Thermodynamically driven self-assembly of pyridinearene to hexameric capsules.
Kiesilä, Anniina; Beyeh, Ngong Kodiah; Moilanen, Jani O.; Puttreddy, Rakesh; Götz, Sven; Rissanen, Kari; Barran, Perdita; Lützen, Arne; Kalenius, Elina; Organic & biomolecular chemistry 17 (2019) 6980–6984; doi:10.1039/c9ob01383k

data_7156952
_publ_section_title
;
 Thermodynamically driven self-assembly of pyridinearene to hexameric
 capsules.
;
_journal_issue                   29
_journal_name_full               'Organic &amp; biomolecular chemistry'
_journal_page_first              6980
_journal_page_last               6984
_journal_paper_doi               10.1039/c9ob01383k
_journal_volume                  17
_journal_year                    2019
_chemical_absolute_configuration unk
_chemical_formula_moiety         '2(C H Cl3), 3(C40 H52 N4 O8)'
_chemical_formula_sum            'C122 H158 Cl6 N12 O24'
_chemical_formula_weight         2389.29
_space_group_crystal_system      monoclinic
_space_group_IT_number           5
_space_group_name_Hall           'I 2y'
_space_group_name_H-M_alt        'I 1 2 1'
_symmetry_space_group_name_Hall  'I 2y'
_symmetry_space_group_name_H-M   'I 1 2 1'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2019-02-24
_audit_creation_method
;
Olex2 1.2
(compiled May 18 2018 14:05:52 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2019-02-26 deposited with the CCDC.    2019-07-01 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 101.549(4)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   23.7456(11)
_cell_length_b                   29.0274(9)
_cell_length_c                   27.4514(14)
_cell_measurement_reflns_used    10533
_cell_measurement_temperature    119.97(11)
_cell_measurement_theta_max      72.7880
_cell_measurement_theta_min      3.0340
_cell_volume                     18538.4(14)
_computing_cell_refinement       'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_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      119.97(11)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.1977
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.997
_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   -115.00 -17.00   0.50   10.00    --  -41.78 -37.00-150.00  196
  2  \w   -114.00 -14.00   0.50   10.00    --  -41.78 -57.00 -30.00  200
  3  \w      1.00  83.00   0.50   10.00    --   41.78 -99.00 120.00  164
  4  \w     29.00 138.00   0.50   60.00    --  105.08 -77.00-180.00  218
  5  \w     29.00 133.00   0.50   60.00    --  105.08 -30.00-120.00  208
  6  \w     48.00 121.00   0.50   60.00    --  105.08-125.00-180.00  146
  7  \w     78.00 178.00   0.50   60.00    --  105.08  30.00 -90.00  200
  8  \w     32.00 114.00   0.50   60.00    --  105.08 -45.00   0.00  164
  9  \w     39.00 109.00   0.50   60.00    --  105.08 -94.00   0.00  140
 10  \w     23.00 155.00   0.50   60.00    --  105.08 -15.00  90.00  264
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0343726000
_diffrn_orient_matrix_UB_12      -0.0068169000
_diffrn_orient_matrix_UB_13      0.0414673000
_diffrn_orient_matrix_UB_21      -0.0287354000
_diffrn_orient_matrix_UB_22      0.0473205000
_diffrn_orient_matrix_UB_23      -0.0123032000
_diffrn_orient_matrix_UB_31      -0.0487562000
_diffrn_orient_matrix_UB_32      -0.0230809000
