Halogenated <i>N</i>-phenylpiperazine and 2-(piperazin-1-yl)pyrimidine as novel cucurbit[7]uril guests: experimental and computational insights into supramolecular binding.
Rincón, David A; Zaorska, Ewelina; Malinska, Maura; RSC advances 15 (2025) 45555–45572; doi:10.1039/d5ra07259j

data_7251315
_publ_section_title
;
 Halogenated <i>N</i>-phenylpiperazine and 2-(piperazin-1-yl)pyrimidine as
 novel cucurbit[7]uril guests: experimental and computational insights
 into supramolecular binding.
;
_journal_issue                   53
_journal_name_full               'RSC advances'
_journal_page_first              45555
_journal_page_last               45572
_journal_paper_doi               10.1039/d5ra07259j
_journal_volume                  15
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety
'C42 H42 N28 O14, 2(H2 O), C10 H15 N2, O, 19[H2O]'
_chemical_formula_sum            'C52 H99 N30 O36'
_chemical_formula_weight         1720.61
_space_group_crystal_system      tetragonal
_space_group_IT_number           79
_space_group_name_Hall           'I 4'
_space_group_name_H-M_alt        'I 4'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2025-11-04
_audit_creation_method
;
Olex2 1.5
(compiled 2025.07.13 svn.rb7424aed for OlexSys, GUI svn.r7314)
;
_audit_update_record
;
2025-11-05 deposited with the CCDC.	2025-11-14 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   28.306(4)
_cell_length_b                   28.306(4)
_cell_length_c                   18.617(4)
_cell_measurement_reflns_used    13714
_cell_measurement_temperature    100
_cell_measurement_theta_max      20
_cell_measurement_theta_min      2
_cell_volume                     14916(4)
_computing_cell_refinement       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.84a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/2 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 1.000
_diffrn_measurement_device_type  synchrotron
_diffrn_radiation_type           synchrotron
_diffrn_radiation_wavelength     0.500
_diffrn_reflns_av_R_equivalents  0.0559
_diffrn_reflns_av_unetI/netI     0.0239
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       36
_diffrn_reflns_limit_h_min       -36
_diffrn_reflns_limit_k_max       36
_diffrn_reflns_limit_k_min       -36
_diffrn_reflns_limit_l_max       24
_diffrn_reflns_limit_l_min       -24
_diffrn_reflns_number            262240
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        17.458
_diffrn_reflns_theta_max         18.945
_diffrn_reflns_theta_min         0.716
_diffrn_source                   synchrotron
_exptl_absorpt_coefficient_mu    0.063
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.532
_exptl_crystal_description       needle
_exptl_crystal_F_000             7272
_exptl_crystal_size_max          0.05
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.613
_refine_diff_density_min         -0.772
_refine_diff_density_rms         0.073
_refine_ls_abs_structure_details
;
 Flack x determined using 5786 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.5(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.089
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     938
_refine_ls_number_reflns         17128
_refine_ls_number_restraints     140
_refine_ls_restrained_S_all      1.102
_refine_ls_R_factor_all          0.0758
_refine_ls_R_factor_gt           0.0671
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1510P)^2^+2.6259P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2083
_refine_ls_wR_factor_ref         0.2229
_reflns_Friedel_coverage         0.940
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     1.000
_reflns_number_gt                13710
_reflns_number_total             17128
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra07259j2.cif
_cod_data_source_block           1
_cod_original_cell_volume        14916(5)
_cod_database_code               7251315
_shelx_shelxl_version_number     2019/2
_shelx_estimated_absorpt_t_max   0.999
_shelx_estimated_absorpt_t_min   0.997
