Pd(II)-Catalyzed Domino Aminopalladation/Desymmetrizative Ring-Opening of Diazabicycles: Synthesis of Indolyl-Functionalized Cyclopentenylamines
Lin, Haoyuan; Meng, Junjie; Zhang, Yue; Li, Zhaodong; Chemical Communications  (2026) –; doi:10.1039/D6CC00349D

data_7135690
_publ_section_title
;
 Pd(II)-catalyzed domino aminopalladation/desymmetrizative ring-opening of
 diazabicycles: synthesis of indolyl-functionalized cyclopentenylamines.
;
_journal_issue                   31
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              8046
_journal_page_last               8050
_journal_paper_doi               10.1039/d6cc00349d
_journal_volume                  62
_journal_year                    2026
_chemical_formula_moiety         'C32 H33 N3 O6 S'
_chemical_formula_sum            'C32 H33 N3 O6 S'
_chemical_formula_weight         587.67
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-05-24
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-12-03 deposited with the CCDC.	2026-03-31 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 99.300(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.9426(3)
_cell_length_b                   23.9740(6)
_cell_length_c                   12.4843(3)
_cell_measurement_reflns_used    10921
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      73.1680
_cell_measurement_theta_min      3.6890
_cell_volume                     2936.69(14)
_computing_cell_refinement       'CrysAlisPro 1.171.43.92a (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 43.92a 64-bit (release 05-10-2023))'
_computing_data_reduction        'CrysAlisPro 1.171.43.92a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/1 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.979
_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    -24.00  27.00   0.50    0.50    --  -46.12  44.00 -60.00  102
  2  \w   -118.00 -64.00   0.50    0.50    --  -46.12 -44.00 148.00  108
  3  \w    -57.00 -31.00   0.50    0.50    --  -46.12 -44.00 148.00   52
  4  \w   -152.00-127.00   0.50    3.00    --  -99.00 -44.00 148.00   50
  5  \w     85.00 110.00   0.50    3.00    --   99.00  44.00 -60.00   50
  6  \w    118.00 170.00   0.50    3.00    --   99.00  44.00 -60.00  104
  7  \w     26.00  51.00   0.50    3.00    --   99.00 -44.00 148.00   50
  8  \w    -24.00  28.00   0.50    0.50    --  -46.12  19.00  90.00  104
  9  \w     75.00 105.00   0.50    0.50    --   46.12  44.00 -60.00   60
 10  \w     19.00  91.00   0.50    0.50    --   46.12-125.00 -90.00  144
 11  \w      4.00  30.00   0.50    0.50    --   46.12 -44.00 148.00   52
 12  \w    -69.00 -35.00   0.50    3.00    --  -99.00  61.00 -60.00   68
 13  \w   -118.00 -75.00   0.50    3.00    --  -99.00-125.00 -90.00   86
 14  \w    -69.00 -41.00   0.50    3.00    --  -99.00  61.00 120.00   56
 15  \w    -72.00 -46.00   0.50    3.00    --  -99.00  77.00-180.00   52
 16  \w    -68.00 -42.00   0.50    3.00    --  -99.00  61.00 -90.00   52
 17  \w     26.00  70.00   0.50    3.00    --   99.00 -61.00 150.00   88
 18  \w     40.00 104.00   0.50    3.00    --   99.00 -94.00  30.00  128
 19  \w     28.00  53.00   0.50    3.00    --   99.00 -45.00  90.00   50
 20  \w     69.00 112.00   0.50    3.00    --   99.00-125.00  30.00   86
 21  \w     27.00  52.00   0.50    3.00    --   99.00 -45.00 -60.00   50
 22  \w     31.00  57.00   0.50    3.00    --   99.00-125.00  30.00   52
 23  \w     27.00  52.00   0.50    3.00    --   99.00 -45.00 120.00   50
 24  \w     27.00  53.00   0.50    3.00    --   99.00 -45.00-180.00   52
 25  \w     27.00  71.00   0.50    3.00    --   99.00 -61.00  60.00   88
 26  \w     97.00 123.00   0.50    3.00    --   99.00  45.00  60.00   52
 27  \w    133.00 169.00   0.50    3.00    --   99.00  45.00  60.00   72
