The synthesis of a pyridine-N-oxide isophthalamide rotaxane utilizing supplementary amide hydrogen bond interactions.
Evans, Nicholas H.; Gell, Charles E.; Peach, Michael J. G.; Organic & biomolecular chemistry 14 (2016) 7972–7981; doi:10.1039/c6ob01435f

data_7155226
_publ_section_title
;
 The synthesis of a pyridine-N-oxide isophthalamide rotaxane utilizing
 supplementary amide hydrogen bond interactions.
;
_journal_issue                   33
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              7972
_journal_page_last               7981
_journal_paper_doi               10.1039/c6ob01435f
_journal_volume                  14
_journal_year                    2016
_chemical_formula_moiety         'C19 H31 N3 O3, C28 H30 N2 O5, C H Cl3'
_chemical_formula_sum            'C48 H62 Cl3 N5 O8'
_chemical_formula_weight         943.37
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_symmetry_space_group_name_Hall  '-P 2yn'
_symmetry_space_group_name_H-M   'P 1 21/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2016-01-08
_audit_creation_method
;
Olex2 1.2
(compiled 2015.01.26 svn.r3150 for OlexSys, GUI svn.r4998)
;
_audit_update_record
;
2016-04-11 deposited with the CCDC.
2016-08-05 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 96.8269(17)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   15.0431(3)
_cell_length_b                   10.80301(18)
_cell_length_c                   29.7705(5)
_cell_measurement_reflns_used    17669
_cell_measurement_temperature    99.9(3)
_cell_measurement_theta_max      74.0130
_cell_measurement_theta_min      3.5190
_cell_volume                     4803.72(15)
_computing_cell_refinement       'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.38.41 (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      99.9(3)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2303
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 1.000
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  1  \w   -124.00  47.00   1.00    6.00    --  -38.50   0.00-180.00  171
  2  \w     17.00 110.00   1.00    6.00    --   41.89  57.00   0.00   93
  3  \w     23.00  96.00   1.00    6.00    --   41.89-125.00 120.00   73
  4  \w     36.00 131.00   1.00   24.00    --  104.55 -61.00  90.00   95
  5  \w     78.00 173.00   1.00   24.00    --  104.55  61.00 150.00   95
  6  \w     74.00 176.00   1.00   24.00    --  104.55  77.00-150.00  102
  7  \w     35.00 127.00   1.00   24.00    --  104.55 -45.00 -30.00   92
  8  \w     84.00 178.00   1.00   24.00    --  104.55  30.00 -90.00   94
  9  \w     25.00 109.00   1.00   24.00    --  104.55 -94.00 -30.00   84
 10  \w     12.00 113.00   1.00    6.00    --   41.89  77.00-180.00  101
 11  \w      1.00  81.00   1.00    6.00    --   41.89 -99.00 -60.00   80
 12  \w     21.00 113.00   1.00    6.00    --   41.89  38.00 120.00   92
 13  \w     35.00 121.00   1.00   24.00    --  104.55-125.00 -60.00   86
 14  \w     84.00 178.00   1.00   24.00    --  104.55  30.00   0.00   94
 15  \w     74.00 176.00   1.00   24.00    --  104.55  77.00  90.00  102
 16  \w     74.00 176.00   1.00   24.00    --  104.55  77.00   0.00  102
 17  \w     78.00 173.00   1.00   24.00    --  104.55  61.00 -60.00   95
 18  \w     82.00 174.00   1.00   24.00    --  104.55  45.00  60.00   92
 19  \w     12.00  37.00   1.00    6.00    --   41.89  77.00  30.00   25
 20  \w     12.00 113.00   1.00    6.00    --   41.89  77.00 -90.00  101
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at zero, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0941977000
_diffrn_orient_matrix_UB_12      0.0566576000
_diffrn_orient_matrix_UB_13      0.0010016000
_diffrn_orient_matrix_UB_21      -0.0208282000
_diffrn_orient_matrix_UB_22      0.0904616000
