Spontaneous Assembly of Rotaxanes from a Primary Amine, Crown Ether and Electrophile.
Fielden, Stephen D. P.; Leigh, David A.; McTernan, Charlie T.; Pérez-Saavedra, Borja; Vitorica-Yrezabal, Iñigo J; Journal of the American Chemical Society 140 (2018) 6049–6052; doi:10.1021/jacs.8b03394

data_4132371
_publ_section_title
;
 Spontaneous Assembly of Rotaxanes from a Primary Amine, Crown Ether and
 Electrophile.
;
_journal_issue                   19
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              6049
_journal_page_last               6052
_journal_paper_doi               10.1021/jacs.8b03394
_journal_volume                  140
_journal_year                    2018
_chemical_formula_moiety
'2(C39 H45 Cl3 N O2), 2(Cl), 2(C16 H32 O8), 4(H2 O)'
_chemical_formula_sum            'C110 H162 Cl8 N2 O24'
_chemical_formula_weight         2180.01
_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'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2018-03-19
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_cell_angle_alpha                90.0
_cell_angle_beta                 95.6287(6)
_cell_angle_gamma                90.0
_cell_formula_units_Z            4
_cell_length_a                   18.85077(14)
_cell_length_b                   15.97613(10)
_cell_length_c                   38.4073(3)
_cell_measurement_reflns_used    24977
_cell_measurement_temperature    100
_cell_measurement_theta_max      31.0531812954
_cell_measurement_theta_min      1.03700441075
_cell_volume                     11511.06(14)
_computing_cell_refinement
'DIALS 2theta refinement, DIALS 1.8.4-g04a6c08a-release'
_computing_data_reduction
;
aimless (Evans, P. R. and Murshudov, G. N., 2013)
ccp4 (Winn, M. D. et al., 2011)
DIALS 1.8.4-g04a6c08a-release (Winter, G. et al., 2018)
pointless (Evans, P., 2006)
XIA2 0.5.487-ge624e5ac-dials-1.8 (Winter, G., 2010)
;
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.0
_diffrn_detector                 'CCD area detector'
_diffrn_detector_area_resol_mean 0.0350
_diffrn_detector_type            'Rigaku Saturn724+'
_diffrn_measured_fraction_theta_full 0.973
_diffrn_measured_fraction_theta_max 0.971
_diffrn_measurement_device       'CrystalLogic Kappa (4 circle)'
_diffrn_measurement_device_type  DLS_I19
_diffrn_measurement_method       'omega rotation'
_diffrn_radiation_collimation    '0.3 x 1.5 Double Pinhole'
_diffrn_radiation_monochromator  'Synchrotron '
_diffrn_radiation_probe          x-ray
_diffrn_radiation_wavelength     0.6889
_diffrn_reflns_av_R_equivalents  0.0655
_diffrn_reflns_av_unetI/netI     0.0647
_diffrn_reflns_Laue_measured_fraction_full 0.973
_diffrn_reflns_Laue_measured_fraction_max 0.971
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       46
_diffrn_reflns_limit_l_min       -46
_diffrn_reflns_number            79585
_diffrn_reflns_point_group_measured_fraction_full 0.973
_diffrn_reflns_point_group_measured_fraction_max 0.971
_diffrn_reflns_theta_full        24.415
_diffrn_reflns_theta_max         24.519