 28  \w     37.00  64.00   0.50    3.00    --   99.00 -61.00   0.00   54
 29  \w     84.00 158.00   0.50    3.00    --   99.00  15.00  60.00  148
 30  \w    150.00 175.00   0.50    3.00    --   99.00  15.00 -90.00   50
 31  \w     99.00 137.00   0.50    3.00    --   99.00  15.00 -90.00   76
 32  \w     28.00  53.00   0.50    3.00    --   99.00 -45.00  60.00   50
 33  \w     27.00  52.00   0.50    3.00    --   99.00 -45.00 -30.00   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1420374000
_diffrn_orient_matrix_UB_12      0.0250025000
_diffrn_orient_matrix_UB_13      0.0401163000
_diffrn_orient_matrix_UB_21      0.0021787000
_diffrn_orient_matrix_UB_22      0.0248811000
_diffrn_orient_matrix_UB_23      -0.1134642000
_diffrn_orient_matrix_UB_31      -0.0669771000
_diffrn_orient_matrix_UB_32      0.0536822000
_diffrn_orient_matrix_UB_33      0.0340025000
_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  0.0541
_diffrn_reflns_av_unetI/netI     0.0435
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.979
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       29
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            23034
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.979
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.378
_diffrn_reflns_theta_min         3.687
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.391
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.73611
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.92a (Rigaku Oxford Diffraction, 2023)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.329
_exptl_crystal_description       block
_exptl_crystal_F_000             1240
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.519
_refine_diff_density_min         -0.591
_refine_diff_density_rms         0.070
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.111
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     428
_refine_ls_number_reflns         5789
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.111
_refine_ls_R_factor_all          0.0887
_refine_ls_R_factor_gt           0.0809
_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^)+(0.0279P)^2^+8.2390P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1770
_refine_ls_wR_factor_ref         0.1811
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5129
_reflns_number_total             5789
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d6cc00349d2.cif
_cod_data_source_block           exp_2823_auto
_cod_depositor_comments          'Adding full bibliography for 7135690.cif.'
_cod_database_code               7135690
_shelx_shelxl_version_number     2018/1
_shelx_estimated_absorpt_t_max   0.873
_shelx_estimated_absorpt_t_min   0.873
_reflns_odcompleteness_completeness 99.84
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     69.95
_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. Others
 Fixed Sof: C21B(0.5) H21a(0.5) H21b(0.5) O1A(0.5) O2A(0.5) O1B(0.5) O2B(0.5)
 C22A(0.5) H22a(0.5) H22b(0.5) H22c(0.5) C21A(0.5) H21c(0.5) H21d(0.5)
 C22B(0.5) H22d(0.5) H22e(0.5) H22f(0.5) C20A(0.5) C20B(0.5)
3.a Ternary CH refined with riding coordinates:
 C15(H15), C19(H19)
3.b Secondary CH2 refined with riding coordinates:
 C18(H18a,H18b), C24(H24a,H24b), C21B(H21a,H21b), C21A(H21c,H21d)
3.c Aromatic/amide H refined with riding coordinates:
 N2(H2), C16(H16), C17(H17), C10(H10), C27(H27), C13(H13), C28(H28), C11(H11),
 C12(H12), C31(H31), C8(H8), C4(H4), C30(H30), C5(H5), C6(H6), C7(H7)
3.d Idealised Me refined as rotating group:
 C32(H32a,H32b,H32c), C25(H25a,H25b,H25c), C22A(H22a,H22b,H22c), C22B(H22d,
 H22e,H22f)
;
_shelx_res_checksum              53756
_shelx_hkl_checksum              57207
_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 2.079
_oxdiff_exptl_absorpt_empirical_full_min 0.448