9-Step synthesis of (-)-larikaempferic acid methyl ester enabled by skeletal rearrangement.
Rivera, Mario E.; Li, Lei; Kolisetti, Aditya; Chi, Nina; Dai, Mingji; Chemical communications (Cambridge, England) 60 (2024) 7164–7167; doi:10.1039/d4cc01462f

data_7133034
_publ_section_title
;
 9-Step synthesis of (-)-larikaempferic acid methyl ester enabled by
 skeletal rearrangement.
;
_journal_issue                   56
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              7164
_journal_page_last               7167
_journal_paper_doi               10.1039/d4cc01462f
_journal_volume                  60
_journal_year                    2024
_chemical_absolute_configuration rmad
_chemical_formula_moiety         'C21 H34 O4'
_chemical_formula_sum            'C21 H34 O4'
_chemical_formula_weight         350.50
_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_Int_Tables_number      4
_atom_sites_solution_primary     dual
_audit_creation_date             2024-01-09
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2023.11.24 svn.r209d9fb2 for OlexSys, GUI svn.r6869)
;
_audit_update_record
;
2024-01-17 deposited with the CCDC.	2024-05-08 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 102.517(6)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   6.1621(4)
_cell_length_b                   11.6465(6)
_cell_length_c                   13.7206(9)
_cell_measurement_reflns_used    1822
_cell_measurement_temperature    105(8)
_cell_measurement_theta_max      72.0970
_cell_measurement_theta_min      3.2810
_cell_volume                     961.28(10)
_computing_cell_refinement       'CrysAlisPro 1.171.42.78a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.78a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.78a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5-alpha (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      105(8)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.9810
_diffrn_measured_fraction_theta_max 0.9332
_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     97.00 128.00   1.00    3.00    --   99.19 125.00-180.00   31
  2  \w    121.00 169.00   1.00    3.00    --   99.19  38.00 -90.00   48
  3  \w    126.00 152.00   1.00    3.00    --   99.19  60.00  -9.00   26
  4  \w     13.00  39.00   1.00    1.00    --   48.16 -60.00-148.00   26
  5  \w     34.00  63.00   1.00    3.00    --   99.19 -60.00-148.00   29
  6  \w     36.00  61.00   1.00    3.00    --   99.19 -57.00-120.00   25
  7  \w     40.00  65.00   1.00    3.00    --   99.19 -57.00 -30.00   25
  8  \w     35.00  60.00   1.00    3.00    --   99.19 -57.00   0.00   25
  9  \w     32.00 106.00   1.00    3.00    --   99.19 -99.00 150.00   74
 10  \w    -62.00   0.00   1.00    1.00    --  -48.16  60.00  -9.00   62
 11  \w     48.00  91.00   1.00    3.00    --   99.19 -99.00 -60.00   43
 12  \w    -28.00  20.00   1.00    1.00    --  -48.16  60.00  -9.00   48
 13  \w    -56.00 -14.00   1.00    3.00    --  -86.25  60.00  -9.00   42
 14  \w    -44.00 -17.00   1.00    3.00    --  -86.25  38.00  90.00   27
 15  \w    -44.00 -13.00   1.00    3.00    --  -86.25  38.00 150.00   31
 16  \w    -41.00 -13.00   1.00    3.00    --  -86.25  38.00 120.00   28
 17  \w    -43.00 -15.00   1.00    3.00    --  -86.25  38.00 -30.00   28
 18  \w    -43.00 -17.00   1.00    3.00    --  -86.25  38.00 -60.00   26
 19  \w    -43.00 -16.00   1.00    3.00    --  -86.25  38.00 -90.00   27
 20  \w    -44.00 -17.00   1.00    3.00    --  -86.25  38.00-180.00   27
 21  \w   -113.00 -37.00   1.00    1.00    --  -48.16 -60.00-148.00   76
 22  \w   -119.00 -38.00   1.00    1.00    --  -48.16 -60.00-148.00   81
 23  \w   -155.00 -73.00   1.00    3.00    --  -86.25 -60.00-148.00   82
 24  \w   -113.00 -86.00   1.00    1.00    --  -48.16-125.00   0.00   27
 25  \w   -102.00 -74.00   1.00    1.00    --  -48.16-125.00  60.00   28
 26  \w     62.00  88.00   1.00    3.00    --   48.16  77.00 -90.00   26
 27  \w     32.00  58.00   1.00    3.00    --   99.19 -57.00  30.00   26
 28  \w     38.00  64.00   1.00    3.00    --   99.19 -60.00-148.00   26
 29  \w   -118.00 -92.00   1.00    3.00    --  -48.16 -19.00  30.00   26
 30  \w    -67.00 -41.00   1.00    3.00    --  -48.16 -19.00  30.00   26
