A systematic study of the interplay between guest molecule structure and intermolecular interactions in crystalline sponges
Carroll, Robert C.; Harrowven, David C.; Pearce, James E.; Coles, Simon J.; IUCrJ 10 (2023) 497–508; doi:10.1107/S2052252523005146

data_1569424
_publ_section_title
;
 A systematic study of the interplay between guest molecule structure and
 intermolecular interactions in crystalline sponges
;
_journal_issue                   4
_journal_name_full               IUCrJ
_journal_page_first              497
_journal_page_last               508
_journal_paper_doi               10.1107/S2052252523005146
_journal_volume                  10
_journal_year                    2023
_chemical_formula_moiety
'C36 H24 I6 N12 Zn3, 0.534(C19 H16 O), 0.35(C6 H12)'
_chemical_formula_sum            'C48.24 H36.74 I6 N12 O0.53 Zn3'
_chemical_formula_weight         1750.56
_chemical_name_common
'Phenyl Biaryl Alcohol-2-Phenyl (absorbed in crystalline sponge)'
_chemical_name_systematic
'2''-methyl-[1,1':3',1''-terphenyl]-4'-ol (absorbed in crystalline sponge)'
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2023-04-04
_audit_creation_method
;
Olex2 1.5
(compiled 2023.03.06 svn.rbb2c1857 for OlexSys, GUI svn.r6748)
;
_cell_angle_alpha                90
_cell_angle_beta                 101.777(2)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   34.9529(6)
_cell_length_b                   14.9266(2)
_cell_length_c                   30.7318(5)
_cell_measurement_reflns_used    9053
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      74.0000
_cell_measurement_theta_min      3.2350
_cell_volume                     15696.1(4)
_computing_cell_refinement       'CrysAlisPro 1.171.41.116a (Rigaku OD, 2021)'
_computing_data_collection       'CrysAlisPro 1.171.41.116a (Rigaku OD, 2021)'
_computing_data_reduction        'CrysAlisPro 1.171.41.116a (Rigaku OD, 2021)'
_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      100(2)
_diffrn_detector                 'hybrid pixel array detector'
_diffrn_detector_area_resol_mean 10
_diffrn_detector_dtime           0.000
_diffrn_detector_type            'Rigaku, HyPix 6000HE'
_diffrn_measured_fraction_theta_full 0.983
_diffrn_measured_fraction_theta_max 0.983
_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   -142.00 -85.00   0.50    1.60    -- -103.00  -9.00 128.00  114
  2  \w    -69.00 -44.00   0.50    1.60    -- -103.00  61.00 -60.00   50
  3  \w    -69.00 -44.00   0.50    1.60    -- -103.00  61.00 -30.00   50
  4  \w   -164.00 -92.00   0.50    1.60    -- -103.00 -61.00  60.00  144
  5  \w    -58.00 -32.00   0.50    1.60    -- -103.00  61.00-120.00   52
  6  \w     85.00 168.00   0.50    1.60    --  101.75   9.00 -57.00  166
  7  \w    134.00 161.00   0.50    1.60    --  101.75  45.00-180.00   54
  8  \w     40.00  75.00   0.50    1.60    --  101.75 -61.00 -60.00   70
  9  \w     29.00 106.00   0.50    1.60    --  101.75 -94.00 -30.00  154
 10  \w     33.00  75.00   0.50    1.60    --  101.75 -94.00-120.00   84
 11  \w     37.00 104.00   0.50    1.60    --  101.75 -94.00  30.00  134
 12  \w     79.00 106.00   0.50    1.60    --  101.75 -94.00  60.00   54
 13  \w     29.00  75.00   0.50    1.60    --  101.75 -61.00  60.00   92
