Dimerization of pillar[5]arene: length-adaptive encapsulation of long-chain guests.
Ohtani, Shunsuke; Nakagawa, Keigo; Akine, Shigehisa; Kato, Kenichi; Ogoshi, Tomoki; Chemical science 16 (2025) 14262–14269; doi:10.1039/d5sc01403d

data_1575002
_publ_section_title
;
 Dimerization of pillar[5]arene: length-adaptive encapsulation of
 long-chain guests.
;
_journal_issue                   31
_journal_name_full               'Chemical science'
_journal_page_first              14262
_journal_page_last               14269
_journal_paper_doi               10.1039/d5sc01403d
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety
'2.001(C55.919 H66.796 O9), 1.5(C6 H14), C2.98 H6.882, C3.02 H7.118'
_chemical_formula_sum            'C126.89 H168.73 O18'
_chemical_formula_weight         1982.08
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2024-07-09
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-12-12 deposited with the CCDC.	2025-07-03 downloaded from the CCDC.
;
_cell_angle_alpha                95.788(7)
_cell_angle_beta                 92.174(7)
_cell_angle_gamma                99.902(8)
_cell_formula_units_Z            2
_cell_length_a                   12.062(5)
_cell_length_b                   21.595(9)
_cell_length_c                   23.1024(10)
_cell_measurement_reflns_used    5039
_cell_measurement_temperature    143.15
_cell_measurement_theta_max      27.3
_cell_measurement_theta_min      3.0
_cell_volume                     5888(3)
_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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      143.15
_diffrn_measured_fraction_theta_full 0.978
_diffrn_measured_fraction_theta_max 0.977
_diffrn_measurement_device_type  'Rigaku Saturn724+ (4x4 bin mode)'
_diffrn_measurement_method       'profile data from \w-scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71075
_diffrn_reflns_av_R_equivalents  0.1070
_diffrn_reflns_av_unetI/netI     0.1826
_diffrn_reflns_Laue_measured_fraction_full 0.978
_diffrn_reflns_Laue_measured_fraction_max 0.977
_diffrn_reflns_limit_h_max       14
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       25
_diffrn_reflns_limit_k_min       -25
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -25
_diffrn_reflns_number            40050
_diffrn_reflns_point_group_measured_fraction_full 0.978
_diffrn_reflns_point_group_measured_fraction_max 0.977
_diffrn_reflns_theta_full        25.000
_diffrn_reflns_theta_max         25.028
_diffrn_reflns_theta_min         3.007
_exptl_absorpt_coefficient_mu    0.073
_exptl_crystal_density_diffrn    1.118
_exptl_crystal_description       Prism
_exptl_crystal_F_000             2148
_exptl_crystal_size_max          0.4
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.401
_refine_diff_density_min         -0.296
_refine_diff_density_rms         0.058
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.125
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1475
_refine_ls_number_reflns         20351
_refine_ls_number_restraints     692
_refine_ls_restrained_S_all      1.121
_refine_ls_R_factor_all          0.2451
_refine_ls_R_factor_gt           0.1375
_refine_ls_shift/su_max          0.012
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0950P)^2^+3.6028P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2709
_refine_ls_wR_factor_ref         0.3390
_reflns_Friedel_coverage         0.000
_reflns_number_gt                9282
_reflns_number_total             20351
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5sc01403d2.cif
_cod_data_source_block           Ph
_cod_depositor_comments
'Adding full bibliography for 1575001--1575002.cif.'
