Mechanistic insights into the base-mediated deuteration of pyridyl phosphonium and ammonium salts
Montoli, Arianna; Dimasi, Alessandro; Guarnaccia, Miriana; Citarella, Andrea; Ronchi, Paolo; Blasi, Delia; Rossi, Sergio; Passarella, Daniele; Fasano, Valerio; RSC Advances 15 (2025) 870–874; doi:10.1039/D4RA07557A

data_7249763
_publ_section_title
;
 Mechanistic insights into the base-mediated deuteration of pyridyl
 phosphonium and ammonium salts
;
_journal_issue                   2
_journal_name_full               'RSC Advances'
_journal_page_first              870
_journal_page_last               874
_journal_paper_doi               10.1039/D4RA07557A
_journal_volume                  15
_journal_year                    2025
_chemical_formula_moiety         'C41 H32 N P2, C1 F3 O3 S1'
_chemical_formula_sum            'C42 H32 F3 N O3 P2 S'
_chemical_formula_weight         749.68
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2024-05-01
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2024-05-01 deposited with the CCDC.	2025-01-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 114.318(7)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   25.4662(14)
_cell_length_b                   13.0867(5)
_cell_length_c                   24.1761(14)
_cell_measurement_reflns_used    11959
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      34.4600
_cell_measurement_theta_min      2.8120
_cell_volume                     7342.3(8)
_computing_cell_refinement       'CrysAlisPro 1.171.43.90 (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 42.72a 64-bit (release 07-10-2022))'
_computing_data_reduction        'CrysAlisPro 1.171.43.90 (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.922
_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     -2.00  59.00   0.50   20.00    --    0.39-104.00  22.00  122
  2  \w    -92.00 -16.00   0.50   20.00    --  -34.63 104.00 124.00  152
  3  \w     -3.00  85.00   0.50   20.00    --   35.41-104.00  22.00  176
  4  \w    -23.00   2.00   0.50   20.00    --  -34.63 -99.00 -90.00   50
  5  \w    -20.00  14.00   0.50   20.00    --  -34.63 -99.00-150.00   68
  6  \w     43.00  82.00   0.50   20.00    --   35.41 178.00-180.00   78
  7  \w    -56.00  -3.00   0.50   20.00    --   35.41 -19.00 -60.00  106
  8  \w    -48.00  -3.00   0.50   20.00    --   35.41 -19.00  60.00   90
  9  \w    -25.00   4.00   0.50   20.00    --   35.41 -19.00 120.00   58
 10  \w    -52.00  21.00   0.50   20.00    --   35.41 -37.00 -90.00  146
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
'XtaLAB Synergy, Single source at offset/far, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0194561000
_diffrn_orient_matrix_UB_12      0.0149677000
_diffrn_orient_matrix_UB_13      0.0295740000
_diffrn_orient_matrix_UB_21      -0.0118327000
_diffrn_orient_matrix_UB_22      0.0499809000
_diffrn_orient_matrix_UB_23      -0.0054987000
_diffrn_orient_matrix_UB_31      -0.0203936000
_diffrn_orient_matrix_UB_32      -0.0146495000
_diffrn_orient_matrix_UB_33      0.0115028000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0705
_diffrn_reflns_av_unetI/netI     0.1114
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.922
_diffrn_reflns_limit_h_max       39
_diffrn_reflns_limit_h_min       -39
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       37
_diffrn_reflns_limit_l_min       -34
_diffrn_reflns_number            45399
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.922
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         34.862
_diffrn_reflns_theta_min         2.819
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.232
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.433
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.90 (Rigaku Oxford Diffraction, 2023)
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            'clear brown'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    brown
_exptl_crystal_density_diffrn    1.356
_exptl_crystal_description       plate
_exptl_crystal_F_000             3104
_exptl_crystal_size_max          0.45
_exptl_crystal_size_mid          0.22
_exptl_crystal_size_min          0.08
_refine_diff_density_max         0.453
_refine_diff_density_min         -0.265
_refine_diff_density_rms         0.050
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.966
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     542
_refine_ls_number_reflns         14751
_refine_ls_number_restraints     247
_refine_ls_restrained_S_all      0.983
_refine_ls_R_factor_all          0.2089
_refine_ls_R_factor_gt           0.0674
_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^)+(0.0851P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1542
_refine_ls_wR_factor_ref         0.2072
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5143
_reflns_number_total             14751
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ra07557a2.cif
_cod_data_source_block           gwl_dppbe_xx1
_cod_original_cell_volume        7342.3(7)
_cod_database_code               7249763
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C42H33F3NO3P2S
_shelx_estimated_absorpt_t_max   0.982
_shelx_estimated_absorpt_t_min   0.903
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
2. Uiso/Uaniso restraints and constraints
S1 \\sim F1 \\sim F2 \\sim F3 \\sim O1 \\sim O2 \\sim O3 \\sim C42 \\sim S1A
\\sim O2A \\sim F2A \\sim F3A \\sim O3A \\sim O1A \\sim F1A \\sim C42A: within
2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
3. Same fragment restrains
{S1, F1, F2, F3, O1, O2, O3, C42} sigma for 1-2: 0.02, 1-3: 0.04
as in
{S1A, F1A, F2A, F3A, O1A, O2A, O3A, C42A}
4. Others
 Sof(S1A)=Sof(F1A)=Sof(F2A)=Sof(F3A)=Sof(O1A)=Sof(O2A)=Sof(O3A)=Sof(C42A)=1-
 FVAR(1)
 Sof(S1)=Sof(F1)=Sof(F2)=Sof(F3)=Sof(O1)=Sof(O2)=Sof(O3)=Sof(C42)=FVAR(1)
5.a Aromatic/amide H refined with riding coordinates:
 C1(H1), C2(H2), C4(H4), C7(H7), C8(H8), C9(H9), C10(H10), C11(H11), C14(H14),
 C15(H15), C16(H16), C17(H17), C19(H19), C20(H20), C21(H21), C22(H22), C23(H23),
  C25(H25), C26(H26), C27(H27), C28(H28), C29(H29), C31(H31), C32(H32),
 C33(H33), C34(H34), C35(H35), C37(H37), C38(H38), C39(H39), C40(H40), C41(H41)
;
_shelx_res_checksum              25656
_shelx_hkl_checksum              4012
_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 1.580
_oxdiff_exptl_absorpt_empirical_full_min 0.668