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_7250996
_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         'C8 H10 Cl N3 O'
_chemical_formula_sum            'C8 H10 Cl N3 O'
_chemical_formula_weight         199.64
_chemical_melting_point          378.0(10)
_chemical_name_systematic        N-(5-chloropyrimidin-2-yl)butyramide
_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     dual
_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                89.4260(10)
_cell_angle_beta                 87.8120(10)
_cell_angle_gamma                77.4270(10)
_cell_formula_units_Z            2
_cell_length_a                   4.48170(10)
_cell_length_b                   8.33370(10)
_cell_length_c                   12.9705(2)
_cell_measurement_reflns_used    8781
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.7310
_cell_measurement_theta_min      3.4040
_cell_volume                     472.475(14)
_computing_cell_refinement       'CrysAlisPro 1.171.43.133a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.133a 64-bit (release 07-08-2024))'
_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  (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 1.000
_diffrn_measured_fraction_theta_max 0.988
_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    -96.00 -20.00   0.50    0.20    --  -48.07 138.00   1.00  152
  2  \w    -90.00 -16.00   0.50    0.20    --  -48.07 131.00-174.00  148
  3  \w   -120.00 -65.00   0.50    0.20    --  -48.07-138.00 -60.00  110
  4  \w   -119.00 -70.00   0.50    0.20    --  -48.07-131.00 115.00   98
  5  \w     42.00 103.00   0.50    0.20    --   48.07-138.00 -60.00  122
  6  \w     38.00  98.00   0.50    0.20    --   48.07-131.00 115.00  120
  7  \w   -158.00 -65.00   0.50    1.00    --  -91.75-138.00 -60.00  186
  8  \w   -162.00 -70.00   0.50    1.00    --  -91.75-131.00 115.00  184
  9  \w    -96.00 -20.00   0.50    1.00    --  -91.75 138.00   1.00  152
 10  \w     43.00 116.00   0.50    1.00    --  113.25-131.00 115.00  146
 11  \w     87.00 175.00   0.50    1.00    --  113.25 138.00   1.00  176
 12  \w     42.00 121.00   0.50    1.00    --  113.25-138.00 -60.00  158
 13  \w     91.00 178.00   0.50    1.00    --  113.25 131.00-174.00  174
 14  \w    -26.00  27.00   0.50    0.20    --  -48.07  19.00  30.00  106
 15  \w   -118.00 -73.00   0.50    0.20    --  -48.07-125.00 150.00   90
 16  \w   -118.00 -73.00   0.50    0.20    --  -48.07-125.00 -90.00   90
 17  \w     36.00 121.00   0.50    0.20    --   48.07  38.00-120.00  170
 18  \w    -26.00  26.00   0.50    0.20    --   48.07 -19.00-180.00  104
 19  \w     36.00 121.00   0.50    0.20    --   48.07  38.00-120.00  170
 20  \w   -163.00 -75.00   0.50    1.00    --  -91.75 -61.00   0.00  176
 21  \w     42.00 105.00   0.50    1.00    --  113.25 -77.00 -30.00  126
 22  \w     44.00 111.00   0.50    1.00    --  113.25-125.00-180.00  134
 23  \w     97.00 178.00   0.50    1.00    --  113.25  61.00  90.00  162
 24  \w     42.00  71.00   0.50    1.00    --  113.25 -61.00-120.00   58
 25  \w     44.00 111.00   0.50    1.00    --  113.25-125.00 -30.00  134
 26  \w     42.00 105.00   0.50    1.00    --  113.25 -77.00 150.00  126
 27  \w     42.00 105.00   0.50    1.00    --  113.25 -77.00   0.00  126
 28  \w     95.00 178.00   0.50    1.00    --  113.25 125.00-150.00  166
 29  \w     97.00 178.00   0.50    1.00    --  113.25  61.00 120.00  162
 30  \w    101.00 178.00   0.50    1.00    --  113.25  45.00-180.00  154
 31  \w     42.00  71.00   0.50    1.00    --  113.25 -61.00-150.00   58
 32  \w    101.00 178.00   0.50    1.00    --  113.25  30.00  30.00  154
 33  \w    101.00 178.00   0.50    1.00    --  113.25  30.00  30.00  154
 34  \w    101.00 178.00   0.50    1.00    --  113.25  45.00-120.00  154
 35  \w     42.00  71.00   0.50    1.00    --  113.25 -61.00  90.00   58
 36  \w     97.00 178.00   0.50    1.00    --  113.25  61.00-150.00  162
 37  \w     42.00  71.00   0.50    1.00    --  113.25 -61.00 -90.00   58
 38  \w    101.00 178.00   0.50    1.00    --  113.25  45.00  60.00  154
 39  \w     42.00 106.00   0.50    1.00    --  113.25 -94.00 120.00  128
 40  \w     67.00  93.00   0.50    1.00    --  113.25 -86.00-107.17   52
