Size-dependent compression of threaded alkyldiphosphate in head to head cyclodextrin [3]pseudorotaxanes
Scelle, Jérémy; Vervoitte, Hugo; Bouteiller, Laurent; Chamoreau, Lise-Marie; Sollogoub, Matthieu; Vives, Guillaume; Hasenknopf, Bernold; Chemical Science 13 (2022) 2218–2225; doi:10.1039/D1SC05697B

data_1565994
_publ_section_title
;
 Size-dependent compression of threaded alkyldiphosphate in head to head
 cyclodextrin [3]pseudorotaxanes
;
_journal_issue                   8
_journal_name_full               'Chemical Science'
_journal_page_first              2218
_journal_page_last               2225
_journal_paper_doi               10.1039/D1SC05697B
_journal_volume                  13
_journal_year                    2022
_chemical_absolute_configuration syn
_chemical_formula_moiety
'4(C36 H60 O30), 2 (C12 H24 P2 O8), 77.5 H2 O, 8 K '
_chemical_formula_sum            'C168 H443 K8 O213.5 P4'
_chemical_formula_weight         6316.88
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2021-10-07
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2021-10-11 deposited with the CCDC.	2022-01-17 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 92.681(8)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   22.944(3)
_cell_length_b                   13.9699(15)
_cell_length_c                   44.772(5)
_cell_measurement_reflns_used    9913
_cell_measurement_temperature    150
_cell_measurement_theta_max      42.29
_cell_measurement_theta_min      3.86
_cell_volume                     14335(3)
_computing_cell_refinement       'Bruker SAINT'
_computing_data_collection       'Bruker APEX2'
_computing_data_reduction        'Bruker SAINT'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'ShelXD (Sheldrick, 2008)'
_diffrn_ambient_temperature      150
_diffrn_measured_fraction_theta_full 0.952
_diffrn_measured_fraction_theta_max 0.952
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0783
_diffrn_reflns_av_unetI/netI     0.0705
_diffrn_reflns_Laue_measured_fraction_full 0.952
_diffrn_reflns_Laue_measured_fraction_max 0.952
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            86361
_diffrn_reflns_point_group_measured_fraction_full 0.954
_diffrn_reflns_point_group_measured_fraction_max 0.954
_diffrn_reflns_theta_full        43.132
_diffrn_reflns_theta_max         43.132
_diffrn_reflns_theta_min         2.964
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    2.386
_exptl_absorpt_correction_T_max  0.7483
_exptl_absorpt_correction_T_min  0.6181
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
'SADABS-2014/5 (Bruker,2014/5) was used for absorption correction. wR2(int) was 0.1180 before and 0.0569 after correction. The Ratio of minimum to maximum transmission is 0.8260. The \l/2 correction factor is 0.00150.'
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.463
_exptl_crystal_description       needle
_exptl_crystal_F_000             6742
_exptl_crystal_recrystallization_method
'recrystallisation from solvent H2O/DMF'
_exptl_crystal_size_max          0.44
_exptl_crystal_size_mid          0.08
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.720
_refine_diff_density_min         -0.430
_refine_diff_density_rms         0.076
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.06(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.033
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     3568
_refine_ls_number_reflns         19449
_refine_ls_number_restraints     2945
_refine_ls_restrained_S_all      0.970
_refine_ls_R_factor_all          0.1136
_refine_ls_R_factor_gt           0.0947
_refine_ls_shift/su_max          1.130
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1613P)^2^+50.2555P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2295
_refine_ls_wR_factor_ref         0.2503
_reflns_Friedel_coverage         0.890
_reflns_Friedel_fraction_full    0.956
_reflns_Friedel_fraction_max     0.956
_reflns_number_gt                15864
_reflns_number_total             19449
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1sc05697b2.cif
_cod_data_source_block           jsc306_06_0m_ap_platon
_cod_depositor_comments
'Adding full bibliography for 1565992--1565995.cif.'
