Green Synthesis of α-Aminophosphonates: From Hydrogen-Bonded Janus Dimers to Pharmaceutical Potential
Kholany, Rawda; Mardini, Alaa A.; Shakirova, Ksenia; Islamov, Daut; Gerasimov, Alexander; Klimovitskii, Alexander; Vavilova, Alena A.; Mostovaya, Olga; Gazizova, Asiya; Stoikov, Ivan; Organic & Biomolecular Chemistry  (2025) –; doi:10.1039/D5OB01712B

data_7160907
_publ_section_title
;
 Green Synthesis of \a-Aminophosphonates: From Hydrogen-Bonded Janus
 Dimers to Pharmaceutical Potential
;
_journal_name_full               'Organic &amp; Biomolecular Chemistry'
_journal_paper_doi               10.1039/D5OB01712B
_journal_year                    2025
_chemical_formula_moiety         'C17 H29 N2 O4 P'
_chemical_formula_sum            'C17 H29 N2 O4 P'
_chemical_formula_weight         356.39
_space_group_crystal_system      orthorhombic
_space_group_IT_number           29
_space_group_name_Hall           'P 2c -2ac'
_space_group_name_H-M_alt        'P c a 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2025-10-17
_audit_creation_method
;
Olex2 1.3-ac4
(compiled 2020.11.27 svn.r5f609507 for Rigaku Oxford Diffraction, GUI svn.r6214)
;
_audit_update_record
;
2025-10-20 deposited with the CCDC.	2025-11-28 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   29.3313(6)
_cell_length_b                   9.2370(2)
_cell_length_c                   14.2141(4)
_cell_measurement_reflns_used    19226
_cell_measurement_temperature    304.7(5)
_cell_measurement_theta_max      75.5330
_cell_measurement_theta_min      3.0460
_cell_volume                     3851.07(16)
_computing_cell_refinement       'CrysAlisPro 1.171.42.80a (Rigaku OD, 2023)'
_computing_data_collection       'CrysAlisPro 1.171.42.80a (Rigaku OD, 2023)'
_computing_data_reduction        'CrysAlisPro 1.171.42.80a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.3-ac4 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3-ac4 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2016/6 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_environment      air
_diffrn_ambient_temperature      304.7(5)
_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 0.990
_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     26.00  52.00   0.50    5.00    --   46.31-106.00 -78.00   52
  2  \w    -39.00  -4.00   0.50    5.00    --  -47.56 106.00  20.00   70
  3  \w    -76.00 -46.00   0.50    5.00    --  -47.56 106.00  20.00   60
  4  \w     45.00  70.00   0.50   15.00    --  103.80-106.00 -78.00   50
  5  \w   -124.00 -98.00   0.50   15.00    -- -105.05-106.00 -78.00   52
  6  \w   -164.00-138.00   0.50   15.00    -- -105.05-106.00 -78.00   52
  7  \w     31.00  94.00   0.50    5.00    --   46.31-125.00-180.00  126
  8  \w     43.00  69.00   0.50    5.00    --   46.31 -77.00  30.00   52
  9  \w     74.00 100.00   0.50    5.00    --   46.31 125.00 -30.00   52
 10  \w    -22.00   3.00   0.50    5.00    --   46.31 -77.00  30.00   50
 11  \w   -119.00 -35.00   0.50    5.00    --  -47.56 -57.00-120.00  168
 12  \w    -40.00  24.00   0.50    5.00    --  -47.56  37.00-150.00  128
 13  \w    -25.00  14.00   0.50    5.00    --  -47.56  19.00 -60.00   78
 14  \w    -42.00  24.00   0.50    5.00    --  -47.56  37.00  30.00  132
 15  \w     33.00  90.00   0.50   15.00    --  103.80-125.00   0.00  114
 16  \w     92.00 175.00   0.50   15.00    --  103.80  45.00 120.00  166
 17  \w     61.00 112.00   0.50   15.00    --  103.80-125.00-180.00  102
 18  \w     31.00  58.00   0.50   15.00    --  103.80-125.00-180.00   54
 19  \w     96.00 175.00   0.50   15.00    --  103.80  45.00  90.00  158
 20  \w     31.00  70.00   0.50   15.00    --  103.80-125.00  60.00   78
 21  \w     33.00  70.00   0.50   15.00    --  103.80 -61.00 -30.00   74
 22  \w    128.00 153.00   0.50   15.00    --  103.80 106.00  20.00   50
 23  \w     68.00 106.00   0.50   15.00    --  103.80 -94.00  30.00   76
 24  \w     96.00 174.00   0.50   15.00    --  103.80  45.00-120.00  156
 25  \w     45.00  97.00   0.50   15.00    --  103.80-125.00 120.00  104
 26  \w   -157.00-102.00   0.50   15.00    -- -105.05 -30.00  60.00  110
 27  \w    -58.00 -32.00   0.50   15.00    -- -105.05  61.00-180.00   52
 28  \w   -110.00 -55.00   0.50   15.00    -- -105.05 125.00-180.00  110
 29  \w   -112.00 -42.00   0.50   15.00    -- -105.05 125.00-120.00  140
 30  \w    -70.00 -38.00   0.50   15.00    -- -105.05  61.00-120.00   64
 31  \w   -112.00 -80.00   0.50   15.00    -- -105.05 125.00  60.00   64
 32  \w    -68.00 -34.00   0.50   15.00    -- -105.05 125.00  60.00   68
 33  \w    -67.00 -35.00   0.50   15.00    -- -105.05  61.00-150.00   64
