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_7250993
_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         'C12 H18 Br N3 O'
_chemical_formula_sum            'C12 H18 Br N3 O'
_chemical_formula_weight         300.20
_chemical_melting_point          372.0(10)
_chemical_name_systematic        N-(5-bromopyrimidin-2-yl)octanamide
_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             2024-05-16
_audit_creation_method
;
Olex2 1.5-ac6-019
(compiled 2024.02.14 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6920)
;
_audit_update_record
;
2025-08-25 deposited with the CCDC.	2025-10-02 downloaded from the CCDC.
;
_cell_angle_alpha                92.709(3)
_cell_angle_beta                 102.343(3)
_cell_angle_gamma                100.682(3)
_cell_formula_units_Z            2
_cell_length_a                   5.4649(2)
_cell_length_b                   10.9705(4)
_cell_length_c                   12.1885(4)
_cell_measurement_reflns_used    4618
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.6950
_cell_measurement_theta_min      3.7150
_cell_volume                     698.59(4)
_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-ac6-019 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-019 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/4 (Sheldrick, 2014)'
_diffrn_ambient_temperature      210.15
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.992
_diffrn_measured_fraction_theta_max 0.957
_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    -53.00 -22.00   0.50    3.00    --  -49.54 109.00-141.00   62
  2  \w     41.00  84.00   0.50    3.00    --   49.54-109.00 122.00   86
  3  \w   -114.00 -85.00   0.50   12.00    --  -90.00-109.00 122.00   58
  4  \w    -77.00 -51.00   0.50   12.00    --  -90.00 109.00-141.00   52
  5  \w     66.00 107.00   0.50   12.00    --  111.50-109.00 122.00   82
  6  \w    106.00 154.00   0.50   12.00    --  111.50 109.00-141.00   96
  7  \w    -26.00  24.00   0.50    3.00    --  -49.54  19.00  90.00  100
  8  \w   -118.00 -93.00   0.50    3.00    --  -49.54-125.00 -60.00   50
  9  \w   -120.00 -40.00   0.50    3.00    --  -49.54 -57.00 150.00  160
 10  \w    -25.00  20.00   0.50    3.00    --  -49.54  19.00 -60.00   90
 11  \w     13.00  68.00   0.50    3.00    --   49.54 -77.00-120.00  110
 12  \w    -18.00   9.00   0.50    3.00    --   49.54 -77.00-120.00   54
 13  \w    -47.00 -18.00   0.50   12.00    --  -90.00  45.00 150.00   58
 14  \w   -161.00 -83.00   0.50   12.00    --  -90.00 -30.00-180.00  156
 15  \w    -69.00 -24.00   0.50   12.00    --  -90.00  61.00  30.00   90
 16  \w     49.00  74.00   0.50   12.00    --  111.50-104.00 -99.86   50
 17  \w     44.00  70.00   0.50   12.00    --  111.50 -61.00  90.00   52
 18  \w    153.00 178.00   0.50   12.00    --  111.50  15.00 150.00   50
 19  \w     81.00 107.00   0.50   12.00    --  111.50-103.00 -50.99   52
 20  \w     45.00  99.00   0.50   12.00    --  111.50 -94.00 150.00  108
 21  \w    145.00 175.00   0.50   12.00    --  111.50  15.00 -90.00   60
 22  \w    108.00 176.00   0.50   12.00    --  111.50  15.00 -30.00  136
 23  \w    104.00 141.00   0.50   12.00    --  111.50  15.00 -90.00   74
 24  \w     42.00  70.00   0.50   12.00    --  111.50 -61.00-120.00   56
 25  \w    143.00 178.00   0.50   12.00    --  111.50  45.00   0.00   70
 26  \w    102.00 138.00   0.50   12.00    --  111.50  45.00   0.00   72
 27  \w     80.00 105.00   0.50   12.00    --  111.50 -94.00  30.00   50
 28  \w    105.00 142.00   0.50   12.00    --  111.50  15.00 150.00   74
 29  \w     42.00  70.00   0.50   12.00    --  111.50 -61.00 -60.00   56
 30  \w     44.00  70.00   0.50   12.00    --  111.50 -61.00  30.00   52
