Base-promoted decarboxylative condensation of cinnamonitriles and phenylacetic acids with sulfur: direct access to azatrithiapentalenes.
Chu, Ngoc Lan; Tran, Quang Huy; Tran, Quynh Trang; Bui, Thai Thanh Thu; Mac, Dinh Hung; Ngo, Quoc Anh; Pham, Quoc Nghi; Nguyen, Le Anh; Retailleau, Pascal; Nguyen, Thanh Binh; Organic & biomolecular chemistry 24 (2026) 1424–1427; doi:10.1039/d5ob01790d

data_7160985
_publ_section_title
;
 Base-promoted decarboxylative condensation of cinnamonitriles and
 phenylacetic acids with sulfur: direct access to azatrithiapentalenes.
;
_journal_issue                   7
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              1424
_journal_page_last               1427
_journal_paper_doi               10.1039/d5ob01790d
_journal_volume                  24
_journal_year                    2026
_chemical_formula_moiety         'C16 H11 N S3'
_chemical_formula_sum            'C16 H11 N S3'
_chemical_formula_weight         313.471
_space_group_crystal_system      orthorhombic
_space_group_IT_number           33
_space_group_name_Hall           'P 2c -2n'
_space_group_name_H-M_alt        'P n a 21'
_symmetry_Int_Tables_number      33
_atom_sites_solution_primary     other
_audit_creation_date             2025-07-18
_audit_creation_method
;
Olex2 1.5-ac6-016
(compiled 2024.01.13 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6897)
;
_audit_update_record
;
2025-07-22 deposited with the CCDC.	2026-01-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   27.8169(10)
_cell_length_b                   12.6863(6)
_cell_length_c                   3.9186(2)
_cell_measurement_reflns_used    5389
_cell_measurement_temperature    123.00(10)
_cell_measurement_theta_max      32.1880
_cell_measurement_theta_min      2.6980
_cell_volume                     1382.85(11)
_computing_cell_refinement       'CrysAlisPro 1.171.43.130a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.130a 64-bit (release 05-07-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.130a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5-ac6-016 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-016 (Dolomanov et al., 2009)'
_computing_structure_refinement
'olex2.refine 1.5-ac6-016 (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      123.00(10)
_diffrn_detector                 'Dectris PILATUS3 R 200K-A area detector'
_diffrn_detector_area_resol_mean 5.811
_diffrn_detector_type            'Hybrid Photon Counting area detector'
_diffrn_measured_fraction_theta_full 0.9986
_diffrn_measured_fraction_theta_max 0.9812
_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    -39.00 106.00   0.50    4.00    --   16.90  38.00 150.00  290
  2  \w    -23.00  44.00   0.50    4.00    --  -17.70  57.00  60.00  134
  3  \w    -23.00  44.00   0.50    4.00    --  -17.70  57.00  60.00  134
  4  \w     18.00  46.00   0.50    4.00    --  -17.70  57.00-180.00   56
  5  \w    -12.00  13.00   0.50    4.00    --  -17.70  57.00-180.00   50
;
_diffrn_measurement_device       'kappa gonio four-circle diffractometer'
_diffrn_measurement_device_type  'Rigaku XtaLAB PRO'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0118600000
_diffrn_orient_matrix_UB_12      -0.0483813000
_diffrn_orient_matrix_UB_13      -0.0340330000
_diffrn_orient_matrix_UB_21      -0.0217130000
_diffrn_orient_matrix_UB_22      0.0276995000
_diffrn_orient_matrix_UB_23      -0.0311162000
_diffrn_orient_matrix_UB_31      0.0061539000
_diffrn_orient_matrix_UB_32      0.0044808000
_diffrn_orient_matrix_UB_33      -0.1749732000
_diffrn_radiation_collimation    '0.3 mm'
_diffrn_radiation_monochromator
'Rigaku Integrated Confocal MaxFlux double bounce multi-layer mirror optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0267
_diffrn_reflns_av_unetI/netI     0.0323
_diffrn_reflns_Laue_measured_fraction_full 0.9986
_diffrn_reflns_Laue_measured_fraction_max 0.9812
_diffrn_reflns_limit_h_max       39
_diffrn_reflns_limit_h_min       -41
