#------------------------------------------------------------------------------ #$Date: 2025-08-18 23:52:38 +0100 (Mon, 18 Aug 2025) $ #$Revision: 301791 $ #$URL: svn://www.crystallography.net/cod/cif/2/00/60/2006082.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. The original data for this entry # were provided by IUCr Journals, http://journals.iucr.org/. # # The file may be used within the scientific community so long as # proper attribution is given to the journal article from which the # data were obtained. # data_2006082 loop_ _publ_author_name 'Bernardinelli, G.' 'Tronchet, J. M. J.' 'Kovacs, I.' _publ_section_title ;Absolute Structure of (Thian-5-one 1,1-dioxide)-3-spiro-3'-(5'-O-tert-butyldimethylsilyl-3'-deoxy-1',2'-O-isopropylidene-\a-D-xylo-pentofuranose), a Novel Type of Spirosugar ; _journal_issue 4 _journal_name_full 'Acta Crystallographica Section C' _journal_page_first 511 _journal_page_last 513 _journal_paper_doi 10.1107/S010827019601445X _journal_volume 53 _journal_year 1997 _chemical_formula_moiety 'C18 H32 O7 S Si' _chemical_formula_structural 'C18 H32 O7 S Si' _chemical_formula_sum 'C18 H32 O7 S Si' _chemical_formula_weight 420.6 _chemical_melting_point 161.0(2) _chemical_name_systematic ; (thian-5-one-1,1-dioxide)-3-spiro-3'-(5'-O-tert-butyldimethylsilyl-3'- deoxy-1',2'-O-isopropylidene-alpha-D-xylo-pentofuranose) ; _space_group_IT_number 19 _symmetry_cell_setting orthorhombic _symmetry_space_group_name_Hall 'P 2ac 2ab' _symmetry_space_group_name_H-M 'P 21 21 21' _audit_creation_method from_xtal_archive_file_using_CIFIO _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 6.6446(5) _cell_length_b 9.4721(8) _cell_length_c 35.046(2) _cell_measurement_reflns_used 20 _cell_measurement_temperature 293 _cell_measurement_theta_max 30.5 _cell_measurement_theta_min 14.5 _cell_volume 2205.7(3) _computing_cell_refinement 'Xtal LATCON (Hall, Flack & Stewart, 1992)' _computing_data_collection 'CAD-4 Software (Enraf-Nonius, 1989)' _computing_data_reduction Xtal_REFCAL_LSABS__SORTRF _computing_molecular_graphics Xtal_ORTEP _computing_publication_material Xtal_BONDLA_CIFIO _computing_structure_refinement Xtal_CRYLSQ _computing_structure_solution 'MULTAN87 (Main et al., 1987)' _diffrn_ambient_temperature 293 _diffrn_measurement_device 'Nonius CAD-4' _diffrn_measurement_method \w-2\q _diffrn_radiation_monochromator graphite _diffrn_radiation_source Sealed-off_tube _diffrn_radiation_type CuK\a _diffrn_radiation_wavelength 1.54184 _diffrn_reflns_av_R_equivalents 0.031 _diffrn_reflns_av_sigmaI/netI 0.048 _diffrn_reflns_limit_h_max 7 _diffrn_reflns_limit_h_min 0 _diffrn_reflns_limit_k_max 