Determination of the Absolute Configuration of Khellactone Esters from Peucedanum japonicum Roots.
Hong, Min Jee; Kim, Jinwoong; Journal of natural products 80 (2017) 1354–1360; doi:10.1021/acs.jnatprod.6b00947

data_1546206
_publ_section_title
;
 Determination of the Absolute Configuration of Khellactone Esters from
 Peucedanum japonicum Roots.
;
_journal_issue                   5
_journal_name_full               'Journal of natural products'
_journal_page_first              1354
_journal_page_last               1360
_journal_paper_doi               10.1021/acs.jnatprod.6b00947
_journal_volume                  80
_journal_year                    2017
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C23 H28 O7'
_chemical_formula_sum            'C23 H28 O7'
_chemical_formula_weight         416.45
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_symmetry_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2016-10-14
_audit_creation_method
;
Olex2 1.2-ac21
(compiled 2015.09.16 svn.r134, GUI svn.r4998)
;
_cell_angle_alpha                90
_cell_angle_beta                 109.128(2)
_cell_angle_gamma                90
_cell_formula_units_Z            12
_cell_length_a                   24.3633(4)
_cell_length_b                   9.12727(13)
_cell_length_c                   31.0898(6)
_cell_measurement_reflns_used    17994
_cell_measurement_temperature    99.9(2)
_cell_measurement_theta_max      76.1950
_cell_measurement_theta_min      3.8400
_cell_volume                     6531.8(2)
_computing_cell_refinement       'CrysAlisPro 1.171.38.43d (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.43d (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.43d (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100(80)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2262
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 0.990
_diffrn_measured_fraction_theta_max 0.974
_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   -116.00 -17.00   1.00    9.33    --  -41.49 -38.00 120.00   99
  2  \w    -66.00  33.00   1.00    9.33    --  -41.49  38.00 120.00   99
  3  \w     84.00 178.00   1.00   36.98    --  112.00  30.00  60.00   94
  4  \w     29.00 109.00   1.00   36.98    --  112.00 -94.00 150.00   80
  5  \w     39.00 138.00   1.00   36.98    --  112.00 -45.00  30.00   99
  6  \w     39.00 138.00   1.00   36.98    --  112.00 -45.00-120.00   99
  7  \w     29.00 109.00   1.00   36.98    --  112.00 -94.00-150.00   80
  8  \w   -118.00  -9.00   1.00    9.33    --  -41.49 -77.00   0.00  109
  9  \w      1.00  82.00   1.00    9.33    --   41.49 -99.00-120.00   81
 10  \w     84.00 178.00   1.00   36.98    --  112.00  30.00-150.00   94
 11  \w     59.00 175.00   1.00   36.98    --  112.00  15.00 -30.00  116
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0655968000
_diffrn_orient_matrix_UB_12      0.0333360000
_diffrn_orient_matrix_UB_13      -0.0173850000
_diffrn_orient_matrix_UB_21      -0.0022644000
_diffrn_orient_matrix_UB_22      -0.0374792000
_diffrn_orient_matrix_UB_23      -0.0488661000
_diffrn_orient_matrix_UB_31      -0.0130566000
_diffrn_orient_matrix_UB_32      -0.1611638000
_diffrn_orient_matrix_UB_33      0.0077862000
_diffrn_radiation_collimation    '0.2 mm sinlge-pinhole'
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0243
_diffrn_reflns_av_unetI/netI     0.0335
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.974
_diffrn_reflns_limit_h_max       29
_diffrn_reflns_limit_h_min       -30
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       39
_diffrn_reflns_limit_l_min       -39
_diffrn_reflns_number            39478
_diffrn_reflns_point_group_measured_fraction_full 0.951
_diffrn_reflns_point_group_measured_fraction_max 0.747
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         76.836
