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_7160506
_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         'C21 H29 N O6'
_chemical_formula_sum            'C21 H29 N O6'
_chemical_formula_weight         391.45
_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             2023-07-19
_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            12
_cell_length_a                   14.7354(2)
_cell_length_b                   15.1012(2)
_cell_length_c                   29.1138(3)
_cell_measurement_reflns_used    32084
_cell_measurement_temperature    160.0(1)
_cell_measurement_theta_max      76.3580
_cell_measurement_theta_min      2.9940
_cell_volume                     6478.47(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 0.995
_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   -116.00 -63.00   1.00    4.00    --  -41.01-147.00  18.00   53
  2  \w    -67.00  35.00   1.00    4.00    --  -41.01  37.00 120.00  102
  3  \w     15.00 117.00   1.00    4.00    --   41.01  37.00 -30.00  102
  4  \w    113.00 178.00   1.00   16.00    --  113.00  61.00 150.00   65
  5  \w    115.00 178.00   1.00   16.00    --  113.00  77.00 -30.00   63
  6  \w     29.00 107.00   1.00   16.00    --  113.00 -94.00 120.00   78
  7  \w    115.00 178.00   1.00   16.00    --  113.00  77.00  60.00   63
  8  \w    115.00 178.00   1.00   16.00    --  113.00  77.00   0.00   63
  9  \w     38.00 109.00   1.00   16.00    --  113.00-111.00  60.00   71
 10  \w    113.00 178.00   1.00   16.00    --  113.00  61.00 120.00   65
 11  \w     97.00 178.00   1.00   16.00    --  113.00  45.00-180.00   81
 12  \w     38.00 109.00   1.00   16.00    --  113.00-111.00  30.00   71
 13  \w     38.00 109.00   1.00   16.00    --  113.00-111.00 -30.00   71
 14  \w     38.00 109.00   1.00   16.00    --  113.00-111.00 -60.00   71
 15  \w    115.00 178.00   1.00   16.00    --  113.00  77.00 -60.00   63
 16  \w    -87.00 -20.00   1.00    4.00    --  -41.01 125.00-120.00   67
 17  \w     11.00 115.00   1.00    4.00    --   41.01  61.00-161.00  104
 18  \w     15.00 117.00   1.00    4.00    --   41.01  37.00 120.00  102
 19  \w     82.00 178.00   1.00   16.00    --  113.00  30.00   0.00   96
 20  \w     82.00 178.00   1.00   16.00    --  113.00  30.00  90.00   96
 21  \w     83.00 178.00   1.00   16.00    --  113.00  61.00-161.00   95
 22  \w     83.00 178.00   1.00   16.00    --  113.00  59.00  28.00   95
 23  \w     82.00 178.00   1.00   16.00    --  113.00  30.00 -90.00   96
;
_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      -0.0454148000
_diffrn_orient_matrix_UB_12      -0.0538679000
_diffrn_orient_matrix_UB_13      0.0386124000
_diffrn_orient_matrix_UB_21      0.0585478000
_diffrn_orient_matrix_UB_22      0.0486262000
_diffrn_orient_matrix_UB_23      0.0358911000
_diffrn_orient_matrix_UB_31      -0.0736595000
_diffrn_orient_matrix_UB_32      0.0717660000
_diffrn_orient_matrix_UB_33      0.0046959000
_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  0.0690
_diffrn_reflns_av_unetI/netI     0.0356
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -18
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -18
_diffrn_reflns_limit_l_max       36
_diffrn_reflns_limit_l_min       -36
_diffrn_reflns_number            69614
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.725
_diffrn_reflns_theta_min         3.036
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.723
_exptl_absorpt_correction_T_max  0.932
_exptl_absorpt_correction_T_min  0.886
_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    1.204
_exptl_crystal_description       plate
_exptl_crystal_F_000             2520
_exptl_crystal_size_max          0.23
_exptl_crystal_size_mid          0.13
_exptl_crystal_size_min          0.10
_refine_diff_density_max         0.451
_refine_diff_density_min         -0.220
_refine_diff_density_rms         0.044
_refine_ls_abs_structure_details
;
 Flack x determined using 5179 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.04(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.040
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     831
_refine_ls_number_reflns         13538
_refine_ls_number_restraints     172
_refine_ls_restrained_S_all      1.085
_refine_ls_R_factor_all          0.0522
_refine_ls_R_factor_gt           0.0480
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0730P)^2^+0.7196P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1262
_refine_ls_wR_factor_ref         0.1319
_reflns_Friedel_coverage         0.815
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.985
_reflns_number_gt                12433
_reflns_number_total             13538
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ob00469a2.cif
_cod_data_source_block           8
_cod_depositor_comments
'Adding full bibliography for 7160505--7160506.cif.'