10 _diffrn_reflns_limit_k_min 0 _diffrn_reflns_limit_l_max 36 _diffrn_reflns_limit_l_min 0 _diffrn_reflns_number 3412 _diffrn_reflns_theta_max 54.96 _diffrn_reflns_theta_min 2.53 _diffrn_standards_decay_% 6.5 _diffrn_standards_interval_count 100 _diffrn_standards_number 2 _exptl_absorpt_coefficient_mu 2.123 _exptl_absorpt_correction_T_max 0.95 _exptl_absorpt_correction_T_min 0.78 _exptl_absorpt_correction_type 'analytical by integration (Blanc, Schwarzenbach & Flack, 1991)' _exptl_absorpt_process_details ;Analytical integration, xtal_lsabs program (Blanc, Schwarzenbach & Flack, 1991) ; _exptl_crystal_colour colourless _exptl_crystal_density_diffrn 1.266 _exptl_crystal_density_meas ? _exptl_crystal_description needle _exptl_crystal_F_000 904 _exptl_crystal_size_max 0.50 _exptl_crystal_size_mid 0.13 _exptl_crystal_size_min 0.026 _refine_diff_density_max 0.738 _refine_diff_density_min -0.314 _refine_ls_abs_structure_details 'Flack (1983)' _refine_ls_abs_structure_Flack '\c = 0.02(5)' _refine_ls_extinction_method none _refine_ls_goodness_of_fit_all 3.432 _refine_ls_goodness_of_fit_obs 3.101 _refine_ls_hydrogen_treatment ; All non-methyl H atoms observed and refined (with fixed U~iso~); all coordinates of methyl H atoms calculated ; _refine_ls_matrix_type full _refine_ls_number_constraints 0 _refine_ls_number_parameters 278 _refine_ls_number_reflns 2501 _refine_ls_number_restraints 0 _refine_ls_R_factor_all 0.068 _refine_ls_R_factor_obs 0.059 _refine_ls_shift/esd_max 0.000182 _refine_ls_shift/esd_mean 0.0000176 _refine_ls_structure_factor_coef F _refine_ls_weighting_details 'w = 1/\s^2^(F~o~)' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_all 0.048 _refine_ls_wR_factor_obs 0.041 _reflns_number_observed 2501 _reflns_number_total 2746 _reflns_observed_criterion F>4\s(F) _cod_data_source_file pa1244.cif _cod_data_source_block KOVA _cod_depositor_comments ; The following automatic conversions were performed: '_chemical_melting_point' value '160.8-161.2' was changed to '161.0(2)' - the average value was taken and precision was estimated. Automatic conversion script Id: cif_fix_values 1715 2011-07-08 13:25:40Z adriana The following automatic conversions were performed: '_exptl_crystal_density_meas' value 'not measured' was changed to '?' - the value is perceived as not measured. Automatic conversion script Id: cif_fix_values 3008 2015-01-20 13:52:24Z robertas The following automatic conversions were performed: '_refine_ls_weighting_scheme' value 'w = 1/\s^2^(F~o~)' was changed to 'calc'. New tag '_refine_ls_weighting_details' was created. The value of the new tag was set to 'w = 1/\s^2^(F~o~)'. Automatic