Synthesis and antiviral activity of novel spirocyclic nucleosides
Cobb, Alexander J. A.; Dell’Isola, Antonio; Abdulsattar, Ban O.; McLachlan, Matthew M. W.; Neuman, Benjamin W.; Müller, Christin; Shankland, Kenneth; Al-Mulla, Hawaa M. N.; Binks, Alexander W. D.; Elvidge, Warren; New Journal of Chemistry 42 (2018) 18363–; doi:10.1039/C8NJ02777C

data_7057827
_publ_section_title
;
 Synthesis and antiviral activity of novel spirocyclic nucleosides
;
_journal_issue                   22
_journal_name_full               'New Journal of Chemistry'
_journal_page_first              18363
_journal_paper_doi               10.1039/C8NJ02777C
_journal_volume                  42
_journal_year                    2018
_chemical_absolute_configuration syn
_chemical_formula_moiety         'C14 H19 N O6 S'
_chemical_formula_sum            'C14 H19 N O6 S'
_chemical_formula_weight         329.37
_chemical_name_systematic
((6R,7S,8R)-7,8-dihydroxy-6-(hydroxymethyl)-5-oxa-2-azaspiro[3.4]octan-2-yl)(\l^3^-oxidaneylidyne)(p-tolyl)-\l^7^-sulfanone
_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_space_group_name_Hall  'P 2yb'
_symmetry_space_group_name_H-M   'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2018-04-23
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_audit_update_record
;
2018-04-28 deposited with the CCDC.
2018-10-15 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 91.524(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.1956(3)
_cell_length_b                   5.6323(2)
_cell_length_c                   20.3477(5)
_cell_measurement_reflns_used    16846
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      70.1930
_cell_measurement_theta_min      3.3480
_cell_volume                     1511.74(7)
_computing_cell_refinement       'CrysAlisPro 1.171.39.34b (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.34b (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.34b (Rigaku OD, 2017)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      150.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.998
_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    -84.00  94.00   0.50    2.00    --    5.00  12.00 -98.00  356
  2  \w   -179.00  -1.00   0.50    2.00    --  -90.00  12.00 -98.00  356
  3  \w    -89.00  89.00   0.50    0.50    --    0.00  60.00  30.00  356
  4  \w    -84.00  94.00   0.50    2.00    --    5.00  14.00 150.00  356
  5  \w    -84.00  94.00   0.50    2.00    --    5.00  29.00 -30.00  356
  6  \w    -72.00   2.00   0.50    2.00    --    5.00  43.00  60.00  148
  7  \w    -34.00  -6.00   0.50    2.00    --    5.00  60.00  60.00   56
  8  \w    -32.00  -1.00   0.50    2.00    --  -90.00  43.00 150.00   62
  9  \w   -160.00-134.00   0.50    2.00    --  -90.00  60.00 150.00   52
 10  \w   -162.00-136.00   0.50    2.00    --  -90.00  43.00 150.00   52
 11  \w    -27.00  -1.00   0.50    2.00    --  -90.00  60.00 150.00   52
 12  \w   -179.00-133.00   0.50    2.00    --  -90.00  43.00  90.00   92
 13  \w    -26.00  -1.00   0.50    2.00    --  -90.00  60.00 120.00   50
 14  \w    -27.00  -1.00   0.50    2.00    --  -90.00  60.00  90.00   52
 15  \w    -35.00  -1.00   0.50    2.00    --  -90.00  43.00-180.00   68
 16  \w    -26.00  -1.00   0.50    2.00    --  -90.00  60.00-180.00   50
 17  \w    -52.00  -2.00   0.50    2.00    --  -90.00  60.00-150.00  100
 18  \w    -43.00  -1.00   0.50    2.00    --  -90.00  43.00 120.00   84
 19  \w   -105.00 -40.00   0.50    2.00    --  -90.00  43.00-180.00  130
 20  \w    -26.00  -1.00   0.50    2.00    --  -90.00  57.00 150.00   50
 21  \w   -144.00-110.00   0.50    2.00    --  -90.00  43.00-180.00   68
 22  \w   -178.00-129.00   0.50    2.00    --  -90.00  60.00-180.00   98
 23  \w    -27.00  -1.00   0.50    2.00    --  -90.00  57.00-180.00   52
 24  \w    -33.00  -1.00   0.50    2.00    --  -90.00  57.00-150.00   64
 25  \w    -28.00  -1.00   0.50    2.00    --  -90.00  57.00 120.00   54
 26  \w    -28.00  -2.00   0.50    2.00    --  -90.00  60.00-120.00   52
 27  \w    -27.00  -1.00   0.50    2.00    --  -90.00  57.00  90.00   52
 28  \w    -45.00 -19.00   0.50    2.00    --  -90.00  29.00 -60.00   52
 29  \w   -179.00  -4.00   0.50    2.00    --  -90.00  43.00-150.00  350
