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_7250991
_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 H11 N3 O'
_chemical_formula_sum            'C8 H11 N3 O'
_chemical_formula_weight         165.20
_chemical_melting_point          376.5(15)
_chemical_name_systematic        N-(pyrimidin-2-yl)butyramide
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-I 2ya'
_space_group_name_H-M_alt        'I 1 2/a 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2023-12-15
_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                 96.210(3)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   17.7106(5)
_cell_length_b                   5.3994(2)
_cell_length_c                   18.1317(5)
_cell_measurement_reflns_used    1358
_cell_measurement_temperature    294.1(2)
_cell_measurement_theta_max      79.2590
_cell_measurement_theta_min      4.9010
_cell_volume                     1723.70(9)
_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    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_environment      air
_diffrn_ambient_temperature      294.1(2)
_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 0.995
_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    -79.00  25.00   0.50   13.00    --  -48.10  95.00  79.00  208
  2  \w     43.00 108.00   0.50    8.00    --   47.98  77.00 150.00  130
  3  \w     67.00 103.00   0.50   30.00    --  113.25 -95.00 -30.00   72
  4  \w    106.00 178.00   0.50   30.00    --  113.25  95.00  79.00  144
  5  \w     52.00  77.00   0.50    6.00    --   47.98  57.00-150.00   50
  6  \w     -7.00  26.00   0.50    6.00    --  -47.98  19.00  30.00   66
  7  \w    -19.00  18.00   0.50    6.00    --  -47.98  19.00   0.00   74
  8  \w   -106.00 -79.00   0.50    6.00    --  -47.98-125.00-150.00   54
  9  \w    -49.00 -23.00   0.50   24.00    --  -91.75  45.00  30.00   52
 10  \w     76.00 109.00   0.50   24.00    --  113.25-125.00 150.00   66
 11  \w     49.00 100.00   0.50   24.00    --  113.25 -94.00   0.00  102
 12  \w     79.00 106.00   0.50   24.00    --  113.25 -94.00  30.00   54
 13  \w    137.00 176.00   0.50   24.00    --  113.25  15.00 -90.00   78
 14  \w     48.00  75.00   0.50   24.00    --  113.25 -94.00  30.00   54
 15  \w     45.00  71.00   0.50   24.00    --  113.25-125.00 150.00   52
 16  \w     81.00 106.00   0.50   24.00    --  113.25-125.00  90.00   50
 17  \w     74.00 104.00   0.50   24.00    --  113.25 -77.00  60.00   60
 18  \w     83.00 109.00   0.50   24.00    --  113.25-125.00   0.00   52
 19  \w    101.00 127.00   0.50   24.00    --  113.25  30.00  30.00   52
 20  \w     48.00  74.00   0.50   24.00    --  113.25-125.00 -30.00   52
 21  \w    137.00 175.00   0.50   24.00    --  113.25  30.00   0.00   76
 22  \w     42.00  91.00   0.50   24.00    --  113.25 -77.00  30.00   98
 23  \w     79.00 106.00   0.50   24.00    --  113.25-125.00 -30.00   54
 24  \w     42.00  71.00   0.50   24.00    --  113.25 -61.00  90.00   58
 25  \w     95.00 124.00   0.50   24.00    --  113.25 125.00 120.00   58
 26  \w    139.00 165.00   0.50   24.00    --  113.25 125.00 120.00   52
 27  \w     42.00  67.00   0.50   24.00    --  113.25 -61.00  30.00   50
 28  \w    132.00 161.00   0.50   24.00    --  113.25  30.00  30.00   58
 29  \w     47.00  73.00   0.50   24.00    --  113.25 -77.00  60.00   52
 30  \w    107.00 134.00   0.50   24.00    --  113.25  30.00   0.00   54
 31  \w     42.00  67.00   0.50   24.00    --  113.25 -61.00   0.00   50
 32  \w     42.00  67.00   0.50   24.00    --  113.25 -61.00-120.00   50
 33  \w     45.00  71.00   0.50   24.00    --  113.25 -61.00 150.00   52
 34  \w     86.00 111.00   0.50   24.00    --  113.25-125.00  60.00   50
 35  \w    100.00 152.00   0.50   24.00    --  113.25 125.00   0.00  104
 36  \w     42.00  67.00   0.50   24.00    --  113.25 -61.00 -90.00   50
 37  \w     43.00  68.00   0.50   24.00    --  113.25 -61.00 120.00   50
 38  \w     45.00 106.00   0.50   24.00    --  113.25 -94.00 150.00  122
 39  \w    104.00 132.00   0.50   24.00    --  113.25 -85.00 -12.13   56
 40  \w     50.00  75.00   0.50   24.00    --  113.25 -77.00 -60.00   50
 41  \w     70.00  96.00   0.50   24.00    --  113.25 -77.00 -30.00   52
 42  \w     67.00  93.00   0.50   24.00    --  113.25 -77.00 150.00   52
 43  \w     79.00 106.00   0.50   24.00    --  113.25 -94.00 120.00   54
 44  \w    114.00 176.00   0.50   24.00    --  113.25  45.00-120.00  124
 45  \w    121.00 146.00   0.50   24.00    --  113.25  15.00  30.00   50
 46  \w     45.00  70.00   0.50   24.00    --  113.25 -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      0.0216109000
_diffrn_orient_matrix_UB_12      0.2417926000
_diffrn_orient_matrix_UB_13      -0.0376075000
_diffrn_orient_matrix_UB_21      0.0272462000
_diffrn_orient_matrix_UB_22      0.1111055000
_diffrn_orient_matrix_UB_23      0.0765373000
_diffrn_orient_matrix_UB_31      0.0802570000
_diffrn_orient_matrix_UB_32      -0.1027232000
_diffrn_orient_matrix_UB_33      -0.0058492000
_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  0.0284
_diffrn_reflns_av_unetI/netI     0.0245
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       6
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            8394
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.933
_diffrn_reflns_theta_min         4.907
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.719
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.92102
_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            white
_exptl_crystal_colour_primary    white
_exptl_crystal_density_diffrn    1.273
_exptl_crystal_description       needle
_exptl_crystal_F_000             704
_exptl_crystal_recrystallization_method 'crystallized from ethylacetate'
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.018
_exptl_crystal_size_min          0.013
_refine_diff_density_max         0.141
_refine_diff_density_min         -0.126
_refine_diff_density_rms         0.029
_refine_ls_extinction_coef       0.0012(2)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     115
_refine_ls_number_reflns         1875
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.060
_refine_ls_R_factor_all          0.0434
_refine_ls_R_factor_gt           0.0359
_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^)+(0.0550P)^2^+0.3545P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1005
_refine_ls_wR_factor_ref         0.1049
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1575
_reflns_number_total             1875
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_821_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '375-378' was changed to
'376.5(15)' -- 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        1723.69(10)
_cod_database_code               7250991
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C8H11N3O
_shelx_estimated_absorpt_t_max   0.991
_shelx_estimated_absorpt_t_min   0.900
_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:
 C9(H9A,H9B), C10(H10A,H10B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5)
2.c Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C)
;
_shelx_res_checksum              74998
_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 2.725
_oxdiff_exptl_absorpt_empirical_full_min 0.499