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_1569415
_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, 0.543(C16 H15 N O), 0.208(C6 H12)'
_chemical_formula_sum            'C45.94 H34.64 I6 N12.54 O0.54 Zn3'
_chemical_formula_weight         1728.59
_chemical_name_common
'Benzyl Biaryl Alcohol-10-Nitrile (absorbed in crystalline sponge)'
_chemical_name_systematic
'2'-(hydroxymethyl)-2,6-dimethyl-[1,1'-biphenyl]-4-carbonitrile (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                 102.899(6)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   35.620(2)
_cell_length_b                   14.9567(3)
_cell_length_c                   30.9945(16)
_cell_measurement_reflns_used    7806
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      71.4210
_cell_measurement_theta_min      2.8920
_cell_volume                     16095.9(13)
_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 2014/5 (Sheldrick, 2014)'
_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 0.990
_diffrn_measured_fraction_theta_max 0.989
_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   -174.00 -94.00   0.50    1.60    -- -103.00 -36.00-166.00  160
  2  \w   -111.00 -82.00   0.50    1.60    -- -103.00 125.00  90.00   58
  3  \w    -60.00 -35.00   0.50    1.60    -- -103.00  61.00  30.00   50
  4  \w    -69.00 -31.00   0.50    1.60    -- -103.00  61.00  90.00   76
  5  \w    -64.00 -38.00   0.50    1.60    -- -103.00  61.00 120.00   52
  6  \w    -64.00 -36.00   0.50    1.60    -- -103.00  61.00 -60.00   56
  7  \w    -64.00 -34.00   0.50    1.60    -- -103.00  61.00 -30.00   60
  8  \w    -66.00 -33.00   0.50    1.60    -- -103.00 125.00  90.00   66
  9  \w     94.00 121.00   0.50    1.60    --  101.75  36.00 -10.00   54
 10  \w     31.00  66.00   0.50    1.60    --  101.75 -61.00 120.00   70
 11  \w     78.00 104.00   0.50    1.60    --  101.75 -94.00 -90.00   52
 12  \w    141.00 174.00   0.50    1.60    --  101.75  15.00 120.00   66
 13  \w     89.00 174.00   0.50    1.60    --  101.75  45.00  60.00  170
 14  \w     31.00  64.00   0.50    1.60    --  101.75 -61.00   0.00   66
 15  \w     41.00  74.00   0.50    1.60    --  101.75 -61.00  60.00   66
 16  \w     29.00  56.00   0.50    1.60    --  101.75 -61.00  90.00   54
 17  \w     97.00 124.00   0.50    1.60    --  101.75  15.00 120.00   54
 18  \w     41.00  73.00   0.50    1.60    --  101.75 -61.00 -90.00   64
 19  \w     32.00  73.00   0.50    1.60    --  101.75 -61.00-180.00   82
 20  \w     33.00  75.00   0.50    1.60    --  101.75 -61.00-150.00   84
 21  \w    -36.00  27.00   0.50    0.40    --  -46.24  36.00 -10.00  126
 22  \w   -119.00 -42.00   0.50    0.40    --  -46.24 -36.00-166.00  154
 23  \w     42.00 118.00   0.50    0.40    --   46.24  36.00 -10.00  152
 24  \w      8.00  33.00   0.50    0.40    --   46.24 -36.00-166.00   50
 25  \w    -37.00  27.00   0.50    0.40    --  -46.24  37.00 120.00  128
 26  \w     -9.00  29.00   0.50    0.40    --  -46.24  19.00 120.00   76
;
_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      -0.0107860000
_diffrn_orient_matrix_UB_12      -0.0010454000
_diffrn_orient_matrix_UB_13      -0.0509707000
_diffrn_orient_matrix_UB_21      -0.0381950000
_diffrn_orient_matrix_UB_22      0.0477168000
_diffrn_orient_matrix_UB_23      0.0006969000
_diffrn_orient_matrix_UB_31      0.0198383000
_diffrn_orient_matrix_UB_32      0.0912801000
_diffrn_orient_matrix_UB_33      -0.0009200000
_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  0.0356
_diffrn_reflns_av_unetI/netI     0.0275
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.989
_diffrn_reflns_limit_h_max       42
_diffrn_reflns_limit_h_min       -34
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       36
_diffrn_reflns_limit_l_min       -37
_diffrn_reflns_number            49545
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.989
