diffrn_orient_matrix_UB_21      -0.1699673000
_diffrn_orient_matrix_UB_22      0.0260882000
_diffrn_orient_matrix_UB_23      -0.0903928000
_diffrn_orient_matrix_UB_31      0.0932672000
_diffrn_orient_matrix_UB_32      -0.0592838000
_diffrn_orient_matrix_UB_33      -0.0555458000
_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  0.0192
_diffrn_reflns_av_unetI/netI     0.0235
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.983
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -4
_diffrn_reflns_limit_k_max       24
_diffrn_reflns_limit_k_min       -25
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            4131
_diffrn_reflns_point_group_measured_fraction_full 0.762
_diffrn_reflns_point_group_measured_fraction_max 0.747
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         70.370
_diffrn_reflns_theta_min         4.146
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.071
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.89310
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.84a (Rigaku Oxford Diffraction, 2020)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.666
_exptl_crystal_description       block
_exptl_crystal_F_000             648
_exptl_crystal_size_max          0.16
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.06
_refine_diff_density_max         0.394
_refine_diff_density_min         -0.299
_refine_diff_density_rms         0.054
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   0.00(2)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.059
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     196
_refine_ls_number_reflns         1782
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.059
_refine_ls_R_factor_all          0.0290
_refine_ls_R_factor_gt           0.0288
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0525P)^2^+0.9093P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0762
_refine_ls_wR_factor_ref         0.0766
_reflns_Friedel_coverage         0.510
_reflns_Friedel_fraction_full    0.522
_reflns_Friedel_fraction_max     0.507
_reflns_number_gt                1772
_reflns_number_total             1782
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            structures_1-7.cif
_cod_data_source_block           k8a4
_cod_database_code               1572516
_shelx_shelxl_version_number     2017/1
_chemical_oxdiff_formula         'C10 H10 N4 O4 S2'
_chemical_oxdiff_usercomment     'yellow block, Cu, 100K, 0.16x0.10x0.06'
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups, All N(H,H) groups
 At 1.5 times of:
  All O(H) groups
2. Restrained distances
 N1-H1
 0.87 with sigma of 0.02
3.a Aromatic/amide H refined with riding coordinates:
 C1(H1A), C9(H9), C4(H4)
3.b X=CH2 refined with riding coordinates:
 N4(H4A,H4B)
;
_shelx_res_checksum              3009
_shelx_hkl_checksum              39431
_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 1.119
_oxdiff_exptl_absorpt_empirical_full_min 0.835