Synthesis of fluorinated carbocyclic pyrimidine nucleoside analogues
Benckendorff, Caecilie M. M.; Slyusarchuk, Valentyna; Huang, Ningwu; Lima, Marcelo A.; Smith, Mark; Miller, Gavin John; Organic & Biomolecular Chemistry  (2022) –; doi:10.1039/D2OB01761J

data_7158992
_publ_section_title
;
 Synthesis of fluorinated carbocyclic pyrimidine nucleoside analogues
;
_journal_name_full               'Organic &amp; Biomolecular Chemistry'
_journal_paper_doi               10.1039/D2OB01761J
_journal_year                    2022
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C17 H17 F N2 O8'
_chemical_formula_sum            'C17 H17 F N2 O8'
_chemical_formula_weight         396.32
_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             2022-08-10
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-11-10 deposited with the CCDC.	2022-11-14 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   6.3601(4)
_cell_length_b                   9.4921(6)
_cell_length_c                   29.8749(18)
_cell_measurement_reflns_used    3916
_cell_measurement_temperature    150.0
_cell_measurement_theta_max      23.479
_cell_measurement_theta_min      2.96
_cell_volume                     1803.57(19)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      150.0
_diffrn_measured_fraction_theta_full 0.997
_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  0.1131
_diffrn_reflns_av_unetI/netI     0.0901
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            26730
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.494
_diffrn_reflns_theta_min         3.275
_diffrn_source_current           20.0
_diffrn_source_power             1.0
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.123
_exptl_absorpt_correction_T_max  0.7456
_exptl_absorpt_correction_T_min  0.6764
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0695 before and 0.0642 after correction.
The Ratio of minimum to maximum transmission is 0.9072.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.460
_exptl_crystal_description       plate
_exptl_crystal_F_000             824
_exptl_crystal_size_max          0.21
_exptl_crystal_size_mid          0.06
_exptl_crystal_size_min          0.01
_refine_diff_density_max         0.260
_refine_diff_density_min         -0.310
_refine_diff_density_rms         0.058
_refine_ls_abs_structure_details
;
 Flack x determined using 827 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.4(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.140
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     255
_refine_ls_number_reflns         4133
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.140
_refine_ls_R_factor_all          0.1134
_refine_ls_R_factor_gt           0.0716
_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^)+(0.0267P)^2^+0.4503P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0921
_refine_ls_wR_factor_ref         0.1010
_reflns_Friedel_coverage         0.720
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     1.000
_reflns_number_gt                2904
_reflns_number_total             4133
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2ob01761j2.cif
_cod_data_source_block           10
_cod_database_code               7158992
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.999
_shelx_estimated_absorpt_t_min   0.975
_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.a Ternary CH refined with riding coordinates:
 C1(H1), C2(H2), C3(H3), C4(H4), C5(H5)
2.b Aromatic/amide H refined with riding coordinates:
 C6(H6), C13(H13), C15(H15), C17(H17)
2.c X=CH2 refined with riding coordinates:
 C7(H7A,H7B)
2.d Idealised Me refined as rotating group:
 C9(H9A,H9B,H9C), C10(H10A,H10B,H10C)
;
_shelx_res_checksum              78097
_olex2_submission_special_instructions 'No special instructions were received'