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_7250987
_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 Br N3 O'
_chemical_formula_sum            'C7 H8 Br N3 O'
_chemical_formula_weight         230.07
_chemical_melting_point          436.0(10)
_chemical_name_systematic        N-(5-bromopyrimidin-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                116.3584(13)
_cell_angle_beta                 103.3625(12)
_cell_angle_gamma                100.5427(10)
_cell_formula_units_Z            8
_cell_length_a                   11.91357(16)
_cell_length_b                   12.78923(14)
_cell_length_c                   13.5543(2)
_cell_measurement_reflns_used    28780
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.8320
_cell_measurement_theta_min      3.8940
_cell_volume                     1701.06(5)
_computing_cell_refinement       'CrysAlisPro 1.171.43.100a (Rigaku OD, 2023)'
_computing_data_collection       'CrysAlisPro 1.171.43.100a (Rigaku OD, 2023)'
_computing_data_reduction        'CrysAlisPro 1.171.43.100a (Rigaku OD, 2023)'
_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 0.999
_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    -75.00  25.00   0.50    0.50    --  -47.98  87.00 104.00  200
  2  \w    -21.00  75.00   0.50    0.50    --   47.98 -87.00 -12.00  192
  3  \w   -163.00 -79.00   0.50    2.80    --  -91.75 -87.00 -12.00  168
  4  \w   -119.00 -19.00   0.50    2.80    --  -91.75  87.00 104.00  200
  5  \w     42.00 141.00   0.50    2.80    --  113.25 -87.00 -12.00  198
  6  \w    115.00 148.00   0.50    2.80    --  113.25  87.00 104.00   66
  7  \w   -117.00 -73.00   0.50    0.50    --  -47.98-125.00  90.00   88
  8  \w   -113.00 -84.00   0.50    0.50    --  -47.98-125.00 120.00   58
  9  \w    -25.00  26.00   0.50    0.50    --  -47.98  19.00   0.00  102
 10  \w    -43.00  23.00   0.50    0.50    --  -47.98  38.00  90.00  132
 11  \w   -108.00 -83.00   0.50    0.50    --  -47.98-125.00 150.00   50
 12  \w   -112.00 -76.00   0.50    0.50    --  -47.98-125.00  30.00   72
 13  \w    -13.00  26.00   0.50    0.50    --   47.98 -19.00  90.00   78
 14  \w    -48.00 -23.00   0.50    2.80    --  -91.75  45.00-120.00   50
 15  \w    -50.00 -20.00   0.50    2.80    --  -91.75  45.00  60.00   60
 16  \w    -48.00 -22.00   0.50    2.80    --  -91.75  45.00 -90.00   52
 17  \w    -50.00 -20.00   0.50    2.80    --  -91.75  45.00 -60.00   60
 18  \w     79.00 104.00   0.50    2.80    --  113.25 -94.00-180.00   50
 19  \w    136.00 177.00   0.50    2.80    --  113.25  45.00 150.00   82
 20  \w     66.00 111.00   0.50    2.80    --  113.25-125.00   0.00   90
 21  \w     42.00  67.00   0.50    2.80    --  113.25 -61.00   0.00   50
 22  \w     71.00 119.00   0.50    2.80    --  113.25 -83.00  74.05   96
 23  \w     46.00  87.00   0.50    2.80    --  113.25 -77.00 -60.00   82
 24  \w     42.00  67.00   0.50    2.80    --  113.25 -61.00-120.00   50
 25  \w     81.00 106.00   0.50    2.80    --  113.25 -94.00  30.00   50
 26  \w     77.00 111.00   0.50    2.80    --  113.25-125.00 150.00   68
 27  \w     85.00 111.00   0.50    2.80    --  113.25-125.00 120.00   52
 28  \w     44.00  84.00   0.50    2.80    --  113.25-125.00-180.00   80
 29  \w     78.00 108.00   0.50    2.80    --  113.25-106.00 -50.12   60
 30  \w     43.00  68.00   0.50    2.80    --  113.25 -77.00   0.00   50
 31  \w     73.00  99.00   0.50    2.80    --  113.25 -77.00   0.00   52
