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_1569416
_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, 0.598(C14 H14 O2), 0.2(C6 H12)'
_chemical_formula_sum            'C45.57 H34.77 I6 N12 O1.2 Zn3'
_chemical_formula_weight         1727.08
_chemical_name_common
'Phenyl Biaryl Alcohol-12-Methoxy (absorbed in crystalline sponge)'
_chemical_name_systematic
'2'-methoxy-6'-methyl-[1,1'-biphenyl]-2-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                 102.979(2)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   35.3379(7)
_cell_length_b                   14.8649(2)
_cell_length_c                   31.6259(7)
_cell_measurement_reflns_used    6933
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      74.7240
_cell_measurement_theta_min      2.8610
_cell_volume                     16188.5(5)
_computing_cell_refinement       'CrysAlisPro 1.171.41.89a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.41.89a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.41.89a (Rigaku OD, 2020)'
_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 0.994
_diffrn_measured_fraction_theta_max 0.993
_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   -173.00 -89.00   0.50    2.00    -- -103.00 -16.00 171.00  168
  2  \w    -58.00 -32.00   0.50    2.00    -- -103.00  61.00 -60.00   52
  3  \w    -68.00 -34.00   0.50    2.00    -- -103.00  61.00 -90.00   68
  4  \w   -110.00 -46.00   0.50    2.00    -- -103.00 125.00  60.00  128
  5  \w    120.00 146.00   0.50    2.00    --  101.75  16.00 -19.00   52
  6  \w     75.00 101.00   0.50    2.00    --  101.75 -94.00   0.00   52
  7  \w     31.00  75.00   0.50    2.00    --  101.75 -61.00  30.00   88
  8  \w    110.00 174.00   0.50    2.00    --  101.75   0.00 -60.00  128
  9  \w    108.00 167.00   0.50    2.00    --  101.75   0.00  60.00  118
 10  \w     34.00  90.00   0.50    2.00    --  101.75 -94.00 -30.00  112
 11  \w     38.00  64.00   0.50    2.00    --  101.75 -94.00 -90.00   52
 12  \w     34.00  62.00   0.50    2.00    --  101.75 -61.00   0.00   56
 13  \w     38.00  64.00   0.50    2.00    --  101.75 -94.00-180.00   52
 14  \w     72.00  97.00   0.50    2.00    --  101.75 -94.00-180.00   50
 15  \w     31.00  56.00   0.50    2.00    --  101.75 -94.00   0.00   50
 16  \w    -11.00  15.00   0.50    0.50    --  -46.64  16.00 -19.00   52
 17  \w   -115.00 -35.00   0.50    0.50    --  -46.64 -16.00 171.00  160
 18  \w     38.00 120.00   0.50    0.50    --   46.64  16.00 -19.00  164
 19  \w    -28.00  -3.00   0.50    0.50    --   46.64 -16.00 171.00   50
 20  \w     -7.00  27.00   0.50    0.50    --  -46.64  19.00 120.00   68
 21  \w     28.00  92.00   0.50    0.50    --   46.64-125.00  30.00  128
;
_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      0.0212220000
_diffrn_orient_matrix_UB_12      -0.0053801000
_diffrn_orient_matrix_UB_13      0.0481446000
_diffrn_orient_matrix_UB_21      -0.0387437000
_diffrn_orient_matrix_UB_22      -0.0213048000
_diffrn_orient_matrix_UB_23      0.0124581000
_diffrn_orient_matrix_UB_31      0.0070336000
_diffrn_orient_matrix_UB_32      -0.1012869000
_diffrn_orient_matrix_UB_33      -0.0051531000
_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     1.54184
_diffrn_reflns_av_R_equivalents  0.0223
_diffrn_reflns_av_unetI/netI     0.0222
_diffrn_reflns_Laue_measured_fraction_full 0.994
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       42
_diffrn_reflns_limit_h_min       -42
_diffrn_reflns_limit_k_max       9
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            48192
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.247
_diffrn_reflns_theta_min         2.868
_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    19.255
_exptl_absorpt_correction_T_max  0.350
