#------------------------------------------------------------------------------ #$Date: 2019-05-17 11:44:18 +0300 (Fri, 17 May 2019) $ #$Revision: 215237 $ #$URL: file:///home/coder/svn-repositories/cod/cif/7/15/68/7156868.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/ # # All data on this site have been placed in the public domain by the # contributors. # data_7156868 loop_ _publ_author_name 'Malassis, Julien' 'Vendeville, Jean-Baptiste' 'Nguyen, Qui-Hien' 'Boujon, Marie' 'Gaignard-Gaillard, Quentin' 'Light, Mark' 'Linclau, Bruno' _publ_section_title ; Synthesis of vicinal dideoxy-difluorinated galactoses. ; _journal_name_full 'Organic & biomolecular chemistry' _journal_paper_doi 10.1039/c9ob00707e _journal_year 2019 _chemical_absolute_configuration unk _chemical_formula_moiety 'C6 H10 F2 O4' _chemical_formula_sum 'C6 H10 F2 O4' _chemical_formula_weight 184.14 _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 2018-11-17 _audit_creation_method ; Olex2 1.2 (compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506) ; _audit_update_record ; 2018-11-17 deposited with the CCDC. 2019-05-08 downloaded from the CCDC. ; _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 8.3866(2) _cell_length_b 8.4182(2) _cell_length_c 10.2320(2) _cell_measurement_reflns_used 13913 _cell_measurement_temperature 100(2) _cell_measurement_theta_max 31.5310 _cell_measurement_theta_min 3.0930 _cell_volume 722.38(3) _computing_cell_refinement 'CrysAlisPro 1.171.40.18b (Rigaku OD, 2018)' _computing_data_collection 'CrysAlisPro 1.171.40.18b (Rigaku OD, 2018)' _computing_data_reduction 'CrysAlisPro 1.171.40.18b (Rigaku OD, 2018)' _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 100(2) _diffrn_detector 'CCD area detector' _diffrn_detector_area_resol_mean 28.5714 _diffrn_detector_type 'Rigaku HG Saturn724+ (2x2 bin mode)' _diffrn_measured_fraction_theta_full 0.999 _diffrn_measured_fraction_theta_max 0.999 _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 -86.00 32.00 0.50 1.00 -- 2.50 -57.00 -30.00 236 2 \w -86.00 36.00 0.50 1.00 -- 2.50 -70.00-150.00 244 3 \w -29.00 91.00 0.50 1.00 -- 2.50 38.00-180.00 240 4 \w -94.00 24.00 0.50 1.00 -- -5.50 -57.00 -60.00 236 5 \w -29.00 -4.00 0.50 1.00 -- 2.50 38.00 -60.00 50 6 \w -37.00 83.00 0.50 1.00 -- -5.50 38.00 60.00 240 ; _diffrn_measurement_device 'four-circle \k diffractometer' _diffrn_measurement_device_type 'Rigaku AFC12 FRE-VHF' _diffrn_measurement_method 'profile data from \w-scans' _diffrn_measurement_specimen_support 'MiTeGen MicroMesh' _diffrn_orient_matrix_type 'CrysAlisPro convention (1999,Acta A55,543-557)' _diffrn_orient_matrix_UB_11 0.0555537000 _diffrn_orient_matrix_UB_12 0.0515073000 _diffrn_orient_matrix_UB_13 -0.0306900000 _diffrn_orient_matrix_UB_21 0.0617594000 _diffrn_orient_matrix_UB_22 -0.0558099000 _diffrn_orient_matrix_UB_23 0.0117631000 _diffrn_orient_matrix_UB_31 -0.0159418000 _diffrn_orient_matrix_UB_32 -0.0364820000 _diffrn_orient_matrix_UB_33 -0.0610299000 _diffrn_radiation_collimation 0.3 _diffrn_radiation_monochromator 'Confocal mirrors, VHF Varimax' _diffrn_radiation_probe x-ray _diffrn_radiation_type MoK\a _diffrn_radiation_wavelength 0.71073 _diffrn_reflns_av_R_equivalents 0.0207 _diffrn_reflns_av_unetI/netI 0.0100 _diffrn_reflns_Laue_measured_fraction_full 0.999 _diffrn_reflns_Laue_measured_fraction_max 0.999 _diffrn_reflns_limit_h_max 11 _diffrn_reflns_limit_h_min -11 _diffrn_reflns_limit_k_max 11 _diffrn_reflns_limit_k_min -11 _diffrn_reflns_limit_l_max 13 _diffrn_reflns_limit_l_min -13 _diffrn_reflns_number 16292 _diffrn_reflns_point_group_measured_fraction_full 0.999 _diffrn_reflns_point_group_measured_fraction_max 0.995 _diffrn_reflns_theta_full 25.242 _diffrn_reflns_theta_max 28.497 _diffrn_reflns_theta_min 3.134 _diffrn_source 'Rotating-anode X-ray tube' _diffrn_source_current 55.0 _diffrn_source_power 2.475 _diffrn_source_target Mo _diffrn_source_type 'Rigaku FR-E+ SuperBright' _diffrn_source_voltage 45.0 _exptl_absorpt_coefficient_mu 0.171 _exptl_absorpt_correction_T_max 1.00000 _exptl_absorpt_correction_T_min 0.64139 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details ; CrysAlisPro 1.171.40.18b (Rigaku Oxford Diffraction, 2018) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. ; _exptl_crystal_colour 'clear colourless' _exptl_crystal_colour_lustre clear _exptl_crystal_colour_primary colourless _exptl_crystal_density_diffrn 1.693 _exptl_crystal_description prism _exptl_crystal_F_000 384 _exptl_crystal_recrystallization_method 'The material was recrystallised from methanol by slow evaporation' _exptl_crystal_size_max 0.28 _exptl_crystal_size_mid 0.085 _exptl_crystal_size_min 0.069 _refine_diff_density_max 0.376 _refine_diff_density_min -0.172 _refine_diff_density_rms 0.039 _refine_ls_abs_structure_details ; Flack x determined using 723 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259). ; _refine_ls_abs_structure_Flack -0.23(13) _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 1.065 _refine_ls_hydrogen_treatment mixed _refine_ls_matrix_type full _refine_ls_number_parameters 121 _refine_ls_number_reflns 1816 _refine_ls_number_restraints 0 _refine_ls_restrained_S_all 1.065 _refine_ls_R_factor_all 0.0223 _refine_ls_R_factor_gt 0.0218 _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^)+(0.0366P)^2^+0.1460P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.0606 _refine_ls_wR_factor_ref 0.0609 _reflns_Friedel_coverage 0.691 _reflns_Friedel_fraction_full 1.000 _reflns_Friedel_fraction_max 0.988 _reflns_number_gt 1779 _reflns_number_total 1816 _reflns_threshold_expression 'I > 2\s(I)' _cod_data_source_file c9ob00707e2.cif _cod_data_source_block 2018sot0037_r1_100k _cod_database_code 7156868 _shelx_shelxl_version_number 2016/6 _chemical_oxdiff_formula C6H10F2O4 _chemical_oxdiff_usercomment JBVLNS42tube7-24 _shelx_space_group_comment ; The symmetry employed for this shelxl refinement is uniquely defined by the following loop, which should always be used as a