Statistical optimization of guest uptake in crystalline sponges: grading structural outcomes.
Carroll, Robert C.; Coles, Simon J.; IUCrJ 11 (2024) –; doi:10.1107/S2052252524004871

data_1571858
_publ_section_title
;
 Statistical optimization of guest uptake in crystalline sponges: grading
 structural outcomes.
;
_journal_coeditor_code           LT5068
_journal_issue                   4
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252524004871
_journal_volume                  11
_journal_year                    2024
_chemical_formula_moiety         'C72 H47.959 I12 N24 Zn6, 0.68(C15 H16 O3)'
_chemical_formula_sum            'C82.19 H58.83 I12 N24 O2.04 Zn6'
_chemical_formula_weight         3330.36
_chemical_name_systematic
; (2',6'-dimethoxy-[1,1'-biphenyl]-2-yl)methanol 
(absorbed in crystalline sponge)
;
_space_group_crystal_system      monoclinic
_space_group_IT_number           13
_space_group_name_Hall           '-P 2yac'
_space_group_name_H-M_alt        'P 1 2/n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-02-07
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2024.01.24 svn.r2f8d729c for OlexSys, GUI svn.r6923)
;
_cell_angle_alpha                90
_cell_angle_beta                 101.834(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   31.4571(13)
_cell_length_b                   14.9918(3)
_cell_length_c                   34.3610(12)
_cell_measurement_reflns_used    10977
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      67.8330
_cell_measurement_theta_min      2.6610
_cell_volume                     15860.2(9)
_computing_cell_refinement       'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.72a (Rigaku OD, 2022)'
_computing_molecular_graphics    'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2016/6 (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 0.996
_diffrn_measured_fraction_theta_max 0.996
_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 -88.00   0.50    4.00    -- -103.00 -59.00  17.00  170
  2  \w    -65.00 -30.00   0.50    4.00    -- -103.00  59.00 157.00   70
  3  \w    -68.00 -39.00   0.50    4.00    -- -103.00  61.00-150.00   58
  4  \w   -121.00 -90.00   0.50    4.00    -- -103.00 -15.00-120.00   62
  5  \w    -69.00 -44.00   0.50    4.00    -- -103.00  61.00 120.00   50
  6  \w   -173.00-148.00   0.50    4.00    -- -103.00 -15.00-120.00   50
  7  \w    -67.00 -42.00   0.50    4.00    -- -103.00  61.00  30.00   50
  8  \w   -161.00-134.00   0.50    4.00    -- -103.00-125.00 120.00   54
  9  \w   -101.00 -76.00   0.50    4.00    -- -103.00-125.00 120.00   50
 10  \w    -68.00 -31.00   0.50    4.00    -- -103.00  61.00  90.00   74
 11  \w   -174.00 -90.00   0.50    4.00    -- -103.00 -45.00  90.00  168
 12  \w    106.00 131.00   0.50    4.00    --  101.75  59.00 157.00   50
 13  \w     30.00  70.00   0.50    4.00    --  101.75 -59.00  17.00   80
 14  \w     43.00  74.00   0.50    4.00    --  101.75 -61.00-120.00   62