 31  \w    -29.00  12.00   1.00    3.00    --  -48.16  19.00-120.00   41
 32  \w     -7.00  20.00   1.00    3.00    --   48.16 -19.00-150.00   27
 33  \w    -26.00  -1.00   1.00    3.00    --   48.16 -19.00-120.00   25
 34  \w   -101.00 -56.00   1.00    3.00    --  -86.25  77.00 -60.00   45
 35  \w   -106.00 -77.00   1.00    3.00    --  -86.25 -38.00  60.00   29
 36  \w   -153.00-110.00   1.00    3.00    --  -86.25 -38.00  60.00   43
 37  \w   -147.00 -74.00   1.00    3.00    --  -86.25 -38.00 120.00   73
 38  \w   -121.00 -75.00   1.00    3.00    --  -86.25 -38.00  30.00   46
 39  \w    -41.00 -15.00   1.00    3.00    --  -86.25  77.00 -60.00   26
 40  \w   -148.00 -63.00   1.00    3.00    --  -86.25 -77.00 120.00   85
 41  \w   -122.00 -97.00   1.00    3.00    --  -86.25 -99.00-180.00   25
 42  \w    118.00 144.00   1.00    3.00    --   99.19  57.00 -30.00   26
 43  \w     86.00 113.00   1.00    3.00    --   99.19  57.00 -30.00   27
 44  \w     27.00  52.00   1.00    3.00    --   99.19 -57.00-180.00   25
 45  \w    107.00 145.00   1.00    3.00    --   99.19  38.00 150.00   38
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1702570000
_diffrn_orient_matrix_UB_12      -0.0177147000
_diffrn_orient_matrix_UB_13      0.0991718000
_diffrn_orient_matrix_UB_21      0.1519157000
_diffrn_orient_matrix_UB_22      0.0917054000
_diffrn_orient_matrix_UB_23      -0.0311811000
_diffrn_orient_matrix_UB_31      -0.1163417000
_diffrn_orient_matrix_UB_32      0.0936514000
_diffrn_orient_matrix_UB_33      0.0492555000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0552
_diffrn_reflns_av_unetI/netI     0.0494
_diffrn_reflns_Laue_measured_fraction_full 0.9810
_diffrn_reflns_Laue_measured_fraction_max 0.9332
_diffrn_reflns_limit_h_max       7
_diffrn_reflns_limit_h_min       -7
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       16
_diffrn_reflns_limit_l_min       -16
_diffrn_reflns_number            11114
_diffrn_reflns_point_group_measured_fraction_full 0.9585
_diffrn_reflns_point_group_measured_fraction_max 0.8954
_diffrn_reflns_theta_full        67.6840
_diffrn_reflns_theta_max         72.97
_diffrn_reflns_theta_min         5.03
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.650
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.649
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.78a (Rigaku Oxford Diffraction, 2022)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.211
_exptl_crystal_description       needle
_exptl_crystal_F_000             385.226
_exptl_crystal_recrystallization_method
'The material was recrystallised from --- by as supplied'
_exptl_crystal_size_max          0.28
_exptl_crystal_size_mid          0.08
_exptl_crystal_size_min          0.07
_refine_diff_density_max         0.3695
_refine_diff_density_min         -0.3879
_refine_diff_density_rms         0.0808
_refine_ls_abs_structure_details
'Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668.'
_refine_ls_abs_structure_Flack   -0.26(13)
_refine_ls_d_res_high            0.8063
_refine_ls_d_res_low             8.7888
_refine_ls_goodness_of_fit_ref   1.0552
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_constraints    19
_refine_ls_number_parameters     405
_refine_ls_number_reflns         3443
_refine_ls_number_restraints     867
_refine_ls_restrained_S_all      0.9309
_refine_ls_R_factor_all          0.0657
_refine_ls_R_factor_gt           0.0649
_refine_ls_shift/su_max          0.0007
_refine_ls_shift/su_mean         0.0001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0000P)^2^+2.1751P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1264
_refine_ls_wR_factor_ref         0.1268
_reflns_Friedel_coverage         0.854
_reflns_limit_h_max              7
_reflns_limit_h_min              -7
_reflns_limit_k_max              13
_reflns_limit_k_min              -13
_reflns_limit_l_max              16
_reflns_limit_l_min              -16
_reflns_number_gt                3410
_reflns_number_total             3443
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d4cc01462f2.cif
_cod_data_source_block           MER-2023-05_Cu
_cod_depositor_comments
;
Adding full bibliography for 7133034--7133036.cif.

