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_7251318
_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
'C10 H13 Cl F N2, 1.5(C42 H42 N28 O14), 53[H2O]'
_chemical_formula_sum            'C73 H182 Cl F N44 O74'
_chemical_formula_weight         2915.07
_space_group_crystal_system      orthorhombic
_space_group_IT_number           20
_space_group_name_Hall           'C 2c 2'
_space_group_name_H-M_alt        'C 2 2 21'
_atom_sites_solution_hydrogens   geom
_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                   32.4607(6)
_cell_length_b                   39.2830(8)
_cell_length_c                   20.2199(3)
_cell_measurement_reflns_used    37070
_cell_measurement_temperature    100.01(10)
_cell_measurement_theta_max      62.1070
_cell_measurement_theta_min      2.8080
_cell_volume                     25783.5(8)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_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    'SHELXD  (Sheldrick, 2008)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.01(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2195
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.991
_diffrn_measured_fraction_theta_max 0.991
_diffrn_measurement_details
;
List of Runs (angles in degrees, time in seconds):

  # Type    Start    End  Width  t~exp~   \w     \q     \k     \f   Frames
  1  \w    -86.00 -34.00   1.00   10.44    --    0.00 178.00 -30.00   52
  2  \w    -22.00  73.00   1.00   10.44    --    0.00  37.00-120.00   95
  3  \w     94.00 154.00   1.00   41.75    --   82.51 125.00-150.00   60
  4  \w     12.00 110.00   1.00   41.75    --   82.51 -61.00  30.00   98
  5  \w     59.00 157.00   1.00   41.75    --   82.51  30.00 -30.00   98
  6  \w     94.00 154.00   1.00   41.75    --   82.51 125.00-120.00   60
  7  \w     11.00 107.00   1.00   41.75    --   82.51 -45.00  60.00   96
  8  \w      8.00 106.00   1.00   41.75    --   82.51 -30.00 150.00   98
  9  \w    -27.00  70.00   1.00   10.44    --    0.00  57.00 -60.00   97
 10  \w    -86.00 -34.00   1.00   10.44    --    0.00 178.00  30.00   52
 11  \w     55.00 153.00   1.00   41.75    --   82.51  61.00 150.00   98
 12  \w     58.00 154.00   1.00   41.75    --   82.51  45.00-120.00   96
 13  \w     58.00 154.00   1.00   41.75    --   82.51  45.00  90.00   96
 14  \w     51.00  84.00   1.00   41.75    --   82.51  77.00   0.00   33
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0113911000
_diffrn_orient_matrix_UB_12      0.0376579000
_diffrn_orient_matrix_UB_13      -0.0112021000
_diffrn_orient_matrix_UB_21      -0.0431482000
_diffrn_orient_matrix_UB_22      -0.0065211000
_diffrn_orient_matrix_UB_23      0.0289776000
_diffrn_orient_matrix_UB_31      0.0161417000
_diffrn_orient_matrix_UB_32      0.0087606000
_diffrn_orient_matrix_UB_33      0.0695863000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0749
_diffrn_reflns_av_unetI/netI     0.0427
_diffrn_reflns_Laue_measured_fraction_full 0.991
_diffrn_reflns_Laue_measured_fraction_max 0.991
_diffrn_reflns_limit_h_max       37
_diffrn_reflns_limit_h_min       -37
_diffrn_reflns_limit_k_max       44
_diffrn_reflns_limit_k_min       -44
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            88456
_diffrn_reflns_point_group_measured_fraction_full 0.985
_diffrn_reflns_point_group_measured_fraction_max 0.985
_diffrn_reflns_theta_full        62.637
_diffrn_reflns_theta_max         62.637
_diffrn_reflns_theta_min         2.249
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.351
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.80147
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46 (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.502
_exptl_crystal_description       block
_exptl_crystal_F_000             12368
_exptl_crystal_size_max          0.4
_exptl_crystal_size_mid          0.25
_exptl_crystal_size_min          0.23
_refine_diff_density_max         0.335
_refine_diff_density_min         -0.234
_refine_diff_density_rms         0.047
_refine_ls_abs_structure_details
;
 Flack x determined using 6551 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.12(3)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.046
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1283
_refine_ls_number_reflns         20353
_refine_ls_number_restraints     173
_refine_ls_restrained_S_all      1.058
_refine_ls_R_factor_all          0.0725
_refine_ls_R_factor_gt           0.0645
_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^)+(0.1403P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1878
_refine_ls_wR_factor_ref         0.1994
_reflns_Friedel_coverage         0.861
_reflns_Friedel_fraction_full    0.978
_reflns_Friedel_fraction_max     0.978
_reflns_number_gt                17074
_reflns_number_total             20353
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra07259j2.cif
_cod_data_source_block           3
_cod_database_code               7251318
_shelx_shelxl_version_number     2019/2
_chemical_oxdiff_formula         'C40 H40 N40 O20 Cl4 F4'
_chemical_oxdiff_usercomment     '100K, colourless prism'
_shelx_estimated_absorpt_t_max   0.746
_shelx_estimated_absorpt_t_min   0.614
_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
2. Restrained distances
 N25-C38
 1.45 with sigma of 0.01
 C44A-N30A
 1.54 with sigma of 0.02
 N30A-C46
 1.54 with sigma of 0.02
 N30A-C46A
 1.54 with sigma of 0.02
 N30A-C44
 1.54 with sigma of 0.02
 N14-C18
 1.45 with sigma of 0.02
 C44A-N29A
 2.34 with sigma of 0.04
 C46A-N29A
 2.34 with sigma of 0.04
 N26-C38 \\sim C38-N25
 with sigma of 0.02
 N2-C42 \\sim C42-N28
 with sigma of 0.02
 C44A-C43A \\sim C44-C45
 with sigma of 0.02
 C44A-C46A \\sim C44-C46
