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_7250989
_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         'C9 H12 Br N3 O'
_chemical_formula_sum            'C9 H12 Br N3 O'
_chemical_formula_weight         258.13
_chemical_melting_point          390.0(10)
_chemical_name_systematic        N-(5-bromopyrimidin-2-yl)pentanamide
_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             2024-02-26
_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                70.2550(10)
_cell_angle_beta                 73.2710(10)
_cell_angle_gamma                78.2360(10)
_cell_formula_units_Z            4
_cell_length_a                   8.16640(10)
_cell_length_b                   10.95870(10)
_cell_length_c                   13.4268(2)
_cell_measurement_reflns_used    16733
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.7010
_cell_measurement_theta_min      3.5890
_cell_volume                     1075.49(2)
_computing_cell_refinement       'CrysAlisPro 1.171.43.105a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.105a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.105a (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  'XL  (Sheldrick, 2008)'
_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 0.999
_diffrn_measured_fraction_theta_max 0.992
_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    -73.00 -12.00   0.50    0.20    --  -49.82 124.00 154.00  122
  2  \w    -83.00 -58.00   0.50    0.20    --  -49.82 149.00 -41.00   50
  3  \w   -103.00 -57.00   0.50    0.20    --  -49.82-149.00 -89.00   92
  4  \w     70.00 109.00   0.50    0.20    --   49.82-149.00 -89.00   78
  5  \w     35.00  91.00   0.50    0.20    --   49.82-124.00  74.00  112
  6  \w   -141.00-116.00   0.50    0.80    --  -90.00-124.00  74.00   50
  7  \w    -77.00 -52.00   0.50    0.80    --  -90.00 124.00 154.00   50
  8  \w    -88.00 -63.00   0.50    0.80    --  -90.00 149.00 -41.00   50
  9  \w     86.00 111.00   0.50    0.80    --  111.50-124.00  74.00   50
 10  \w    141.00 175.00   0.50    0.80    --  111.50 124.00 154.00   68
 11  \w     57.00  83.00   0.50    0.80    --  111.50-124.00  74.00   52
 12  \w     94.00 129.00   0.50    0.80    --  111.50-149.00 -89.00   70
 13  \w     91.00 136.00   0.50    0.80    --  111.50 149.00 -41.00   90
 14  \w   -109.00 -31.00   0.50    0.20    --  -49.82 -77.00 -30.00  156
 15  \w   -119.00 -94.00   0.50    0.20    --  -49.82-125.00 -30.00   50
 16  \w   -101.00 -73.00   0.50    0.20    --  -49.82-125.00 -60.00   56
 17  \w    -22.00  14.00   0.50    0.20    --   49.82 -19.00-180.00   72
 18  \w    -22.00   3.00   0.50    0.20    --   49.82 -19.00 -90.00   50
 19  \w    -19.00  25.00   0.50    0.20    --   49.82 -19.00 -30.00   88
 20  \w    -48.00 -21.00   0.50    0.80    --  -90.00  45.00 -60.00   54
 21  \w   -161.00 -83.00   0.50    0.80    --  -90.00 -15.00 -60.00  156
 22  \w   -128.00-103.00   0.50    0.80    --  -90.00-149.00 -89.00   50
 23  \w    127.00 175.00   0.50    0.80    --  111.50  15.00  90.00   96
 24  \w     69.00 106.00   0.50    0.80    --  111.50-100.00 -13.96   74
 25  \w    105.00 138.00   0.50    0.80    --  111.50  30.00  30.00   66
 26  \w     48.00 122.00   0.50    0.80    --  111.50  -2.00 -48.87  148
 27  \w     76.00 104.00   0.50    0.80    --  111.50 -94.00  30.00   56
 28  \w     41.00  66.00   0.50    0.80    --  111.50 -61.00 150.00   50
 29  \w     47.00 101.00   0.50    0.80    --  111.50 -94.00 -90.00  108
 30  \w     45.00  70.00   0.50    0.80    --  111.50 -94.00 150.00   50
 31  \w    111.00 161.00   0.50    0.80    --  111.50  15.00  60.00  100
 32  \w     56.00  92.00   0.50    0.80    --  111.50 -94.00  60.00   72
 33  \w     42.00  68.00   0.50    0.80    --  111.50 -61.00 -30.00   52
 34  \w    140.00 166.00   0.50    0.80    --  111.50 125.00 -90.00   52
 35  \w     80.00 105.00   0.50    0.80    --  111.50 -94.00 150.00   50
 36  \w     43.00  68.00   0.50    0.80    --  111.50 -61.00  30.00   50
 37  \w     54.00  80.00   0.50    0.80    --  111.50 -77.00-120.00   52
 38  \w    108.00 135.00   0.50    0.80    --  111.50  15.00 120.00   54
 39  \w    141.00 166.00   0.50    0.80    --  111.50  15.00 120.00   50
 40  \w     48.00  74.00   0.50    0.80    --  111.50 -77.00   0.00   52
 41  \w     43.00  68.00   0.50    0.80    --  111.50 -94.00  30.00   50
 42  \w     41.00  75.00   0.50    0.80    --  111.50 -94.00 -30.00   68
 43  \w     43.00  90.00   0.50    0.80    --  111.50-125.00-120.00   94
 44  \w     42.00  70.00   0.50    0.80    --  111.50 -61.00  60.00   56
 45  \w     49.00 108.00   0.50    0.80    --  111.50-125.00 -90.00  118
 46  \w     86.00 111.00   0.50    0.80    --  111.50-125.00-180.00   50
 47  \w     43.00  71.00   0.50    0.80    --  111.50-125.00-180.00   56
 48  \w    138.00 169.00   0.50    0.80    --  111.50  30.00 -60.00   62
 49  \w     43.00  94.00   0.50    0.80    --  111.50 -77.00  60.00  102
 50  \w     44.00  69.00   0.50    0.80    --  111.50-125.00  30.00   50
