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_7245969
_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         'C10 H16 N3 O2, N O3, H2 O'
_chemical_formula_sum            'C10 H18 N4 O6'
_chemical_formula_weight         290.28
_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   mixed
_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                81.938(4)
_cell_angle_beta                 74.159(4)
_cell_angle_gamma                62.779(3)
_cell_formula_units_Z            4
_cell_length_a                   9.9111(9)
_cell_length_b                   10.2045(9)
_cell_length_c                   15.5393(14)
_cell_measurement_reflns_used    9600
_cell_measurement_temperature    100.0
_cell_measurement_theta_max      68.23
_cell_measurement_theta_min      2.96
_cell_volume                     1344.3(2)
_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 0.997
_diffrn_measured_fraction_theta_max 0.991
_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  0.0535
_diffrn_reflns_av_unetI/netI     0.0222
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.991
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            91370
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.991
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         68.497
_diffrn_reflns_theta_min         2.956
_exptl_absorpt_coefficient_mu    1.020
_exptl_absorpt_correction_T_max  0.7531
_exptl_absorpt_correction_T_min  0.5539
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1511 before and 0.0842 after correction.
The Ratio of minimum to maximum transmission is 0.7355.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.434
_exptl_crystal_description       block
_exptl_crystal_F_000             616
_exptl_crystal_size_max          0.42
_exptl_crystal_size_mid          0.35
_exptl_crystal_size_min          0.28
_refine_diff_density_max         0.274
_refine_diff_density_min         -0.238
_refine_diff_density_rms         0.051
_refine_ls_extinction_coef       0.0033(6)
_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   1.076
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     370
_refine_ls_number_reflns         4906
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.076
_refine_ls_R_factor_all          0.0367
_refine_ls_R_factor_gt           0.0362
_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^)+(0.0537P)^2^+0.4833P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0996
_refine_ls_wR_factor_ref         0.1001
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4786
_reflns_number_total             4906
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ce01293f2.cif
_cod_data_source_block           1_a_CCDC1
_cod_depositor_comments
'Adding full bibliography for 7245964--7245971.cif.'
_cod_database_code               7245969
_shelx_shelxl_version_number     2019/1
_shelx_estimated_absorpt_t_max   0.763
_shelx_estimated_absorpt_t_min   0.674
_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, All O(H,H) groups
2.a Free rotating group:
 O1W(H1WA,H1WB), O2W(H2WA,H2WB)
2.b Secondary CH2 refined with riding coordinates:
 C3A(H3AA,H3AB), C4A(H4AA,H4AB), C5A(H5AA,H5AB), C6A(H6AA,H6AB), C7A(H7AB,
 H7AA), C3B(H3BA,H3BB), C4B(H4BA,H4BB), C5B(H5BA,H5BB), C6B(H6BA,H6BB),
 C7B(H7BA,H7BB)
2.c Aromatic/amide H refined with riding coordinates:
 N8A(H8A), N1A'(H1A'), C4A'(H4A'), C5A'(H5A'), C6A'(H6A'), N8B(H8B),
 N1B'(H1B'), C4B'(H4B'), C5B'(H5B'), C6B'(H6B')
2.d Idealised tetrahedral OH refined as rotating group:
 O1A(H1A), O1B(H1B)
;
_shelx_res_checksum              75035
_shelx_hkl_checksum              53270
_olex2_submission_special_instructions 'No special instructions were received'