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.247
_diffrn_reflns_theta_min         2.545
_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    19.362
_exptl_absorpt_correction_T_max  0.385
_exptl_absorpt_correction_T_min  0.114
_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    1.427
_exptl_crystal_description       block
_exptl_crystal_F_000             6483
_exptl_crystal_size_max          0.18
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.06
_refine_diff_density_max         1.483
_refine_diff_density_min         -1.335
_refine_diff_density_rms         0.220
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.094
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     940
_refine_ls_number_reflns         14578
_refine_ls_number_restraints     389
_refine_ls_restrained_S_all      1.084
_refine_ls_R_factor_all          0.1468
_refine_ls_R_factor_gt           0.1280
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1229P)^2^+651.1928P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3303
_refine_ls_wR_factor_ref         0.3424
_reflns_Friedel_coverage         0.000
_reflns_number_gt                11166
_reflns_number_total             14578
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5059.cif
_cod_data_source_block           BBA-10-Nitrile_CrystallineSponge
_cod_original_cell_volume        16096.0(14)
_cod_database_code               1569415
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         '(Zn3 I6 N12 H24 C36) (C16 H15 N O)2 (C6 H12)2'
_chemical_oxdiff_usercomment     JP-9300-25
_shelx_estimated_absorpt_t_max   0.390
_shelx_estimated_absorpt_t_min   0.128
_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
 C16A-C10A
 1.54 with sigma of 0.02
 O1B-C14B
 1.43 with sigma of 0.02
 N1A-C16A
 1.2 with sigma of 0.02
 C5B-C14B
 1.54 with sigma of 0.02
 N1B-C16B
 1.2 with sigma of 0.02
 C13A-C8A = C15A-C12A
 1.54 with sigma of 0.02
 C7A-C4A
 1.54 with sigma of 0.02
 C15B-C12B = C8B-C13B
 1.54 with sigma of 0.02
 C14A-C5A
 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
 C9B-C16B
 2.5 with sigma of 0.04
 C11A-C16A
 2.5 with sigma of 0.04
 C11B-C16B
 2.5 with sigma of 0.04
 C9A-C16A
 2.5 with sigma of 0.04
 C5A-O1A
 2.4 with sigma of 0.04
 C6A-C14A
 2.5 with sigma of 0.04
 C4A-C14A
 2.5 with sigma of 0.04
 C801-C803 = C801-C805 = C802-C804 = C803-C805 = C804-C806
 2.54 with sigma of 0.04
 N1A-C9A \\sim N1A-C11A
 with sigma of 0.01
 C5A-C7A \\sim C7A-C3A
 with sigma of 0.04
 C12A-C4A \\sim C4A-C8A
 with sigma of 0.04
 I302-Zn31 \\sim I402-Zn41
 with sigma of 0.02
 I301-Zn31 \\sim I401-Zn41
 with sigma of 0.02
 Zn31-N301 \\sim Zn41-N301
 with sigma of 0.02
 I301-N301 \\sim I401-N301
 with sigma of 0.04
 I302-I301 \\sim I402-I401
 with sigma of 0.04
 I302-N301 \\sim I402-N301
 with sigma of 0.04
 I403-N306 \\sim I303-N306
 with sigma of 0.04
 I403-I404 \\sim I303-I304
 with sigma of 0.04
 I403-Zn42 \\sim I303-Zn32
 with sigma of 0.02
 I404-N307 \\sim I304-N307
 with sigma of 0.04
 I403-N307 \\sim I303-N307
 with sigma of 0.04
 I404-Zn42 \\sim I304-Zn32
 with sigma of 0.02
 I404-N306 \\sim I304-N306
 with sigma of 0.04
 Zn42-N307 \\sim Zn32-N307
 with sigma of 0.02
 Zn42-N306 \\sim Zn32-N306
 with sigma of 0.02
 I405-N312 \\sim I305-N312
 with sigma of 0.04
 I405-I406 \\sim I305-I306
 with sigma of 0.04
 Zn43-N312 \\sim Zn33-N312
 with sigma of 0.02
 I406-N312 \\sim I306-N312
 with sigma of 0.04
 I405-Zn43 \\sim I305-Zn33
 with sigma of 0.02
 I406-Zn43 \\sim I306-Zn33
 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
 C801-C802 \\sim C802-C803 \\sim C803-C804 \\sim C804-C805 \\sim C805-C806
\\sim C806-C801
 with sigma of 0.02
3. Restrained planarity
 C9A, C10A, C11A, C16A, N1A
 with sigma of 0.05
 C9B, C10B, C11B, C16B, N1B
 with sigma of 0.05
4. Uiso/Uaniso restraints and constraints
C5B \\sim O1B \\sim C14B \\sim C4B \\sim C6B \\sim C3B \\sim C7B \\sim C1B