_diffrn_oxdiff_ac3_digest_hkl    0186924a6347c0937a416943ca1404d98ef3ee
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H,H) groups
 At 1.5 times of:
  All O(H,H) groups
2. Restrained distances
 C45B-C46B
 1.54 with sigma of 0.02
 C44B-C43B
 1.54 with sigma of 0.02
 H3WB-O5
 3 with sigma of 0.04
 O6-H3WA = H3WB-O5
 3 with sigma of 0.04
 C47-N30A \\sim C47-N30B
 with sigma of 0.02
 C47-C44A \\sim C47-C45B
 with sigma of 0.04
 C47-C45A \\sim C47-C44B
 with sigma of 0.04
 C44A-N29A \\sim C45B-N29B
 with sigma of 0.04
 C45A-N29A \\sim C44B-N29B
 with sigma of 0.04
 N30A-C44A \\sim N30B-C45B
 with sigma of 0.02
 N30A-C45A \\sim N30B-C44B
 with sigma of 0.02
 C44A-C43A \\sim C45B-C46B
 with sigma of 0.02
 C45A-C46A \\sim C44B-C43B
 with sigma of 0.02
 N29B-C43B \\sim N29B-C46B \\sim N29A-C43A \\sim N29A-C46A
 with sigma of 0.01
 N30A-C43A \\sim N30B-C46B
 with sigma of 0.04
 N30A-C46A \\sim N30B-C43B
 with sigma of 0.04
 C44A-C45A \\sim C45B-C44B
 with sigma of 0.04
 C43A-C46A \\sim C46B-C43B
 with sigma of 0.04
3. Restrained angles
 C44B-C43B-N29B
 fixed at 110 with sigma of 0.02
 C43B-N29B-C46B
 fixed at 110 with sigma of 0.02
4. Rigid bond restraints
 C43A, N29A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 N29B, C46B, C43B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C43A, N29A, C46A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 N30A, C44B, C44A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
C43A \\sim N29A: within 1.7A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 1.7A
C43A \\sim N29A \\sim C46A: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08 within 1.7A
C43B \\sim N29B \\sim C46B: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08 within 1.7A
N30A \\sim C44B \\sim C44A: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08 within 1.7A
Uanis(C45A) = Uanis(C45B)
Uanis(C44A) = Uanis(C44B)
6. Rigid body (RIGU) restrains
 N1, C1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N11, C16
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C47, C52
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C50, C51
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N14, C19
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N13, C23
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N15, C24
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C2, C3
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N10, C11
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N7, C10
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N19, C30
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C21, C20
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
7. Others
 Sof(N30B)=Sof(C44B)=Sof(H44C)=Sof(H44D)=Sof(C46B)=Sof(H46C)=Sof(H46D)=
 Sof(N29B)=Sof(H29E)=Sof(H29F)=Sof(C45B)=Sof(H45C)=Sof(H45D)=Sof(C43B)=
 Sof(H43C)=Sof(H43D)=Sof(O1W)=1-FVAR(1)
 Sof(N30A)=Sof(C44A)=Sof(H44A)=Sof(H44B)=Sof(C45A)=Sof(H45A)=Sof(H45B)=
 Sof(C43A)=Sof(H43A)=Sof(H43B)=Sof(N29A)=Sof(H29C)=Sof(H29D)=Sof(C46A)=
 Sof(H46A)=Sof(H46B)=Sof(O15)=FVAR(1)
8.a Free rotating group:
 O2W(H2WA,H2WB), O3W(H3WA,H3WB)
8.b Ternary CH refined with riding coordinates:
 C2(H2), C14(H14), C8(H8), C38(H38), C21(H21), C20(H20), C32(H32), C15(H15),
 C27(H27), C3(H3), C26(H26), C39(H39), C9(H9), C33(H33)
8.c Secondary CH2 refined with riding coordinates:
 C42(H42A,H42B), C17(H17A,H17B), C30(H30A,H30B), C41(H41A,H41B), C36(H36A,
 H36B), C24(H24A,H24B), C35(H35A,H35B), C5(H5A,H5B), C6(H6A,H6B), C12(H12A,
 H12B), C23(H23A,H23B), C18(H18A,H18B), C11(H11A,H11B), C29(H29A,H29B),
 C44A(H44A,H44B), C45A(H45A,H45B), C43A(H43A,H43B), N29A(H29C,H29D), C46A(H46A,
 H46B), C44B(H44C,H44D), C46B(H46C,H46D), N29B(H29E,H29F), C45B(H45C,H45D),
 C43B(H43C,H43D)
8.d Aromatic/amide H refined with riding coordinates:
 C52(H52), C51(H51), C50(H50), C49(H49), C48(H48)
8.e Fitted hexagon refined as free rotating group:
 C47(C52,C51,C50,C49,C48)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              59386
_shelx_fab_checksum              74909
_olex2_submission_special_instructions 'No special instructions were received'