The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic Reagents - A Route to Thymidine (6-4) Photoproduct Analogues.
Wrigstedt, Pauli; Kavakka, Jari; Heikkinen, Sami; Nieger, Martin; Räisänen, Minna; Repo, Timo; The Journal of organic chemistry 81 (2016) 3848–3859; doi:10.1021/acs.joc.6b00495

data_4036781
_publ_section_title
;
 The Reactivity of Thymine and Thymidine 5,6-Epoxides with Organometallic
 Reagents - A Route to Thymidine (6-4) Photoproduct Analogues.
;
_journal_issue                   9
_journal_name_full               'The Journal of organic chemistry'
_journal_page_first              3848
_journal_page_last               3859
_journal_paper_doi               10.1021/acs.joc.6b00495
_journal_volume                  81
_journal_year                    2016
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C28 H48 N2 O6 Si2'
_chemical_formula_sum            'C28 H48 N2 O6 Si2'
_chemical_formula_weight         564.86
_chemical_name_systematic
;
 1-(4-((tert-butyldimethylsilyl)oxy)-5-(((2-(trimethylsilyl)propan-
2-yl)oxy)methyl)tetrahydrofuran-2-yl)-5-hydroxy-5-methyl-
6-phenyldihydropyrimidine-2,4(1H,3H)-dione
;
_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   difmap
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           SHELXL-2014/7
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   6.3869(2)
_cell_length_b                   23.9885(7)
_cell_length_c                   41.8744(14)
_cell_measurement_reflns_used    8327
_cell_measurement_temperature    123(2)
_cell_measurement_theta_max      71.8
_cell_measurement_theta_min      2.8
_cell_volume                     6415.7(3)
_computing_cell_refinement       'APEX3 v2015.9-RC2 (Bruker AXS)'
_computing_data_collection       'APEX3 v2015.9-RC2 (Bruker AXS)'
_computing_data_reduction        'SAINT V8.35A (Bruker AXS Inc., 2015)'
_computing_molecular_graphics    Shelxtl
_computing_publication_material  publCIF
_computing_structure_refinement  'SHELXL-2014/7 (Sheldrick, 2014)'
_computing_structure_solution    'SHELXS-97 (Sheldrick, 1997)'
_diffrn_ambient_temperature      123(2)
_diffrn_detector_area_resol_mean 10.4167
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.985
_diffrn_measurement_device_type  'Bruker D8 VENTURE with Photon100 detector'
_diffrn_measurement_method       'rotation in \f and \w, 0.5\%, shutterless'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0932
_diffrn_reflns_av_unetI/netI     0.0910
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.985
_diffrn_reflns_limit_h_max       7
_diffrn_reflns_limit_h_min       -7
_diffrn_reflns_limit_k_max       29
_diffrn_reflns_limit_k_min       -29
_diffrn_reflns_limit_l_max       50
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            38957
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.980
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         72.595
_diffrn_reflns_theta_min         2.110
_diffrn_source                   'INCOATEC microfocus sealed tube'
_exptl_absorpt_coefficient_mu    1.329
_exptl_absorpt_correction_T_max  0.9705
_exptl_absorpt_correction_T_min  0.8057
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details   'SADABS V2014/5 (Bruker AXS Inc.)'
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.170
_exptl_crystal_description       needles
_exptl_crystal_F_000             2448
_exptl_crystal_size_max          0.180
_exptl_crystal_size_mid          0.040
_exptl_crystal_size_min          0.020
_refine_diff_density_max         0.342
_refine_diff_density_min         -0.269
_refine_diff_density_rms         0.059
_refine_ls_abs_structure_details
;

 The absolute configuration has been established by 
 anomalous dispersion effects in diffraction measurement
 on the crystal. In addition, the enantiomer has been assigned by
 reference to an unchanging chiral centre in the synthetic
 procedure.

 Determination of absolute structure using Bayesian statistics 
 on Bijvoet differences (Hooft, Straver and Spek, 2008): 
 Hooft's y = 0.07(2) (Platon: Spek, 2009).
 
 Flack x determined using 2925 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.071(19)
_refine_ls_extinction_coef       0.00013(4)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2014/7 (Sheldrick 2014'
_refine_ls_goodness_of_fit_ref   1.026
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     698
_refine_ls_number_reflns         12462
_refine_ls_number_restraints     4
_refine_ls_restrained_S_all      1.026
_refine_ls_R_factor_all          0.0891
_refine_ls_R_factor_gt           0.0556
_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^)+(0.0474P)^2^+1.1250P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1117
_refine_ls_wR_factor_ref         0.1258
_reflns_Friedel_coverage         0.761
_reflns_Friedel_fraction_full    0.997
_reflns_Friedel_fraction_max     0.975
_reflns_number_gt                9129
_reflns_number_total             12462
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            jo6b00495_si_001.cif
_cod_data_source_block           les134
_cod_database_code               4036781
_shelx_shelxl_version_number     2014/7
_shelx_estimated_absorpt_t_min   0.796
_shelx_estimated_absorpt_t_max   0.974