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_7063161
_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         '2(C20 H20 N3 O2 Zn0.5), C2 H3 N1'
_chemical_formula_sum            'C42 H43 N7 O4 Zn'
_chemical_formula_weight         775.20
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 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                90
_cell_angle_beta                 93.3260(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.61490(10)
_cell_length_b                   10.83280(10)
_cell_length_c                   25.0497(3)
_cell_measurement_reflns_used    8435
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      75.1550
_cell_measurement_theta_min      3.4810
_cell_volume                     3688.29(6)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_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 (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 1.000
_diffrn_measured_fraction_theta_max 0.985
_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    -66.00  32.00   1.00    1.00    --  -41.76  37.00 150.00   98
  2  \w    -55.00   4.00   1.00    1.00    --  -41.76  37.00  30.00   59
  3  \w    -77.00   6.00   1.00    1.00    --  -41.76 115.00-171.00   83
  4  \w     37.00 102.00   1.00    4.00    --  109.50-125.00   0.00   65
  5  \w     99.00 126.00   1.00    4.00    --  109.50 125.00  60.00   27
  6  \w     63.00 113.00   1.00    4.00    --  109.50-125.00 -60.00   50
  7  \w     90.00 173.00   1.00    4.00    --  109.50  30.00 -60.00   83
  8  \w     37.00 100.00   1.00    4.00    --  109.50-125.00  90.00   63
  9  \w     65.00 117.00   1.00    4.00    --  109.50-125.00 150.00   52
 10  \w     40.00  99.00   1.00    4.00    --  109.50 -94.00 150.00   59
 11  \w     37.00  77.00   1.00    4.00    --  109.50 -94.00  90.00   40
 12  \w     68.00  96.00   1.00    4.00    --  109.50-125.00  30.00   28
 13  \w     84.00 174.00   1.00    4.00    --  109.50  45.00-180.00   90
;
_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      0.0244799000
_diffrn_orient_matrix_UB_12      -0.0782220000
_diffrn_orient_matrix_UB_13      -0.0488433000
_diffrn_orient_matrix_UB_21      0.0133832000
_diffrn_orient_matrix_UB_22      -0.1145311000
_diffrn_orient_matrix_UB_23      0.0361437000
_diffrn_orient_matrix_UB_31      -0.1098494000
_diffrn_orient_matrix_UB_32      -0.0314329000
_diffrn_orient_matrix_UB_33      -0.0101769000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0237
_diffrn_reflns_av_unetI/netI     0.0272
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.985
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       10
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       -30
_diffrn_reflns_number            17736
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.985
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         75.288
_diffrn_reflns_theta_min         3.535
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.358
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.27566
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46e (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.396
_exptl_crystal_description       plate
_exptl_crystal_F_000             1624
_exptl_crystal_size_max          0.35
_exptl_crystal_size_mid          0.3
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.345
_refine_diff_density_min         -0.371
_refine_diff_density_rms         0.050
_refine_ls_extinction_coef       0.00091(6)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.033
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     551
_refine_ls_number_reflns         7509
_refine_ls_number_restraints     18
_refine_ls_restrained_S_all      1.040
_refine_ls_R_factor_all          0.0360
_refine_ls_R_factor_gt           0.0315
_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^)+(0.0476P)^2^+1.0446P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0828
_refine_ls_wR_factor_ref         0.0870
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6690
_reflns_number_total             7509
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4nj00235k2.cif
_cod_data_source_block           17
_cod_depositor_comments
'Adding full bibliography for 7063150--7063171.cif.'
_cod_database_code               7063161
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.935
_shelx_estimated_absorpt_t_min   0.648
_reflns_odcompleteness_completeness 99.97
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     71.98
_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. Restrained distances
 C45A-C44 \\sim C45-C44
 with sigma of 0.01
 C46-C45 \\sim C46A-C45A
 with sigma of 0.01
 C47-C46 \\sim C47-C46A
 with sigma of 0.01
 C48A-C47 \\sim C48-C47
 with sigma of 0.01
 C49A-C48A \\sim C49-C48
 with sigma of 0.01
 C49A-C44 \\sim C49-C44
 with sigma of 0.01
 N5-C51 \\sim N5A-C51A
 with sigma of 0.02
 C51-C52 \\sim C51A-C52A
 with sigma of 0.02
 N5-C52 \\sim N5A-C52A
 with sigma of 0.04
3. Rigid body (RIGU) restrains
 N5, C51, C52
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
4. Others
 Sof(H47A)=Sof(C45A)=Sof(H45A)=Sof(C46A)=Sof(H46A)=Sof(C48A)=Sof(H48A)=
 Sof(C49A)=Sof(H49A)=1-FVAR(1)
 Sof(H47)=Sof(C45)=Sof(H45)=Sof(C46)=Sof(H46)=Sof(C48)=Sof(H48)=Sof(C49)=
 Sof(H49)=FVAR(1)
 Sof(N5A)=Sof(C51A)=Sof(C52A)=Sof(H52D)=Sof(H52E)=Sof(H52F)=1-FVAR(2)
 Sof(N5)=Sof(C51)=Sof(C52)=Sof(H52A)=Sof(H52B)=Sof(H52C)=FVAR(2)
5.a Secondary CH2 refined with riding coordinates:
 C20(H20A,H20B), C21(H21A,H21B), C22(H22A,H22B), C23(H23A,H23B), C40(H40A,
 H40B), C41(H41A,H41B), C42(H42A,H42B), C43(H43A,H43B)
5.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), C31(H31), C32(H32), C33(H33), C34(H34),
  C36(H36), C37(H37), C47(H47), C47(H47A), C45(H45), C46(H46), C48(H48),
 C49(H49), C45A(H45A), C46A(H46A), C48A(H48A), C49A(H49A)
5.c Idealised Me refined as rotating group:
 C52(H52A,H52B,H52C), C52A(H52D,H52E,H52F)
;
_shelx_res_checksum              32660
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 3.259
_oxdiff_exptl_absorpt_empirical_full_min 0.567