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_7250990
_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         'C7 H9 N3 O'
_chemical_formula_sum            'C7 H9 N3 O'
_chemical_formula_weight         151.17
_chemical_melting_point          400.0(10)
_chemical_name_systematic        N-(pyrimidin-2-yl)propionamide
_space_group_crystal_system      monoclinic
_space_group_IT_number           12
_space_group_name_Hall           '-I 2y'
_space_group_name_H-M_alt        'I 1 2/m 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2023-12-16
_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                 98.060(16)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.4300(16)
_cell_length_b                   6.8202(14)
_cell_length_c                   12.068(2)
_cell_measurement_reflns_used    2050
_cell_measurement_temperature    294.20(10)
_cell_measurement_theta_max      71.4440
_cell_measurement_theta_min      5.4510
_cell_volume                     768.5(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    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      air
_diffrn_ambient_temperature      294.20(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.987
_diffrn_measured_fraction_theta_max 0.987
_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    -74.00   6.00   0.50    0.70    --  -48.94 103.00-133.00  160
  2  \w     15.00  70.00   0.50    0.70    --   48.94-103.00 125.00  110
  3  \w    -81.00 -50.00   0.50    3.00    --  -90.00 103.00-133.00   62
  4  \w   -156.00 -84.00   0.50    3.00    --  -90.00-103.00 125.00  144
  5  \w    110.00 168.00   0.50    3.00    --  111.50 103.00-133.00  116
  6  \w     55.00 107.00   0.50    3.00    --  111.50-103.00 125.00  104
  7  \w   -116.00 -79.00   0.50    0.70    --  -48.94-125.00  30.00   74
  8  \w   -117.00 -85.00   0.50    0.70    --  -48.94-125.00-180.00   64
  9  \w   -109.00 -38.00   0.50    0.70    --  -48.94 -77.00 120.00  142
 10  \w   -116.00 -78.00   0.50    0.70    --  -48.94-125.00 -60.00   76
 11  \w    -20.00  16.00   0.50    0.70    --   48.94 -19.00 120.00   72
 12  \w   -160.00 -85.00   0.50    3.00    --  -90.00 -30.00-180.00  150
 13  \w   -161.00-103.00   0.50    3.00    --  -90.00 -45.00 150.00  116
 14  \w     96.00 173.00   0.50    3.00    --  111.50 125.00-180.00  154
 15  \w     57.00 105.00   0.50    3.00    --  111.50 -94.00 150.00   96
 16  \w     43.00 104.00   0.50    3.00    --  111.50 -77.00 -90.00  122
 17  \w    108.00 147.00   0.50    3.00    --  111.50  45.00-180.00   78
 18  \w     97.00 165.00   0.50    3.00    --  111.50 125.00 -90.00  136
 19  \w     56.00  94.00   0.50    3.00    --  111.50 -94.00-150.00   76
 20  \w     68.00 100.00   0.50    3.00    --  111.50 -94.00-180.00   64
 21  \w     64.00  98.00   0.50    3.00    --  111.50 -77.00-150.00   68
 22  \w     49.00  98.00   0.50    3.00    --  111.50 -94.00 -90.00   98
 23  \w     41.00  70.00   0.50    3.00    --  111.50 -61.00-120.00   58
 24  \w    113.00 171.00   0.50    3.00    --  111.50  30.00  30.00  116
 25  \w     43.00  85.00   0.50    3.00    --  111.50 -77.00 -60.00   84
 26  \w     52.00 109.00   0.50    3.00    --  111.50-125.00-150.00  114
 27  \w    105.00 152.00   0.50    3.00    --  111.50  15.00  30.00   94
 28  \w   -129.00-103.00   0.50    3.00    --  -90.00 -93.00  22.00   52
 29  \w   -110.00 -84.00   0.50    0.70    --  -49.69 -57.00   0.00   52
 30  \w    -86.00 -48.00   0.50    0.70    --  -49.69 -19.00-150.00   76
 31  \w   -122.00 -86.00   0.50    0.70    --  -49.69 -19.00   0.00   72
 32  \w    -66.00 -40.00   0.50    0.70    --  -49.69 -57.00   0.00   52
 33  \w    -67.00 -42.00   0.50    0.70    --  -49.69 -19.00   0.00   50
 34  \w     86.00 116.00   0.50    0.70    --   49.69  77.00  90.00   60
 35  \w     31.00  57.00   0.50    0.70    --   49.69  77.00 -30.00   52
 36  \w     31.00  57.00   0.50    0.70    --   49.69  77.00  90.00   52
 37  \w     31.00  57.00   0.50    0.70    --   49.69  77.00 -60.00   52
 38  \w     61.00  89.00   0.50    0.70    --   49.69  77.00 -90.00   56
 39  \w     30.00  84.00   0.50    0.70    --   49.69  77.00-150.00  108
 40  \w     30.00  74.00   0.50    0.70    --   49.69  77.00 150.00   88
 41  \w     37.00  67.00   0.50    0.70    --   49.69  57.00   0.00   60
 42  \w     29.00  55.00   0.50    0.70    --   49.69  77.00 120.00   52
 43  \w     29.00  55.00   0.50    0.70    --   49.69  77.00  30.00   52
 44  \w     49.00  84.00   0.50    0.70    --   49.69  38.00 120.00   70
 45  \w     29.00  59.00   0.50    0.70    --   49.69  77.00 -90.00   60
 46  \w    -61.00 -35.00   0.50    3.00    --  -90.00  57.00-150.00   52
 47  \w   -139.00-113.00   0.50    3.00    --  -90.00 -59.00  88.57   52
 48  \w    -66.00 -41.00   0.50    3.00    --  -90.00  57.00-180.00   50
 49  \w   -125.00 -75.00   0.50    3.00    --  -90.00 -62.00 -71.67  100
