Piperidine and piperazine analogs in action: zinc(ii)-mediated formation of amidines
Podjed, Nina; Košmrlj, Janez; Modec, Barbara; New Journal of Chemistry 48 (2024) 8844–8859; doi:10.1039/D4NJ00235K

data_7063162
_publ_section_title
;
 Piperidine and piperazine analogs in action: zinc(ii)-mediated formation
 of amidines
;
_journal_issue                   19
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              8844
_journal_page_last               8859
_journal_paper_doi               10.1039/D4NJ00235K
_journal_volume                  48
_journal_year                    2024
_chemical_formula_moiety         'C22 H18 N4 O4 Zn, 1.333(C2 H3 N), 0.2(H2 O)'
_chemical_formula_sum            'C24.66 H22.4 N5.34 O4.2 Zn'
_chemical_formula_weight         526.12
_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             2024-04-03
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2024-04-04 deposited with the CCDC.	2024-04-16 downloaded from the CCDC.
;
_cell_angle_alpha                77.896(4)
_cell_angle_beta                 78.984(3)
_cell_angle_gamma                84.021(3)
_cell_formula_units_Z            2
_cell_length_a                   8.1567(3)
_cell_length_b                   9.9520(4)
_cell_length_c                   15.1357(6)
_cell_measurement_reflns_used    3997
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      29.7160
_cell_measurement_theta_min      3.1240
_cell_volume                     1176.56(8)
_computing_cell_refinement       'CrysAlisPro 1.171.40.68a (Rigaku OD, 2019)'
_computing_data_collection       'CrysAlisPro 1.171.40.68a (Rigaku OD, 2019)'
_computing_data_reduction        'CrysAlisPro 1.171.40.68a (Rigaku OD, 2019)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (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      150.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.4933
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.999
_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    -60.00  29.00   1.00   22.50    --   14.05 -57.00 120.00   89
  2  \w    -10.00  89.00   1.00   22.50    --   14.05  37.00 -90.00   99
  3  \w     39.00 103.00   1.00   22.50    --   14.05 178.00  90.00   64
  4  \w    -26.00  17.00   1.00   22.50    --  -14.36 -77.00   0.00   43
  5  \w    -25.00  18.00   1.00   22.50    --  -14.36 -77.00-150.00   43
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0070109000
_diffrn_orient_matrix_UB_12      -0.0692137000
_diffrn_orient_matrix_UB_13      0.0236916000
_diffrn_orient_matrix_UB_21      -0.0354813000
_diffrn_orient_matrix_UB_22      0.0233536000
_diffrn_orient_matrix_UB_23      0.0411286000
_diffrn_orient_matrix_UB_31      -0.0810898000
_diffrn_orient_matrix_UB_32      0.0011083000
_diffrn_orient_matrix_UB_33      -0.0107700000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0280
_diffrn_reflns_av_unetI/netI     0.0515
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.988
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            10357
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.998
_diffrn_reflns_theta_min         2.550
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    1.088
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.78984
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.68a (Rigaku Oxford Diffraction, 2019)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.485
_exptl_crystal_description       needle
_exptl_crystal_F_000             543
_exptl_crystal_size_max          0.5
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.03
_refine_diff_density_max         0.518
_refine_diff_density_min         -0.462
_refine_diff_density_rms         0.067
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     361
_refine_ls_number_reflns         5608
_refine_ls_number_restraints     26
_refine_ls_restrained_S_all      1.036
_refine_ls_R_factor_all          0.0529
_refine_ls_R_factor_gt           0.0388
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0391P)^2^+0.1943P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0825
_refine_ls_wR_factor_ref         0.0894
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4591
_reflns_number_total             5608
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4nj00235k2.cif
_cod_data_source_block           23
_cod_depositor_comments
'Adding full bibliography for 7063150--7063171.cif.'
_cod_original_formula_sum        'C24.66 H22.40 N5.34 O4.20 Zn'
_cod_database_code               7063162
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.968
_shelx_estimated_absorpt_t_min   0.612
_reflns_odcompleteness_completeness 99.93
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     27.50
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 N6-C61
 1.14 with sigma of 0.02
 C61-N6
 1.137 with sigma of 0.01
 C61-C62
 1.456 with sigma of 0.01
 C62-N6
 2.593 with sigma of 0.02
 N6-C62
 2.59 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
N6 \\sim C61 \\sim C62: within 2A with sigma of 0.001 and sigma for terminal
atoms of 0.002 within 2A
4. Rigid body (RIGU) restrains
 N6, C61, C62
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N6, C61, C62, H62A, H62B, H62C
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Fixed Sof: O3(0.2) H3A(0.2) H3B(0.2) N6(0.3333) C61(0.3333) C62(0.3333)
 H62A(0.3333) H62B(0.3333) H62C(0.3333)
6.a Free rotating group:
 O3(H3A,H3B)
6.b Aromatic/amide H refined with riding coordinates:
 C11(H11), C12(H12), C13(H13), C14(H14), C16(H16), C17(H17), C21(H21),
 C22(H22), C23(H23), C24(H24), C26(H26), C27(H27)
6.c Idealised Me refined as rotating group:
 C32(H32A,H32B,H32C), C52(H52A,H52B,H52C), C62(H62A,H62B,H62C)
;
_shelx_res_checksum              76192
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.283
_oxdiff_exptl_absorpt_empirical_full_min 0.689