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_7251000
_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 H17 N3 O'
_chemical_formula_sum            'C11 H17 N3 O'
_chemical_formula_weight         207.27
_chemical_melting_point          358.5(15)
_chemical_name_systematic        N-(pyrimidin-2-yl)heptanamide
_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
_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                86.634(3)
_cell_angle_beta                 78.835(3)
_cell_angle_gamma                74.900(4)
_cell_formula_units_Z            2
_cell_length_a                   5.4040(3)
_cell_length_b                   9.4516(4)
_cell_length_c                   11.8359(3)
_cell_measurement_reflns_used    3628
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      77.8910
_cell_measurement_theta_min      3.7900
_cell_volume                     572.59(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-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)'
_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 0.994
_diffrn_measured_fraction_theta_max 0.959
_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    -59.00 -33.00   0.50   10.00    --  -47.57 118.00 173.00   52
  2  \w    -94.00 -50.00   0.50   10.00    --  -47.57-160.00 -64.00   88
  3  \w     63.00 118.00   0.50   10.00    --   47.57-160.00 -64.00  110
  4  \w     45.00  86.00   0.50   10.00    --   47.57-118.00  87.00   82
  5  \w     72.00  97.00   0.50   10.00    --   47.57 160.00 -34.00   50
  6  \w   -115.00 -78.00   0.50   40.00    --  -91.75-118.00  87.00   74
  7  \w   -102.00 -76.00   0.50   40.00    --  -91.75 160.00 -34.00   52
  8  \w    -78.00 -53.00   0.50   40.00    --  -91.75 118.00 173.00   50
  9  \w     55.00  82.00   0.50   40.00    --  113.25-118.00  87.00   54
 10  \w    124.00 150.00   0.50   40.00    --  113.25 118.00 173.00   52
 11  \w    111.00 136.00   0.50   40.00    --  113.25-160.00 -64.00   50
 12  \w     83.00 110.00   0.50   40.00    --  113.25-118.00  87.00   54
 13  \w    -26.00  28.00   0.50   10.00    --  -47.57  19.00 150.00  108
 14  \w    -26.00  28.00   0.50   10.00    --  -47.57  19.00  90.00  108
 15  \w    -19.00   6.00   0.50   10.00    --  -47.57  19.00 -60.00   50
 16  \w    -26.00  25.00   0.50   10.00    --  -47.57  19.00  30.00  102
 17  \w    -26.00  19.00   0.50   10.00    --   47.57 -19.00 -60.00   90
 18  \w    -50.00 -21.00   0.50   40.00    --  -91.75  45.00 -60.00   58
 19  \w   -156.00-105.00   0.50   40.00    --  -91.75 -61.00   0.00  102
 20  \w   -162.00-112.00   0.50   40.00    --  -91.75 -45.00 150.00  100
 21  \w    -51.00 -24.00   0.50   40.00    --  -91.75  45.00 120.00   54
 22  \w     43.00  69.00   0.50   40.00    --  113.25 -61.00 -30.00   52
 23  \w     46.00 110.00   0.50   40.00    --  113.25-125.00  60.00  128
 24  \w     78.00 104.00   0.50   40.00    --  113.25 -94.00-120.00   52
 25  \w     62.00 101.00   0.50   40.00    --  113.25 -94.00 -30.00   78
 26  \w     43.00  71.00   0.50   40.00    --  113.25 -61.00 150.00   56
 27  \w     43.00  68.00   0.50   40.00    --  113.25 -94.00-120.00   50
 28  \w    103.00 174.00   0.50   40.00    --  113.25  45.00 -30.00  142
 29  \w    115.00 144.00   0.50   40.00    --  113.25  45.00-120.00   58
 30  \w     42.00  68.00   0.50   40.00    --  113.25 -61.00-120.00   52
 31  \w    152.00 178.00   0.50   40.00    --  113.25  30.00  90.00   52
 32  \w    104.00 145.00   0.50   40.00    --  113.25  30.00  90.00   82
 33  \w     48.00 102.00   0.50   40.00    --  113.25 -94.00  90.00  108
 34  \w     70.00 106.00   0.50   40.00    --  113.25-101.00-160.75   72
 35  \w     47.00  79.00   0.50   40.00    --  113.25 -77.00-120.00   64
 36  \w    118.00 166.00   0.50   40.00    --  113.25  45.00 150.00   96
 37  \w     42.00  67.00   0.50   40.00    --  113.25 -61.00  90.00   50
