Three-dimensional protonic conductivity in porous organic cage solids
Ming Liu; Linjiang Chen; Scott Lewis; Samantha Y. Chong; Marc A. Little; Tom Hasell; Iain M. Aldous; Craig M. Brown; Martin W. Smith; Carole A. Morrison; Laurence J. Hardwick; Andrew I. Cooper; Nature Communications 7 (2016) 12750–; doi:10.1038/ncomms12750

data_1547995
_publ_section_title
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 Three-dimensional protonic conductivity in porous organic cage solids
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_journal_name_full               'Nature Communications'
_journal_page_first              12750
_journal_paper_doi               10.1038/ncomms12750
_journal_volume                  7
_journal_year                    2016
_chemical_formula_moiety         '12(Cl), 4(H2 O), C48 H84 N12'
_chemical_formula_sum            'C48 H91 Cl12 N12 O4'
_chemical_formula_weight         1325.73
_space_group_crystal_system      tetragonal
_space_group_IT_number           76
_space_group_name_H-M_alt        'P 41'
_symmetry_space_group_name_Hall  'P 4w'
_symmetry_space_group_name_H-M   'P 41'
_atom_sites_solution_hydrogens   geom
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   20.2276(15)
_cell_length_b                   20.2276(15)
_cell_length_c                   32.016(3)
_cell_measurement_reflns_used    2862
_cell_measurement_temperature    100
_cell_measurement_theta_max      11.551
_cell_measurement_theta_min      2.312
_cell_volume                     13099.5(18)
_computing_cell_refinement       'SAINT v7.68A (Bruker, 2009)'
_computing_data_collection       'CrystalClear v2 (Rigaku)'
_computing_data_reduction        'SAINT v7.68A (Bruker, 2009)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXS (Sheldrick, 2008)'
_diffrn_ambient_temperature      100.0
_diffrn_detector                 'CCD area detector'
_diffrn_detector_area_resol_mean 0.0350
_diffrn_detector_type            'Rigaku Saturn724+'
_diffrn_measured_fraction_theta_full 0.877
_diffrn_measured_fraction_theta_max 1.000
_diffrn_measurement_device       'CrystalLogic Kappa (4 circle)'
_diffrn_measurement_device_type  DLS_I19
_diffrn_measurement_method       'omega rotation'
_diffrn_radiation_collimation    '0.3 x 1.5 Double Pinhole'
_diffrn_radiation_monochromator  'Synchrotron '
_diffrn_radiation_probe          x-ray
_diffrn_radiation_wavelength     0.6889
_diffrn_reflns_av_R_equivalents  0.0704
_diffrn_reflns_av_unetI/netI     0.0444
_diffrn_reflns_Laue_measured_fraction_full 0.877
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -24
_diffrn_reflns_limit_k_max       24
_diffrn_reflns_limit_k_min       -22
_diffrn_reflns_limit_l_max       39
_diffrn_reflns_limit_l_min       -39
_diffrn_reflns_number            147618
_diffrn_reflns_point_group_measured_fraction_full 0.876
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        26.000
_diffrn_reflns_theta_max         24.814
_diffrn_reflns_theta_min         0.616
_diffrn_source                   Synchrotron
_diffrn_source_type              'Undulator, I19, DLS, RAL'
_exptl_absorpt_coefficient_mu    0.513
_exptl_absorpt_correction_T_max  0.7452
_exptl_absorpt_correction_T_min  0.5585
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2008/1 (Bruker,2008) was used for absorption correction.
wR2(int) was 0.1057 before and 0.0826 after correction.
The Ratio of minimum to maximum transmission is 0.7495.
The \l/2 correction factor is 0.0000.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.344
_exptl_crystal_description       block
_exptl_crystal_F_000             5592
_exptl_crystal_size_max          0.214
_exptl_crystal_size_mid          0.201
_exptl_crystal_size_min          0.174
_refine_diff_density_max         1.413
_refine_diff_density_min         -0.418
_refine_diff_density_rms         0.172
_refine_ls_abs_structure_details
;
 Flack x determined using 10326 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.23(2)
_refine_ls_extinction_coef       .
