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_7250994
_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         'C7 H8 Cl N3 O'
_chemical_formula_sum            'C7 H8 Cl N3 O'
_chemical_formula_weight         185.61
_chemical_melting_point          426.0(10)
_chemical_name_systematic        'N-(5- chloropyrimidin-2-yl)propionamide'
_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     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                116.5720(10)
_cell_angle_beta                 103.2490(10)
_cell_angle_gamma                99.7370(10)
_cell_formula_units_Z            8
_cell_length_a                   11.72860(10)
_cell_length_b                   12.73070(10)
_cell_length_c                   13.53730(10)
_cell_measurement_reflns_used    24656
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.7010
_cell_measurement_theta_min      3.8910
_cell_volume                     1671.82(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 0.990
_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  25.00   0.50    1.00    --  -48.07  80.00 107.00  194
  2  \w    -21.00  72.00   0.50    1.00    --   48.07 -80.00 -15.00  186
  3  \w   -163.00 -79.00   0.50    4.00    --  -91.75 -80.00 -15.00  168
  4  \w   -116.00 -19.00   0.50    4.00    --  -91.75  80.00 107.00  194
  5  \w    101.00 178.00   0.50    4.00    --  113.25  80.00 107.00  154
  6  \w    101.00 137.00   0.50    4.00    --  113.25  80.00 107.00   72
  7  \w   -117.00 -79.00   0.50    1.00    --  -48.07-125.00  90.00   76
  8  \w    -20.00  13.00   0.50    1.00    --  -48.07  80.00 107.00   66
  9  \w    -25.00   6.00   0.50    1.00    --  -48.07  19.00  30.00   62
 10  \w   -112.00 -75.00   0.50    1.00    --  -48.07-125.00 120.00   74
 11  \w   -105.00 -73.00   0.50    1.00    --  -48.07-125.00 -30.00   64
 12  \w     34.00  91.00   0.50    1.00    --   48.07-125.00-120.00  114
 13  \w    -24.00  39.00   0.50    1.00    --   48.07 -38.00   0.00  126
 14  \w    -25.00  25.00   0.50    1.00    --   48.07 -38.00  60.00  100
 15  \w    -18.00  26.00   0.50    1.00    --   48.07 -19.00  90.00   88
 16  \w    -49.00 -21.00   0.50    4.00    --  -91.75  45.00 -30.00   56
 17  \w    -49.00 -24.00   0.50    4.00    --  -91.75  45.00-120.00   50
 18  \w     48.00  73.00   0.50    4.00    --  113.25-125.00-120.00   50
 19  \w     75.00 108.00   0.50    4.00    --  113.25-106.00 137.41   66
 20  \w     83.00 111.00   0.50    4.00    --  113.25-125.00-120.00   56
 21  \w    107.00 138.00   0.50    4.00    --  113.25  15.00-150.00   62
 22  \w     85.00 111.00   0.50    4.00    --  113.25-125.00  90.00   52
 23  \w    112.00 178.00   0.50    4.00    --  113.25  45.00  90.00  132
 24  \w    119.00 176.00   0.50    4.00    --  113.25  45.00   0.00  114
 25  \w     61.00 106.00   0.50    4.00    --  113.25 -94.00-120.00   90
 26  \w     42.00 101.00   0.50    4.00    --  113.25 -94.00 -30.00  118
 27  \w     60.00 102.00   0.50    4.00    --  113.25-101.00-178.60   84
 28  \w     55.00  80.00   0.50    4.00    --  113.25-125.00  90.00   50
 29  \w    137.00 163.00   0.50    4.00    --  113.25 125.00 150.00   52
 30  \w     56.00  96.00   0.50    4.00    --  113.25 -77.00  90.00   80
 31  \w    153.00 178.00   0.50    4.00    --  113.25  15.00-150.00   50
 32  \w    101.00 143.00   0.50    4.00    --  113.25  30.00-120.00   84
 33  \w    153.00 178.00   0.50    4.00    --  113.25  30.00-120.00   50
 34  \w     43.00  68.00   0.50    4.00    --  113.25 -61.00-150.00   50
 35  \w     43.00 105.00   0.50    4.00    --  113.25 -77.00   0.00  124
 36  \w     49.00 102.00   0.50    4.00    --  113.25 -77.00 120.00  106
 37  \w     83.00 111.00   0.50    4.00    --  113.25-125.00   0.00   56
 38  \w    102.00 136.00   0.50    4.00    --  113.25  30.00 120.00   68
 39  \w     43.00  68.00   0.50    4.00    --  113.25 -61.00 -90.00   50
 40  \w    121.00 172.00   0.50    4.00    --  113.25 125.00-180.00  102
 41  \w     78.00 111.00   0.50    4.00    --  113.25-125.00 120.00   66
 42  \w     45.00  70.00   0.50    4.00    --  113.25 -61.00-120.00   50
 43  \w     98.00 135.00   0.50    4.00    --  113.25  61.00  30.00   74
 44  \w     54.00  80.00   0.50    4.00    --  113.25 -87.00 105.41   52
 45  \w    102.00 172.00   0.50    4.00    --  113.25  45.00 -30.00  140
 46  \w     51.00  77.00   0.50    4.00    --  113.25-125.00 120.00   52
 47  \w    106.00 175.00   0.50    4.00    --  113.25  30.00  60.00  138
 48  \w     65.00  90.00   0.50    4.00    --  113.25 -88.00 158.65   50
 49  \w     99.00 138.00   0.50    4.00    --  113.25 -88.00 158.65   78
 50  \w     43.00  96.00   0.50    4.00    --  113.25 -77.00-120.00  106
 51  \w     42.00  76.00   0.50    4.00    --  113.25 -77.00 -30.00   68
 52  \w    104.00 130.00   0.50    4.00    --  113.25 125.00 150.00   52
 53  \w    102.00 149.00   0.50    4.00    --  113.25  45.00 150.00   94
 54  \w     42.00  67.00   0.50    4.00    --  113.25 -61.00 150.00   50