 15  \w     89.00 166.00   0.50    4.00    --  101.75  45.00 -90.00  154
 16  \w     30.00  69.00   0.50    4.00    --  101.75 -61.00-180.00   78
 17  \w     35.00  75.00   0.50    4.00    --  101.75 -61.00 -30.00   80
 18  \w     39.00  64.00   0.50    4.00    --  101.75 -61.00 150.00   50
 19  \w     31.00  81.00   0.50    4.00    --  101.75-125.00 -90.00  100
 20  \w   -117.00 -39.00   0.50    0.68    --  -46.24 -59.00  17.00  156
 21  \w    -39.00  26.00   0.50    0.68    --  -46.24  59.00 157.00  130
 22  \w     51.00  76.00   0.50    0.68    --   46.24  59.00 157.00   50
 23  \w    -23.00  17.00   0.50    0.68    --   46.24 -59.00  17.00   80
 24  \w    -23.00  24.00   0.50    0.68    --   46.24 -19.00-150.00   94
 25  \w    -26.00  24.00   0.50    0.68    --   46.24 -19.00  30.00  100
;
_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      0.0500274000
_diffrn_orient_matrix_UB_12      -0.0038272000
_diffrn_orient_matrix_UB_13      0.0104949000
_diffrn_orient_matrix_UB_21      -0.0004809000
_diffrn_orient_matrix_UB_22      -0.0720064000
_diffrn_orient_matrix_UB_23      -0.0321285000
_diffrn_orient_matrix_UB_31      0.0022683000
_diffrn_orient_matrix_UB_32      0.0731730000
_diffrn_orient_matrix_UB_33      -0.0308759000
_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  0.0569
_diffrn_reflns_av_unetI/netI     0.0442
_diffrn_reflns_Laue_measured_fraction_full 0.996
_diffrn_reflns_Laue_measured_fraction_max 0.996
_diffrn_reflns_limit_h_max       37
_diffrn_reflns_limit_h_min       -37
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       40
_diffrn_reflns_limit_l_min       -41
_diffrn_reflns_number            97907
_diffrn_reflns_point_group_measured_fraction_full 0.996
_diffrn_reflns_point_group_measured_fraction_max 0.996
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.251
_diffrn_reflns_theta_min         2.628
_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    19.630
_exptl_absorpt_correction_T_max  0.329
_exptl_absorpt_correction_T_min  0.100
_exptl_absorpt_correction_type   analytical
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.72a (Rigaku Oxford Diffraction, 2022)
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            'light yellow'
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.395
_exptl_crystal_description       block
_exptl_crystal_F_000             6209
_exptl_crystal_size_max          0.23
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.08
_refine_diff_density_max         1.168
_refine_diff_density_min         -0.828
_refine_diff_density_rms         0.219
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.057
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1563
_refine_ls_number_reflns         28916
_refine_ls_number_restraints     494
_refine_ls_restrained_S_all      1.052
_refine_ls_R_factor_all          0.1477
_refine_ls_R_factor_gt           0.1135
_refine_ls_shift/su_max          0.004