_exptl_absorpt_correction_T_min  0.117
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.89a (Rigaku Oxford Diffraction, 2020)
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    1.417
_exptl_crystal_description       block
_exptl_crystal_F_000             6478
_exptl_crystal_size_max          0.21
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.07
_refine_diff_density_max         1.171
_refine_diff_density_min         -0.864
_refine_diff_density_rms         0.191
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.045
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     894
_refine_ls_number_reflns         14718
_refine_ls_number_restraints     314
_refine_ls_restrained_S_all      1.039
_refine_ls_R_factor_all          0.0694
_refine_ls_R_factor_gt           0.0637
_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^)+(0.1441P)^2^+38.3580P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2014
_refine_ls_wR_factor_ref         0.2097
_reflns_Friedel_coverage         0.000
_reflns_number_gt                12644
_reflns_number_total             14718
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5059.cif
_cod_data_source_block           PBA-12-Methoxy_CrystallineSponge
_cod_original_formula_sum        'C45.57 H34.77 I6 N12 O1.20 Zn3'
_cod_database_code               1569416
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         '(Zn3 I6 N12 H24 C36) (C14 H14 O2)2 (C6 H12)3'
_chemical_oxdiff_usercomment     'Methoxy Biaryl Alcohol'
_shelx_estimated_absorpt_t_max   0.346
_shelx_estimated_absorpt_t_min   0.107
_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
 C5B-O1B
 1.38 with sigma of 0.02
 O2B-C14B
 1.43 with sigma of 0.02
 O2B-C12B
 1.43 with sigma of 0.02
 C808-C809 = C808-C807 = C809-C810 = C810-C811 = C811-C812 = C812-C807
 1.54 with sigma of 0.02
 C806-C801 = C806-C805 = C801-C802 = C802-C803 = C803-C804 = C804-C805
 1.54 with sigma of 0.02
 C9B-C13B
 2.5 with sigma of 0.04
 C7B-C13B
 2.5 with sigma of 0.04
 C4B-O1B
 2.3 with sigma of 0.04
 O1B-C6B
 2.3 with sigma of 0.04
 C806-C802 = C806-C804 = C801-C803 = C802-C804 = C803-C805
 2.54 with sigma of 0.04
 C808-C810 = C808-C812 = C809-C811 = C810-C812 = C811-C807
 2.54 with sigma of 0.04
 C808-C809 \\sim C809-C810 \\sim C810-C811 \\sim C811-C812 \\sim C812-C807
\\sim C807-C808
 with sigma of 0.02
 C806-C801 \\sim C801-C802 \\sim C802-C803 \\sim C803-C804 \\sim C804-C805
\\sim C805-C806
 with sigma of 0.02
 C808-C812 \\sim C810-C812 \\sim C809-C807 \\sim C809-C811 \\sim C811-C807
\\sim C808-C810
 with sigma of 0.04
 C806-C804 \\sim C802-C804 \\sim C801-C805 \\sim C801-C803 \\sim C803-C805
\\sim C806-C802
 with sigma of 0.04
 Zn33-N312 \\sim Zn43-N312
 with sigma of 0.02
 I306-I305 \\sim I406-I405
 with sigma of 0.04
 I306-N312 \\sim I406-N312
 with sigma of 0.04
 I306-Zn33 \\sim I406-Zn43
 with sigma of 0.02
 I305-N312 \\sim I405-N312
 with sigma of 0.04
 I305-Zn33 \\sim I405-Zn43
 with sigma of 0.02
3. Restrained angles
 C13B-C8B-C9B
 fixed at 120 with sigma of 0.02
 C7B-C8B-C13B
 fixed at 120 with sigma of 0.02
4. Restrained planarity
 C4B, C5B, C6B, O1B
 with sigma of 0.05
5. Uiso/Uaniso restraints and constraints
C12A \\sim O2A \\sim C14A \\sim C7A \\sim C11A \\sim C4A \\sim C8A \\sim C10A
\\sim C5A \\sim C3A \\sim C13A \\sim C9A \\sim C6A \\sim O1A \\sim C2A \\sim
C1A: within 1.7A with sigma of 0.04 and sigma for terminal atoms of 0.08 within
1.7A
C806 \\sim C801 \\sim C802 \\sim C803 \\sim C804 \\sim C805: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
C7B \\sim C5B \\sim C6B \\sim C4B \\sim O1B \\sim C1B \\sim C3B \\sim C2B \\sim
C8B \\sim C12B \\sim C9B \\sim C13B \\sim C11B \\sim C10B \\sim O2B \\sim C14B:
within 1.7A with sigma of 0.04 and sigma for terminal atoms of 0.08 within 1.7A