_cod_original_formula_sum        'C168 H443 K8 O213.50 P4'
_cod_database_code               1565994
_shelx_shelxl_version_number     2017/1
_shelx_estimated_absorpt_t_max   0.954
_shelx_estimated_absorpt_t_min   0.420
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.94(7)
 0.06(7)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
3. Restrained distances
 C15-C14
 1.5 with sigma of 0.02
 C21-C20
 1.54 with sigma of 0.02
 O12-C13
 1.45 with sigma of 0.02
 O12B-C13B
 1.45 with sigma of 0.02
 C14B-C13B = C14-C13
 1.54 with sigma of 0.02
 C19B-C18 = C19-C18 = C20-C19B = C19-C20
 1.54 with sigma of 0.02
 C18-C17
 1.54 with sigma of 0.02
 C20-C22B
 2.45 with sigma of 0.04
 O13-O16
 2.45 with sigma of 0.04
 P3-O12B \\sim P3-O12
 with sigma of 0.02
 O6B2-C6B2 \\sim O7B2-C6B2
 with sigma of 0.02
4. Uiso/Uaniso restraints and constraints
C6A2 \\sim C5A2: within 1.7A with sigma of 0.04 and sigma for terminal atoms of
0.08
: with sigma of 0.1 and sigma for terminal atoms of 0.2
: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(O1W) \\sim Ueq, Uanis(O2W) \\sim Ueq, Uanis(O3W) \\sim Ueq, Uanis(O4W)
\\sim Ueq, Uanis(O5W) \\sim Ueq, Uanis(O6W) \\sim Ueq, Uanis(O9W) \\sim Ueq,
Uanis(O11W) \\sim Ueq, Uanis(O12W) \\sim Ueq, Uanis(O13W) \\sim Ueq,
Uanis(O15W) \\sim Ueq, Uanis(O16W) \\sim Ueq, Uanis(O17W) \\sim Ueq,
Uanis(O18W) \\sim Ueq, Uanis(O20W) \\sim Ueq, Uanis(O21W) \\sim Ueq,
Uanis(O22W) \\sim Ueq, Uanis(O24W) \\sim Ueq, Uanis(O25W) \\sim Ueq,
Uanis(O26W) \\sim Ueq, Uanis(O27W) \\sim Ueq, Uanis(O28W) \\sim Ueq,
Uanis(O29W) \\sim Ueq, Uanis(O30W) \\sim Ueq, Uanis(O31W) \\sim Ueq,
Uanis(O32W) \\sim Ueq, Uanis(O33W) \\sim Ueq, Uanis(O34W) \\sim Ueq,
Uanis(O35W) \\sim Ueq, Uanis(O36W) \\sim Ueq, Uanis(O37W) \\sim Ueq,
Uanis(O38W) \\sim Ueq, Uanis(O39W) \\sim Ueq, Uanis(O41W) \\sim Ueq,
Uanis(O42W) \\sim Ueq, Uanis(O43W) \\sim Ueq, Uanis(O44W) \\sim Ueq,
Uanis(O45W) \\sim Ueq, Uanis(O46W) \\sim Ueq, Uanis(O47W) \\sim Ueq,
Uanis(O48W) \\sim Ueq, Uanis(O49W) \\sim Ueq, Uanis(O50W) \\sim Ueq,
Uanis(O51W) \\sim Ueq, Uanis(O53W) \\sim Ueq, Uanis(O54W) \\sim Ueq,
Uanis(O55W) \\sim Ueq, Uanis(O57W) \\sim Ueq, Uanis(O58W) \\sim Ueq,
Uanis(O59W) \\sim Ueq, Uanis(O60W) \\sim Ueq, Uanis(K1) \\sim Ueq, Uanis(O62W)
\\sim Ueq, Uanis(O63W) \\sim Ueq, Uanis(O64W) \\sim Ueq, Uanis(O66W) \\sim Ueq,
Uanis(O69W) \\sim Ueq, Uanis(O68W) \\sim Ueq, Uanis(O70W) \\sim Ueq,
Uanis(O71W) \\sim Ueq, Uanis(O72W) \\sim Ueq, Uanis(O73W) \\sim Ueq,
Uanis(O74W) \\sim Ueq, Uanis(O75W) \\sim Ueq, Uanis(O76W) \\sim Ueq,
Uanis(O77W) \\sim Ueq, Uanis(O78W) \\sim Ueq, Uanis(O80W) \\sim Ueq,
Uanis(O81W) \\sim Ueq, Uanis(O82W) \\sim Ueq, Uanis(O83W) \\sim Ueq,
Uanis(O86W) \\sim Ueq, Uanis(O87W) \\sim Ueq, Uanis(O17) \\sim Ueq, Uanis(O89W)
