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_7251316
_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_formula_moiety
'2(Cl), C42 H42 N28 O14, C10 H13 F2 N2, 16[H2O]'
_chemical_formula_sum            'C52 H87 Cl2 F2 N30 O30'
_chemical_formula_weight         1721.41
_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   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                   28.61260(10)
_cell_length_b                   28.61260(10)
_cell_length_c                   18.3038(2)
_cell_measurement_reflns_used    75686
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      72.6680
_cell_measurement_theta_min      2.8100
_cell_volume                     14984.97(18)
_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_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 5.2195
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.996
_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    -88.00  -7.00   1.00    1.97    --  -41.28 126.00-137.00   81
  2  \w   -116.00 -17.00   1.00    1.97    --  -41.28 -38.00  60.00   99
  3  \w   -116.00 -17.00   1.00    1.97    --  -41.28 -38.00 150.00   99
  4  \w    -87.00  -6.00   1.00    1.97    --  -41.28 125.00 -60.00   81
  5  \w     28.00  98.00   1.00    1.97    --   41.28-126.00 146.00   70
  6  \w     78.00 177.00   1.00    7.87    --  103.66  45.00-180.00   99
  7  \w     31.00 133.00   1.00    7.87    --  103.66 -61.00  30.00  102
  8  \w     27.00 109.00   1.00    7.87    --  103.66-111.00  60.00   82
  9  \w     27.00 109.00   1.00    7.87    --  103.66-111.00 150.00   82
 10  \w    104.00 178.00   1.00    7.87    --  103.66 111.00 120.00   74
 11  \w     31.00 133.00   1.00    7.87    --  103.66 -61.00-120.00  102
 12  \w    103.00 178.00   1.00    7.87    --  103.66  77.00   0.00   75
 13  \w     37.00 127.00   1.00    7.87    --  103.66-144.00 -22.00   90
 14  \w     27.00 109.00   1.00    7.87    --  103.66-111.00   0.00   82
 15  \w     78.00 177.00   1.00    7.87    --  103.66  45.00  90.00   99
 16  \w     28.00 136.00   1.00    7.87    --  103.66 -77.00-180.00  108
 17  \w     16.00 178.00   1.00    7.87    --  103.66   0.00   0.00  162
 18  \w   -113.00 -13.00   1.00    1.97    --  -41.28 -57.00   0.00  100
 19  \w   -113.00 -13.00   1.00    1.97    --  -41.28 -57.00-180.00  100
 20  \w   -113.00 -13.00   1.00    1.97    --  -41.28 -57.00 -90.00  100
 21  \w   -114.00 -65.00   1.00    1.97    --  -41.28-144.00 -22.00   49
 22  \w     75.00 176.00   1.00    7.87    --  103.66  61.00  90.00  101
 23  \w     75.00 176.00   1.00    7.87    --  103.66  61.00-150.00  101
 24  \w     75.00 176.00   1.00    7.87    --  103.66  61.00 120.00  101
 25  \w     78.00 177.00   1.00    7.87    --  103.66  45.00   0.00   99
 26  \w     75.00 176.00   1.00    7.87    --  103.66  61.00  30.00  101
 27  \w     75.00 176.00   1.00    7.87    --  103.66  61.00  60.00  101
 28  \w     78.00 177.00   1.00    7.87    --  103.66  45.00 -90.00   99
 29  \w     75.00 176.00   1.00    7.87    --  103.66  61.00 150.00  101
 30  \w     75.00 162.00   1.00    7.87    --  103.66  61.00-180.00   87
 31  \w     75.00 176.00   1.00    7.87    --  103.66  61.00 -60.00  101
;
_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      0.0535604000
_diffrn_orient_matrix_UB_12      -0.0035578000
_diffrn_orient_matrix_UB_13      -0.0061474000
_diffrn_orient_matrix_UB_21      0.0041139000
_diffrn_orient_matrix_UB_22      0.0531388000
_diffrn_orient_matrix_UB_23      0.0123074000
_diffrn_orient_matrix_UB_31      0.0033479000
_diffrn_orient_matrix_UB_32      -0.0081406000
_diffrn_orient_matrix_UB_33      0.0830112000
_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  0.0259
_diffrn_reflns_av_unetI/netI     0.0112
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       35
_diffrn_reflns_limit_h_min       -35
_diffrn_reflns_limit_k_max       35
_diffrn_reflns_limit_k_min       -35
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -19
_diffrn_reflns_number            142724
_diffrn_reflns_point_group_measured_fraction_full 0.947
_diffrn_reflns_point_group_measured_fraction_max 0.939
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         72.720
_diffrn_reflns_theta_min         2.184
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.736
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.84036
