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_7251001
_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 H16 Cl N3 O'
_chemical_formula_sum            'C11 H16 Cl N3 O'
_chemical_formula_weight         241.72
_chemical_melting_point          356.5(15)
_chemical_name_systematic        N-(5-chloropyrimidin-2-yl)heptanamide
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_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                90
_cell_angle_beta                 107.3484(18)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   14.1859(2)
_cell_length_b                   4.43507(5)
_cell_length_c                   20.7479(4)
_cell_measurement_reflns_used    7193
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.2760
_cell_measurement_theta_min      3.2630
_cell_volume                     1245.98(4)
_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    'SHELXS  (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 0.992
_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   -122.00 -35.00   0.50    0.60    --  -48.07 -14.00 147.00  174
  2  \w    -22.00  22.00   0.50    0.60    --  -48.07  14.00 -42.00   88
  3  \w     -2.00  23.00   0.50    0.60    --   48.07 -14.00 147.00   50
  4  \w     72.00  99.00   0.50    0.60    --   48.07  14.00 -42.00   54
  5  \w   -146.00-121.00   0.50    2.40    --  -91.75 -14.00 147.00   50
  6  \w     99.00 170.00   0.50    2.40    --  113.25  14.00 -42.00  142
  7  \w   -118.00 -74.00   0.50    0.60    --  -48.07-125.00 150.00   88
  8  \w    -25.00  43.00   0.50    0.60    --   48.07 -38.00  30.00  136
  9  \w     36.00  89.00   0.50    0.60    --   48.07-125.00   0.00  106
 10  \w     42.00  68.00   0.50    2.40    --  113.25 -61.00 150.00   52
 11  \w     80.00 105.00   0.50    2.40    --  113.25 -77.00   0.00   50
 12  \w    104.00 145.00   0.50    2.40    --  113.25  15.00-120.00   82
 13  \w     45.00  71.00   0.50    2.40    --  113.25 -77.00   0.00   52
 14  \w     42.00  72.00   0.50    2.40    --  113.25 -94.00 -60.00   60
 15  \w     78.00 105.00   0.50    2.40    --  113.25 -94.00 -60.00   54
 16  \w    123.00 170.00   0.50    2.40    --  113.25 125.00-150.00   94
 17  \w     49.00  79.00   0.50    2.40    --  113.25-125.00 120.00   60
 18  \w     86.00 111.00   0.50    2.40    --  113.25-125.00 120.00   50
 19  \w     44.00  70.00   0.50    2.40    --  113.25 -94.00   0.00   52
 20  \w     81.00 106.00   0.50    2.40    --  113.25 -94.00   0.00   50
 21  \w     45.00  70.00   0.50    2.40    --  113.25 -61.00 -90.00   50
 22  \w    113.00 177.00   0.50    2.40    --  113.25  45.00 -30.00  128
 23  \w     43.00  70.00   0.50    2.40    --  113.25 -61.00   0.00   54
 24  \w    148.00 178.00   0.50    2.40    --  113.25  15.00-120.00   60
 25  \w    101.00 127.00   0.50    2.40    --  113.25  30.00  60.00   52
 26  \w    131.00 169.00   0.50    2.40    --  113.25  30.00  60.00   76
 27  \w     42.00  67.00   0.50    2.40    --  113.25 -61.00  30.00   50
 28  \w     42.00  67.00   0.50    2.40    --  113.25 -61.00-180.00   50
 29  \w     42.00  79.00   0.50    2.40    --  113.25 -77.00  60.00   74
 30  \w     43.00  73.00   0.50    2.40    --  113.25 -94.00 150.00   60
 31  \w     80.00 106.00   0.50    2.40    --  113.25 -94.00 150.00   52
 32  \w    138.00 175.00   0.50    2.40    --  113.25  30.00 150.00   74
 33  \w    118.00 178.00   0.50    2.40    --  113.25 125.00-120.00  120
 34  \w    106.00 157.00   0.50    2.40    --  113.25  45.00-120.00  102
 35  \w     64.00  90.00   0.50    2.40    --  113.25 -77.00  30.00   52
 36  \w     74.00  99.00   0.50    2.40    --  113.25 -94.00 -30.00   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      0.0961951000
_diffrn_orient_matrix_UB_12      -0.0405141000
_diffrn_orient_matrix_UB_13      0.0583059000
_diffrn_orient_matrix_UB_21      -0.0607372000
_diffrn_orient_matrix_UB_22      -0.0527072000
_diffrn_orient_matrix_UB_23      0.0493757000
_diffrn_orient_matrix_UB_31      -0.0019859000
_diffrn_orient_matrix_UB_32      -0.3409850000
_diffrn_orient_matrix_UB_33      -0.0145333000
_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  0.0270
_diffrn_reflns_av_unetI/netI     0.0291
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.992
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       3
_diffrn_reflns_limit_k_min       -5
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -26
_diffrn_reflns_number            10186
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.725
_diffrn_reflns_theta_min         3.264
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.588
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.87584
_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    1.289
_exptl_crystal_description       plate
_exptl_crystal_F_000             512
_exptl_crystal_recrystallization_method 'crystallized from ethylacetate'
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.07
_exptl_crystal_size_min          0.01
_refine_diff_density_max         0.184
_refine_diff_density_min         -0.177
_refine_diff_density_rms         0.038
_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         2692
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.052
_refine_ls_R_factor_all          0.0350
_refine_ls_R_factor_gt           0.0322
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0488P)^2^+0.2202P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0891
_refine_ls_wR_factor_ref         0.0918
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2455
_reflns_number_total             2692
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_928_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '355-358' was changed to
'356.5(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               7251001
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C11H16Cl1N3O
_shelx_estimated_absorpt_t_max   0.975
_shelx_estimated_absorpt_t_min   0.564
_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), C5(H5)
2.c Idealised Me refined as rotating group:
 C15(H15A,H15B,H15C)
;
_shelx_res_checksum              96112
_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 1.296
_oxdiff_exptl_absorpt_empirical_full_min 0.639