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_7250984
_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         'C10 H15 N3 O'
_chemical_formula_sum            'C10 H15 N3 O'
_chemical_formula_weight         193.25
_chemical_melting_point          384.0(10)
_chemical_name_systematic        N-(pyrimidin-2-yl)hexanamide
_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     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                86.598(2)
_cell_angle_beta                 83.945(2)
_cell_angle_gamma                76.146(2)
_cell_formula_units_Z            2
_cell_length_a                   5.48770(10)
_cell_length_b                   9.4348(3)
_cell_length_c                   10.5745(3)
_cell_measurement_reflns_used    1241
_cell_measurement_temperature    292.66(13)
_cell_measurement_theta_max      78.7710
_cell_measurement_theta_min      4.2160
_cell_volume                     528.28(2)
_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      292.66(13)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.980
_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     -2.00  24.00   0.50    0.20    --  -47.98  88.00-178.00   52
  2  \w    -53.00 -13.00   0.50    0.20    --  -47.98  88.00-178.00   80
  3  \w    -18.00  73.00   0.50    0.20    --   47.98 -88.00  65.00  182
  4  \w   -151.00-125.00   0.50    1.00    --  -91.75 -88.00  65.00   52
  5  \w    -93.00 -66.00   0.50    1.00    --  -91.75  88.00-178.00   54
  6  \w    115.00 158.00   0.50    1.00    --  113.25  88.00-178.00   86
  7  \w   -111.00 -86.00   0.50    0.20    --  -47.98-125.00 -30.00   50
  8  \w   -115.00 -80.00   0.50    0.20    --  -47.98-125.00-180.00   70
  9  \w     -2.00  28.00   0.50    0.20    --  -47.98  19.00  60.00   60
 10  \w   -118.00 -73.00   0.50    0.20    --  -47.98-125.00 150.00   90
 11  \w     -5.00  24.00   0.50    0.20    --   47.98 -19.00 150.00   58
 12  \w     -3.00  42.00   0.50    0.20    --   47.98 -38.00  60.00   90
 13  \w    -21.00  41.00   0.50    0.20    --   47.98 -38.00 120.00  124
 14  \w    -50.00 -20.00   0.50    1.00    --  -91.75  45.00 -30.00   60
 15  \w    -51.00 -21.00   0.50    1.00    --  -91.75  45.00  30.00   60
 16  \w     63.00  99.00   0.50    1.00    --  113.25 -94.00-150.00   72
 17  \w    122.00 147.00   0.50    1.00    --  113.25  45.00 -30.00   50
 18  \w    102.00 138.00   0.50    1.00    --  113.25 -86.00 127.30   72
 19  \w     42.00  69.00   0.50    1.00    --  113.25 -61.00  60.00   54
 20  \w     42.00  68.00   0.50    1.00    --  113.25 -61.00 -60.00   52
 21  \w     44.00  70.00   0.50    1.00    --  113.25 -61.00   0.00   52
 22  \w    135.00 173.00   0.50    1.00    --  113.25  15.00-180.00   76
 23  \w     79.00 104.00   0.50    1.00    --  113.25 -94.00  30.00   50
 24  \w    109.00 177.00   0.50    1.00    --  113.25  45.00 -60.00  136
 25  \w    122.00 148.00   0.50    1.00    --  113.25 125.00-180.00   52
 26  \w    148.00 176.00   0.50    1.00    --  113.25  15.00  90.00   56
 27  \w     62.00 106.00   0.50    1.00    --  113.25 -94.00 -90.00   88
 28  \w     51.00  77.00   0.50    1.00    --  113.25 -86.00 127.30   52
 29  \w     58.00  84.00   0.50    1.00    --  113.25 -77.00  60.00   52
 30  \w     92.00 118.00   0.50    1.00    --  113.25  77.00 -90.00   52
 31  \w    133.00 159.00   0.50    1.00    --  113.25  30.00  90.00   52
 32  \w     43.00  84.00   0.50    1.00    --  113.25 -94.00 120.00   82
 33  \w     42.00  67.00   0.50    1.00    --  113.25 -61.00-180.00   50
 34  \w    108.00 159.00   0.50    1.00    --  113.25  45.00-180.00  102
 35  \w    140.00 165.00   0.50    1.00    --  113.25  45.00-120.00   50
 36  \w    115.00 157.00   0.50    1.00    --  113.25  45.00 120.00   84
 37  \w    107.00 133.00   0.50    1.00    --  113.25  15.00-180.00   52
 38  \w    129.00 178.00   0.50    1.00    --  113.25  45.00  30.00   98
 39  \w     71.00  96.00   0.50    1.00    --  113.25 -94.00-180.00   50
 40  \w     79.00 105.00   0.50    1.00    --  113.25 -94.00   0.00   52
 41  \w     50.00 100.00   0.50    1.00    --  113.25 -77.00 -60.00  100
 42  \w    128.00 154.00   0.50    1.00    --  113.25 125.00  30.00   52
 43  \w    105.00 138.00   0.50    1.00    --  113.25  30.00  30.00   66
 44  \w    148.00 176.00   0.50    1.00    --  113.25  30.00  30.00   56
 45  \w    147.00 172.00   0.50    1.00    --  113.25 125.00 -60.00   50
