XCage: A Tricyclic Octacationic Receptor for Perylene Diimide with Picomolar Affinity in Water.
Liu, Wenqi; Bobbala, Sharan; Stern, Charlotte L.; Hornick, Jessica; Liu, Yugang; Enciso, Alan Enrique; Scott, Evan A.; Stoddart, J. Fraser; Journal of the American Chemical Society  (2020) –; doi:10.1021/jacs.9b12982

data_4134127
_publ_section_title
;
 XCage: A Tricyclic Octacationic Receptor for Perylene Diimide with
 Picomolar Affinity in Water.
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_paper_doi               10.1021/jacs.9b12982
_journal_year                    2020
_chemical_absolute_configuration ad
_chemical_formula_moiety
'C96 H76 N8, C32 H28 N4 O4, 7(F6 P), 4(C2 H3 N), 2(H O)'
_chemical_formula_sum            'C136 H118 F42 N16 O6 P7'
_chemical_formula_weight         3087.25
_space_group_crystal_system      tetragonal
_space_group_IT_number           96
_space_group_name_Hall           'P 4nw 2abw'
_space_group_name_H-M_alt        'P 43 21 2'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2019-06-13
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   40.109(4)
_cell_length_b                   40.109(4)
_cell_length_c                   10.8259(13)
_cell_measurement_reflns_used    9940
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      53.390
_cell_measurement_theta_min      2.463
_cell_volume                     17416(3)
_computing_cell_refinement       'SAINT V8.34A (Bruker, 2017)'
_computing_data_collection       'APEX2 V2017.3 (Bruker, 2017)'
_computing_data_reduction        'SAINT V8.38A (?, 2016)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXD (Sheldrick, 2008)'
_diffrn_ambient_temperature      100.0
_diffrn_detector_area_resol_mean 8
_diffrn_measured_fraction_theta_full 0.968
_diffrn_measured_fraction_theta_max 0.968
_diffrn_measurement_device_type  'Bruker Kappa APEX CCD area detector'
_diffrn_measurement_method       '\w and \f scans'
_diffrn_radiation_monochromator  'MX optics'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0658
_diffrn_reflns_av_unetI/netI     0.0634
_diffrn_reflns_Laue_measured_fraction_full 0.968
_diffrn_reflns_Laue_measured_fraction_max 0.968
_diffrn_reflns_limit_h_max       39
_diffrn_reflns_limit_h_min       -28
_diffrn_reflns_limit_k_max       40
_diffrn_reflns_limit_k_min       -40
_diffrn_reflns_limit_l_max       10
_diffrn_reflns_limit_l_min       -11
_diffrn_reflns_number            37061
_diffrn_reflns_point_group_measured_fraction_full 0.950
_diffrn_reflns_point_group_measured_fraction_max 0.950
_diffrn_reflns_theta_full        54.261
_diffrn_reflns_theta_max         54.261
_diffrn_reflns_theta_min         1.558
_diffrn_source                   microsource
_exptl_absorpt_coefficient_mu    1.492
_exptl_absorpt_correction_T_max  0.7507
_exptl_absorpt_correction_T_min  0.6158
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2016/2 (Bruker,2016/2) was used for absorption correction. wR2(int) was 0.1224 before and 0.0582 after correction. The Ratio of minimum to maximum transmission is 0.8203. The \l/2 correction factor is Not present.'
_exptl_crystal_colour            pink
_exptl_crystal_colour_primary    pink
_exptl_crystal_density_diffrn    1.177
_exptl_crystal_description       needle
_exptl_crystal_F_000             6308
_exptl_crystal_recrystallization_method
'The material was recrystallised from --- by as supplied'
_exptl_crystal_size_max          0.74
_exptl_crystal_size_mid          0.067
_exptl_crystal_size_min          0.023
_refine_diff_density_max         0.823
_refine_diff_density_min         -0.448
_refine_diff_density_rms         0.104
_refine_ls_abs_structure_details
;
 Flack x determined using 2409 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.128(16)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.142
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1079
_refine_ls_number_reflns         10132
_refine_ls_number_restraints     1320
_refine_ls_restrained_S_all      1.146
_refine_ls_R_factor_all          0.1341
