Chemical synthesis of 4'-thio and 4'-sulfinyl pyrimidine nucleoside analogues.
Guinan, Mieke; Huang, Ningwu; Hawes, Chris S.; Lima, Marcelo A.; Smith, Mark; Miller, Gavin J.; Organic & biomolecular chemistry 20 (2022) 1401–1406; doi:10.1039/d1ob02097h

data_7158397
_publ_section_title
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 Chemical synthesis of 4'-thio and 4'-sulfinyl pyrimidine nucleoside
 analogues.
;
_journal_issue                   7
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              1401
_journal_page_last               1406
_journal_paper_doi               10.1039/d1ob02097h
_journal_volume                  20
_journal_year                    2022
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C20 H18 F2 O7 S2'
_chemical_formula_sum            'C20 H18 F2 O7 S2'
_chemical_formula_weight         472.46
_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   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2020-02-27
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
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2021-10-12 deposited with the CCDC.	2021-11-11 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   5.4744(3)
_cell_length_b                   17.6020(11)
_cell_length_c                   21.4574(14)
_cell_measurement_reflns_used    9139
_cell_measurement_temperature    150.0
_cell_measurement_theta_max      27.582
_cell_measurement_theta_min      2.99
_cell_volume                     2067.6(2)
_computing_cell_refinement       'SAINT V8.40A (?, 2016)'
_computing_data_reduction        'SAINT V8.40A (?, 2016)'
_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_temperature      150.0
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0783
_diffrn_reflns_av_unetI/netI     0.0511
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       6
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -26
_diffrn_reflns_number            24500
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         25.996
_diffrn_reflns_theta_min         2.501
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.316
_exptl_absorpt_correction_T_max  0.7456
_exptl_absorpt_correction_T_min  0.6085
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.1092 before and 0.0790 after correction. The Ratio of minimum to maximum transmission is 0.8161. The \l/2 correction factor is Not present.'
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.518
_exptl_crystal_description       rod
_exptl_crystal_F_000             976
_exptl_crystal_size_max          0.31
_exptl_crystal_size_mid          0.08
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.609
_refine_diff_density_min         -0.402
_refine_diff_density_rms         0.079
_refine_ls_abs_structure_details
;
 Flack x determined using 1213 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.01(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.179
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     306
_refine_ls_number_reflns         4070
_refine_ls_number_restraints     142
_refine_ls_restrained_S_all      1.178
_refine_ls_R_factor_all          0.0753
_refine_ls_R_factor_gt           0.0620
_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^)+(0.0497P)^2^+2.8680P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1354
_refine_ls_wR_factor_ref         0.1412
_reflns_Friedel_coverage         0.716
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     1.000
_reflns_number_gt                3505
_reflns_number_total             4070
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1ob02097h2.cif
_cod_data_source_block           mgu239_664_0m
_cod_depositor_comments          'Adding full bibliography for 7158397.cif.'
_cod_database_code               7158397
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   0.984
_shelx_estimated_absorpt_t_min   0.908
_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
 C13-C15 \\sim C13-C19 \\sim C15-C19
 with sigma of 0.02
 C14-C13 \\sim C14-C15 \\sim C14-C19
 with sigma of 0.02
 C7-C8 \\sim C7-C12 \\sim C12-C11 \\sim C10-C11 \\sim C10-C9 \\sim C9-C8 \\sim
C8-C7A \\sim C12A-C7A ~
 C11A-C12A \\sim C11A-C10A \\sim C10A-C9
 with sigma of 0.01
3. Uiso/Uaniso restraints and constraints
Uanis(C11) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.02
Uanis(C7A) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.02
Uanis(C10) = Uanis(C10A)
Uanis(C7A) = Uanis(C7)
4. Rigid body (RIGU) restrains
 C8, C9, C7A, C10A, C11A, C12A, C7, C10, C11, C12
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Sof(H8B)=Sof(H9B)=Sof(C7)=Sof(C10)=Sof(H10)=Sof(C11)=Sof(H11)=Sof(C12)=
 Sof(H12)=1-FVAR(1)
 Sof(H8A)=Sof(H9A)=Sof(C7A)=Sof(C10A)=Sof(H10A)=Sof(C11A)=Sof(H11A)=Sof(C12A)=
 Sof(H12A)=FVAR(1)
6.a Ternary CH refined with riding coordinates:
 C1(H1), C3(H3), C4(H4)
6.b Secondary CH2 refined with riding coordinates:
 C5(H5A,H5B)
6.c Aromatic/amide H refined with riding coordinates:
 C8(H8A), C8(H8B), C9(H9A), C9(H9B), C15(H15), C16(H16), C17(H17), C18(H18),
 C19(H19), C10A(H10A), C11A(H11A), C12A(H12A), C10(H10), C11(H11), C12(H12)
6.d Idealised Me refined as rotating group:
 C20(H20A,H20B,H20C)
;
_shelx_res_checksum              51008
_olex2_submission_special_instructions 'No special instructions were received'