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_7250992
_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         'C8 H10 Br N3 O'
_chemical_formula_sum            'C8 H10 Br N3 O'
_chemical_formula_weight         244.10
_chemical_melting_point          410.0(10)
_chemical_name_systematic        N-(5-bromopyrimidin-2-yl)butyramide
_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                89.593(2)
_cell_angle_beta                 87.432(2)
_cell_angle_gamma                76.571(2)
_cell_formula_units_Z            2
_cell_length_a                   4.59547(11)
_cell_length_b                   8.48559(18)
_cell_length_c                   12.8938(4)
_cell_measurement_reflns_used    8780
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      78.7570
_cell_measurement_theta_min      3.4160
_cell_volume                     488.56(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    'XT  (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 0.980
_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   -121.00 -60.00   0.50    0.70    --  -49.82-145.00 -89.00  122
  2  \w   -100.00 -23.00   0.50    0.70    --  -49.82 145.00 -37.00  154
  3  \w   -120.00 -73.00   0.50    0.70    --  -49.82-126.00  77.00   94
  4  \w     45.00 107.00   0.50    0.70    --   49.82-145.00 -89.00  124
  5  \w     35.00  95.00   0.50    0.70    --   49.82-126.00  77.00  120
  6  \w   -153.00 -60.00   0.50    2.80    --  -90.00-145.00 -89.00  186
  7  \w    -87.00 -20.00   0.50    2.80    --  -90.00 126.00 154.00  134
  8  \w   -100.00 -23.00   0.50    2.80    --  -90.00 145.00 -37.00  154
  9  \w     81.00 170.00   0.50    2.80    --  111.50 145.00 -37.00  178
 10  \w     42.00 113.00   0.50    2.80    --  111.50-126.00  77.00  142
 11  \w     95.00 178.00   0.50    2.80    --  111.50 126.00 154.00  166
 12  \w     45.00 126.00   0.50    2.80    --  111.50-145.00 -89.00  162
 13  \w    -26.00  24.00   0.50    0.70    --  -49.82  19.00  90.00  100
 14  \w    -26.00  24.00   0.50    0.70    --  -49.82  19.00 -60.00  100
 15  \w   -121.00 -37.00   0.50    0.70    --  -49.82 -57.00 150.00  168
 16  \w   -162.00 -82.00   0.50    2.80    --  -90.00 -30.00-120.00  160
 17  \w   -161.00 -69.00   0.50    2.80    --  -90.00 -77.00 150.00  184
 18  \w   -162.00 -82.00   0.50    2.80    --  -90.00 -30.00-120.00  160
 19  \w     41.00 105.00   0.50    2.80    --  111.50 -94.00 -90.00  128
 20  \w     41.00 105.00   0.50    2.80    --  111.50 -94.00 -90.00  128
 21  \w     41.00  71.00   0.50    2.80    --  111.50 -61.00 -90.00   60
 22  \w     41.00  71.00   0.50    2.80    --  111.50 -61.00 -30.00   60
 23  \w     41.00  71.00   0.50    2.80    --  111.50 -61.00  30.00   60
 24  \w     43.00 111.00   0.50    2.80    --  111.50-125.00-180.00  136
 25  \w     43.00 111.00   0.50    2.80    --  111.50-125.00-180.00  136
 26  \w     41.00 105.00   0.50    2.80    --  111.50 -94.00 -60.00  128
 27  \w     41.00  71.00   0.50    2.80    --  111.50 -61.00 150.00   60
 28  \w    104.00 178.00   0.50    2.80    --  111.50  30.00 -30.00  148
 29  \w     41.00  71.00   0.50    2.80    --  111.50 -61.00  60.00   60
 30  \w     41.00 105.00   0.50    2.80    --  111.50 -77.00 -60.00  128
 31  \w     95.00 178.00   0.50    2.80    --  111.50 125.00-180.00  166
 32  \w    102.00 178.00   0.50    2.80    --  111.50  45.00 120.00  152
 33  \w     91.00 178.00   0.50    2.80    --  111.50  77.00 -30.00  174
 34  \w     41.00 105.00   0.50    2.80    --  111.50 -94.00-120.00  128
 35  \w     41.00 105.00   0.50    2.80    --  111.50 -94.00-120.00  128
 36  \w     43.00 111.00   0.50    2.80    --  111.50-125.00  30.00  136
 37  \w     41.00 105.00   0.50    2.80    --  111.50 -77.00-180.00  128
