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_7245971
_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
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_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         'C9 H14 N3 O2, N O3'
_chemical_formula_sum            'C9 H14 N4 O5'
_chemical_formula_weight         258.235
_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'
_symmetry_Int_Tables_number      14
_atom_sites_solution_primary     dual
_audit_creation_date             2022-11-14
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-11-14 deposited with the CCDC.	2022-11-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 109.840(1)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   9.3661(3)
_cell_length_b                   36.0462(12)
_cell_length_c                   7.5101(3)
_cell_measurement_reflns_used    9916
_cell_measurement_temperature    298.0
_cell_measurement_theta_max      66.661
_cell_measurement_theta_min      4.909
_cell_volume                     2385.01(15)
_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  'olex2.refine 1.5 (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      298.00
_diffrn_measured_fraction_theta_full 0.9929
_diffrn_measured_fraction_theta_max 0.9929
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0418
_diffrn_reflns_av_unetI/netI     0.0385
_diffrn_reflns_Laue_measured_fraction_full 0.9929
_diffrn_reflns_Laue_measured_fraction_max 0.9929
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       42
_diffrn_reflns_limit_k_min       -42
_diffrn_reflns_limit_l_max       8
_diffrn_reflns_limit_l_min       -8
_diffrn_reflns_number            21222
_diffrn_reflns_point_group_measured_fraction_full 0.9929
_diffrn_reflns_point_group_measured_fraction_max 0.9929
_diffrn_reflns_theta_full        66.7859
_diffrn_reflns_theta_max         66.79
_diffrn_reflns_theta_min         2.45
_exptl_absorpt_coefficient_mu    1.016
_exptl_absorpt_correction_T_max  0.7528
_exptl_absorpt_correction_T_min  0.5696
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1321 before and 0.0732 after correction.
The Ratio of minimum to maximum transmission is 0.7566.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.438
_exptl_crystal_description       block
_exptl_crystal_F_000             1092.523
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.19
_exptl_crystal_size_min          0.14
_refine_diff_density_max         0.3378
_refine_diff_density_min         -0.2609
_refine_diff_density_rms         0.0397
_refine_ls_d_res_high            0.8388
_refine_ls_d_res_low             18.0231
_refine_ls_goodness_of_fit_ref   1.0445
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    48
_refine_ls_number_parameters     327
_refine_ls_number_reflns         4206
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.0445
_refine_ls_R_factor_all          0.0621
_refine_ls_R_factor_gt           0.0597
_refine_ls_shift/su_max          -0.0005
_refine_ls_shift/su_mean         0.0001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0521P)^2^+1.1353P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1507
_refine_ls_wR_factor_ref         0.1523
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              10
_reflns_limit_h_min              -11
_reflns_limit_k_max              42
_reflns_limit_k_min              0
_reflns_limit_l_max              8
_reflns_limit_l_min              0
_reflns_number_gt                3929
_reflns_number_total             4206
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d2ce01293f2.cif
_cod_data_source_block           1_a_CCDC2
_cod_depositor_comments
'Adding full bibliography for 7245964--7245971.cif.'
_cod_database_code               7245971
_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:
 C6B(H6Ba,H6Bb), C5B(H5Ba,H5Bb), C4B(H4Ba,H4Bb), C3B(H3Ba,H3Bb), C6A(H6Aa,
 H6Ab), C5A(H5Aa,H5Ab), C4A(H4Aa,H4Ab), C3A(H3Aa,H3Ab)
2.b Aromatic/amide H refined with riding coordinates:
 N1B'(H1B'), C4B'(H4B'), C5B'(H5B'), C6B'(H6B'), N7B(H7B), N1A'(H1A'),
 C4A'(H4A'), C5A'(H5A'), C6A'(H6A'), N7A(H7A)
2.c Idealised tetrahedral OH refined as rotating group:
 O1B(H1B), O1A(H1A)
;
_olex2_submission_special_instructions 'No special instructions were received'