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_7250982
_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         'C9 H13 N3 O'
_chemical_formula_sum            'C9 H13 N3 O'
_chemical_formula_weight         179.22
_chemical_melting_point          380.0(10)
_chemical_name_systematic        N-(pyrimidin-2-yl)pentanamide
_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             2023-12-17
_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                 114.958(4)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   14.1135(5)
_cell_length_b                   9.5709(3)
_cell_length_c                   15.7423(5)
_cell_measurement_reflns_used    1427
_cell_measurement_temperature    294.25(10)
_cell_measurement_theta_max      75.0640
_cell_measurement_theta_min      5.5520
_cell_volume                     1927.88(13)
_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      294.25(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 0.994
_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   -105.00 -80.00   0.50    0.60    --  -49.82  -8.00 -25.00   50
  2  \w    -23.00  20.00   0.50    0.60    --  -49.82   8.00 149.00   86
  3  \w     -7.00  23.00   0.50    0.60    --   49.82  -8.00 -25.00   60
  4  \w     55.00  81.00   0.50    0.60    --   49.82   8.00 149.00   52
  5  \w   -145.00-120.00   0.50    2.50    --  -90.00  -8.00 -25.00   50
  6  \w    118.00 165.00   0.50    2.50    --  111.50   8.00 149.00   94
  7  \w    -76.00 -45.00   0.50    0.60    --  -49.82 125.00-180.00   62
  8  \w    -42.00  22.00   0.50    0.60    --  -49.82  38.00-150.00  128
  9  \w    -23.00  23.00   0.50    0.60    --  -49.82  19.00 -90.00   92
 10  \w     46.00  92.00   0.50    0.60    --   49.82-125.00-120.00   92
 11  \w      6.00  38.00   0.50    0.60    --   49.82 -57.00-120.00   64
 12  \w     46.00  71.00   0.50    2.50    --  111.50 -77.00 -30.00   50
 13  \w    108.00 159.00   0.50    2.50    --  111.50  15.00 -90.00  102
 14  \w     41.00  67.00   0.50    2.50    --  111.50 -61.00-180.00   52
 15  \w     44.00  74.00   0.50    2.50    --  111.50-125.00-150.00   60
 16  \w     95.00 121.00   0.50    2.50    --  111.50 -87.00 177.05   52
 17  \w     61.00  99.00   0.50    2.50    --  111.50 -94.00 150.00   76
 18  \w     97.00 139.00   0.50    2.50    --  111.50  61.00  60.00   84
 19  \w    137.00 176.00   0.50    2.50    --  111.50  77.00  90.00   78
 20  \w    138.00 175.00   0.50    2.50    --  111.50  30.00-180.00   74
 21  \w     41.00  67.00   0.50    2.50    --  111.50 -61.00   0.00   52
 22  \w     74.00 104.00   0.50    2.50    --  111.50 -77.00-180.00   60
 23  \w    111.00 178.00   0.50    2.50    --  111.50  61.00 -90.00  134
 24  \w     49.00  74.00   0.50    2.50    --  111.50 -87.00 177.05   50
 25  \w    105.00 135.00   0.50    2.50    --  111.50  30.00 120.00   60
 26  \w    113.00 170.00   0.50    2.50    --  111.50  61.00 -30.00  114
 27  \w     69.00 103.00   0.50    2.50    --  111.50 -94.00 -90.00   68
 28  \w     86.00 111.00   0.50    2.50    --  111.50-125.00-150.00   50
 29  \w     79.00 111.00   0.50    2.50    --  111.50-125.00 -90.00   64
 30  \w     86.00 111.00   0.50    2.50    --  111.50-125.00 -60.00   50
 31  \w     42.00 113.00   0.50    2.50    --  111.50 -87.00  96.71  142
 32  \w     92.00 125.00   0.50    2.50    --  111.50  77.00  90.00   66
 33  \w    125.00 178.00   0.50    2.50    --  111.50 125.00 120.00  106
 34  \w    112.00 167.00   0.50    2.50    --  111.50  15.00  60.00  110
 35  \w    104.00 129.00   0.50    2.50    --  111.50 125.00-120.00   50
 36  \w    142.00 178.00   0.50    2.50    --  111.50 125.00-120.00   72
 37  \w     42.00  71.00   0.50    2.50    --  111.50 -61.00 -90.00   58
 38  \w    129.00 154.00   0.50    2.50    --  111.50  15.00-150.00   50
 39  \w     62.00  88.00   0.50    2.50    --  111.50 -77.00-150.00   52
 40  \w     41.00 100.00   0.50    2.50    --  111.50 -77.00-120.00  118
 41  \w     76.00 102.00   0.50    2.50    --  111.50 -77.00   0.00   52
 42  \w     56.00  82.00   0.50    2.50    --  111.50 -77.00  60.00   52
 43  \w     58.00  84.00   0.50    2.50    --  111.50 -94.00   0.00   52
 44  \w     80.00 105.00   0.50    2.50    --  111.50 -94.00 120.00   50
 45  \w     54.00  90.00   0.50    2.50    --  111.50 -94.00 -60.00   72
 46  \w     41.00  67.00   0.50    2.50    --  111.50 -61.00-120.00   52
 47  \w    131.00 156.00   0.50    2.50    --  111.50 125.00  60.00   50
 48  \w     54.00 105.00   0.50    2.50    --  111.50 -94.00-180.00  102
;
_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      -0.0451454000
_diffrn_orient_matrix_UB_12      -0.1479037000
_diffrn_orient_matrix_UB_13      -0.0053629000
_diffrn_orient_matrix_UB_21      0.0954777000
_diffrn_orient_matrix_UB_22      -0.0619093000
_diffrn_orient_matrix_UB_23      -0.0100804000
_diffrn_orient_matrix_UB_31      0.0579131000
_diffrn_orient_matrix_UB_32      -0.0132321000
_diffrn_orient_matrix_UB_33      0.1073868000
_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  0.0322
_diffrn_reflns_av_unetI/netI     0.0295
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.994
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            11115
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.994
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.922
_diffrn_reflns_theta_min         5.565
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.681
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.71838
_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            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.235
_exptl_crystal_description       irregular
_exptl_crystal_F_000             768
_exptl_crystal_recrystallization_method 'crystallized from ethylacetate'
_exptl_crystal_size_max          0.164
_exptl_crystal_size_mid          0.099
_exptl_crystal_size_min          0.029
_refine_diff_density_max         0.128
_refine_diff_density_min         -0.190
_refine_diff_density_rms         0.045
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.080
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     123
_refine_ls_number_reflns         2088
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.080
_refine_ls_R_factor_all          0.0519
_refine_ls_R_factor_gt           0.0441
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0732P)^2^+0.3194P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1278
_refine_ls_wR_factor_ref         0.1360
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1677
_reflns_number_total             2088
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_824_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '379-381' was changed to
'380.0(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        1927.87(13)
_cod_database_code               7250982
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C9H13N3O
_shelx_estimated_absorpt_t_max   0.981
_shelx_estimated_absorpt_t_min   0.897
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H) groups
2.a Secondary CH2 refined with riding coordinates:
 C10(H10A,H10B), C11(H11A,H11B), C12(H12A,H12B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5)
2.c Idealised Me refined as rotating group:
 C13(H13A,H13B,H13C)
;
_shelx_res_checksum              78782
_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 1.288
_oxdiff_exptl_absorpt_empirical_full_min 0.876