 31  \w     41.00 104.00   0.50   12.00    --  111.50 -94.00-120.00  126
 32  \w     77.00 103.00   0.50    3.00    --   49.79  19.00 -90.00   52
 33  \w     46.00  74.00   0.50   12.00    --  111.50 -94.00   0.00   56
 34  \w     76.00 102.00   0.50   12.00    --  111.50 -94.00   0.00   52
 35  \w     41.00  76.00   0.50   12.00    --  111.50 -94.00-180.00   70
 36  \w    105.00 172.00   0.50   12.00    --  111.50  30.00  30.00  134
 37  \w     41.00  69.00   0.50   12.00    --  111.50 -61.00 120.00   56
 38  \w     52.00  90.00   0.50   12.00    --  111.50 -77.00 -90.00   76
 39  \w     60.00 100.00   0.50   12.00    --  111.50 -94.00  60.00   80
 40  \w     67.00 111.00   0.50   12.00    --  111.50-125.00  30.00   88
 41  \w     43.00  93.00   0.50   12.00    --  111.50   0.00 -90.00  100
 42  \w    119.00 158.00   0.50   12.00    --  111.50   0.00 -90.00   78
 43  \w     41.00  71.00   0.50   12.00    --  111.50 -94.00-150.00   60
 44  \w     43.00  68.00   0.50   12.00    --  111.50 -77.00  30.00   50
 45  \w     80.00 105.00   0.50   12.00    --  111.50 -77.00  30.00   50
 46  \w    102.00 128.00   0.50   12.00    --  111.50  45.00 120.00   52
 47  \w    147.00 178.00   0.50   12.00    --  111.50  45.00 120.00   62
 48  \w     86.00 111.00   0.50   12.00    --  111.50-125.00 -60.00   50
 49  \w     79.00 106.00   0.50   12.00    --  111.50-102.00-178.76   54
 50  \w     86.00 111.00   0.50   12.00    --  111.50-125.00 -90.00   50
 51  \w     46.00  72.00   0.50   12.00    --  111.50-125.00 120.00   52
 52  \w     41.00  69.00   0.50   12.00    --  111.50 -61.00 -90.00   56
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0530
_diffrn_reflns_av_unetI/netI     0.0456
_diffrn_reflns_Laue_measured_fraction_full 0.992
_diffrn_reflns_Laue_measured_fraction_max 0.957
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            8672
_diffrn_reflns_point_group_measured_fraction_full 0.992
_diffrn_reflns_point_group_measured_fraction_max 0.957
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.976
_diffrn_reflns_theta_min         3.728
_exptl_absorpt_coefficient_mu    3.926
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.54087
_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    1.427
_exptl_crystal_description       needle
_exptl_crystal_F_000             308
_exptl_crystal_recrystallization_method 'crystallized from ethyl acetate'
_exptl_crystal_size_max          0.135
_exptl_crystal_size_mid          0.013
_exptl_crystal_size_min          0.011
_refine_diff_density_max         0.800
_refine_diff_density_min         -0.537
_refine_diff_density_rms         0.073
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.033
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     159
_refine_ls_number_reflns         2908
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.033
_refine_ls_R_factor_all          0.0472
_refine_ls_R_factor_gt           0.0407
_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^)+(0.0477P)^2^+0.5852P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1018
_refine_ls_wR_factor_ref         0.1050
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2558
_reflns_number_total             2908
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_891_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '371-373' was changed to
'372.0(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               7250993
_shelx_shelxl_version_number     2018/3
_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), C15(H15A,H15B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
2.c Idealised Me refined as rotating group:
 C16(H16A,H16B,H16C)
;
_shelx_res_checksum              3012
_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
;