_diffrn_orient_matrix_UB_33      -0.0375146000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0721
_diffrn_reflns_av_unetI/netI     0.0852
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -28
_diffrn_reflns_limit_k_max       34
_diffrn_reflns_limit_k_min       -34
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -32
_diffrn_reflns_number            52848
_diffrn_reflns_point_group_measured_fraction_full 0.928
_diffrn_reflns_point_group_measured_fraction_max 0.928
_diffrn_reflns_theta_full        66.499
_diffrn_reflns_theta_max         66.499
_diffrn_reflns_theta_min         2.239
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.249
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.695
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.43c (Rigaku Oxford Diffraction, 2018)
Numerical absorption correction based on gaussian integration over
            a multifaceted crystal model
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    0.856
_exptl_crystal_description       block
_exptl_crystal_F_000             5072
_exptl_crystal_size_max          0.205
_exptl_crystal_size_mid          0.144
_exptl_crystal_size_min          0.089
_refine_diff_density_max         2.382
_refine_diff_density_min         -0.891
_refine_diff_density_rms         0.221
_refine_ls_abs_structure_details
;
 Flack x determined using 4712 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.43(2)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.789
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     835
_refine_ls_number_reflns         30370
_refine_ls_number_restraints     323
_refine_ls_restrained_S_all      1.819
_refine_ls_R_factor_all          0.2432
_refine_ls_R_factor_gt           0.2056
_refine_ls_shift/su_max          0.008
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4494
_refine_ls_wR_factor_ref         0.5139
_reflns_Friedel_coverage         0.821
_reflns_Friedel_fraction_full    0.856
_reflns_Friedel_fraction_max     0.856
_reflns_number_gt                19960
_reflns_number_total             30370
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c9ob01383k2.cif
_cod_data_source_block           1_6
_cod_depositor_comments          'Adding full bibliography for 7156952.cif.'
_cod_database_code               7156952
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C100 H100 N16 O16'
_chemical_oxdiff_usercomment     CHCl3+DIPE
_reflns_odcompleteness_completeness 99.75
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.49
_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 C(H,H,H) groups, All O(H) groups
2. Restrained distances
 Cl2-C1S
 1.79 with sigma of 0.01
 Cl1-C1S
 1.79 with sigma of 0.01
 C1S-Cl3
 1.79 with sigma of 0.01
 C32-C12
 1.54 with sigma of 0.001
 C109-C110
 1.54 with sigma of 0.001
 C109-C108
 1.54 with sigma of 0.001
 C56-C67
 1.54 with sigma of 0.001
 C68-C67
 1.54 with sigma of 0.001
 C64-C65
 1.54 with sigma of 0.001
 C18-C28
 1.54 with sigma of 0.001
 C115-C113
 1.54 with sigma of 0.001
 C38-C39
 1.54 with sigma of 0.001
 C38-C37
 1.54 with sigma of 0.001
 C117-C119
 1.54 with sigma of 0.001
 C34-C35
 1.54 with sigma of 0.001
 C97-C116
 1.54 with sigma of 0.001
 C117-C116
 1.54 with sigma of 0.001
 C72-C71
 1.54 with sigma of 0.001
 C103-C104