 32  \w    128.00 154.00   0.50    2.80    --  113.25  30.00   0.00   52
 33  \w     46.00 106.00   0.50    2.80    --  113.25 -94.00  60.00  120
 34  \w     60.00  86.00   0.50    2.80    --  113.25 -77.00-120.00   52
 35  \w     77.00 105.00   0.50    2.80    --  113.25-103.00-128.00   56
 36  \w     46.00  71.00   0.50    2.80    --  113.25 -77.00  90.00   50
 37  \w     45.00  77.00   0.50    2.80    --  113.25-125.00 120.00   64
 38  \w     45.00  72.00   0.50    2.80    --  113.25-125.00 150.00   54
 39  \w     81.00 111.00   0.50    2.80    --  113.25-125.00-150.00   60
 40  \w     44.00  70.00   0.50    2.80    --  113.25 -77.00 -90.00   52
 41  \w     58.00 108.00   0.50    2.80    --  113.25-106.00-153.61  100
 42  \w    101.00 178.00   0.50    2.80    --  113.25  45.00 -30.00  154
 43  \w    102.00 127.00   0.50    2.80    --  113.25  15.00 -60.00   50
 44  \w    133.00 159.00   0.50    2.80    --  113.25 125.00-180.00   52
 45  \w     46.00 105.00   0.50    2.80    --  113.25 -94.00-120.00  118
 46  \w     84.00 110.00   0.50    2.80    --  113.25 -81.00 -90.54   52
 47  \w     64.00 100.00   0.50    2.80    --  113.25 -94.00   0.00   72
 48  \w     43.00  69.00   0.50    2.80    --  113.25 -94.00  30.00   52
 49  \w     85.00 111.00   0.50    2.80    --  113.25-125.00  60.00   52
 50  \w     96.00 165.00   0.50    2.80    --  113.25 125.00  60.00  138
 51  \w    114.00 157.00   0.50    2.80    --  113.25  45.00   0.00   86
 52  \w    111.00 153.00   0.50    2.80    --  113.25  30.00  60.00   84
 53  \w     61.00 100.00   0.50    2.80    --  113.25 -94.00-150.00   78
 54  \w     72.00 104.00   0.50    2.80    --  113.25 -94.00 120.00   64
 55  \w    104.00 138.00   0.50    2.80    --  113.25  30.00-150.00   68
 56  \w    147.00 176.00   0.50    2.80    --  113.25  30.00-150.00   58
 57  \w     95.00 123.00   0.50    2.80    --  113.25 125.00  30.00   56
 58  \w    149.00 174.00   0.50    2.80    --  113.25 125.00  30.00   50
 59  \w     42.00  67.00   0.50    2.80    --  113.25 -61.00-180.00   50
 60  \w     42.00  74.00   0.50    2.80    --  113.25 -94.00-180.00   64
 61  \w     99.00 162.00   0.50    2.80    --  113.25 125.00 -90.00  126
 62  \w    153.00 178.00   0.50    2.80    --  113.25  45.00  90.00   50
 63  \w     85.00 111.00   0.50    2.80    --  113.25-125.00  30.00   52
 64  \w    130.00 171.00   0.50    2.80    --  113.25  15.00 -90.00   82
 65  \w     93.00 168.00   0.50    2.80    --  113.25  77.00 -60.00  150
 66  \w     91.00 127.00   0.50    2.80    --  113.25  77.00   0.00   72
 67  \w    133.00 178.00   0.50    2.80    --  113.25  77.00   0.00   90
 68  \w     62.00  87.00   0.50    2.80    --  113.25 -77.00  60.00   50
 69  \w     45.00  71.00   0.50    2.80    --  113.25 -77.00  30.00   52
 70  \w    147.00 178.00   0.50    2.80    --  113.25  61.00  60.00   62
 71  \w     99.00 125.00   0.50    2.80    --  113.25 -79.00-152.68   52
 72  \w     48.00  73.00   0.50    2.80    --  113.25 -79.00-152.68   50
 73  \w     43.00  72.00   0.50    2.80    --  113.25 -77.00 120.00   58
 74  \w     76.00 102.00   0.50    2.80    --  113.25 -94.00 -60.00   52
 75  \w     97.00 141.00   0.50    2.80    --  113.25  61.00  60.00   88
 76  \w     71.00  99.00   0.50    2.80    --  113.25 -94.00 150.00   56
 77  \w    108.00 137.00   0.50    2.80    --  113.25  45.00  90.00   58
 78  \w    120.00 146.00   0.50    2.80    --  113.25  61.00-120.00   52
