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_7250988
_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         'C9 H12 Cl N3 O'
_chemical_formula_sum            'C9 H12 Cl N3 O'
_chemical_formula_weight         213.67
_chemical_melting_point          375.0(10)
_chemical_name_systematic        N-(5-chloropyrimidin-2-yl)pentanamide
_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     dual
_audit_creation_date             2024-09-22
_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                 99.8219(9)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   8.51521(9)
_cell_length_b                   26.9519(2)
_cell_length_c                   9.59636(7)
_cell_measurement_reflns_used    14939
_cell_measurement_temperature    240.00(10)
_cell_measurement_theta_max      78.7290
_cell_measurement_theta_min      4.9510
_cell_volume                     2170.09(3)
_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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      240.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_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   -100.00 -67.00   0.50    0.50    --  -49.79-143.00 121.00   66
  2  \w    -85.00 -17.00   0.50    0.50    --  -49.79 127.00   6.00  136
  3  \w   -110.00 -82.00   0.50    0.50    --  -49.79-127.00 -68.00   56
  4  \w     57.00  82.00   0.50    0.50    --   49.79-127.00 -68.00   50
  5  \w     75.00 102.00   0.50    0.50    --   49.79-143.00 121.00   54
  6  \w    -78.00 -53.00   0.50    4.00    --  -90.00 127.00   6.00   50
  7  \w    -85.00 -60.00   0.50    4.00    --  -90.00 143.00 176.00   50
  8  \w     69.00 125.00   0.50    4.00    --  111.50-143.00 121.00  112
  9  \w    103.00 128.00   0.50    4.00    --  111.50 143.00 176.00   50
 10  \w     85.00 113.00   0.50    4.00    --  111.50-127.00 -68.00   56
 11  \w     51.00  77.00   0.50    4.00    --  111.50-127.00 -68.00   52
 12  \w    -26.00  18.00   0.50    0.50    --  -49.79  19.00 -90.00   88
 13  \w    -17.00  20.00   0.50    0.50    --  -49.79  19.00 -60.00   74
 14  \w    -26.00  24.00   0.50    0.50    --  -49.79  19.00-150.00  100
 15  \w   -140.00-115.00   0.50    4.00    --  -90.00-127.00 -68.00   50
 16  \w    -47.00 -18.00   0.50    4.00    --  -90.00  45.00-120.00   58
 17  \w     41.00  68.00   0.50    4.00    --  111.50 -61.00  60.00   54
 18  \w     71.00  97.00   0.50    4.00    --  111.50-125.00   0.00   52
 19  \w     42.00  68.00   0.50    4.00    --  111.50 -77.00  90.00   52
 20  \w     83.00 111.00   0.50    4.00    --  111.50-125.00 -30.00   56
 21  \w     44.00  70.00   0.50    4.00    --  111.50-125.00 -30.00   52
 22  \w     71.00 106.00   0.50    4.00    --  111.50-125.00 120.00   70
 23  \w     75.00 101.00   0.50    4.00    --  111.50 -94.00  90.00   52
 24  \w    120.00 162.00   0.50    4.00    --  111.50 125.00  30.00   84
 25  \w    103.00 155.00   0.50    4.00    --  111.50  45.00 120.00  104
 26  \w    152.00 178.00   0.50    4.00    --  111.50  30.00   0.00   52
 27  \w    105.00 178.00   0.50    4.00    --  111.50  30.00  30.00  146
 28  \w     82.00 111.00   0.50    4.00    --  111.50-125.00  30.00   58
 29  \w     44.00  69.00   0.50    4.00    --  111.50 -61.00 -30.00   50
 30  \w    112.00 174.00   0.50    4.00    --  111.50  61.00 -60.00  124
 31  \w     42.00  67.00   0.50    4.00    --  111.50 -61.00 -60.00   50
 32  \w     47.00  72.00   0.50    4.00    --  111.50 -77.00 120.00   50
 33  \w     62.00  88.00   0.50    4.00    --  111.50 -94.00-150.00   52
 34  \w     60.00  96.00   0.50    4.00    --  111.50 -77.00 -60.00   72
 35  \w     41.00  66.00   0.50    4.00    --  111.50 -61.00 150.00   50
 36  \w     47.00  72.00   0.50    4.00    --  111.50-125.00 -60.00   50
 37  \w     79.00 111.00   0.50    4.00    --  111.50-125.00 -60.00   64
 38  \w     54.00 103.00   0.50    4.00    --  111.50 -77.00   0.00   98
 39  \w     77.00 103.00   0.50    4.00    --  111.50 -77.00  60.00   52
 40  \w     43.00  79.00   0.50    4.00    --  111.50-125.00 -90.00   72
 41  \w     85.00 134.00   0.50    4.00    --  111.50 -82.00-105.83   98
 42  \w     48.00  77.00   0.50    4.00    --  111.50-125.00  30.00   58
