A Squaramide Cage Capable of Binding and Extracting H2PO4- and HP2O73- in Highly Polar Protic Media
Kim, Sung Kuk; Yang, Ju Ho; Chemical Communications  (2023) –; doi:10.1039/D3CC02611F

data_7131931
_publ_section_title
;
 A Squaramide Cage Capable of Binding and Extracting H2PO4- and HP2O73- in
 Highly Polar Protic Media
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D3CC02611F
_journal_year                    2023
_chemical_formula_moiety
'C60 H59.962 Cl0.038 N6 O9, C16 H36 N, 3(C H4 O), C H Cl2.864, 1.045(C H Cl3), H2 O4 P'
_chemical_formula_sum            'C81.04 H112.01 Cl6.04 N7 O16 P'
_chemical_formula_weight         1685.32
_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
_atom_sites_solution_primary     dual
_audit_creation_date             2022-09-07
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2023-05-30 deposited with the CCDC.	2023-07-25 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 96.6710(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   13.13170(10)
_cell_length_b                   19.00400(10)
_cell_length_c                   34.9608(2)
_cell_measurement_reflns_used    40929
_cell_measurement_temperature    100(1)
_cell_measurement_theta_max      76.8940
_cell_measurement_theta_min      2.5390
_cell_volume                     8665.57(10)
_computing_cell_refinement       'CrysAlisPro 1.171.41.123a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.41.123a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.41.123a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100(1)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.992
_diffrn_measured_fraction_theta_max 0.955
_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   -120.00 -30.00   0.50   27.00    --  -48.70 -67.00-104.00  180
  2  \w    -67.00  24.00   0.50   27.00    --  -48.70  67.00  29.00  182
  3  \w    -23.00  67.00   0.50   27.00    --   48.70 -67.00-104.00  180
  4  \w     35.00 127.00   0.50  103.00    --  107.75 -67.00-104.00  184
  5  \w     89.00 178.00   0.50  103.00    --  107.75  67.00  29.00  178
  6  \w   -120.00 -73.00   0.50   27.00    --  -48.70-125.00  30.00   94
  7  \w     30.00 120.00   0.50   27.00    --   48.70  67.00  29.00  180
  8  \w     35.00 120.00   0.50  103.00    --  107.75 -38.00-120.00  170
  9  \w     35.00 106.00   0.50  103.00    --  107.75 -99.00-180.00  142
 10  \w     95.00 178.00   0.50  103.00    --  107.75  38.00 -60.00  166
 11  \w     85.00 178.00   0.50  103.00    --  107.75  77.00   0.00  186
 12  \w     35.00 106.00   0.50  103.00    --  107.75 -99.00 120.00  142
 13  \w   -120.00 -45.00   0.50   27.00    --  -48.70 -77.00 -30.00  150
 14  \w   -120.00 -73.50   0.50   27.00    --  -48.70 -77.00 150.00   93
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0655290000
_diffrn_orient_matrix_UB_12      0.0507183000
_diffrn_orient_matrix_UB_13      0.0213322000
_diffrn_orient_matrix_UB_21      -0.0980693000
_diffrn_orient_matrix_UB_22      -0.0371224000
_diffrn_orient_matrix_UB_23      -0.0182669000
_diffrn_orient_matrix_UB_31      0.0063044000
_diffrn_orient_matrix_UB_32      -0.0512052000
_diffrn_orient_matrix_UB_33      0.0343418000
_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  0.0320
_diffrn_reflns_av_unetI/netI     0.0238
_diffrn_reflns_Laue_measured_fraction_full 0.992
_diffrn_reflns_Laue_measured_fraction_max 0.955
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -14
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       44
_diffrn_reflns_limit_l_min       -41
_diffrn_reflns_number            65351
_diffrn_reflns_point_group_measured_fraction_full 0.992
_diffrn_reflns_point_group_measured_fraction_max 0.955
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.117
_diffrn_reflns_theta_min         2.545
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.538
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.653
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.123a (Rigaku Oxford Diffraction, 2022)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.292
