Examining intermolecular interactions in crystal structures of amide-substituted 2-aminopyrimidine derivatives
Marasinghe, Aloka A.; Averkiev, Boris B.; Aakeröy, Christer B.; CrystEngComm 27 (2025) 7000–7011; doi:10.1039/D5CE00839E

data_7250995
_publ_section_title
;
 Examining intermolecular interactions in crystal structures of
 amide-substituted 2-aminopyrimidine derivatives
;
_journal_issue                   43
_journal_name_full               CrystEngComm
_journal_page_first              7000
_journal_page_last               7011
_journal_paper_doi               10.1039/D5CE00839E
_journal_volume                  27
_journal_year                    2025
_chemical_formula_moiety         'C6 H6 Cl N3 O'
_chemical_formula_sum            'C6 H6 Cl N3 O'
_chemical_formula_weight         171.59
_chemical_melting_point          480.0(10)
_chemical_name_systematic        N-(5-chloropyrimidin-2-yl)acetamide
_space_group_crystal_system      orthorhombic
_space_group_IT_number           66
_space_group_name_Hall           '-C 2 2c'
_space_group_name_H-M_alt        'C c c m'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-09-18
_audit_creation_method
;
Olex2 1.5-ac5-024
(compiled 2022.04.12 svn.rca3783a0 for Rigaku Oxford Diffraction, GUI svn.r6498)
;
_audit_update_record
;
2025-08-25 deposited with the CCDC.	2025-10-02 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   11.52290(10)
_cell_length_b                   18.7942(3)
_cell_length_c                   6.59400(10)
_cell_measurement_reflns_used    2685
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.6120
_cell_measurement_theta_min      4.4910
_cell_volume                     1428.02(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5-ac5-024 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac5-024 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      210.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.998
_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     70.00 106.00   0.50    0.40    --  113.25-100.00   6.00   72
  2  \w     44.00  94.00   0.50    0.40    --  113.25 -94.00  60.00  100
  3  \w     43.00  76.00   0.50    0.40    --  113.25-140.00 -59.00   66
  4  \w     44.00 103.00   0.50    0.40    --  113.25 -94.00 -60.00  118
  5  \w     69.00 102.00   0.50    0.40    --  113.25 -77.00   0.00   66
  6  \w     45.00  70.00   0.50    0.40    --  113.25 -77.00  60.00   50
  7  \w     42.00  67.00   0.50    0.40    --  113.25 -61.00 150.00   50
  8  \w     44.00  69.00   0.50    0.40    --  113.25 -61.00   0.00   50
  9  \w     52.00  92.00   0.50    0.40    --  113.25 -77.00-150.00   80
 10  \w     46.00  71.00   0.50    0.40    --  113.25 -61.00-180.00   50
 11  \w    106.00 158.00   0.50    0.40    --  113.25  15.00 -60.00  104
 12  \w    109.00 170.00   0.50    0.40    --  113.25 100.00 111.00  122
 13  \w    111.00 161.00   0.50    0.40    --  113.25 125.00 120.00  100
 14  \w    -30.00  11.00   0.50    0.10    --  -48.07  24.00 -31.00   82
 15  \w    -77.00 -52.00   0.50    0.40    --  -91.75 140.00  -0.00   50
 16  \w    -25.00  15.00   0.50    0.10    --  -48.07  19.00  30.00   80
 17  \w   -118.00 -69.00   0.50    0.10    --  -48.07-140.00 -59.00   98
 18  \w   -110.00 -71.00   0.50    0.10    --  -48.07-130.00 113.00   78
 19  \w   -146.00-121.00   0.50    0.40    --  -91.75 -24.00 164.00   50
;
_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      -0.0165669000
_diffrn_orient_matrix_UB_12      0.0399850000
_diffrn_orient_matrix_UB_13      0.2019257000
_diffrn_orient_matrix_UB_21      -0.0377563000
_diffrn_orient_matrix_UB_22      0.0669995000
_diffrn_orient_matrix_UB_23      -0.1172848000
_diffrn_orient_matrix_UB_31      -0.1271654000
_diffrn_orient_matrix_UB_32      -0.0251050000
_diffrn_orient_matrix_UB_33      0.0085577000
_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  0.0210
_diffrn_reflns_av_unetI/netI     0.0181
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -24
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -7
_diffrn_reflns_number            3405
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.885
_diffrn_reflns_theta_min         4.501
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.261
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.85607
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.133a (Rigaku Oxford Diffraction, 2024)
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    1.596
_exptl_crystal_description       irregular
_exptl_crystal_F_000             704
_exptl_crystal_recrystallization_method
'crystallized from acetonitrile, methanol, ethylacetate'
_exptl_crystal_size_max          0.16
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.308
_refine_diff_density_min         -0.381
_refine_diff_density_rms         0.127
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.147
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     71
_refine_ls_number_reflns         854
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.147
_refine_ls_R_factor_all          0.0397
_refine_ls_R_factor_gt           0.0385
_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^)+(0.0703P)^2^+0.2779P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1004
_refine_ls_wR_factor_ref         0.1020
_reflns_Friedel_coverage         0.000
_reflns_number_gt                808
_reflns_number_total             854
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_932_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '479-481' was changed to
'480.0(10)' -- the average value was taken and precision was
estimated.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 

 Adding full bibliography for 7250982--7251002.cif.
;
_cod_database_code               7250995
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C6H6Cl1N3O
_shelx_estimated_absorpt_t_max   0.727
_shelx_estimated_absorpt_t_min   0.549
_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. Others
 Fixed Sof: H10A(0.5) H10B(0.5) H10C(0.5)
3.a Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
3.b Idealised Me refined as rotating group:
 C10(H10A,H10B,H10C)
;
_shelx_res_checksum              84297
_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 1.301
_oxdiff_exptl_absorpt_empirical_full_min 0.846