_refine_ls_R_factor_gt           0.1051
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2703
_refine_ls_wR_factor_ref         0.2963
_reflns_Friedel_coverage         0.745
_reflns_Friedel_fraction_full    0.926
_reflns_Friedel_fraction_max     0.926
_reflns_number_gt                7288
_reflns_number_total             10132
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja9b12982_si_003.cif
_cod_data_source_block           cx1582a
_cod_original_cell_volume        17416(4)
_cod_database_code               4134127
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   0.966
_shelx_estimated_absorpt_t_min   0.405
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All H(H) groups, All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 P4-F20 = P4-F24 = P4-F22 = P4-F23 = P4-F19 = P4-F21
 1.6 with sigma of 0.02
 C69-C68
 2.4 with sigma of 0.02
 O2S-H2S = O1S-H1S
 1 with sigma of 0.02
 C67_$1-C66 \\sim C67-C66 \\sim C63_$1-C62_$1 \\sim C63-C62
 with sigma of 0.01
 F7-F9 \\sim F7-F10 \\sim F7-F11 \\sim F7-F12 \\sim F8-F9 \\sim F8-F10 \\sim
F8-F11 \\sim F8-F12 \\sim F9-F10
 \\sim F9-F12 \\sim F10-F11 \\sim F11-F12
 with sigma of 0.02
 P2-F7 \\sim P2-F8 \\sim P2-F9 \\sim P2-F10 \\sim P2-F11 \\sim P2-F12
 with sigma of 0.01
 F7A-F9A \\sim F7A-F10A \\sim F7A-F11A \\sim F7A-F12A \\sim F8A-F9A \\sim
F8A-F10A \\sim F8A-F11A ~
 F8A-F12A \\sim F9A-F10A \\sim F9A-F12A \\sim F10A-F11A \\sim F11A-F12A
 with sigma of 0.02
 P2A-F7A \\sim P2A-F8A \\sim P2A-F9A \\sim P2A-F10A \\sim P2A-F11A \\sim
P2A-F12A
 with sigma of 0.01
 F19-F21 \\sim F19-F22 \\sim F19-F23 \\sim F19-F24 \\sim F20-F21 \\sim F20-F22
\\sim F20-F23 \\sim F20-F24
 \\sim F21-F22 \\sim F21-F24 \\sim F22-F23 \\sim F23-F24
 with sigma of 0.02
 P4-F19 \\sim P4-F20 \\sim P4-F21 \\sim P4-F22 \\sim P4-F23 \\sim P4-F24
 with sigma of 0.01
 N7-C66 \\sim N8_$1-C69_$1 \\sim N8_$1-C67_$1 \\sim N8_$1-C68_$1 \\sim N8-C68
\\sim N8-C67 \\sim N8-
 C69 \\sim N6-C63 \\sim N6-C63_$1 \\sim N5-C62 \\sim N5-C62_$1 \\sim N6-C64_$1
\\sim N6-C64
 with sigma of 0.01
3. Uiso/Uaniso restraints and constraints
Uanis(C69) \\sim Ueq, Uanis(N8) \\sim Ueq, Uanis(C68) \\sim Ueq, Uanis(N6)
\\sim Ueq, Uanis(C64) \\sim Ueq, Uanis(O2S) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
4. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
5. Others
 Sof(P2A)=Sof(F7A)=Sof(F8A)=Sof(F9A)=Sof(F10A)=Sof(F11A)=Sof(F12A)=1-FVAR(1)
 Sof(P2)=Sof(F7)=Sof(F8)=Sof(F9)=Sof(F10)=Sof(F11)=Sof(F12)=FVAR(1)
 Fixed Sof: N8(0.5) C62(0.5) H62A(0.5) H62B(0.5) C63(0.5) H63A(0.5) H63B(0.5)
 H66A(0.5) H66B(0.5) C67(0.5) H67A(0.5) H67B(0.5) C68(0.5) H68A(0.5) H68B(0.5)
 H68C(0.5) C69(0.5) H69A(0.5) H69B(0.5) H69C(0.5) P4(0.5) F19(0.5) F20(0.5)
 F21(0.5) F22(0.5) F23(0.5) F24(0.5) H2S(0.5) H1S(0.5) O1S(0.5) O2S(0.5)
6.a Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C18(H18A,H18B), C25(H25A,H25B), C42(H42A,H42B), C62(H62A,H62B),
 C63(H63A,H63B), C66(H66A,H66B), C67(H67A,H67B)
6.b Me refined with riding coordinates:
 C69(H69A,H69B,H69C)
6.c Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C5(H5), C6(H6), C8(H8), C10(H10), C12(H12), C14(H14),
 C15(H15), C16(H16), C17(H17), C20(H20), C21(H21), C23(H23), C24(H24), C26(H26),
  C27(H27), C29(H29), C30(H30), C32(H32), C34(H34), C36(H36), C38(H38),
 C39(H39), C40(H40), C41(H41), C44(H44), C45(H45), C47(H47), C48(H48), C50(H50),
  C51(H51), C56(H56), C57(H57)
6.d Idealised Me refined as rotating group:
 C64(H64A,H64B,H64C), C68(H68A,H68B,H68C), C2S(H2SA,H2SB,H2SC), C4S(H4SA,H4SB,
 H4SC)
;
_shelx_res_checksum              81039
_shelx_hkl_checksum              13654
_shelx_fab_checksum              57328
_olex2_date_sample_data_collection 2019-06-10
_olex2_date_sample_submission    2019-06-06
_olex2_diffrn_ambient_temperature_device 'Oxford Cryosystems'
_olex2_exptl_crystal_mounting_method
'The crystal was mounted on a MITIGEN holder'
_olex2_submission_original_sample_id cx1582a
_olex2_submission_special_instructions 'No special instructions were received'