 1.54 with sigma of 0.01
 C91-C112
 1.54 with sigma of 0.02
 C77-C76
 1.54 with sigma of 0.001
 C76-C45
 1.54 with sigma of 0.02
 C103-C81
 1.47 with sigma of 0.01
 C80-O10
 1.43 with sigma of 0.01
 C84-O11
 1.43 with sigma of 0.01
 C86-O12
 1.43 with sigma of 0.01
 C90-O13
 1.43 with sigma of 0.01
 C96-O15
 1.43 with sigma of 0.01
 O16-C98
 1.3 with sigma of 0.01
 C102-O9
 1.43 with sigma of 0.01
 C97-C99
 1.54 with sigma of 0.001
 O3-C5
 1.3 with sigma of 0.01
 C1-O4
 1.43 with sigma of 0.01
 C11-O1
 1.3 with sigma of 0.01
 C7-O2
 1.43 with sigma of 0.01
 O7-C17
 1.43 with sigma of 0.01
 C13-O8
 1.43 with sigma of 0.01
 C23-O6
 1.43 with sigma of 0.01
 C61-O24
 1.3 with sigma of 0.01
 C57-O17
 1.43 with sigma of 0.01
 C46-O21
 1.43 with sigma of 0.01
 O22-C44
 1.43 with sigma of 0.01
 C43-C45
 1.47 with sigma of 0.01
 C40-O23
 1.43 with sigma of 0.01
 C55-O18
 1.43 with sigma of 0.001
 C51-O19
 1.43 with sigma of 0.001
3. Uiso/Uaniso restraints and constraints
Uanis(C26) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C107) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C1S) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C6) \\sim Ueq, Uanis(C114) \\sim Ueq, Uanis(C77) \\sim Ueq: with sigma of
0.01 and sigma for terminal atoms of 0.01
Uanis(C118) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C2S) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C70) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(Cl1) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C56) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.05
Uanis(O20) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C30) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(O22) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(O5) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C116) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C33) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C75) \\sim Ueq, Uanis(C73) \\sim Ueq, Uanis(C74) \\sim Ueq: with sigma of
0.01 and sigma for terminal atoms of 0.01
Uanis(C78) \\sim Ueq, Uanis(C79) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.01
Uanis(C91) \\sim Ueq, Uanis(C112) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.01
Uanis(C12) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C103) \\sim Ueq, Uanis(C111) \\sim Ueq, Uanis(C110) \\sim Ueq,
Uanis(C105) \\sim Ueq, Uanis(C35) \\sim Ueq, Uanis(C37) \\sim Ueq, Uanis(C38)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C45) \\sim Ueq, Uanis(C71) \\sim Ueq, Uanis(C62) \\sim Ueq, Uanis(C97)
\\sim Ueq, Uanis(C76) \\sim Ueq, Uanis(C18) \\sim Ueq, Uanis(C12) \\sim Ueq:
with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C29) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(O11) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(O15) \\sim Ueq, Uanis(O3) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.01
Uanis(O1) \\sim Ueq, Uanis(O9) \\sim Ueq, Uanis(O7) \\sim Ueq, Uanis(O10) \\sim
Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.01
Uanis(C85) = Uanis(C108) = Uanis(C109)
Uanis(C106) = Uanis(C105) = Uanis(C107)
Uanis(C118) = Uanis(C117) = Uanis(C119)
Uanis(C63) = Uanis(C64) = Uanis(C65)
Uanis(C64) = Uanis(C66)
Uanis(C26) = Uanis(C25)
Uanis(C114) = Uanis(C113) = Uanis(C115)
Uanis(C120) = Uanis(C24)
