P-Stereodefined morpholino dinucleoside 3',5'-phosphorothioates.
Jastrzębska, Katarzyna; Antończyk, Patrycja; Dolot, Rafał; Organic & biomolecular chemistry 22 (2024) 8737–8742; doi:10.1039/d4ob01437e

data_7160180
_publ_section_title
;
 P-Stereodefined morpholino dinucleoside 3',5'-phosphorothioates.
;
_journal_issue                   44
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              8737
_journal_page_last               8742
_journal_paper_doi               10.1039/d4ob01437e
_journal_volume                  22
_journal_year                    2024
_chemical_absolute_configuration ad
_chemical_compound_source        synthetic
_chemical_formula_moiety         'C16 H24 N3 O5 P S2'
_chemical_formula_sum            'C16 H24 N3 O5 P S2'
_chemical_formula_weight         433.47
_chemical_name_systematic
(R)-2-(uracil-1-yl)-(RP)-N-(2-thio-4,4-pentamethylene-1,3,2-oxathiaphospholane-2-yl)-(S)-6-hydroxymethyl-morpholine
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-07-12
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-07-12 deposited with the CCDC.	2024-10-02 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.566(2)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   7.4472(2)
_cell_length_b                   6.4902(2)
_cell_length_c                   20.4323(5)
_cell_measurement_reflns_used    7794
_cell_measurement_temperature    293.88(10)
_cell_measurement_theta_max      76.2630
_cell_measurement_theta_min      4.2650
_cell_volume                     987.20(5)
_computing_cell_refinement       'CrysAlisPro 1.171.41.100a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.100a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.100a (Rigaku OD, 2021)'
_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)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      air
_diffrn_ambient_temperature      293.88(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.961
_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    101.00 139.00   0.50    0.05    --  107.22  38.00  60.00   76
  2  \w    131.00 173.00   0.50    0.05    --  107.22  57.00  90.00   84
  3  \w    142.00 176.00   0.50    0.05    --  107.22  38.00  60.00   68
  4  \w     96.00 121.00   0.50    0.05    --  107.22  38.00 120.00   50
  5  \w    107.00 174.00   0.50    0.05    --  107.22  19.00 -90.00  134
  6  \w    142.00 178.00   0.50    0.05    --  107.22  57.00-150.00   72
  7  \w    104.00 130.00   0.50    0.05    --  107.22  57.00-150.00   52
  8  \w    -16.00  25.00   0.50    0.05    --  -47.84  19.00  90.00   82
  9  \w    -25.00  28.00   0.50    0.05    --  -47.84  19.00 150.00  106
 10  \w    -60.00 -35.00   0.50    0.05    --  -91.75  57.00-180.00   50
 11  \w    -65.00 -20.00   0.50    0.05    --  -91.75  57.00   0.00   90
 12  \w    -54.00 -23.00   0.50    0.05    --  -91.75  57.00 120.00   62
 13  \w    -73.00  25.00   0.50    0.05    --  -47.84  84.00 162.00  196
 14  \w    -84.00 -20.00   0.50    0.05    --  -91.75 125.00 150.00  128
 15  \w    -67.00 -19.00   0.50    0.05    --  -91.75  84.00 162.00   96
 16  \w   -114.00 -79.00   0.50    0.05    --  -47.84-125.00 120.00   70
 17  \w   -139.00-113.00   0.50    0.05    --  -91.75 -84.00  42.00   52
 18  \w   -106.00 -76.00   0.50    0.05    --  -47.84-125.00 -90.00   60
 19  \w   -107.00 -75.00   0.50    0.05    --  -47.84-125.00-180.00   64
 20  \w   -160.00-134.00   0.50    0.05    --  -91.75 -19.00-120.00   52
 21  \w   -112.00 -81.00   0.50    0.05    --  -91.75 -19.00-120.00   62
 22  \w   -142.00-104.00   0.50    0.05    --  -91.75 -38.00 -60.00   76
 23  \w   -163.00 -70.00   0.50    0.05    --  -91.75 -77.00   0.00  186
 24  \w   -145.00-119.00   0.50    0.05    --  -91.75 -77.00 120.00   52
 25  \w   -109.00 -70.00   0.50    0.05    --  -91.75 -77.00 120.00   78
 26  \w     -2.00  23.00   0.50    0.05    --   47.84 -19.00 -30.00   50
 27  \w     42.00  68.00   0.50    0.05    --  107.22 -77.00-150.00   52
 28  \w     73.00  98.00   0.50    0.05    --  107.22 -77.00-150.00   50
 29  \w    101.00 178.00   0.50    0.05    --  107.22  84.00 162.00  154
