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_7063166
_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         'C8 H15 N3 O'
_chemical_formula_sum            'C8 H15 N3 O'
_chemical_formula_weight         169.23
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 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                90
_cell_angle_beta                 100.9800(10)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   4.96280(10)
_cell_length_b                   12.41770(10)
_cell_length_c                   7.50220(10)
_cell_measurement_reflns_used    8666
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      72.5330
_cell_measurement_theta_min      3.5230
_cell_volume                     453.871(12)
_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 0.998
_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   -115.00 -13.00   1.00    1.00    --  -41.63 -57.00 150.00  102
  2  \w   -115.00 -13.00   1.00    1.00    --  -41.63 -57.00-120.00  102
  3  \w   -115.00 -13.00   1.00    1.00    --  -41.63 -57.00   0.00  102
  4  \w   -115.00 -60.00   1.00    1.00    --  -41.63-151.00  62.00   55
  5  \w    -87.00  -6.00   1.00    1.00    --  -41.63 125.00-150.00   81
  6  \w     17.00 116.00   1.00    1.00    --   41.63  37.00 120.00   99
  7  \w      6.00  83.00   1.00    1.00    --   41.63 -99.00 120.00   77
  8  \w     10.00 116.00   1.00    1.00    --   41.63  71.00 142.39  106
  9  \w    -21.00  74.00   1.00    1.00    --   41.63 -77.00  30.00   95
 10  \w     13.00 115.00   1.00    1.00    --   41.63  57.00 -30.00  102
 11  \w     97.00 178.00   1.00    4.00    --  104.43 125.00  90.00   81
 12  \w     22.00 106.00   1.00    4.00    --  104.43 -94.00-120.00   84
 13  \w     79.00 177.00   1.00    4.00    --  104.43  45.00  30.00   98
 14  \w     75.00 177.00   1.00    4.00    --  104.43  61.00  30.00  102
 15  \w     28.00 137.00   1.00    4.00    --  104.43 -77.00   0.00  109
 16  \w     78.00 177.00   1.00    4.00    --  104.43  47.00  10.64   99
 17  \w     76.00 178.00   1.00    4.00    --  104.43  59.00 118.79  102
 18  \w     79.00 177.00   1.00    4.00    --  104.43  45.00 -60.00   98
 19  \w     75.00 177.00   1.00    4.00    --  104.43  61.00-150.00  102
 20  \w     75.00 177.00   1.00    4.00    --  104.43  61.00-120.00  102
 21  \w     75.00 177.00   1.00    4.00    --  104.43  61.00  60.00  102
 22  \w     75.00 177.00   1.00    4.00    --  104.43  61.00 -60.00  102
 23  \w     75.00 177.00   1.00    4.00    --  104.43  62.00-170.06  102
 24  \w     75.00 177.00   1.00    4.00    --  104.43  61.00  90.00  102
 25  \w     75.00 177.00   1.00    4.00    --  104.43  61.00-180.00  102
 26  \w     79.00 177.00   1.00    4.00    --  104.43  45.00 150.00   98
 27  \w     75.00 177.00   1.00    4.00    --  104.43  61.00 -90.00  102
 28  \w    103.00 178.00   1.00    4.00    --  104.43  77.00  60.00   75
 29  \w     75.00 177.00   1.00    4.00    --  104.43  61.00 -30.00  102
 30  \w     31.00 112.00   1.00    4.00    --  104.43-125.00-150.00   81
 31  \w     79.00 177.00   1.00    4.00    --  104.43  45.00-180.00   98
 32  \w     79.00 177.00   1.00    4.00    --  104.43  45.00 120.00   98
 33  \w     79.00 177.00   1.00    4.00    --  104.43  45.00 -30.00   98
 34  \w     75.00 177.00   1.00    4.00    --  104.43  61.00 150.00  102
 35  \w     75.00 177.00   1.00    4.00    --  104.43  62.00  72.03  102
 36  \w     79.00 177.00   1.00    4.00    --  104.43  45.00-120.00   98
 37  \w   -115.00 -13.00   1.00    1.00    --  -41.63 -57.00 -90.00  102
 38  \w   -116.00 -17.00   1.00    1.00    --  -41.63 -37.00   0.00   99
 39  \w    -47.00 130.00   1.00    1.00    --   41.63   0.00-120.00  177
 40  \w    -47.00 130.00   1.00    1.00    --   41.63   0.00-150.00  177
 41  \w    -47.00 130.00   1.00    1.00    --   41.63   0.00-180.00  177
 42  \w    -47.00 130.00   1.00    1.00    --   41.63   0.00 -90.00  177
 43  \w     27.00  98.00   1.00    1.00    --   41.63-125.00 -30.00   71
;
_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      -0.0635568000
_diffrn_orient_matrix_UB_12      -0.0106238000
_diffrn_orient_matrix_UB_13      -0.2084238000
_diffrn_orient_matrix_UB_21      0.0371417000
_diffrn_orient_matrix_UB_22      -0.1229710000
_diffrn_orient_matrix_UB_23      0.0175406000
_diffrn_orient_matrix_UB_31      -0.3074352000
_diffrn_orient_matrix_UB_32      -0.0126618000
_diffrn_orient_matrix_UB_33      0.0042555000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0290
_diffrn_reflns_av_unetI/netI     0.0118
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.985
_diffrn_reflns_limit_h_max       5
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       15
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       9
_diffrn_reflns_limit_l_min       -9
_diffrn_reflns_number            12090
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.980
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         72.558
_diffrn_reflns_theta_min         6.008
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.684
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.16134
_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    1.238
_exptl_crystal_description       block
_exptl_crystal_F_000             184
_exptl_crystal_size_max          0.5
_exptl_crystal_size_mid          0.4
_exptl_crystal_size_min          0.2
_refine_diff_density_max         0.142
_refine_diff_density_min         -0.178
_refine_diff_density_rms         0.044
_refine_ls_abs_structure_details
;
 Flack x determined using 826 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.09(8)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.056
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     122
_refine_ls_number_reflns         1759
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.056
_refine_ls_R_factor_all          0.0309
_refine_ls_R_factor_gt           0.0307
_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^)+(0.0522P)^2^+0.0582P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0790
_refine_ls_wR_factor_ref         0.0791
_reflns_Friedel_coverage         0.895
_reflns_Friedel_fraction_full    0.996
_reflns_Friedel_fraction_max     0.974
_reflns_number_gt                1755
_reflns_number_total             1759
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4nj00235k2.cif
_cod_data_source_block           8
_cod_depositor_comments
'Adding full bibliography for 7063150--7063171.cif.'
_cod_database_code               7063166
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.875
_shelx_estimated_absorpt_t_min   0.726
_reflns_odcompleteness_completeness 99.76
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_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 Ternary CH refined with riding coordinates:
 C23(H23)
2.b Secondary CH2 refined with riding coordinates:
 C21(H21A,H21B), C22(H22C,H22D), C24(H24A,H24B), C25(H25A,H25B)
2.c Idealised Me refined as rotating group:
 C12(H12A,H12B,H12C)
;
_shelx_res_checksum              16409
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 4.292
_oxdiff_exptl_absorpt_empirical_full_min 0.445