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_7250394
_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         'C7 H8 N2 O4, 2(H2 O)'
_chemical_formula_sum            'C7 H12 N2 O6'
_chemical_formula_weight         220.19
_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
_audit_creation_date             2023-11-02
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2025-01-27 deposited with the CCDC.	2025-05-07 downloaded from the CCDC.
;
_cell_angle_alpha                77.211(9)
_cell_angle_beta                 89.735(9)
_cell_angle_gamma                76.363(10)
_cell_formula_units_Z            2
_cell_length_a                   5.1105(6)
_cell_length_b                   7.7802(9)
_cell_length_c                   13.1733(13)
_cell_measurement_reflns_used    1899
_cell_measurement_temperature    293
_cell_measurement_theta_max      28.5460
_cell_measurement_theta_min      2.8530
_cell_volume                     495.76(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)'
_diffrn_ambient_temperature      293
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 8.0303
_diffrn_detector_type            EosS2
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.996
_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     -9.00  42.00   1.00   14.82    --   13.76  77.00-120.00   51
  2  \w     15.00  50.00   1.00   14.82    --   13.76 -99.00 150.00   35
  3  \w     -3.00  24.00   1.00   14.82    --   13.76  77.00   0.00   27
  4  \w    -71.00  53.00   1.00   14.82    --  -15.95   0.00-180.00  124
  5  \w    -86.00 -57.00   1.00   14.82    --  -15.95 178.00-180.00   29
  6  \w    -83.00  -3.00   1.00   14.82    --  -15.95 -38.00 -30.00   80
;
_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      -0.1206527000
_diffrn_orient_matrix_UB_12      0.0631292000
_diffrn_orient_matrix_UB_13      0.0063035000
_diffrn_orient_matrix_UB_21      -0.0767528000
_diffrn_orient_matrix_UB_22      -0.0556671000
_diffrn_orient_matrix_UB_23      -0.0154975000
_diffrn_orient_matrix_UB_31      -0.0006097000
_diffrn_orient_matrix_UB_32      -0.0468314000
_diffrn_orient_matrix_UB_33      0.0526911000
_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  0.0217
_diffrn_reflns_av_unetI/netI     0.0346
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            3756
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.996
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         26.367
_diffrn_reflns_theta_min         2.766
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.130
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.74353
_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            'light colourless'
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.475
_exptl_crystal_description       prism
_exptl_crystal_F_000             232
_exptl_crystal_size_max          0.071
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.042
_refine_diff_density_max         0.386
_refine_diff_density_min         -0.227
_refine_diff_density_rms         0.071
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.074
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     150
_refine_ls_number_reflns         2026
_refine_ls_number_restraints     6
_refine_ls_restrained_S_all      1.073
_refine_ls_R_factor_all          0.0673
_refine_ls_R_factor_gt           0.0566
_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^)+(0.0772P)^2^+0.2394P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1543
_refine_ls_wR_factor_ref         0.1627
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1665
_reflns_number_total             2026
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00362h2.cif
_cod_data_source_block           c3
_cod_depositor_comments
'Adding full bibliography for 7250393--7250394.cif.'
_cod_database_code               7250394
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N O'
_shelx_estimated_absorpt_t_max   0.995
_shelx_estimated_absorpt_t_min   0.991
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups, All O(H,H) groups
2. Restrained distances
 O5-H5D = O5-H5E
 0.85 with sigma of 0.02
 O6-H6C = O6-H6D
 0.85 with sigma of 0.02
 H5D-H5E
 1.34 with sigma of 0.04
 H6C-H6D
 1.34 with sigma of 0.04
3.a Secondary CH2 refined with riding coordinates:
 C6(H6A,H6B)
3.b Aromatic/amide H refined with riding coordinates:
 N1(H1), C4(H4A)
3.c Idealised Me refined as rotating group:
 C5(H5A,H5B,H5C)
3.d Idealised tetrahedral OH refined as rotating group:
 O4(H4)
;
_shelx_res_checksum              7332
_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 1.672
_oxdiff_exptl_absorpt_empirical_full_min 0.700