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1381P)^2^+193.4743P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3243
_refine_ls_wR_factor_ref         0.3480
_reflns_Friedel_coverage         0.000
_reflns_number_gt                18549
_reflns_number_total             28916
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5068.cif
_cod_data_source_block           50_1_24a
_cod_database_code               1571858
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         '(Zn3 I6 N12 H24 C36) (C15 H16 O3)2 (C6 H12)2'
_chemical_oxdiff_usercomment     JP-9300-04
_shelx_estimated_absorpt_t_max   0.303
_shelx_estimated_absorpt_t_min   0.093
_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-C13B
 1.51 with sigma of 0.02
 O2B-C8B = O3B-C12B
 1.37 with sigma of 0.02
 C7A-C4A
 1.5 with sigma of 0.02
 C5A-C13A
 1.51 with sigma of 0.02
 O1B-C13B = O2B-C14B = O3B-C15B
 1.43 with sigma of 0.02
 O1A-C13A = O2A-C14A = O3A-C15A
 1.43 with sigma of 0.02
 O3A-C12A = O2A-C8A
 1.37 with sigma of 0.02
 C7B-C4B
 1.5 with sigma of 0.02
 C5A-O1A
 2.4 with sigma of 0.02
 O1B-C5B
 2.4 with sigma of 0.04
 C14B-C8B
 2.4 with sigma of 0.04
 C12B-C15B
 2.4 with sigma of 0.04
 C9B-O2B
 2.4 with sigma of 0.04
 C7B-O2B
 2.4 with sigma of 0.04
 C6B-C13B = C13B-C4B
 2.5 with sigma of 0.04
 C5A-C4A \\sim C6A-C5A \\sim C6A-C1A \\sim C2A-C1A \\sim C3A-C2A \\sim C4A-C3A
 with sigma of 0.02
 C8A-C7A \\sim C7A-C12A \\sim C12A-C11A \\sim C11A-C10A \\sim C9A-C10A \\sim
C9A-C8A
 with sigma of 0.02
 C1A-C5A \\sim C4A-C6A
 with sigma of 0.02
 C8B-C4B \\sim C4B-C12B
 with sigma of 0.04
 C5B-C7B \\sim C7B-C3B
 with sigma of 0.04
 I312-Zn36 \\sim I412-Zn46
 with sigma of 0.02
 I303-Zn32 \\sim I403-Zn42
 with sigma of 0.02
 I311-Zn36 \\sim I411-Zn46
 with sigma of 0.02
 I304-Zn32 \\sim I404-Zn42
 with sigma of 0.02
 Zn36-N319 \\sim Zn46-N319
 with sigma of 0.02
 Zn32-N305 \\sim Zn42-N305
 with sigma of 0.02
 I504-Zn52 \\sim I404-Zn42
 with sigma of 0.02
 Zn36-N318 \\sim Zn46-N318
 with sigma of 0.02
 I312-I311 \\sim I412-I411
 with sigma of 0.04
 I503-Zn52 \\sim I403-Zn42
 with sigma of 0.02
 I312-N319 \\sim I412-N319
 with sigma of 0.04
 I312-N318 \\sim I412-N318
 with sigma of 0.04
 I311-N319 \\sim I411-N319
 with sigma of 0.04
 I311-N318 \\sim I411-N318
 with sigma of 0.04
 I409-Zn45 \\sim I309-Zn35
 with sigma of 0.02
 I410-Zn45 \\sim I310-Zn35
 with sigma of 0.02
 Zn45-N317 \\sim Zn35-N317
 with sigma of 0.02
 I409-I410 \\sim I309-I310
 with sigma of 0.04
 I409-N317 \\sim I309-N317
 with sigma of 0.04
 I410-N317 \\sim I310-N317
 with sigma of 0.04
 I402-Zn41 \\sim I302-Zn31
 with sigma of 0.02
 I401-Zn41 \\sim I301-Zn31
 with sigma of 0.02
 Zn41-N301 \\sim Zn31-N301
 with sigma of 0.02
 I402-I401 \\sim I302-I301
 with sigma of 0.04
 I402-N301 \\sim I302-N301
 with sigma of 0.04
 I401-N301 \\sim I301-N301
 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
 Zn43-N307 \\sim Zn33-N307
 with sigma of 0.02
 Zn43-N306 \\sim Zn33-N306
 with sigma of 0.02
 I405-I406 \\sim I305-I306
