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#$Date: 2024-12-07 19:12:45 +0200 (Sat, 07 Dec 2024) $
#$Revision: 296788 $
#$URL: file:///home/coder/svn-repositories/cod/cif/2/02/32/2023287.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_2023287
loop_
_publ_author_name
'Peixoto de Abreu Lima, Alejandro'
'Pandolfi, Enrique'
'Schapiro, Valeria'
'Suescun, Leopoldo'
_publ_section_title
;
 Synthesis, crystal structure and absolute configuration of
 (3aS,4R,5S,7aR)-7-(but-3-en-1-yn-1-yl)-2,2-dimethyl-3a,4,5,7a-tetrahydro-2H-1,3-benzodioxole-4,5-diol
;
_journal_coeditor_code           EE2008
_journal_issue                   11
_journal_name_full
'Acta Crystallographica Section E Crystallographic Communications'
_journal_page_first              1165
_journal_page_last               1169
_journal_paper_doi               10.1107/S2056989024009733
_journal_volume                  80
_journal_year                    2024
_chemical_absolute_configuration syn
_chemical_formula_iupac          'C13 H16 O4'
_chemical_formula_moiety         'C13 H16 O4'
_chemical_formula_sum            'C13 H16 O4'
_chemical_formula_weight         236.26
_chemical_name_common
(1S,2R,3S,4R)-5-(But-3-en-1-ynyl)-1,2-dihydroxy-3,4-isopropylidenedioxocycle-5-hexene
_chemical_name_systematic
(3aS,4R,5S,7aR)-7-(But-3-en-1-yn-1-yl)-2,2-dimethyl-3a,4,5,7a-tetrahydro-2H-1,3-benzodioxole-4,5-diol
_space_group_crystal_system      monoclinic
_space_group_IT_number           5
_space_group_name_Hall           'C 2y'
_space_group_name_H-M_alt        'C 1 2 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_method           SHELXL-2019/3
_cell_angle_alpha                90
_cell_angle_beta                 109.652(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   17.4126(13)
_cell_length_b                   5.0996(4)
_cell_length_c                   14.9856(11)
_cell_measurement_reflns_used    7392
_cell_measurement_temperature    296(2)
_cell_measurement_theta_max      77.75
_cell_measurement_theta_min      5.225
_cell_volume                     1253.17(16)
_computing_cell_refinement
;
SAINT V8.38A (Bruker, 2018)
;
_computing_data_collection
;
APEX3 (Bruker, 2018)
;
_computing_data_reduction
;
SAINT V8.38A (Bruker, 2018)
;
_computing_molecular_graphics
;
ShelXle (Hübschle et al., 2011)
;
_computing_publication_material
;
ShelXle (Hübschle et al., 2011)
;
_computing_structure_refinement
;
SHELXL2019/2 (Sheldrick, 2015)
;
_computing_structure_solution
;
olex2.solve 1.5 (Bourhis et al.,  2015, Dolomanov et
al.,  2009)
;
_diffrn_ambient_temperature      296(2)
_diffrn_detector_area_resol_mean 10.4167
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.961
_diffrn_measurement_device_type  'Bruker D8 Venture/Photon 100 CMOS'
_diffrn_measurement_method       '\j and ω scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0489
_diffrn_reflns_av_unetI/netI     0.0590
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       6
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -18
_diffrn_reflns_number            10420
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         81.635
_diffrn_reflns_theta_min         5.249
_diffrn_source                   'Cu Incoatec microsource'
_exptl_absorpt_coefficient_mu    0.765
_exptl_absorpt_correction_T_max  0.7543
_exptl_absorpt_correction_T_min  0.6456
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
(SADABS; Krause et al.,  2015)
;
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.252
_exptl_crystal_description       plate
_exptl_crystal_F_000             504
_exptl_crystal_size_max          0.379
_exptl_crystal_size_mid          0.256
_exptl_crystal_size_min          0.120
_refine_diff_density_max         0.412
_refine_diff_density_min         -0.206
_refine_ls_abs_structure_details
;
Flack x determined using 752 quotients
[(I⁺)-(I⁻)]/[(I⁺)+(I⁻)]
(Parsons et al.,  2013)
;
_refine_ls_abs_structure_Flack   0.1(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.128
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     157
_refine_ls_number_reflns         2628
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.130
_refine_ls_R_factor_all          0.0908
_refine_ls_R_factor_gt           0.0804
_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/[σ²(Fo²)+(0.1316P)²+0.6357P] where P=(Fo²+2Fc²)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2344
_refine_ls_wR_factor_ref         0.2483
_reflns_number_gt                2138
_reflns_number_total             2628
_reflns_threshold_expression     'I > 2σ(I)'
_cod_data_source_file            ee2008.cif
_cod_data_source_block           I
_cod_depositor_comments          'Adding full bibliography for 2023287.cif.'