conversion script Id: cif_fix_values 3143 2015-03-26 13:38:13Z robertas ; _cod_original_cell_volume 2205.7(2) _cod_original_sg_symbol_Hall P_2ac_2ab _cod_original_formula_sum 'C18 H32 O7 Si S' _cod_database_code 2006082 loop_ _symmetry_equiv_pos_as_xyz +x,+y,+z 1/2-x,-y,1/2+z 1/2+x,1/2-y,-z -x,1/2+y,1/2-z loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_22 _atom_site_aniso_U_23 _atom_site_aniso_U_33 S .0522(15) .0016(14) -.0090(14) .0458(14) -.0028(13) .0469(13) Si .0426(16) .0017(17) -.0031(16) .0633(18) -.0149(16) .0635(18) O1 .039(4) .000(4) .018(3) .034(4) -.002(4) .064(4) O2 .107(7) .030(6) .052(5) .070(5) .029(5) .070(5) O3 .052(4) .012(4) .000(4) .047(4) .015(4) .053(4) O4 .036(4) .018(5) .003(4) .078(5) -.007(5) .084(5) O5 .101(6) .018(6) -.032(4) .078(5) .004(4) .055(4) O6 .057(4) -.005(4) -.007(4) .044(4) -.018(4) .060(4) O7 .043(4) .003(4) .002(4) .054(4) -.022(4) .047(4) C1 .064(8) -.014(6) .022(7) .038(6) -.003(5) .062(7) C2 .035(6) .001(5) .008(5) .041(6) -.001(5) .042(6) C3 .028(5) -.001(4) -.001(4) .022(5) -.008(4) .041(5) C4 .033(6) .002(5) -.005(5) .034(5) .002(5) .048(6) C5 .077(9) .011(7) .009(7) .052(7) .004(6) .050(7) C6 .089(9) .014(6) .018(7) .042(6) .017(5) .062(7) C7 .144(12) .018(10) -.007(9) .083(8) -.008(8) .075(8) C8 .041(6) -.000(6) -.010(5) .039(6) -.001(5) .038(6) C9 .041(7) -.017(6) .009(5) .045(6) .000(6) .054(7) C10 .061(7) -.006(7) .009(6) .046(5) .000(6) .048(6) C11 .035(6) .001(6) -.007(5) .046(6) -.002(6) .053(6) C12 .054(8) .005(6) -.010(6) .040(6) -.013(6) .061(8) C13 .062(7) .009(7) .026(7) .066(7) -.030(7) .110(9) C14 .047(7) -.000(7) -.014(7) .087(8) -.018(7) .085(8) C15 .058(9) -.003(9) .006(7) .125(11) .005(8) .076(9) C16 .179(16) .020(13) -.002(10) .120(10) .035(9) .082(9) C17 .104(11) .015(12) .013(10) .222(18) .022(12) .112(11) C18 .118(12) -.006(15) -.019(10) .242(18) .005(12) .101(11) loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_thermal_displace_type S .1791(4) .2593(3) .22982(7) .0483(14) Uani Si -.0859(4) .5710(3) .41245(8) .0565(17) Uani O1 .0216(8) .2615(6) .35621(15) .046(4) Uani O2 .1626(12) .0576(7) .38055(18) .083(6) Uani O3 .4167(9) .0756(6) .33743(15) .051(4) Uani O4 .6747(9) .1723(7) .25697(17) .066(5) Uani O5 .0581(11) .3294(7) .20139(15) .078(5) Uani O6 .1866(9) .1077(6) .22938(17) .054(4) Uani O7 .1147(9) .5428(6) .38610(15) .048(4) Uani C1 .0741(16) .1182(10) .3485(3) .055(7) Uani C2 .2405(13) .1221(9) .3178(3) .040(6) Uani C3 .2621(11) .2814(8) .3084(3) .030(5) Uani C4 .1886(14) .3464(8) .3460(3) .038(6) Uani C5 .3619(18) .0119(10) .3729(3) .060(8) Uani C6 .3701(16) -.1453(9) .3701(3) .064(7) Uani C7 .5031(19) .0690(12) .4030(3) .101(9) Uani C8 .4804(14) .3237(10) .2981(3) .039(6) Uani C9 .5472(13) .2636(10) .2606(3) .047(6) Uani C10 .4351(15) .3178(10) .2260(3) .052(6) Uani C11 .1182(13) .3216(10) .2760(3) .044(6) Uani C12 .1312(16) .4992(10) .3474(3) .052(7) Uani C13 -.1093(15) .7646(10) .4207(3) .080(8) Uani C14 -.3187(15) .5064(11) .3875(3) .073(7) Uani C15 -.0474(17) .4783(14) .4586(4) .086(10) Uani C16 -.035(3) .3242(15) .4537(4) .127(11) Uani C17 -.2099(19) .5165(18) .4864(4) .146(13) Uani C18 .144(3) .5290(18) .4769(4) .154(14) Uani H1 -.035(11) .082(9) .338(3) .05000 Uiso H2 .211(11) .061(8) .2931(18) .05000 Uiso H4 .298(11) .324(8) .3630(19) .05000 Uiso H61 .52502 -.17605 .36201 .05000 Uiso H62 .32944 -.19432 .39636 .05000 Uiso H63 .27122 -.18831 .34714 .05000 Uiso H71 .45537 .02241 .43056 .05000 Uiso H72 .65095 .04069 .39621 .05000 Uiso H73 .48936 .18437 .40627 .05000 Uiso H81 .485(11) .435(8) .2963(18) .05000 Uiso H82 .541(12) .285(8) .316(2) .05000 Uiso H101 .426(11) .414(7) .229(3) .05000 Uiso H102 .510(11) .284(8) .2018(18) .05000 Uiso H111 .095(11) .433(8) .2760(19) .05000 Uiso H112 .004(11) .289(9) .280(3) .05000 Uiso H121 .254(11) .573(7) .3323(19) .05000 Uiso H122 .024(12) .514(9) .337(3) .05000 Uiso H131 .01976 .80520 .43464 .05000 Uiso H132 -.13014 .81778 .39268 .05000 Uiso H133 -.24620 .78278 .43756 .05000 Uiso H141 -.33700 .56231 .36098 .05000 Uiso H142 -.30499 .39371 .38257 .05000 Uiso H143 -.45271 .52479 .40549 .05000 Uiso H161 -.18606 .28531 .44165 .05000 Uiso H162 .07897 .29136 .43446 .05000 Uiso H163 -.02013 .26576 .48098 .05000 Uiso H171 -.20921 .62800 .49266 .05000 Uiso H172 -.35461 .48254 .47611 .05000 Uiso H173 -.18638 .46075 .51489 .05000 Uiso H181 .27623 .49908 .45810 .05000 Uiso H182 .14935 .63875 .48209 .05000 Uiso H183 .17546 .47146 .50444 .05000 Uiso loop_ _atom_type_symbol _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C .017 .009 'Int. Tables Vol IV Tables 2.2B and 2.3.1' H 0 0 'Int. Tables Vol IV Tables 2.2B and 2.3.1' O .047 .032 'Int. Tables Vol IV Tables 2.2B and 2.3.1' S .319 .557 'Int. Tables Vol IV Tables 2.2B and 2.3.1' Si .244 .33 'Int. Tables Vol IV Tables 2.2B and 2.3.1' loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_publ_flag O5 S O6 118.2(4) yes O5 S C10 109.6(5) no O5 S C11 110.6(4) no O6 S C10 105.9(4) no O6 S C11 110.5(4) no C10 S C11 100.5(5) yes O7 Si C13 108.4(4) no O7 Si C14 110.7(4) no O7 Si C15 107.5(5) no C13 Si C14 108.9(5) no C13 Si C15 109.9(5) no C14 Si C15 111.3(5) no C1 O1 C4 107.5(7) yes C1 O2 C5 111.6(8) yes C2 O3 C5 109.9(7) yes Si O7 C12 130.2(6) no O1 C1 O2 110.1(8) no O1 C1 C2 106.5(7) yes O1 C1 H1 104(6) no O2 C1 C2 