Regioselective N1-ribosylation of hydantoin: synthesis and properties of the first contracted uridine analog.
Bsoul, Odai; Lampel, Yakir; Rofe, Maayan; Pariente-Cohen, Natalie; Timsit, Chen; Fischer, Bilha; Chemical communications (Cambridge, England) 61 (2025) 2281–2284; doi:10.1039/d4cc06033d

data_7134062
_publ_section_title
;
 Regioselective N1-ribosylation of hydantoin: synthesis and properties of
 the first contracted uridine analog.
;
_journal_issue                   11
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              2281
_journal_page_last               2284
_journal_paper_doi               10.1039/d4cc06033d
_journal_volume                  61
_journal_year                    2025
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C8 H12 N2 O6'
_chemical_formula_sum            'C8 H12 N2 O6'
_chemical_formula_weight         232.20
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_block_doi                 10.5517/ccdc.csd.cc2l0lz6
_audit_creation_date             2024-07-21
_audit_creation_method
;
Olex2 1.5
(compiled 2024.01.12 svn.r2f8d729c for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-09-13 deposited with the CCDC.	2024-12-16 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   9.08590(10)
_cell_length_b                   9.16110(10)
_cell_length_c                   11.4717(2)
_cell_measurement_reflns_used    8528
_cell_measurement_theta_max      74.4010
_cell_measurement_theta_min      4.8570
_cell_volume                     954.87(2)
_computing_cell_refinement       'CrysAlisPro 1.171.43.108a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.108a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.108a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2016/4 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_type            'HyPix-Arc 150'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.985
_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   -110.00 -85.00   0.50    0.05    --  -70.00 -55.00 116.01   50
  2  \w   -109.00 -84.00   0.50    0.05    --  -74.00 -72.00  -2.04   50
  3  \w   -102.00 -77.00   0.50    0.05    --  -70.00 -75.00 -81.64   50
  4  \w   -113.00 -88.00   0.50    0.05    --  -68.75 -22.00 -60.00   50
  5  \w   -109.00 -81.00   0.50    0.05    --  -65.92 -22.00 -60.00   56
  6  \w    -78.00 -53.00   0.50    0.05    --  -65.92 109.00 -70.00   50
  7  \w    -82.00 -36.00   0.50    0.05    --  -68.75 109.00 -70.00   92
  8  \w    -83.00 -57.00   0.50    0.05    --  -68.75 114.00-165.00   52
  9  \w    -58.00 -32.00   0.50    0.05    --  -65.92 114.00-165.00   52
 10  \w     49.00  77.00   0.50    0.05    --   38.00  63.00 -92.63   56
 11  \w     62.00  88.00   0.50    0.05    --   46.00  54.00-136.97   52
 12  \w     81.00 123.00   0.50    0.05    --   77.50  26.00-146.21   84
 13  \w     95.00 121.00   0.50    0.05    --   77.50  38.00-132.25   52
 14  \w     89.00 114.00   0.50    0.05    --   77.50  65.00 -53.94   50
 15  \w     58.00 116.00   0.50    0.05    --   77.37  15.00  60.00  116
 16  \w     70.00 103.00   0.50    0.05    --   77.37  22.00 105.00   66
 17  \w     65.00  90.00   0.50    0.05    --   73.12  22.00 105.00   50
 18  \w     51.00  77.00   0.50    0.05    --   38.00  55.00 150.09   52
 19  \w     54.00  79.00   0.50    0.05    --   65.58  22.00 105.00   50
 20  \w     58.00  96.00   0.50    0.05    --   77.50   8.00   4.02   76
 21  \w     60.00 109.00   0.50    0.05    --   77.37   0.00 -60.00   98
 22  \w     59.00 108.00   0.50    0.05    --   77.37   0.00-120.00   98
 23  \w     43.00  88.00   0.50    0.05    --   77.37   0.00-180.00   90
 24  \w     30.00  55.00   0.50    0.05    --   65.58-109.00-166.00   50
 25  \w     67.00  92.00   0.50    0.05    --   77.37-125.00-150.00   50
 26  \w     41.00  93.00   0.50    0.05    --   77.37-125.00 -60.00  104
 27  \w     74.00 100.00   0.50    0.05    --   77.37-125.00 -30.00   52
 28  \w     42.00  68.00   0.50    0.05    --   77.37-125.00   0.00   52
