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_7063165
_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         'C40 H40 N6 O4 Zn, 2(C2 H5 N O)'
_chemical_formula_sum            'C44 H50 N8 O6 Zn'
_chemical_formula_weight         852.29
_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             2022-05-05
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2022-06-25 deposited with the CCDC.	2024-04-16 downloaded from the CCDC.
;
_cell_angle_alpha                101.629(4)
_cell_angle_beta                 101.475(3)
_cell_angle_gamma                101.582(3)
_cell_formula_units_Z            1
_cell_length_a                   7.9641(2)
_cell_length_b                   10.7052(4)
_cell_length_c                   12.7812(5)
_cell_measurement_reflns_used    7996
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      30.0410
_cell_measurement_theta_min      2.9250
_cell_volume                     1012.52(7)
_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 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_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 0.904
_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    -67.00  60.00   1.00    5.00    --   14.05 -19.00  30.00  127
  2  \w    -12.00  87.00   1.00    5.00    --   14.05  37.00 -90.00   99
  3  \w    -12.00  90.00   1.00    5.00    --   14.05  37.00-180.00  102
  4  \w    -15.00  56.00   1.00    5.00    --   14.05 -99.00   0.00   71
  5  \w    -12.00  89.00   1.00    5.00    --   14.05  37.00  60.00  101
  6  \w    -40.00  48.00   1.00    5.00    --   14.05 -77.00-120.00   88
  7  \w    -48.00  -1.00   1.00    5.00    --  -14.36  77.00-180.00   47
  8  \w    -89.00 -60.00   1.00    5.00    --  -14.36 151.00  -7.39   29
  9  \w    -32.00  18.00   1.00    5.00    --  -14.36 -77.00-120.00   50
;
_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      -0.0254171000
_diffrn_orient_matrix_UB_12      -0.0155234000
_diffrn_orient_matrix_UB_13      -0.0584580000
_diffrn_orient_matrix_UB_21      -0.0279547000
_diffrn_orient_matrix_UB_22      0.0591578000
_diffrn_orient_matrix_UB_23      0.0023721000
_diffrn_orient_matrix_UB_31      0.0859438000
_diffrn_orient_matrix_UB_32      0.0338064000
_diffrn_orient_matrix_UB_33      -0.0005697000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0358
_diffrn_reflns_av_unetI/netI     0.0361
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.904
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            20001
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.904
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         30.371
_diffrn_reflns_theta_min         2.696
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.667
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.95894
_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    1.398
_exptl_crystal_description       block
_exptl_crystal_F_000             448
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.339
_refine_diff_density_min         -0.385
_refine_diff_density_rms         0.056
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.057
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     281
_refine_ls_number_reflns         5524
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.057
_refine_ls_R_factor_all          0.0412
_refine_ls_R_factor_gt           0.0335
_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^)+(0.0280P)^2^+0.4458P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0748
_refine_ls_wR_factor_ref         0.0801
_reflns_Friedel_coverage         0.000
_reflns_number_gt                4918
_reflns_number_total             5524
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4nj00235k2.cif
_cod_data_source_block           18a
_cod_depositor_comments
'Adding full bibliography for 7063150--7063171.cif.'
_cod_original_cell_volume        1012.52(6)
_cod_database_code               7063165
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.936
_shelx_estimated_absorpt_t_min   0.851
_reflns_odcompleteness_completeness 99.87
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     27.50
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2.a Secondary CH2 refined with riding coordinates:
 C20(H20A,H20B), C21(H21A,H21B), C22(H22A,H22B), C23(H23A,H23B)
2.b Aromatic/amide H refined with riding coordinates:
 C11(H11), C12(H12), C13(H13), C14(H14), C16(H16), C17(H17), C25(H25),
 C26(H26), C27(H27), C28(H28), C29(H29)
2.c Idealised Me refined as rotating group:
 C32(H32A,H32B,H32C)
;
_shelx_res_checksum              87450
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.156
_oxdiff_exptl_absorpt_empirical_full_min 0.890