Synthesis of 2-acetylnoviosamine derivatives by hydrogenolytic cleavage of a spirocyclopropane.
Salim, Maruan D.; Ferrara, Isabella; Blacque, Olivier; Gademann, Karl; Organic & biomolecular chemistry 23 (2025) 4873–4878; doi:10.1039/d5ob00469a

data_7160505
_publ_section_title
;
 Synthesis of 2-acetylnoviosamine derivatives by hydrogenolytic cleavage
 of a spirocyclopropane.
;
_journal_issue                   20
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              4873
_journal_page_last               4878
_journal_paper_doi               10.1039/d5ob00469a
_journal_volume                  23
_journal_year                    2025
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C20 H27 N O6'
_chemical_formula_sum            'C20 H27 N O6'
_chemical_formula_weight         377.42
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2023-07-13
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_audit_update_record
;
2025-03-10 deposited with the CCDC.	2025-04-17 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   9.5296(2)
_cell_length_b                   9.5745(2)
_cell_length_c                   45.0172(7)
_cell_measurement_reflns_used    24352
_cell_measurement_temperature    160.0(1)
_cell_measurement_theta_max      75.7490
_cell_measurement_theta_min      1.9340
_cell_volume                     4107.42(14)
_computing_cell_refinement       'CrysAlisPro 1.171.42.93a (Rigaku OD, 2023)'
_computing_data_collection       'CrysAlisPro 1.171.42.93a (Rigaku OD, 2023)'
_computing_data_reduction        'CrysAlisPro 1.171.42.93a (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 (Sheldrick, 2015b)'
_computing_structure_solution    'SHELXT (Sheldrick, 2015a)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      160.0(1)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.3801
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 1.000
_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    -87.00 -20.00   1.00    3.73    --  -41.01 125.00-120.00   67
  2  \w    -67.00  35.00   1.00    3.73    --  -41.01  37.00-120.00  102
  3  \w     13.00  41.00   1.00    3.73    --   41.01  50.00  68.34   28
  4  \w     12.00  38.00   1.00    3.73    --   41.01  52.00 -85.34   26
  5  \w     12.00  38.00   1.00    3.73    --   41.01  52.00 160.32   26
  6  \w     12.00  38.00   1.00    3.73    --   41.01  52.00-131.00   26
  7  \w     13.00  41.00   1.00    3.73    --   41.01  50.00 178.76   28
  8  \w     12.00  38.00   1.00    3.73    --   41.01  52.00-167.20   26
  9  \w    -11.00  75.00   1.00    3.73    --   41.01 -77.00 120.00   86
 10  \w     13.00  41.00   1.00    3.73    --   41.01  50.00-110.79   28
 11  \w      6.00  82.00   1.00    3.73    --   41.01 -99.00 150.00   76
 12  \w     12.00  39.00   1.00    3.73    --   41.01  51.00-142.39   27
 13  \w     13.00  41.00   1.00    3.73    --   41.01  50.00 143.02   28
 14  \w     12.00  38.00   1.00    3.73    --   41.01  52.00 127.76   26
 15  \w     13.00  45.00   1.00    3.73    --   41.01  48.00  94.62   32
 16  \w     13.00  41.00   1.00    3.73    --   41.01  50.00  39.23   28
 17  \w     13.00  43.00   1.00    3.73    --   41.01  49.00 120.38   30
 18  \w     38.00 109.00   1.00   10.93    --  113.00-111.00 -60.00   71
 19  \w     97.00 178.00   1.00   10.93    --  113.00  45.00 120.00   81
 20  \w     61.00 146.00   1.00   10.93    --  113.00 178.00-150.00   85
 21  \w     38.00 109.00   1.00   10.93    --  113.00-111.00-120.00   71