 51  \w     82.00 107.00   0.50    0.80    --  111.50-125.00  30.00   50
 52  \w     74.00 100.00   0.50    0.80    --  111.50-125.00 120.00   52
 53  \w    112.00 148.00   0.50    0.80    --  111.50  15.00 -60.00   72
 54  \w     73.00 101.00   0.50    0.80    --  111.50 -94.00   0.00   56
 55  \w     95.00 136.00   0.50    0.80    --  111.50 125.00 -90.00   82
 56  \w     96.00 148.00   0.50    0.80    --  111.50 125.00   0.00  104
 57  \w     79.00 105.00   0.50    0.80    --  111.50 -94.00-120.00   52
 58  \w    111.00 137.00   0.50    0.80    --  111.50  30.00 -60.00   52
 59  \w    104.00 141.00   0.50    0.80    --  111.50  45.00-150.00   74
 60  \w     86.00 111.00   0.50    0.80    --  111.50-125.00 -30.00   50
 61  \w     42.00  68.00   0.50    0.80    --  111.50 -77.00-180.00   52
 62  \w     73.00  99.00   0.50    0.80    --  111.50 -77.00-180.00   52
 63  \w    127.00 153.00   0.50    0.80    --  111.50  15.00-180.00   52
 64  \w    111.00 136.00   0.50    0.80    --  111.50  61.00 -90.00   50
 65  \w     98.00 123.00   0.50    0.80    --  111.50 -87.00 -83.49   50
 66  \w     63.00  89.00   0.50    0.80    --  111.50 -77.00 -60.00   52
 67  \w     46.00  71.00   0.50    0.80    --  111.50 -77.00 -30.00   50
 68  \w    129.00 177.00   0.50    0.80    --  111.50  15.00   0.00   96
 69  \w     52.00  77.00   0.50    0.80    --  111.50 -77.00  90.00   50
 70  \w     42.00  67.00   0.50    0.80    --  111.50 -77.00 120.00   50
 71  \w     47.00  86.00   0.50    0.80    --  111.50 -77.00 150.00   78
 72  \w     52.00  77.00   0.50    0.80    --  111.50-125.00 -30.00   50
 73  \w     76.00 101.00   0.50    0.80    --  111.50 -94.00  90.00   50
 74  \w     84.00 110.00   0.50    0.80    --  111.50-125.00 150.00   52
 75  \w     85.00 110.00   0.50    0.80    --  111.50 -78.00 -54.02   50
 76  \w     41.00  99.00   0.50    0.80    --  111.50 -94.00 120.00  116
 77  \w    142.00 168.00   0.50    0.80    --  111.50  30.00 150.00   52
 78  \w    141.00 166.00   0.50    0.80    --  111.50 125.00-120.00   50
 79  \w    137.00 168.00   0.50    0.80    --  111.50 125.00  60.00   62
 80  \w    122.00 178.00   0.50    0.80    --  111.50  77.00 150.00  112
 81  \w     85.00 110.00   0.50    0.80    --  111.50 -82.00-163.42   50
 82  \w     45.00  70.00   0.50    0.80    --  111.50 -61.00 -60.00   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      0.1525674000
_diffrn_orient_matrix_UB_12      -0.0188183000
_diffrn_orient_matrix_UB_13      0.0517082000
_diffrn_orient_matrix_UB_21      0.1164134000
_diffrn_orient_matrix_UB_22      0.0543336000
_diffrn_orient_matrix_UB_23      -0.1138174000
_diffrn_orient_matrix_UB_31      -0.0502481000
_diffrn_orient_matrix_UB_32      0.1389925000
_diffrn_orient_matrix_UB_33      0.0110558000
_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  0.0228
_diffrn_reflns_av_unetI/netI     0.0195
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.992
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            20918
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         80.023
_diffrn_reflns_theta_min         3.601
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.999
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.79296
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.105a (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    1.594
_exptl_crystal_description       block
_exptl_crystal_F_000             520
_exptl_crystal_recrystallization_method 'crystallized from acetonitrile'
_exptl_crystal_size_max          0.148
_exptl_crystal_size_mid          0.103
_exptl_crystal_size_min          0.044
_refine_diff_density_max         0.322
_refine_diff_density_min         -0.657
_refine_diff_density_rms         0.068
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.050
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     263
_refine_ls_number_reflns         4659
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.050
_refine_ls_R_factor_all          0.0243
_refine_ls_R_factor_gt           0.0232
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0382P)^2^+0.2606P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0633
_refine_ls_wR_factor_ref         0.0640
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4406
_reflns_number_total             4659
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_862a_autored
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '389-391' was changed to
'390.0(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               7250989
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         C7H8Br1N3O
_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), C11A(H11A,H11B), C12A(H12A,H12B), C10B(H10C,H10D), C11B(H11C,
 H11D), C12B(H12C,H12D)
2.b Aromatic/amide H refined with riding coordinates:
 C3A(H3A), C5A(H5A), C3B(H3B), C5B(H5B)
2.c Idealised Me refined as rotating group:
 C13A(H13A,H13B,H13C), C13B(H13D,H13E,H13F)
;
_shelx_res_checksum              76240
_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 1.282
_oxdiff_exptl_absorpt_empirical_full_min 0.799