Exploring uracil derivatives: synthesis, crystal structure insights, and antibacterial activity
Mal, Susital; Franco, Chris H. J.; Kumar, Binay; Kirillov, Alexander M.; Das, Subrata; CrystEngComm 27 (2025) 3456–3466; doi:10.1039/D5CE00362H

data_7250393
_publ_section_title
;
 Exploring uracil derivatives: synthesis, crystal structure insights, and
 antibacterial activity
;
_journal_issue                   21
_journal_name_full               CrystEngComm
_journal_page_first              3456
_journal_page_last               3466
_journal_paper_doi               10.1039/D5CE00362H
_journal_volume                  27
_journal_year                    2025
_chemical_formula_moiety         'C8 H12 N4 O2, H2 O'
_chemical_formula_sum            'C8 H14 N4 O3'
_chemical_formula_weight         214.23
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2023-06-23
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_audit_update_record
;
2025-01-27 deposited with the CCDC.	2025-05-07 downloaded from the CCDC.
;
_cell_angle_alpha                65.458(10)
_cell_angle_beta                 78.475(9)
_cell_angle_gamma                73.773(10)
_cell_formula_units_Z            2
_cell_length_a                   8.0489(9)
_cell_length_b                   8.2275(8)
_cell_length_c                   8.8795(9)
_cell_measurement_reflns_used    1817
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      28.9080
_cell_measurement_theta_min      3.3390
_cell_volume                     511.22(10)
_computing_cell_refinement       'CrysAlisPro 1.171.40.69a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.69a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.69a (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 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 8.0303
_diffrn_detector_type            EosS2
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.997
_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     -8.00  19.00   1.00    7.50    --   13.76  77.00 -90.00   27
  2  \w     -7.00  23.00   1.00    7.50    --   13.76  77.00  30.00   30
  3  \w     -3.00  25.00   1.00    7.50    --   13.76  77.00 150.00   28
  4  \w    -40.00  42.00   1.00    7.50    --  -15.95  77.00  30.00   82
  5  \w    -37.00  41.00   1.00    7.50    --  -15.95  77.00 150.00   78
  6  \w    -41.00  41.00   1.00    7.50    --  -15.95  77.00 -90.00   82
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Single source at offset/far, EosS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0216125000
_diffrn_orient_matrix_UB_12      -0.0550228000
_diffrn_orient_matrix_UB_13      -0.0479613000
_diffrn_orient_matrix_UB_21      0.0006681000
_diffrn_orient_matrix_UB_22      0.0795332000
_diffrn_orient_matrix_UB_23      -0.0739660000
_diffrn_orient_matrix_UB_31      0.0896336000
_diffrn_orient_matrix_UB_32      -0.0093562000
_diffrn_orient_matrix_UB_33      0.0034169000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0179
_diffrn_reflns_av_unetI/netI     0.0332
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       11
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            3641
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.997
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         26.364
_diffrn_reflns_theta_min         2.533
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.108
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.72786
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.69a (Rigaku Oxford Diffraction, 2020)
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    1.392
_exptl_crystal_description       block
_exptl_crystal_F_000             228
_exptl_crystal_size_max          0.11
_exptl_crystal_size_mid          0.095
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.242
_refine_diff_density_min         -0.276
_refine_diff_density_rms         0.052
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.051
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     154
_refine_ls_number_reflns         2074
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.051
_refine_ls_R_factor_all          0.0645
_refine_ls_R_factor_gt           0.0507
_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^)+(0.0829P)^2^+0.0423P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1373
_refine_ls_wR_factor_ref         0.1494
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1617
_reflns_number_total             2074
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00362h2.cif
_cod_data_source_block           c1
_cod_depositor_comments
'Adding full bibliography for 7250393--7250394.cif.'
_cod_database_code               7250393
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C2 H2 N2 O2 '
_shelx_estimated_absorpt_t_max   0.991
_shelx_estimated_absorpt_t_min   0.988
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Others
 Fixed Sof: O3(0.5) H3A(0.5) H3B(0.5) O3A(0.5) H3AA(0.5) H3AB(0.5)
3.a Free rotating group:
 O3(H3A,H3B), O3A(H3AA,H3AB)
3.b Aromatic/amide H refined with riding coordinates:
 N1(H1), C3(H3), C5(H5)
3.c Idealised Me refined as rotating group:
 C6(H6A,H6B,H6C), C8(H8A,H8B,H8C), C7(H7A,H7B,H7C)
;
_shelx_res_checksum              59579
_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 1.495
_oxdiff_exptl_absorpt_empirical_full_min 0.578