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_7250986
_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         'C10 H14 Br N3 O'
_chemical_formula_sum            'C10 H14 Br N3 O'
_chemical_formula_weight         272.15
_chemical_name_systematic        N-(5-bromopyrimidin-2-yl)hexanamide
_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             2024-02-23
_audit_creation_method
;
Olex2 1.5-ac6-016
(compiled 2024.01.13 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6897)
;
_audit_update_record
;
2025-08-25 deposited with the CCDC.	2025-10-02 downloaded from the CCDC.
;
_cell_angle_alpha                83.8025(13)
_cell_angle_beta                 88.2380(13)
_cell_angle_gamma                77.2224(13)
_cell_formula_units_Z            2
_cell_length_a                   4.22728(7)
_cell_length_b                   9.25178(15)
_cell_length_c                   15.5113(2)
_cell_measurement_reflns_used    8013
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.6560
_cell_measurement_theta_min      2.8590
_cell_volume                     588.149(16)
_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-ac6-016 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-016 (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 0.999
_diffrn_measured_fraction_theta_max 0.986
_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   -104.00 -78.00   0.50    1.00    --  -47.98-143.00  -3.00   52
  2  \w    -74.00 -48.00   0.50    1.00    --  -47.98 143.00  51.00   52
  3  \w    -88.00 -46.00   0.50    1.00    --  -47.98 127.00-118.00   84
  4  \w   -118.00 -72.00   0.50    1.00    --  -47.98-127.00 166.00   92
  5  \w     70.00 106.00   0.50    1.00    --   47.98-143.00  -3.00   72
  6  \w     39.00  84.00   0.50    1.00    --   47.98-127.00 166.00   90
  7  \w   -132.00-107.00   0.50    4.00    --  -91.75-143.00  -3.00   50
  8  \w    -85.00 -60.00   0.50    4.00    --  -91.75 143.00  51.00   50
  9  \w    -78.00 -53.00   0.50    4.00    --  -91.75 127.00-118.00   50
 10  \w     54.00  79.00   0.50    4.00    --  113.25-127.00 166.00   50
 11  \w    102.00 128.00   0.50    4.00    --  113.25 143.00  51.00   52
 12  \w     99.00 125.00   0.50    4.00    --  113.25-143.00  -3.00   52
 13  \w    151.00 176.00   0.50    4.00    --  113.25 127.00-118.00   50
 14  \w   -118.00 -74.00   0.50    1.00    --  -47.98-125.00   0.00   88
 15  \w    -26.00  28.00   0.50    1.00    --  -47.98  19.00 -90.00  108
 16  \w    -25.00  28.00   0.50    1.00    --  -47.98  19.00-180.00  106
 17  \w    -14.00  26.00   0.50    1.00    --   47.98 -19.00 -90.00   80
 18  \w    -49.00 -21.00   0.50    4.00    --  -91.75  45.00  60.00   56
 19  \w   -145.00 -78.00   0.50    4.00    --  -91.75 -15.00  30.00  134
 20  \w     42.00  88.00   0.50    4.00    --  113.25 -77.00 -30.00   92
 21  \w     45.00  70.00   0.50    4.00    --  113.25-125.00-150.00   50
 22  \w     42.00  71.00   0.50    4.00    --  113.25 -61.00-120.00   58
 23  \w    130.00 178.00   0.50    4.00    --  113.25  45.00  60.00   96
 24  \w     77.00 103.00   0.50    4.00    --  113.25 -94.00-150.00   52
 25  \w     44.00 100.00   0.50    4.00    --  113.25 -77.00  90.00  112
 26  \w     61.00 107.00   0.50    4.00    --  113.25-125.00 -90.00   92
 27  \w    136.00 172.00   0.50    4.00    --  113.25  61.00  30.00   72
 28  \w    103.00 130.00   0.50    4.00    --  113.25  45.00  90.00   54
 29  \w    148.00 174.00   0.50    4.00    --  113.25  30.00-120.00   52
 30  \w     42.00  71.00   0.50    4.00    --  113.25 -61.00  30.00   58
 31  \w     81.00 106.00   0.50    4.00    --  113.25 -94.00  30.00   50
 32  \w    105.00 143.00   0.50    4.00    --  113.25  45.00 120.00   76
 33  \w    129.00 164.00   0.50    4.00    --  113.25 125.00 -90.00   70
 34  \w     46.00 106.00   0.50    4.00    --  113.25 -94.00-180.00  120
 35  \w     58.00 104.00   0.50    4.00    --  113.25 -94.00 -60.00   92
 36  \w    131.00 157.00   0.50    4.00    --  113.25  30.00  30.00   52
 37  \w     91.00 123.00   0.50    4.00    --  113.25  77.00-120.00   64
 38  \w    131.00 162.00   0.50    4.00    --  113.25  77.00-120.00   62
 39  \w    103.00 143.00   0.50    4.00    --  113.25  45.00 -60.00   80