_diffrn_reflns_limit_k_max       19
_diffrn_reflns_limit_k_min       -18
_diffrn_reflns_limit_l_max       5
_diffrn_reflns_limit_l_min       -5
_diffrn_reflns_number            12784
_diffrn_reflns_point_group_measured_fraction_full 0.9552
_diffrn_reflns_point_group_measured_fraction_max 0.9047
_diffrn_reflns_theta_full        25.2417
_diffrn_reflns_theta_max         30.50
_diffrn_reflns_theta_min         2.17
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'Rigaku micromax 003'
_exptl_absorpt_coefficient_mu    0.523
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.743
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.130a (Rigaku Oxford Diffraction, 2024)
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            red
_exptl_crystal_colour_primary    red
_exptl_crystal_density_diffrn    1.506
_exptl_crystal_description       needle
_exptl_crystal_F_000             648
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: dichloromethane'
_exptl_crystal_size_max          0.51
_exptl_crystal_size_mid          0.11
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.1691
_refine_diff_density_min         -0.1383
_refine_diff_density_rms         0.0373
_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   0.30(3)
_refine_ls_d_res_high            0.7001
_refine_ls_d_res_low             9.3729
_refine_ls_goodness_of_fit_ref   1.0449
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    1
_refine_ls_number_parameters     344
_refine_ls_number_reflns         3826
_refine_ls_number_restraints     406
_refine_ls_restrained_S_all      0.9890
_refine_ls_R_factor_all          0.0247
_refine_ls_R_factor_gt           0.0213
_refine_ls_shift/su_max          0.0277
_refine_ls_shift/su_mean         0.0002
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0028P)^2^+0.0384P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0329
_refine_ls_wR_factor_ref         0.0337
_reflns_Friedel_coverage         0.805
_reflns_limit_h_max              39
_reflns_limit_h_min              -39
_reflns_limit_k_max              18
_reflns_limit_k_min              -17
_reflns_limit_l_max              5
_reflns_limit_l_min              -5
_reflns_number_gt                3530
_reflns_number_total             3826
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            d5ob01790d2.cif
_cod_data_source_block           B21666
_cod_original_sg_symbol_Hall     ' P 2c -2n'
_cod_database_code               7160985
_chemical_oxdiff_formula         'C15 H10 N1 S3'
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
2. Rigid bond restraints
 C1B, N2B, S1B, C3, S2, C4B, S3B, C5B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 C1, C2, S1, C3, S2, N4, S3, C5
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
3. Uiso/Uaniso restraints and constraints
C1 \\sim C2 \\sim N2B \\sim S1 \\sim C3 \\sim S2 \\sim C4B \\sim N4 \\sim S3
\\sim C5 \\sim S3B \\sim C5B \\sim C1B \\sim S1B: within 2A with sigma of 0.02
and sigma for terminal atoms of 0.04 within 2A
Uanis(N2B) \\sim Ueq, Uanis(C4B) \\sim Ueq: with sigma of 0.02 and sigma for
terminal atoms of 0.04
Uanis(H4B) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(N4) \\sim Ueq, Uanis(C2) \\sim Ueq: with sigma of 0.03 and sigma for
terminal atoms of 0.06
4. Rigid body (RIGU) restrains
 C1, C2, N2B, S1, C3, S2, C4B, N4, S3, C5, S3B, C5B, C1B, S1B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Others
 Sof(S3B)=Sof(C5B)=Sof(N2B)=Sof(C4B)=Sof(H4B)=Sof(C1B)=Sof(S1B)=1-FVAR(1)
 Sof(S1)=Sof(C1)=Sof(C2)=Sof(H2)=Sof(N4)=Sof(C5)=Sof(S3)=FVAR(1)
;
_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 5.0
   PARTITIONING:   NoSpherA2
   INT ACCURACY:   Normal
   METHOD:         R2SCAN
   BASIS SET:      def2-TZVP
   CHARGE:         0
   MULTIPLICITY:   1
   SOLVATION:      CH2CL2
   DATE:           2025-07-21_19-04-05
;
_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 1.205
_oxdiff_exptl_absorpt_empirical_full_min 0.858