The crystal structure of a matrine derivative, 13-(methylamine-1-yl) carbodithioate matrine, C17H27N3OS2
Hui-Qing, He; Fang-Yun, Dong; Han-Hui, Zhang; Jing-Min, Ye; Chun-Can, Tan; Xu-Hong, Jiang; Zi-Zhao, Zheng; Xiao-Jing, Lv; Xing-An, Cheng; Zeitschrift für Kristallographie - New Crystal Structures 235 (2020) 685–687; doi:10.1515/ncrs-2019-0899

data_8105257
_publ_section_title
;
 The crystal structure of a matrine derivative, 13-(methylamine-1-yl)
 carbodithioate matrine, C17H27N3OS2
;
_journal_issue                   3
_journal_name_full
'Zeitschrift f\"ur Kristallographie - New Crystal Structures'
_journal_page_first              685
_journal_page_last               687
_journal_paper_doi               10.1515/ncrs-2019-0899
_journal_volume                  235
_journal_year                    2020
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C17 H27 N3 O S2'
_chemical_formula_sum            'C17 H27 N3 O S2'
_chemical_formula_weight         353.53
_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   geom
_atom_sites_solution_primary     iterative
_atom_sites_solution_secondary   difmap
_cell_angle_alpha                90
_cell_angle_beta                 99.2730(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   8.80520(10)
_cell_length_b                   10.88600(10)
_cell_length_c                   18.6705(2)
_cell_measurement_reflns_used    15270
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      73.5510
_cell_measurement_theta_min      4.7680
_cell_volume                     1766.24(3)
_computing_cell_refinement       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.33c (Rigaku OD, 2017)'
_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    'olex2.solve (Bourhis et al., 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.983
_diffrn_measured_fraction_theta_max 0.983
_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    -42.00 -14.70   0.35    0.50    --    0.00 -77.00-180.00   78
  2  \w    -41.00  25.85   0.35    0.50    --    0.00 -77.00  60.00  191
  3  \w     43.00  85.00   0.35    0.50    --    0.00  38.00  90.00  120
  4  \w      3.00  28.20   0.35    0.50    --    0.00 -77.00-180.00   72
  5  \w     -6.00  28.30   0.35    0.50    --    0.00 -77.00-120.00   98
  6  \w    -33.00  -5.00   0.35    0.50    --    0.00 -82.00-120.00   80
  7  \w    -17.00  27.10   0.35    0.50    --    0.00  38.00  90.00  126
  8  \w     78.00 160.25   0.35    3.00    --   94.60  30.00-120.00  235
  9  \w     78.00 182.65   0.35    3.00    --   94.60  30.00 -90.00  299
 10  \w    116.00 182.85   0.35    3.00    --   94.60  82.00 -60.00  191
 11  \w    157.00 183.25   0.35    3.00    --   94.60  30.00 120.00   75
 12  \w     87.00 142.65   0.35    3.00    --   94.60  30.00 120.00  159
 13  \w     65.00  99.30   0.35    3.00    --   94.60 -45.00 -30.00   98
 14  \w    106.00 168.65   0.35    3.00    --   94.60  30.00 150.00  179
 15  \w     80.00 113.25   0.35    3.00    --   94.60  77.00  90.00   95
 16  \w     86.00 124.85   0.35    3.00    --   94.60 -82.00  60.00  111
 17  \w     48.00 123.25   0.35    3.00    --   94.60 -82.00 150.00  215
 18  \w     14.00 124.95   0.35    3.00    --   94.60 -82.00   0.00  317
 19  \w    108.00 169.25   0.35    3.00    --   94.60  15.00 -30.00  175
 20  \w     17.00 109.05   0.35    3.00    --   94.60 -61.00   0.00  263
 21  \w      6.00  79.15   0.35    3.00    --   94.60 -30.00  60.00  209
 22  \w      6.00  46.25   0.35    3.00    --   94.60 -30.00   0.00  115
 23  \w     84.00 110.25   0.35    3.00    --   94.60  77.00 -90.00   75
 24  \w     23.00 100.00   0.35    3.00    --   94.60 -30.00-150.00  220
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0962561000
_diffrn_orient_matrix_UB_12      -0.0298103000
_diffrn_orient_matrix_UB_13      0.0743768000
_diffrn_orient_matrix_UB_21      -0.0519606000
_diffrn_orient_matrix_UB_22      0.1216660000
_diffrn_orient_matrix_UB_23      0.0305437000
_diffrn_orient_matrix_UB_31      -0.1394888000
_diffrn_orient_matrix_UB_32      -0.0659426000
_diffrn_orient_matrix_UB_33      0.0228404000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0350
_diffrn_reflns_av_unetI/netI     0.0202
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.983
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            16370
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.912
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.861
_diffrn_reflns_theta_min         4.718
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.788
_exptl_absorpt_correction_T_max  0.601
_exptl_absorpt_correction_T_min  0.573
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.33c (Rigaku Oxford Diffraction, 2017)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.330
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             760
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.2
_refine_diff_density_max         0.441
_refine_diff_density_min         -0.294
_refine_diff_density_rms         0.061
_refine_ls_abs_structure_details
;
Flack H D (1983), Acta Cryst. A39, 876-881'    

 Flack x determined using 2781 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.058(9)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.031
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     417
_refine_ls_number_reflns         6521
_refine_ls_number_restraints     2
_refine_ls_restrained_S_all      1.032
_refine_ls_R_factor_all          0.0306
_refine_ls_R_factor_gt           0.0305
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0572P)^2^+0.4852P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0809
_refine_ls_wR_factor_ref         0.0810
_reflns_Friedel_coverage         0.758
_reflns_Friedel_fraction_full    0.881
_reflns_Friedel_fraction_max     0.832
_reflns_number_gt                6505
_reflns_number_total             6521
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            suppl_ncrs-2019-0899_suppl.cif
_cod_data_source_block           a
_cod_database_code               8105257
_chemical_oxdiff_formula         'C50 H50 O50 Cl0 S1 N1 '
_reflns_odcompleteness_completeness 99.94
_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, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Rigid bond restraints
 C20, S21
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.005
 S21, C20
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
3.a Ternary CH refined with riding coordinates:
 C5(H5), C28(H28), C11(H11), C7(H7), C34(H34), C30(H30), C13(H13), C29(H29),
 C6(H6), C36(H36)
3.b Secondary CH2 refined with riding coordinates:
 C12(H12A,H12B), C17(H17A,H17B), C14(H14A,H14B), C40(H40A,H40B), C9(H9A,H9B),
 C3(H3A,H3B), C2(H2A,H2B), C35(H35A,H35B), C10(H10A,H10B), C37(H37A,H37B),
 C31(H31A,H31B), C27(H27A,H27B), C4(H4A,H4B), C8(H8A,H8B), C25(H25A,H25B),
 C26(H26A,H26B), C32(H32A,H32B), C33(H33A,H33B)
3.c Aromatic/amide H refined with riding coordinates:
 N22(H22), N45(H45)
3.d Idealised Me refined as rotating group:
 C23(H23A,H23B,H23C), C46(H46A,H46B,H46C)
;