Charge-assisted hydrogen bonding in a bicyclic amide cage: an effective approach to anion recognition and catalysis in water.
Xu, Chengkai; Tran, Quy Gia; Liu, Dexin; Zhai, Canjia; Wojtas, Lukasz; Liu, Wenqi; Chemical science 15 (2024) 16040–16049; doi:10.1039/d4sc05236f

data_1572627
_publ_section_title
;
 Charge-assisted hydrogen bonding in a bicyclic amide cage: an effective
 approach to anion recognition and catalysis in water.
;
_journal_issue                   39
_journal_name_full               'Chemical science'
_journal_page_first              16040
_journal_page_last               16049
_journal_paper_doi               10.1039/d4sc05236f
_journal_volume                  15
_journal_year                    2024
_chemical_formula_moiety
'C54 H66 N9 O6, 4.103(C2 F3 O2), C2 H F3 O2, 1.5(O)'
_chemical_formula_sum            'C64.2 H67 F15.31 N9 O17.7'
_chemical_formula_weight         1538.84
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2024-01-31
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2024-02-21 deposited with the CCDC.	2024-09-10 downloaded from the CCDC.
;
_cell_angle_alpha                113.091(5)
_cell_angle_beta                 99.699(5)
_cell_angle_gamma                92.773(5)
_cell_formula_units_Z            4
_cell_length_a                   13.0460(10)
_cell_length_b                   25.708(2)
_cell_length_c                   27.482(2)
_cell_measurement_reflns_used    9921
_cell_measurement_temperature    100.00
_cell_measurement_theta_max      36.27
_cell_measurement_theta_min      3.08
_cell_volume                     8290.6(12)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL  (Sheldrick, 2008)'
_diffrn_ambient_temperature      100.00
_diffrn_detector                 'Bruker PHOTON III CPAD area detector'
_diffrn_detector_type            'CPAD area detector'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_diffrn_measurement_device       'Kappa stage four-circle diffractometer'
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  mirrors
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.1251
_diffrn_reflns_av_unetI/netI     0.0891
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       19
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            54411
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        35.732
_diffrn_reflns_theta_max         35.732
_diffrn_reflns_theta_min         3.078
_diffrn_source                   'Microfocus sealed X-ray tube'
_diffrn_source_current           1.1
_diffrn_source_power             0.05500000000000001
_diffrn_source_type              'Incoatec ImuS 3.0,HELIOS EF Cu optic (ELM70)'
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.983
_exptl_absorpt_correction_T_max  0.7472
_exptl_absorpt_correction_T_min  0.4929
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1458 before and 0.1099 after correction.
The Ratio of minimum to maximum transmission is 0.6597.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.233
_exptl_crystal_description       needle
_exptl_crystal_F_000             3179
_refine_diff_density_max         0.687
_refine_diff_density_min         -0.371
_refine_diff_density_rms         0.077
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.367
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2051
_refine_ls_number_reflns         7551
_refine_ls_number_restraints     3397
_refine_ls_restrained_S_all      1.200
_refine_ls_R_factor_all          0.1366
_refine_ls_R_factor_gt           0.1091
_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          0.3060
_refine_ls_wR_factor_ref         0.3349
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5066
_reflns_number_total             7551
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc05236f2.cif
_cod_data_source_block           127_7
_cod_depositor_comments
'Adding full bibliography for 1572625--1572628.cif.'