source of symmetry information in preference to the above space-group names. They are only intended as comments. ; _shelx_estimated_absorpt_t_max 0.988 _shelx_estimated_absorpt_t_min 0.954 _diffrn_measurement_device_type2 'Rigaku AFC12 (Right)' _reflns_odcompleteness_completeness 99.89 _reflns_odcompleteness_iscentric 1 _reflns_odcompleteness_theta 26.32 _olex2_refinement_description ; 1. Fixed Uiso At 1.2 times of: All C(H) groups, All C(H,H) groups 2.a Ternary CH refined with riding coordinates: C1(H1), C2(H2A), C3(H3A), C4(H4A), C5(H5) 2.b Secondary CH2 refined with riding coordinates: C6(H6A,H6B) ; _shelx_res_file ; TITL 2018sot0037_r1_100k_a.res in P2(1)2(1)2(1) 2018sot0037_r1_100k.res created by SHELXL-2016/6 at 10:50:28 on 17-Nov-2018 REM Old TITL 2018sot0037_R1_100K in P2(1)2(1)2(1) REM SHELXT solution in P2(1)2(1)2(1) REM R1 0.081, Rweak 0.020, Alpha 0.001, Orientation as input REM Flack x = 0.185 ( 0.086 ) from Parsons' quotients REM Formula found by SHELXT: C6 O F5 CELL 0.71073 8.3866 8.4182 10.232 90 90 90 ZERR 4 0.0002 0.0002 0.0002 0 0 0 LATT -1 SYMM 0.5-X,-Y,0.5+Z SYMM -X,0.5+Y,0.5-Z SYMM 0.5+X,0.5-Y,-Z SFAC C H F O UNIT 24 40 8 16 L.S. 4 0 0 PLAN 20 SIZE 0.069 0.085 0.28 TEMP -173(2) BOND $H list 4 fmap 2 53 ACTA OMIT -3 57 REM REM REM WGHT 0.036600 0.146000 FVAR 0.97802 F1 3 0.865340 0.802542 0.688662 11.00000 0.01383 0.01603 = 0.02933 -0.00619 -0.00306 -0.00443 F2 3 0.854662 0.502041 0.783913 11.00000 0.02044 0.02271 = 0.01138 -0.00122 -0.00417 0.00695 O1 4 0.592957 0.407276 0.633611 11.00000 0.00943 0.00896 = 0.01511 0.00222 0.00283 0.00168 O2 4 0.363336 0.550938 0.641501 11.00000 0.00832 0.01317 = 0.02069 -0.00228 0.00120 0.00024 H2 2 0.309280 0.493704 0.587932 11.00000 0.04727 O3 4 0.540049 0.839493 0.623150 11.00000 0.01389 0.00854 = 0.01419 0.00021 0.00122 0.00216 H3 2 0.486059 0.866228 0.680881 11.00000 0.02607 O4 4 0.719922 0.114749 0.551038 11.00000 0.01978 0.00949 = 0.02487 0.00097 0.00655 -0.00004 H4 2 0.685271 0.056371 0.603561 11.00000 0.03534 C1 1 0.518728 0.555013 0.596290 11.00000 0.00936 0.00853 = 0.01318 0.00103 0.00017 0.00147 AFIX 13 H1 2 0.520635 0.567949 0.499151 11.00000 -1.20000 AFIX 0 C2 1 0.606881 0.691619 0.662265 11.00000 0.01026 0.00915 = 0.01043 0.00029 -0.00016 0.00085 AFIX 13 H2A 2 0.599140 0.680357 0.759350 11.00000 -1.20000 AFIX 0 C3 1 0.780283 0.685914 0.620886 11.00000 0.01062 0.01102 = 0.01492 -0.00089 0.00077 -0.00225 AFIX 13 H3A 2 0.787234 0.708367 0.525084 11.00000 -1.20000 AFIX 0 C4 1 0.853966 0.524912 0.647846 11.00000 0.01127 0.01547 = 0.01086 -0.00010 0.00064 0.00184 AFIX 13 H4A 2 0.965255 0.520934 0.612913 11.00000 -1.20000 AFIX 0 C5 1 0.753610 0.395016 0.586375 11.00000 0.01037 0.01158 = 0.01063 0.00117 0.00279 0.00198 AFIX 13 H5 2 0.753577 0.409258 0.489347 11.00000 -1.20000 AFIX 0 C6 1 0.814277 0.230161 0.618498 11.00000 0.01420 0.01263 = 0.01687 0.00198 0.00285 0.00394 AFIX 23 H6A 2 0.927273 0.220258 0.591715 11.00000 -1.20000 H6B 2 0.807702 0.211762 0.713910 11.00000 -1.20000 AFIX 0 HKLF 4 REM 2018sot0037_r1_100k_a.res in P2(1)2(1)2(1) REM R1 = 0.0218 for 1779 Fo > 4sig(Fo) and 0.0223 for all 1816 data REM 121 parameters refined using 0 restraints END WGHT 0.0376 0.1388 REM Highest difference peak 0.376, deepest hole -0.172, 1-sigma level 0.039 Q1 1 0.5654 0.6219 0.6301 11.00000 0.05 0.38 Q2 1 0.8141 0.6048 0.6344 11.00000 0.05 0.35 Q3 1 0.6950 0.6930 0.6395 11.00000 0.05 0.34 Q4 1 0.7878 0.3151 0.6068 11.00000 0.05 0.32 Q5 1 0.8082 0.4572 0.6186 11.00000 0.05 0.31 Q6 1 0.5616 0.4737 0.6213 11.00000 0.05 0.20 Q7 1 0.6787 0.3998 0.6148 11.00000 0.05 0.18 Q8 1 0.5759 0.7627 0.6395 11.00000 0.05 0.18 Q9 1 0.4409 0.5446 0.6215 11.00000 0.05 0.15 Q10 1 0.8193 0.7493 0.6465 11.00000 0.05 0.15 Q11 1 0.6031 0.6781 0.7251 11.00000 0.05 0.15 Q12 1 0.5954 0.4053 0.7009 11.00000 0.05 0.14 Q13 1 0.5441 0.3318 0.6094 11.00000 0.05 0.14 Q14 1 0.7511 0.4072 0.5251 11.00000 0.05 0.13 Q15 1 0.7760 0.1579 0.5984 11.00000 0.05 0.13 Q16 1 0.8553 0.5129 0.7172 11.00000 0.05 0.13 Q17 1 0.8045 0.4389 0.7821 11.00000 0.05 0.12 Q18 1 0.9435 0.5225 0.6383 11.00000 0.05 0.12 Q19 1 0.8476 0.7787 0.7602 11.00000 0.05 0.11 Q20 1 0.7564 0.0997 0.4826 11.00000 0.05 0.11 ; _shelx_res_checksum 57845 _olex2_date_sample_data_collection 2018-11-07 _olex2_date_sample_submission 2018-11-06 _olex2_diffrn_ambient_temperature_device 'Oxford Cryosystems' _olex2_exptl_crystal_mounting_method 'The crystal was mounted on a MITIGEN holder silicon oil' _olex2_submission_original_sample_id JBVLNS42tube7-24 _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 1.567 _oxdiff_exptl_absorpt_empirical_full_min 0.533 loop_ _space_group_symop_operation_xyz 'x, y, z' '-x+1/2, -y, z+1/2' '-x, y+1/2, -z+1/2' 'x+1/2, -y+1/2, -z' 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_site_symmetry_order _atom_site_calc_flag _atom_site_refinement_flags_posn F1 F 0.86534(10) 0.80254(10) 0.68866(9) 0.0197(2) Uani 1 1 d . F2 F 0.85466(10) 0.50204(10) 0.78391(8) 0.01818(19) Uani 1 1 d . O1 O 0.59296(11) 0.40728(10) 0.63361(10) 0.0112(2) Uani 1 1 d . O2 O 0.36334(11) 0.55094(11) 0.64150(10) 0.0141(2) Uani 1 1 d . H2 H 0.309(3) 0.494(3) 0.588(3) 0.047(7) Uiso 1 1 d . O3 O 0.54005(12) 0.83949(11) 0.62315(10) 0.0122(2) Uani 1 1 d . H3 H 0.486(3) 0.866(3) 0.681(2) 0.026(5) Uiso 1 1 d . O4 O 0.71992(13) 0.11475(12) 0.55104(12) 0.0180(2) Uani 1 1 d . H4 H 0.685(3) 0.056(3) 0.604(2) 0.035(6) Uiso 1 1 d . C1 C 0.51873(14) 0.55501(15) 0.59629(13) 0.0104(2) Uani 1 1 d . H1 H 0.520635 0.567949 0.499151 0.012 Uiso 1 1 calc R C2 C 0.60688(15) 0.69162(14) 0.66226(12) 0.0099(2) Uani 1 1 d . H2A H 0.599140 0.680357 0.759350 0.012 Uiso 1 1 calc R C3 C 0.78028(15) 0.68591(15) 0.62089(13) 0.0122(2) Uani 1 1 d . H3A H 0.787234 0.708367 0.525084 0.015 Uiso 1 1 calc R C4 C 0.85397(16) 0.52491(15) 0.64785(12) 0.0125(2) Uani 1 1 d . H4A H 0.965255 0.520934 0.612913 0.015 Uiso 1 1 calc R C5 C 0.75361(15) 0.39502(15) 0.58637(12) 0.0109(2) Uani 1 1 d . H5 H 0.753577 0.409258 0.489347 0.013 Uiso 