 55  \w     43.00 105.00   0.50    4.00    --  113.25 -77.00  60.00  124
 56  \w     43.00 103.00   0.50    4.00    --  113.25 -94.00   0.00  120
 57  \w     47.00  92.00   0.50    4.00    --  113.25-125.00  60.00   90
 58  \w     45.00  71.00   0.50    4.00    --  113.25 -61.00-180.00   52
 59  \w    123.00 152.00   0.50    4.00    --  113.25  61.00 -90.00   58
 60  \w     96.00 145.00   0.50    4.00    --  113.25 125.00 -90.00   98
 61  \w    133.00 172.00   0.50    4.00    --  113.25 125.00  60.00   78
 62  \w    145.00 171.00   0.50    4.00    --  113.25  77.00 120.00   52
 63  \w     84.00 109.00   0.50    4.00    --  113.25-125.00 -30.00   50
 64  \w     65.00 112.00   0.50    4.00    --  113.25 -86.00-113.29   94
 65  \w     42.00  88.00   0.50    4.00    --  113.25 -77.00-180.00   92
 66  \w     49.00  75.00   0.50    4.00    --  113.25 -77.00 -90.00   52
 67  \w     60.00  86.00   0.50    4.00    --  113.25 -77.00  30.00   52
 68  \w     55.00  81.00   0.50    4.00    --  113.25 -77.00 150.00   52
 69  \w     54.00  80.00   0.50    4.00    --  113.25-125.00 -30.00   52
 70  \w     82.00 108.00   0.50    4.00    --  113.25-106.00  21.96   52
 71  \w     81.00 106.00   0.50    4.00    --  113.25 -94.00  90.00   50
 72  \w     42.00  74.00   0.50    4.00    --  113.25 -94.00-150.00   64
 73  \w    133.00 159.00   0.50    4.00    --  113.25  45.00  60.00   52
 74  \w    103.00 164.00   0.50    4.00    --  113.25  45.00 -90.00  122
 75  \w    109.00 151.00   0.50    4.00    --  113.25  30.00 -90.00   84
 76  \w    122.00 148.00   0.50    4.00    --  113.25  30.00   0.00   52
 77  \w     45.00 111.00   0.50    4.00    --  113.25-125.00 -90.00  132
 78  \w    146.00 171.00   0.50    4.00    --  113.25  61.00  30.00   50
 79  \w     99.00 133.00   0.50    4.00    --  113.25  61.00  90.00   68
 80  \w    153.00 178.00   0.50    4.00    --  113.25  61.00  90.00   50
 81  \w    107.00 134.00   0.50    4.00    --  113.25  77.00  90.00   54
 82  \w     85.00 111.00   0.50    4.00    --  113.25 -82.00 -29.30   52
 83  \w     45.00  71.00   0.50    4.00    --  113.25 -61.00 120.00   52
 84  \w     87.00 113.00   0.50    4.00    --  113.25 -87.00 105.41   52
 85  \w    100.00 126.00   0.50    4.00    --  113.25 -80.00 -15.00   52
;
_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      0.0682111000
_diffrn_orient_matrix_UB_12      0.0113175000
_diffrn_orient_matrix_UB_13      -0.0811569000
_diffrn_orient_matrix_UB_21      -0.1206833000
_diffrn_orient_matrix_UB_22      -0.0096060000
_diffrn_orient_matrix_UB_23      -0.0831430000
_diffrn_orient_matrix_UB_31      0.0309270000
_diffrn_orient_matrix_UB_32      0.1416381000
_diffrn_orient_matrix_UB_33      0.0699324000
_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  0.0219
_diffrn_reflns_av_unetI/netI     0.0176
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            37773
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.923
_diffrn_reflns_theta_min         3.891
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.683
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.88710
_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    1.475
_exptl_crystal_description       irregular
_exptl_crystal_F_000             768
_exptl_crystal_recrystallization_method 'crystallized from methanol'
_exptl_crystal_size_max          0.135
_exptl_crystal_size_mid          0.123
_exptl_crystal_size_min          0.083
_refine_diff_density_max         0.260
_refine_diff_density_min         -0.506
_refine_diff_density_rms         0.055
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.091
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     453
_refine_ls_number_reflns         7231
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.091
_refine_ls_R_factor_all          0.0343
_refine_ls_R_factor_gt           0.0326
_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^)+(0.0547P)^2^+0.2431P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0945
_refine_ls_wR_factor_ref         0.0961
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6691
_reflns_number_total             7231
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_929_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '425-427' was changed to
'426.0(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               7250994
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C7H8ClN3O
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2.a Secondary CH2 refined with riding coordinates:
 C10A(H10A,H10B), C10B(H10C,H10D), C10C(H10E,H10F), C10D(H10G,H10H)
2.b Aromatic/amide H refined with riding coordinates:
 C3A(H3A), C5A(H5A), C3B(H3B), C5B(H5B), C3C(H3C), C5C(H5C), C3D(H3D), C5D(H5D)
2.c Idealised Me refined as rotating group:
 C11A(H11A,H11B,H11C), C11B(H11D,H11E,H11F), C11C(H11G,H11H,H11I), C11D(H11J,
 H11K,H11L)
;
_shelx_res_checksum              7876
_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 1.244
_oxdiff_exptl_absorpt_empirical_full_min 0.842