_cod_database_code               1575002
_shelx_shelxl_version_number     2018/3
_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
2. Restrained distances
 C5-C6 = C6-C7 = C7-C8 = C8-C9 = C9-C10
 1.52 with sigma of 0.02
 C11-C12 = C12-C13 = C13-C14 = C14-C15 = C15-C17
 1.52 with sigma of 0.02
 C18-C19 = C19-C1A = C1A-C1B = C1B-C1C = C1C-C1D
 1.52 with sigma of 0.02
 C5-C7 = C8-C10
 2.53 with sigma of 0.04
 C6-C8 = C7-C9
 2.54 with sigma of 0.04
 C11-C13 = C14-C17
 2.53 with sigma of 0.04
 C12-C14 = C13-C15
 2.54 with sigma of 0.04
 C18-C1A = C1B-C1D
 2.53 with sigma of 0.04
 C19-C1B = C1A-C1C
 2.54 with sigma of 0.04
 O00H-C40 \\sim O00H-C40A
 with sigma of 0.02
 C40-C16 \\sim C40A-C16A
 with sigma of 0.02
 O00H-C16 \\sim O00H-C16A
 with sigma of 0.04
 O003-C010 \\sim O0-C010
 with sigma of 0.02
 O003-C02U \\sim O0-C3
 with sigma of 0.02
 C02U-C03B \\sim C3-C4
 with sigma of 0.02
 O003-C03B \\sim O0-C4
 with sigma of 0.04
 C010-C02U \\sim C010-C3
 with sigma of 0.04
 C5-C6 \\sim C6-C7 \\sim C7-C8 \\sim C8-C9 \\sim C9-C10
 with sigma of 0.02
 C5-C7 \\sim C7-C9 \\sim C6-C8 \\sim C8-C10
 with sigma of 0.04
 C11-C12 \\sim C12-C13 \\sim C13-C14 \\sim C14-C15 \\sim C15-C17
 with sigma of 0.02
 C11-C13 \\sim C13-C15 \\sim C12-C14 \\sim C14-C17
 with sigma of 0.04
 C18-C19 \\sim C19-C1A \\sim C1A-C1B \\sim C1B-C1C \\sim C1C-C1D
 with sigma of 0.02
 C18-C1A \\sim C1A-C1C \\sim C19-C1B \\sim C1B-C1D
 with sigma of 0.04
 C18-C19 \\sim C18A-C19A
 with sigma of 0.02
 C19-C1A \\sim C19A-C1F
 with sigma of 0.02
 C1A-C1B \\sim C1F-C1E
 with sigma of 0.02
 C1B-C1C \\sim C1E-C20
 with sigma of 0.02
 C1C-C1D \\sim C20-C1D
 with sigma of 0.02
 C18-C1A \\sim C18A-C1F
 with sigma of 0.04
 C19-C1B \\sim C19A-C1E
 with sigma of 0.04
 C1A-C1C \\sim C1F-C20
 with sigma of 0.04
 C1B-C1D \\sim C1E-C1D
 with sigma of 0.04
 C1C-C1D \\sim C1C-C21
 with sigma of 0.02
 O10-C03P \\sim O10-C03Q
 with sigma of 0.02
 C03P-C41 \\sim C03Q-C41A
 with sigma of 0.02
 O10-C41 \\sim O10-C41A
 with sigma of 0.04
 O00C-C01P \\sim O2-C01P
 with sigma of 0.02
 O00C-C034 \\sim O2-C0
 with sigma of 0.02
 C034-C03O \\sim C0-C22
 with sigma of 0.02
 O00C-C03O \\sim O2-C22
 with sigma of 0.04
 C01P-C034 \\sim C01P-C0
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
C40: within 1.7A with sigma of 0.01 and sigma for terminal atoms of 0.01 within
1.7A
C5 \\sim C6 \\sim C7 \\sim C8 \\sim C9 \\sim C10: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08 within 2A
C11 \\sim C12 \\sim C13 \\sim C14 \\sim C15 \\sim C17: within 2A with sigma of
0.04 and sigma for terminal atoms of 0.08 within 2A
C18 \\sim C19 \\sim C1A \\sim C1B \\sim C1C \\sim C1D: within 2A with sigma of
0.04 and sigma for terminal atoms of 0.08 within 2A
C18A \\sim C18: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C19A \\sim C19: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C1A \\sim C1F: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C1C \\sim C20: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C1D \\sim C21: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C03P \\sim C03Q: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C41A \\sim C41: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C40 \\sim C40A: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C16A \\sim C16: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