_exptl_crystal_description       plate
_exptl_crystal_F_000             3572
_exptl_crystal_size_max          0.182
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.058
_refine_diff_density_max         0.963
_refine_diff_density_min         -0.654
_refine_diff_density_rms         0.057
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.032
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1097
_refine_ls_number_reflns         17522
_refine_ls_number_restraints     79
_refine_ls_restrained_S_all      1.035
_refine_ls_R_factor_all          0.0482
_refine_ls_R_factor_gt           0.0444
_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^)+(0.0642P)^2^+6.9455P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1205
_refine_ls_wR_factor_ref         0.1229
_reflns_Friedel_coverage         0.000
_reflns_number_gt                15869
_reflns_number_total             17522
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3cc02611f2.cif
_cod_data_source_block           yjh-4
_cod_database_code               7131931
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C81H106N7O16Cl6P
_shelx_estimated_absorpt_t_max   0.867
_shelx_estimated_absorpt_t_min   0.655
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 H34-O10
 1.85 with sigma of 0.05
 C77A-Cl6A
 1.77 with sigma of 0.02
 C77A-Cl4A
 1.77 with sigma of 0.02
 C77A-Cl5A
 1.77 with sigma of 0.02
 C81-O16 = C81A-O16A
 1.45 with sigma of 0.01
 Cl6-C77
 1.77 with sigma of 0.02
 Cl4-C77
 1.77 with sigma of 0.02
 Cl5-C77
 1.77 with sigma of 0.02
 Cl6-C77 \\sim Cl6A-C77
 with sigma of 0.02
 Cl4-C77 \\sim Cl4A-C77
 with sigma of 0.02
 Cl5-C77 \\sim Cl5A-C77
 with sigma of 0.02
 Cl4-Cl5 \\sim Cl4-Cl6 \\sim Cl5-Cl6 \\sim Cl4A-Cl5A \\sim Cl4A-Cl6A \\sim
Cl5A-Cl6A
 with sigma of 0.03
 O16-C81 \\sim O16A-C81A
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Cl4 \\sim Cl4A \\sim Cl5 \\sim Cl5A \\sim Cl6 \\sim Cl6A: within 2A with sigma
of 0.01 and sigma for terminal atoms of 0.02 within 2A
C81 \\sim C81A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
O16 \\sim O16A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
Uanis(C81) \\sim Ueq, Uanis(C81A) \\sim Ueq, Uanis(O16) \\sim Ueq, Uanis(O16A)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O16) \\sim Ueq, Uanis(O16A) \\sim Ueq, Uanis(C81) \\sim Ueq, Uanis(C81A)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(Cl4) = Uanis(Cl4A)
Uanis(Cl6) = Uanis(Cl6A)
Uanis(Cl5) = Uanis(Cl5A)
4. Others
 Sof(O16A)=Sof(H19)=Sof(C81A)=Sof(H27)=Sof(H28)=Sof(H29)=1-FVAR(1)
 Sof(O16)=Sof(H18)=Sof(C81)=Sof(H24)=Sof(H25)=Sof(H26)=FVAR(1)
 Sof(Cl4A)=Sof(Cl5A)=Sof(Cl6A)=Sof(C77A)=Sof(H31)=1-FVAR(2)
 Sof(Cl4)=Sof(Cl5)=Sof(Cl6)=FVAR(2)
 Fixed Sof: Cl7(0.038) H7(0.962)
 Fixed Uiso: C77A(0.03797)
5.a Ternary CH refined with riding coordinates:
 C77A(H31), C78(H42)
5.b Secondary CH2 refined with riding coordinates:
 C11(H11A,H11B), C18(H18A,H18B), C29(H29A,H29B), C36(H36A,H36B), C37(H37A,
 H37B), C48(H48A,H48B), C49(H49A,H49B), C51(H51A,H51B), C53(H53A,H53B),
 C55(H55A,H55B), C57(H57A,H57B), C59(H59A,H59B), C61(H,HA), C62(HB,HC), C63(HD,
 HE), C65(HI,HJ), C66(HK,HL), C67(HM,HN), C69(HR,HS), C70(HT,HU), C71(HV,HW),
 C73(H8,H10), C74(H11,H12), C75(H13,H14)
5.c Aromatic/amide H refined with riding coordinates:
 C6(H6A), C7(H7A), C9(H9), C20(H20), C21(H21), C22(H22), C23(H23), C43(H43),
 C44(H44), C45(H45), C46(H46)
5.d Idealised Me refined as rotating group:
 C50(H50A,H50B,H50C), C52(H52A,H52B,H52C), C54(H54A,H54B,H54C), C56(H56A,H56B,
 H56C), C58(H58A,H58B,H58C), C60(H60A,H60B,H60C), C64(HF,HG,HH), C68(HO,HP,HQ),
 C72(HX,HY,HZ), C76(H15,H16,H17), C81(H24,H25,H26), C81A(H27,H28,H29), C80(H35,
 H36,H37), C79(H39,H40,H41)
5.e Idealised tetrahedral OH refined as rotating group:
 O16(H18), O16A(H19), O15(H34)
;
_shelx_res_checksum              55522
_shelx_hkl_checksum              82923
_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 1.901
_oxdiff_exptl_absorpt_empirical_full_min 0.585