_diffrn_reflns_theta_min         1.126
_diffrn_source                   Synchrotron
_diffrn_source_type              'Undulator, I19, DLS, RAL'
_exptl_absorpt_coefficient_mu    0.245
_exptl_absorpt_correction_T_max  1.0
_exptl_absorpt_correction_T_min  0.987306213249
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details
'CCP4 7.0.048: AIMLESS, version 0.5.32 : 29/03/17 Scaling & analysis of unmerged intensities, absorption correction using spherical harmonics'
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.258
_exptl_crystal_description       plate
_exptl_crystal_F_000             4656
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.07
_refine_diff_density_max         1.505
_refine_diff_density_min         -0.641
_refine_diff_density_rms         0.112
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.334
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1631
_refine_ls_number_reflns         20484
_refine_ls_number_restraints     1107
_refine_ls_restrained_S_all      1.361
_refine_ls_R_factor_all          0.1369
_refine_ls_R_factor_gt           0.1111
_refine_ls_shift/su_max          0.002
_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          0.3306
_refine_ls_wR_factor_ref         0.3547
_reflns_Friedel_coverage         0.000
_reflns_number_gt                14057
_reflns_number_total             20484
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja8b03394_si_003.cif
_cod_data_source_block           shelxt_a
_cod_original_cell_volume        11511.07(10)
_cod_database_code               4132371
_shelxl_version_number           2014/6
_shelx_estimated_absorpt_t_max   0.983
_shelx_estimated_absorpt_t_min   0.964
_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,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 O3-H3A = O3-H3B
 0.85 with sigma of 0.02
 C140-C139
 1.54 with sigma of 0.02
 C55-C41
 2.4 with sigma of 0.02
 C80-C94
 2.4 with sigma of 0.02
 C81-C80 = C41-C42
 1.5 with sigma of 0.002
 C43-C42 = C42-C55 = C42-C49
 1.45 with sigma of 0.002
 C82-C81 = C81-C88 = C81-C94
 1.45 with sigma of 0.002
 O4-H4A = O4-H4B
 0.87 with sigma of 0.02
 C80-C79
 1.54 with sigma of 0.02
 C41-C40 = C80-C79
 1.54 with sigma of 0.002
 H3A-H3B
 1.34 with sigma of 0.04
 H4A-H4B
 1.38 with sigma of 0.04
 O16-C109 \\sim O16-C119 \\sim O26-C120 \\sim O17-C110 \\sim O17-C111 \\sim
O26-C121 \\sim O10-C112 ~
 O10-C122
 with sigma of 0.002
 C111-C112 \\sim C122-C121 \\sim C119-C120 \\sim C110-C109
 with sigma of 0.002
 O28-C61 \\sim O7-C61
 with sigma of 0.02
 O8-C61 \\sim O27-C61
 with sigma of 0.02
 C73-C71 \\sim C71-C101 \\sim C72-C71 \\sim C100-C71 \\sim C74-C71 \\sim
C71-C102
 with sigma of 0.002
 O22-C143 \\sim O29-C135 \\sim O23-C136 \\sim O23-C144 \\sim O23-C137
 with sigma of 0.02
 C136-C135 \\sim C144-C143 \\sim C140-C139 \\sim C141-C142
 with sigma of 0.02
 C89-C81 \\sim C81-C93
 with sigma of 0.02
 O28-C79 \\sim O28-C40
 with sigma of 0.02
 C41-C79 \\sim C80-C40
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
