Generation and application of Cu-bound alkyl nitrene for the catalyst-controlled synthesis of cyclic β-amino acids
Tak, Raj K.; Amemiya, Fuyuki; Noda, Hidetoshi; Shibasaki, Masakatsu; Chemical Science  (2021) –; doi:10.1039/D1SC01419F

data_1562234
_publ_section_title
;
 Generation and application of Cu-bound alkyl nitrene for the
 catalyst-controlled synthesis of cyclic \b-amino acids
;
_journal_name_full               'Chemical Science'
_journal_paper_doi               10.1039/D1SC01419F
_journal_year                    2021
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C18 H19 N O2'
_chemical_formula_sum            'C18 H19 N O2'
_chemical_formula_weight         281.34
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2020-06-29
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2020-12-10 deposited with the CCDC.	2021-04-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 99.0810(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   10.47410(10)
_cell_length_b                   10.48660(10)
_cell_length_c                   13.73150(10)
_cell_measurement_reflns_used    25043
_cell_measurement_temperature    93.15
_cell_measurement_theta_max      76.0470
_cell_measurement_theta_min      3.2570
_cell_volume                     1489.33(2)
_computing_cell_refinement       'CrysAlisPro 1.171.40.14a (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.40.14a (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.40.14a (Rigaku OD, 2018)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      93.15
_diffrn_detector                 'Rigaku HyPix-6000 area detector'
_diffrn_detector_area_resol_mean 10.0
_diffrn_detector_type            'HPC area detector'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.967
_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    -26.00  60.00   0.50    0.05    --   47.95 -25.00  20.00  172
  2  \w     41.00  68.00   0.50    0.05    --   47.95  38.00 -90.00   54
  3  \w     36.00 122.00   0.50    0.05    --   47.95  25.00-175.00  172
  4  \w     93.00 174.00   0.50    0.11    --  106.49  25.00-175.00  162
  5  \w    144.00 170.00   0.50    0.11    --  106.49  61.00 -60.00   52
  6  \w     91.00 119.00   0.50    0.11    --  106.49  61.00 -60.00   56
  7  \w     92.00 118.00   0.50    0.11    --  106.49  61.00 -90.00   52
  8  \w     98.00 127.00   0.50    0.11    --  106.49  45.00-120.00   58
  9  \w     86.00 112.00   0.50    0.11    --  106.49  77.00 -90.00   52
 10  \w     85.00 111.00   0.50    0.11    --  106.49  77.00-120.00   52
 11  \w     85.00 120.00   0.50    0.11    --  106.49  77.00-150.00   70
 12  \w     84.00 111.00   0.50    0.11    --  106.49  77.00-180.00   54
 13  \w     33.00 110.00   0.50    0.05    --   47.95  57.00 -60.00  154
 14  \w     31.00  60.00   0.50    0.11    --  106.49 -25.00  20.00   58
 15  \w     36.00  93.00   0.50    0.05    --   47.95  38.00-120.00  114
 16  \w    -60.00  27.00   0.50    0.05    --  -47.95  25.00-175.00  174
 17  \w    -66.00 -25.00   0.50    0.11    -- -100.00  25.00-175.00   82
 18  \w    -81.00 -32.00   0.50    0.11    -- -100.00  45.00 -60.00   98
 19  \w    -67.00 -25.00   0.50    0.11    -- -100.00  30.00   0.00   84
 20  \w    -77.00 -30.00   0.50    0.11    -- -100.00  61.00  30.00   94
 21  \w    -70.00 -28.00   0.50    0.11    -- -100.00  45.00   0.00   84
 22  \w    -66.00 -27.00   0.50    0.11    -- -100.00 125.00 -60.00   78
 23  \w    -96.00 -20.00   0.50    0.05    --  -47.95 125.00 -60.00  152
 24  \w   -102.00 -33.00   0.50    0.11    -- -100.00  61.00 -60.00  138
 25  \w   -116.00 -90.00   0.50    0.11    -- -100.00  61.00  30.00   52
 26  \w   -116.00 -80.00   0.50    0.11    -- -100.00 125.00 -60.00   72
 27  \w   -122.00 -36.00   0.50    0.05    --  -47.95 -25.00  20.00  172
 28  \w    -70.00 -31.00   0.50    0.11    -- -100.00  45.00 150.00   78
 29  \w   -110.00 -84.00   0.50    0.11    -- -100.00 -61.00   0.00   52
 30  \w   -102.00 -77.00   0.50    0.11    -- -100.00 -78.00 -19.05   50
 31  \w   -103.00 -77.00   0.50    0.11    -- -100.00 -77.00 -60.00   52
 32  \w   -104.00 -78.00   0.50    0.11    -- -100.00 -77.00 -73.19   52
 33  \w   -101.00 -76.00   0.50    0.11    -- -100.00 -79.00 -59.08   50
 34  \w   -104.00 -78.00   0.50    0.11    -- -100.00 -77.00 -30.00   52
 35  \w   -109.00 -83.00   0.50    0.11    -- -100.00 -64.00 -70.68   52
 36  \w   -101.00 -75.00   0.50    0.11    -- -100.00 -82.00-104.47   52
 37  \w   -103.00 -77.00   0.50    0.11    -- -100.00 -77.00 -90.00   52
 38  \w   -110.00 -84.00   0.50    0.11    -- -100.00 -61.00 -60.00   52
 39  \w   -111.00 -85.00   0.50    0.11    -- -100.00 -61.00 -30.00   52
 40  \w   -114.00 -87.00   0.50    0.11    -- -100.00 -43.00 -75.11   54
 41  \w   -117.00 -84.00   0.50    0.11    -- -100.00 -61.00-120.00   66
 42  \w   -114.00 -84.00   0.50    0.11    -- -100.00 -60.00 -96.28   60