105.6(8) yes O2 C1 H1 122(5) no C2 C1 H1 108(5) no O3 C2 C1 104.2(7) yes O3 C2 C3 109.1(7) yes O3 C2 H2 112(4) no C1 C2 C3 103.8(7) yes C1 C2 H2 115(4) no C3 C2 H2 112(4) no C2 C3 C4 100.2(6) yes C2 C3 C8 112.9(7) no C2 C3 C11 110.0(7) no C4 C3 C8 113.2(7) no C4 C3 C11 109.7(7) no C8 C3 C11 110.4(7) yes O1 C4 C3 103.7(6) yes O1 C4 C12 110.0(8) no O1 C4 H4 108(5) no C3 C4 C12 119.7(8) no C3 C4 H4 102(5) no C12 C4 H4 112(5) no O2 C5 O3 105.8(8) yes O2 C5 C6 110.5(9) no O2 C5 C7 109.8(8) no O3 C5 C6 110.7(8) no O3 C5 C7 107.4(8) no C6 C5 C7 112.4(9) no C5 C6 H61 108.2(8) no C5 C6 H62 111.5(8) no C5 C6 H63 113.0(8) no H61 C6 H62 110.0(8) no H61 C6 H63 105.5(7) no H62 C6 H63 108.4(8) no C5 C7 H71 106.7(10) no C5 C7 H72 109.3(9) no C5 C7 H73 112.0(10) no H71 C7 H72 111.5(10) no H71 C7 H73 106.4(9) no H72 C7 H73 110.8(11) no C3 C8 C9 112.5(7) yes C3 C8 H81 107(4) no C3 C8 H82 99(6) no C9 C8 H81 109(4) no C9 C8 H82 111(5) no H81 C8 H82 118(7) no O4 C9 C8 124.5(8) no O4 C9 C10 120.1(8) no C8 C9 C10 115.3(8) yes S C10 C9 107.7(7) yes S C10 H101 103(5) no S C10 H102 115(4) no C9 C10 H101 106(5) no C9 C10 H102 108(4) no H101 C10 H102 116(6) no S C11 C3 116.8(6) yes S C11 H111 111(4) no S C11 H112 103(6) no C3 C11 H111 110(4) no C3 C11 H112 111(6) no H111 C11 H112 104(7) no O7 C12 C4 109.3(8) no O7 C12 H121 108(4) no O7 C12 H122 107(6) no C4 C12 H121 112(4) no C4 C12 H122 112(6) no H121 C12 H122 108(7) no Si C13 H131 111.2(7) no Si C13 H132 108.6(7) no Si C13 H133 107.9(7) no H131 C13 H132 110.1(8) no H131 C13 H133 111.5(9) no H132 C13 H133 107.5(8) no Si C14 H141 109.5(7) no Si C14 H142 109.0(7) no Si C14 H143 110.3(7) no H141 C14 H142 110.8(9) no H141 C14 H143 108.9(9) no H142 C14 H143 108.3(9) no Si C15 C16 112.0(8) no Si C15 C17 110.7(9) no Si C15 C18 109.7(9) no C16 C15 C17 110.7(12) no C16 C15 C18 108.7(12) no C17 C15 C18 104.7(10) no C15 C16 H161 108.3(12) no C15 C16 H162 113.8(12) no C15 C16 H163 113.6(10) no H161 C16 H162 107.2(10) no H161 C16 H163 103.7(11) no H162 C16 H163 109.6(13) no C15 C17 H171 111.4(12) no C15 C17 H172 110.7(12) no C15 C17 H173 111.1(12) no H171 C17 H172 111.3(13) no H171 C17 H173 106.0(12) no H172 C17 H173 106.1(12) no C15 C18 H181 109.1(11) no C15 C18 H182 114.6(13) no C15 C18 H183 111.6(13) no H181 C18 H182 108.7(13) no H181 C18 H183 103.5(12) no H182 C18 H183 108.8(12) no loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_publ_flag S O5 1.442(7) yes S O6 1.437(6) yes S C10 1.794(11) yes S C11 1.771(10) yes Si O7 1.643(6) no Si C13 1.863(10) no Si C14 1.879(10) no Si C15 1.858(12) no O1 C1 1.427(11) yes O1 C4 1.416(10) yes O2 C1 1.392(12) yes O2 C5 1.418(14) yes O3 C2 