The crystal structure of a matrine derivative: 41 S,7aS,12S,13aR,13bR)-12-(4-methylpiperazin-1-yl)dodecahydro-1H,5H,10H-dipyrido[2,1-f:3′,2′,1′-ij][1,6]naphthyridin-10-one, C20H34N4O
Cheng, Xing-An; Zhan-Mei, Liu; Bo, Wu; Su-Qing, Huang; Xia-Ling, Xiong; Xu-Hong, Jiang; Zeitschrift für Kristallographie - New Crystal Structures 233 (2018) 283–285; doi:10.1515/ncrs-2017-0282

data_8106127
_publ_section_title
;
 The crystal structure of a matrine derivative: 41
 S,7aS,12S,13aR,13bR)-12-(4-methylpiperazin-1-yl)dodecahydro-1H,5H,10H-dipyrido[2,1-f:3&#x2032;,2&#x2032;,1&#x2032;-ij][1,6]naphthyridin-10-one,
 C20H34N4O
;
_journal_issue                   2
_journal_name_full
'Zeitschrift f\"ur Kristallographie - New Crystal Structures'
_journal_page_first              283
_journal_page_last               285
_journal_paper_doi               10.1515/ncrs-2017-0282
_journal_volume                  233
_journal_year                    2018
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C20 H34 N4 O'
_chemical_formula_sum            'C20 H34 N4 O'
_chemical_formula_weight         346.509
_space_group_crystal_system      triclinic
_space_group_IT_number           1
_space_group_name_Hall           'P 1'
_space_group_name_H-M_alt        'P 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_cell_angle_alpha                73.200(7)
_cell_angle_beta                 75.372(6)
_cell_angle_gamma                71.091(7)
_cell_formula_units_Z            2
_cell_length_a                   7.8545(6)
_cell_length_b                   10.8802(9)
_cell_length_c                   12.3714(9)
_cell_measurement_reflns_used    3348
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      73.7300
_cell_measurement_theta_min      3.8490
_cell_volume                     942.65(14)
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'XS (Sheldrick, 2008)'
_diffrn_ambient_temperature      293(2)
_diffrn_measured_fraction_theta_full 0.962
_diffrn_measured_fraction_theta_max 0.962
_diffrn_measurement_device_type  'multiwire proportional'
_diffrn_measurement_method       'phi and omega scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0172
_diffrn_reflns_av_unetI/netI     0.0165
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -10
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            6049
_diffrn_reflns_theta_full        74.32
_diffrn_reflns_theta_max         74.32
_diffrn_reflns_theta_min         3.79
_diffrn_source                   'fine-focus sealed tube'
_exptl_absorpt_coefficient_mu    0.598
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.77445
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.221
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             380
_exptl_crystal_size_max          0.6
_exptl_crystal_size_mid          0.4
_exptl_crystal_size_min          0.3
_refine_diff_density_max         0.844
_refine_diff_density_min         -0.296
_refine_diff_density_rms         0.063
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   -0.1(3)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.026
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     453
_refine_ls_number_reflns         4265
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.026
_refine_ls_R_factor_all          0.0598
_refine_ls_R_factor_gt           0.0591
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.1160P)^2^+0.4070P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1632
_refine_ls_wR_factor_ref         0.1641
_reflns_number_gt                4193
_reflns_number_total             4265
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            suppl_ncrs-2017-0282_suppl.cif
_cod_data_source_block           p1
_cod_depositor_comments
;

2025-04-27
Z value fixed to be consistent with given formula
                 miguel
;
_cod_original_formula_units_Z            19
_cod_original_cell_volume        942.65(13)
_cod_database_code               8106127
_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:
 C13(H13), C6'(H6'), C5'(H5'), C6(H6), C7'(H7'), C7(H7), C5(H5), C11'(H11'),
 C13'(H13'), C11(H11)
2.b Secondary CH2 refined with riding coordinates:
 C14(H14A,H14B), C10(H10A,H10B), C4'(H4'A,H4'B), C9(H9A,H9B), C21(H21A,H21B),
 C23(H23A,H23B), C3'(H3'A,H3'B), C17'(H17C,H17D), C24(H24A,H24B), C20(H20A,
 H20B), C2(H2A,H2B), C24'(H24C,H24D), C20'(H20C,H20D), C8(H8A,H8B), C4(H4A,H4B),
  C3(H3A,H3B), C9'(H9'A,H9'B), C14'(H14C,H14D), C23'(H23C,H23D), C21'(H21C,
 H21D), C10'(H10C,H10D), C12(H12A,H12B), C2'(H2'A,H2'B), C8'(H8'A,H8'B),
 C12'(H12C,H12D), C17(H17A,H17B)
2.c Idealised Me refined as rotating group:
 C25(H25A,H25B,H25C), C25'(H25D,H25E,H25F)
;
_olex2_submission_special_instructions 'No special instructions were received'