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_7250983
_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 H19 N3 O'
_chemical_formula_sum            'C12 H19 N3 O'
_chemical_formula_weight         221.30
_chemical_melting_point          369.0(10)
_chemical_name_systematic        N-(pyrimidin-2-yl)octanamide
_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     direct
_audit_creation_date             2024-05-14
_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                 97.8206(19)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.4878(2)
_cell_length_b                   5.36366(9)
_cell_length_c                   24.6068(5)
_cell_measurement_reflns_used    3479
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      78.9760
_cell_measurement_theta_min      3.6150
_cell_volume                     1240.58(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-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    'XS  (Sheldrick, 2008)'
_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 0.951
_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   -121.00 -22.00   0.50    1.00    --  -48.07  -5.00  81.00  198
  2  \w    -28.00  17.00   0.50    1.00    --  -48.07   5.00-101.00   90
  3  \w     63.00 107.00   0.50    1.00    --   48.07   5.00-101.00   88
  4  \w   -137.00 -82.00   0.50    5.00    --  -91.75  -5.00  81.00  110
  5  \w     73.00 170.00   0.50    5.00    --  113.25   5.00-101.00  194
  6  \w     -8.00  43.00   0.50    1.00    --   48.07 -38.00 -30.00  102
  7  \w    -46.00 -20.00   0.50    5.00    --  -91.75  45.00-120.00   52
  8  \w    -72.00 -41.00   0.50    5.00    --  -91.75 125.00 -30.00   62
  9  \w    -96.00 -70.00   0.50    5.00    --  -91.75  77.00  90.00   52
 10  \w    -64.00 -21.00   0.50    5.00    --  -91.75  77.00  90.00   86
 11  \w     53.00 110.00   0.50    5.00    --  113.25-125.00  30.00  114
 12  \w     68.00 110.00   0.50    5.00    --  113.25-125.00 -90.00   84
 13  \w     42.00  70.00   0.50    5.00    --  113.25 -61.00-150.00   56
 14  \w     73.00 106.00   0.50    5.00    --  113.25-125.00   0.00   66
 15  \w    101.00 178.00   0.50    5.00    --  113.25  15.00 150.00  154
 16  \w     42.00  68.00   0.50    5.00    --  113.25 -61.00 -90.00   52
 17  \w     42.00  69.00   0.50    5.00    --  113.25 -61.00 120.00   54
 18  \w     79.00 111.00   0.50    5.00    --  113.25-125.00 -30.00   64
 19  \w     42.00  89.00   0.50    5.00    --  113.25 -94.00  90.00   94
;
_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      -0.1579846000
_diffrn_orient_matrix_UB_12      0.0182863000
_diffrn_orient_matrix_UB_13      0.0079200000
_diffrn_orient_matrix_UB_21      0.0423754000
_diffrn_orient_matrix_UB_22      -0.0037571000
_diffrn_orient_matrix_UB_23      0.0626770000
_diffrn_orient_matrix_UB_31      0.0107080000
_diffrn_orient_matrix_UB_32      0.2866576000
_diffrn_orient_matrix_UB_33      0.0003790000
_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  0.0341
_diffrn_reflns_av_unetI/netI     0.0397
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.951
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       6
_diffrn_reflns_limit_k_min       -3
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       -28
_diffrn_reflns_number            7258
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.951
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.614
_diffrn_reflns_theta_min         3.626
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.617
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.83896
_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    1.185
_exptl_crystal_description       needle
_exptl_crystal_F_000             480
_exptl_crystal_recrystallization_method 'crystallized from ethyl acetate'
_exptl_crystal_size_max          0.318
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.017
_refine_diff_density_max         0.141
_refine_diff_density_min         -0.252
_refine_diff_density_rms         0.041
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.052
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     150
_refine_ls_number_reflns         2554
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.052
_refine_ls_R_factor_all          0.0493
_refine_ls_R_factor_gt           0.0417
_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^)+(0.0600P)^2^+0.1593P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1108
_refine_ls_wR_factor_ref         0.1166
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2153
_reflns_number_total             2554
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_887_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '368-370' was changed to
'369.0(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               7250983
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C12H19N3O1
_shelx_estimated_absorpt_t_max   0.990
_shelx_estimated_absorpt_t_min   0.828
_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), C4(H4), C5(H5)
2.c Idealised Me refined as rotating group:
 C16(H16A,H16B,H16C)
;
_shelx_res_checksum              42458
_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 1.392
_oxdiff_exptl_absorpt_empirical_full_min 0.582