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_1571843
_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         'C108 H72 I18 N36 Zn9, 0.771(C15 H16 O3)'
_chemical_formula_sum            'C119.57 H84.34 I18 N36 O2.31 Zn9'
_chemical_formula_weight         4934.99
_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           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             2024-01-29
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2023.11.24 svn.r209d9fb2 for OlexSys, GUI svn.r6869)
;
_cell_angle_alpha                90
_cell_angle_beta                 100.1020(10)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   78.8715(10)
_cell_length_b                   14.95020(10)
_cell_length_c                   41.6531(4)
_cell_measurement_reflns_used    39883
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      74.0720
_cell_measurement_theta_min      2.1340
_cell_volume                     48353.6(8)
_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-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 0.993
_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    -56.00 -31.00   0.25    0.80    -- -103.00  53.00 -25.00  100
  2  \w   -173.00 -92.00   0.25    0.80    -- -103.00 -53.00-169.00  324
  3  \w   -167.00 -80.00   0.25    0.80    -- -103.00 -77.00  90.00  348
  4  \w   -118.00 -93.00   0.25    0.80    -- -103.00 -45.00-120.00  100
  5  \w   -102.00 -39.00   0.25    0.80    -- -103.00  77.00 -30.00  252
  6  \w   -173.00-142.00   0.25    0.80    -- -103.00 -45.00-120.00  124
  7  \w    -61.00 -36.00   0.25    0.80    -- -103.00  61.00-180.00  100
  8  \w    107.00 132.00   0.25    0.80    --  101.75  53.00 -25.00  100
  9  \w     29.00  62.00   0.25    0.80    --  101.75 -53.00-169.00  132
 10  \w     93.00 121.00   0.25    0.80    --  101.75  45.00 -90.00  112
 11  \w    121.00 168.00   0.25    0.80    --  101.75  61.00-120.00  188
 12  \w    131.00 173.00   0.25    0.80    --  101.75  45.00 -90.00  168
 13  \w     33.00  73.00   0.25    0.80    --  101.75 -61.00   0.00  160
 14  \w     29.00  71.00   0.25    0.80    --  101.75 -61.00 -30.00  168
 15  \w     33.00  62.00   0.25    0.80    --  101.75 -61.00  90.00  116
 16  \w     35.00  73.00   0.25    0.80    --  101.75 -61.00  30.00  152
 17  \w     94.00 120.00   0.25    0.80    --  101.75  61.00-120.00  104
 18  \w   -117.00 -41.00   0.25    0.25    --  -46.48 -53.00-169.00  304
 19  \w     -2.00  25.00   0.25    0.25    --  -46.48  53.00 -25.00  108
 20  \w    -24.00  45.00   0.25    0.25    --   46.48 -53.00-169.00  276
 21  \w     50.00 116.00   0.25    0.25    --   46.48  53.00 -25.00  264
 22  \w    -19.00   6.00   0.25    0.25    --  -46.48  19.00-150.00  100
 23  \w    -17.00   9.00   0.25    0.25    --  -46.48  19.00 120.00  104
 24  \w    -23.00  28.00   0.25    0.25    --  -46.48  19.00 -30.00  204
;
_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      0.0121541000
_diffrn_orient_matrix_UB_12      -0.0085390000
_diffrn_orient_matrix_UB_13      -0.0250430000
_diffrn_orient_matrix_UB_21      0.0113463000
_diffrn_orient_matrix_UB_22      -0.0659623000
_diffrn_orient_matrix_UB_23      0.0227387000
_diffrn_orient_matrix_UB_31      -0.0108352000
_diffrn_orient_matrix_UB_32      -0.0786540000
_diffrn_orient_matrix_UB_33      -0.0163477000
_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  0.0498
_diffrn_reflns_av_unetI/netI     0.0413
_diffrn_reflns_Laue_measured_fraction_full 0.993
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       94
_diffrn_reflns_limit_h_min       -94
_diffrn_reflns_limit_k_max       18
_diffrn_reflns_limit_k_min       -17
_diffrn_reflns_limit_l_max       50
_diffrn_reflns_limit_l_min       -50
_diffrn_reflns_number            157610
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.993
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         68.251
_diffrn_reflns_theta_min         2.155
_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    19.307
_exptl_absorpt_correction_T_max  0.327
_exptl_absorpt_correction_T_min  0.076