 40  \w     42.00 105.00   0.50    4.00    --  113.25 -94.00 -30.00  126
 41  \w    104.00 130.00   0.50    4.00    --  113.25  61.00  30.00   52
 42  \w     78.00 103.00   0.50    4.00    --  113.25 -94.00 -90.00   50
 43  \w     56.00  97.00   0.50    4.00    --  113.25 -94.00  90.00   82
 44  \w     42.00  77.00   0.50    4.00    --  113.25 -94.00  30.00   70
 45  \w     42.00  67.00   0.50    4.00    --  113.25 -61.00 -30.00   50
 46  \w    101.00 147.00   0.50    4.00    --  113.25  45.00-150.00   92
 47  \w    102.00 127.00   0.50    4.00    --  113.25  45.00   0.00   50
 48  \w    130.00 156.00   0.50    4.00    --  113.25  45.00   0.00   52
 49  \w    101.00 149.00   0.50    4.00    --  113.25  15.00  30.00   96
 50  \w     66.00 105.00   0.50    4.00    --  113.25 -94.00  60.00   78
 51  \w     73.00  99.00   0.50    4.00    --  113.25-125.00-120.00   52
 52  \w     46.00 108.00   0.50    4.00    --  113.25-125.00 -60.00  124
 53  \w    102.00 142.00   0.50    4.00    --  113.25  30.00-120.00   80
 54  \w    119.00 147.00   0.50    4.00    --  113.25  61.00 -60.00   56
 55  \w     97.00 152.00   0.50    4.00    --  113.25 125.00 120.00  110
 56  \w     93.00 138.00   0.50    4.00    --  113.25  77.00-180.00   90
 57  \w     93.00 177.00   0.50    4.00    --  113.25  77.00 -60.00  168
 58  \w    103.00 138.00   0.50    4.00    --  113.25 -83.00  84.57   70
 59  \w     72.00 113.00   0.50    4.00    --  113.25 -85.00  25.91   82
 60  \w    102.00 145.00   0.50    4.00    --  113.25  77.00 120.00   86
;
_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      -0.0478439000
_diffrn_orient_matrix_UB_12      0.0846581000
_diffrn_orient_matrix_UB_13      -0.0914389000
_diffrn_orient_matrix_UB_21      0.1634216000
_diffrn_orient_matrix_UB_22      -0.1437336000
_diffrn_orient_matrix_UB_23      -0.0398701000
_diffrn_orient_matrix_UB_31      -0.3326181000
_diffrn_orient_matrix_UB_32      -0.0405308000
_diffrn_orient_matrix_UB_33      -0.0056414000
_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  0.0185
_diffrn_reflns_av_unetI/netI     0.0159
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.986
_diffrn_reflns_limit_h_max       4
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            8938
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.986
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.969
_diffrn_reflns_theta_min         2.866
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.601
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.79079
_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    1.537
_exptl_crystal_description       plate
_exptl_crystal_F_000             276
_exptl_crystal_recrystallization_method 'crystallized from acetonitrile'
_exptl_crystal_size_max          0.147
_exptl_crystal_size_mid          0.088
_exptl_crystal_size_min          0.022
_refine_diff_density_max         0.449
_refine_diff_density_min         -0.443
_refine_diff_density_rms         0.064
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.076
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     141
_refine_ls_number_reflns         2536
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.076
_refine_ls_R_factor_all          0.0237
_refine_ls_R_factor_gt           0.0235
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0357P)^2^+0.2164P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0614
_refine_ls_wR_factor_ref         0.0616
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2499
_reflns_number_total             2536
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_865_auto
_cod_depositor_comments
'Adding full bibliography for 7250982--7251002.cif.'
_cod_original_cell_volume        588.148(16)
_cod_database_code               7250986
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C10H14Br1N3O1
_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:
 C10(H10A,H10B), C11(H11A,H11B), C12(H12A,H12B), C13(H13A,H13B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
2.c Idealised Me refined as rotating group:
 C14(H14A,H14B,H14C)
;
_shelx_res_checksum              8324
_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 1.287
_oxdiff_exptl_absorpt_empirical_full_min 0.833