# Supplementary Material (ESI) for Organic & Biomolecular Chemistry # This journal is (c) The Royal Society of Chemistry 2008 data_global _journal_coden_Cambridge 182 loop_ _publ_author_name 'T Donohoe' 'Matthew D Cheeseman' 'Jessica A Kershaw' "Timothy J C O'Riordan" _publ_contact_author_name 'T Donohoe' _publ_contact_author_email TIMOTHY.DONOHOE@CHEM.OX.AC.UK _publ_section_title ; Synthesis of (+)-DGDP and (-)-7-Epialexine ; # Attachment 'Compound_4.cif' #============================================================================== data_Compound-4-(DGDP) _database_code_depnum_ccdc_archive 'CCDC 695945' #============================================================================== _audit_creation_date 08-07-15 _audit_creation_method CRYSTALS_ver_12.84 _oxford_structure_analysis_title 'TJD 050' _chemical_name_systematic (+)-2,5-dideoxy-2,5-imino-d-glucitol _chemical_melting_point 139-141 _cell_length_a 5.9247(2) _cell_length_b 7.2417(3) _cell_length_c 17.4475(9) _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 _cell_volume 748.58(6) _symmetry_cell_setting Orthorhombic _symmetry_space_group_name_H-M 'P 21 21 21 ' _symmetry_space_group_name_Hall 'P 2ac 2ab' loop_ _symmetry_equiv_pos_as_xyz x,y,z x+1/2,-y+1/2,-z -x,y+1/2,-z+1/2 -x+1/2,-y,z+1/2 loop_ _atom_type_symbol _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_Cromer_Mann_a1 _atom_type_scat_Cromer_Mann_b1 _atom_type_scat_Cromer_Mann_a2 _atom_type_scat_Cromer_Mann_b2 _atom_type_scat_Cromer_Mann_a3 _atom_type_scat_Cromer_Mann_b3 _atom_type_scat_Cromer_Mann_a4 _atom_type_scat_Cromer_Mann_b4 _atom_type_scat_Cromer_Mann_c _atom_type_scat_source C 0.0033 0.0016 2.3100 20.8439 1.0200 10.2075 1.5886 0.5687 0.8650 51.6512 0.2156 'International Tables Vol C 4.2.6.8 and 6.1.1.4' H 0.0000 0.0000 0.4930 10.5109 0.3229 26.1257 0.1402 3.1424 0.0408 57.7998 0.0030 'International Tables Vol C 4.2.6.8 and 6.1.1.4' O 0.0106 0.0060 3.0485 13.2771 2.2868 5.7011 1.5463 0.3239 0.8670 32.9089 0.2508 'International Tables Vol C 4.2.6.8 and 6.1.1.4' N 0.0061 0.0033 12.2126 0.0057 3.1322 9.8933 2.0125 28.9975 1.1663 0.5826 -11.5290 'International Tables Vol C 4.2.6.8 and 6.1.1.4' _cell_formula_units_Z 4 # Given Formula = C6 H13 N1 O4 # Dc = 1.45 Fooo = 352.00 Mu = 1.21 M = 163.17 # Found Formula = C6 H13 N1 O4 # Dc = 1.45 FOOO = 352.00 Mu = 1.21 M = 163.17 _chemical_formula_sum 'C6 H13 N1 O4' _chemical_formula_moiety 'C6 H13 N1 O4' _chemical_compound_source . _chemical_formula_weight 163.17 _cell_measurement_reflns_used 1013 _cell_measurement_theta_min 5 _cell_measurement_theta_max 27 _cell_measurement_temperature 150 _exptl_crystal_description plate _exptl_crystal_colour colourless _exptl_crystal_size_min 0.10 _exptl_crystal_size_mid 0.20 _exptl_crystal_size_max 0.60 _exptl_crystal_density_diffrn 1.448 _exptl_crystal_density_meas 'not measured' # Non-dispersive F(000): _exptl_crystal_F_000 352 _exptl_absorpt_coefficient_mu 0.121 # Sheldrick geometric approximatio 0.98 0.99 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details 'DENZO/SCALEPACK (Otwinowski & Minor, 1997)' _exptl_absorpt_correction_T_min 0.98 _exptl_absorpt_correction_T_max 0.99 # For a Kappa CCD, set Tmin to 1.0 and # Tmax to the