 with sigma of 0.02
 C43A-N29A \\sim C45-N29
 with sigma of 0.02
 N29A-C45A \\sim N29-C43
 with sigma of 0.02
 C45A-C46A \\sim C43-C46
 with sigma of 0.02
 N30A-C44A \\sim N30A-C44
 with sigma of 0.04
 N30A-C43A \\sim N30A-C45
 with sigma of 0.04
 N30A-C45A \\sim N30A-C43
 with sigma of 0.04
 N30A-C46A \\sim N30A-C46
 with sigma of 0.04
 C44A-N29A \\sim C44-N29
 with sigma of 0.04
 C44A-C45A \\sim C44-C43
 with sigma of 0.04
 C43A-C45A \\sim C45-C43
 with sigma of 0.04
 C43A-C46A \\sim C45-C46
 with sigma of 0.04
 N29A-C46A \\sim N29-C46
 with sigma of 0.04
 N14-C18 \\sim C18-N12
 with sigma of 0.02
 N17-C23 \\sim C23-N15
 with sigma of 0.02
 N19-C27 \\sim C27-N20
 with sigma of 0.02
3. Rigid bond restraints
 Cl1, C50
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.001
 N29A, C45A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C43A, C44A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C44A, N30A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C46, N30A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 N30A, C44A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 N29A, C43A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
Cl1 \\sim C50: within 1.7A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 1.7A
C46 \\sim N30A: within 1.7A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 1.7A
N30A \\sim C44A: within 1.7A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 1.7A
C43A \\sim N29A: within 1.7A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 1.7A
Uanis(C43A) = Uanis(C43)
Uanis(N29) = Uanis(N29A)
Uanis(C45) = Uanis(C44)
Uanis(C46A) = Uanis(C44)
5. Rigid body (RIGU) restrains
 N13A, C18A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N13A, C17A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N5A, C9A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N8A, C14A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 O10, C16
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N2, C42
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C22, O11
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N3, C5
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N4, C3
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N5, C7
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N6, C6
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N11, C15
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N13, C19
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N14, C22
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N17, C23
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N22, C30
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N27, C37
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C8, C9
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C33, C32
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 C38, C39
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N2A, C2A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N6A, C8A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N7A, C11A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N9A, C12A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N9A, C15A
 with sigma for 1-2 distances of 0.002 and sigma for 1-3 distances of 0.002
 N11A, C17A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N14A, C20A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C51, C52
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N30A, C46A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N10A, C12A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O6, C31
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C26, H15A, C27
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O1, C1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N12, C16
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N28, C40
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C34, N24
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N1A, C2A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C47, N30A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(N29)=Sof(H29E)=Sof(H29F)=Sof(C43)=Sof(H43C)=Sof(H43D)=Sof(C44)=Sof(H44C)=
 Sof(H44D)=Sof(C46)=Sof(H46C)=Sof(H46D)=Sof(C45)=Sof(H45C)=Sof(H45D)=1-FVAR(1)
 Sof(C44A)=Sof(H44A)=Sof(H44B)=Sof(C43A)=Sof(H43A)=Sof(H43B)=Sof(N29A)=
 Sof(H29C)=Sof(H29D)=Sof(C45A)=Sof(H45A)=Sof(H45B)=Sof(C46A)=Sof(H46A)=
 Sof(H46B)=FVAR(1)
7.a Ternary CH refined with riding coordinates:
 C8(H8), C7A(H7A), C9(H9), C39(H39), C33(H33), C6A(H6AA), C38(H38), C32(H32),
 C13A(H13A), C14(H14), C2(H2), C3(H3), C12A(H12C), C19A(H19A), C27(H27),
 C21(H21), C15(H15), C18A(H18C), C20(H20), C26(H26), C2A(H2A)
7.b Secondary CH2 refined with riding coordinates:
 C4A(H4AA,H4AB), C9A(H9AA,H9AB), C16A(H16A,H16B), C3A(H3AA,H3AB), C6(H6A,H6B),
 C36(H36A,H36B), C41(H41A,H41B), C29(H29A,H29B), C17(H17A,H17B), C10A(H10A,
 H10B), C5(H5A,H5B), C35(H35A,H35B), C24(H24A,H24B), C11(H11A,H11B), C12(H12A,
 H12B), C21A(H21A,H21B), C42(H42A,H42B), C18(H18A,H18B), C44A(H44A,H44B),
 C23(H23A,H23B), C43A(H43A,H43B), C15A(H15A,H15B), N29A(H29C,H29D), C45A(H45A,
 H45B), C46A(H46A,H46B), C30(H30A,H30B), N29(H29E,H29F), C43(H43C,H43D),
 C44(H44C,H44D), C46(H46C,H46D), C45(H45C,H45D)
7.c Aromatic/amide H refined with riding coordinates:
 C52(H52), C51(H51), C49(H49)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              69863
_shelx_fab_checksum              34534
_olex2_submission_special_instructions 'No special instructions were received'
_oxdiff_exptl_absorpt_empirical_details
;
Empirical correction (ABSPACK) includes:
- Absorption correction using spherical harmonics
- Frame scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.559
_oxdiff_exptl_absorpt_empirical_full_min 0.520