 22  \w     38.00 109.00   1.00   10.93    --  113.00-111.00 150.00   71
 23  \w    113.00 178.00   1.00   10.93    --  113.00  61.00 150.00   65
 24  \w     97.00 178.00   1.00   10.93    --  113.00  45.00  90.00   81
 25  \w    105.00 178.00   1.00   10.93    --  113.00 111.00   0.00   73
 26  \w     39.00 143.00   1.00   10.93    --  113.00 -61.00 -90.00  104
 27  \w    113.00 178.00   1.00   10.93    --  113.00  61.00   0.00   65
 28  \w     29.00 107.00   1.00   10.93    --  113.00 -94.00 -90.00   78
 29  \w     38.00 109.00   1.00   10.93    --  113.00-111.00  90.00   71
 30  \w    115.00 178.00   1.00   10.93    --  113.00  77.00 120.00   63
 31  \w    115.00 178.00   1.00   10.93    --  113.00  77.00 -30.00   63
 32  \w     38.00 109.00   1.00   10.93    --  113.00-111.00  30.00   71
 33  \w     38.00 109.00   1.00   10.93    --  113.00-111.00-180.00   71
 34  \w     86.00 178.00   1.00   10.93    --  113.00  41.00 -50.44   92
 35  \w     38.00 109.00   1.00   10.93    --  113.00-111.00  60.00   71
 36  \w     34.00 108.00   1.00   10.93    --  113.00-104.00 -96.00   74
 37  \w     38.00 109.00   1.00   10.93    --  113.00-111.00 -30.00   71
 38  \w     35.00 144.00   1.00   10.93    --  113.00 -30.00-120.00  109
 39  \w     38.00 109.00   1.00   10.93    --  113.00-111.00-150.00   71
 40  \w     38.00 109.00   1.00   10.93    --  113.00-111.00 120.00   71
 41  \w     38.00 141.00   1.00   10.93    --  113.00 -45.00 -30.00  103
 42  \w     38.00 109.00   1.00   10.93    --  113.00-111.00   0.00   71
 43  \w     86.00 178.00   1.00   10.93    --  113.00  42.00  57.23   92
 44  \w    -71.00  30.00   1.00    3.73    --  -41.01  57.00  60.00  101
 45  \w   -117.00 -15.00   1.00    3.73    --  -41.01 -37.00  60.00  102
 46  \w    -67.00  35.00   1.00    3.73    --  -41.01  37.00   0.00  102
 47  \w     12.00  38.00   1.00    3.73    --   41.01  52.00 -52.50   26
 48  \w     12.00  38.00   1.00    3.73    --   41.01  52.00 -30.61   26
 49  \w     13.00  53.00   1.00    3.73    --   41.01  45.00 -32.18   40
 50  \w     12.00  38.00   1.00    3.73    --   41.01  52.00  89.62   26
 51  \w     15.00 117.00   1.00    3.73    --   41.01  37.00-150.00  102
 52  \w     13.00  53.00   1.00    3.73    --   41.01  45.00  54.86   40
 53  \w     12.00  38.00   1.00    3.73    --   41.01  52.00  17.06   26
 54  \w     12.00  39.00   1.00    3.73    --   41.01  51.00   4.46   27
 55  \w     15.00 117.00   1.00    3.73    --   41.01  37.00 -60.00  102
 56  \w     86.00 178.00   1.00   10.93    --  113.00  42.00   1.65   92
 57  \w     82.00 151.00   1.00   10.93    --  113.00  30.00-120.00   69
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1086011000
_diffrn_orient_matrix_UB_12      -0.0993001000
_diffrn_orient_matrix_UB_13      -0.0140047000
_diffrn_orient_matrix_UB_21      -0.1116706000
_diffrn_orient_matrix_UB_22      -0.1161226000
_diffrn_orient_matrix_UB_23      -0.0016830000
_diffrn_orient_matrix_UB_31      -0.0428221000
_diffrn_orient_matrix_UB_32      0.0506133000
_diffrn_orient_matrix_UB_33      -0.0311933000
_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  0.0591
_diffrn_reflns_av_unetI/netI     0.0261
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       49
_diffrn_reflns_limit_l_min       -56
_diffrn_reflns_number            83504
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.490
_diffrn_reflns_theta_min         1.963