 14  \w     47.00  72.00   0.50    1.60    --  101.75 -94.00  60.00   50
 15  \w     45.00  73.00   0.50    1.60    --  101.75 -61.00 150.00   56
 16  \w     89.00 114.00   0.50    1.60    --  101.75  45.00-180.00   50
 17  \w   -113.00 -35.00   0.50    0.40    --  -46.77  -9.00 128.00  156
 18  \w     28.00  53.00   0.50    0.40    --   46.77   9.00 -57.00   50
 19  \w     65.00 121.00   0.50    0.40    --   46.77   9.00 -57.00  112
 20  \w    -13.00  18.00   0.50    0.40    --   46.77  -9.00 128.00   62
 21  \w     -9.00  24.00   0.50    0.40    --  -46.77   9.00 -57.00   66
 22  \w    -38.00  16.00   0.50    0.40    --  -46.77  37.00 120.00  108
 23  \w    -26.00  44.00   0.50    0.40    --   46.77 -37.00   0.00  140
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_details
'Rigaku Oxford Difffraction, UG2 \k goniometer'
_diffrn_measurement_device_type
'Rigaku 007HF equipped with Varimax confocal mirrors and a UG2 goniometer and HyPix 6000HE detector'
_diffrn_measurement_method       'profile data from \w-scans'
_diffrn_measurement_specimen_support 'MiTeGen loops'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0105016000
_diffrn_orient_matrix_UB_12      0.0102437000
_diffrn_orient_matrix_UB_13      -0.0509370000
_diffrn_orient_matrix_UB_21      -0.0435871000
_diffrn_orient_matrix_UB_22      0.0073778000
_diffrn_orient_matrix_UB_23      0.0019466000
_diffrn_orient_matrix_UB_31      0.0041727000
_diffrn_orient_matrix_UB_32      0.1024097000
_diffrn_orient_matrix_UB_33      0.0049496000
_diffrn_radiation_collimation    0.3
_diffrn_radiation_monochromator  'Varimax focusing mirrors'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.0280
_diffrn_reflns_av_unetI/netI     0.0266
_diffrn_reflns_Laue_measured_fraction_full 0.983
_diffrn_reflns_Laue_measured_fraction_max 0.983
_diffrn_reflns_limit_h_max       40
_diffrn_reflns_limit_h_min       -42
_diffrn_reflns_limit_k_max       17
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       35
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            49673
_diffrn_reflns_point_group_measured_fraction_full 0.983
_diffrn_reflns_point_group_measured_fraction_max 0.983
_diffrn_reflns_theta_full        67.679
_diffrn_reflns_theta_max         68.245
_diffrn_reflns_theta_min         2.583
_diffrn_source                   'Rotating anode'
_diffrn_source_current           30.0
_diffrn_source_power             1.2
_diffrn_source_target            Cu
_diffrn_source_type              'Rigaku 007 HF'
_diffrn_source_voltage           40.0
_exptl_absorpt_coefficient_mu    19.861
_exptl_absorpt_correction_T_max  0.400
_exptl_absorpt_correction_T_min  0.081
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.116a (Rigaku Oxford Diffraction, 2021)
Analytical numeric absorption correction using a multifaceted crystal
model based on expressions derived by R.C. Clark & J.S. Reid.
(Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
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    1.482
_exptl_crystal_description       block
_exptl_crystal_F_000             6580
_exptl_crystal_size_max          0.31
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.06
_refine_diff_density_max         1.029
_refine_diff_density_min         -0.861
_refine_diff_density_rms         0.165
