Bio-inspired total synthesis of daphnepapytone A
Pereira, Joan; Casaretto, Nicolas; Frison, Gilles; Nay, Bastien; Chemical Science 16 (2025) 11375–11380; doi:10.1039/D5SC02953H

data_1574664
_publ_section_title
;
 Bio-inspired total synthesis of daphnepapytone A
;
_journal_issue                   25
_journal_name_full               'Chemical Science'
_journal_page_first              11375
_journal_page_last               11380
_journal_paper_doi               10.1039/D5SC02953H
_journal_volume                  16
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety         '0.5(C21 H34 O2 Si), 0.5(C21 H33 O2 Si)'
_chemical_formula_sum            'C21 H34 O2 Si'
_chemical_formula_weight         346.57
_space_group_crystal_system      triclinic
_space_group_IT_number           1
_space_group_name_Hall           'P 1'
_space_group_name_H-M_alt        'P 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-01-23
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-01-24 deposited with the CCDC.	2025-05-19 downloaded from the CCDC.
;
_cell_angle_alpha                96.641(6)
_cell_angle_beta                 101.339(6)
_cell_angle_gamma                99.843(7)
_cell_formula_units_Z            2
_cell_length_a                   7.4300(6)
_cell_length_b                   10.0076(8)
_cell_length_c                   14.9814(12)
_cell_measurement_reflns_used    7949
_cell_measurement_temperature    150
_cell_measurement_theta_max      24.74
_cell_measurement_theta_min      2.33
_cell_volume                     1063.22(15)
_computing_cell_refinement
;
X-Area Recipe 2.0.2 (STOE, 2024)
;
_computing_data_collection
;
X-Area Pilatus3_SV 1.31.194.0 (STOE, 2023)
;
_computing_data_reduction
;
X-Area Integrate 2.5.18.0 (STOE, 2024)
X-Area LANA 2.8.4 (STOE, 2024)
;
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material
;
STOE & Cie GmbH, X-Area, software package for collecting single-crystal or
multi-domain crystal data on STOE area-detector diffractometers, for image 
processing, for the correction and scaling of reflection intensities and 
for outlier rejection, version 2.4, Darmstadt 2024
;
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      150
_diffrn_detector                 'EIGER2 1M CDTE'
_diffrn_detector_area_resol_mean 13.33
_diffrn_measured_fraction_theta_full 0.991
_diffrn_measured_fraction_theta_max 0.991
_diffrn_measurement_details
;
 599 frames, detector distance = 60 mm
;
_diffrn_measurement_device       'Eulerian 4-circle diffractometer'
_diffrn_measurement_device_type  'STOE STADIVARI'
_diffrn_measurement_method       'rotation method, \w scans'
_diffrn_radiation_collimation    '1.2 0.6 mm diameter'
_diffrn_radiation_monochromator  'Graded multilayer mirror'
_diffrn_radiation_polarisn_norm  270
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0649
_diffrn_reflns_av_unetI/netI     0.0786
_diffrn_reflns_Laue_measured_fraction_full 0.991
_diffrn_reflns_Laue_measured_fraction_max 0.991
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       15
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            8759
_diffrn_reflns_point_group_measured_fraction_full 0.712
_diffrn_reflns_point_group_measured_fraction_max 0.712
_diffrn_reflns_theta_full        25.024
_diffrn_reflns_theta_max         25.024
_diffrn_reflns_theta_min         2.331
_diffrn_source                   Axo_Mo
_diffrn_source_current           1.00
_diffrn_source_power             0.050
_diffrn_source_voltage           50
_exptl_absorpt_coefficient_mu    0.120
_exptl_absorpt_correction_T_max  1.0000
_exptl_absorpt_correction_T_min  1.0000
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
STOE LANA, absorption correction by scaling of reflection intensities.
