Asymmetric Synthesis of the Aminocyclitol Pactamycin, a Universal Translocation Inhibitor
Robert J. Sharpe; Justin T. Malinowski; Jeffrey S. Johnson; Journal of the American Chemical Society 135 (2013) 17990–17998; doi:10.1021/ja409944u

data_4121229
_publ_contact_author_name
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;
_publ_section_title
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 Asymmetric Synthesis of the Aminocyclitol Pactamycin, a Universal
 Translocation Inhibitor
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_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              17990
_journal_page_last               17998
_journal_paper_doi               10.1021/ja409944u
_journal_volume                  135
_journal_year                    2013
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C25 H28 N4 O9'
_chemical_formula_sum            'C25 H28 N4 O9'
_chemical_formula_weight         528.51
_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'
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_atom_sites_solution_secondary   difmap
_audit_creation_date             2012-12-05
_audit_creation_method
;
  Olex2 1.2-beta
  (compiled Nov 28 2012 18:30:28, GUI svn.r4385)
;
_cell_angle_alpha                90.00
_cell_angle_beta                 113.3690(10)
_cell_angle_gamma                90.00
_cell_formula_units_Z            2
_cell_length_a                   10.8826(2)
_cell_length_b                   10.0476(2)
_cell_length_c                   12.7530(2)
_cell_measurement_reflns_used    9993
_cell_measurement_temperature    100
_cell_measurement_theta_max      70.08
_cell_measurement_theta_min      4.40
_cell_volume                     1280.08(4)
_computing_data_reduction        'SAINT v8.27A (Bruker, 2012)'
_computing_molecular_graphics
;
O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.
;
_computing_publication_material
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O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.
;
_computing_structure_refinement
;
XL, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122
;
_computing_structure_solution
;
olex2.solve (L.J. Bourhis, O.V. Dolomanov, R.J. Gildea, J.A.K. Howard,
H. Puschmann, in preparation, 2011)
;
_diffrn_ambient_temperature      100
_diffrn_measured_fraction_theta_full 0.977
_diffrn_measured_fraction_theta_max 0.977
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0135
_diffrn_reflns_av_unetI/netI     0.0160
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -13
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -15
_diffrn_reflns_number            13034
_diffrn_reflns_theta_full        70.08
_diffrn_reflns_theta_max         70.08
_diffrn_reflns_theta_min         4.43
_diffrn_source                   'fine-focus sealed tube'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.890
_exptl_absorpt_correction_T_max  0.8434
_exptl_absorpt_correction_T_min  0.7394
_exptl_absorpt_correction_type   numerical
_exptl_absorpt_process_details
;
SADABS-2012/1 (Bruker,2012) was used for absorption correction.
wR2(int) was 0.0463 before and 0.0257 after correction.
The Ratio of minimum to maximum transmission is 0.8767.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.371
_exptl_crystal_description       block
_exptl_crystal_F_000             556
_exptl_crystal_size_max          0.522
_exptl_crystal_size_mid          0.409
_exptl_crystal_size_min          0.3
_refine_diff_density_max         0.213
_refine_diff_density_min         -0.247
_refine_diff_density_rms         0.038
_refine_ls_abs_structure_details 'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack   0.12(10)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.062
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     347
_refine_ls_number_reflns         4663
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.062
_refine_ls_R_factor_all          0.0259
_refine_ls_R_factor_gt           0.0258
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0425P)^2^+0.2427P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0678
_refine_ls_wR_factor_ref         0.0679
_reflns_number_gt                4643
_reflns_number_total             4663
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja409944u_si_001.cif
_cod_data_source_block           x1211017
_cod_original_cell_volume        1280.07(4)
_cod_database_code               4121229
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  {H19A,H19B} of C19, H13 of C13, H17 of C17, H14 of C14, H16 of C16, H25 of
  C25, H24 of C24, H23 of C23, H22 of C22, H21 of C21, H1 of N1, H4 of N4, H2
  of C2, H3 of C3, H4A of C4
 At 1.5 times of:
  {H10A,H10B,H10C} of C10, {H6A,H6B,H6C} of C6, {H7A,H7B,H7C} of C7, {H9A,H9B,
  H9C} of C9
2.a Ternary CH refined with riding coordinates:
 C2(H2), C3(H3), C4(H4A)
2.b Secondary CH2 refined with riding coordinates:
 C19(H19A,H19B)
2.c Aromatic/amide H refined with riding coordinates:
 N1(H1), N4(H4), C13(H13), C14(H14), C16(H16), C17(H17), C21(H21), C22(H22),
 C23(H23), C24(H24), C25(H25)
2.d Idealised Me refined as rotating group:
 C6(H6A,H6B,H6C), C7(H7A,H7B,H7C), C9(H9A,H9B,H9C), C10(H10A,H10B,H10C)
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