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_7250998
_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 H18 Cl N3 O'
_chemical_formula_sum            'C12 H18 Cl N3 O'
_chemical_formula_weight         255.74
_chemical_name_systematic        N-(5-chloropyrimidin-2-yl)octanamide
_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             2024-09-18
_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                98.463(2)
_cell_angle_beta                 97.059(2)
_cell_angle_gamma                100.985(2)
_cell_formula_units_Z            2
_cell_length_a                   4.79170(10)
_cell_length_b                   7.8274(2)
_cell_length_c                   18.7292(4)
_cell_measurement_reflns_used    6160
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.7480
_cell_measurement_theta_min      2.4180
_cell_volume                     673.80(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.133a (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    'SHELXT 2018/2 (Sheldrick, 2018)'
_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 0.997
_diffrn_measured_fraction_theta_max 0.990
_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   -119.00 -94.00   0.50    2.50    --  -48.07-131.00 113.00   50
  2  \w    -84.00 -51.00   0.50    2.50    --  -48.07 131.00-176.00   66
  3  \w   -120.00 -65.00   0.50    2.50    --  -48.07-138.00 -62.00  110
  4  \w    -82.00 -57.00   0.50    2.50    --  -48.07 138.00  -0.00   50
  5  \w     45.00 101.00   0.50    2.50    --   48.07-138.00 -62.00  112
  6  \w     40.00  66.00   0.50    2.50    --   48.07-131.00 113.00   52
  7  \w    -80.00 -55.00   0.50   10.00    --  -91.75 131.00-176.00   50
  8  \w   -116.00 -91.00   0.50   10.00    --  -91.75-131.00 113.00   50
  9  \w    -82.00 -57.00   0.50   10.00    --  -91.75 138.00  -0.00   50
 10  \w     80.00 119.00   0.50   10.00    --  113.25-138.00 -62.00   78
 11  \w     58.00  83.00   0.50   10.00    --  113.25-131.00 113.00   50
 12  \w    110.00 135.00   0.50   10.00    --  113.25 131.00-176.00   50
 13  \w    107.00 133.00   0.50   10.00    --  113.25 138.00  -0.00   52
 14  \w   -116.00 -76.00   0.50    2.50    --  -48.07-125.00 120.00   80
 15  \w    -21.00  26.00   0.50    2.50    --  -48.07  19.00 150.00   94
 16  \w    -26.00  16.00   0.50    2.50    --  -48.07  19.00 120.00   84
 17  \w   -118.00 -35.00   0.50    2.50    --  -48.07 -19.00 -30.00  166
 18  \w   -118.00 -93.00   0.50    2.50    --  -48.07-125.00-180.00   50
 19  \w    -49.00 -22.00   0.50   10.00    --  -91.75  45.00 -30.00   54
 20  \w   -164.00-117.00   0.50   10.00    --  -91.75 -15.00 -30.00   94
 21  \w     46.00  71.00   0.50   10.00    --  113.25-125.00-120.00   50
 22  \w    101.00 134.00   0.50   10.00    --  113.25  30.00 150.00   66
 23  \w    125.00 151.00   0.50   10.00    --  113.25  45.00  90.00   52
 24  \w    123.00 175.00   0.50   10.00    --  113.25  45.00  30.00  104
 25  \w    140.00 166.00   0.50   10.00    --  113.25  30.00 150.00   52
 26  \w    101.00 170.00   0.50   10.00    --  113.25  45.00  60.00  138
 27  \w     46.00  71.00   0.50   10.00    --  113.25 -61.00 -30.00   50
 28  \w     51.00  77.00   0.50   10.00    --  113.25 -77.00  90.00   52
 29  \w     45.00 108.00   0.50   10.00    --  113.25-125.00  60.00  126
 30  \w     42.00  70.00   0.50   10.00    --  113.25 -61.00-120.00   56
 31  \w     96.00 139.00   0.50   10.00    --  113.25 125.00 -30.00   86
 32  \w    145.00 178.00   0.50   10.00    --  113.25 125.00 -30.00   66
 33  \w    117.00 178.00   0.50   10.00    --  113.25  45.00 -30.00  122
 34  \w     59.00 108.00   0.50   10.00    --  113.25-106.00 112.66   98
 35  \w     63.00 104.00   0.50   10.00    --  113.25 -77.00 -90.00   82
 36  \w     55.00  81.00   0.50   10.00    --  113.25 -77.00 -30.00   52
 37  \w     57.00 106.00   0.50   10.00    --  113.25 -94.00 -90.00   98
 38  \w     57.00  83.00   0.50   10.00    --  113.25 -77.00   0.00   52
 39  \w    136.00 161.00   0.50   10.00    --  113.25 125.00  60.00   50
 40  \w    105.00 131.00   0.50   10.00    --  113.25  77.00 -90.00   52
 41  \w    136.00 161.00   0.50   10.00    --  113.25  77.00 -90.00   50
 42  \w     42.00  67.00   0.50   10.00    --  113.25 -61.00-180.00   50
 43  \w     43.00  68.00   0.50   10.00    --  113.25 -77.00 120.00   50
