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_7251002
_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         'C10 H14 Br N3 O'
_chemical_formula_sum            'C10 H14 Br N3 O'
_chemical_formula_weight         272.15
_chemical_melting_point          379.0(10)
_chemical_name_systematic        N-(5-bromopyrimidin-2-yl)hexanamide
_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             2024-02-23
_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                 93.5077(7)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   26.6198(2)
_cell_length_b                   10.98094(8)
_cell_length_c                   8.05204(5)
_cell_measurement_reflns_used    17704
_cell_measurement_temperature    210.00(10)
_cell_measurement_theta_max      79.7830
_cell_measurement_theta_min      3.3130
_cell_volume                     2349.29(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.105a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.105a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.105a (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 0.988
_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   -120.00 -95.00   0.50    0.80    --  -49.82-129.00 168.00   50
  2  \w    -88.00 -15.00   0.50    0.80    --  -49.82 129.00-118.00  146
  3  \w    -95.00 -63.00   0.50    0.80    --  -49.82-141.00  -3.00   64
  4  \w     50.00  75.00   0.50    0.80    --   49.82-141.00  -3.00   50
  5  \w     59.00  84.00   0.50    0.80    --   49.82-129.00 168.00   50
  6  \w   -140.00-115.00   0.50    3.20    --  -90.00-129.00 168.00   50
  7  \w    -84.00 -59.00   0.50    3.20    --  -90.00 141.00  54.00   50
  8  \w     46.00 114.00   0.50    3.20    --  111.50-129.00 168.00  136
  9  \w    111.00 136.00   0.50    3.20    --  111.50 129.00-118.00   50
 10  \w     88.00 122.00   0.50    3.20    --  111.50-141.00  -3.00   68
 11  \w    118.00 144.00   0.50    3.20    --  111.50 141.00  54.00   52
 12  \w    -25.00  13.00   0.50    0.80    --  -49.82  19.00 150.00   76
 13  \w    -25.00   9.00   0.50    0.80    --  -49.82  19.00 -60.00   68
 14  \w    -23.00  21.00   0.50    0.80    --  -49.82  19.00-180.00   88
 15  \w    -21.00  24.00   0.50    0.80    --   49.82 -19.00 150.00   90
 16  \w    -51.00 -26.00   0.50    3.20    --  -90.00  45.00 120.00   50
 17  \w     76.00 111.00   0.50    3.20    --  111.50-125.00  30.00   70
 18  \w    110.00 135.00   0.50    3.20    --  111.50  61.00  60.00   50
 19  \w    148.00 178.00   0.50    3.20    --  111.50  15.00-120.00   60
 20  \w     86.00 111.00   0.50    3.20    --  111.50-125.00   0.00   50
 21  \w     71.00 107.00   0.50    3.20    --  111.50-125.00 120.00   72
 22  \w     42.00  70.00   0.50    3.20    --  111.50 -61.00-120.00   56
 23  \w     47.00 103.00   0.50    3.20    --  111.50 -77.00   0.00  112
 24  \w    125.00 151.00   0.50    3.20    --  111.50  15.00 -90.00   52
 25  \w    108.00 133.00   0.50    3.20    --  111.50  15.00  90.00   50
 26  \w    120.00 146.00   0.50    3.20    --  111.50  15.00-120.00   52
 27  \w     66.00  92.00   0.50    3.20    --  111.50 -94.00   0.00   52
 28  \w     78.00 103.00   0.50    3.20    --  111.50 -77.00  60.00   50
 29  \w     43.00  69.00   0.50    3.20    --  111.50 -61.00 150.00   52
 30  \w    139.00 164.00   0.50    3.20    --  111.50 125.00  30.00   50
 31  \w     54.00 102.00   0.50    3.20    --  111.50-125.00-120.00   96
 32  \w     82.00 108.00   0.50    3.20    --  111.50-125.00-180.00   52
 33  \w     46.00  96.00   0.50    3.20    --  111.50 -77.00 -60.00  100
 34  \w     41.00  66.00   0.50    3.20    --  111.50 -61.00 -30.00   50
 35  \w     45.00  72.00   0.50    3.20    --  111.50-125.00-180.00   54
 36  \w     44.00  69.00   0.50    3.20    --  111.50 -94.00 150.00   50
 37  \w     73.00  98.00   0.50    3.20    --  111.50 -94.00 150.00   50
 38  \w     95.00 165.00   0.50    3.20    --  111.50 125.00-150.00  140
 39  \w     86.00 111.00   0.50    3.20    --  111.50-125.00 -60.00   50
 40  \w    107.00 147.00   0.50    3.20    --  111.50  15.00-180.00   80
 41  \w    146.00 174.00   0.50    3.20    --  111.50  15.00  90.00   56
 42  \w     63.00  97.00   0.50    3.20    --  111.50 -77.00 150.00   68
 43  \w    114.00 150.00   0.50    3.20    --  111.50  15.00 -60.00   72
 44  \w     97.00 130.00   0.50    3.20    --  111.50  61.00-120.00   66