_diffrn_orient_matrix_UB_23      0.0373281000
_diffrn_orient_matrix_UB_31      0.0365194000
_diffrn_orient_matrix_UB_32      -0.0946098000
_diffrn_orient_matrix_UB_33      0.0363415000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0550
_diffrn_reflns_av_unetI/netI     0.0283
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -17
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       35
_diffrn_reflns_limit_l_min       -35
_diffrn_reflns_number            52573
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        67.075
_diffrn_reflns_theta_max         67.075
_diffrn_reflns_theta_min         2.990
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.196
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.66024
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.38.41 (Rigaku Oxford Diffraction, 2015)
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    1.304
_exptl_crystal_description       plate
_exptl_crystal_F_000             2000
_exptl_crystal_size_max          0.432
_exptl_crystal_size_mid          0.212
_exptl_crystal_size_min          0.038
_refine_diff_density_max         0.472
_refine_diff_density_min         -0.552
_refine_diff_density_rms         0.086
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.074
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     599
_refine_ls_number_reflns         8552
_refine_ls_number_restraints     9
_refine_ls_restrained_S_all      1.073
_refine_ls_R_factor_all          0.0776
_refine_ls_R_factor_gt           0.0692
_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^)+(0.0977P)^2^+11.4370P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2014
_refine_ls_wR_factor_ref         0.2091
_reflns_Friedel_coverage         0.000
_reflns_number_gt                7388
_reflns_number_total             8552
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c6ob01435f5.cif
_cod_data_source_block           ne105
_cod_depositor_comments
'Adding full bibliography for 7155225--7155226.cif.'
_cod_original_cell_volume        4803.73(15)
_cod_database_code               7155226
_chemical_oxdiff_formula         'C47 H61 N5 O8 Cl3'
_chemical_oxdiff_usercomment     TO21
_reflns_odcompleteness_completeness 99.99
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Rigid bond restraints
 C44, C45, C46A, C47B
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.02
 C44, C45, C46, C47
 with sigma for 1-2 distances of 0.02 and sigma for 1-3 distances of 0.02
3. Others
 Sof(H45C)=Sof(H45D)=Sof(C47B)=Sof(H47D)=Sof(H47E)=Sof(H47F)=Sof(C46A)=
 Sof(H46C)=Sof(H46D)=1-FVAR(1)
 Sof(H45A)=Sof(H45B)=Sof(C46)=Sof(H46A)=Sof(H46B)=Sof(C47)=Sof(H47A)=Sof(H47B)=
 Sof(H47C)=FVAR(1)
4.a Ternary CH refined with riding coordinates:
 C48(H48)
4.b Secondary CH2 refined with riding coordinates:
 C35(H35A,H35B), C36(H36A,H36B), C37(H37A,H37B), C38(H38A,H38B), C39(H39A,
 H39B), C42(H42A,H42B), C43(H43A,H43B), C44(H44A,H44B), C45(H45A,H45B),
 C45(H45C,H45D), C46(H46A,H46B), C8(H8A,H8B), C15(H15A,H15B), C16(H16A,H16B),
 C17(H17A,H17B), C18(H18A,H18B), C19(H19A,H19B), C20(H20A,H20B), C27(H27A,H27B),
  C46A(H46C,H46D)
4.c Aromatic/amide H refined with riding coordinates:
 C29(H29), C31(H31), C33(H33), N4(H4), N5(H5), C1(H1), C3(H3), C4(H4A),
 C5(H5A), C10(H10), C11(H11), C13(H13), C14(H14), C22(H22), C23(H23), C25(H25),
 C26(H26), N1(H1A), N2(H2)
4.d Idealised Me refined as rotating group:
 C40(H40A,H40B,H40C), C47(H47A,H47B,H47C), C47B(H47D,H47E,H47F)
;
_shelx_shelxl_version_number     2014/7
_olex2_exptl_crystal_mounting_method
'The crystal was mounted on a polyimide loop using Paratone-N oil'
_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 1.763
_oxdiff_exptl_absorpt_empirical_full_min 0.726