_cod_original_cell_volume        8290.6(11)
_cod_original_formula_sum        'C64.20 H67 F15.31 N9 O17.70'
_cod_database_code               1572627
_shelx_shelxl_version_number     2019/1
_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
 O2_20-O2_21
 -2.6 with sigma of 0.02
 O2_21-H23A_1$1
 -2.6 with sigma of 0.02
 C44A_1-C43A_1 = C45A_1-C44A_1 = C46A_1-C45A_1 = C47A_1-C46A_1 = C48A_1-C47A_1
 = C48A_1-C43A_1 = C64A_1-C63A_1 = C65A_1-C64A_1 = C66A_1-C65A_1 = C67A_1-
 C66A_1 = C68A_1-C67A_1 = C68A_1-C63A_1 = C48B_2-C43B_2 = C44B_2-C43B_2 =
 C45B_2-C44B_2 = C46B_2-C45B_2 = C47B_2-C46B_2 = C48B_2-C47B_2 = C64B_2-C63B_2 =
  C65B_2-C64B_2 = C66B_2-C65B_2 = C67B_2-C66B_2 = C68B_2-C67B_2 = C68B_2-C63B_2
 = C4A_1-C3A_1 = C5A_1-C4A_1 = C6A_1-C5A_1 = C7A_1-C6A_1 = C14A_1-C13A_1 =
 C15A_1-C14A_1 = C16A_1-C15A_1 = C17A_1-C16A_1 = C24A_1-C23A_1 = C25A_1-C24A_1 =
  C26A_1-C25A_1 = C27A_1-C26A_1 = C4B_2-C3B_2 = C5B_2-C4B_2 = C6B_2-C5B_2 =
 C7B_2-C6B_2 = C14B_2-C13B_2 = C15B_2-C14B_2 = C16B_2-C15B_2 = C17B_2-C16B_2 =
 C24B_2-C23B_2 = C25B_2-C24B_2 = C26B_2-C25B_2 = C27B_2-C26B_2
 1.39 with sigma of 0.02
 C8A_1-C4A_1 \\sim C6A_1-C10A_1 \\sim C20A_1-C16A_1 \\sim C18A_1-C14A_1 \\sim
C28A_1-C24A_1 ~
 C30A_1-C26A_1 \\sim C8B_2-C4B_2 \\sim C6B_2-C10B_2 \\sim C18B_2-C14B_2 \\sim
C20B_2-C16B_2 ~
 C28B_2-C24B_2 \\sim C30B_2-C26B_2
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 2A
4. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(O1)=Sof(O2)=Sof(C3)=Sof(C4)=Sof(F5)=Sof(F6)=Sof(F7)=Sof(O1)=Sof(O2)=
 Sof(C3)=Sof(C4)=Sof(F5)=Sof(F6)=Sof(F7)=FVAR(1)
 Sof(O1)=Sof(O2)=Sof(C3)=Sof(C4)=Sof(F5)=Sof(F6)=Sof(F7)=FVAR(2)
 Sof(O1)=Sof(O2)=Sof(C3)=Sof(C4)=Sof(F5)=Sof(F6)=Sof(F7)=FVAR(3)
 Fixed Sof: F5(0.5) F5(0.5) F6(0.5) F6(0.5) F7(0.5) F7(0.5) F5(0.5) F5(0.5)
 F6(0.5) F6(0.5) F7(0.5) F7(0.5) O1(0.5) O2(0.5) C3(0.5) C4(0.5) F5(0.25)
 F5(0.25) F6(0.25) F6(0.25) F7(0.25) F7(0.25)
6.a Secondary CH2 refined with riding coordinates:
 C32A(H32A,H32B), C34A(H34A,H34B), C36A(H36A,H36B), C37A(H37A,H37B), C39A(H39A,
 H39B), C41A(H41A,H41B), C52A(H52A,H52B), C54A(H54A,H54B), C56A(H56A,H56B),
 C57A(H57A,H57B), C59A(H59A,H59B), C61A(H61A,H61B), C32B(H32A,H32B), C34B(H34A,
 H34B), C36B(H36A,H36B), C37B(H37A,H37B), C39B(H39A,H39B), C41B(H41A,H41B),
 C52B(H52A,H52B), C54B(H54A,H54B), C56B(H56A,H56B), C57B(H57A,H57B), C59B(H59A,
 H59B), C61B(H61A,H61B)
6.b Aromatic/amide H refined with riding coordinates:
 C3A(H3A), C5A(H5A), C7A(H7A), C13A(H13A), C15A(H15A), C17A(H17A), C23A(H23A),
 C25A(H25A), C27A(H27A), N31A(H31A), N33A(H33A), N35A(H35A), N51A(H51A),
 N53A(H53A), N55A(H55A), C3B(H3B), C5B(H5B), C7B(H7B), C13B(H13B), C15B(H15B),
 C17B(H17B), C23B(H23B), C25B(H25B), C27B(H27B), N31B(H31B), N33B(H33B),
 N35B(H35B), N51B(H51B), N53B(H53B), N55B(H55B)
6.c Tetrahedral OH refined with riding coordinates:
 O2(H2), O2(H2)
6.d Idealised Me refined as rotating group:
 C1A(H1AA,H1AB,H1AC), C11A(H11A,H11B,H11C), C21A(H21A,H21B,H21C), C38A(H38A,
 H38B,H38C), C40A(H40A,H40B,H40C), C42A(H42A,H42B,H42C), C58A(H58A,H58B,H58C),
 C60A(H60A,H60B,H60C), C62A(H62A,H62B,H62C), C1B(H1BA,H1BB,H1BC), C11B(H11A,
 H11B,H11C), C21B(H21A,H21B,H21C), C38B(H38A,H38B,H38C), C40B(H40A,H40B,H40C),
 C42B(H42A,H42B,H42C), C58B(H58A,H58B,H58C), C60B(H60A,H60B,H60C), C62B(H62A,
 H62B,H62C)
;
_smtbx_masks_void_probe_radius   0.6
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              43742
_shelx_hkl_checksum              92143
_shelx_fab_checksum              80900
_olex2_submission_special_instructions 'No special instructions were received'