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.84a (Rigaku Oxford Diffraction, 2020)
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    1.526
_exptl_crystal_description       block
_exptl_crystal_F_000             7208
_exptl_crystal_size_max          0.23
_exptl_crystal_size_mid          0.17
_exptl_crystal_size_min          0.16
_refine_diff_density_max         0.659
_refine_diff_density_min         -0.306
_refine_diff_density_rms         0.049
_refine_ls_abs_structure_details
;
 Flack x determined using 5536 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.502(6)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.067
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     916
_refine_ls_number_reflns         14038
_refine_ls_number_restraints     69
_refine_ls_restrained_S_all      1.080
_refine_ls_R_factor_all          0.0551
_refine_ls_R_factor_gt           0.0514
_refine_ls_shift/su_max          0.004
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0866P)^2^+12.5155P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1457
_refine_ls_wR_factor_ref         0.1515
_reflns_Friedel_coverage         0.826
_reflns_Friedel_fraction_full    0.892
_reflns_Friedel_fraction_max     0.879
_reflns_number_gt                13014
_reflns_number_total             14038
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5ra07259j2.cif
_cod_data_source_block           2
_cod_original_cell_volume        14984.97(19)
_cod_database_code               7251316
_shelx_shelxl_version_number     2019/2
_chemical_oxdiff_formula         'C60 H60 N20 F2 O10'
_chemical_oxdiff_usercomment     '100 K'
_shelx_estimated_absorpt_t_max   0.769
_shelx_estimated_absorpt_t_min   0.691
_diffrn_oxdiff_digest_hkl
;
01f3286ed818fe3ce1f67eebfe488599a7cef8
;
_reflns_odcompleteness_completeness 99.99
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_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
 C44B-C43B
 1.54 with sigma of 0.02
 N29A-C45B
 1.54 with sigma of 0.02
 C43A-N29A
 1.54 with sigma of 0.001
 C44A-C43A
 1.54 with sigma of 0.001
 N29A-C45A \\sim N29A-C43A
 with sigma of 0.02
 C43A-C44A \\sim C43B-C44B
 with sigma of 0.02
3. Restrained planarity
 F2B, C51, C50, C49, C47
 with sigma of 0.01
 F2A, C48, C47, C52, C51, C50, C49
 with sigma of 0.01
4. Rigid bond restraints
 C48, C47, C49, F2A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
C48 \\sim C47 \\sim C49 \\sim F2A: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08 within 1.7A
Uanis(F2A) \\sim Ueq, Uanis(F2B) \\sim Ueq: with sigma of 0.1 and sigma for
terminal atoms of 0.2
Uanis(N29B) = Uanis(N29A)
Uanis(C44B) = Uanis(C44A)
Uanis(C46B) = Uanis(C45B)
Uanis(C43B) = Uanis(C43A)
Uanis(C43B) = Uanis(C45B)
Uanis(C46B) = Uanis(C46A)
Uanis(C45B) = Uanis(C45A)
6. Rigid body (RIGU) restrains
 N25, C37
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C47, C48, C49, F2A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
7. Others
 Sof(H48)=Sof(C43B)=Sof(H43A)=Sof(H43B)=Sof(F2B)=Sof(N29B)=Sof(H29C)=Sof(H29D)=
 Sof(C46B)=Sof(H46C)=Sof(H46D)=Sof(C44B)=Sof(H44C)=Sof(H44D)=Sof(C45B)=
 Sof(H45C)=Sof(H45D)=1-FVAR(1)
 Sof(H52)=Sof(C45A)=Sof(H45A)=Sof(H45B)=Sof(F2A)=Sof(C44A)=Sof(H44A)=Sof(H44B)=
 Sof(C46A)=Sof(H46A)=Sof(H46B)=Sof(N29A)=Sof(H29E)=Sof(H29F)=Sof(C43A)=
 Sof(H43C)=Sof(H43D)=FVAR(1)
8.a Ternary CH refined with riding coordinates:
 C14(H14), C40(H40), C15(H15), C26(H26), C27(H27), C2(H2), C34(H34), C32(H32),
 C8(H8), C38(H38), C3(H3), C9(H9), C21(H21), C20(H20)
8.b Secondary CH2 refined with riding coordinates:
 C24(H24A,H24B), C30(H30A,H30B), C5(H5A,H5B), C42(H42A,H42B), C41(H41A,H41B),
 C18(H18A,H18B), C36(H36A,H36B), C23(H23A,H23B), C35(H35A,H35B), C17(H17A,H17B),
  C11(H11A,H11B), C6(H6A,H6B), C29(H29A,H29B), C12(H12A,H12B), C43B(H43A,H43B),
 C45A(H45A,H45B), C44A(H44A,H44B), C46A(H46A,H46B), N29B(H29C,H29D), C46B(H46C,
 H46D), N29A(H29E,H29F), C44B(H44C,H44D), C43A(H43C,H43D), C45B(H45C,H45D)
8.c Aromatic/amide H refined with riding coordinates:
 C51(H51), C52(H52), C48(H48), C49(H49)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              52230
_shelx_fab_checksum              91537
_olex2_date_sample_data_collection 2021-04-13
_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 1.256
_oxdiff_exptl_absorpt_empirical_full_min 0.833