# Supplementary Material (ESI) for Organic and Biomolecular Chemistry # This journal is © The Royal Society of Chemistry 2009 data_global _journal_name_full Org.Biomol.Chem. _journal_coden_Cambridge 0177 _publ_contact_author_name 'Feng-Ling Qing' _publ_contact_author_email zfmonster@mail.sioc.ac.cn _publ_section_title ; Synthesis and conformational analysis of D-2-deoxy-2,2-difluoro-4-dihydro-4-thionucleosides ; loop_ _publ_author_name 'Feng-Ling Qing' 'Lin Fu' 'Renxiao Wang' # Attachment 'cd28358.cif' data_cd28358 _database_code_depnum_ccdc_archive 'CCDC 740876' _audit_creation_method SHELXL-97 _chemical_name_systematic ; ? ; _chemical_name_common ? _chemical_melting_point ? _chemical_formula_moiety ? _chemical_formula_sum 'C8 H8 F2 N2 O3 S' _chemical_formula_weight 250.22 loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' S S 0.1246 0.1234 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' _symmetry_cell_setting Monoclinic _symmetry_space_group_name_H-M P2(1)/n loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x-1/2, -y-1/2, z-1/2' _cell_length_a 6.1849(8) _cell_length_b 18.082(2) _cell_length_c 8.9343(11) _cell_angle_alpha 90.00 _cell_angle_beta 100.122(2) _cell_angle_gamma 90.00 _cell_volume 983.6(2) _cell_formula_units_Z 4 _cell_measurement_temperature 293(2) _cell_measurement_reflns_used 1759 _cell_measurement_theta_min 5.150 _cell_measurement_theta_max 53.977 _exptl_crystal_description prismatic _exptl_crystal_colour colorless _exptl_crystal_size_max 0.480 _exptl_crystal_size_mid 0.202 _exptl_crystal_size_min 0.097 _exptl_crystal_density_meas ? _exptl_crystal_density_diffrn 1.690 _exptl_crystal_density_method 'not measured' _exptl_crystal_F_000 512 _exptl_absorpt_coefficient_mu 0.353 _exptl_absorpt_correction_type empirical _exptl_absorpt_correction_T_min 0.8286 _exptl_absorpt_correction_T_max 1.0000 _exptl_absorpt_process_details sadabs _exptl_special_details ; ? ; _diffrn_ambient_temperature 293(2) _diffrn_radiation_wavelength 0.71073 _diffrn_radiation_type MoK\a _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_monochromator graphite _diffrn_measurement_device_type 'CCD area detector' _diffrn_measurement_method 'phi and omega scans' _diffrn_detector_area_resol_mean ? _diffrn_standards_number ? _diffrn_standards_interval_count ? _diffrn_standards_interval_time ? _diffrn_standards_decay_% ? _diffrn_reflns_number 5594 _diffrn_reflns_av_R_equivalents 0.0244 _diffrn_reflns_av_sigmaI/netI 0.0377 _diffrn_reflns_limit_h_min -6 _diffrn_reflns_limit_h_max 7 _diffrn_reflns_limit_k_min -22 _diffrn_reflns_limit_k_max 23 _diffrn_reflns_limit_l_min -10 _diffrn_reflns_limit_l_max 11 _diffrn_reflns_theta_min 2.25 _diffrn_reflns_theta_max 26.99 _reflns_number_total 2129 _reflns_number_gt 1605 _reflns_threshold_expression >2sigma(I) _computing_data_collection 'Bruker SMART' _computing_cell_refinement 'Bruker SMART' _computing_data_reduction 'Bruker SHELXTL' _computing_structure_solution 'SHELXS-97 (Sheldrick, 1990)' _computing_structure_refinement 'SHELXL-97 (Sheldrick, 1997)' _computing_molecular_graphics 'Bruker SHELXTL' _computing_publication_material 'Bruker SHELXTL' _refine_special_details ; Refinement of F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. ; _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_weighting_scheme calc _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0632P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_ls_hydrogen_treatment mixed _refine_ls_extinction_method none _refine_ls_extinction_coef ? _refine_ls_number_reflns 2129 _refine_ls_number_parameters 153 _refine_ls_number_restraints 2 _refine_ls_R_factor_all 0.0597 _refine_ls_R_factor_gt 0.0433 _refine_ls_wR_factor_ref 0.1168 _refine_ls_wR_factor_gt 0.1110 _refine_ls_goodness_of_fit_ref 1.025 _refine_ls_restrained_S_all 1.025 _refine_ls_shift/su_max 0.000 _refine_ls_shift/su_mean 0.000 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_symmetry_multiplicity _atom_site_calc_flag _atom_site_refinement_flags _atom_site_disorder_assembly _atom_site_disorder_group F1 F 1.1680(2) 0.10956(8) 0.49407(17) 0.0530(4) Uani 1 1 d . . . F2 F 1.1821(2) 0.19602(8) 0.66274(17) 0.0596(5) Uani 1 1 d . . . S1 S 0.65193(11) 0.14828(4) 0.38384(7) 0.0503(2) Uani 1 1 d . . . O1 O 1.0260(3) 0.05258(10) 0.7333(2) 0.0527(5) Uani 1 1 d D . . O2 O 1.1544(3) 0.31505(9) 0.39599(19) 0.0456(4) Uani 1 1 d . . . O3 O 0.7658(3) 0.48949(9) 0.59412(19) 0.0457(4) Uani 1 1 d . . . N1 N 0.8596(3) 0.27635(9) 0.49555(18) 0.0287(4) Uani 1 1 d . . . N2 N 0.9549(3) 0.40062(10) 0.4961(2) 0.0324(4) Uani 1 1 d D . . C1 C 0.7238(4) 0.07566(14) 0.5228(3) 0.0522(7) Uani 1 1 d . . . H1A H 0.5960 0.0606 0.5645 0.063 Uiso 1 1 calc R . . H1B H 0.7803 0.0330 0.4765 0.063 Uiso 1 1 calc R . . C2 C 0.8973(4) 0.10721(13) 0.6462(3) 0.0379(6) Uani 1 1 d . . . H2 H 0.8272 0.1384 0.7135 0.046 Uiso 1 1 calc R . . C3 C 1.0392(3) 0.15374(11) 0.5663(2) 0.0320(5) Uani 1 1 d . . . C4 C 0.8992(3) 0.20096(11) 0.4457(2) 0.0314(5) Uani 1 1 d . . . H4 H 0.9766 0.2049 0.3593 0.038 Uiso 1 1 calc R . . C5 C 1.0017(3) 0.32991(12) 0.4580(2) 0.0307(5) Uani 1 1 d . . . C6 C 0.7863(4) 0.42319(12) 0.5663(2) 0.0321(5) Uani 1 1 d . . . C7 C 0.6456(4) 0.36523(12) 0.5989(2) 0.0352(5) Uani 1 1 d . . . H7 H 0.5259 0.3762 0.6450 0.042 Uiso 1 1 calc R . . C8 C 0.6841(4) 0.29546(12) 0.5638(2) 0.0337(5) Uani 1 1 d . . . H8 H 0.5899 0.2585 0.5860 0.040 Uiso 1 1 calc R . . H1 H 0.944(5) 0.0322(18) 0.782(3) 0.097(13) Uiso 1 1 d D . . H2A H 1.048(3) 0.4308(12) 0.473(3) 0.043(7) Uiso 1 1 d D . . loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 F1 0.0482(9) 0.0449(9) 0.0740(10) 0.0078(7) 0.0331(8) 0.0113(7) F2 0.0575(10) 0.0437(9) 0.0663(10) 0.0006(7) -0.0204(8) -0.0130(7) S1 0.0503(4) 0.0382(4) 0.0545(4) -0.0044(3) -0.0128(3) -0.0099(3) O1 0.0546(11) 0.0497(12) 0.0561(11) 0.0223(9) 0.0160(9) 0.0083(9) O2 0.0427(10) 0.0357(9) 0.0666(11) 0.0002(8) 0.0318(9) -0.0008(7) O3 0.0503(10) 0.0282(9) 0.0637(11) -0.0078(8) 0.0236(8) -0.0025(7) N1 0.0308(9) 0.0249(9) 0.0318(9) -0.0005(7) 0.0091(7) -0.0029(7) N2 0.0324(10) 0.0253(10) 0.0418(10) 0.0010(8) 0.0129(9) -0.0040(8) C1 0.0397(14) 0.0340(14) 0.0809(19) 0.0096(13) 0.0051(14) -0.0080(11) C2 0.0390(13) 0.0373(13) 0.0407(13) 0.0057(10) 0.0160(11) 0.0028(10) C3 0.0293(12) 0.0264(11) 0.0406(12) -0.0038(9) 0.0069(9) -0.0023(9) C4 0.0378(12) 0.0259(11) 0.0316(11) -0.0021(9) 0.0094(9) -0.0028(9) C5 0.0303(11) 0.0279(12) 0.0346(11) 0.0025(9) 0.0076(9) -0.0033(9) C6 0.0338(12) 0.0299(12) 0.0329(11) -0.0014(9) 0.0072(9) 0.0002(9) C7 0.0344(12) 0.0332(13) 0.0412(12) 0.0006(10) 0.0158(10) -0.0006(9) C8 0.0323(12) 0.0341(13) 0.0374(12) 0.0024(10) 0.0139(10) -0.0039(9) _geom_special_details ; All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. ; loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 _geom_bond_publ_flag F1 C3 1.368(2) . ? F2 C3 1.356(2) . ? S1 C4 1.804(2) . ? S1 C1 1.808(3) . ? O1 C2 1.414(3) . ? O1 H1 0.813(18) . ? O2 C5 1.206(2) . ? O3 C6 1.235(3) . ? N1 C8 1.380(3) . ? N1 C5 1.388(3) . ? N1 C4 1.468(3) . ? N2 C5 1.367(3) . ? N2 C6 1.370(3) . ? N2 H2A 0.844(16) . ? C1 C2 1.509(3) . ? C1 H1A 0.9700 . ? C1 H1B 0.9700 . ? C2 C3 1.486(3) . ? C2 H2 0.9800 . ? C3 C4 1.521(3) . ? C4 H4 0.9800 . ? C6 C7 1.425(3) . ? C7 C8 1.331(3) . ? C7 H7 0.9300 . ? C8 H8 0.9300 . ? loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 _geom_angle_publ_flag C4 S1 C1 94.62(11) . . ? C2 O1 H1 106(2) . . ? C8 N1 C5 120.87(18) . . ? C8 N1 C4 123.56(17) . . ? C5 N1 C4 115.36(16) . . ? C5 N2 C6 127.16(19) . . ? C5 N2 H2A 111.1(17) . . ? C6 N2 H2A 121.7(17) . . ? C2 C1 S1 106.53(16) . . ? C2 C1 H1A 110.4 . . ? S1 C1 H1A 110.4 . . ? C2 C1 H1B 110.4 . . ? S1 C1 H1B 110.4 . . ? H1A C1 H1B 108.6 . . ? O1 C2 C3 109.71(18) . . ? O1 C2 C1 113.4(2) . . ? C3 C2 C1 105.54(18) . . ? O1 C2 H2 109.4 . . ? C3 C2 H2 109.4 . . ? C1 C2 H2 109.4 . . ? F2 C3 F1 105.10(17) . . ? F2 C3 C2 112.85(18) . . ? F1 C3 C2 109.76(18) . . ? F2 C3 C4 111.10(16) . . ? F1 C3 C4 107.43(16) . . ? C2 C3 C4 110.33(17) . . ? N1 C4 C3 114.24(16) . . ? N1 C4 S1 113.95(14) . . ? C3 C4 S1 105.49(13) . . ? N1 C4 H4 107.6 . . ? C3 C4 H4 107.6 . . ? S1 C4 H4 107.6 . . ? O2 C5 N2 122.7(2) . . ? O2 C5 N1 122.4(2) . . ? N2 C5 N1 114.93(18) . . ? O3 C6 N2 119.6(2) . . ? O3 C6 C7 125.8(2) . . ? N2 C6 C7 114.57(19) . . ? C8 C7 C6 120.6(2) . . ? C8 C7 H7 119.7 . . ? C6 C7 H7 119.7 . . ? C7 C8 N1 121.89(19) . . ? C7 C8 H8 119.1 . . ? N1 C8 H8 119.1 . . ? loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_site_symmetry_1 _geom_torsion_site_symmetry_2 _geom_torsion_site_symmetry_3 _geom_torsion_site_symmetry_4 _geom_torsion_publ_flag C4 S1 C1 C2 19.25(19) . . . . ? S1 C1 C2 O1 -158.66(16) . . . . ? S1 C1 C2 C3 -38.5(2) . . . . ? O1 C2 C3 F2 -67.8(2) . . . . ? C1 C2 C3 F2 169.65(18) . . . . ? O1 C2 C3 F1 49.1(2) . . . . ? C1 C2 C3 F1 -73.5(2) . . . . ? O1 C2 C3 C4 167.26(17) . . . . ? C1 C2 C3 C4 44.7(2) . . . . ? C8 N1 C4 C3 -89.6(2) . . . . ? C5 N1 C4 C3 95.7(2) . . . . ? C8 N1 C4 S1 31.8(2) . . . . ? C5 N1 C4 S1 -142.96(16) . . . . ? F2 C3 C4 N1 -29.6(2) . . . . ? F1 C3 C4 N1 -144.09(17) . . . . ? C2 C3 C4 N1 96.3(2) . . . . ? F2 C3 C4 S1 -155.58(14) . . . . ? F1 C3 C4 S1 89.98(16) . . . . ? C2 C3 C4 S1 -29.6(2) . . . . ? C1 S1 C4 N1 -120.86(16) . . . . ? C1 S1 C4 C3 5.25(16) . . . . ? C6 N2 C5 O2 180.0(2) . . . . ? C6 N2 C5 N1 0.2(3) . . . . ? C8 N1 C5 O2 -178.75(19) . . . . ? C4 N1 C5 O2 -3.9(3) . . . . ? C8 N1 C5 N2 1.0(3) . . . . ? C4 N1 C5 N2 175.92(17) . . . . ? C5 N2 C6 O3 179.6(2) . . . . ? C5 N2 C6 C7 -1.2(3) . . . . ? O3 C6 C7 C8 -179.9(2) . . . . ? N2 C6 C7 C8 1.0(3) . . . . ? C6 C7 C8 N1 0.1(3) . . . . ? C5 N1 C8 C7 -1.2(3) . . . . ? C4 N1 C8 C7 -175.7(2) . . . . ? loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A O1 H1 O3 0.813(18) 2.002(19) 2.813(2) 176(4) 2_646 N2 H2A O3 0.844(16) 2.002(17) 2.841(2) 172(2) 3_766 _diffrn_measured_fraction_theta_max 0.994 _diffrn_reflns_theta_full 26.99 _diffrn_measured_fraction_theta_full 0.994 _refine_diff_density_max 0.342 _refine_diff_density_min -0.295 _refine_diff_density_rms 0.051