 46  \w     47.00  93.00   0.50    1.00    --  113.25 -77.00-120.00   92
 47  \w     45.00  80.00   0.50    1.00    --  113.25 -77.00 150.00   70
 48  \w     64.00 103.00   0.50    1.00    --  113.25 -94.00-120.00   78
 49  \w     57.00 111.00   0.50    1.00    --  113.25-125.00-180.00  108
 50  \w     45.00  84.00   0.50    1.00    --  113.25 -94.00  60.00   78
 51  \w     57.00  91.00   0.50    1.00    --  113.25 -77.00 -90.00   68
 52  \w     73.00 102.00   0.50    1.00    --  113.25 -77.00   0.00   58
 53  \w     97.00 122.00   0.50    1.00    --  113.25 125.00 -60.00   50
 54  \w     43.00  69.00   0.50    1.00    --  113.25 -94.00 -30.00   52
 55  \w     76.00 101.00   0.50    1.00    --  113.25 -94.00 -30.00   50
 56  \w    103.00 128.00   0.50    1.00    --  113.25  45.00-150.00   50
 57  \w     42.00  74.00   0.50    1.00    --  113.25 -94.00   0.00   64
 58  \w    104.00 164.00   0.50    1.00    --  113.25  45.00 -90.00  120
 59  \w    105.00 131.00   0.50    1.00    --  113.25  15.00 150.00   52
 60  \w    142.00 167.00   0.50    1.00    --  113.25 125.00 120.00   50
 61  \w     99.00 131.00   0.50    1.00    --  113.25  77.00-150.00   64
 62  \w    146.00 178.00   0.50    1.00    --  113.25  77.00-150.00   64
 63  \w    106.00 140.00   0.50    1.00    --  113.25 -88.00 -86.02   68
 64  \w     62.00  88.00   0.50    1.00    --  113.25 -88.00  65.00   52
 65  \w     67.00  92.00   0.50    1.00    --  113.25 -88.00  65.00   50
 66  \w     42.00  67.00   0.50    1.00    --  113.25 -61.00  90.00   50
 67  \w     76.00 102.00   0.50    1.00    --  113.25 -94.00 -60.00   52
 68  \w     46.00  72.00   0.50    1.00    --  113.25 -94.00 -30.00   52
 69  \w     81.00 106.00   0.50    1.00    --  113.25 -94.00 150.00   50
 70  \w    109.00 146.00   0.50    1.00    --  113.25  30.00  60.00   74
;
_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      0.0039303000
_diffrn_orient_matrix_UB_12      -0.1455632000
_diffrn_orient_matrix_UB_13      0.0748358000
_diffrn_orient_matrix_UB_21      0.1687082000
_diffrn_orient_matrix_UB_22      -0.0833659000
_diffrn_orient_matrix_UB_23      -0.1105005000
_diffrn_orient_matrix_UB_31      0.2363783000
_diffrn_orient_matrix_UB_32      0.0133514000
_diffrn_orient_matrix_UB_33      0.0606579000
_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  0.0306
_diffrn_reflns_av_unetI/netI     0.0364
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.980
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            8131
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.980
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.941
_diffrn_reflns_theta_min         4.207
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.656
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.47851
_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    1.215
_exptl_crystal_description       irregular
_exptl_crystal_F_000             208
_exptl_crystal_recrystallization_method 'crystallized from ethylacetate'
_exptl_crystal_size_max          0.258
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.097
_refine_diff_density_max         0.167
_refine_diff_density_min         -0.197
_refine_diff_density_rms         0.042
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.059
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     132
_refine_ls_number_reflns         2263
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.059
_refine_ls_R_factor_all          0.0475
_refine_ls_R_factor_gt           0.0438
_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^)+(0.0847P)^2^+0.0291P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1312
_refine_ls_wR_factor_ref         0.1360
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1952
_reflns_number_total             2263
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_822_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '383-385' was changed to
'384.0(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               7250984
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C8H11N3O
_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)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5)
2.c Idealised Me refined as rotating group:
 C14(H14A,H14B,H14C)
;
_shelx_res_checksum              66751
_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 2.124
_oxdiff_exptl_absorpt_empirical_full_min 0.630