C121 \\sim C111: within 2A with sigma of 0.002 and sigma for terminal atoms of
0.004
C90 \\sim C91 \\sim C92 \\sim C93 \\sim C88 \\sim C89 \\sim C49 \\sim C50 \\sim
C51 \\sim C52 \\sim C53 \\sim C54: within 2A with sigma of 0.04 and sigma for
terminal atoms of 0.08
O28 \\sim O7 \\sim O27 \\sim O8: within 2A with sigma of 0.002 and sigma for
terminal atoms of 0.004
C102 \\sim C74 \\sim C100 \\sim C72 \\sim C101 \\sim C73: within 2A with sigma
of 0.002 and sigma for terminal atoms of 0.004
C43 \\sim C94: within 2A with sigma of 0.002 and sigma for terminal atoms of
0.004
C81 \\sim C42: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
Uanis(O27) \\sim Ueq, Uanis(O8) \\sim Ueq, Uanis(O28) \\sim Ueq, Uanis(O7)
\\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
4. Rigid body (RIGU) restrains
 O12, O10, C113, C112, C122, C114, C111, C121, O11, O17, O26, C115, C123, C110,
  C120, C116, C124, C109, C119, O16, C117, C108, C118, C107, O13, O15, C103,
 C106, C104, C105, O14
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 Cl8, C44, C43, C47, C45, C48, C46, C94, C95, C96, C97, C98, C99, Cl10
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C90, C91, C92, C93, C89, C49, C50, C51, C52, C53, C54, Cl7, Cl11, C88
 with sigma for 1-2 distances of 0.0002 and sigma for 1-3 distances of 0.0002
 C134, O21, C132, C133, C131, O22, O20, C143, C130, C144, C129, O23, O19, C137,
  C128, C127, C138, O18, O24, C126, C139, C125, C140, O25
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C136, O21, C132, C133, C131, C134, O22, O29, O20, C143, C135, C130, C144,
 C129, O23, O19, C137, C128, C138, C127, O18, O24, C126, C139, C141, C125, C140,
  C142, O25
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O28, O27, C61, C40, O7, O8, C79
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C82, C81, C42, C55, C83, C87, C85, C86, C58, C59, C57, C84, C56, C41, C80,
 C79, C40, O28, O7, C61, C62, C63
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
5. Others
 Sof(Cl11)=Sof(O28)=Sof(O27)=Sof(C88)=Sof(C89)=Sof(H89)=Sof(C90)=Sof(H90)=
 Sof(C91)=Sof(C92)=Sof(H92)=Sof(C93)=Sof(H93)=Sof(C80)=Sof(H80A)=Sof(H80B)=
 Sof(C79)=Sof(H79A)=Sof(H79B)=Sof(C81)=Sof(C94)=Sof(C99)=Sof(H99)=Sof(C98)=
 Sof(H98)=Sof(C97)=Sof(C96)=Sof(H96)=Sof(C95)=Sof(H95)=Sof(Cl10)=Sof(C82)=
 Sof(C83)=Sof(H83)=Sof(C84)=Sof(H84)=Sof(C85)=Sof(C86)=Sof(H86)=Sof(C87)=
 Sof(H87)=Sof(Cl9)=1-FVAR(1)
 Sof(Cl8)=Sof(Cl6)=Sof(C55)=Sof(C42)=Sof(C56)=Sof(H56)=Sof(C60)=Sof(H60)=
 Sof(C43)=Sof(C48)=Sof(H48)=Sof(C47)=Sof(H47)=Sof(C46)=Sof(C45)=Sof(H45)=
 Sof(C44)=Sof(H44)=Sof(C57)=Sof(H57)=Sof(C40)=Sof(H40A)=Sof(H40B)=Sof(C58)=
 Sof(C59)=Sof(H59)=Sof(C41)=Sof(H41A)=Sof(H41B)=Sof(C49)=Sof(C50)=Sof(H50)=
 Sof(C51)=Sof(H51)=Sof(C52)=Sof(C53)=Sof(H53)=Sof(C54)=Sof(H54)=Sof(Cl7)=
 Sof(O7)=Sof(O8)=FVAR(1)
 Sof(C102)=Sof(H10A)=Sof(H10B)=Sof(H10C)=Sof(C101)=Sof(H10D)=Sof(H10E)=
 Sof(H10F)=Sof(C100)=Sof(H10G)=Sof(H10H)=Sof(H10I)=1-FVAR(2)
 Sof(C72)=Sof(H72A)=Sof(H72B)=Sof(H72C)=Sof(C73)=Sof(H73A)=Sof(H73B)=Sof(H73C)=
 Sof(C74)=Sof(H74A)=Sof(H74B)=Sof(H74C)=FVAR(2)