 50  \w   -123.00 -98.00   0.50    3.00    --  -90.00 -47.00 -49.83   50
 51  \w   -103.00 -70.00   0.50    3.00    --  -90.00 -77.00  60.00   66
 52  \w   -118.00 -80.00   0.50    3.00    --  -90.00 -53.00 -14.88   76
 53  \w   -139.00-108.00   0.50    3.00    --  -90.00 -71.00  68.56   62
 54  \w    -99.00 -74.00   0.50    3.00    --  -90.00 -71.00  68.56   50
 55  \w   -149.00-123.00   0.50    3.00    --  -90.00 -77.00 -90.00   52
 56  \w   -156.00-127.00   0.50    3.00    --  -90.00 -67.00 175.57   58
 57  \w   -131.00 -70.00   0.50    3.00    --  -90.00 -76.00 -39.17  122
 58  \w   -113.00 -69.00   0.50    3.00    --  -90.00 -77.00 -90.00   88
 59  \w   -107.00 -81.00   0.50    3.00    --  -90.00 -48.00  94.36   52
 60  \w    -94.00 -69.00   0.50    3.00    --  -90.00 -77.00   0.00   50
 61  \w   -100.00 -75.00   0.50    3.00    --  -90.00 -62.00-166.60   50
 62  \w   -115.00 -76.00   0.50    3.00    --  -90.00 -59.00-124.78   78
 63  \w   -155.00-129.00   0.50    3.00    --  -90.00 -62.00-166.60   52
 64  \w    -97.00 -71.00   0.50    3.00    --  -90.00 -77.00 120.00   52
 65  \w   -112.00 -81.00   0.50    3.00    --  -90.00 -52.00 137.13   62
 66  \w   -157.00-131.00   0.50    3.00    --  -90.00 -77.00  60.00   52
 67  \w    -98.00 -73.00   0.50    3.00    --  -90.00 -67.00 175.57   50
 68  \w   -105.00 -79.00   0.50    3.00    --  -90.00 -57.00 120.00   52
 69  \w    -96.00 -71.00   0.50    3.00    --  -90.00 -77.00-120.00   50
 70  \w   -160.00-124.00   0.50    3.00    --  -90.00 -52.00 137.13   72
 71  \w    -95.00 -70.00   0.50    3.00    --  -90.00 -76.00  85.52   50
 72  \w   -102.00 -74.00   0.50    3.00    --  -90.00 -74.00 -15.67   56
 73  \w    -96.00 -71.00   0.50    3.00    --  -90.00 -74.00 148.79   50
 74  \w    -95.00 -70.00   0.50    3.00    --  -90.00 -75.00 -68.91   50
 75  \w   -157.00-144.50   0.50    3.00    --  -90.00 -76.00  85.52   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      -0.0049277000
_diffrn_orient_matrix_UB_12      -0.2165696000
_diffrn_orient_matrix_UB_13      -0.0364243000
_diffrn_orient_matrix_UB_21      0.1583553000
_diffrn_orient_matrix_UB_22      0.0113105000
_diffrn_orient_matrix_UB_23      -0.0182484000
_diffrn_orient_matrix_UB_31      0.0466051000
_diffrn_orient_matrix_UB_32      -0.0626051000
_diffrn_orient_matrix_UB_33      0.1223269000
_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  0.0599
_diffrn_reflns_av_unetI/netI     0.0280
_diffrn_reflns_Laue_measured_fraction_full 0.987
_diffrn_reflns_Laue_measured_fraction_max 0.987
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            4507
_diffrn_reflns_point_group_measured_fraction_full 0.987
_diffrn_reflns_point_group_measured_fraction_max 0.987
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.219
_diffrn_reflns_theta_min         5.589
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.759
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.640
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.100a (Rigaku Oxford Diffraction, 2023)
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    1.307
_exptl_crystal_description       irregular
_exptl_crystal_F_000             320
_exptl_crystal_recrystallization_method 'crystallized from ethylacetate'
_exptl_crystal_size_max          0.187
_exptl_crystal_size_mid          0.132
_exptl_crystal_size_min          0.078
_refine_diff_density_max         0.349
_refine_diff_density_min         -0.201
_refine_diff_density_rms         0.065
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.045
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     71
_refine_ls_number_reflns         756
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.045
_refine_ls_R_factor_all          0.0775
_refine_ls_R_factor_gt           0.0615
_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^)+(0.1328P)^2^+0.1580P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1712
_refine_ls_wR_factor_ref         0.1980
_reflns_Friedel_coverage         0.000
_reflns_number_gt                563
_reflns_number_total             756
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_823a_autor
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '399-401' was changed to
'400.0(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               7250990
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C7H9N3O1
_shelx_estimated_absorpt_t_max   0.943
_shelx_estimated_absorpt_t_min   0.871
_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. Others
 Fixed Sof: H10A(0.5) H10B(0.5) H11A(0.5) H11B(0.5) H11C(0.5)
3.a Secondary CH2 refined with riding coordinates:
 C10(H10A,H10B)
3.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5)
3.c Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C)
;
_shelx_res_checksum              77882
_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 7.587
_oxdiff_exptl_absorpt_empirical_full_min 0.436