C034 \\sim C0: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C03O \\sim C22: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
O00C \\sim O2: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C02R: within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within
2A
C03C: within 2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within
2A
C4 \\sim C03B: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C3 \\sim C02U: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
O003 \\sim O0: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C18 \\sim C18A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C19 \\sim C19A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C1F \\sim C1A: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C1E \\sim C1B: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C20 \\sim C1C: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
C21 \\sim C1D: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02 within 2A
Uanis(C40) \\sim Ueq: with sigma of 1.5 and sigma for terminal atoms of 0.01
Uanis(O1) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O10) \\sim Ueq, Uanis(C03P) \\sim Ueq, Uanis(C03Q) \\sim Ueq, Uanis(C41)
\\sim Ueq, Uanis(C41A) \\sim Ueq: with sigma of 0.1 and sigma for terminal
atoms of 0.2
Uanis(C03P) \\sim Ueq, Uanis(C03Q) \\sim Ueq, Uanis(C41) \\sim Ueq, Uanis(C41A)
\\sim Ueq, Uanis(O10) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(C40) \\sim Ueq, Uanis(C40A) \\sim Ueq, Uanis(C16A) \\sim Ueq, Uanis(C16)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O00C) \\sim Ueq, Uanis(O2) \\sim Ueq, Uanis(C034) \\sim Ueq, Uanis(C0)
\\sim Ueq, Uanis(C03O) \\sim Ueq, Uanis(C22) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(C4) \\sim Ueq, Uanis(C03B) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C02U) \\sim Ueq, Uanis(C3) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(O003) \\sim Ueq, Uanis(O0) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C18) \\sim Ueq, Uanis(C18A) \\sim Ueq, Uanis(C19A) \\sim Ueq, Uanis(C19)
\\sim Ueq, Uanis(C1F) \\sim Ueq, Uanis(C1A) \\sim Ueq, Uanis(C1B) \\sim Ueq,
Uanis(C1E) \\sim Ueq, Uanis(C20) \\sim Ueq, Uanis(C1C) \\sim Ueq, Uanis(C21)
\\sim Ueq, Uanis(C1D) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(C11) \\sim Ueq, Uanis(C12) \\sim Ueq, Uanis(C13) \\sim Ueq, Uanis(C14)
\\sim Ueq, Uanis(C15) \\sim Ueq, Uanis(C17) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(C40A) = Uanis(C40)
Uanis(O0) = Uanis(O003)
Uanis(C3) = Uanis(C02U)
Uanis(C1D) = Uanis(C21)
Uanis(O2) = Uanis(O00C)
4. Rigid body (RIGU) restrains
 C5, C6, C7, C8, C9, C10
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C11, C12, C13, C14, C15, C17
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C18, C19, C1A, C1B, C1C, C1D
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O10, C03Q, C41A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O10, C03P, C41
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C028, C02W, C02J, C01I, C02A, C02S
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(C40A)=Sof(H40C)=Sof(H40D)=Sof(C16A)=Sof(H16D)=Sof(H16E)=Sof(H16F)=1-FVAR(1)
 Sof(C40)=Sof(H40A)=Sof(H40B)=Sof(C16)=Sof(H16A)=Sof(H16B)=Sof(H16C)=FVAR(1)