 43  \w    152.00 178.00   0.50    4.00    --  111.50  15.00 -30.00   52
 44  \w    107.00 133.00   0.50    4.00    --  111.50  15.00 -30.00   52
 45  \w     55.00  85.00   0.50    4.00    --  111.50 -94.00 -30.00   60
 46  \w    140.00 176.00   0.50    4.00    --  111.50  30.00  90.00   72
 47  \w    103.00 143.00   0.50    4.00    --  111.50  45.00 -60.00   80
 48  \w     69.00 105.00   0.50    4.00    --  111.50 -94.00-120.00   72
 49  \w     75.00 101.00   0.50    4.00    --  111.50 -94.00 -90.00   52
 50  \w     44.00  75.00   0.50    4.00    --  111.50 -94.00 -60.00   62
 51  \w     80.00 105.00   0.50    4.00    --  111.50 -94.00 -60.00   50
 52  \w     43.00  76.00   0.50    4.00    --  111.50-125.00  90.00   66
 53  \w    106.00 131.00   0.50    4.00    --  111.50  30.00 -60.00   50
 54  \w    123.00 148.00   0.50    4.00    --  111.50  15.00  60.00   50
 55  \w    124.00 153.00   0.50    4.00    --  111.50  77.00   0.00   58
 56  \w    112.00 147.00   0.50    4.00    --  111.50  30.00   0.00   70
;
_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      0.0922250000
_diffrn_orient_matrix_UB_12      0.0488860000
_diffrn_orient_matrix_UB_13      -0.0065572000
_diffrn_orient_matrix_UB_21      0.1562658000
_diffrn_orient_matrix_UB_22      -0.0294320000
_diffrn_orient_matrix_UB_23      0.0073506000
_diffrn_orient_matrix_UB_31      -0.0280239000
_diffrn_orient_matrix_UB_32      -0.0032955000
_diffrn_orient_matrix_UB_33      -0.1626390000
_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  0.0274
_diffrn_reflns_av_unetI/netI     0.0218
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       33
_diffrn_reflns_limit_k_min       -34
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -12
_diffrn_reflns_number            27544
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.955
_diffrn_reflns_theta_min         3.280
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.905
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.85444
_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    1.308
_exptl_crystal_description       block
_exptl_crystal_F_000             896
_exptl_crystal_recrystallization_method 'crystallized from ethylacetate'
_exptl_crystal_size_max          0.172
_exptl_crystal_size_mid          0.102
_exptl_crystal_size_min          0.097
_refine_diff_density_max         0.199
_refine_diff_density_min         -0.228
_refine_diff_density_rms         0.038
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.047
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     283
_refine_ls_number_reflns         4696
_refine_ls_number_restraints     4
_refine_ls_restrained_S_all      1.053
_refine_ls_R_factor_all          0.0495
_refine_ls_R_factor_gt           0.0466
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0636P)^2^+0.5694P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1302
_refine_ls_wR_factor_ref         0.1325
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4264
_reflns_number_total             4696
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_936
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '374-376' was changed to
'375.0(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               7250988
_shelx_shelxl_version_number     2018/3
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C12C-C11B = C12B-C11B = C13C-C12C = C12B-C13B
 1.51 with sigma of 0.02
3. Others
 Sof(H11C)=Sof(H11D)=Sof(C12C)=Sof(H12C)=Sof(H12D)=Sof(C13C)=Sof(H13D)=
 Sof(H13E)=Sof(H13F)=1-FVAR(1)
 Sof(H11A)=Sof(H11B)=Sof(C12B)=Sof(H12A)=Sof(H12B)=Sof(C13B)=Sof(H13A)=
 Sof(H13B)=Sof(H13C)=FVAR(1)
4.a Secondary CH2 refined with riding coordinates:
 C10A(H10C,H10D), C11A(H11E,H11F), C12A(H12E,H12F), C10B(H10A,H10B), C11B(H11A,
 H11B), C11B(H11C,H11D), C12B(H12A,H12B), C12C(H12C,H12D)
4.b Aromatic/amide H refined with riding coordinates:
 C3A(H3A), C5A(H5A), C3B(H3B), C5B(H5B)
4.c Idealised Me refined as rotating group:
 C13A(H13G,H13H,H13I), C13B(H13A,H13B,H13C), C13C(H13D,H13E,H13F)
;
_shelx_res_checksum              9252
_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 1.249
_oxdiff_exptl_absorpt_empirical_full_min 0.796