 29  \w     39.00  64.00   0.50    0.05    --   77.37-125.00 -30.00   50
 30  \w     43.00  95.00   0.50    0.05    --   77.37-125.00-120.00  104
 31  \w     40.00  98.00   0.50    0.05    --   77.37-125.00  30.00  116
 32  \w     64.00  94.00   0.50    0.05    --   77.37-114.00 103.00   60
 33  \w     36.00  63.00   0.50    0.05    --   73.12-114.00 103.00   54
 34  \w     41.00  67.00   0.50    0.05    --   77.37-125.00 150.00   52
 35  \w     28.00  53.00   0.50    0.05    --   65.58-114.00 103.00   50
 36  \w     42.00  67.00   0.50    0.05    --   77.37-109.00-166.00   50
 37  \w     58.00  87.00   0.50    0.05    --   73.12-109.00-166.00   58
 38  \w   -107.00 -82.00   0.50    0.05    --  -74.00 -83.00 113.07   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, HyPix-Arc 150'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0438541000
_diffrn_orient_matrix_UB_12      -0.1420937000
_diffrn_orient_matrix_UB_13      -0.0628532000
_diffrn_orient_matrix_UB_21      -0.0182786000
_diffrn_orient_matrix_UB_22      0.0853027000
_diffrn_orient_matrix_UB_23      -0.1148406000
_diffrn_orient_matrix_UB_31      0.1627586000
_diffrn_orient_matrix_UB_32      -0.0286621000
_diffrn_orient_matrix_UB_33      -0.0298362000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0181
_diffrn_reflns_av_unetI/netI     0.0115
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.985
_diffrn_reflns_limit_h_max       10
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       11
_diffrn_reflns_limit_k_min       -11
_diffrn_reflns_limit_l_max       14
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            10131
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.974
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.672
_diffrn_reflns_theta_min         6.182
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'PhotonJet R (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.214
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.82623
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.108a (Rigaku Oxford Diffraction, 2024)
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    1.615
_exptl_crystal_description       prism
_exptl_crystal_F_000             488
_exptl_crystal_size_max          0.35
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.165
_refine_diff_density_min         -0.215
_refine_diff_density_rms         0.047
_refine_ls_abs_structure_details
;
 Flack x determined using 764 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.06(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.061
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     148
_refine_ls_number_reflns         1910
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.061
_refine_ls_R_factor_all          0.0245
_refine_ls_R_factor_gt           0.0243
_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^)+(0.0351P)^2^+0.2630P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0629
_refine_ls_wR_factor_ref         0.0631
_reflns_Friedel_coverage         0.683
_reflns_Friedel_fraction_full    0.997
_reflns_Friedel_fraction_max     0.959
_reflns_number_gt                1891
_reflns_number_total             1910
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4cc06033d2.cif
_cod_data_source_block           bf8_auto
_cod_depositor_comments          'Adding full bibliography for 7134062.cif.'
_cod_database_code               7134062
_shelx_shelxl_version_number     2016/4
_chemical_oxdiff_formula         C8O6N2H4
_chemical_oxdiff_usercomment     'Odai Bsoul  Bilha Fischer BIU'
_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:
 C1(H1), C3(H3A), C4(H4A), C5(H5)
2.b Secondary CH2 refined with riding coordinates:
 C2(H2B,H2C), C8(H8A,H8B)
2.c Aromatic/amide H refined with riding coordinates:
 N2(H2A)
2.d Idealised tetrahedral OH refined as rotating group:
 O2(H2), O3(H3), O4(H4)
;
_shelx_res_checksum              62504
_shelx_hkl_checksum              82310
_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 1.255
_oxdiff_exptl_absorpt_empirical_full_min 0.775