Copper-catalyzed direct regioselective C5-H alkylation reactions of functionalized indoles with α-diazomalonates.
Isono, Tomohiro; Harada, Shingo; Yanagawa, Mai; Nemoto, Tetsuhiro; Chemical science 16 (2025) 14967–14975; doi:10.1039/d5sc03417e

data_1575092
_publ_section_title
;
 Copper-catalyzed direct regioselective C5-H alkylation reactions of
 functionalized indoles with &#x3b1;-diazomalonates.
;
_journal_issue                   33
_journal_name_full               'Chemical science'
_journal_page_first              14967
_journal_page_last               14975
_journal_paper_doi               10.1039/d5sc03417e
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C24 H23 N O5'
_chemical_formula_sum            'C24 H23 N O5'
_chemical_formula_weight         405.43
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-02-27
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2025-05-02 deposited with the CCDC.	2025-07-14 downloaded from the CCDC.
;
_cell_angle_alpha                80.226(6)
_cell_angle_beta                 71.038(5)
_cell_angle_gamma                81.929(6)
_cell_formula_units_Z            2
_cell_length_a                   8.1618(2)
_cell_length_b                   11.0202(3)
_cell_length_c                   12.1858(3)
_cell_measurement_reflns_used    8888
_cell_measurement_temperature    93(2)
_cell_measurement_theta_max      136.370
_cell_measurement_theta_min      7.740
_cell_volume                     1017.24(6)
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/2 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      93.15
_diffrn_detector                 'Rigaku curved IP area detector'
_diffrn_detector_area_resol_mean 10.000
_diffrn_detector_type            'Rigaku Imaging plate area detector'
_diffrn_measured_fraction_theta_full 0.982
_diffrn_measured_fraction_theta_max 0.981
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Rigaku VariMax RAPID'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_collimation    1.0
_diffrn_radiation_monochromator  'multi-layer mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54187
_diffrn_reflns_av_R_equivalents  0.0356
_diffrn_reflns_av_unetI/netI     0.0445
_diffrn_reflns_Laue_measured_fraction_full 0.982
_diffrn_reflns_Laue_measured_fraction_max 0.981
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            11746
_diffrn_reflns_point_group_measured_fraction_full 0.982
_diffrn_reflns_point_group_measured_fraction_max 0.981
_diffrn_reflns_theta_full        67.687
_diffrn_reflns_theta_max         68.186
_diffrn_reflns_theta_min         3.870
_diffrn_source                   'rotating anode X-ray generator'
_diffrn_source_current           30.0
_diffrn_source_power             1.2
_diffrn_source_target            Cu
_diffrn_source_type              'MicroMax 007'
_diffrn_source_voltage           40.0
_exptl_absorpt_coefficient_mu    0.760
_exptl_absorpt_correction_T_max  1.0000
_exptl_absorpt_correction_T_min  0.7707
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'ABSCOR (Rigaku, 1995)'
_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    1.324
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             428
_exptl_crystal_preparation       As-Grown
_exptl_crystal_recrystallization_method 'Batch Method'
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.211
_refine_diff_density_min         -0.190
_refine_diff_density_rms         0.043
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.054
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     305
_refine_ls_number_reflns         3652
_refine_ls_number_restraints     2
_refine_ls_restrained_S_all      1.057
_refine_ls_R_factor_all          0.0563
_refine_ls_R_factor_gt           0.0429
_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^)+(0.0579P)^2^+0.1884P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1096
_refine_ls_wR_factor_ref         0.1165
_reflns_Friedel_coverage         0.000
_reflns_number_gt                2920
_reflns_number_total             3652
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc03417e2.cif
_cod_data_source_block           shelxl
_cod_depositor_comments          'Adding full bibliography for 1575092.cif.'
_cod_database_code               1575092
_shelx_shelxl_version_number     2019/2
_shelx_estimated_absorpt_t_max   0.928
_shelx_estimated_absorpt_t_min   0.928
_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. Restrained distances
 O5-C00O \\sim O5A-C00O
 with sigma of 0.02
 O5-C00U \\sim O5A-C00U
 with sigma of 0.02
 O5-C00U \\sim O5-C00V
 with sigma of 0.02
 O4-C00O \\sim O4A-C00O
 with sigma of 0.02
 O4-O5A \\sim O4A-O5A
 with sigma of 0.02
 O4-C00V \\sim O4A-C00V
 with sigma of 0.02
3. Others
 Sof(O5A)=1-FVAR(1)
 Sof(O5)=FVAR(1)
 Sof(C00V)=Sof(H00X)=Sof(H00Y)=Sof(H)=1-FVAR(2)
 Sof(C00U)=Sof(H00U)=Sof(H00V)=Sof(H00W)=FVAR(2)
 Sof(O4A)=1-FVAR(3)
 Sof(O4)=FVAR(3)
4.a Ternary CH refined with riding coordinates:
 C00J(H00J)
4.b Secondary CH2 refined with riding coordinates:
 C00I(H00C,H00D)
4.c Aromatic/amide H refined with riding coordinates:
 C00A(H00A), C00B(H00B), C00E(H00E), C00F(H00F), C00H(H00H), C00L(H00L),
 C00M(H00M), C00N(H00N), C00Q(H00Q), C00R(H00R), C00S(H00S)
4.d Idealised Me refined as rotating group:
 C00P(H00G,H00I,H00K), C00T(H00O,H00P,H00T), C00U(H00U,H00V,H00W), C00V(H00X,
 H00Y,H)
;
_shelx_res_checksum              84312
_olex2_exptl_crystal_mounting_method 'MiTeGen MicroLoops'
_olex2_submission_special_instructions 'No special instructions were received'