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_1572628
_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
'3(I), C54 H66 N9 O6, 5.519(C2 H3 N), 1.39(H2 O), 0.994(O)'
_chemical_formula_sum            'C65.04 H85.33 I3 N14.52 O8.39'
_chemical_formula_weight         1585.36
_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
_audit_creation_date             2024-01-18
_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                90
_cell_angle_beta                 102.8042(7)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   14.8832(2)
_cell_length_b                   32.8405(5)
_cell_length_c                   15.3240(2)
_cell_measurement_reflns_used    9578
_cell_measurement_temperature    100.00
_cell_measurement_theta_max      78.81
_cell_measurement_theta_min      5.41
_cell_volume                     7303.69(18)
_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 0.998
_diffrn_measured_fraction_theta_max 0.982
_diffrn_measurement_device       'three-circle diffractometer'
_diffrn_measurement_device_type  'Bruker D8 Venture Photon III'
_diffrn_measurement_method       'omega scans'
_diffrn_radiation_monochromator  mirrors
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0518
_diffrn_reflns_av_unetI/netI     0.0296
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.982
_diffrn_reflns_limit_h_max       18
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       41
_diffrn_reflns_limit_k_min       -40
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            156372
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.982
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         79.261
_diffrn_reflns_theta_min         2.691
_diffrn_source                   'Microfocus sealed X-ray tube'
_diffrn_source_current           1.1
_diffrn_source_power             0.05500000000000001
_diffrn_source_type              'Incoatec ImuS'
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    10.573
_exptl_absorpt_correction_T_max  0.3292
_exptl_absorpt_correction_T_min  0.1725
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.1253 before and 0.0812 after correction.
The Ratio of minimum to maximum transmission is 0.5240.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.442
_exptl_crystal_description       plate
_exptl_crystal_F_000             3213
_exptl_crystal_size_max          0.09
_exptl_crystal_size_mid          0.04
_exptl_crystal_size_min          0.02
_refine_diff_density_max         1.765
_refine_diff_density_min         -1.273
_refine_diff_density_rms         0.091
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.039
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     963
_refine_ls_number_reflns         15540
_refine_ls_number_restraints     197
_refine_ls_restrained_S_all      1.036
_refine_ls_R_factor_all          0.0367
_refine_ls_R_factor_gt           0.0355
_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^)+(0.0559P)^2^+10.7768P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1003
_refine_ls_wR_factor_ref         0.1012
_reflns_Friedel_coverage         0.000
_reflns_number_gt                14802
_reflns_number_total             15540
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc05236f2.cif
_cod_data_source_block           cu_vl_cx_2098pf6_teai_1_acn_et2o
_cod_depositor_comments
'Adding full bibliography for 1572625--1572628.cif.'
_cod_database_code               1572628
_shelx_shelxl_version_number     2019/1
_shelx_estimated_absorpt_t_max   0.816
_shelx_estimated_absorpt_t_min   0.450
_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,H) groups
2. Restrained distances
 O31D_$1-H52B
 1.9 with sigma of 0.02
 H52A-I3_$2
 2.6 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
C42N \\sim C43N \\sim N41N \\sim C42H \\sim N41H \\sim C43H: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
C42J \\sim N41J \\sim C43J \\sim C43I \\sim N41I \\sim C42I: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
4. Rigid body (RIGU) restrains
 N41K, C42K, C43K, N41L, C42L, C43L, C43M, N41M, C42M, C43J, N41J, C42J, C43I,
 N41I, C42I, C43N, C42N, N41N, C42H, N41H, C43H
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(N41J)=Sof(C42J)=Sof(C43J)=Sof(H43M)=Sof(H43N)=Sof(H43O)=1-FVAR(1)
 Sof(N41I)=Sof(C42I)=Sof(C43I)=Sof(H43J)=Sof(H43K)=Sof(H43L)=FVAR(1)
 Sof(N41L)=Sof(C42L)=Sof(C43L)=Sof(H43S)=Sof(H43T)=Sof(H43U)=Sof(O53)=Sof(O55)=
 1-FVAR(2)
 Sof(N41K)=Sof(C42K)=Sof(C43K)=Sof(H43P)=Sof(H43Q)=Sof(H43R)=FVAR(2)
 Sof(C42N)=Sof(C43N)=Sof(H43Y)=Sof(H)=Sof(HA)=Sof(N41N)=1-FVAR(3)
 Sof(N41H)=Sof(C42H)=Sof(C43H)=Sof(H43G)=Sof(H43H)=Sof(H43I)=FVAR(3)
 Sof(N41M)=Sof(C42M)=Sof(C43M)=Sof(H43V)=Sof(H43W)=Sof(H43X)=FVAR(4)
 Sof(O52)=Sof(H52A)=Sof(H52B)=FVAR(5)
6.a Secondary CH2 refined with riding coordinates:
 C7A(H7AA,H7AB), C9A(H9AA,H9AB), C11A(H11A,H11B), C13A(H13A,H13B), C15A(H15A,
 H15B), C17A(H17A,H17B), C7B(H7BA,H7BB), C9B(H9BA,H9BB), C11B(H11C,H11D),
 C13B(H13C,H13D), C15B(H15C,H15D), C17B(H17C,H17D)
6.b Aromatic/amide H refined with riding coordinates:
 N8A(H8A), N10A(H10A), N12A(H12A), N8B(H8B), N10B(H10B), N12B(H12B),
 C23C(H23C), C25C(H25C), C27C(H27C), C23D(H23D), C25D(H25D), C27D(H27D),
 C23E(H23E), C25E(H25E), C27E(H27E)
6.c Idealised Me refined as rotating group:
 C14A(H14A,H14B,H14C), C16A(H16A,H16B,H16C), C18A(H18A,H18B,H18C), C14B(H14D,
 H14E,H14F), C16B(H16D,H16E,H16F), C18B(H18D,H18E,H18F), C21C(H21A,H21B,H21C),
 C21D(H21D,H21E,H21F), C21E(H21G,H21H,H21I), C43F(H43A,H43B,H43C), C43G(H43D,
 H43E,H43F), C43H(H43G,H43H,H43I), C43I(H43J,H43K,H43L), C43J(H43M,H43N,H43O),
 C43K(H43P,H43Q,H43R), C43L(H43S,H43T,H43U), C43M(H43V,H43W,H43X), C43N(H43Y,H,
 HA)
;
_shelx_res_checksum              27540
_shelx_hkl_checksum              56802
_olex2_submission_special_instructions 'No special instructions were received'