 41  \w    107.00 137.00   0.50    1.00    --  113.25 -86.00-107.17   60
 42  \w    105.00 177.00   0.50    1.00    --  113.25  45.00 -90.00  144
 43  \w    104.00 148.00   0.50    1.00    --  113.25  61.00 150.00   88
 44  \w     73.00 110.00   0.50    1.00    --  113.25-125.00-120.00   74
 45  \w     47.00  72.00   0.50    1.00    --  113.25-125.00-120.00   50
 46  \w     77.00 102.00   0.50    1.00    --  113.25 -94.00 150.00   50
 47  \w     50.00  96.00   0.50    1.00    --  113.25 -94.00 -30.00   92
 48  \w     42.00  71.00   0.50    1.00    --  113.25 -61.00-180.00   58
 49  \w     44.00  85.00   0.50    1.00    --  113.25 -77.00  30.00   82
 50  \w     66.00 105.00   0.50    1.00    --  113.25 -94.00 -60.00   78
 51  \w    118.00 144.00   0.50    1.00    --  113.25  45.00 -30.00   52
 52  \w     70.00  95.00   0.50    1.00    --  113.25 -77.00  60.00   50
 53  \w     44.00  70.00   0.50    1.00    --  113.25 -77.00  90.00   52
 54  \w     48.00  74.00   0.50    1.00    --  113.25 -94.00  30.00   52
 55  \w     70.00  96.00   0.50    1.00    --  113.25 -94.00  60.00   52
 56  \w     42.00  70.00   0.50    1.00    --  113.25 -61.00 150.00   56
 57  \w    123.00 149.00   0.50    1.00    --  113.25  15.00 -30.00   52
 58  \w    146.00 175.00   0.50    1.00    --  113.25  77.00 150.00   58
 59  \w    113.00 139.00   0.50    1.00    --  113.25  61.00  90.00   52
;
_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      0.0933112000
_diffrn_orient_matrix_UB_12      0.0604390000
_diffrn_orient_matrix_UB_13      0.1033441000
_diffrn_orient_matrix_UB_21      0.1763776000
_diffrn_orient_matrix_UB_22      0.1140386000
_diffrn_orient_matrix_UB_23      -0.0586479000
_diffrn_orient_matrix_UB_31      -0.2905059000
_diffrn_orient_matrix_UB_32      0.1386208000
_diffrn_orient_matrix_UB_33      0.0029057000
_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  0.0263
_diffrn_reflns_av_unetI/netI     0.0185
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.988
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -5
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            10560
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.932
_diffrn_reflns_theta_min         3.410
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.297
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.454
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.133a (Rigaku Oxford Diffraction, 2024)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
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    1.403
_exptl_crystal_description       plate
_exptl_crystal_F_000             208
_exptl_crystal_recrystallization_method 'crystallized from chloroform'
_exptl_crystal_size_max          0.235
_exptl_crystal_size_mid          0.056
_exptl_crystal_size_min          0.031
_refine_diff_density_max         0.314
_refine_diff_density_min         -0.235
_refine_diff_density_rms         0.061
_refine_ls_extinction_coef       0.0186(18)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.103
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     124
_refine_ls_number_reflns         2039
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.103
_refine_ls_R_factor_all          0.0306
_refine_ls_R_factor_gt           0.0301
_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^)+(0.0471P)^2^+0.0933P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0817
_refine_ls_wR_factor_ref         0.0821
_reflns_Friedel_coverage         0.000
_reflns_number_gt                1983
_reflns_number_total             2039
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_933
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '377-379' was changed to
'378.0(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               7250996
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C8HH10Cl1N3O1
_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)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5)
2.c Idealised Me refined as rotating group:
 C12(H12A,H12B,H12C)
;
_shelx_res_checksum              18472
_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 1.219
_oxdiff_exptl_absorpt_empirical_full_min 0.812