Synthesis of chiral hexynones for use as precursors to native photosynthetic hydroporphyrins
Chau Nguyen, Khiem; Chung, Duy T. M.; Nalaoh, Phattananawee; Lindsey, Jonathan S.; New Journal of Chemistry 48 (2024) 2097–2117; doi:10.1039/D3NJ03900E

data_7062963
_publ_section_title
;
 Synthesis of chiral hexynones for use as precursors to native
 photosynthetic hydroporphyrins
;
_journal_issue                   5
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              2097
_journal_page_last               2117
_journal_paper_doi               10.1039/D3NJ03900E
_journal_volume                  48
_journal_year                    2024
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C19 H36 N2 O4 Si'
_chemical_formula_sum            'C19 H36 N2 O4 Si'
_chemical_formula_weight         384.59
_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'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-07-27
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_audit_update_record
;
2023-08-06 deposited with the CCDC.	2023-12-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90.692(3)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   9.5029(4)
_cell_length_b                   44.825(2)
_cell_length_c                   11.1259(6)
_cell_measurement_reflns_used    9769
_cell_measurement_temperature    100.00
_cell_measurement_theta_max      67.64
_cell_measurement_theta_min      3.94
_cell_volume                     4738.9(4)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      100.00
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device_type  'Bruker D8 Venture'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0563
_diffrn_reflns_av_unetI/netI     0.0472
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       11
_diffrn_reflns_limit_h_min       -10
_diffrn_reflns_limit_k_max       53
_diffrn_reflns_limit_k_min       -53
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            60586
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.996
_diffrn_reflns_theta_full        66.592
_diffrn_reflns_theta_max         66.592
_diffrn_reflns_theta_min         3.945
_diffrn_source_current           1.1
_diffrn_source_power             0.05500000000000001
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    1.057
_exptl_absorpt_correction_T_max  0.7531
_exptl_absorpt_correction_T_min  0.6677
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1076 before and 0.0776 after correction.
The Ratio of minimum to maximum transmission is 0.8866.
The \l/2 correction factor is Not present.
;
_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    1.078
_exptl_crystal_description       plate
_exptl_crystal_F_000             1680
_exptl_crystal_size_max          0.327
_exptl_crystal_size_mid          0.137
_exptl_crystal_size_min          0.044
_refine_diff_density_max         0.861
_refine_diff_density_min         -0.341
_refine_diff_density_rms         0.055
_refine_ls_abs_structure_details
;
 Flack x determined using 5558 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.022(15)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.025
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1044
_refine_ls_number_reflns         16704
_refine_ls_number_restraints     4
_refine_ls_restrained_S_all      1.027
_refine_ls_R_factor_all          0.0918
_refine_ls_R_factor_gt           0.0799
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1540P)^2^+1.5583P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2241
_refine_ls_wR_factor_ref         0.2413
_reflns_Friedel_coverage         0.966
_reflns_Friedel_fraction_full    0.993
_reflns_Friedel_fraction_max     0.993
_reflns_number_gt                13934
_reflns_number_total             16704
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3nj03900e2.cif
_cod_data_source_block           ncsu_pn36_a
_cod_depositor_comments
'Adding full bibliography for 7062961--7062963.cif.'
_cod_original_cell_volume        4739.0(4)
_cod_database_code               7062963
_shelx_shelxl_version_number     2019/1
_shelx_estimated_absorpt_t_max   0.955
_shelx_estimated_absorpt_t_min   0.724
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All C(H,H,H,H,H,H) groups
2. Restrained distances
 Si4-C9 \\sim Si4A-C9A
 with sigma of 0.02
 Si4-C69 \\sim Si4A-C69
 with sigma of 0.02
 C9-C69 \\sim C9A-C69
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
Uanis(C74) = Uanis(C9A)
4. Others
 Fixed Sof: Si4(0.5) C9(0.5) H9A(0.5) H9B(0.5) H9C(0.5) H62(0.5) H62A(0.5)
 H74A(0.5) H74B(0.5) H74C(0.5) H74D(0.5) H74E(0.5) H74F(0.5) H75A(0.5)
 H75B(0.5) H75C(0.5) H75D(0.5) H75E(0.5) H75F(0.5) O14(0.5) C10(0.5) H10A(0.5)
 H10B(0.5) H10C(0.5) C63(0.5) H63(0.5) C64A(0.5) H64A(0.5) H64B(0.5) H64C(0.5)
 C70(0.5) H70A(0.5) H70B(0.5) H70C(0.5) C80(0.5) H80A(0.5) H80B(0.5) H80C(0.5)
 O10(0.5) C59(0.5) H59A(0.5) H59B(0.5) H59C(0.5) C64(0.5) H64D(0.5) H64E(0.5)
 H64F(0.5) C77(0.5) H77(0.5) C78(0.5) H78A(0.5) H78B(0.5) H78C(0.5) C79(0.5)
 H79A(0.5) H79B(0.5) H79C(0.5) Si4A(0.5) C9A(0.5) H9AA(0.5) H9AB(0.5) H9AC(0.5)
5.a Ternary CH refined with riding coordinates:
 C13(H13), C14(H14), C15(H15), C16(H16), C30(H30), C31(H31), C33(H33),
 C34(H34), C47(H47), C48(H48), C51(H51), C52(H52), C62(H62), C62(H62A),
 C66(H66), C67(H67), C63(H63), C77(H77)
5.b Secondary CH2 refined with riding coordinates:
 C20(H20A,H20B), C23(H23A,H23B), C38(H38A,H38B), C41(H41A,H41B), C46(H46A,
 H46B), C55(H55A,H55B), C61(H61A,H61B), C72(H72A,H72B)
5.c Aromatic/amide H refined with riding coordinates:
 N7(H7), N8(H8), N5(H5), N6(H6)
5.d Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C), C17(H17A,H17B,H17C), C18(H18A,H18B,H18C), C19(H19A,H19B,
 H19C), C21(H21A,H21B,H21C), C22(H22A,H22B,H22C), C25(H25A,H25B,H25C), C26(H26A,
 H26B,H26C), C27(H27A,H27B,H27C), C4(H4A,H4B,H4C), C28(H28A,H28B,H28C),
 C35(H35A,H35B,H35C), C36(H36A,H36B,H36C), C37(H37A,H37B,H37C), C39(H39A,H39B,
 H39C), C40(H40A,H40B,H40C), C43(H43A,H43B,H43C), C44(H44A,H44B,H44C), C5(H5A,
 H5B,H5C), C7(H7A,H7B,H7C), C45(H45A,H45B,H45C), C49(H49A,H49B,H49C), C54(H54A,
 H54B,H54C), C56(H56A,H56B,H56C), C57(H57A,H57B,H57C), C58(H58A,H58B,H58C),
 C76(H76A,H76B,H76C), C9(H9A,H9B,H9C), C71(H71A,H71B,H71C), C73(H73A,H73B,H73C),
  C74(H74A,H74B,H74C), C74(H74D,H74E,H74F), C75(H75A,H75B,H75C), C75(H75D,H75E,
 H75F), C10(H10A,H10B,H10C), C64A(H64A,H64B,H64C), C70(H70A,H70B,H70C),
 C80(H80A,H80B,H80C), C59(H59A,H59B,H59C), C64(H64D,H64E,H64F), C78(H78A,H78B,
 H78C), C79(H79A,H79B,H79C), C9A(H9AA,H9AB,H9AC)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              5778
_shelx_hkl_checksum              81650
_shelx_fab_checksum              71882
_olex2_submission_special_instructions 'No special instructions were received'