NaHMDS/B(C6F5)3-promoted diastereoselective Friedel–Crafts alkylation of indoles/pyrroles with N-tert-butanesulfinylimines: towards the asymmetric synthesis of bisindole alkaloid Calcicamide B
Zhang, Guangshuai; Chen, Xin; Liu, Yan; Peng, Rui; Xu, Mengwei; Yan, Si; Xiao, Jin; Liu, Zishu; Min, Qing; Liao, Gang; Wang, Xiaoji; Qin, Shuanglin; RSC Advances 15 (2025) 43421–43425; doi:10.1039/D5RA06138E

data_7251245
_publ_section_title
;
 NaHMDS/B(C6F5)3-promoted diastereoselective Friedel--Crafts alkylation of
 indoles/pyrroles with N-tert-butanesulfinylimines: towards the asymmetric
 synthesis of bisindole alkaloid Calcicamide B
;
_journal_issue                   51
_journal_name_full               'RSC Advances'
_journal_page_first              43421
_journal_page_last               43425
_journal_paper_doi               10.1039/D5RA06138E
_journal_volume                  15
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C21 H21 N3 O5'
_chemical_formula_sum            'C21 H21 N3 O5'
_chemical_formula_weight         395.41
_space_group_crystal_system      trigonal
_space_group_IT_number           152
_space_group_name_Hall           'P 31 2"'
_space_group_name_H-M_alt        'P 31 2 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-09-16
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2025-10-09 deposited with the CCDC.	2025-11-04 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                120
_cell_formula_units_Z            6
_cell_length_a                   9.5132(2)
_cell_length_b                   9.5132(2)
_cell_length_c                   39.0933(15)
_cell_measurement_reflns_used    5643
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      57.3930
_cell_measurement_theta_min      2.2603
_cell_volume                     3063.98(15)
_computing_cell_refinement       'CrysAlisPro 1.171.41.89a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.41.89a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.41.89a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      293.00
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.996
_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     17.00  76.00   0.50    0.50    --   42.30  77.00-180.00  118
  2  \w     28.00  70.00   0.50    0.50    --   42.30 -82.00 -90.00   84
  3  \w    -47.00  26.00   0.50    0.50    --   42.30 -65.00 120.00  146
  4  \w     80.00 126.00   0.50    0.50    --   42.30  77.00-180.00   92
  5  \w    -38.00  26.00   0.50    0.50    --   42.30 -54.00 -60.00  128
  6  \w    -10.00  16.00   0.50    0.50    --   42.30 -82.00  90.00   52
  7  \w     12.00  69.00   0.50    0.50    --   42.30 -82.00 150.00  114
  8  \w    -27.00  69.00   0.50    0.50    --   42.30 -82.00   0.00  192
  9  \w     32.00  66.00   0.50    0.50    --   42.30 -82.00 -60.00   68
 10  \w    -35.00  -9.00   0.50    0.50    --   42.30 -82.00 -90.00   52
 11  \w     36.00  61.00   0.50    0.50    --   42.30 -54.00 -60.00   50
 12  \w    -47.00  72.00   0.50    0.50    --   42.30 -54.00  30.00  238
 13  \w     36.00  65.00   0.50    0.50    --   42.30 -77.00-180.00   58
 14  \w    -39.00  15.00   0.50    0.50    --   42.30 -82.00 -60.00  108
 15  \w     66.00  97.00   0.50    0.50    --   42.30  82.00-120.00   62
 16  \w     34.00  71.00   0.50    0.50    --   42.30 -32.00 120.00   74