C808 \\sim C809 \\sim C810 \\sim C811 \\sim C812 \\sim C807: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
6. Rigid body (RIGU) restrains
 C806, C801, C802, C803, C804, C805
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C808, C809, C810, C811, C812, C807
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
7. Others
 1*[Sof(I301)+Sof(I302)+Sof(Zn31)]+1*[Sof(I402)+Sof(Zn41)+Sof(I401)]+1*
 [Sof(I502)+Sof(I501)+Sof(Zn51)]+1*[Sof(I602)+Sof(I601)+Sof(Zn61)]=1 with esd
 of 0.00001
 1*[Sof(I306)+Sof(I305)+Sof(Zn33)]+1*[Sof(I405)+Sof(Zn43)+Sof(I406)]+1*
 [Sof(I506)+Sof(I505)+Sof(Zn53)]=1 with esd of 0.00001
 Sof(I403)=1-FVAR(1)
 Sof(I303)=FVAR(1)
 Sof(I301)=Sof(I302)=Sof(Zn31)=FVAR(2)
 Sof(I402)=Sof(Zn41)=Sof(I401)=FVAR(3)
 Sof(I502)=Sof(I501)=Sof(Zn51)=FVAR(4)
 Sof(I602)=Sof(I601)=Sof(Zn61)=FVAR(5)
 Sof(I306)=Sof(I305)=Sof(Zn33)=FVAR(6)
 Sof(I405)=Sof(Zn43)=Sof(I406)=FVAR(7)
 Sof(I506)=Sof(I505)=Sof(Zn53)=FVAR(8)
 Fixed Sof: O2A(0.33203) C3A(0.33203) H3A(0.33203) C2A(0.33203) H2A(0.33203)
 C1A(0.33203) H1A(0.33203) C6A(0.33203) H6A(0.33203) C5A(0.33203) C4A(0.33203)
 C13A(0.33203) H13A(0.33203) H13B(0.33203) H13C(0.33203) C14A(0.33203)
 H14A(0.33203) H14B(0.33203) H14C(0.33203) C9A(0.33203) H9A(0.33203)
 C8A(0.33203) C7A(0.33203) C12A(0.33203) C11A(0.33203) H11A(0.33203)
 C10A(0.33203) H10A(0.33203) O1A(0.33203) H1AA(0.33203) C5B(0.26573)
 C6B(0.26573) H6B(0.26573) C1B(0.26573) H1B(0.26573) C2B(0.26573) H2B(0.26573)
 C3B(0.26573) H3B(0.26573) C4B(0.26573) C8B(0.26573) C9B(0.26573) H9B(0.26573)
 C10B(0.26573) H10B(0.26573) C11B(0.26573) H11B(0.26573) C12B(0.26573)
 C7B(0.26573) O1B(0.26573) H1BA(0.26573) C13B(0.26573) H13D(0.26573)
 H13E(0.26573) H13F(0.26573) O2B(0.26573) C14B(0.26573) H14D(0.26573)
 H14E(0.26573) H14F(0.26573) C808(0.1) H80A(0.1) H80B(0.1) C809(0.1) H80C(0.1)
 H80D(0.1) C810(0.1) H81A(0.1) H81B(0.1) C811(0.1) H81C(0.1) H81D(0.1)
 C812(0.1) H81E(0.1) H81F(0.1) C807(0.1) H80E(0.1) H80F(0.1) C806(0.1)
 H80G(0.1) H80H(0.1) C801(0.1) H80I(0.1) H80J(0.1) C802(0.1) H80K(0.1)
 H80L(0.1) C803(0.1) H80M(0.1) H80N(0.1) C804(0.1) H80O(0.1) H80P(0.1)
 C805(0.1) H80Q(0.1) H80R(0.1)
 Fixed Uiso: I506(0.08) I505(0.08) Zn53(0.08) C808(0.08) C809(0.08) C810(0.08)
 C811(0.08) C812(0.08) C807(0.08) C806(0.08) C801(0.08) C802(0.08) C803(0.08)
 C804(0.08) C805(0.08)
8.a Secondary CH2 refined with riding coordinates:
 C808(H80A,H80B), C809(H80C,H80D), C810(H81A,H81B), C811(H81C,H81D), C812(H81E,
 H81F), C807(H80E,H80F), C806(H80G,H80H), C801(H80I,H80J), C802(H80K,H80L),
 C803(H80M,H80N), C804(H80O,H80P), C805(H80Q,H80R)
8.b Aromatic/amide H refined with riding coordinates:
 C304(H304), C328(H328), C314(H314), C305(H305), C320(H320), C315(H315),
 C329(H329), C319(H319), C335(H335), C311(H311), C331(H331), C302(H302),
 C330(H330), C313(H313), C336(H336), C310(H310), C312(H312), C317(H317),
 C301(H301), C318(H318), C333(H333), C332(H332), C322(H322), C323(H323),
 C3A(H3A), C2A(H2A), C1A(H1A), C6A(H6A), C9A(H9A), C11A(H11A), C10A(H10A),
 C6B(H6B), C1B(H1B), C2B(H2B), C3B(H3B), C9B(H9B), C10B(H10B), C11B(H11B)
8.c Fitted hexagon refined as free rotating group:
 C3A(C2A,C1A,C6A,C5A,C4A), C9A(C8A,C7A,C12A,C11A,C10A), C5B(C6B,C1B,C2B,C3B,
 C4B), C8B(C9B,C10B,C11B,C12B,C7B)
8.d Tetrahedral OH refined with everything fixed:
 O1A(H1AA), O1B(H1BA)
8.e Idealised Me refined with everything fixed:
 C13A(H13A,H13B,H13C), C14A(H14A,H14B,H14C), C13B(H13D,H13E,H13F), C14B(H14D,
 H14E,H14F)
;
_shelx_res_checksum              61477
_shelx_hkl_checksum              70260
_olex2_date_sample_data_collection 2021-09-13
_olex2_date_sample_submission    2021-09-13
_olex2_submission_original_sample_id 'Phenyl Biaryl Alcohol-12-Methoxy'
_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 2.684
_oxdiff_exptl_absorpt_empirical_full_min 0.519