 43  \w   -124.00 -84.00   0.50    0.11    -- -100.00 -66.00  -7.30   80
 44  \w   -105.00 -80.00   0.50    0.11    -- -100.00 -77.00   0.00   50
 45  \w   -120.00 -25.00   0.50    0.05    --  -47.95 -77.00 -30.00  190
 46  \w   -120.00 -25.00   0.50    0.05    --  -47.95 -77.00-120.00  190
 47  \w   -120.00 -25.00   0.50    0.05    --  -47.95 -77.00 -90.00  190
 48  \w   -125.00 -86.00   0.50    0.11    -- -100.00 -52.00 -94.98   78
 49  \w   -156.00 -86.00   0.50    0.11    -- -100.00 -54.00 -15.14  140
 50  \w   -167.00-141.00   0.50    0.11    -- -100.00 -82.00-104.47   52
 51  \w   -172.00-125.00   0.50    0.11    -- -100.00 -77.00 -73.19   94
 52  \w   -173.00 -87.00   0.50    0.11    -- -100.00 -25.00  20.00  172
 53  \w   -173.00-119.00   0.50    0.11    -- -100.00 -79.00 -59.08  108
 54  \w   -173.00-140.00   0.50    0.11    -- -100.00 -77.00 -90.00   66
 55  \w   -171.00 -85.00   0.50    0.11    -- -100.00 -58.00 -29.21  172
 56  \w   -173.00 -77.00   0.50    0.11    -- -100.00 -77.00-123.75  192
 57  \w   -172.00-146.00   0.50    0.11    -- -100.00 -78.00 -19.05   52
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Rigaku XtaLAB Synergy-Custom'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.1370458000
_diffrn_orient_matrix_UB_12      0.0104251000
_diffrn_orient_matrix_UB_13      0.0266659000
_diffrn_orient_matrix_UB_21      0.0512671000
_diffrn_orient_matrix_UB_22      -0.0470031000
_diffrn_orient_matrix_UB_23      0.1051868000
_diffrn_orient_matrix_UB_31      0.0276338000
_diffrn_orient_matrix_UB_32      0.1388643000
_diffrn_orient_matrix_UB_33      0.0335880000
_diffrn_radiation_monochromator  'multi-layer mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0291
_diffrn_reflns_av_unetI/netI     0.0203
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.967
_diffrn_reflns_limit_h_max       13
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            28665
_diffrn_reflns_point_group_measured_fraction_full 0.976
_diffrn_reflns_point_group_measured_fraction_max 0.929
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.213
_diffrn_reflns_theta_min         3.259
_diffrn_source                   'rotating anode X-ray generator'
_diffrn_source_type              micromax007
_exptl_absorpt_coefficient_mu    0.648
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.56816
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.14a (Rigaku Oxford Diffraction, 2018)
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    1.255
_exptl_crystal_description       prism
_exptl_crystal_F_000             600
_exptl_crystal_size_max          0.3
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.341
_refine_diff_density_min         -0.307
_refine_diff_density_rms         0.035
_refine_ls_abs_structure_details
;
 Flack x determined using 2511 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.02(6)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.038
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     381
_refine_ls_number_reflns         5802
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.038
_refine_ls_R_factor_all          0.0292
_refine_ls_R_factor_gt           0.0287
_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^)+(0.0436P)^2^+0.2272P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0743
_refine_ls_wR_factor_ref         0.0746
_reflns_Friedel_coverage         0.818
_reflns_Friedel_fraction_full    0.949
_reflns_Friedel_fraction_max     0.887
_reflns_number_gt                5673
_reflns_number_total             5802
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1sc01419f2.cif
_cod_data_source_block           exp_387
_cod_depositor_comments
;

2022-05-30
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_moiety     '2(C18 H19 N O2)'
_cod_original_formula_sum        'C36 H38 N2 O4'
_cod_original_formula_units_Z    2
_cod_original_formula_weight     562.68
_cod_database_code               1562234
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N O'
_chemical_oxdiff_usercomment     Raj
_reflns_odcompleteness_completeness 100.00
_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.a Riding coordinates:
 N2(H2)
2.b Secondary CH2 refined with riding coordinates:
 C00C(H00A,H00C), C00J(H00D,H00E), C00O(H00Q,H00S), C00T(H00F,H00H), C00U(H00U,
 H00V), C00W(H00W,H00Y)
2.c Aromatic/amide H refined with riding coordinates:
 N1(H1), C00B(H00B), C00G(H00G), C00H(H00O), C00I(H00I), C00K(H00P),
 C00L(H00L), C00M(H00M), C00Q(H00T), C00R(H00R), C00X(H00X), C00Y(H00Z),
 C010(H010), C011(H011), C012(H012), C013(H013), C014(H014), C015(H015),
 C016(H016)
2.d Idealised Me refined as rotating group:
 C00V(H00J,H00K,H00N), C00Z(H00,H,HA)
;
_shelx_res_checksum              7369
_shelx_hkl_checksum              72309
_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 1.472
_oxdiff_exptl_absorpt_empirical_full_min 0.614