_cod_original_sg_symbol_H-M      'C 2'
_cod_database_code               2023287
_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_min   0.760
_shelx_estimated_absorpt_t_max   0.914
loop_
_space_group_symop_operation_xyz
'x, y, z'
'-x, y, -z'
'x+1/2, y+1/2, z'
'-x+1/2, y+1/2, -z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
C C2 0.3746(3) 0.1116(12) 0.4110(3) 0.0683(11) Uani d 1 . .
H H2 0.398970 0.279483 0.437829 0.082 Uiso calc 1 . .
C C1 0.2844(3) 0.1188(12) 0.3889(4) 0.0709(12) Uani d 1 . .
H H1A 0.261212 -0.053188 0.365494 0.085 Uiso calc 1 . .
O O1 0.2645(3) 0.1853(10) 0.4702(3) 0.0957(14) Uani d 1 . .
H H1 0.252857 0.051859 0.493396 0.144 Uiso calc 1 . .
O O3 0.47692(19) 0.0935(9) 0.3375(3) 0.0779(11) Uani d 1 . .
O O4 0.4120(2) 0.4298(8) 0.2405(3) 0.0750(10) Uani d 1 . .
C C3 0.3927(3) 0.0527(10) 0.3215(3) 0.0635(11) Uani d 1 . .
H H3 0.377713 -0.128755 0.301629 0.076 Uiso calc 1 . .
C C4 0.3504(3) 0.2420(11) 0.2399(3) 0.0661(11) Uani d 1 . .
H H4 0.333731 0.145670 0.179805 0.079 Uiso calc 1 . .
C C5 0.2776(3) 0.3908(12) 0.2485(4) 0.0714(12) Uani d 1 . .
O O2 0.4080(3) -0.0979(11) 0.4766(3) 0.0939(13) Uani d 1 . .
H H2A 0.433176 -0.036444 0.528898 0.141 Uiso calc 1 . .
C C6 0.2469(3) 0.3234(12) 0.3150(5) 0.0791(15) Uani d 1 . .
H H6 0.199730 0.407119 0.315916 0.095 Uiso calc 1 . .
C C7 0.2395(3) 0.5872(13) 0.1767(4) 0.0790(14) Uani d 1 . .
C C8 0.2085(4) 0.7380(16) 0.1167(5) 0.0968(19) Uani d 1 . .
C C9 0.1732(7) 0.918(2) 0.0403(7) 0.139(4) Uani d 1 . .
H H9 0.190917 0.900463 -0.011464 0.167 Uiso calc 1 . .
C C10 0.1213(9) 1.096(3) 0.0339(11) 0.197(7) Uani d 1 . .
H H10A 0.101128 1.123418 0.083313 0.295 Uiso calc 1 . .
H H10B 0.103243 1.200024 -0.020116 0.295 Uiso calc 1 . .
C C11 0.4859(3) 0.2806(12) 0.2714(4) 0.0750(14) Uani d 1 . .
C C12 0.5552(4) 0.4617(17) 0.3208(8) 0.119(3) Uani d 1 . .