J. Koziskova, F. Hahn, J. Richter, J. Kozisek, "Comparison of different
absorption corrections on the model structure of tetrakis(\m~2~-acetato)-
diaqua-di-copper(II)", Acta Chimica Slovaca, vol. 9, no. 2, 2016, pp. 136 - 140.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.083
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             380
_refine_diff_density_max         0.287
_refine_diff_density_min         -0.255
_refine_diff_density_rms         0.058
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   0.1(2)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.961
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     518
_refine_ls_number_reflns         5325
_refine_ls_number_restraints     228
_refine_ls_restrained_S_all      0.981
_refine_ls_R_factor_all          0.0960
_refine_ls_R_factor_gt           0.0713
_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^)+(0.1273P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1761
_refine_ls_wR_factor_ref         0.1893
_reflns_Friedel_coverage         0.436
_reflns_Friedel_fraction_full    0.432
_reflns_Friedel_fraction_max     0.432
_reflns_number_gt                3638
_reflns_number_total             5325
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc02953h3.cif
_cod_data_source_block           jp359-1f1
_cod_depositor_comments
'Adding full bibliography for 1574658--1574665.cif.'
_cod_database_code               1574664
_shelx_shelxl_version_number     2018/3
_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. Restrained distances
 Si00-C01B = Si00-C019
 1.88 with sigma of 0.02
 Si00-C01A
 1.87 with sigma of 0.02
 C01A-C017 = C3-C01A = C01A-C018
 1.53 with sigma of 0.02
 Si-C01C = Si-C2
 1.88 with sigma of 0.02
 Si-C4
 1.87 with sigma of 0.02
 C4-C0 = C4-C1 = C3A-C4
 1.53 with sigma of 0.02
 Si00-O004 = Si-O004
 1.66 with sigma of 0.02
 Si00-O004 \\sim Si-O004
 with sigma of 0.02
 Si00-C019 \\sim Si-C2
 with sigma of 0.02
 Si00-C01A \\sim Si-C4
 with sigma of 0.02
 Si00-C01B \\sim Si-C01C
 with sigma of 0.02
 C017-C01A \\sim C0-C4
 with sigma of 0.02
 C018-C01A \\sim C1-C4
 with sigma of 0.02
 C01A-C3 \\sim C4-C3A
 with sigma of 0.02
 Si00-C017 \\sim Si-C0
 with sigma of 0.04
 Si00-C018 \\sim Si-C1
 with sigma of 0.04
 Si00-C3 \\sim Si-C3A
 with sigma of 0.04
 O004-C019 \\sim O004-C2
 with sigma of 0.04
 O004-C01A \\sim O004-C4
 with sigma of 0.04
 O004-C01B \\sim O004-C01C
 with sigma of 0.04
 C017-C018 \\sim C0-C1
 with sigma of 0.04
 C017-C3 \\sim C0-C3A
 with sigma of 0.04
 C018-C3 \\sim C1-C3A
 with sigma of 0.04
 C019-C01A \\sim C2-C4
 with sigma of 0.04
 C019-C01B \\sim C2-C01C
 with sigma of 0.04
 C01A-C01B \\sim C4-C01C
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
Si00 \\sim C017 \\sim C018 \\sim C019 \\sim C01A \\sim C01B \\sim C3: within 2A
with sigma of 0.004 and sigma for terminal atoms of 0.008 within 2A
Si00 \\sim C017 \\sim C018 \\sim C019 \\sim C01A \\sim C01B \\sim C3 \\sim Si
\\sim C0 \\sim C1 \\sim C2 \\sim C4 \\sim C01C \\sim C3A: within 2A with sigma
of 0.004 and sigma for terminal atoms of 0.008 within 2A
C5 \\sim C6 \\sim C7 \\sim C00R: within 2A with sigma of 0.004 and sigma for
terminal atoms of 0.008 within 2A
4. Others
 Sof(Si)=Sof(C0)=Sof(H0A)=Sof(H0B)=Sof(H0C)=Sof(C1)=Sof(H1A)=Sof(H1B)=Sof(H1C)=
 Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(H2C)=Sof(C4)=Sof(C01C)=Sof(H01M)=Sof(H01N)=