Uanis(C35) = Uanis(C34)
Uanis(C34) = Uanis(C32)
Uanis(C72) = Uanis(C73)
Uanis(C77) = Uanis(C76)
Uanis(C82) = Uanis(C83) = Uanis(C84) = Uanis(N6) = Uanis(C80) = Uanis(C81)
Uanis(N7) = Uanis(C90) = Uanis(C88) = Uanis(C87) = Uanis(C86) = Uanis(C89)
Uanis(C92) = Uanis(N8) = Uanis(C96) = Uanis(C95) = Uanis(C94) = Uanis(C93)
Uanis(C98) = Uanis(C99) = Uanis(C100) = Uanis(C101) = Uanis(C102) = Uanis(N5)
Uanis(C98) = Uanis(O16)
Uanis(C5) = Uanis(C4) = Uanis(C3) = Uanis(C2) = Uanis(C1) = Uanis(N2)
Uanis(C9) = Uanis(C10) = Uanis(C11) = Uanis(N1) = Uanis(C7) = Uanis(C8)
Uanis(C7) = Uanis(O2)
Uanis(O2) = Uanis(C7)
Uanis(N4) = Uanis(C13) = Uanis(C14) = Uanis(C15) = Uanis(C16) = Uanis(C17)
Uanis(C22) = Uanis(C21) = Uanis(C20) = Uanis(C19) = Uanis(C23) = Uanis(N3)
Uanis(C23) = Uanis(O6)
Uanis(C57) = Uanis(N10) = Uanis(C61) = Uanis(C60) = Uanis(C59) = Uanis(C58)
Uanis(O24) = Uanis(C61)
Uanis(C56) = Uanis(C58)
Uanis(C50) = Uanis(C49) = Uanis(C48) = Uanis(C47) = Uanis(C46) = Uanis(N12)
Uanis(C40) = Uanis(N9) = Uanis(C44) = Uanis(C43) = Uanis(C41) = Uanis(C42)
Uanis(C40) = Uanis(O23)
Uanis(N11) = Uanis(C55) = Uanis(C54) = Uanis(C53) = Uanis(C52) = Uanis(C51)
Uanis(O19) = Uanis(C51)
Uanis(O18) = Uanis(C55)
Uanis(C92) = Uanis(O14)
Uanis(C90) = Uanis(O13)
4.a Riding coordinates:
 O1(H1), O3(H3), O5(H5), O7(H7), O10(H10), O12(H12A), O14(H13), O16(H16),
 O18(H17), O20(H20), O22(H22), O24(H24)
4.b Ternary CH refined with riding coordinates:
 C1S(H1S), C2S(H2S), C6(H6), C12(H12), C18(H18), C25(H25), C29(H29), C34(H34),
 C38(H38), C45(H45), C56(H56), C62(H62), C64(H64), C68(H68), C71(H71), C73(H73),
  C77(H77), C85(H85), C91(H91), C97(H97), C103(H103), C105(H105), C109(H109),
 C113(H113), C117(H117), C120(H120)
4.c Secondary CH2 refined with riding coordinates:
 C24(H24A,H24B), C28(H28A,H28B), C32(H32A,H32B), C36(H36A,H36B), C63(H63A,
 H63B), C67(H67A,H67B), C72(H72A,H72B), C76(H76A,H76B), C104(H10A,H10B),
 C108(H10I,H10J), C112(H11G,H11H), C116(H11O,H11P)
4.d Aromatic/amide H refined with riding coordinates:
 N3(H3A), C21(H21), N4(H4), C15(H15), N5(H5A), C100(H100), N6(H6A), C82(H82),
 N7(H7A), C88(H88), N8(H8), C94(H94), N9(H9A), C42(H42), N10(H10K), C59(H59),
 N11(H11), C53(H53), N12(H12B), C48(H48), C3(H3B), N2(H2), N1(H1A), C9(H9)
4.e Fitted hexagon refined as free rotating group:
 N3(C19,C20,C21,C22,C23), N4(C13,C14,C15,C16,C17), N5(C102,C101,C100,C99,C98),
 N6(C84,C83,C82,C81,C80), N7(C90,C89,C88,C87,C86), N8(C96,C95,C94,C93,C92),
 N9(C40,C41,C42,C43,C44), N10(C61,C60,C59,C58,C57), N11(C51,C52,C53,C54,C55),
 N12(C50,C49,C48,C47,C46), C3(C2,C1,N2,C5,C4), C7(N1,C11,C10,C9,C8)
4.f Idealised Me refined as rotating group:
 C26(H26A,H26B,H26C), C27(H27A,H27B,H27C), C30(H30A,H30B,H30C), C31(H31A,H31B,
 H31C), C33(H33A,H33B,H33C), C35(H35A,H35B,H35C), C37(H37A,H37B,H37C), C39(H39A,
 H39B,H39C), C65(H65A,H65B,H65C), C66(H66A,H66B,H66C), C69(H69A,H69B,H69C),
 C70(H70A,H70B,H70C), C74(H74A,H74B,H74C), C75(H75A,H75B,H75C), C78(H78A,H78B,
 H78C), C79(H79A,H79B,H79C), C106(H10C,H10D,H10E), C107(H10F,H10G,H10H),
 C110(H11A,H11B,H11C), C111(H11D,H11E,H11F), C114(H11I,H11J,H11K), C115(H11L,
 H11M,H11N), C118(H11Q,H11R,H11S), C119(H11T,H11U,H11V)
;
_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 2.065
_oxdiff_exptl_absorpt_empirical_full_min 0.659