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.105
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1465
_refine_ls_number_reflns         24799
_refine_ls_number_restraints     103
_refine_ls_restrained_S_all      1.108
_refine_ls_R_factor_all          0.0803
_refine_ls_R_factor_gt           0.0751
_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^)+(0.1290P)^2^+5.9410P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1844
_refine_ls_wR_factor_ref         0.1911
_reflns_Friedel_coverage         0.962
_reflns_Friedel_fraction_full    0.875
_reflns_Friedel_fraction_max     1.000
_reflns_number_gt                23190
_reflns_number_total             24799
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ncomms12750-s2.cif
_cod_data_source_block           rCC1_12-chloride_4-H2O
_cod_original_cell_volume        13100(2)
_cod_database_code               1547995
_olex2_refinement_description
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1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups, All N(H,H)
  groups, All N(H,H,H,H) groups
2. Restrained distances
 N3A-C44A
 1.51 with sigma of 0.02
 N3A-C9
 1.51 with sigma of 0.02
 N3A-C44A \\sim N3B-C44B
 with sigma of 0.02
 C44A-C43A \\sim C44B-C43B
 with sigma of 0.02
 N3A-C9 \\sim N3B-C9
 with sigma of 0.02
 N4-C43A \\sim N4-C43B
 with sigma of 0.02
3. Rigid bond restraints
 C27, N12, C38, C37, N11, C36
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C7, N8, C46, C45, N7, C34
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
C27 \\sim N12 \\sim C38 \\sim C37 \\sim N11 \\sim C36: within 1.7A with sigma
of 0.04 and sigma for terminal atoms of 0.08
C7 \\sim N8 \\sim C46 \\sim C45 \\sim N7 \\sim C34: within 1.7A with sigma of
0.04 and sigma for terminal atoms of 0.08
Uanis(C63) \\sim Ueq, Uanis(C69) \\sim Ueq, Uanis(C13) \\sim Ueq: with sigma of
0.001 and sigma for terminal atoms of 0.002
Uiso(N3B) = Uiso(C44B) = Uiso(C43B)
5. Others
 Sof(Cl26)=1-FVAR(1)
 Sof(Cl25)=FVAR(1)
 Sof(Cl23)=1-FVAR(2)
 Sof(Cl24)=FVAR(2)
 Sof(Cl6)=1-FVAR(3)
 Sof(Cl7)=FVAR(3)
 Sof(Cl1)=1-FVAR(4)
 Sof(Cl14)=FVAR(4)
 Sof(Cl32)=1-FVAR(5)
 Sof(Cl33)=FVAR(5)
 Sof(Cl37)=1-FVAR(6)
 Sof(Cl38)=FVAR(6)
 Sof(Cl22)=1-FVAR(7)
 Sof(Cl21)=FVAR(7)
 Sof(Cl16)=1-FVAR(8)
 Sof(Cl15)=FVAR(8)
 Fixed Sof: Cl2(0.65) Cl46(0.8) Cl3(0.75) Cl4(0.8) Cl42(0.225) Cl5(0.2)
 Cl29(0.2) Cl34(0.5) Cl35(0.25) Cl36(0.25) Cl40(0.475) Cl9(0.33333)
 Cl10(0.33333) Cl11(0.33333) Cl44(0.25) Cl12(0.25) Cl13(0.75) Cl30(0.8)
 Cl17(0.5) Cl18(0.5) Cl19(0.2) Cl41(0.3) Cl20(0.8) Cl43(0.2) Cl31(0.35) O1(0.5)
 O10(0.5) O2(0.5) O12(0.25) O3(0.5) O9(0.5) O4(0.5) O11(0.5) O5(0.5) O13(0.25)
 O6(0.5) N3A(0.6) HX(0.6) HY(0.6) N3B(0.4) HZ(0.4) H1(0.4) HD(0.6) HE(0.6)