 44  \w     45.00  70.00   0.50   10.00    --  113.25 -94.00  60.00   50
 45  \w     42.00  69.00   0.50   10.00    --  113.25 -61.00-150.00   54
 46  \w     51.00  84.00   0.50   10.00    --  113.25 -94.00   0.00   66
 47  \w    148.00 174.00   0.50   10.00    --  113.25  15.00  60.00   52
 48  \w     66.00 110.00   0.50   10.00    --  113.25-125.00-150.00   88
 49  \w     76.00 102.00   0.50   10.00    --  113.25 -94.00  60.00   52
 50  \w     95.00 178.00   0.50   10.00    --  113.25  77.00  60.00  166
 51  \w     82.00 110.00   0.50   10.00    --  113.25-125.00   0.00   56
 52  \w    123.00 177.00   0.50   10.00    --  113.25  45.00 -60.00  108
 53  \w     43.00  69.00   0.50   10.00    --  113.25 -61.00 -60.00   52
 54  \w     53.00  85.00   0.50   10.00    --  113.25 -77.00 150.00   64
 55  \w     99.00 139.00   0.50   10.00    --  113.25 125.00 120.00   80
 56  \w     43.00  75.00   0.50   10.00    --  113.25 -94.00 120.00   64
 57  \w     90.00 131.00   0.50   10.00    --  113.25 -81.00 -46.96   82
 58  \w     88.00 115.00   0.50   10.00    --  113.25 -85.00-122.63   54
 59  \w     88.00 133.00   0.50   10.00    --  113.25 -88.00  94.54   90
 60  \w     83.00 111.00   0.50   10.00    --  113.25-125.00-120.00   56
 61  \w     80.00 105.00   0.50   10.00    --  113.25 -77.00  30.00   50
 62  \w     61.00  87.00   0.50   10.00    --  113.25-125.00-180.00   52
 63  \w    126.00 172.00   0.50   10.00    --  113.25  45.00 -90.00   92
 64  \w    100.00 126.00   0.50   10.00    --  113.25  61.00-180.00   52
 65  \w    101.00 126.00   0.50   10.00    --  113.25  61.00 150.00   50
 66  \w     42.00  67.00   0.50   10.00    --  113.25 -61.00  90.00   50
 67  \w     57.00  82.00   0.50   10.00    --  113.25  -2.00 100.39   50
 68  \w     45.00  70.00   0.50   10.00    --  113.25 -61.00 120.00   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      0.2088223000
_diffrn_orient_matrix_UB_12      0.0220549000
_diffrn_orient_matrix_UB_13      0.0717733000
_diffrn_orient_matrix_UB_21      0.2461057000
_diffrn_orient_matrix_UB_22      -0.0223636000
_diffrn_orient_matrix_UB_23      -0.0439396000
_diffrn_orient_matrix_UB_31      0.0757842000
_diffrn_orient_matrix_UB_32      0.2011993000
_diffrn_orient_matrix_UB_33      0.0021670000
_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  0.0299
_diffrn_reflns_av_unetI/netI     0.0312
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -7
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            10790
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         80.040
_diffrn_reflns_theta_min         2.414
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.420
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.94135
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.133a (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    1.261
_exptl_crystal_description       needle
_exptl_crystal_F_000             272
_exptl_crystal_recrystallization_method 'crystallized from acetonitrile'
_exptl_crystal_size_max          0.21
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.251
_refine_diff_density_min         -0.263
_refine_diff_density_rms         0.050
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.063
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     159
_refine_ls_number_reflns         2900
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.063
_refine_ls_R_factor_all          0.0408
_refine_ls_R_factor_gt           0.0374
_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^)+(0.0475P)^2^+0.1560P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0989
_refine_ls_wR_factor_ref         0.1010
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2627
_reflns_number_total             2900
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_926_auto
_cod_depositor_comments
'Adding full bibliography for 7250982--7251002.cif.'
_cod_database_code               7250998
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C12H18Cl1N3O
_shelx_estimated_absorpt_t_max   0.953
_shelx_estimated_absorpt_t_min   0.630
_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), C5(H5)
2.c Idealised Me refined as rotating group:
 C16(H16A,H16B,H16C)
;
_shelx_res_checksum              32766
_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 1.299
_oxdiff_exptl_absorpt_empirical_full_min 0.772