 30  \w     38.00  64.00   0.50    0.05    --  107.22 -57.00  90.00   52
 31  \w     37.00  63.00   0.50    0.05    --  107.22 -57.00  60.00   52
 32  \w     56.00  83.00   0.50    0.05    --  107.22 -84.00  42.00   54
 33  \w     45.00 103.00   0.50    0.05    --  107.22 -99.00 120.00  116
 34  \w     78.00 110.00   0.50    0.05    --  107.22-125.00  30.00   64
 35  \w     80.00 105.00   0.50    0.05    --  107.22 -99.00  60.00   50
 36  \w     38.00  63.00   0.50    0.05    --  107.22-125.00  30.00   50
 37  \w     40.00  69.00   0.50    0.05    --  107.22-125.00   0.00   58
 38  \w     55.00 100.00   0.50    0.05    --  107.22-125.00-120.00   90
 39  \w     -9.00  47.00   0.50    0.05    --   47.84 -84.00  42.00  112
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.1784621000
_diffrn_orient_matrix_UB_12      0.0437920000
_diffrn_orient_matrix_UB_13      -0.0337929000
_diffrn_orient_matrix_UB_21      -0.0182748000
_diffrn_orient_matrix_UB_22      -0.2047612000
_diffrn_orient_matrix_UB_23      -0.0377040000
_diffrn_orient_matrix_UB_31      -0.1032889000
_diffrn_orient_matrix_UB_32      0.1118664000
_diffrn_orient_matrix_UB_33      -0.0558632000
_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  0.0390
_diffrn_reflns_av_unetI/netI     0.0384
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.961
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       7
_diffrn_reflns_limit_k_min       -7
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            10844
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.934
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.662
_diffrn_reflns_theta_min         4.329
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.508
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.14779
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.100a (Rigaku Oxford Diffraction, 2021)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.458
_exptl_crystal_description       prism
_exptl_crystal_F_000             456
_exptl_crystal_recrystallization_method
'Crystallization from the mixture of chloroform : methanol (1:1)'
_exptl_crystal_size_max          0.67
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.187
_refine_diff_density_min         -0.249
_refine_diff_density_rms         0.048
_refine_ls_abs_structure_details
;
 Flack x determined using 1558 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.022(10)
_refine_ls_extinction_coef       0.0059(6)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.048
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     249
_refine_ls_number_reflns         3894
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.048
_refine_ls_R_factor_all          0.0310
_refine_ls_R_factor_gt           0.0299
_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^)+(0.0387P)^2^+0.0868P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0760
_refine_ls_wR_factor_ref         0.0768
_reflns_Friedel_coverage         0.781
_reflns_Friedel_fraction_full    0.997
_reflns_Friedel_fraction_max     0.902
_reflns_number_gt                3729
_reflns_number_total             3894
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ob01437e2.cif
_cod_data_source_block           kjmu_2_01_auto
_cod_depositor_comments
'Adding full bibliography for 7160179--7160180.cif.'
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               7160180
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.721
_shelx_estimated_absorpt_t_min   0.202
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
2.a Ternary CH refined with riding coordinates:
 C6(H6), C2(H2)
2.b Secondary CH2 refined with riding coordinates:
 C20(H20A,H20B), C14(H14A,H14B), C16(H16A,H16B), C19(H19A,H19B), C13(H13A,
 H13B), C3(H3A,H3B), C5(H5A,H5B), C17(H17A,H17B), C18(H18A,H18B)
2.c Aromatic/amide H refined with riding coordinates:
 N9(H9), C11(H11), C12(H12)
;
_shelx_res_checksum              40261
_olex2_exptl_crystal_mounting_method
'Crystal was glued to a support using CA glue'
_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 2.645
_oxdiff_exptl_absorpt_empirical_full_min 0.538