ratio of max:min frame scales in scale_all.log _diffrn_measurement_device_type 'Nonius KappaCCD' _diffrn_radiation_monochromator graphite _diffrn_radiation_type 'Mo K\a' _diffrn_radiation_wavelength 0.71073 _diffrn_measurement_method \w # If a reference occurs more than once, delete the author # and date from subsequent references. _computing_data_collection 'COLLECT (Nonius, 1997-2001).' _computing_cell_refinement 'DENZO/SCALEPACK (Otwinowski & Minor, 1997)' _computing_data_reduction 'DENZO/SCALEPACK (Otwinowski & Minor, 1997)' _computing_structure_solution 'SIR92 (Altomare et al., 1994)' _computing_structure_refinement 'CRYSTALS (Betteridge et al., 2003)' _computing_publication_material 'CRYSTALS (Betteridge et al., 2003)' _computing_molecular_graphics 'CAMERON (Watkin et al., 1996)' _diffrn_standards_interval_time . _diffrn_standards_interval_count . _diffrn_standards_number 0 _diffrn_standards_decay_% . _diffrn_ambient_temperature 150 _diffrn_reflns_number 1703 _reflns_number_total 1018 _diffrn_reflns_av_R_equivalents 0.031 # Number of reflections with Friedels Law is 1018 # Number of reflections without Friedels Law is 0 # Theoretical number of reflections is about 855 _diffrn_reflns_theta_min 5.458 _diffrn_reflns_theta_max 27.448 _diffrn_measured_fraction_theta_max 0.989 _diffrn_reflns_theta_full 27.448 _diffrn_measured_fraction_theta_full 0.989 _diffrn_reflns_limit_h_min -7 _diffrn_reflns_limit_h_max 7 _diffrn_reflns_limit_k_min -9 _diffrn_reflns_limit_k_max 9 _diffrn_reflns_limit_l_min -22 _diffrn_reflns_limit_l_max 22 _reflns_limit_h_min 0 _reflns_limit_h_max 7 _reflns_limit_k_min 0 _reflns_limit_k_max 9 _reflns_limit_l_min 0 _reflns_limit_l_max 22 _oxford_diffrn_Wilson_B_factor 1.83 _oxford_diffrn_Wilson_scale 1.92 _atom_sites_solution_primary direct #heavy,direct,difmap,geom # _atom_sites_solution_secondary difmap _atom_sites_solution_hydrogens geom _refine_diff_density_min -0.37 _refine_diff_density_max 0.40 # The current dictionary definitions do not cover the # situation where the reflections used for refinement were # selected by a user-defined sigma threshold # The values actually used during refinement _oxford_reflns_threshold_expression_ref I>-3.0\s(I) _refine_ls_number_reflns 1018 _refine_ls_number_restraints 0 _refine_ls_number_parameters 100 _oxford_refine_ls_R_factor_ref 0.0548 _refine_ls_wR_factor_ref 0.0978 _refine_ls_goodness_of_fit_ref 0.9153 _refine_ls_shift/su_max 0.000295 # The values computed from all data _oxford_reflns_number_all 1018 _refine_ls_R_factor_all 0.0548 _refine_ls_wR_factor_all 0.0978 # The values computed with a 2 sigma cutoff - a la SHELX _reflns_threshold_expression I>2.0\s(I) _reflns_number_gt 796 _refine_ls_R_factor_gt 0.0382 _refine_ls_wR_factor_gt 0.0911 # choose from: rm (reference molecule of known chirality), # ad (anomolous dispersion - Flack), rmad (rm and ad), # syn (from synthesis), unk (unknown) or . (not applicable). _chemical_absolute_configuration unk _refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_hydrogen_treatment mixed # none, undef, noref, refall, # refxyz, refU, constr or mixed _refine_ls_weighting_scheme calc _refine_ls_weighting_details ; Method= Modified Sheldrick w=1/[\s^2^(F^2^) + ( 0.04P)^2^ + 0.06P], where P=(max(Fo^2^,0) + 2Fc^2^)/3 ; # Insert your own references if required - in alphabetical order _publ_section_references ; Altomare, A., Cascarano, G., Giacovazzo, G., Guagliardi, A., Burla, M.C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435. Betteridge, P.W., Carruthers, J.R., Cooper, R.I., Prout, K. & Watkin, D.J. (2003). J. Appl. Cryst. 