\\sim C2B \\sim C8B \\sim C12B \\sim C9B \\sim C13B \\sim C11B \\sim C15B \\sim
C10B \\sim C16B \\sim N1B: within 1.7A with sigma of 0.02 and sigma for
terminal atoms of 0.04 within 1.7A
C4A \\sim C5A \\sim C3A \\sim C7A \\sim C6A \\sim C14A \\sim C2A \\sim C12A
\\sim C8A \\sim C1A \\sim O1A \\sim C15A \\sim C11A \\sim C13A \\sim C9A \\sim
C10A \\sim C16A \\sim N1A: 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
Uanis(Zn32) = Uanis(Zn42)
Uanis(Zn53) = Uanis(Zn43) = Uanis(Zn33)
Uanis(I506) = Uanis(I306) = Uanis(I406)
5. Rigid body (RIGU) restrains
 C801, C802, C803, C804, C805, C806
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 1*[Sof(I302)+Sof(I301)+Sof(Zn31)]+1*[Sof(Zn41)+Sof(I402)+Sof(I401)]+1*
 [Sof(I502)+Sof(I501)+Sof(Zn51)]=1 with esd of 0.00001
 1*[Sof(I405)+Sof(I406)+Sof(Zn43)]+1*[Sof(I305)+Sof(Zn33)+Sof(I306)]+1*
 [Sof(I505)+Sof(I506)+Sof(Zn53)]=1 with esd of 0.00001
 Sof(I304)=Sof(I303)=Sof(Zn32)=1-FVAR(1)
 Sof(I403)=Sof(I404)=Sof(Zn42)=FVAR(1)
 Sof(I302)=Sof(I301)=Sof(Zn31)=FVAR(2)
 Sof(Zn41)=Sof(I402)=Sof(I401)=FVAR(3)
 Sof(I502)=Sof(I501)=Sof(Zn51)=FVAR(4)
 Sof(I405)=Sof(I406)=Sof(Zn43)=FVAR(5)
 Sof(I305)=Sof(Zn33)=Sof(I306)=FVAR(6)
 Sof(I505)=Sof(I506)=Sof(Zn53)=FVAR(7)
 Fixed Sof: O1B(0.271) H1BA(0.271) C4B(0.271) C3B(0.271) H3B(0.271) C2B(0.271)
 H2B(0.271) C1B(0.271) H1B(0.271) C6B(0.271) H6B(0.271) C5B(0.271) C7B(0.271)
 C8B(0.271) C9B(0.271) H9B(0.271) C10B(0.271) C11B(0.271) H11B(0.271)
 C12B(0.271) N1B(0.271) C16B(0.271) C15B(0.271) H16A(0.271) H16B(0.271)
 H16C(0.271) C14B(0.271) H14A(0.271) H14B(0.271) C13B(0.271) H13A(0.271)
 H13B(0.271) H13C(0.271) C4A(0.27213) C5A(0.27213) C6A(0.27213) H6A(0.27213)
 C1A(0.27213) H1A(0.27213) C2A(0.27213) H2A(0.27213) C3A(0.27213) H3A(0.27213)
 C15A(0.27213) H16D(0.27213) H16E(0.27213) H16F(0.27213) C13A(0.27213)
 H13D(0.27213) H13E(0.27213) H13F(0.27213) C7A(0.27213) C12A(0.27213)
 C11A(0.27213) H11A(0.27213) C10A(0.27213) C9A(0.27213) H9A(0.27213)
 C8A(0.27213) O1A(0.27213) H1AA(0.27213) C14A(0.27213) H14C(0.27213)
 H14D(0.27213) C16A(0.27213) N1A(0.27213) C801(0.20804) H80A(0.20804)
 H80B(0.20804) C802(0.20804) H80C(0.20804) H80D(0.20804) C803(0.20804)
 H80E(0.20804) H80F(0.20804) C804(0.20804) H80G(0.20804) H80H(0.20804)
 C805(0.20804) H80I(0.20804) H80J(0.20804) C806(0.20804) H80K(0.20804)
 H80L(0.20804)
 Fixed Uiso: I502(0.08) I501(0.08) Zn51(0.08)
7.a Secondary CH2 refined with riding coordinates:
 C14B(H14A,H14B), C14A(H14C,H14D), C801(H80A,H80B), C802(H80C,H80D), C803(H80E,
 H80F), C804(H80G,H80H), C805(H80I,H80J), C806(H80K,H80L)
7.b Aromatic/amide H refined with riding coordinates:
 C332(H332), C333(H333), C312(H312), C301(H301), C317(H317), C335(H335),
 C329(H329), C313(H313), C323(H323), C322(H322), C302(H302), C336(H336),
 C315(H315), C318(H318), C330(H330), C320(H320), C314(H314), C319(H319),
 C328(H328), C331(H331), C310(H310), C304(H304), C311(H311), C305(H305),
 C3B(H3B), C2B(H2B), C1B(H1B), C6B(H6B), C9B(H9B), C11B(H11B), C6A(H6A),
 C1A(H1A), C2A(H2A), C3A(H3A), C11A(H11A), C9A(H9A)
7.c Fitted hexagon refined as free rotating group:
 C4B(C3B,C2B,C1B,C6B,C5B), C7B(C8B,C9B,C10B,C11B,C12B), C4A(C5A,C6A,C1A,C2A,
 C3A), C7A(C12A,C11A,C10A,C9A,C8A)
7.d Tetrahedral OH refined with riding coordinates:
 O1A(H1AA)
7.e Idealised Me refined with everything fixed:
 C15B(H16A,H16B,H16C), C15A(H16D,H16E,H16F), C13A(H13D,H13E,H13F)
7.f Idealised Me refined as rotating group:
 C13B(H13A,H13B,H13C)
7.g Idealised tetrahedral OH refined as rotating group:
 O1B(H1BA)
;
_shelx_res_checksum              46600
_shelx_hkl_checksum              21681
_olex2_date_sample_data_collection 2022-02-21
_olex2_date_sample_submission    2022-01-21
_olex2_submission_original_sample_id 'Benzyl Biaryl Alcohol-10-Nitrile'
_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 1.896
_oxdiff_exptl_absorpt_empirical_full_min 0.562