 HF(0.4) HG(0.4) H7(0.6) H8(0.6) H9(0.4) H10(0.4) C43A(0.6) H3(0.6) H2AA(0.6)
 C43B(0.4) H2AA(0.4) H3AA(0.4) C44A(0.6) H3AA(0.6) H4AA(0.6) C44B(0.4)
 H4AA(0.4) H5AA(0.4)
6.a Secondary CH2 refined with riding coordinates:
 N1(H,HA), N2(HB,HC), N3A(HX,HY), N3B(HZ,H1), N4(HD,HE), N4(HF,HG), N5(HH,HI),
 N6(HJ,HK), N7(HL,HM), N8(HN,HO), N9(HP,HQ), N10(HR,HS), N11(HT,HU), N12(HV,HW),
  C7(H4,H5), C8(H6,H6AA), C9(H7,H8), C9(H9,H10), C16(H0BA,H1BA), C17(H2BA,H3BA),
  C18(H4BA,H5BA), C25(H9BA,H0CA), C26(H1CA,H2CA), C27(H3CA,H4CA), C34(H8CA,
 H9CA), C35(H0DA,H1DA), C36(H2DA,H3DA), C37(H4DA,H5DA), C38(H6DA,H7DA),
 C39(H8DA,H9DA), C40(H0EA,H1EA), C41(H2EA,H3EA), C42(H4EA,H5EA), C43A(H3,H2AA),
 C43B(H2AA,H3AA), C44A(H3AA,H4AA), C44B(H4AA,H5AA), C45(H6EA,H7EA), C46(H8EA,
 H9EA), C47(H0FA,H1FA), C48(H2FA,H3FA), N13(H4FA,H5FA), N14(H6FA,H7FA),
 N15(H8FA,H9FA), N16(H0GA,H1GA), N17(H2GA,H3GA), N18(H4GA,H5GA), N19(H6GA,H7GA),
  N20(H8GA,H9GA), N21(H0HA,H1HA), N22(H2HA,H3HA), N23(H4HA,H5HA), N24(H6HA,
 H7HA), C55(H1IA,H2IA), C56(H3IA,H4IA), C57(H5IA,H6IA), C64(H0JA,H1JA),
 C65(H2JA,H3JA), C66(H4JA,H5JA), C73(H9JA,H0KA), C74(H1KA,H2KA), C75(H3KA,H4KA),
  C82(H8KA,H9KA), C83(H0LA,H1LA), C84(H2LA,H3LA), C85(H4LA,H5LA), C86(H6LA,
 H7LA), C87(H8LA,H9LA), C88(H0MA,H1MA), C89(H2MA,H3MA), C90(H4MA,H5MA),
 C91(H6MA,H7MA), C92(H8MA,H9MA), C93(H0NA,H1NA), C94(H2NA,H3NA), C95(H4NA,H5NA),
  C96(H6NA,H7NA)
6.b Aromatic/amide H refined with riding coordinates:
 C2(H0AA), C4(H1AA), C6(H2), C11(H7AA), C13(H8AA), C15(H9AA), C20(H6BA),
 C22(H7BA), C24(H8BA), C29(H5CA), C31(H6CA), C33(H7CA), C50(H8HA), C52(H9HA),
 C54(H0IA), C59(H7IA), C61(H8IA), C63(H9IA), C68(H6JA), C70(H7JA), C72(H8JA),
 C77(H5KA), C79(H6KA), C81(H7KA)
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_plat201_alert_2_b
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Problem: Isotropic non-H Atoms in Main Residue(s) ....... 4 Report
Response: One of the cage vertices was disordered over two positions. 
Disordered atoms were refined isotropically.
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_plat306_alert_2_b
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Problem: Isolated Oxygen Atom (H-atoms Missing ?)
Response: It was not possible to accurately locate H-atoms for the H2O
molecules in the crystal structure.  
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_plat340_alert_3_b
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Problem: LLow Bond Precision on C-C Bonds ............... 0.0115 Ang.
Response: Disorder in the crystal structure resulted in low
bond precision on C-C bonds.
;
_shelx_res_checksum              70023
_shelx_hkl_checksum              91231
_olex2_submission_special_instructions 'No special instructions were received'