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.743
_exptl_absorpt_correction_T_max  0.963
_exptl_absorpt_correction_T_min  0.918
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.93a (Rigaku Oxford Diffraction, 2023)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.221
_exptl_crystal_description       plate
_exptl_crystal_F_000             1616
_exptl_crystal_size_max          0.14
_exptl_crystal_size_mid          0.07
_exptl_crystal_size_min          0.06
_refine_diff_density_max         0.215
_refine_diff_density_min         -0.271
_refine_diff_density_rms         0.034
_refine_ls_abs_structure_details
;
 Flack x determined using 3015 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.00(7)
_refine_ls_extinction_coef       0.00078(14)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL (Sheldrick, 2015b)'
_refine_ls_goodness_of_fit_ref   1.030
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     550
_refine_ls_number_reflns         8376
_refine_ls_number_restraints     286
_refine_ls_restrained_S_all      1.065
_refine_ls_R_factor_all          0.0445
_refine_ls_R_factor_gt           0.0383
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0527P)^2^+0.7290P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0968
_refine_ls_wR_factor_ref         0.1022
_reflns_Friedel_coverage         0.764
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     1.000
_reflns_number_gt                7498
_reflns_number_total             8376
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ob00469a2.cif
_cod_data_source_block           2
_cod_depositor_comments
'Adding full bibliography for 7160505--7160506.cif.'
_cod_database_code               7160505
_shelx_estimated_absorpt_t_max   0.957
_shelx_estimated_absorpt_t_min   0.903
_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. Restrained distances
 C40A-C38A = C40B-C38B = C39B-C38B = C39A-C38A
 1.54 with sigma of 0.005
 C40B-C39B
 2.5 with sigma of 0.01
 C40B-C37B
 2.5 with sigma of 0.01
 C37B-C39B
 2.5 with sigma of 0.01
 O11-C37A \\sim O11-C37B
 with sigma of 0.01
 O12B-C37B \\sim O12A-C37A
 with sigma of 0.01
 C38B-C37B \\sim C38A-C37A
 with sigma of 0.01
3. Uiso/Uaniso restraints and constraints
C37A \\sim C37B \\sim C38A \\sim C38B \\sim C39A \\sim C39B \\sim C40A \\sim
C40B \\sim O11 \\sim O12A \\sim O12B: within 3A with sigma of 0.005 and sigma
for terminal atoms of 0.01 within 3A
4. Others
 Sof(C37B)=Sof(C38B)=Sof(H38B)=Sof(C39B)=Sof(H39D)=Sof(H39E)=Sof(H39F)=
 Sof(C40B)=Sof(H40D)=Sof(H40E)=Sof(H40F)=Sof(O12B)=1-FVAR(1)
 Sof(C37A)=Sof(C38A)=Sof(H38A)=Sof(C39A)=Sof(H39A)=Sof(H39B)=Sof(H39C)=
 Sof(C40A)=Sof(H40A)=Sof(H40B)=Sof(H40C)=Sof(O12A)=FVAR(1)
5.a Ternary CH refined with riding coordinates:
 C3(H3), C4(H4), C6(H6), C7(H7), C11(H11), C23(H23), C24(H24), C26(H26),
 C27(H27), C38A(H38A), C38B(H38B)
5.b Secondary CH2 refined with riding coordinates:
 C14(H14A,H14B), C30(H30A,H30B)
5.c Aromatic/amide H refined with riding coordinates:
 C16(H16), C17(H17), C18(H18), C19(H19), C20(H20), C32(H32), C33(H33),
 C34(H34), C35(H35), C36(H36)
5.d X=CH2 refined with riding coordinates:
 C9(H9A,H9B), C29(H29A,H29B)
5.e Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C8(H8A,H8B,H8C), C12(H12A,H12B,H12C), C13(H13A,H13B,H13C),
 C21(H21A,H21B,H21C), C28(H28A,H28B,H28C), C39A(H39A,H39B,H39C), C39B(H39D,H39E,
 H39F), C40A(H40A,H40B,H40C), C40B(H40D,H40E,H40F)
;
_shelx_res_checksum              90780