 with sigma of 0.04
 I405-N307 \\sim I305-N307
 with sigma of 0.04
 I405-N306 \\sim I305-N306
 with sigma of 0.04
 I406-N307 \\sim I306-N307
 with sigma of 0.04
 I406-N306 \\sim I306-N306
 with sigma of 0.04
 I307-Zn34 \\sim I407-Zn44
 with sigma of 0.02
 I308-Zn34 \\sim I408-Zn44
 with sigma of 0.02
 Zn34-N313 \\sim Zn44-N313
 with sigma of 0.02
 Zn34-N312 \\sim Zn44-N312
 with sigma of 0.02
 I307-I308 \\sim I407-I408
 with sigma of 0.04
 I307-N313 \\sim I407-N313
 with sigma of 0.04
 I307-N312 \\sim I407-N312
 with sigma of 0.04
 I308-N313 \\sim I408-N313
 with sigma of 0.04
 I308-N312 \\sim I408-N312
 with sigma of 0.04
 I306-Zn33 \\sim I506-Zn53
 with sigma of 0.02
 I505-Zn53 \\sim I305-Zn33
 with sigma of 0.02
 I303-I304 \\sim I403-I404
 with sigma of 0.04
 I303-N305 \\sim I403-N305
 with sigma of 0.04
 I304-N305 \\sim I404-N305
 with sigma of 0.04
 I511-Zn56 \\sim I411-Zn46
 with sigma of 0.02
 I512-Zn56 \\sim I412-Zn46
 with sigma of 0.02
 I508-Zn54 \\sim I308-Zn34
 with sigma of 0.02
 I507-Zn54 \\sim I407-Zn44
 with sigma of 0.02
 I509-Zn55 \\sim I309-Zn35
 with sigma of 0.02
 I310-Zn35 \\sim I510-Zn55
 with sigma of 0.02
 N307-C423 \\sim N307-C323
 with sigma of 0.02
 C321-C422 \\sim C321-C322
 with sigma of 0.02
 C422-C423 \\sim C322-C323
 with sigma of 0.02
 N307-C422 \\sim N307-C322
 with sigma of 0.04
 C321-C423 \\sim C321-C323
 with sigma of 0.04
 Zn55-N317 \\sim Zn35-N317
 with sigma of 0.02
3. Restrained planarity
 C7A, C12A, C9A, C8A, C11A, C10A
 with sigma of 0.1
 C3B, C4B, C5B, C13B
 with sigma of 0.1
 O2B, C8B, C7B, C12B, O3B
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
C7A \\sim O3A \\sim C12A \\sim C15A \\sim C11A \\sim C4A \\sim C8A \\sim C10A
\\sim C3A \\sim C5A \\sim O2A \\sim C9A \\sim C2A \\sim C6A \\sim C13A \\sim
C14A \\sim C1A \\sim O1A: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
C7B \\sim C4B \\sim C5B \\sim C3B \\sim C6B \\sim C13B \\sim C2B \\sim C12B
\\sim C8B \\sim C1B \\sim O1B \\sim C11B \\sim O3B \\sim C9B \\sim O2B \\sim
C10B \\sim C15B \\sim C14B: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
Uanis(Zn32) = Uanis(Zn42)
Uanis(Zn41) = Uanis(Zn31)
Uanis(C423) = Uanis(C323) = Uanis(C322) = Uanis(C422)
5. Rigid body (RIGU) restrains
 C7B, C4B, C5B, C3B, C6B, C13B, C2B, C12B, C8B, C1B, O1B, C11B, O3B, C9B, O2B,
 C10B, C15B, C14B
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 1*[Sof(I409)+Sof(I410)+Sof(Zn45)]+1*[Sof(I309)+Sof(Zn35)+Sof(I310)]+1*
 [Sof(H366)+Sof(I510)+Sof(I509)+Sof(Zn55)]=1 with esd of 0.00001
 Sof(I301)=Sof(Zn31)=Sof(I302)=1-FVAR(1)
 Sof(I402)=Sof(I401)=Sof(Zn41)=FVAR(1)
 Sof(I409)=Sof(I410)=Sof(Zn45)=FVAR(2)
 Sof(I309)=Sof(Zn35)=Sof(I310)=FVAR(3)
 Sof(H366)=1-FVAR(4)
 Sof(I510)=Sof(I509)=Sof(Zn55)=FVAR(4)
 Sof(C323)=Sof(H323)=Sof(C322)=Sof(H322)=1-FVAR(5)
 Sof(C422)=Sof(H422)=Sof(C423)=Sof(H423)=FVAR(5)
 Fixed Sof: I312(0.54169) I405(0.29363) I307(0.45395) I311(0.54169)
 I308(0.45395) I303(0.45097) I304(0.45097) I406(0.29363) Zn36(0.54169)