\\sim Ueq, Uanis(O90W) \\sim Ueq: with sigma of 0.1 and sigma for terminal
atoms of 0.2
Uanis(C6C1) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(C6A2) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
5. Rigid body (RIGU) restrains
 O3E4, C1A4, C2A4, O1A4, O5A4, C3A4, O2A4, C4B4, C5A4, C4A4, O3A4, C3B4, C5B4,
 C6A4, O1F4, C2B4, O3B4, C6B4, O5B4, O6A4, C1F4, C1B4, O2B4, O6B4, C2F4, O5F4,
 O1B4, C3F4, O2F4, C5F4, C4C4, C4F4, O3F4, C6F4, C3C4, C5C4, O1E4, O6F4, O7F4,
 C2C4, O3C4, C6C4, O5C4, C1E4, C1C4, O2C4, O6C4, C2E4, O5E4, O1C4, C3E4, O2E4,
 C5E4, C4D4, C4E4, C6E4, C3D4, C5D4, O1D4, O6E4, C2D4, O3D4, C6D4, O5D4, C1D4,
 O2D4, O6D4
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O5E3, C1A3, C2A3, O1A3, O5A3, C3A3, O2A3, C4B3, C5A3, C4A3, O3A3, C3B3, C5B3,
 C6A3, O1F3, C2B3, O3B3, C6B3, O5B3, O6A3, C1F3, C1B3, O2B3, O6B3, O5F3, C2F3,
 O1B3, C5F3, O2F3, C3F3, C4C3, C4F3, C6F3, O3F3, C3C3, C5C3, O1E3, O6F3, C2C3,
 O3C3, C6C3, O5C3, C1E3, C1C3, O2C3, O6C3, C2E3, O1C3, C3E3, O2E3, C5E3, C4D3,
 C4E3, O3E3, C6E3, C3D3, C5D3, O1D3, O6E3, C2D3, O3D3, C6D3, O5D3, C1D3, O2D3,
 O6D3
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O2A2, C1A2, C2A2, O1A2, O5A2, C3A2, C4B2, C5A2, C4A2, O3A2, C3B2, C5B2, C6A2,
 O1F2, C2B2, O3B2, C6B2, O5B2, O6A2, C1F2, C1B2, O2B2, O6B2, O7B2, C2F2, O5F2,
 O1B2, C3F2, O2F2, C5F2, C4C2, C4F2, O3F2, C6F2, C3C2, C5C2, O1E2, O6F2, C2C2,
 O3C2, C6C2, O5C2, C1E2, C1C2, O2C2, O6C2, O7C2, C2E2, O5E2, O1C2, C3E2, O2E2,
 C5E2, C4D2, C4E2, O3E2, C6E2, C3D2, C5D2, O1D2, O6E2, C2D2, O3D2, C6D2, O5D2,
 C1D2, O2D2, O6D2
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C1F1, C1A1, C2A1, O1A1, O5A1, C3A1, O2A1, C4B1, C5A1, C4A1, O3A1, C3B1, C5B1,
 C6A1, O1F1, C2B1, O3B1, C6B1, O5B1, O6A1, O7A1, C1B1, O2B1, O6B1, C2F1, O5F1,
 O1B1, C3F1, O2F1, C5F1, C4C1, C4F1, O3F1, C6F1, C3C1, C5C1, O1E1, O6F1, C2C1,
 O3C1, C6C1, O5C1, C1E1, C1C1, O2C1, O6C1, C2E1, O5E1, O1C1, C3E1, O2E1, C5E1,
 C4D1, C4E1, O3E1, C6E1, C3D1, C5D1, O1D1, O6E1, C2D1, O3D1, C6D1, O5D1, C1D1,
 O2D1, O6D1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C10, P1, O0AA, O2, O3, O1B, O2B, O3B, O4, C1, C2, C3, C4, C5, C6, C7, C8, C9,
 C11, C12, O5, P2, O6, O7, O8
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O12, O12B, P3, O11, O11B, O9B, O9, O10B, O10
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 P4A, O13, O14, O15, O16
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Fixed Sof: O6A1(0.5) O7A1(0.5) O6B2(0.5) O7B2(0.5) O6C2(0.5) O7C2(0.5)
 H6F4(0.5) H6FE(0.5) O6F4(0.5) O7F4(0.5) O0AA(0.5) O2(0.5) O3(0.5) O1B(0.5)
 O2B(0.5) O3B(0.5) O9(0.5) O10(0.5) O11(0.5) O12(0.5) O9B(0.5) O10B(0.5)
