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_7250997
_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         'C11 H16 Br N3 O'
_chemical_formula_sum            'C11 H16 Br N3 O'
_chemical_formula_weight         286.18
_chemical_melting_point          383.0(10)
_chemical_name_systematic        N-(5-bromopyrimidin-2-yl)heptanamide
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-05-16
_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                90
_cell_angle_beta                 104.0832(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   11.27079(12)
_cell_length_b                   5.29124(5)
_cell_length_c                   21.5186(2)
_cell_measurement_reflns_used    10241
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.5180
_cell_measurement_theta_min      4.0680
_cell_volume                     1244.72(2)
_computing_cell_refinement       'CrysAlisPro 1.171.43.116a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.116a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.116a (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 2014/4 (Sheldrick, 2014)'
_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 0.999
_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    -62.00  24.00   0.50    0.30    --  -48.07  55.00 -58.00  172
  2  \w   -119.00 -34.00   0.50    0.30    --  -48.07 -55.00 158.00  170
  3  \w    -23.00  63.00   0.50    0.30    --   48.07 -55.00 158.00  172
  4  \w   -163.00 -77.00   0.50    1.20    --  -91.75 -55.00 158.00  172
  5  \w    -63.00 -19.00   0.50    1.20    --  -91.75  55.00 -58.00   88
  6  \w     99.00 178.00   0.50    1.20    --  113.25  55.00 -58.00  158
  7  \w   -118.00 -73.00   0.50    0.30    --  -48.07-125.00-120.00   90
  8  \w   -118.00 -73.00   0.50    0.30    --  -48.07-125.00 120.00   90
  9  \w    -51.00 -20.00   0.50    1.20    --  -91.75  45.00  90.00   62
 10  \w    -51.00 -20.00   0.50    1.20    --  -91.75  45.00 150.00   62
 11  \w    -51.00 -20.00   0.50    1.20    --  -91.75  45.00 120.00   62
 12  \w     42.00  71.00   0.50    1.20    --  113.25 -61.00  30.00   58
 13  \w     42.00  71.00   0.50    1.20    --  113.25 -61.00 150.00   58
 14  \w    101.00 178.00   0.50    1.20    --  113.25  45.00-150.00  154
 15  \w     42.00  71.00   0.50    1.20    --  113.25 -61.00   0.00   58
 16  \w     42.00  71.00   0.50    1.20    --  113.25 -61.00-180.00   58
 17  \w     42.00  96.00   0.50    1.20    --  113.25 -94.00 150.00  108
 18  \w    146.00 178.00   0.50    1.20    --  113.25  30.00-120.00   64
 19  \w     94.00 126.00   0.50    1.20    --  113.25  77.00-150.00   64
 20  \w    133.00 166.00   0.50    1.20    --  113.25  77.00-150.00   66
 21  \w     42.00  68.00   0.50    1.20    --  113.25 -61.00-150.00   52
 22  \w    116.00 142.00   0.50    1.20    --  113.25  45.00-180.00   52
 23  \w     44.00  91.00   0.50    1.20    --  113.25 -77.00-150.00   94
 24  \w     48.00  99.00   0.50    1.20    --  113.25 -94.00 120.00  102
 25  \w    148.00 174.00   0.50    1.20    --  113.25  45.00-180.00   52
 26  \w    101.00 144.00   0.50    1.20    --  113.25 125.00-180.00   86
 27  \w     94.00 125.00   0.50    1.20    --  113.25  77.00-120.00   62
 28  \w     42.00  97.00   0.50    1.20    --  113.25 -77.00 150.00  110
 29  \w     96.00 121.00   0.50    1.20    --  113.25  77.00-180.00   50
 30  \w    139.00 177.00   0.50    1.20    --  113.25  77.00-180.00   76
 31  \w     77.00 103.00   0.50    1.20    --  113.25-125.00  30.00   52
 32  \w     67.00  93.00   0.50    1.20    --  113.25 -94.00-120.00   52
 33  \w    102.00 172.00   0.50    1.20    --  113.25  45.00  90.00  140
 34  \w    112.00 138.00   0.50    1.20    --  113.25  15.00   0.00   52
 35  \w    112.00 178.00   0.50    1.20    --  113.25 125.00-120.00  132
 36  \w     44.00  70.00   0.50    1.20    --  113.25 -77.00-120.00   52
 37  \w     64.00  90.00   0.50    1.20    --  113.25 -77.00 120.00   52
 38  \w    119.00 155.00   0.50    1.20    --  113.25  45.00 -90.00   72
 39  \w     61.00  87.00   0.50    1.20    --  113.25 -94.00  30.00   52
 40  \w     71.00 107.00   0.50    1.20    --  113.25-125.00 -60.00   72
 41  \w     91.00 116.00   0.50    1.20    --  113.25  77.00 -90.00   50
 42  \w     43.00  95.00   0.50    1.20    --  113.25 -94.00  90.00  104
;
_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      -0.1112916000
_diffrn_orient_matrix_UB_12      -0.1249143000
_diffrn_orient_matrix_UB_13      -0.0455877000
_diffrn_orient_matrix_UB_21      0.0862853000
_diffrn_orient_matrix_UB_22      -0.1475109000
_diffrn_orient_matrix_UB_23      -0.0324456000
_diffrn_orient_matrix_UB_31      0.0054092000
_diffrn_orient_matrix_UB_32      -0.2177215000
_diffrn_orient_matrix_UB_33      0.0481442000
_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  0.0329
_diffrn_reflns_av_unetI/netI     0.0247
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       6
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -27
_diffrn_reflns_number            14677
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.855
_diffrn_reflns_theta_min         4.083
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.378
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.60816
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.116a (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    1.527
_exptl_crystal_description       needle
_exptl_crystal_F_000             584
_exptl_crystal_recrystallization_method 'crystallized from ethyl acetate'
_exptl_crystal_size_max          0.284
_exptl_crystal_size_mid          0.024
_exptl_crystal_size_min          0.019
_refine_diff_density_max         0.574
_refine_diff_density_min         -0.538
_refine_diff_density_rms         0.057
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.082
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     150
_refine_ls_number_reflns         2713
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.082
_refine_ls_R_factor_all          0.0315
_refine_ls_R_factor_gt           0.0287
_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^)+(0.0323P)^2^+0.8193P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0744
_refine_ls_wR_factor_ref         0.0767
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2476
_reflns_number_total             2713
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_892_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '382-384' was changed to
'383.0(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               7250997
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C11H16Br1N3O1
_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), C14(H14A,H14B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
2.c Idealised Me refined as rotating group:
 C15(H15A,H15B,H15C)
;
_shelx_res_checksum              55094
_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 1.512
_oxdiff_exptl_absorpt_empirical_full_min 0.559