2025-03-31
Z value and formula fixed to values more according to usual
chemical conventions.                 miguel
;
_cod_original_formula_sum            'C42 H68 O8'
_cod_original_formula_weight         701.003
_cod_original_formula_moiety         '2(C21 H34 O4)'
_cod_original_formula_units_Z            1
_cod_original_sg_symbol_Hall     ' P 2yb'
_cod_database_code               7133034
_chemical_oxdiff_formula         'C42  H68  O8  '
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.8(3)
 0.10(3) 0.2(3) -0.08(3)
2. Fixed Uiso
 At 1.5 times of:
  All C(H) groups, All C(H,H) groups
3. Restrained distances
 H1-O1
 0.955 with sigma of 0.02
 C19-H19C = C20-H20C = C21-H21A = C15-H15B
 1.01 with sigma of 0.01
4. Uiso/Uaniso restraints and constraints
Uiso(H5B) = Uiso(H5A) = Uiso(H6B) = Uiso(H6A)
Uiso(H7B) = Uiso(H7A)
5. Rigid body (RIGU) restrains
 C8, O1, C1, C2, C10, C3, C15, C7, C14, C9, C11, C4, C6, O2, C13, C12, C16,
 C21, C5, C18, O4, O3, C20, C19, C17
 with sigma for 1-2 distances of 0.0002 and sigma for 1-3 distances of 0.002
 C10, O1, C1, C2, C8, C3, C15, C7, C14, C9, C11, C4, C6, O2, C13, C12, C16,
 C21, C5, C18, O4, O3, C20, C19, C17
 with sigma for 1-2 distances of 0.0002 and sigma for 1-3 distances of 0.004
 O1, H1
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.004
 O1, H1, C2, C14, C3, H3, C1, C8, H8, C11, H11A, H11B, C15, H15A, H15C, C18,
 H18, C12, H12, C9, H9A, H9B, C10, H10A, H10B, C13, H13A, H13B, C20, H20A, H20B,
  H20C, C19, H19A, H19B, H19C, H15B, C7, C4, O2
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.004
 O3, C17, H17A, H17B, H17C
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.004
 C6, H6A, H6B, H5A, H5B, C7, H7A, H7B, C4, C2, C5
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.004
 C21, H21A, H21B, H21C, C4, C16, C3, C5
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.004
6. Others
 Fixed Uiso: H12(0.031303) H8(0.01831) H9A(0.021919) H9B(0.021919)
7.a Ternary CH refined with riding coordinates:
 C18(H18)
7.b Secondary CH2 refined with riding coordinates and stretchable bonds:
 C6(H6A,H6B), C5(H5A,H5B), C7(H7A,H7B), C13(H13A,H13B), C11(H11A,H11B),
 C10(H10A,H10B), C9(H9A,H9B)
7.c Idealised Me refined with riding coordinates and stretchable bonds:
 C15(H15A,H15B,H15C), C19(H19A,H19B,H19C), C20(H20A,H20B,H20C), C21(H21A,H21B,
 H21C)
7.d Idealised tetrahedral OH refined with riding coordinates and stretchable
bonds:
 O1(H1)
;
_olex2_refine_details
;
Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors.

The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
 - for a fragment of the crystal.
This fragment can be embedded in an electrostatic crystal field by employing cluster charges
or modelled using implicit solvation models, depending on the software used.
The following options were used:
   SOFTWARE:       ORCA
   PARTITIONING:   NoSpherA2
   INT ACCURACY:   Normal
   METHOD:         PBE
   BASIS SET:      def2-TZVP
   CHARGE:         0
   MULTIPLICITY:   1
   SOLVATION:      Methanol
   DATE:           2024-01-09_17-42-45
;
_olex2_diffrn_ambient_temperature_device 'Oxford Cryosystems'
_olex2_exptl_crystal_mounting_method 'The crystal was mounted on a loop'
_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 1.226
_oxdiff_exptl_absorpt_empirical_full_min 0.807