 30  \w   -175.00-127.00   0.50    2.00    --  -90.00  29.00 -60.00   96
 31  \w    -27.00  -1.00   0.50    2.00    --  -90.00  43.00  90.00   52
 32  \w    -34.00  -1.00   0.50    2.00    --  -90.00  57.00-120.00   66
 33  \w   -151.00-108.00   0.50    2.00    --  -90.00  60.00-150.00   86
 34  \w   -179.00  -2.00   0.50    2.00    --  -90.00  60.00 -90.00  354
 35  \w   -178.00  -1.00   0.50    2.00    --  -90.00  29.00 150.00  354
 36  \w   -178.00 -90.00   0.50    2.00    --  -90.00  60.00 120.00  176
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC11 (RCD3): quarter-chi single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0807173000
_diffrn_orient_matrix_UB_12      0.0565296000
_diffrn_orient_matrix_UB_13      0.0538019000
_diffrn_orient_matrix_UB_21      0.0831918000
_diffrn_orient_matrix_UB_22      -0.0080478000
_diffrn_orient_matrix_UB_23      -0.0516820000
_diffrn_orient_matrix_UB_31      -0.0145408000
_diffrn_orient_matrix_UB_32      0.2674677000
_diffrn_orient_matrix_UB_33      -0.0129814000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_unetI/netI     0.0186
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       6
_diffrn_reflns_limit_k_min       -6
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -24
_diffrn_reflns_number            14940
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         70.559
_diffrn_reflns_theta_min         3.350
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.180
_exptl_absorpt_correction_T_max  0.929
_exptl_absorpt_correction_T_min  0.816
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.34b (Rigaku Oxford Diffraction, 2017)
Analytical numeric absorption correction using a multifaceted crystal
            model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_density_diffrn    1.452
_exptl_crystal_description       block
_exptl_crystal_F_000             700
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.072
_exptl_crystal_size_min          0.04
_refine_diff_density_max         0.439
_refine_diff_density_min         -0.394
_refine_diff_density_rms         0.070
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   -0.020(10)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.069
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     408
_refine_ls_number_reflns         14940
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.0474
_refine_ls_R_factor_gt           0.0440
_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^)+(0.0871P)^2^+0.8068P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1405
_refine_ls_wR_factor_ref         0.1497
_reflns_Friedel_coverage         0.793
_reflns_Friedel_fraction_full    0.999
_reflns_Friedel_fraction_max     0.985
_reflns_number_gt                14053
_reflns_number_total             14940
_reflns_threshold_expression     'I > 2\s(I)'
_twin_special_details
;
Component 2 rotated by 179.9928\% 
 around [1.00 -0.00 -0.00] (reciprocal) or [1.00 -0.00 0.02] (direct)
Component 3 rotated by -179.9914\% 
 around [1.00 -0.00 -0.02] (reciprocal) or [1.00 -0.00 0.01] (direct)
Component 4 rotated by 0.8780\% 
 around [-0.22 -0.94 0.27] (reciprocal) or [-0.04 -1.00 0.02] (direct)
;
_cod_data_source_file            c8nj02777c2.cif
_cod_data_source_block           28B
_cod_depositor_comments
'Adding full bibliography for 7057826--7057827.cif.'
_cod_database_code               7057827
_shelx_shelxl_version_number     2017/1
_chemical_oxdiff_formula         'C14 H19 N1 O6 S1'
_chemical_oxdiff_usercomment     ADI-7(2)-6
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.425(4)
 0.3540(16) 0.1066(9) 0.114(4)
2. 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 C(H,H,H) groups, All O(H) groups
3.a Ternary CH refined with riding coordinates:
3.b Secondary CH2 refined with riding coordinates:
3.c Aromatic/amide H refined with riding coordinates:
3.d Idealised Me refined as rotating group:
3.e Idealised tetrahedral OH refined as rotating group:

;
_shelx_res_checksum              59353
_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 1.593
_oxdiff_exptl_absorpt_empirical_full_min 0.758
_oxdiff_twin_integration_method  simultaneous
_oxdiff_twin_items               4