 17  \w    -30.00  -5.00   0.50    0.50    --   42.30 -32.00 120.00   50
 18  \w     44.00  69.00   0.50    0.50    --   42.30 -82.00  30.00   50
 19  \w     30.00  55.00   0.50    0.50    --   42.30  82.00-120.00   50
 20  \w    -29.00  62.00   0.50    0.50    --   42.30 -65.00-150.00  182
 21  \w    -39.00   9.00   0.50    0.50    --   42.30 -77.00-180.00   96
 22  \w      4.00 124.00   0.50    0.50    --   93.70 -42.00 120.00  240
 23  \w     11.00 182.00   0.50    0.50    --   93.70   8.00  60.00  342
 24  \w     44.00  88.00   0.50    0.50    --   93.70 -82.00 -60.00   88
 25  \w     36.00  96.00   0.50    0.50    --   93.70 -82.00-120.00  120
 26  \w      4.00 120.00   0.50    0.50    --   93.70 -50.00 -90.00  232
 27  \w     47.00 109.00   0.50    0.50    --   93.70 -82.00  30.00  124
 28  \w    140.00 176.00   0.50    0.50    --   93.70  17.00 -90.00   72
 29  \w     13.00 112.00   0.50    0.50    --   93.70  17.00 -90.00  198
 30  \w     28.00 127.00   0.50    0.50    --   93.70 -33.00 -90.00  198
 31  \w      6.00  82.00   0.50    0.50    --   93.70 -59.00  60.00  152
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Pro II 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      0.0056189000
_diffrn_orient_matrix_UB_12      0.0370445000
_diffrn_orient_matrix_UB_13      -0.0385015000
_diffrn_orient_matrix_UB_21      -0.1288900000
_diffrn_orient_matrix_UB_22      0.0509315000
_diffrn_orient_matrix_UB_23      0.0052391000
_diffrn_orient_matrix_UB_31      0.1354337000
_diffrn_orient_matrix_UB_32      0.1760075000
_diffrn_orient_matrix_UB_33      0.0065572000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0559
_diffrn_reflns_av_unetI/netI     0.0416
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       46
_diffrn_reflns_limit_l_min       -47
_diffrn_reflns_number            22638
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.303
_diffrn_reflns_theta_min         3.392
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.772
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.51276
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.89a (Rigaku Oxford Diffraction, 2020)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.286
_exptl_crystal_description       block
_exptl_crystal_F_000             1248
_exptl_crystal_size_max          0.06
_exptl_crystal_size_mid          0.05
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.216
_refine_diff_density_min         -0.176
_refine_diff_density_rms         0.036
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   -0.1(4)
_refine_ls_extinction_coef       0.0032(5)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2019/2 (Sheldrick 2019)'
_refine_ls_goodness_of_fit_ref   1.053
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     354
_refine_ls_number_reflns         3728
_refine_ls_number_restraints     380
_refine_ls_restrained_S_all      1.066
_refine_ls_R_factor_all          0.0662
_refine_ls_R_factor_gt           0.0496
_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^)+(0.0774P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1253
_refine_ls_wR_factor_ref         0.1435
_reflns_Friedel_coverage         0.676
_reflns_Friedel_fraction_full    0.985
_reflns_Friedel_fraction_max     0.976
_reflns_number_gt                2775
_reflns_number_total             3728
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra06138e2.cif