36, 1487. Larson, A.C. (1970) Crystallographic Computing, Ed Ahmed, F.R., Munksgaard, Copenhagen, 291-294. Nonius (1997-2001). COLLECT. Nonius BV, Delft, The Netherlands. Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, edited by C. W. Carter Jr & R. M. Sweet, pp. 307--326. New York: Academic Press. Watkin, D.J., Prout, C.K. & Pearce, L.J. (1996). CAMERON, Chemical Crystallography Laboratory, Oxford, UK. ; # Uequiv = arithmetic mean of Ui i.e. Ueqiv = (U1+U2+U3)/3 # Replace last . with number of unfound hydrogen atomsattached to an atom. # ..._refinement_flags_... # . no refinement constraints S special position constraint on site # G rigid group refinement of site R riding atom # D distance or angle restraint on site T thermal displacement constraints # U Uiso or Uij restraint (rigid bond) P partial occupancy constraint 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_occupancy _atom_site_adp_type _atom_site_refinement_flags_posn _atom_site_refinement_flags_adp _atom_site_refinement_flags_occupancy _atom_site_disorder_assembly _atom_site_disorder_group _atom_site_attached_hydrogens C1 C 0.4815(3) 0.8964(3) 0.57327(11) 0.0181 1.0000 Uani . . . . . . C2 C 0.4736(3) 0.7494(3) 0.63553(10) 0.0167 1.0000 Uani . . . . . . C3 C 0.2217(3) 0.7114(3) 0.64524(10) 0.0150 1.0000 Uani . . . . . . N4 N 0.1279(3) 0.8993(2) 0.64106(9) 0.0160 1.0000 Uani . . . . . . C5 C 0.2543(3) 1.0008(3) 0.58061(11) 0.0152 1.0000 Uani . . . . . . C6 C 0.2728(4) 1.2004(3) 0.60435(11) 0.0225 1.0000 Uani . . . . . . O7 O 0.3633(2) 1.30799(19) 0.54230(7) 0.0234 1.0000 Uani . . . . . . C8 C 0.1645(3) 0.6168(3) 0.71920(11) 0.0181 1.0000 Uani . . . . . . O9 O -0.07373(18) 0.5817(2) 0.72149(7) 0.0235 1.0000 Uani . . . . . . O10 O 0.5977(2) 0.58735(17) 0.61636(7) 0.0211 1.0000 Uani . . . . . . O11 O 0.6789(2) 1.0052(2) 0.58346(8) 0.0268 1.0000 Uani . . . . . . H11 H 0.4882 0.8317 0.5216 0.0212 1.0000 Uiso R . . . . . H21 H 0.5331 0.7965 0.6845 0.0198 1.0000 Uiso R . . . . . H31 H 0.1713 0.6348 0.6024 0.0181 1.0000 Uiso R . . . . . H51 H 0.1713 0.9917 0.5322 0.0181 1.0000 Uiso R . . . . . H61 H 0.3781 1.2118 0.6478 0.0272 1.0000 Uiso R . . . . . H62 H 0.1223 1.2472 0.6191 0.0273 1.0000 Uiso R . . . . . H81 H 0.2086 0.6931 0.7636 0.0210 1.0000 Uiso R . . . . . H82 H 0.2442 0.5004 0.7213 0.0226 1.0000 Uiso R . . . . . H4 H -0.1060 0.5241 0.7616 0.0353 1.0000 Uiso R . . . . . H6 H 0.7020 0.5831 0.6476 0.0317 1.0000 Uiso R . . . . . H8 H 0.7015 1.0677 0.5445 0.0400 1.0000 Uiso R . . . . . H12 H -0.015(4) 0.899(3) 0.6286(11) 0.0247 1.0000 Uiso . . . . . . H1 H 0.4513 1.3849 0.5583 0.0356 1.0000 Uiso 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 C1 0.0148(9) 0.0216(10) 0.0180(9) 0.0022(9) 0.0022(8) 0.0007(10) C2 0.0177(9) 0.0165(10) 0.0160(9) 0.0002(8) -0.0010(8) 0.0020(9) C3 0.0153(9) 