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     962
_refine_ls_number_reflns         14120
_refine_ls_number_restraints     368
_refine_ls_restrained_S_all      1.037
_refine_ls_R_factor_all          0.0643
_refine_ls_R_factor_gt           0.0587
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1072P)^2^+78.6030P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1757
_refine_ls_wR_factor_ref         0.1807
_reflns_Friedel_coverage         0.000
_reflns_number_gt                12203
_reflns_number_total             14120
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5059.cif
_cod_data_source_block           PBA-2-Phenyl_CrystallineSponge
_cod_database_code               1569424
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         '(Zn3 I6 N12 H24 C36) (C19 H16 O)2 (C6 H14)'
_chemical_oxdiff_usercomment     'Phenyl Biaryl '
_shelx_estimated_absorpt_t_max   0.382
_shelx_estimated_absorpt_t_min   0.063
_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
 C2A-C14A
 1.54 with sigma of 0.02
 C7A-C4A
 1.54 with sigma of 0.02
 C801-C802 = C801-C806 = C802-C803 = C803-C804 = C804-C805 = C805-C806
 1.54 with sigma of 0.02
 C7B-C13B
 2.5 with sigma of 0.04
 C9B-C13B
 2.5 with sigma of 0.04
 C4B-O1B
 2.4 with sigma of 0.04
 C6B-O1B
 2.4 with sigma of 0.04
 C13A-C7A
 2.5 with sigma of 0.04
 C13A-C9A
 2.5 with sigma of 0.04
 C4B-C7B \\sim C14B-C2B
 with sigma of 0.02
 C3A-C7A \\sim C7A-C5A
 with sigma of 0.04
 C12A-C4A \\sim C4A-C8A
 with sigma of 0.04
 I303-Zn32 \\sim I403-Zn42 \\sim I304-Zn32 \\sim I404-Zn42
 with sigma of 0.02
 C801-C805 \\sim C803-C805 \\sim C802-C806 \\sim C802-C804 \\sim C804-C806
\\sim C801-C803
 with sigma of 0.04
 I301-I302 \\sim I401-I402 \\sim I501-I502
 with sigma of 0.04
 I502-Zn51 \\sim I402-Zn41 \\sim I302-Zn31 \\sim I501-Zn51 \\sim I401-Zn41
\\sim I301-Zn31
 with sigma of 0.02
 Zn53-N306 \\sim Zn43-N306
 with sigma of 0.02
 I506-N307 \\sim I406-N307
 with sigma of 0.04
 Zn53-N307 \\sim Zn43-N307
 with sigma of 0.02
 I506-N306 \\sim I406-N306
 with sigma of 0.04
 I505-I506 \\sim I405-I406
 with sigma of 0.04
 I505-N306 \\sim I405-N306
 with sigma of 0.04
 I505-N307 \\sim I405-N307
 with sigma of 0.04
 I506-Zn53 \\sim I406-Zn43
 with sigma of 0.02
 I505-Zn53 \\sim I405-Zn43
 with sigma of 0.02
3. Restrained planarity
 C4A, C5A, C6A, O1A
 with sigma of 0.05
4. Uiso/Uaniso restraints and constraints
C5B \\sim C14B \\sim C15B \\sim C19B \\sim C2B \\sim C16B \\sim C18B \\sim C1B
\\sim C3B \\sim C17B \\sim C6B \\sim C4B \\sim C7B \\sim O1B \\sim C8B \\sim
C12B \\sim C9B \\sim C13B \\sim C11B \\sim C10B: within 1.7A with sigma of 0.02
and sigma for terminal atoms of 0.04 within 1.7A
C801 \\sim C802 \\sim C803 \\sim C804 \\sim C805 \\sim C806: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
O1A \\sim C5A \\sim C6A \\sim C4A \\sim C1A \\sim C3A \\sim C7A \\sim C2A \\sim
C8A \\sim C12A \\sim C14A \\sim C9A \\sim C13A \\sim C11A \\sim C15A \\sim C19A
\\sim C10A \\sim C16A \\sim C18A \\sim C17A: within 1.7A with sigma of 0.04 and
sigma for terminal atoms of 0.08 within 1.7A
5. Others
 1*[Sof(I302)+Sof(I301)+Sof(Zn31)]+1*[Sof(I401)+Sof(Zn41)+Sof(I402)]+1*
 [Sof(Zn51)+Sof(I502)+Sof(I501)]=1 with esd of 0.00001
 1*[Sof(I505)+Sof(I506)+Sof(Zn53)]+1*[Sof(Zn43)+Sof(I405)+Sof(I406)]+1*