 34  \w   -125.00 -84.00   0.50   15.00    -- -105.05 -77.00-150.00   82
 35  \w   -170.00-139.00   0.50   15.00    -- -105.05 -77.00-150.00   62
 36  \w    -66.00 -36.00   0.50   15.00    -- -105.05  61.00 120.00   60
 37  \w    -70.00 -37.00   0.50   15.00    -- -105.05  61.00 150.00   66
 38  \w    -71.00 -46.00   0.50   15.00    -- -105.05  61.00 -90.00   50
 39  \w    -59.00 -34.00   0.50   15.00    -- -105.05 125.00 150.00   50
 40  \w   -112.00 -85.00   0.50   15.00    -- -105.05 125.00 150.00   54
 41  \w    -65.00 -40.00   0.50   15.00    -- -105.05  61.00 -30.00   50
 42  \w   -105.00 -64.00   0.50   15.00    -- -105.05 106.00  20.00   82
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type
'XtaLAB Synergy, Single source at home/near, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0258689000
_diffrn_orient_matrix_UB_12      -0.0292946000
_diffrn_orient_matrix_UB_13      -0.0923444000
_diffrn_orient_matrix_UB_21      0.0451512000
_diffrn_orient_matrix_UB_22      0.0418784000
_diffrn_orient_matrix_UB_23      0.0483647000
_diffrn_orient_matrix_UB_31      0.0071006000
_diffrn_orient_matrix_UB_32      -0.1587550000
_diffrn_orient_matrix_UB_33      0.0297077000
_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  0.0470
_diffrn_reflns_av_unetI/netI     0.0271
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       36
_diffrn_reflns_limit_h_min       -36
_diffrn_reflns_limit_k_max       8
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            44008
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.981
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         75.947
_diffrn_reflns_theta_min         3.013
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.452
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.752
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.80a (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            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.229
_exptl_crystal_description       prism
_exptl_crystal_F_000             1536
_exptl_crystal_size_max          0.218
_exptl_crystal_size_mid          0.142
_exptl_crystal_size_min          0.105
_refine_diff_density_max         7.018
_refine_diff_density_min         -0.759
_refine_diff_density_rms         0.374
_refine_ls_abs_structure_details
;
 Flack x determined using 3024 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.370(15)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   2.459
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     440
_refine_ls_number_reflns         7886
_refine_ls_number_restraints     38
_refine_ls_restrained_S_all      2.458
_refine_ls_R_factor_all          0.2606
_refine_ls_R_factor_gt           0.2583
_refine_ls_shift/su_max          0.060
_refine_ls_shift/su_mean         0.008
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4849
_refine_ls_wR_factor_ref         0.4896
_reflns_Friedel_coverage         0.901
_reflns_Friedel_fraction_full    0.998
_reflns_Friedel_fraction_max     0.971
_reflns_number_gt                7257
_reflns_number_total             7886
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ob01712b2.cif
_cod_data_source_block           stoi871_corr
_cod_database_code               7160907
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         C17H29N2O4P
_shelx_estimated_absorpt_t_max   0.868
_shelx_estimated_absorpt_t_min   0.741
_reflns_odcompleteness_completeness 99.92
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.49
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Rigid bond restraints
 P2, C12
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
3. Uiso/Uaniso restraints and constraints
Uanis(C33) = Uanis(C2)
4. Rigid body (RIGU) restrains
 C32, C2, C33, O8
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 O7, C22, C7, C31
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5.a Ternary CH refined with riding coordinates:
 C22(H22), C32(H32), C23(H23), C29(H29)
5.b Me refined with riding coordinates:
 C19(H19A,H19B,H19C)
5.c Aromatic/amide H refined with riding coordinates:
 N1(H1A), C1(H1), N4(H4), C10(H10), N2(H2), C18(H18), N3(H3), C24(H24),
 C26(H26), C28(H28), C17(H17), C9(H9)
5.d Idealised Me refined as rotating group:
 C30(H30A,H30B,H30C), C5(H5A,H5B,H5C), C21(H21A,H21B,H21C), C11(H11A,H11B,
 H11C), C3(H3A,H3B,H3C), C25(H25A,H25B,H25C), C13(H13A,H13B,H13C), C27(H27A,
 H27B,H27C), C7(H7A,H7B,H7C), C15(H15A,H15B,H15C), C31(H31A,H31B,H31C), C2(H2A,
 H2B,H2C), C33(H33A,H33B,H33C)
;
_shelx_res_checksum              75510
_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 1.929
_oxdiff_exptl_absorpt_empirical_full_min 0.671