 O11B(0.5) O12B(0.5) C13(0.5) C14(0.5) C15(0.5) C13B(0.5) C14B(0.5) C15B(0.5)
 C19(0.5) C19B(0.5) P4A(0.5) O13(0.5) O14(0.5) O15(0.5) O16(0.5) O5W(0.75)
 O6W(0.5) O7W(0.5) O8W(0.5) O10W(0.25) O11W(0.5) O17W(0.5) O26W(0.5) O28W(0.5)
 O32W(0.5) O57W(0.5) O65W(0.5) O66W(0.5) O80W(0.5) O82W(0.5) O83W(0.5)
 O84W(0.5) O85W(0.5) O86W(0.5) O87W(0.5) O17(0.5) O89W(0.5) O90W(0.5) O26X(0.5)
 O92W(0.5)
7.a Ternary CH refined with riding coordinates:
 C1A1(H1A1), C2A1(H2A1), C3A1(H3A1), C4A1(H4A1), C5A1(H5A1), C1B1(H1B1),
 C2B1(H2B1), C3B1(H3B1), C4B1(H4B1), C5B1(H5B1), C1C1(H1C1), C2C1(H2C1),
 C3C1(H3C1), C4C1(H4C1), C5C1(H5C1), C1D1(H1D1), C2D1(H2D1), C3D1(H3D1),
 C4D1(H4D1), C5D1(H5D1), C1E1(H1E1), C2E1(H2E1), C3E1(H3E1), C4E1(H4E1),
 C5E1(H5E1), C1F1(H1F1), C2F1(H2F1), C3F1(H3F1), C4F1(H4F1), C5F1(H5F1),
 C1A2(H1A2), C2A2(H2A2), C3A2(H3A2), C4A2(H4A2), C5A2(H5A2), C1B2(H1B2),
 C2B2(H2B2), C3B2(H3B2), C4B2(H4B2), C5B2(H5B2), C1C2(H1C2), C2C2(H2C2),
 C3C2(H3C2), C4C2(H4C2), C5C2(H5C2), C1D2(H1D2), C2D2(H2D2), C3D2(H3D2),
 C4D2(H4D2), C5D2(H5D2), C1E2(H1E2), C2E2(H2E2), C3E2(H3E2), C4E2(H4E2),
 C5E2(H5E2), C1F2(H1F2), C2F2(H2F2), C3F2(H3F2), C4F2(H4F2), C5F2(H5F2),
 C1A3(H1A3), C2A3(H2A3), C3A3(H3A3), C4A3(H4A3), C5A3(H5A3), C1B3(H1B3),
 C2B3(H2B3), C3B3(H3B3), C4B3(H4B3), C5B3(H5B3), C1C3(H1C3), C2C3(H2C3),
 C3C3(H3C3), C4C3(H4C3), C5C3(H5C3), C1D3(H1D3), C2D3(H2D3), C3D3(H3D3),
 C4D3(H4D3), C5D3(H5D3), C1E3(H1E3), C2E3(H2E3), C3E3(H3E3), C4E3(H4E3),
 C5E3(H5E3), C1F3(H1F3), C2F3(H2F3), C3F3(H3F3), C4F3(H4F3), C5F3(H5F3),
 C1A4(H1A4), C2A4(H2A4), C3A4(H3A4), C4A4(H4A4), C5A4(H5A4), C1B4(H1B4),
 C2B4(H2B4), C3B4(H3B4), C4B4(H4B4), C5B4(H5B4), C1C4(H1C4), C2C4(H2C4),
 C3C4(H3C4), C4C4(H4C4), C5C4(H5C4), C1D4(H1D4), C2D4(H2D4), C3D4(H3D4),
 C4D4(H4D4), C5D4(H5D4), C1E4(H1E4), C2E4(H2E4), C3E4(H3E4), C4E4(H4E4),
 C5E4(H5E4), C1F4(H1F4), C2F4(H2F4), C3F4(H3F4), C4F4(H4F4), C5F4(H5F4)
7.b Secondary CH2 refined with riding coordinates:
 C6C1(H6CA,H6CB), C6D1(H6DA,H6DB), C6E1(H6EA,H6EB), C6F1(H6FA,H6FB), C6A2(H6AA,
 H6AB), C6D2(H6DC,H6DD), C6E2(H6EC,H6ED), C6F2(H6FC,H6FD), C6A3(H6AE,H6AF),
 C6B3(H6BC,H6BD), C6C3(H6CE,H6CF), C6D3(H6DG,H6DH), C6E3(H6EG,H6EH), C6F3(H6FF,
 H6FG), C6A4(H6AC,H6AD), C6B4(H6BA,H6BB), C6C4(H6CC,H6CD), C6D4(H6DE,H6DF),
 C6E4(H6EE,H6EF), C1(H1A,H1B), C2(H2A,H2B), C3(H3A,H3B), C4(H4A,H4B), C5(H5A,
 H5B), C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B), C10(H10A,H10B),
 C11(H11A,H11B), C12(H12A,H12B)
7.c Aromatic/amide H refined with riding coordinates:
 C6F4(H6F4), C6F4(H6FE)
;
_shelx_res_checksum              71600
_shelx_hkl_checksum              39543
_olex2_exptl_crystal_mounting_method cryoloop
_olex2_submission_special_instructions 'No special instructions were received'