 [Sof(I305)+Sof(I306)+Sof(Zn33)]=1 with esd of 0.00001
 Sof(I403)=Sof(Zn42)=Sof(I404)=1-FVAR(1)
 Sof(I303)=Sof(I304)=Sof(Zn32)=FVAR(1)
 Sof(I302)=Sof(I301)=Sof(Zn31)=FVAR(2)
 Sof(I401)=Sof(Zn41)=Sof(I402)=FVAR(3)
 Sof(Zn51)=Sof(I502)=Sof(I501)=FVAR(4)
 Sof(I505)=Sof(I506)=Sof(Zn53)=FVAR(5)
 Sof(Zn43)=Sof(I405)=Sof(I406)=FVAR(6)
 Sof(I305)=Sof(I306)=Sof(Zn33)=FVAR(7)
 Fixed Sof: C2A(0.3066) C3A(0.3066) H3A(0.3066) C4A(0.3066) C5A(0.3066)
 C6A(0.3066) H6A(0.3066) C1A(0.3066) H1A(0.3066) C14A(0.3066) C15A(0.3066)
 H15A(0.3066) C16A(0.3066) H16A(0.3066) C17A(0.3066) H17A(0.3066) C18A(0.3066)
 H18A(0.3066) C19A(0.3066) H19A(0.3066) C14B(0.22708) C15B(0.22708)
 H15B(0.22708) C16B(0.22708) H16B(0.22708) C17B(0.22708) H17B(0.22708)
 C18B(0.22708) H18B(0.22708) C19B(0.22708) H19B(0.22708) C7B(0.22708)
 C8B(0.22708) C9B(0.22708) H9B(0.22708) C10B(0.22708) H10B(0.22708)
 C11B(0.22708) H11B(0.22708) C12B(0.22708) H12B(0.22708) C4B(0.22708)
 C5B(0.22708) C6B(0.22708) H6B(0.22708) C1B(0.22708) H1B(0.22708) C2B(0.22708)
 C3B(0.22708) H3B(0.22708) O1A(0.3066) H1AA(0.3066) C7A(0.3066) C12A(0.3066)
 H12A(0.3066) C11A(0.3066) H11A(0.3066) C10A(0.3066) H10A(0.3066) C9A(0.3066)
 H9A(0.3066) C8A(0.3066) C13A(0.3066) H13A(0.3066) H13B(0.3066) H13C(0.3066)
 C13B(0.22708) H13D(0.22708) H13E(0.22708) H13F(0.22708) O1B(0.22708)
 H1BA(0.22708) C801(0.35) H80A(0.35) H80B(0.35) C802(0.35) H80C(0.35)
 H80D(0.35) C803(0.35) H80E(0.35) H80F(0.35) C804(0.35) H80G(0.35) H80H(0.35)
 C805(0.35) H80I(0.35) H80J(0.35) C806(0.35) H80K(0.35) H80L(0.35)
 Fixed Uiso: I505(0.08) I506(0.08) Zn53(0.08) Zn51(0.08) I502(0.08) I501(0.08)
6.a Secondary CH2 refined with riding coordinates:
 C801(H80A,H80B), C802(H80C,H80D), C803(H80E,H80F), C804(H80G,H80H), C805(H80I,
 H80J), C806(H80K,H80L)
6.b Aromatic/amide H refined with riding coordinates:
 C333(H333), C332(H332), C322(H322), C302(H302), C313(H313), C304(H304),
 C335(H335), C315(H315), C301(H301), C310(H310), C317(H317), C312(H312),
 C336(H336), C318(H318), C331(H331), C323(H323), C311(H311), C305(H305),
 C330(H330), C328(H328), C314(H314), C329(H329), C320(H320), C319(H319),
 C3A(H3A), C6A(H6A), C1A(H1A), C15A(H15A), C16A(H16A), C17A(H17A), C18A(H18A),
 C19A(H19A), C15B(H15B), C16B(H16B), C17B(H17B), C18B(H18B), C19B(H19B),
 C9B(H9B), C10B(H10B), C11B(H11B), C12B(H12B), C6B(H6B), C1B(H1B), C3B(H3B),
 C12A(H12A), C11A(H11A), C10A(H10A), C9A(H9A)
6.c Fitted hexagon refined as free rotating group:
 C2A(C3A,C4A,C5A,C6A,C1A), C14A(C15A,C16A,C17A,C18A,C19A), C14B(C15B,C16B,C17B,
 C18B,C19B), C7B(C8B,C9B,C10B,C11B,C12B), C4B(C5B,C6B,C1B,C2B,C3B), C7A(C12A,
 C11A,C10A,C9A,C8A)
6.d Tetrahedral OH refined with riding coordinates:
 O1A(H1AA), O1B(H1BA)
6.e Idealised Me refined with everything fixed:
 C13A(H13A,H13B,H13C), C13B(H13D,H13E,H13F)
;
_shelx_res_checksum              90328
_shelx_hkl_checksum              96914
_olex2_date_sample_data_collection 2021-11-08
_olex2_date_sample_submission    2021-11-08
_olex2_submission_original_sample_id 'Phenyl Biaryl Alcohol-2-Phenyl'
_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
- Detector area scaling
- B-factor correction
;
_oxdiff_exptl_absorpt_empirical_full_max 2.720
_oxdiff_exptl_absorpt_empirical_full_min 0.506