 38  \w     48.00  74.00   0.50    2.80    --  111.50 -77.00 120.00   52
 39  \w     79.00 104.00   0.50    2.80    --  111.50 -77.00 120.00   50
 40  \w     61.00 105.00   0.50    2.80    --  111.50 -94.00  90.00   88
 41  \w     97.00 130.00   0.50    2.80    --  111.50 125.00  60.00   66
 42  \w    147.00 176.00   0.50    2.80    --  111.50 125.00  60.00   58
 43  \w    102.00 128.00   0.50    2.80    --  111.50  45.00 120.00   52
 44  \w    119.00 145.00   0.50    2.80    --  111.50   0.00 -90.00   52
 45  \w     53.00  99.00   0.50    2.80    --  111.50   0.00 -90.00   92
 46  \w     68.00 105.00   0.50    2.80    --  111.50 -94.00  60.00   74
 47  \w     95.00 136.00   0.50    2.80    --  111.50 125.00-150.00   82
 48  \w     41.00  66.00   0.50    2.80    --  111.50 -77.00 150.00   50
 49  \w     60.00  86.00   0.50    2.80    --  111.50 -94.00-180.00   52
 50  \w     78.00 104.00   0.50    2.80    --  111.50 -94.00-150.00   52
 51  \w     44.00 101.00   0.50    2.80    --  111.50 -94.00  30.00  114
 52  \w    125.00 151.00   0.50    2.80    --  111.50  30.00 -90.00   52
 53  \w     45.00  70.00   0.50    2.80    --  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      0.2267886000
_diffrn_orient_matrix_UB_12      0.0867053000
_diffrn_orient_matrix_UB_13      -0.0526067000
_diffrn_orient_matrix_UB_21      0.1118314000
_diffrn_orient_matrix_UB_22      0.0311635000
_diffrn_orient_matrix_UB_23      0.1071118000
_diffrn_orient_matrix_UB_31      0.2347005000
_diffrn_orient_matrix_UB_32      -0.1623299000
_diffrn_orient_matrix_UB_33      -0.0080045000
_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  0.0342
_diffrn_reflns_av_unetI/netI     0.0253
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.980
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            10411
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.980
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.319
_diffrn_reflns_theta_min         3.431
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    5.465
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.88070
_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    1.659
_exptl_crystal_description       needle
_exptl_crystal_F_000             244
_exptl_crystal_recrystallization_method 'crystallized from acetone'
_exptl_crystal_size_max          0.208
_exptl_crystal_size_mid          0.025
_exptl_crystal_size_min          0.014
_refine_diff_density_max         0.286
_refine_diff_density_min         -0.536
_refine_diff_density_rms         0.074
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.111
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     123
_refine_ls_number_reflns         2074
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.111
_refine_ls_R_factor_all          0.0250
_refine_ls_R_factor_gt           0.0241
_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^)+(0.0411P)^2^+0.1055P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0657
_refine_ls_wR_factor_ref         0.0662
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1978
_reflns_number_total             2074
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_861_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '409-411' was changed to
'410.0(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               7250992
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         C8H10Br1N3O
_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)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
2.c Idealised Me refined as rotating group:
 C12(H12A,H12B,H12C)
;
_shelx_res_checksum              83048
_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 1.520
_oxdiff_exptl_absorpt_empirical_full_min 0.630