 79  \w    153.00 178.00   0.50    2.80    --  113.25  61.00-120.00   50
 80  \w    103.00 129.00   0.50    2.80    --  113.25  61.00  90.00   52
 81  \w     95.00 151.00   0.50    2.80    --  113.25 125.00 -30.00  112
 82  \w    119.00 165.00   0.50    2.80    --  113.25 125.00   0.00   92
 83  \w    106.00 132.00   0.50    2.80    --  113.25  77.00 -90.00   52
 84  \w    139.00 178.00   0.50    2.80    --  113.25  77.00 -90.00   78
 85  \w     46.00  72.00   0.50    2.80    --  113.25 -80.00  88.94   52
 86  \w     43.00  69.00   0.50    2.80    --  113.25 -81.00 -90.54   52
 87  \w     75.00 108.00   0.50    2.80    --  113.25-125.00 -30.00   66
 88  \w    108.00 138.00   0.50    2.80    --  113.25 -82.00 -15.49   60
 89  \w    110.00 136.00   0.50    2.80    --  113.25  15.00  60.00   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      0.0609048000
_diffrn_orient_matrix_UB_12      0.0138029000
_diffrn_orient_matrix_UB_13      -0.0841571000
_diffrn_orient_matrix_UB_21      -0.1259703000
_diffrn_orient_matrix_UB_22      -0.0294178000
_diffrn_orient_matrix_UB_23      -0.0874156000
_diffrn_orient_matrix_UB_31      0.0145121000
_diffrn_orient_matrix_UB_32      0.1385249000
_diffrn_orient_matrix_UB_33      0.0606611000
_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  0.0285
_diffrn_reflns_av_unetI/netI     0.0223
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_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            38605
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.992
_diffrn_reflns_theta_min         3.893
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    6.235
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.88994
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.100a (Rigaku Oxford Diffraction, 2023)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            orange
_exptl_crystal_colour_primary    orange
_exptl_crystal_density_diffrn    1.797
_exptl_crystal_description       prism
_exptl_crystal_F_000             912
_exptl_crystal_recrystallization_method 'crystallized from acetone and methanol'
_exptl_crystal_size_max          0.063
_exptl_crystal_size_mid          0.032
_exptl_crystal_size_min          0.031
_refine_diff_density_max         0.654
_refine_diff_density_min         -0.973
_refine_diff_density_rms         0.064
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.059
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     453
_refine_ls_number_reflns         7366
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.059
_refine_ls_R_factor_all          0.0277
_refine_ls_R_factor_gt           0.0257
_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^)+(0.0390P)^2^+0.6880P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0700
_refine_ls_wR_factor_ref         0.0713
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6792
_reflns_number_total             7366
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_860_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '435-437' was changed to
'436.0(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_original_cell_volume        1701.06(4)
_cod_database_code               7250987
_shelx_shelxl_version_number     2018/3
_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), 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              68259
_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 1.157
_oxdiff_exptl_absorpt_empirical_full_min 0.843