 Sof(H01O)=Sof(C3A)=Sof(H3AA)=Sof(H3AB)=Sof(H3AC)=1-FVAR(1)
 Sof(Si00)=Sof(C017)=Sof(H01A)=Sof(H01B)=Sof(H01C)=Sof(C018)=Sof(H01D)=
 Sof(H01E)=Sof(H01F)=Sof(C019)=Sof(H01G)=Sof(H01H)=Sof(H01I)=Sof(C01A)=
 Sof(C01B)=Sof(H01J)=Sof(H01K)=Sof(H01L)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(H3C)=
 FVAR(1)
5.a Ternary CH refined with riding coordinates:
 C009(H009), C00C(H00N), C00H(H00H), C00R(H00R)
5.b Secondary CH2 refined with riding coordinates:
 C00D(H00O,H00P), C00F(H00Q,H00S), C00G(H00A,H00B), C00Q(H00Z,H), C00S(H00C,
 H00D), C00Z(H00L,H00M)
5.c X=CH2 refined with riding coordinates:
 C011(H01P,H01Q), C7(H7A,H7B)
5.d Idealised Me refined as rotating group:
 C00M(H00T,H00U,H00V), C00P(H00W,H00X,H00Y), C00T(H00,HA,HB), C00U(H1,HC,HD),
 C00V(H00E,H00F,H00G), C00W(H00I,H00J,H00K), C00X(H2,HE,HF), C012(H01R,H01S,
 H01T), C013(H01U,H01V,H01W), C015(H01X,H01Y,HG), C017(H01A,H01B,H01C),
 C018(H01D,H01E,H01F), C019(H01G,H01H,H01I), C01B(H01J,H01K,H01L), C3(H3A,H3B,
 H3C), C0(H0A,H0B,H0C), C1(H1A,H1B,H1C), C2(H2A,H2B,H2C), C01C(H01M,H01N,H01O),
 C3A(H3AA,H3AB,H3AC), C6(H6A,H6B,H6C)
;
_shelx_res_checksum              8626
_olex2_submission_special_instructions 'No special instructions were received'
_stoe_detector_distance          '60.0 mm'
_stoe_detector_pixelsize_x       '0.075 mm'
_stoe_detector_pixelsize_y       '0.075 mm'
_stoe_detector_size_x            '8.0 cm'
_stoe_detector_size_y            '7.7 cm'
_stoe_evaluation_integration_a   10.1
_stoe_evaluation_integration_b   0.1
_stoe_evaluation_integration_ems 0.011
_stoe_evaluation_lana_bis_l_even_max -
_stoe_evaluation_lana_bis_l_odd_max -
_stoe_evaluation_lana_bos_l_even_max 4
_stoe_evaluation_lana_bos_l_odd_max 1
_stoe_evaluation_lana_completeness 59.5
_stoe_evaluation_lana_dxs_max_order 3
_stoe_evaluation_lana_dys_max_order 3
_stoe_evaluation_lana_fs_max_order 3
_stoe_evaluation_lana_max_2theta_available 58.5
_stoe_evaluation_lana_max_2theta_desired 58.5
_stoe_evaluation_lana_mean_redundancy 1.6
_stoe_evaluation_lana_number_refls_after_or 10828
_stoe_evaluation_lana_number_refls_outliers 365
_stoe_evaluation_lana_number_refls_total 11193
_stoe_evaluation_lana_number_refls_unique 6892
_stoe_evaluation_lana_number_refls_written 10828
_stoe_evaluation_lana_or_c1      0.050
_stoe_evaluation_lana_or_c2      0
_stoe_evaluation_lana_or_c3      0
_stoe_evaluation_lana_or_c4      1.0
_stoe_evaluation_lana_point_group 1
_stoe_evaluation_lana_table
;
2Theta           6.7   12.9   19.1   25.3   31.5   37.7   43.9   50.1   56.3
<Resolution>    5.24   3.11   2.16   1.60   1.30   1.10   0.95   0.84   0.77
N(total)         169    506    658   1017   1516   1962   2211   2328    826
<Redundancy>     2.5    2.2    1.8    1.7    1.7    1.7    1.5    1.4    1.2
Complet. [%%]    98.3   94.4   76.1   75.5   74.6   71.5   68.2   62.0   25.7
<I/sigma>      191.0   92.6   50.5   23.2   14.0    6.1    2.2    0.9    0.5
R(int)         0.055  0.041  0.070  0.080  0.081  0.108  0.194  0.318  0.432
;
_stoe_measurement_identifier     JP359-1F1
_stoe_measurement_max_exposure_per_frame '90.0 s'
_stoe_measurement_mean_exposure_per_frame '90.0 s'
_stoe_measurement_min_exposure_per_frame '90.0 s'
_stoe_measurement_total_exposure_time '15.0 h'
_stoe_measurement_total_frame_number 599
_stoe_measurement_total_run_number 10
_stoe_measurement_tube_power     '50.0 W'