 45  \w     63.00  89.00   0.50    3.20    --  111.50 -77.00-180.00   52
 46  \w     45.00  70.00   0.50    3.20    --  111.50 -61.00 -60.00   50
 47  \w     48.00  73.00   0.50    3.20    --  111.50 -94.00-180.00   50
 48  \w     73.00  98.00   0.50    3.20    --  111.50 -94.00 -90.00   50
 49  \w    131.00 156.00   0.50    3.20    --  111.50  30.00  60.00   50
 50  \w    104.00 130.00   0.50    3.20    --  111.50  45.00-120.00   52
 51  \w    109.00 164.00   0.50    3.20    --  111.50  61.00-180.00  110
 52  \w    130.00 176.00   0.50    3.20    --  111.50  61.00 -90.00   92
 53  \w    108.00 178.00   0.50    3.20    --  111.50  61.00 150.00  140
 54  \w     41.00  66.00   0.50    3.20    --  111.50 -61.00   0.00   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      0.0247159000
_diffrn_orient_matrix_UB_12      -0.1268365000
_diffrn_orient_matrix_UB_13      0.0111420000
_diffrn_orient_matrix_UB_21      -0.0524532000
_diffrn_orient_matrix_UB_22      -0.0596090000
_diffrn_orient_matrix_UB_23      -0.0050524000
_diffrn_orient_matrix_UB_31      -0.0007150000
_diffrn_orient_matrix_UB_32      -0.0057988000
_diffrn_orient_matrix_UB_33      -0.1913057000
_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  0.0344
_diffrn_reflns_av_unetI/netI     0.0273
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.988
_diffrn_reflns_limit_h_max       33
_diffrn_reflns_limit_h_min       -33
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       7
_diffrn_reflns_limit_l_min       -9
_diffrn_reflns_number            28790
_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         79.934
_diffrn_reflns_theta_min         3.327
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.608
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.82316
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.105a (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    1.539
_exptl_crystal_description       plate
_exptl_crystal_F_000             1104
_exptl_crystal_recrystallization_method 'crystallized from acetonitrile'
_exptl_crystal_size_max          0.217
_exptl_crystal_size_mid          0.118
_exptl_crystal_size_min          0.01
_refine_diff_density_max         0.622
_refine_diff_density_min         -0.483
_refine_diff_density_rms         0.075
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.090
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     319
_refine_ls_number_reflns         5067
_refine_ls_number_restraints     8
_refine_ls_restrained_S_all      1.090
_refine_ls_R_factor_all          0.0331
_refine_ls_R_factor_gt           0.0307
_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^)+(0.0572P)^2^+0.5327P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0884
_refine_ls_wR_factor_ref         0.0904
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4631
_reflns_number_total             5067
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ce00839e2.cif
_cod_data_source_block           exp_863_auto
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_chemical_melting_point' value '378-380' was changed to
'379.0(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_original_cell_volume        2349.28(3)
_cod_database_code               7251002
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C10H14Br1N3O
_shelx_estimated_absorpt_t_max   0.955
_shelx_estimated_absorpt_t_min   0.435
_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
 C11C-C10B = C11B-C10B = C12C-C11C = C12B-C11B = C13C-C12C = C13B-C12B = C14B-
 C13B = C14C-C13C
 1.52 with sigma of 0.02
3. Others
 Sof(H10C)=Sof(H10D)=Sof(C11C)=Sof(H11C)=Sof(H11D)=Sof(C12C)=Sof(H12C)=
 Sof(H12D)=Sof(C13C)=Sof(H13C)=Sof(H13D)=Sof(C14C)=Sof(H14D)=Sof(H14E)=
 Sof(H14F)=1-FVAR(1)
 Sof(H10A)=Sof(H10B)=Sof(C11B)=Sof(H11A)=Sof(H11B)=Sof(C12B)=Sof(H12A)=
 Sof(H12B)=Sof(C13B)=Sof(H13A)=Sof(H13B)=Sof(C14B)=Sof(H14A)=Sof(H14B)=
 Sof(H14C)=FVAR(1)
4.a Secondary CH2 refined with riding coordinates:
 C10A(H10E,H10F), C11A(H11E,H11F), C12A(H12E,H12F), C13A(H13E,H13F), C10B(H10A,
 H10B), C10B(H10C,H10D), C11B(H11A,H11B), C11C(H11C,H11D), C12B(H12A,H12B),
 C12C(H12C,H12D), C13B(H13A,H13B), C13C(H13C,H13D)
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:
 C14A(H14G,H14H,H14I), C14B(H14A,H14B,H14C), C14C(H14D,H14E,H14F)
;
_shelx_res_checksum              7664
_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 1.414
_oxdiff_exptl_absorpt_empirical_full_min 0.728