_diffrn_reflns_theta_min         3.637
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.774
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.62998
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.43d (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.270
_exptl_crystal_description       needle
_exptl_crystal_F_000             2664
_exptl_crystal_size_max          0.3
_exptl_crystal_size_mid          0.101
_exptl_crystal_size_min          0.031
_refine_diff_density_max         0.360
_refine_diff_density_min         -0.266
_refine_diff_density_rms         0.039
_refine_ls_abs_structure_details
;
 Flack x determined using 5322 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.08(6)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.031
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1668
_refine_ls_number_reflns         20639
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.031
_refine_ls_R_factor_all          0.0464
_refine_ls_R_factor_gt           0.0417
_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^)+(0.0600P)^2^+0.9138P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1069
_refine_ls_wR_factor_ref         0.1107
_reflns_Friedel_coverage         0.442
_reflns_Friedel_fraction_full    0.899
_reflns_Friedel_fraction_max     0.490
_reflns_number_gt                18836
_reflns_number_total             20639
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            np6b00947_si_001.cif
_cod_data_source_block           exp_376
_cod_database_code               1546206
_chemical_oxdiff_formula         'C23 H28 O7'
_reflns_odcompleteness_completeness 99.91
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     69.95
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Others
 Sof(C4AA)=Sof(H4AA)=Sof(H4AB)=Sof(H4AC)=1-FVAR(1)
 Sof(C1P)=Sof(H1PA)=Sof(H1PB)=Sof(H1PC)=FVAR(1)
3.a Ternary CH refined with riding coordinates:
 C1AA(H1AA), C2"E(H2"E), C3'E(H3'E), C4'E(H4'F), C2"D(H2"D), C3'D(H3'G),
 C4'D(H4'H), C18(H18), C2"(H2"), C2'"(H2'"), C3'(H3'), C4'(H4'), C1M(H1M),
 C2"A(H2"A), C3'A(H3'C), C4'A(H4'D), C2"B(H2"B), C3'B(H3'F), C4'B(H4'G),
 C5AA(H5AA), C2"C(H2"C), C2BA(H2BA), C3'C(H3'D), C4'C(H4'E)
3.b Secondary CH2 refined with riding coordinates:
 C2AA(H2AA,H2AB), C1C(H1CA,H1CB), C3'"(H3'a,H3'b), C1L(H1LA,H1LB), C6AA(H6AA,
 H6AB), C0BA(H0BA,H0BB)
3.c Aromatic/amide H refined with riding coordinates:
 C3E(H3E), C4E(H4E), C5E(H5E), C6E(H6E), C3D(H3D), C4D(H4D), C5D(H5D),
 C6D(H6D), C3(H3), C4(H4), C5(H5), C6(H6), C3A(H3A), C4A(H4A), C5A(H5A),
 C6A(H6A), C3B(H3B), C4B(H4B), C5B(H5B), C6B(H6B), C3C(H3C), C4C(H4C), C5C(H5C),
  C6C(H6C)
3.d Idealised Me refined as rotating group:
 C1P(H1PA,H1PB,H1PC), C3"E(H3"J,H3"K,H3"L), C3AA(H3AA,H3AB,H3AC), C4"E(H4"D,
 H4"E,H4"F), C4AA(H4AA,H4AB,H4AC), C5'E(H6'D,H6'E,H6'F), C6'E(H5'G,H5'H,H5'I),
 C1A(H1AB,H1AC,H1AD), C1B(H1BA,H1BB,H1BC), C3"D(H3"M,H3"N,H3"O), C4"D(H4"M,H4"N,
 H4"O), C5'D(H6'P,H6'Q,H6'R), C6'D(H5'S,H5'T,H5'U), C3"(H3"a,H3"b,H3"c),
 C4"(H4"a,H4"b,H4"c), C4'"(H4'a,H4'b,H4'c), C5'(H5'a,H5'b,H5'c), C5'"(H5'd,H5'e,
 H5'f), C6'(H6'a,H6'b,H6'c), C1N(H1NA,H1NB,H1NC), C1O(H1OA,H1OB,H1OC),
 C3"A(H3"D,H3"E,H3"F), C4"A(H4"P,H4"Q,H4"R), C5'A(H6'G,H6'H,H6'I), C6'A(H5'J,
 H5'K,H5'L), C3"B(H3"P,H3"Q,H3"R), C4"B(H4"G,H4"H,H4"I), C5'B(H5'P,H5'Q,H5'R),
 C6'B(H6'M,H6'N,H6'O), C7AA(H7AA,H7AB,H7AC), C8AA(H8AA,H8AB,H8AC), C1BA(H1BD,
 H1BE,H1BF), C3"C(H3"G,H3"H,H3"I), C3BA(H3BA,H3BB,H3BC), C4"C(H4"J,H4"K,H4"L),
 C6'C(H5'M,H5'N,H5'O), C5'C(H6'J,H6'K,H6'L)
;
_shelx_res_checksum              21944
_shelx_hkl_checksum              29464
_shelx_shelxl_version_number     2014/7
_olex2_date_sample_data_collection 2016-06-24
_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 1.508
_oxdiff_exptl_absorpt_empirical_full_min 0.643