H H12A 0.562490 0.585508 0.276005 0.179 Uiso calc 1 . .
H H12B 0.604292 0.361554 0.347503 0.179 Uiso calc 1 . .
H H12C 0.543123 0.553832 0.370311 0.179 Uiso calc 1 . .
C C13 0.5005(5) 0.131(2) 0.1907(5) 0.113(3) Uani d 1 . .
H H13A 0.459372 -0.001682 0.167864 0.170 Uiso calc 1 . .
H H13B 0.553287 0.049946 0.213143 0.170 Uiso calc 1 . .
H H13C 0.497907 0.250061 0.140183 0.170 Uiso calc 1 . .
loop_
_atom_type_symbol
_atom_type_description
_atom_type_scat_dispersion_real
_atom_type_scat_dispersion_imag
_atom_type_scat_source
C C 0.0181 0.0091 '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'
O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
_geom_angle
_geom_angle_publ_flag
O2 C2 C1 . . 108.9(4) ?
O2 C2 C3 . . 107.6(5) ?
C1 C2 C3 . . 109.1(4) ?
O2 C2 H2 . . 110.4 ?
C1 C2 H2 . . 110.4 ?
C3 C2 H2 . . 110.4 ?
O1 C1 C2 . . 111.0(4) ?
O1 C1 C6 . . 107.3(5) ?
C2 C1 C6 . . 110.1(4) ?
O1 C1 H1A . . 109.4 ?
C2 C1 H1A . . 109.4 ?
C6 C1 H1A . . 109.4 ?
C1 O1 H1 . . 109.5 ?
C3 O3 C11 . . 109.3(4) ?
C11 O4 C4 . . 103.6(4) ?
O3 C3 C2 . . 109.5(4) ?
O3 C3 C4 . . 103.5(4) ?
C2 C3 C4 . . 113.2(4) ?
O3 C3 H3 . . 110.1 ?
C2 C3 H3 . . 110.1 ?
C4 C3 H3 . . 110.1 ?
O4 C4 C5 . . 108.0(4) ?
O4 C4 C3 . . 104.9(4) ?
C5 C4 C3 . . 115.8(4) ?
O4 C4 H4 . . 109.3 ?
C5 C4 H4 . . 109.3 ?
C3 C4 H4 . . 109.3 ?
C6 C5 C7 . . 122.4(5) ?
C6 C5 C4 . . 119.6(5) ?
C7 C5 C4 . . 117.7(5) ?
C2 O2 H2A . . 109.5 ?
C5 C6 C1 . . 123.4(5) ?
C5 C6 H6 . . 118.3 ?
C1 C6 H6 . . 118.3 ?
C8 C7 C5 . . 177.7(7) ?
C7 C8 C9 . . 176.9(10) ?
C10 C9 C8 . . 128.6(13) ?
C10 C9 H9 . . 115.7 ?
C8 C9 H9 . . 115.7 ?
C9 C10 H10A . . 120.0 ?
C9 C10 H10B . . 120.0 ?
H10A C10 H10B . . 120.0 ?
O3 C11 O4 . . 106.5(4) ?
O3 C11 C12 . . 109.1(5) ?
O4 C11 C12 . . 108.5(5) ?
O3 C11 C13 . . 107.7(6) ?
O4 C11 C13 . . 112.4(5) ?
C12 C11 C13 . . 112.3(6) ?
C11 C12 H12A . . 109.5 ?
C11 C12 H12B . . 109.5 ?
H12A C12 H12B . . 109.5 ?
C11 C12 H12C . . 109.5 ?
H12A C12 H12C . . 109.5 ?
H12B C12 H12C . . 109.5 ?
C11 C13 H13A . . 109.5 ?
C11 C13 H13B . . 109.5 ?
H13A C13 H13B . . 109.5 ?
C11 C13 H13C . . 109.5 ?
H13A C13 H13C . . 109.5 ?