 38  \w    115.00 150.00   0.50   40.00    --  113.25   0.00 120.00   70
 39  \w     44.00 109.00   0.50   40.00    --  113.25-125.00   0.00  130
 40  \w     47.00  72.00   0.50   40.00    --  113.25-125.00-180.00   50
 41  \w     82.00 107.00   0.50   40.00    --  113.25-125.00-180.00   50
 42  \w     52.00  80.00   0.50   40.00    --  113.25   0.00 120.00   56
 43  \w     50.00  89.00   0.50   40.00    --  113.25 -77.00  90.00   78
 44  \w     42.00  67.00   0.50   40.00    --  113.25 -61.00 -90.00   50
 45  \w     42.00  67.00   0.50   40.00    --  113.25 -61.00 120.00   50
 46  \w     58.00  83.00   0.50   40.00    --  113.25 -77.00 -90.00   50
 47  \w     47.00  75.00   0.50   40.00    --  113.25 -77.00 120.00   56
 48  \w     79.00 105.00   0.50   40.00    --  113.25 -77.00 120.00   52
 49  \w    102.00 170.00   0.50   40.00    --  113.25  45.00-150.00  136
 50  \w     91.00 116.00   0.50   40.00    --  113.25 160.00 -34.00   50
 51  \w    114.00 139.00   0.50   40.00    --  113.25 118.00 173.00   50
 52  \w     80.00 105.00   0.50   40.00    --  113.25 -77.00   0.00   50
 53  \w     43.00  69.00   0.50   40.00    --  113.25 -61.00 -90.00   52
 54  \w     81.00  93.50   0.50   40.00    --  113.25-125.00 -60.00   25
;
_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      -0.0051297000
_diffrn_orient_matrix_UB_12      -0.1287558000
_diffrn_orient_matrix_UB_13      0.0857488000
_diffrn_orient_matrix_UB_21      0.1209748000
_diffrn_orient_matrix_UB_22      -0.1091999000
_diffrn_orient_matrix_UB_23      -0.0995258000
_diffrn_orient_matrix_UB_31      0.2749864000
_diffrn_orient_matrix_UB_32      -0.0012875000
_diffrn_orient_matrix_UB_33      0.0185651000
_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  0.0216
_diffrn_reflns_av_unetI/netI     0.0275
_diffrn_reflns_Laue_measured_fraction_full 0.994
_diffrn_reflns_Laue_measured_fraction_max 0.959
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -4
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            6602
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.959
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.132
_diffrn_reflns_theta_min         3.807
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.637
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.72150
_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    1.202
_exptl_crystal_description       needle
_exptl_crystal_F_000             224
_exptl_crystal_recrystallization_method 'crystallized from ethyl acetate'
_exptl_crystal_size_max          0.185
_exptl_crystal_size_mid          0.023
_exptl_crystal_size_min          0.017
_refine_diff_density_max         0.215
_refine_diff_density_min         -0.175
_refine_diff_density_rms         0.044
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.074
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     141
_refine_ls_number_reflns         2366
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.074
_refine_ls_R_factor_all          0.0544
_refine_ls_R_factor_gt           0.0474
_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^)+(0.0762P)^2^+0.1021P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1306
_refine_ls_wR_factor_ref         0.1361
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2059
_reflns_number_total             2366
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_888_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '357-360' was changed to
'358.5(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_database_code               7251000
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C12H19N3O1
_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), C4(H4), C5(H5)
2.c Idealised Me refined as rotating group:
 C15(H15A,H15B,H15C)
;
_shelx_res_checksum              14279
_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 1.441
_oxdiff_exptl_absorpt_empirical_full_min 0.672