 Sof(C124)=Sof(H12A)=Sof(H12B)=Sof(C123)=Sof(H12C)=Sof(H12D)=1-FVAR(3)
 Sof(C116)=Sof(H11M)=Sof(H11N)=Sof(C115)=Sof(H11Q)=Sof(H11R)=FVAR(3)
 Sof(C122)=Sof(H12E)=Sof(H12F)=Sof(C121)=Sof(H12G)=Sof(H12H)=Sof(O26)=
 Sof(C120)=Sof(H12I)=Sof(H12J)=Sof(C119)=Sof(H11S)=Sof(H11T)=1-FVAR(4)
 Sof(O17)=Sof(C109)=Sof(H10N)=Sof(H10O)=Sof(C110)=Sof(H11I)=Sof(H11J)=
 Sof(C112)=Sof(H11K)=Sof(H11L)=Sof(C111)=Sof(H11O)=Sof(H11P)=FVAR(4)
 Sof(C142)=Sof(H14G)=Sof(H14H)=Sof(C141)=Sof(H14I)=Sof(H14J)=1-FVAR(5)
 Sof(C139)=Sof(H13Q)=Sof(H13R)=Sof(C140)=Sof(H14E)=Sof(H14F)=FVAR(5)
 Sof(C136)=Sof(H13S)=Sof(H13T)=1-FVAR(6)
 Sof(C144)=Sof(H14C)=Sof(H14D)=FVAR(6)
 Sof(H13I)=Sof(H13J)=Sof(C135)=Sof(H13U)=Sof(H13V)=Sof(O29)=1-FVAR(7)
 Sof(O22)=Sof(C143)=Sof(H14A)=Sof(H14B)=Sof(H13G)=Sof(H13H)=FVAR(7)
6.a Free rotating group:
 O2(H2E,H2F), O1(H1E,H1F)
6.b Secondary CH2 refined with riding coordinates:
 N1(H1A,H1B), N2(H2A,H2B), C24(H24A,H24B), C23(H23A,H23B), C1(H1C,H1D),
 C25(H25A,H25B), C2(H2C,H2D), C63(H63A,H63B), C64(H64A,H64B), C62(H62A,H62B),
 C114(H11A,H11B), C132(H13A,H13B), C113(H11C,H11D), C126(H12K,H12L), C117(H11E,
 H11F), C108(H10J,H10K), C130(H13C,H13D), C106(H10L,H10M), C118(H11G,H11H),
 C125(H12M,H12N), C109(H10N,H10O), C129(H12O,H12P), C138(H13E,H13F), C143(H14A,
 H14B), C134(H13G,H13H), C134(H13I,H13J), C133(H13K,H13L), C105(H10P,H10Q),
 C128(H12Q,H12R), C137(H13M,H13N), C131(H13O,H13P), C104(H10R,H10S), C40(H40A,
 H40B), C107(H10T,H10U), C127(H12S,H12T), C110(H11I,H11J), C112(H11K,H11L),
 C80(H80A,H80B), C103(H10V,H10W), C144(H14C,H14D), C116(H11M,H11N), C139(H13Q,
 H13R), C140(H14E,H14F), C111(H11O,H11P), C115(H11Q,H11R), C79(H79A,H79B),
 C41(H41A,H41B), C124(H12A,H12B), C123(H12C,H12D), C122(H12E,H12F), C121(H12G,
 H12H), C120(H12I,H12J), C119(H11S,H11T), C142(H14G,H14H), C141(H14I,H14J),
 C136(H13S,H13T), C135(H13U,H13V)
6.c Me refined with riding coordinates:
 C38(H38A,H38B,H38C), C37(H37A,H37B,H37C), C39(H39A,H39B,H39C), C35(H35A,H35B,
 H35C), C34(H34A,H34B,H34C), C33(H33A,H33B,H33C), C78(H78A,H78B,H78C), C76(H76A,
 H76B,H76C), C77(H77A,H77B,H77C), C72(H72A,H72B,H72C), C73(H73A,H73B,H73C),
 C74(H74A,H74B,H74C), C102(H10A,H10B,H10C), C101(H10D,H10E,H10F), C100(H10G,
 H10H,H10I)
6.d Aromatic/amide H refined with riding coordinates:
 C27(H27), C70(H70), C20(H20), C21(H21), C15(H15), C31(H31), C29(H29),
 C17(H17), C5(H5), C14(H14), C66(H66), C18(H18), C9(H9), C89(H89), C90(H90),
 C92(H92), C93(H93), C6(H6), C8(H8), C11(H11), C68(H68), C12(H12), C56(H56),
 C60(H60), C48(H48), C47(H47), C45(H45), C44(H44), C57(H57), C59(H59), C99(H99),
  C98(H98), C96(H96), C95(H95), C83(H83), C84(H84), C86(H86), C87(H87),
 C50(H50), C51(H51), C53(H53), C54(H54)
6.e Fitted hexagon refined as free rotating group:
 C88(C89,C90,C91,C92,C93), C43(C48,C47,C46,C45,C44), C94(C99,C98,C97,C96,C95),
 C82(C83,C84,C85,C86,C87), C49(C50,C51,C52,C53,C54)
;
_shelx_res_checksum              7535
_shelx_hkl_checksum              53207
_olex2_submission_special_instructions 'No special instructions were received'