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_7160179
_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)-(SP)-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                 93.4520(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   6.80030(10)
_cell_length_b                   28.6550(3)
_cell_length_c                   10.60610(10)
_cell_measurement_reflns_used    11272
_cell_measurement_temperature    293.88(10)
_cell_measurement_theta_max      76.0000
_cell_measurement_theta_min      3.0600
_cell_volume                     2062.98(4)
_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_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 0.997
_diffrn_measured_fraction_theta_max 0.949
_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    103.00 128.00   0.50    0.70    --  107.66  15.00  30.00   50
  2  \w    101.00 133.00   0.50    0.70    --  107.66  15.00  60.00   64
  3  \w    101.00 131.00   0.50    0.70    --  107.66  15.00 -30.00   60
  4  \w    104.00 135.00   0.50    0.70    --  107.66  15.00 -90.00   62
  5  \w    103.00 135.00   0.50    0.70    --  107.66  15.00-120.00   64
  6  \w    102.00 136.00   0.50    0.70    --  107.66  15.00-150.00   68
  7  \w    101.00 126.00   0.50    0.70    --  107.66  15.00-180.00   50
  8  \w    -19.00  29.00   0.50    0.18    --  -45.53  38.00 120.00   96
  9  \w     -9.00  29.00   0.50    0.18    --  -45.53  38.00 150.00   76
 10  \w    -18.00  30.00   0.50    0.18    --  -45.53  38.00  60.00   96
 11  \w    -50.00 -20.00   0.50    0.70    --  -93.75  61.00 150.00   60
 12  \w    -72.00 -26.00   0.50    0.70    --  -93.75  77.00  60.00   92
 13  \w    -51.00 -26.00   0.50    0.70    --  -93.75  61.00  30.00   50
 14  \w    -51.00 -23.00   0.50    0.70    --  -93.75  61.00-180.00   56
 15  \w   -154.00-103.00   0.50    0.70    --  -93.75 -77.00 -90.00  102
 16  \w   -144.00-102.00   0.50    0.70    --  -93.75 -88.00 139.00   84
 17  \w    -67.00 -27.00   0.50    0.70    --  -93.75  88.00-104.00   80
 18  \w    -51.00   8.00   0.50    0.18    --  -45.53  88.00-104.00  118
 19  \w    -76.00 -31.00   0.50    0.18    --  -45.53 125.00   0.00   90
 20  \w     40.00  71.00   0.50    0.70    --  107.66 -77.00-150.00   62
 21  \w     65.00  92.00   0.50    0.70    --  107.66 -95.00-180.00   54
 22  \w     35.00  91.00   0.50    0.70    --  107.66 -95.00-150.00  112
 23  \w     40.00  65.00   0.50    0.18    --   45.53 -88.00 139.00   50
 24  \w     36.00  87.00   0.50    0.70    --  107.66-125.00 120.00  102
 25  \w     46.00  84.00   0.50    0.70    --  107.66 -88.00 139.00   76
 26  \w    134.00 160.00   0.50    0.70    --  107.66  88.00-104.00   52
;
_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      -0.0680598000
_diffrn_orient_matrix_UB_12      -0.0465219000
_diffrn_orient_matrix_UB_13      0.0558724000
_diffrn_orient_matrix_UB_21      -0.0867221000
_diffrn_orient_matrix_UB_22      -0.0149471000
_diffrn_orient_matrix_UB_23      -0.1313468000
_diffrn_orient_matrix_UB_31      0.1983564000
_diffrn_orient_matrix_UB_32      -0.0224562000
_diffrn_orient_matrix_UB_33      -0.0282085000
_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  0.0366
_diffrn_reflns_av_unetI/netI     0.0319
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.949
_diffrn_reflns_limit_h_max       8
_diffrn_reflns_limit_h_min       -6
_diffrn_reflns_limit_k_max       35
_diffrn_reflns_limit_k_min       -34
_diffrn_reflns_limit_l_max       13
_diffrn_reflns_limit_l_min       -13
_diffrn_reflns_number            12241
_diffrn_reflns_point_group_measured_fraction_full 0.821
_diffrn_reflns_point_group_measured_fraction_max 0.761
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.114
_diffrn_reflns_theta_min         3.084
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    3.357
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.29204
_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    1.396
_exptl_crystal_description       prism
_exptl_crystal_F_000             912
_exptl_crystal_recrystallization_method
'Crystallization from the mixture of acetonitrile : methanol (1:1 v/v)'
_exptl_crystal_size_max          0.57
_exptl_crystal_size_mid          0.57
_exptl_crystal_size_min          0.28
_refine_diff_density_max         0.498
_refine_diff_density_min         -0.399
_refine_diff_density_rms         0.063
_refine_ls_abs_structure_details
;
 Flack x determined using 2257 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.001(19)
_refine_ls_extinction_coef       0.0018(4)
_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   1.028
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     498
_refine_ls_number_reflns         6583
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.027
_refine_ls_R_factor_all          0.0491
_refine_ls_R_factor_gt           0.0486
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0989P)^2^+0.5314P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1313
_refine_ls_wR_factor_ref         0.1319
_reflns_Friedel_coverage         0.570
_reflns_Friedel_fraction_full    0.637
_reflns_Friedel_fraction_max     0.564
_reflns_number_gt                6454
_reflns_number_total             6583
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4ob01437e2.cif
_cod_data_source_block           kjmu_02
_cod_depositor_comments
'Adding full bibliography for 7160179--7160180.cif.'
_cod_original_sg_symbol_H-M      'P 21'
_cod_database_code               7160179
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C H N O P S'
_shelx_estimated_absorpt_t_max   0.453
_shelx_estimated_absorpt_t_min   0.251
_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 O(H) groups
2.a Ternary CH refined with riding coordinates:
 C6A(H6A), C6B(H6B), C2A(H2A), C2B(H2B)
2.b Secondary CH2 refined with riding coordinates:
 C3B(H3BA,H3BB), C3A(H3AA,H3AB), C13A(H13A,H13B), C5A(H5AA,H5AB), C16A(H16A,
 H16B), C5B(H5BA,H5BB), C14A(H14A,H14B), C16B(H16C,H16D), C14B(H14C,H14D),
 C17A(H17A,H17B), C17B(H17C,H17D), C19B(H19C,H19D), C20A(H20A,H20B), C18B(H18C,
 H18D), C20B(H20C,H20D), C18A(H18A,H18B), C19A(H19A,H19B)
2.c Aromatic/amide H refined with riding coordinates:
 N9B(H9B), N9A(H9A), C12A(H12A), C11A(H11A), C11B(H11B), C12B(H12B)
2.d Idealised tetrahedral OH refined as rotating group:
 O5A(H5A), O5B(H5B)
;
_shelx_res_checksum              41344
_olex2_exptl_crystal_mounting_method
'The crystal was glued to a support using the 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 2.170
_oxdiff_exptl_absorpt_empirical_full_min 0.503