 Sof(O0)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(C4)=Sof(H4A)=Sof(H4B)=Sof(H4C)=1-FVAR(2)
 Sof(O003)=Sof(C02U)=Sof(H02Q)=Sof(H02R)=Sof(C03B)=Sof(H03K)=Sof(H03L)=
 Sof(H03M)=FVAR(2)
 Sof(C20)=Sof(H20A)=Sof(H20B)=Sof(C1E)=Sof(H1EA)=Sof(H1EB)=Sof(C1F)=Sof(H1FA)=
 Sof(H1FB)=Sof(C19A)=Sof(H19C)=Sof(H19D)=Sof(C18A)=Sof(H18D)=Sof(H18E)=
 Sof(H18F)=1-FVAR(3)
 Sof(C18)=Sof(H18A)=Sof(H18B)=Sof(H18C)=Sof(C19)=Sof(H19A)=Sof(H19B)=Sof(C1A)=
 Sof(H1AA)=Sof(H1AB)=Sof(C1B)=Sof(H1BA)=Sof(H1BB)=Sof(C1C)=Sof(H1CA)=Sof(H1CB)=
 FVAR(3)
 Sof(C03Q)=Sof(H12)=Sof(HV)=Sof(C41A)=Sof(H41D)=Sof(H41E)=Sof(H41F)=1-FVAR(4)
 Sof(C03P)=Sof(H11)=Sof(HU)=Sof(C41)=Sof(H41A)=Sof(H41B)=Sof(H41C)=FVAR(4)
 Sof(O2)=Sof(C0)=Sof(H0A)=Sof(H0B)=Sof(C22)=Sof(H22A)=Sof(H22B)=Sof(H22C)=1-
 FVAR(5)
 Sof(O00C)=Sof(C034)=Sof(H03C)=Sof(H03D)=Sof(C03O)=Sof(H03T)=Sof(H03U)=
 Sof(H03V)=FVAR(5)
 Sof(C02R)=Sof(H02M)=Sof(H02N)=Sof(C03C)=Sof(H03N)=Sof(H03O)=Sof(H03P)=FVAR(6)
 Sof(C03K)=Sof(H10)=Sof(HS)=Sof(HT)=FVAR(7)
 Fixed Sof: C11(0.5) H11A(0.5) H11B(0.5) H11C(0.5) C12(0.5) H12A(0.5)
 H12B(0.5) C13(0.5) H13A(0.5) H13B(0.5) C14(0.5) H14A(0.5) H14B(0.5) C15(0.5)
 H15A(0.5) H15B(0.5) C17(0.5) H17A(0.5) H17B(0.5) H17C(0.5) C1D(0.40692)
 H1DA(0.40692) H1DB(0.40692) H1DC(0.40692) C21(0.59308) H21A(0.59308)
 H21B(0.59308) H21C(0.59308)
6.a Secondary CH2 refined with riding coordinates:
 C013(H01M,H01N), C018(H01A,H01B), C01D(H01D,H01E), C01E(H01F,H01G), C01O(H01R,
 H01T), C01Q(H01U,H01V), C01R(H01I,H01J), C01T(H01K,H01L), C024(H02U,H02V),
 C02D(H02A,H02B), C02I(H02C,H02D), C02P(H02,H), C02Q(H1,HA), C02R(H02M,H02N),
 C02T(H02O,H02P), C02U(H02Q,H02R), C02V(H2,HB), C02X(H3,HC), C02Y(H02S,H02T),
 C030(H03W,H03X), C031(H03Y,HF), C033(H03A,H03B), C034(H03C,H03D), C038(H5,HK),
 C03E(H7,HN), C03P(H11,HU), C40(H40A,H40B), C40A(H40C,H40D), C3(H3A,H3B),
 C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B), C12(H12A,H12B), C13(H13A,
 H13B), C14(H14A,H14B), C15(H15A,H15B), C19(H19A,H19B), C1A(H1AA,H1AB),
 C1B(H1BA,H1BB), C1C(H1CA,H1CB), C20(H20A,H20B), C1E(H1EA,H1EB), C1F(H1FA,H1FB),
  C19A(H19C,H19D), C03Q(H12,HV), C0(H0A,H0B), C1(H1A,H1B)
6.b Aromatic/amide H refined with riding coordinates:
 C00L(H00L), C00N(H00N), C00P(H00P), C00V(H00V), C012(H012), C014(H014),
 C01B(H01C), C01H(H01H), C01J(H01O), C01L(H01P), C01M(H01Q), C01S(H01S),
 C01U(H01X), C01W(H01W), C01X(H01Y), C020(H020), C022(H022), C027(H027),
 C02W(H02W), C02A(H02X), C02C(H02Y), C02F(H02F), C02H(H02Z), C02K(H02K)
6.c Fitted hexagon refined as free rotating group:
 C028(C02W,C02J,C01I,C02A,C02S)
6.d Idealised Me refined as rotating group:
 C02L(H02E,H02G,H02H), C02N(H02I,H02J,H02L), C02Z(H4,HD,HE), C032(H03Z,HG,HH),
 C035(H03E,H03F,H03G), C036(H03,HI,HJ), C037(H03H,H03I,H03J), C039(H6,HL,HM),
 C03B(H03K,H03L,H03M), C03C(H03N,H03O,H03P), C03G(H8,HO,HP), C03I(H9,HQ,HR),
 C03J(H03Q,H03R,H03S), C03K(H10,HS,HT), C03O(H03T,H03U,H03V), C41(H41A,H41B,
 H41C), C16(H16A,H16B,H16C), C16A(H16D,H16E,H16F), C4(H4A,H4B,H4C), C5(H5A,H5B,
 H5C), C10(H10A,H10B,H10C), C11(H11A,H11B,H11C), C17(H17A,H17B,H17C), C18(H18A,
 H18B,H18C), C1D(H1DA,H1DB,H1DC), C18A(H18D,H18E,H18F), C21(H21A,H21B,H21C),
 C41A(H41D,H41E,H41F), C22(H22A,H22B,H22C), C2(H2A,H2B,H2C)
;
_shelx_res_checksum              69214
_olex2_submission_special_instructions 'No special instructions were received'