1.428(10) yes O3 C5 1.430(11) yes O4 C9 1.217(11) yes O7 C12 1.421(12) no C1 C2 1.542(14) yes C1 H1 .88(8) no C2 C3 1.551(11) yes C2 H2 1.06(7) no C3 C4 1.537(11) yes C3 C8 1.547(12) yes C3 C11 1.530(12) yes C4 C12 1.497(13) no C4 H4 .96(7) no C5 C6 1.494(12) no C5 C7 1.512(15) no C6 H61 1.107(11) no C6 H62 1.066(9) no C6 H63 1.115(10) no C7 H71 1.107(11) no C7 H72 1.046(13) no C7 H73 1.102(11) no C8 C9 1.501(12) yes C8 H81 1.06(8) no C8 H82 .84(8) no C9 C10 1.510(13) yes C10 H101 .92(7) no C10 H102 1.04(7) no C11 H111 1.07(7) no C11 H112 .83(8) no C12 H121 1.20(7) no C12 H122 .80(8) no C13 H131 1.059(10) no C13 H132 1.113(10) no C13 H133 1.098(10) no C14 H141 1.077(10) no C14 H142 1.086(10) no C14 H143 1.104(10) no C15 C16 1.472(19) no C15 C17 1.499(18) no C15 C18 1.504(18) no C16 H161 1.148(15) no C16 H162 1.063(14) no C16 H163 1.109(12) no C17 H171 1.079(17) no C17 H172 1.076(13) no C17 H173 1.140(14) no C18 H181 1.134(14) no C18 H182 1.056(17) no C18 H183 1.127(14) no 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_publ_flag O5 S C10 C9 169.6(6) no O6 S C10 C9 -61.9(7) no C11 S C10 C9 53.1(7) yes O5 S C11 C3 -167.5(6) no O6 S C11 C3 59.8(7) no C10 S C11 C3 -51.7(7) yes C13 Si O7 C12 -109.1(8) no C14 Si O7 C12 10.3(8) no C15 Si O7 C12 132.1(8) no O7 Si C15 C16 -64.3(10) no O7 Si C15 C17 171.6(9) no O7 Si C15 C18 56.5(10) no C13 Si C15 C16 177.9(9) no C13 Si C15 C17 53.8(11) no C13 Si C15 C18 -61.3(10) no C14 Si C15 C16 57.1(10) no C14 Si C15 C17 -67.0(11) no C14 Si C15 C18 177.9(9) no C4 O1 C1 O2 90.2(9) no C4 O1 C1 C2 -23.9(9) yes C1 O1 C4 C3 41.6(8) yes C1 O1 C4 C12 170.8(8) no C5 O2 C1 O1 -119.3(8) no C5 O2 C1 C2 -4.7(10) yes C1 O2 C5 O3 13.6(10) yes C1 O2 C5 C6 -106.3(9) no C1 O2 C5 C7 129.2(8) no C5 O3 C2 C1 14.5(8) yes C5 O3 C2 C3 124.9(7) no C2 O3 C5 O2 -17.6(9) yes C2 O3 C5 C6 102.2(9) no C2 O3 C5 C7 -134.8(8) no Si O7 C12 C4 -103.5(8) no O1 C1 C2 O3 111.0(8) no O1 C1 C2 C3 -3.2(9) yes O2 C1 C2 O3 -6.0(9) yes O2 C1 C2 C3 -120.2(7) no O3 C2 C3 C4 -84.6(7) no O3 C2 C3 C8 36.0(9) no O3 C2 C3 C11 159.9(7) no C1 C2 C3 C4 26.0(8) yes C1 C2 C3 C8 146.6(7) no C1 C2 C3 C11 -89.5(8) no C2 C3 C4 O1 -41.0(8) yes C2 C3 C4 C12 -164.0(8) no C8 C3 C4 O1 -161.5(7) no C8 C3 C4 C12 75.5(10) no C11 C3 C4 O1 74.6(8) no C11 C3 C4 C12 -48.4(10) no C2 C3 C8 C9 69.2(9) no C4 C3 C8 C9 -177.9(7) no C11 C3 C8 C9 -54.4(9) yes C2 C3 C11 S -71.8(8) no C4 C3 C11 S 178.9(6) no C8 C3 C11 S 53.4(9) yes O1 C4 C12 O7 73.7(9) no C3 C4 C12 O7 -166.4(7) no C3 C8 C9 O4 -111.2(10) no C3 C8 C9 C10 65.1(10) yes O4 C9 C10 S 111.0(9) no C8 C9 C10 S -65.4(9) yes loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 PubChem 101708174