_cod_database_code               7160506
_shelx_estimated_absorpt_t_max   0.931
_shelx_estimated_absorpt_t_min   0.851
_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
 C35B-C33B \\sim C33B-C34B \\sim C35A-C33A \\sim C34A-C33A
 with sigma of 0.005
 C33B-C32 \\sim C33A-C32
 with sigma of 0.005
 O16-C53A \\sim O16-C53B
 with sigma of 0.005
 C53A-C54 \\sim C53B-C54
 with sigma of 0.005
 O18B-C60 \\sim O18A-C60
 with sigma of 0.005
3. Uiso/Uaniso restraints and constraints
C32 \\sim C33A \\sim C34A \\sim C34B \\sim C35A \\sim C35B: within 3A with
sigma of 0.01 and sigma for terminal atoms of 0.02 within 3A
C53A \\sim C53B \\sim C54 \\sim O16: within 3A with sigma of 0.01 and sigma for
terminal atoms of 0.02 within 3A
C60 \\sim O17 \\sim O18A \\sim O18B: within 3A with sigma of 0.002 and sigma
for terminal atoms of 0.004 within 3A
4. Others
 Sof(C33B)=Sof(H33B)=Sof(C34B)=Sof(H34D)=Sof(H34E)=Sof(H34F)=Sof(C35B)=
 Sof(H35D)=Sof(H35E)=Sof(H35F)=1-FVAR(1)
 Sof(C33A)=Sof(H33A)=Sof(C34A)=Sof(H34A)=Sof(H34B)=Sof(H34C)=Sof(C35A)=
 Sof(H35A)=Sof(H35B)=Sof(H35C)=FVAR(1)
 Sof(C53B)=Sof(H53C)=Sof(H53D)=1-FVAR(2)
 Sof(C53A)=Sof(H53A)=Sof(H53B)=FVAR(2)
 Sof(O18B)=1-FVAR(3)
 Sof(O18A)=FVAR(3)
5.a Ternary CH refined with riding coordinates:
 C3(H3A), C4(H4), C6(H6), C7(H7), C12(H12), C24(H24), C25(H25), C27(H27),
 C28(H28), C33A(H33A), C33B(H33B), C45(H45), C46(H46), C48(H48), C49(H49),
 C61(H61)
5.b Secondary CH2 refined with riding coordinates:
 C9(H9A,H9B), C10(H10A,H10B), C15(H15A,H15B), C30(H30A,H30B), C31(H31A,H31B),
 C36(H36A,H36B), C51(H51A,H51B), C52(H52A,H52B), C53A(H53A,H53B), C53B(H53C,
 H53D)
5.c Aromatic/amide H refined with riding coordinates:
 C17(H17), C18(H18), C19(H19), C20(H20), C21(H21), C38(H38), C39(H39),
 C40(H40), C41(H41), C42(H42), C55(H55), C56(H56), C57(H57), C58(H58), C59(H59)
5.d Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C8(H8A,H8B,H8C), C13(H13A,H13B,H13C), C14(H14A,H14B,H14C),
 C22(H22A,H22B,H22C), C29(H29A,H29B,H29C), C34A(H34A,H34B,H34C), C34B(H34D,H34E,
 H34F), C35A(H35A,H35B,H35C), C35B(H35D,H35E,H35F), C43(H43A,H43B,H43C),
 C50(H50A,H50B,H50C), C62(H62A,H62B,H62C), C63(H63A,H63B,H63C)
;
_shelx_res_checksum              89530