H13B C13 H13C . . 109.5 ?
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_site_symmetry_2
_geom_bond_distance
_geom_bond_publ_flag
C2 O2 . 1.437(7) ?
C2 C1 . 1.492(6) ?
C2 C3 . 1.508(7) ?
C2 H2 . 0.9800 ?
C1 O1 . 1.414(7) ?
C1 C6 . 1.502(8) ?
C1 H1A . 0.9800 ?
O1 H1 . 0.8200 ?
O3 C3 . 1.420(5) ?
O3 C11 . 1.422(7) ?
O4 C11 . 1.431(6) ?
O4 C4 . 1.436(6) ?
C3 C4 . 1.538(7) ?
C3 H3 . 0.9800 ?
C4 C5 . 1.520(7) ?
C4 H4 . 0.9800 ?
C5 C6 . 1.324(8) ?
C5 C7 . 1.457(8) ?
O2 H2A . 0.8200 ?
C6 H6 . 0.9300 ?
C7 C8 . 1.168(9) ?
C8 C9 . 1.433(12) ?
C9 C10 . 1.264(16) ?
C9 H9 . 0.9300 ?
C10 H10A . 0.9300 ?
C10 H10B . 0.9300 ?
C11 C12 . 1.502(9) ?
C11 C13 . 1.521(10) ?
C12 H12A . 0.9600 ?
C12 H12B . 0.9600 ?
C12 H12C . 0.9600 ?
C13 H13A . 0.9600 ?
C13 H13B . 0.9600 ?
C13 H13C . 0.9600 ?
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_site_symmetry_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_publ_flag
O1 H1 O1 4_546 0.82 2.00 2.803(3) 166.8 yes
O2 H2A O3 2_656 0.82 2.19 2.995(6) 167.7 yes
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_site_symmetry_1
_geom_torsion_site_symmetry_2
_geom_torsion_site_symmetry_3
_geom_torsion_site_symmetry_4
_geom_torsion
_geom_torsion_publ_flag
O2 C2 C1 O1 . . . . 65.4(6) ?
C3 C2 C1 O1 . . . . -177.4(5) ?
O2 C2 C1 C6 . . . . -175.9(5) ?
C3 C2 C1 C6 . . . . -58.7(6) ?
C11 O3 C3 C2 . . . . -122.7(5) ?
C11 O3 C3 C4 . . . . -1.7(5) ?
O2 C2 C3 O3 . . . . -72.8(5) ?
C1 C2 C3 O3 . . . . 169.2(4) ?
O2 C2 C3 C4 . . . . 172.3(4) ?
C1 C2 C3 C4 . . . . 54.2(6) ?
C11 O4 C4 C5 . . . . 156.9(4) ?
C11 O4 C4 C3 . . . . 32.8(5) ?
O3 C3 C4 O4 . . . . -19.4(5) ?
C2 C3 C4 O4 . . . . 99.0(5) ?
O3 C3 C4 C5 . . . . -138.4(4) ?
C2 C3 C4 C5 . . . . -19.9(6) ?
O4 C4 C5 C6 . . . . -127.6(5) ?
C3 C4 C5 C6 . . . . -10.4(7) ?
O4 C4 C5 C7 . . . . 58.1(6) ?
C3 C4 C5 C7 . . . . 175.4(5) ?
C7 C5 C6 C1 . . . . 179.1(5) ?
C4 C5 C6 C1 . . . . 5.1(9) ?
O1 C1 C6 C5 . . . . 151.3(6) ?
C2 C1 C6 C5 . . . . 30.3(8) ?
C3 O3 C11 O4 . . . . 22.5(6) ?
C3 O3 C11 C12 . . . . 139.5(5) ?
C3 O3 C11 C13 . . . . -98.3(5) ?
C4 O4 C11 O3 . . . . -34.5(5) ?
C4 O4 C11 C12 . . . . -151.9(6) ?
C4 O4 C11 C13 . . . . 83.2(6) ?