_cod_data_source_block           1-3_auto
_cod_original_cell_volume        3063.98(17)
_cod_database_code               7251245
_shelx_shelxl_version_number     2019/3
_shelx_estimated_absorpt_t_max   0.970
_shelx_estimated_absorpt_t_min   0.955
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 1.1(4)
 -0.1(4)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups, All N(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
3. Restrained distances
 O1-C9 \\sim O1A-C9A
 with sigma of 0.02
 O2-C11 \\sim O2A-C11
 with sigma of 0.04
 O1-C11 \\sim O1A-C11
 with sigma of 0.04
 O1-O2 \\sim O1A-O2A
 with sigma of 0.04
 C18-C21 \\sim C18A-C21A
 with sigma of 0.04
 O5-C19 \\sim O5A-C19A
 with sigma of 0.04
 N3-C14 \\sim N3-C14A
 with sigma of 0.02
 C15-C17 \\sim C15A-C17A
 with sigma of 0.04
 C15-C14 \\sim C15A-C14A
 with sigma of 0.02
 C15-C20 \\sim C15A-C20A
 with sigma of 0.02
 C14-C16 \\sim C14A-C16A
 with sigma of 0.04
 C20-C16 \\sim C20A-C16A
 with sigma of 0.04
 C19-C17 \\sim C19A-C17A
 with sigma of 0.04
 C15-C16 \\sim C15A-C16A
 with sigma of 0.02
 O5-C18 \\sim O5A-C18A
 with sigma of 0.02
 O5-C21 \\sim O5A-C21A
 with sigma of 0.02
 O5-C17 \\sim O5A-C17A
 with sigma of 0.04
 C20-C19 \\sim C20A-C19A
 with sigma of 0.02
 C14-C20 \\sim C14A-C20A
 with sigma of 0.04
 C19-C18 \\sim C19A-C18A
 with sigma of 0.02
 C20-C18 \\sim C20A-C18A
 with sigma of 0.04
 C18-C17 \\sim C18A-C17A
 with sigma of 0.02
 C18-C16 \\sim C18A-C16A
 with sigma of 0.04
 C16-C17 \\sim C16A-C17A
 with sigma of 0.02
 N3-C15 \\sim N3-C15A
 with sigma of 0.04
 C15-C19 \\sim C15A-C19A
 with sigma of 0.04
4. Uiso/Uaniso restraints and constraints
O1 \\sim O2 \\sim C10 \\sim C9 \\sim O2A \\sim O1A \\sim C9A \\sim C11: within
2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
N3 \\sim C15 \\sim O5 \\sim C14 \\sim C20 \\sim C19 \\sim C18 \\sim C16 \\sim
C17 \\sim C21 \\sim C14A \\sim C15A \\sim C16A \\sim C17A \\sim C18A \\sim C19A
\\sim C20A \\sim O5A \\sim C21A: within 2A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 2A
5. Others
 Sof(O2A)=Sof(O1A)=Sof(C9A)=Sof(H9AA)=Sof(H9AB)=Sof(H9AC)=1-FVAR(1)
 Sof(O1)=Sof(O2)=Sof(C9)=Sof(H9A)=Sof(H9B)=Sof(H9C)=FVAR(1)
 Sof(H3B)=Sof(C14A)=Sof(H14C)=Sof(H14D)=Sof(C16A)=Sof(H16A)=Sof(C15A)=
 Sof(C20A)=Sof(H20A)=Sof(C19A)=Sof(H19A)=Sof(C18A)=Sof(C17A)=Sof(H17A)=Sof(O5A)=
 Sof(C21A)=Sof(H21D)=Sof(H21E)=Sof(H21F)=1-FVAR(2)
 Sof(H3A)=Sof(C15)=Sof(C20)=Sof(H20)=Sof(C19)=Sof(H19)=Sof(C18)=Sof(C17)=
 Sof(H17)=Sof(C16)=Sof(H16)=Sof(O5)=Sof(C14)=Sof(H14A)=Sof(H14B)=Sof(C21)=
 Sof(H21A)=Sof(H21B)=Sof(H21C)=FVAR(2)
6.a Ternary CH refined with riding coordinates:
 C12(H12)
6.b Secondary CH2 refined with riding coordinates:
 C14(H14A,H14B), C14A(H14C,H14D)
6.c Aromatic/amide H refined with riding coordinates:
 N2(H2), N1(H1), N3(H3A), N3(H3B), C7(H7), C20(H20), C19(H19), C17(H17),
 C16(H16), C4(H4), C1(H1A), C3(H3), C2(H2A), C16A(H16A), C20A(H20A), C19A(H19A),
  C17A(H17A)
6.d Fitted hexagon refined as free rotating group:
 C15(C20,C19,C18,C17,C16), C16A(C15A,C20A,C19A,C18A,C17A)
6.e Idealised Me refined as rotating group:
 C9(H9A,H9B,H9C), C21(H21A,H21B,H21C), C9A(H9AA,H9AB,H9AC), C21A(H21D,H21E,H21F)
;
_shelx_res_checksum              55391
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.722
_oxdiff_exptl_absorpt_empirical_full_min 0.592