Synthesis, structural characterization and DFT study of N-(pyrimidyl)-ω-amino acids/peptide: β-alanine, γ-aminobutyric acid, 5-aminovaleric acid, 6-aminohexanoic acid and glycylglycine
García-Raso, Angel; Terrón, Angel; Fiol, Juan J.; López-Zafra, Adela; Picó, Gemma; Vázquez-López, Ezequiel M.; Barceló-Oliver, Miquel; Frontera, Antonio; CrystEngComm 25 (2023) 233–244; doi:10.1039/D2CE01293F

data_7245966
_publ_section_title
;
 Synthesis, structural characterization and DFT study of
 N-(pyrimidyl)-\w-amino acids/peptide: \b-alanine, \g-aminobutyric acid,
 5-aminovaleric acid, 6-aminohexanoic acid and glycylglycine
;
_journal_issue                   2
_journal_name_full               CrystEngComm
_journal_page_first              233
_journal_page_last               244
_journal_paper_doi               10.1039/D2CE01293F
_journal_volume                  25
_journal_year                    2023
_chemical_formula_moiety         'C8 H12 N3 O2, N O3'
_chemical_formula_sum            'C8 H12 N4 O5'
_chemical_formula_weight         244.22
_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   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-11-15
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-11-15 deposited with the CCDC.	2022-11-24 downloaded from the CCDC.
;
_cell_angle_alpha                101.543(3)
_cell_angle_beta                 96.517(3)
_cell_angle_gamma                94.398(2)
_cell_formula_units_Z            8
_cell_length_a                   9.8280(10)
_cell_length_b                   14.0136(14)
_cell_length_c                   15.9826(16)
_cell_measurement_reflns_used    9738
_cell_measurement_temperature    100.0
_cell_measurement_theta_max      66.492
_cell_measurement_theta_min      5.311
_cell_volume                     2131.6(4)
_computing_cell_refinement       'Bruker Apex3, 2016'
_computing_data_collection       'Bruker Apex3, 2016'
_computing_data_reduction        'SAINT v8.40A (Bruker, 2019)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100.00
_diffrn_measured_fraction_theta_full 0.988
_diffrn_measured_fraction_theta_max 0.988
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0634
_diffrn_reflns_av_unetI/netI     0.0578
_diffrn_reflns_Laue_measured_fraction_full 0.988
_diffrn_reflns_Laue_measured_fraction_max 0.988
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       16
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            33594
_diffrn_reflns_point_group_measured_fraction_full 0.988
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        66.558
_diffrn_reflns_theta_max         66.558
_diffrn_reflns_theta_min         2.847
_exptl_absorpt_coefficient_mu    1.103
_exptl_absorpt_correction_T_max  0.7528
_exptl_absorpt_correction_T_min  0.3844
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1442 before and 0.1014 after correction.
The Ratio of minimum to maximum transmission is 0.5106.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.522
_exptl_crystal_description       prism
_exptl_crystal_F_000             1024
_exptl_crystal_size_max          0.49
_exptl_crystal_size_mid          0.28
_exptl_crystal_size_min          0.24
_refine_diff_density_max         0.362
_refine_diff_density_min         -0.301
_refine_diff_density_rms         0.070
_refine_ls_extinction_coef       0.0095(10)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2019/1 (Sheldrick 2019)'
_refine_ls_goodness_of_fit_ref   1.069
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     618
_refine_ls_number_reflns         7442
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.0547
_refine_ls_R_factor_gt           0.0535
_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^)+(0.0990P)^2^+0.6163P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1558
_refine_ls_wR_factor_ref         0.1572
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7193
_reflns_number_total             7442
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ce01293f2.cif
_cod_data_source_block           1_a
_cod_depositor_comments
'Adding full bibliography for 7245964--7245971.cif.'
_cod_database_code               7245966
_shelx_shelxl_version_number     2019/1
_shelx_estimated_absorpt_t_max   0.778
_shelx_estimated_absorpt_t_min   0.614
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All O(H) groups
2.a Secondary CH2 refined with riding coordinates:
 C3B(H3BA,H3BB), C4B(H4BA,H4BB), C5B(H5BA,H5BB), C3D(H3DA,H3DB), C4D(H4DA,
 H4DB), C5D(H5DA,H5DB), C3C(H3CA,H3CB), C4C(H4CA,H4CB), C5C(H5CA,H5CB),
 C3A(H3AA,H3AB), C4A(H4AA,H4AB), C5A(H5AA,H5AB)
2.b Aromatic/amide H refined with riding coordinates:
 N6B(H6B), N1B'(H1B'), C4B'(H4B'), C5B'(H5B'), C6B'(H6B'), N6D(H6D),
 N1D'(H1D'), C4D'(H4D'), C5D'(H5D'), C6D'(H6D'), N6C(H6C), N1C'(H1C'),
 C4C'(H4C'), C5C'(H5C'), C6C'(H6C'), N6A(H6A), N1A'(H1A'), C4A'(H4A'),
 C5A'(H5A'), C6A'(H6A')
2.c Idealised tetrahedral OH refined as rotating group:
 O1B(H1B), O1D(H1D), O1C(H1C), O1A(H1A)
;
_shelx_res_checksum              31747
_shelx_hkl_checksum              69276
_olex2_submission_special_instructions 'No special instructions were received'