1 1 calc R C6 C 0.81428(16) 0.23016(16) 0.61850(14) 0.0146(3) Uani 1 1 d . H6A H 0.927273 0.220258 0.591715 0.017 Uiso 1 1 calc R H6B H 0.807702 0.211762 0.713910 0.017 Uiso 1 1 calc R 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 0.0138(4) 0.0160(4) 0.0293(5) -0.0062(3) -0.0031(4) -0.0044(3) F2 0.0204(4) 0.0227(4) 0.0114(4) -0.0012(3) -0.0042(3) 0.0070(3) O1 0.0094(4) 0.0090(4) 0.0151(4) 0.0022(3) 0.0028(4) 0.0017(3) O2 0.0083(4) 0.0132(4) 0.0207(5) -0.0023(4) 0.0012(4) 0.0002(3) O3 0.0139(4) 0.0085(4) 0.0142(4) 0.0002(4) 0.0012(4) 0.0022(3) O4 0.0198(5) 0.0095(4) 0.0249(5) 0.0010(4) 0.0066(4) 0.0000(4) C1 0.0094(5) 0.0085(5) 0.0132(6) 0.0010(4) 0.0002(4) 0.0015(4) C2 0.0103(5) 0.0092(5) 0.0104(5) 0.0003(5) -0.0002(4) 0.0008(4) C3 0.0106(5) 0.0110(5) 0.0149(6) -0.0009(5) 0.0008(5) -0.0022(4) C4 0.0113(5) 0.0155(6) 0.0109(6) -0.0001(4) 0.0006(4) 0.0018(5) C5 0.0104(5) 0.0116(6) 0.0106(5) 0.0012(4) 0.0028(5) 0.0020(4) C6 0.0142(6) 0.0126(6) 0.0169(6) 0.0020(5) 0.0029(5) 0.0039(5) 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' F F 0.0171 0.0103 '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' loop_ _exptl_crystal_face_index_h _exptl_crystal_face_index_k _exptl_crystal_face_index_l _exptl_crystal_face_perp_dist -5 1 2 0.0354 5 -1 -2 0.0354 2 2 5 0.1082 -2 -2 -5 0.1082 0 -1 0 0.0344 0 1 0 0.0344 loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle C5 O1 C1 112.21(10) C1 O2 H2 107.3(17) C2 O3 H3 105.6(16) C6 O4 H4 107.5(17) O1 C1 H1 110.5 O1 C1 C2 108.90(10) O2 C1 O1 107.26(10) O2 C1 H1 110.5 O2 C1 C2 109.11(10) C2 C1 H1 110.5 O3 C2 C1 110.14(10) O3 C2 H2A 109.7 O3 C2 C3 109.10(10) C1 C2 H2A 109.7 C3 C2 C1 108.53(10) C3 C2 H2A 109.7 F1 C3 C2 109.20(10) F1 C3 H3A 108.9 F1 C3 C4 109.26(10) C2 C3 H3A 108.9 C4 C3 C2 111.65(11) C4 C3 H3A 108.9 F2 C4 C3 107.74(10) F2 C4 H4A 110.2 F2 C4 C5 108.32(10) C3 C4 H4A 110.2 C3 C4 C5 110.07(10) C5 C4 H4A 110.2 O1 C5 C4 109.24(10) O1 C5 H5 109.0 O1 C5 C6 107.95(10) C4 C5 H5 109.0 C6 C5 C4 112.60(10) C6 C5 H5 109.0 O4 C6 C5 109.38(10) O4 C6 H6A 109.8 O4 C6 H6B 109.8 C5 C6 H6A 109.8 C5 C6 H6B 109.8 H6A C6 H6B 108.2 loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance F1 C3 1.3977(15) F2 C4 1.4055(14) O1 C1 1.4423(14) O1 C5 1.4351(15) O2 H2 0.86(3) O2 C1 1.3833(15) O3 H3 0.78(3) O3 C2 1.4227(15) O4 H4 0.78(3) O4 C6 1.4306(17) C1 H1 1.0000 C1 C2 1.5247(17) C2 H2A 1.0000 C2 C3 1.5154(17) C3 H3A 1.0000 C3 C4 1.5149(17) C4 H4A 1.0000 C4 C5 1.5165(18) C5 H5 1.0000 C5 C6 1.5142(17) C6 H6A 0.9900 C6 H6B 0.9900 loop_ _exptl_oxdiff_crystal_face_indexfrac_h _exptl_oxdiff_crystal_face_indexfrac_k _exptl_oxdiff_crystal_face_indexfrac_l _exptl_oxdiff_crystal_face_x _exptl_oxdiff_crystal_face_y _exptl_oxdiff_crystal_face_z -4.9982 0.9984 1.9983 -0.2876 -0.3409 -0.0787 4.9982 -0.9984 -1.9983 0.2876 0.3409 0.0787 1.9985 1.9999 4.9975 0.0607 0.0706 -0.4098 -1.9985 -1.9999 -4.9975 -0.0607 -0.0706 0.4098 0.0000 -0.9994 0.0000 -0.0515 0.0558 0.0365 -0.0000 0.9994 -0.0000 0.0515 -0.0558 -0.0365