0.0144(9) 0.0153(9) -0.0010(9) -0.0004(7) 0.0017(8) N4 0.0119(8) 0.0159(8) 0.0201(8) 0.0018(8) 0.0005(6) 0.0018(8) C5 0.0133(9) 0.0190(9) 0.0135(9) 0.0002(10) 0.0011(8) 0.0006(8) C6 0.0250(10) 0.0206(10) 0.0220(10) 0.0016(9) 0.0039(9) -0.0026(10) O7 0.0250(7) 0.0200(7) 0.0251(7) 0.0048(6) 0.0017(6) -0.0044(7) C8 0.0141(9) 0.0185(10) 0.0215(10) 0.0004(9) -0.0011(7) 0.0009(9) O9 0.0155(7) 0.0320(8) 0.0230(7) 0.0116(7) 0.0000(5) -0.0038(6) O10 0.0181(7) 0.0206(7) 0.0245(7) -0.0032(6) -0.0026(5) 0.0053(7) O11 0.0137(7) 0.0322(8) 0.0346(9) 0.0167(8) -0.0013(6) -0.0038(8) _refine_ls_extinction_method None _oxford_refine_ls_scale 0.694(2) loop_ _geom_bond_atom_site_label_1 _geom_bond_site_symmetry_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_2 _geom_bond_distance _geom_bond_publ_flag C1 . C2 . 1.521(3) yes C1 . C5 . 1.549(2) yes C1 . O11 . 1.421(2) yes C1 . H11 . 1.017 no C2 . C3 . 1.527(3) yes C2 . O10 . 1.425(2) yes C2 . H21 . 0.986 no C3 . N4 . 1.472(2) yes C3 . C8 . 1.500(2) yes C3 . H31 . 0.978 no N4 . C5 . 1.488(2) yes N4 . H12 . 0.87(2) no C5 . C6 . 1.507(3) yes C5 . H51 . 0.980 no C6 . O7 . 1.438(2) yes C6 . H61 . 0.986 no C6 . H62 . 0.988 no O7 . H1 . 0.812 no C8 . O9 . 1.435(2) yes C8 . H81 . 0.987 no C8 . H82 . 0.967 no O9 . H4 . 0.837 no O10 . H6 . 0.825 no O11 . H8 . 0.827 no loop_ _geom_angle_atom_site_label_1 _geom_angle_site_symmetry_1 _geom_angle_atom_site_label_2 _geom_angle_site_symmetry_2 _geom_angle_atom_site_label_3 _geom_angle_site_symmetry_3 _geom_angle _geom_angle_publ_flag C2 . C1 . C5 . 104.82(15) yes C2 . C1 . O11 . 108.90(15) yes C5 . C1 . O11 . 115.70(14) yes C2 . C1 . H11 . 108.2 no C5 . C1 . H11 . 109.4 no O11 . C1 . H11 . 109.5 no C1 . C2 . C3 . 103.62(15) yes C1 . C2 . O10 . 113.12(14) yes C3 . C2 . O10 . 112.44(15) yes C1 . C2 . H21 . 111.5 no C3 . C2 . H21 . 108.4 no O10 . C2 . H21 . 107.7 no C2 . C3 . N4 . 101.36(15) yes C2 . C3 . C8 . 113.50(15) yes N4 . C3 . C8 . 112.31(15) yes C2 . C3 . H31 . 108.4 no N4 . C3 . H31 . 111.8 no C8 . C3 . H31 . 109.3 no C3 . N4 . C5 . 107.56(14) yes C3 . N4 . H12 . 111.9(14) no C5 . N4 . H12 . 108.3(13) no C1 . C5 . N4 . 104.76(14) yes C1 . C5 . C6 . 115.33(16) yes N4 . C5 . C6 . 108.38(15) yes C1 . C5 . H51 . 109.4 no N4 . C5 . H51 . 109.0 no C6 . C5 . H51 . 109.8 no C5 . C6 . O7 . 109.86(15) yes C5 . C6 . H61 . 109.7 no O7 . C6 . H61 . 107.3 no C5 . C6 . H62 . 109.6 no O7 . C6 . H62 . 110.3 no H61 . C6 . H62 . 110.0 no C6 . O7 . H1 . 110.6 no C3 . C8 . O9 . 109.10(14) yes C3 . C8 . H81 . 111.1 no O9 . C8 . H81 . 109.7 no C3 . C8 . H82 . 108.6 no O9 . C8 . H82 . 109.0 no H81 . C8 . H82 . 109.3 no C8 . O9 . H4 . 109.6 no C2 . O10 . H6 . 105.2 no C1 . O11 . H8 . 109.5 no loop_ _geom_hbond_atom_site_label_D _geom_hbond_site_symmetry_D _geom_hbond_atom_site_label_H _geom_hbond_site_symmetry_H _geom_hbond_atom_site_label_A _geom_hbond_site_symmetry_A _geom_hbond_angle_DHA _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_publ_flag O9 . H4 . N4 3_546 170 0.84 1.93 2.757(2) yes O10 . H6 . O9 1_655 177 0.82 1.85 2.675(2) yes O11 . H8 . O7 2_576 161 0.83 2.01 2.800(2) yes N4 . H12 . O11 1_455 157 0.87(2) 2.12(2) 2.945(2) yes O7 . H1 . O10 1_565 164 0.81 1.98 2.773(2) yes