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_7063152
_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(C16 H20 N3 O2 Zn0.5), 0.5(C2 H3 N)'
_chemical_formula_sum            'C33 H41.5 N6.5 O4 Zn'
_chemical_formula_weight         658.59
_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             2022-05-04
_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                72.156(4)
_cell_angle_beta                 86.674(3)
_cell_angle_gamma                86.036(3)
_cell_formula_units_Z            2
_cell_length_a                   10.5552(4)
_cell_length_b                   12.0176(5)
_cell_length_c                   13.4817(6)
_cell_measurement_reflns_used    5917
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      30.2690
_cell_measurement_theta_min      3.4100
_cell_volume                     1622.75(12)
_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 (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 0.864
_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     -7.00  25.00   1.00   50.00    --  -14.36 -99.00-120.00   32
  2  \w    -53.00 -27.00   1.00   50.00    --   14.52 -57.00   0.00   26
  3  \w    -20.00  56.00   1.00   50.00    --   14.52 -99.00  30.00   76
  4  \w      7.00  88.00   1.00   50.00    --   14.52  57.00-120.00   81
  5  \w    -64.00  48.00   1.00   50.00    --   14.52 -77.00 120.00  112
;
_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      -0.0498652000
_diffrn_orient_matrix_UB_12      -0.0374818000
_diffrn_orient_matrix_UB_13      0.0023279000
_diffrn_orient_matrix_UB_21      0.0431092000
_diffrn_orient_matrix_UB_22      -0.0494408000
_diffrn_orient_matrix_UB_23      0.0166016000
_diffrn_orient_matrix_UB_31      -0.0141185000
_diffrn_orient_matrix_UB_32      -0.0025595000
_diffrn_orient_matrix_UB_33      0.0527109000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0231
_diffrn_reflns_av_unetI/netI     0.0404
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.864
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -16
_diffrn_reflns_limit_l_max       18
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            14788
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.864
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         30.393
_diffrn_reflns_theta_min         2.456
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.804
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.81084
_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    1.348
_exptl_crystal_description       needle
_exptl_crystal_F_000             694
_exptl_crystal_size_max          0.5
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.415
_refine_diff_density_min         -0.401
_refine_diff_density_rms         0.062
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.023
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     449
_refine_ls_number_reflns         8464
_refine_ls_number_restraints     2
_refine_ls_restrained_S_all      1.023
_refine_ls_R_factor_all          0.0506
_refine_ls_R_factor_gt           0.0371
_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^)+(0.0361P)^2^+0.9064P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0866
_refine_ls_wR_factor_ref         0.0948
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6753
_reflns_number_total             8464
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4nj00235k2.cif
_cod_data_source_block           13
_cod_depositor_comments
'Adding full bibliography for 7063150--7063171.cif.'
_cod_original_formula_sum        'C33 H41.50 N6.50 O4 Zn'
_cod_database_code               7063152
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.961
_shelx_estimated_absorpt_t_min   0.689
_reflns_odcompleteness_completeness 99.95
_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. Restrained distances
 N44-C45 \\sim N44-C45A
 with sigma of 0.01
 C45A-C46A \\sim C46-C45
 with sigma of 0.01
3. Others
 Sof(C45A)=Sof(H45C)=Sof(H45D)=Sof(C46A)=Sof(H46D)=Sof(H46E)=Sof(H46F)=1-FVAR(1)
 Sof(C45)=Sof(H45A)=Sof(H45B)=Sof(C46)=Sof(H46A)=Sof(H46B)=Sof(H46C)=FVAR(1)
 Fixed Sof: N5(0.5) C51(0.5) C52(0.5) H52A(0.5) H52B(0.5) H52C(0.5)
4.a Secondary CH2 refined with riding coordinates:
 C21(H21A,H21B), C22(H22A,H22B), C23(H23A,H23B), C24(H24A,H24B), C25(H25A,
 H25B), C41(H41A,H41B), C42(H42A,H42B), C43(H43A,H43B), C44(H44A,H44B),
 C45(H45A,H45B), C45A(H45C,H45D)
4.b Aromatic/amide H refined with riding coordinates:
 C11(H11), C12(H12), C13(H13), C14(H14), C16(H16), C17(H17), C31(H31),
 C32(H32), C33(H33), C34(H34), C36(H36), C37(H37)
4.c Idealised Me refined as rotating group:
 C26(H26A,H26B,H26C), C52(H52A,H52B,H52C), C46(H46A,H46B,H46C), C46A(H46D,H46E,
 H46F)
;
_shelx_res_checksum              63853
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.287
_oxdiff_exptl_absorpt_empirical_full_min 0.699