 Zn43(0.29363) Zn34(0.45395) Zn32(0.45097) O3A(0.51152) O2A(0.51152)
 C4A(0.51152) C3A(0.51152) H3A(0.51152) C7A(0.51152) C1A(0.51152) H1A(0.51152)
 O1A(0.51152) H1AA(0.51152) C5A(0.51152) C12A(0.51152) C9A(0.51152)
 H9A(0.51152) C8A(0.51152) C2A(0.51152) H2A(0.51152) C6A(0.51152) H6A(0.51152)
 C14A(0.51152) H14A(0.51152) H14B(0.51152) H14C(0.51152) C11A(0.51152)
 H11A(0.51152) C10A(0.51152) H10A(0.51152) C13A(0.51152) H13A(0.51152)
 H13B(0.51152) I412(0.43626) Zn46(0.43626) I411(0.43626) I305(0.37749)
 Zn33(0.37749) I306(0.37749) I407(0.44602) Zn44(0.44602) I408(0.44602)
 I505(0.32888) Zn53(0.32888) I506(0.32888) I403(0.34484) Zn42(0.34484)
 I404(0.34484) I512(0.02205) Zn56(0.02205) I511(0.02205) I503(0.20418)
 I504(0.20418) Zn52(0.20418) I508(0.10004) I507(0.10004) Zn54(0.10004)
 C15A(0.51152) H15A(0.51152) H15B(0.51152) H15C(0.51152) C4B(0.16811)
 C5B(0.16811) C6B(0.16811) H6B(0.16811) C1B(0.16811) H1B(0.16811) C2B(0.16811)
 H2B(0.16811) C3B(0.16811) H3B(0.16811) C7B(0.16811) C12B(0.16811)
 C11B(0.16811) H11B(0.16811) C10B(0.16811) H10B(0.16811) C9B(0.16811)
 H9B(0.16811) C8B(0.16811) O3B(0.16811) O2B(0.16811) O1B(0.16811) H1BA(0.16811)
 C13B(0.16811) H13C(0.16811) H13D(0.16811) C15B(0.16811) H15D(0.16811)
 H15E(0.16811) H15F(0.16811) C14B(0.16811) H14D(0.16811) H14E(0.16811)
 H14F(0.16811)
 Fixed Uiso: I512(0.08) Zn56(0.08) I511(0.08) I508(0.08) I507(0.08) Zn54(0.08)
 I510(0.08) I509(0.08) Zn55(0.08)
7.a Secondary CH2 refined with riding coordinates:
 C13A(H13A,H13B), C13B(H13C,H13D)
7.b Aromatic/amide H refined with riding coordinates:
 C365(H365), C329(H329), C304(H304), C364(H364), C349(H349), C356(H356),
 C312(H312), C314(H314), C302(H302), C328(H328), C318(H318), C311(H311),
 C353(H353), C320(H320), C313(H313), C354(H354), C351(H351), C355(H355),
 C331(H331), C337(H337), C310(H310), C358(H358), C317(H317), C305(H305),
 C315(H315), C346(H346), C330(H330), C338(H338), C341(H341), C359(H359),
 C350(H350), C319(H319), C301(H301), C369(H369), C336(H336), C348(H348),
 C335(H335), C368(H368), C340(H340), C347(H347), C332(H332), C367(H367),
 C371(H371), C333(H333), C372(H372), C366(H366), C3A(H3A), C1A(H1A), C9A(H9A),
 C2A(H2A), C6A(H6A), C422(H422), C423(H423), C11A(H11A), C10A(H10A), C323(H323),
  C322(H322), C6B(H6B), C1B(H1B), C2B(H2B), C3B(H3B), C11B(H11B), C10B(H10B),
 C9B(H9B)
7.c Fitted hexagon refined as free rotating group:
 C4B(C5B,C6B,C1B,C2B,C3B), C7B(C12B,C11B,C10B,C9B,C8B)
7.d Tetrahedral OH refined with riding coordinates:
 O1A(H1AA), O1B(H1BA)
7.e Idealised Me refined with everything fixed:
 C14A(H14A,H14B,H14C), C15A(H15A,H15B,H15C), C15B(H15D,H15E,H15F), C14B(H14D,
 H14E,H14F)
;
_shelx_res_checksum              4201
_shelx_hkl_checksum              55265
_olex2_date_sample_data_collection 2022-01-25
_olex2_date_sample_submission    2022-01-25
_olex2_submission_original_sample_id 50_1_24a
_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 3.635
_oxdiff_exptl_absorpt_empirical_full_min 0.414