Novel 1′-homo-N-2′-deoxy-α-nucleosides: synthesis, characterization and biological activity
Carnero, Alejandro; Martín-Nieves, Virginia; Sanghvi, Yogesh S.; Russel, Olivia O.; Bassit, Leda; Schinazi, Raymond F.; Fernández, Susana; Ferrero, Miguel; RSC Advances 10 (2020) 15815–15824; doi:10.1039/D0RA03254A

data_7240369
_publ_section_title
;
 Novel 1&#x2032;-homo-N-2&#x2032;-deoxy-\a-nucleosides: synthesis,
 characterization and biological activity
;
_journal_issue                   27
_journal_name_full               'RSC Advances'
_journal_page_first              15815
_journal_page_last               15824
_journal_paper_doi               10.1039/D0RA03254A
_journal_volume                  10
_journal_year                    2020
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C11 H15 N5 O3'
_chemical_formula_sum            'C11 H15 N5 O3'
_chemical_formula_weight         265.28
_chemical_name_systematic        1'-Homo-N-2'-deoxy-alfa-adenosine
_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'
_symmetry_cell_setting           monoclinic
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2018-07-10
_audit_creation_method           'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_audit_update_record
;
2020-01-28 deposited with the CCDC.	2020-04-15 downloaded from the CCDC.
;
_cell_angle_alpha                90.0
_cell_angle_beta                 117.058(4)
_cell_angle_gamma                90.0
_cell_formula_units_Z            6
_cell_length_a                   15.8711(6)
_cell_length_b                   8.04111(18)
_cell_length_c                   16.4342(5)
_cell_measurement_reflns_used    5358
_cell_measurement_temperature    150(2)
_cell_measurement_theta_max      68.9410
_cell_measurement_theta_min      3.0090
_cell_volume                     1867.79(12)
_computing_cell_refinement       'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.46 (Rigaku OD, 2015)'
_computing_structure_refinement  'SHELXL-2018/3 (Sheldrick, 2018)'
_computing_structure_solution    'SIR2004 (Burla, 2005)'
_diffrn_ambient_temperature      150(2)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 8.2640
_diffrn_detector_type            Onyx
_diffrn_measured_fraction_theta_full 0.9954
_diffrn_measured_fraction_theta_max 0.6925
_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    -68.00  18.90   1.10    8.00    --  -43.48  37.00  90.00   79
  2  \w   -112.00 -80.10   1.10    8.00    --  -43.48 -99.00  30.00   29
  3  \w   -125.00 -82.10   1.10    8.00    --  -43.48 -99.00 150.00   39
  4  \w     54.00 125.50   1.10   37.50    --   94.50 -77.00 -30.00   65
  5  \w     70.00  97.50   1.10   37.50    --   94.50-125.00   0.00   25
  6  \w     62.00  87.30   1.10   37.50    --   94.50 -45.00 -30.00   23
  7  \w     69.00 164.70   1.10   37.50    --   94.50  30.00 -60.00   87
  8  \w    120.00 158.50   1.10   37.50    --   94.50  45.00-180.00   35
  9  \w    127.00 153.40   1.10   37.50    --   94.50 125.00-150.00   24
 10  \w     95.00 120.30   1.10   37.50    --   94.50 125.00-180.00   23
 11  \w     72.00  96.20   1.10   37.50    --   94.50  45.00-180.00   22
 12  \w     49.00 111.70   1.10   37.50    --   94.50 -45.00-180.00   57
 13  \w     26.00  60.10   1.10   37.50    --   94.50 -45.00 -30.00   31
 14  \w     78.00 109.90   1.10   37.50    --   94.50 -30.00 120.00   29
 15  \w     99.00 124.30   1.10   37.50    --   94.50 -77.00 120.00   23
 16  \w     27.00  71.00   1.10   37.50    --   94.50 -77.00 120.00   40
 17  \w     24.00  58.10   1.10   37.50    --   94.50 -30.00 120.00   31
 18  \w   -107.00 -80.60   1.10    8.00    --  -43.48 -99.00-180.00   24
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'Xcalibur, Onyx, Nova'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0978495000
_diffrn_orient_matrix_UB_12      0.0388436000
_diffrn_orient_matrix_UB_13      -0.0063636000
_diffrn_orient_matrix_UB_21      0.0448463000
_diffrn_orient_matrix_UB_22      0.0135189000
_diffrn_orient_matrix_UB_23      0.1049244000
_diffrn_orient_matrix_UB_31      0.0171318000
_diffrn_orient_matrix_UB_32      0.1870617000
_diffrn_orient_matrix_UB_33      -0.0062373000
_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  0.0354
_diffrn_reflns_av_sigmaI/netI    0.0486
_diffrn_reflns_av_unetI/netI     0.0367
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.987
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -19
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            9891
_diffrn_reflns_point_group_measured_fraction_full 0.704
_diffrn_reflns_point_group_measured_fraction_max 0.693
_diffrn_reflns_theta_full        68.1328
_diffrn_reflns_theta_max         69.5376
_diffrn_reflns_theta_min         3.0195
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'Nova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.892
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.88784
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.46 (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear intense white'
_exptl_crystal_density_diffrn    1.415
_exptl_crystal_description       plate
_exptl_crystal_F_000             840
_exptl_crystal_recrystallization_method 'Re-crystallisation from solvent: EtOH'
_exptl_crystal_size_max          0.300
_exptl_crystal_size_mid          0.160
_exptl_crystal_size_min          0.030
_refine_diff_density_max         0.255
_refine_diff_density_min         -0.224
_refine_diff_density_rms         0.043
_refine_ls_abs_structure_details
;
 Flack x determined using 898 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).

 The absolute configuration was assigned by prior knowledge of
 chiral centers.
;
_refine_ls_abs_structure_Flack   0.2(2)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.037
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     520
_refine_ls_number_reflns         4865
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.037
_refine_ls_R_factor_all          0.0485
_refine_ls_R_factor_gt           0.0424
_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^)+(0.0756P)^2^+0.0248P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1102
_refine_ls_wR_factor_ref         0.1183
_reflns_Friedel_coverage         0.304
_reflns_Friedel_fraction_full    0.362
_reflns_Friedel_fraction_max     0.349
_reflns_number_gt                4279
_reflns_number_total             4865
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d0ra03254a2.cif
_cod_data_source_block           18030_vm1_c
_cod_depositor_comments          'Adding full bibliography for 7240369.cif.'
_cod_original_cell_volume        1867.77(12)
_cod_database_code               7240369
_cell_oxdiff_length_a            15.8723(8)
_cell_oxdiff_length_b            8.0435(2)
_cell_oxdiff_length_c            16.4284(8)
_cell_oxdiff_angle_alpha         90.000(3)
_cell_oxdiff_angle_beta          117.061(5)
_cell_oxdiff_angle_gamma         90.025(3)
_cell_oxdiff_volume              1867.77(15)
_cell_oxdiff_measurement_reflns_used 5358
_oxdiff_exptl_absorpt_empirical_full_min 0.719
_oxdiff_exptl_absorpt_empirical_full_max 1.704
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_reflns_odcompleteness_completeness 99.54
_reflns_odcompleteness_theta     68.13
_reflns_odcompleteness_iscentric 1
_chemical_oxdiff_formula         C11H15N5O3
_shelx_estimated_absorpt_t_min   0.776
_shelx_estimated_absorpt_t_max   0.974
_shelx_res_checksum              75871