Asymmetric Synthesis of 2'-<i>C</i>-Methyl-4'-selenonucleosides as Anti-Hepatitis C Virus Agents.
Lee, Hyejin; Jarhad, Dnyandev B.; Yu, Jinha; Lee, Choongho; Jeong, Lak Shin; The Journal of organic chemistry  (2019) –; doi:10.1021/acs.joc.9b01462

data_4033648
_publ_section_title
;
 Asymmetric Synthesis of 2'-<i>C</i>-Methyl-4'-selenonucleosides as
 Anti-Hepatitis C Virus Agents.
;
_journal_name_full               'The Journal of organic chemistry'
_journal_paper_doi               10.1021/acs.joc.9b01462
_journal_year                    2019
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C10 H14 N2 O5 Se, H2 O'
_chemical_formula_sum            'C10 H16 N2 O6 Se'
_chemical_formula_weight         339.21
_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'
_symmetry_space_group_name_Hall  'P 2ac 2ab'
_symmetry_space_group_name_H-M   'P 21 21 21'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2017-11-23
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   6.71850(4)
_cell_length_b                   7.05778(4)
_cell_length_c                   27.0126(2)
_cell_measurement_reflns_used    20206
_cell_measurement_temperature    296(2)
_cell_measurement_theta_max      73.7010
_cell_measurement_theta_min      3.2620
_cell_volume                     1280.875(14)
_computing_cell_refinement       'CrysAlisPro 1.171.39.29d (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.29d (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.29d (Rigaku OD, 2017)'
_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_environment      air
_diffrn_ambient_temperature      296(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2262
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.997
_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   -130.00  46.00   1.00    1.00    --  -41.82   0.00  90.00  176
  2  \w     23.00  98.00   1.00    1.00    --   41.82-125.00 -30.00   75
  3  \w     78.00 178.00   1.00    2.87    --  105.87  30.00-120.00  100
  4  \w     30.00 138.00   1.00    2.87    --  105.87 -77.00-150.00  108
  5  \w     94.00 178.00   1.00    2.87    --  105.87 125.00-180.00   84
  6  \w     80.00 178.00   1.00    2.87    --  105.87  45.00 150.00   98
  7  \w     94.00 178.00   1.00    2.87    --  105.87 125.00  30.00   84
  8  \w   -115.00 -14.00   1.00    1.00    --  -41.82 -57.00  60.00  101
  9  \w      9.00 118.00   1.00    1.00    --   41.82  77.00 -30.00  109
 10  \w     30.00 134.00   1.00    2.87    --  105.87 -30.00  60.00  104
 11  \w     73.00 178.00   1.00    2.87    --  105.87  77.00 -60.00  105
 12  \w     73.00 178.00   1.00    2.87    --  105.87  77.00  90.00  105
 13  \w     78.00 178.00   1.00    2.87    --  105.87  30.00  60.00  100
 14  \w      9.00 118.00   1.00    1.00    --   41.82  77.00-120.00  109
 15  \w      1.00  83.00   1.00    1.00    --   41.82 -99.00 120.00   82
 16  \w     23.00 109.00   1.00    2.87    --  105.87 -94.00 120.00   86
 17  \w     77.00 178.00   1.00    2.87    --  105.87  61.00 -90.00  101
 18  \w     73.00 178.00   1.00    2.87    --  105.87  77.00 150.00  105
 19  \w     77.00 178.00   1.00    2.87    --  105.87  61.00   0.00  101
 20  \w   -118.00  -9.00   1.00    1.00    --  -41.82 -77.00  30.00  109
 21  \w      9.00 118.00   1.00    1.00    --   41.82  77.00 150.00  109
 22  \w     33.00 122.00   1.00    2.87    --  105.87-125.00  30.00   89
 23  \w     73.00 178.00   1.00    2.87    --  105.87  77.00-180.00  105
 24  \w     77.00 178.00   1.00    2.87    --  105.87  61.00-120.00  101
 25  \w     73.00 178.00   1.00    2.87    --  105.87  77.00  60.00  105
 26  \w   -114.00 -67.00   1.00    1.00    --  -41.82-134.00  95.00   47
 27  \w   -115.00 -14.00   1.00    1.00    --  -41.82 -57.00 -90.00  101
 28  \w     73.00 178.00   1.00    2.87    --  105.87  77.00 -30.00  105
 29  \w     73.00 178.00   1.00    2.87    --  105.87  77.00 -90.00  105
 30  \w     73.00 110.00   1.00    2.87    --  105.87  77.00-150.00   37
 31  \w     77.00 178.00   1.00    2.87    --  105.87  61.00  30.00  101
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1600198000
_diffrn_orient_matrix_UB_12      -0.1361269000
_diffrn_orient_matrix_UB_13      -0.0200734000
_diffrn_orient_matrix_UB_21      0.1281407000
_diffrn_orient_matrix_UB_22      0.1706425000
_diffrn_orient_matrix_UB_23      -0.0158047000
_diffrn_orient_matrix_UB_31      0.1027560000
_diffrn_orient_matrix_UB_32      -0.0006976000
_diffrn_orient_matrix_UB_33      0.0509818000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0434
_diffrn_reflns_av_unetI/netI     0.0172
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -8
_diffrn_reflns_limit_l_max       33
_diffrn_reflns_limit_l_min       -32
_diffrn_reflns_number            24115
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         73.882
_diffrn_reflns_theta_min         3.272
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.241
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.61659
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.29d (Rigaku Oxford Diffraction, 2017)
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    1.759
_exptl_crystal_description       'rect. Prism'
_exptl_crystal_F_000             688
_exptl_crystal_size_max          0.301
_exptl_crystal_size_mid          0.151
_exptl_crystal_size_min          0.07
_refine_diff_density_max         0.329
_refine_diff_density_min         -0.234
_refine_diff_density_rms         0.041
_refine_ls_abs_structure_details
;
 Flack x determined using 1034 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.023(6)
_refine_ls_extinction_coef       0.0028(2)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2017/1 (Sheldrick 2017)'
_refine_ls_goodness_of_fit_ref   1.066
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     183
_refine_ls_number_reflns         2588
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.066
_refine_ls_R_factor_all          0.0181
_refine_ls_R_factor_gt           0.0180
_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^)+(0.0278P)^2^+0.2262P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0465
_refine_ls_wR_factor_ref         0.0466
_reflns_Friedel_coverage         0.683
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.992
_reflns_number_gt                2569
_reflns_number_total             2588
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            jo9b01462_si_003.cif
_cod_data_source_block           exp_1090
_cod_database_code               4033648
_shelx_shelxl_version_number     2017/1
_chemical_oxdiff_formula         C10H14N2O5Se
_shelx_estimated_absorpt_t_max   0.756
_shelx_estimated_absorpt_t_min   0.362
_reflns_odcompleteness_completeness 99.93
_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, All O(H) groups, All O(H,H) groups
2.a Free rotating group:
 O1W(H1WA,H1WB)
2.b Ternary CH refined with riding coordinates:
 C1'(H1'A), C3'(H3'A), C4'(H4')
2.c Secondary CH2 refined with riding coordinates:
 C5'(H5'A,H5'B)
2.d Aromatic/amide H refined with riding coordinates:
 N2(H2), C3(H3), C4(H4)
2.e Idealised Me refined as rotating group:
 C6'(H6'A,H6'B,H6'C)
2.f Idealised tetrahedral OH refined as rotating group:
 O2'(H2'), O3'(H3')
;
_shelx_res_checksum              77831
_shelx_hkl_checksum              10560
_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 3.341
_oxdiff_exptl_absorpt_empirical_full_min 0.659