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_4121231
_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_formula_moiety         'C34 H55 N3 O5 Si2'
_chemical_formula_sum            'C34 H55 N3 O5 Si2'
_chemical_formula_weight         641.99
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_symmetry_space_group_name_Hall  '-P 1'
_symmetry_space_group_name_H-M   'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     iterative
_atom_sites_solution_secondary   difmap
_audit_creation_date             2012-10-15
_audit_creation_method
;
  Olex2 1.2-beta
  (compiled Oct  2 2012 15:58:45, GUI svn.r4355)
;
_cell_angle_alpha                111.1370(10)
_cell_angle_beta                 97.9440(10)
_cell_angle_gamma                92.2430(10)
_cell_formula_units_Z            2
_cell_length_a                   7.46250(10)
_cell_length_b                   16.3138(2)
_cell_length_c                   17.2618(2)
_cell_measurement_reflns_used    9896
_cell_measurement_temperature    100
_cell_measurement_theta_max      66.65
_cell_measurement_theta_min      2.92
_cell_volume                     1932.26(4)
_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 0.963
_diffrn_measured_fraction_theta_max 0.963
_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  0.0394
_diffrn_reflns_av_unetI/netI     0.0357
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       19
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            21614
_diffrn_reflns_theta_full        66.64
_diffrn_reflns_theta_max         66.64
_diffrn_reflns_theta_min         2.92
_diffrn_source                   'fine-focus sealed tube'
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.146
_exptl_absorpt_correction_T_max  0.9370
_exptl_absorpt_correction_T_min  0.8107
_exptl_absorpt_correction_type   numerical
_exptl_absorpt_process_details
;
SADABS was used for absorption correction.
wR2(int) was 0.0562 before and 0.0463 after correction.
The Ratio of minimum to maximum transmission is 0.8652.
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    1.103
_exptl_crystal_description       block
_exptl_crystal_F_000             696
_exptl_crystal_size_max          0.348
_exptl_crystal_size_mid          0.127
_exptl_crystal_size_min          0.082
_refine_diff_density_max         0.320
_refine_diff_density_min         -0.331
_refine_diff_density_rms         0.046
_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     430
_refine_ls_number_reflns         6576
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.040
_refine_ls_R_factor_all          0.0556
_refine_ls_R_factor_gt           0.0441
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'calc w=1/[\s^2^(Fo^2^)+(0.0624P)^2^+0.5833P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1125
_refine_ls_wR_factor_ref         0.1183
_reflns_number_gt                5304
_reflns_number_total             6576
_reflns_threshold_expression     >2sigma(I)
_cod_data_source_file            ja409944u_si_003.cif
_cod_data_source_block           x1210004
_cod_database_code               4121231
_olex2_refinement_description
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1. Fixed Uiso
 At 1.2 times of:
  H11 of C11, H10 of C10, H9 of C9, H8 of C8, H7 of C7, H20 of C20, H27 of
  C27, {H17A,H17B} of C17, H19 of C19, H2 of N2, H1 of C1, H2A of C2, H3A of C3,
   H4 of C4, H5 of C5
 At 1.5 times of:
  {H33A,H33B,H33C} of C33, {H32A,H32B,H32C} of C32, {H34A,H34B,H34C} of C34,
  {H15A,H15B,H15C} of C15, {H14A,H14B,H14C} of C14, {H16A,H16B,H16C} of C16,
  {H25A,H25B,H25C} of C25, {H23A,H23B,H23C} of C23, {H26A,H26B,H26C} of C26,
  {H28A,H28B,H28C} of C28, {H28D,H28E,H28F} of C28A, {H29A,H29B,H29C} of C29,
  {H29D,H29E,H29F} of C29A, {H31A,H31B,H31C} of C31, H3 of O3
2. Uiso/Uaniso restraints and constraints
Uanis(Si2) = Uanis(Si2A)
Uanis(C28) = Uanis(C28A)
Uanis(C29) = Uanis(C29A)
3. others
 Sof(Si2)=1-Sof(Si2A)=Sof(C28)=Sof(H28A)=Sof(H28B)=Sof(H28C)=1-Sof(Si2A)=1-
 Sof(Si2A)=1-Sof(Si2A)=1-Sof(Si2A)=Sof(C29)=Sof(H29A)=Sof(H29B)=Sof(H29C)=1-
 Sof(Si2A)=1-Sof(Si2A)=1-Sof(Si2A)=1-Sof(Si2A)
4.a Ternary CH refined with riding coordinates:
 C19(H19), C20(H20), C27(H27)
4.b Secondary CH2 refined with riding coordinates:
 C17(H17A,H17B)
4.c Aromatic/amide H refined with riding coordinates:
 N2(H2), C1(H1), C2(H2A), C3(H3A), C4(H4), C5(H5), C7(H7), C8(H8), C9(H9),
 C10(H10), C11(H11)
4.d Idealised Me refined as rotating group:
 C14(H14A,H14B,H14C), C15(H15A,H15B,H15C), C16(H16A,H16B,H16C), C23(H23A,H23B,
 H23C), C25(H25A,H25B,H25C), C26(H26A,H26B,H26C), C28(H28A,H28B,H28C),
 C28A(H28D,H28E,H28F), C29(H29A,H29B,H29C), C29A(H29D,H29E,H29F), C31(H31A,H31B,
 H31C), C32(H32A,H32B,H32C), C33(H33A,H33B,H33C), C34(H34A,H34B,H34C)
4.e Idealised tetrahedral OH refined as rotating group:
 O3(H3)
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