_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            'light yellow'
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.356
_exptl_crystal_description       block
_exptl_crystal_F_000             18370
_exptl_crystal_size_max          0.21
_exptl_crystal_size_mid          0.19
_exptl_crystal_size_min          0.08
_refine_diff_density_max         1.768
_refine_diff_density_min         -1.206
_refine_diff_density_rms         0.254
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.055
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1925
_refine_ls_number_reflns         43958
_refine_ls_number_restraints     254
_refine_ls_restrained_S_all      1.061
_refine_ls_R_factor_all          0.1120
_refine_ls_R_factor_gt           0.0940
_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^)+(0.1560P)^2^+853.9998P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2889
_refine_ls_wR_factor_ref         0.3037
_reflns_Friedel_coverage         0.000
_reflns_number_gt                32869
_reflns_number_total             43958
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5068.cif
_cod_data_source_block           25_1_96a
_cod_database_code               1571843
_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 96h [1] 25'
_shelx_estimated_absorpt_t_max   0.307
_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
 C2A-C1A = C3A-C2A = C4A-C3A = C5A-C4A = C6A-C5A = C6A-C1A
 1.39 with sigma of 0.02
 C5A-C13A
 1.51 with sigma of 0.02
 O3A-C15A
 1.43 with sigma of 0.02
 C5A-O1A
 2.4 with sigma of 0.02
 C8A-C7A \\sim C9A-C8A \\sim C9A-C10A \\sim C11A-C10A \\sim C12A-C11A \\sim
C7A-C12A
 with sigma of 0.02
 C1A-C3A \\sim C2A-C4A \\sim C3A-C5A \\sim C4A-C6A \\sim C5A-C1A \\sim C6A-C2A
 with sigma of 0.04
 C1A-C4A \\sim C2A-C5A \\sim C3A-C6A
 with sigma of 0.04
 I315-Zn38 \\sim I415-Zn48
 with sigma of 0.02
 C9A-C11A \\sim C10A-C12A \\sim C11A-C7A
 with sigma of 0.04
 O1A-C13A \\sim O2A-C14A
 with sigma of 0.02
 I316-Zn38 \\sim I416-Zn48
 with sigma of 0.02
 Zn38-N329 \\sim Zn48-N329
 with sigma of 0.02
 I315-I316 \\sim I415-I416
 with sigma of 0.04
 I315-N329 \\sim I415-N329
 with sigma of 0.04
 I316-N329 \\sim I416-N329
 with sigma of 0.04
 I309-Zn35 \\sim I409-Zn45
 with sigma of 0.02
 I310-Zn35 \\sim I410-Zn45
 with sigma of 0.02
 Zn35-N318 \\sim Zn45-N318
 with sigma of 0.02
 Zn35-N319 \\sim Zn45-N319
 with sigma of 0.02
 I309-I310 \\sim I409-I410
 with sigma of 0.04
 I309-N318 \\sim I409-N318
 with sigma of 0.04
 I309-N319 \\sim I409-N319
 with sigma of 0.04
 I310-N318 \\sim I410-N318
 with sigma of 0.04
 I310-N319 \\sim I410-N319
 with sigma of 0.04
 I312-Zn36 \\sim I412-Zn46
 with sigma of 0.02
 I311-Zn36 \\sim I411-Zn46
 with sigma of 0.02
 Zn36-N323 \\sim Zn46-N323
 with sigma of 0.02
 I312-I311 \\sim I412-I411
 with sigma of 0.04
 I312-N323 \\sim I412-N323
 with sigma of 0.04
 I311-N323 \\sim I411-N323
 with sigma of 0.04
 I313-Zn37 \\sim I413-Zn47
 with sigma of 0.02
 I314-Zn37 \\sim I414-Zn47
 with sigma of 0.02
 Zn37-N325 \\sim Zn47-N325
 with sigma of 0.02
 Zn37-N324 \\sim Zn47-N324
 with sigma of 0.02
 I313-I314 \\sim I413-I414
 with sigma of 0.04
 I313-N325 \\sim I413-N325
 with sigma of 0.04
 I313-N324 \\sim I413-N324
 with sigma of 0.04
 I314-N325 \\sim I414-N325
 with sigma of 0.04
 I314-N324 \\sim I414-N324
 with sigma of 0.04
 I509-Zn55 \\sim I409-Zn45
 with sigma of 0.02
 I510-Zn55 \\sim I410-Zn45
 with sigma of 0.02
 I303-Zn32 \\sim I403-Zn42
 with sigma of 0.02
 I304-Zn32 \\sim I404-Zn42
 with sigma of 0.02
 Zn32-N305 \\sim Zn42-N305
 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
 I305-Zn33 \\sim I405-Zn43
 with sigma of 0.02
 I306-Zn33 \\sim I406-Zn43
 with sigma of 0.02
 Zn33-N306 \\sim Zn43-N306
 with sigma of 0.02
 Zn33-N307 \\sim Zn43-N307
 with sigma of 0.02
 I305-I306 \\sim I405-I406
 with sigma of 0.04
 I305-N306 \\sim I405-N306
 with sigma of 0.04
 I305-N307 \\sim I405-N307
 with sigma of 0.04
 I306-N306 \\sim I406-N306
 with sigma of 0.04
 I306-N307 \\sim I406-N307
 with sigma of 0.04
 I302-Zn31 \\sim I402-Zn31
 with sigma of 0.02
 I301-Zn31 \\sim I401-Zn31
 with sigma of 0.02
 I308-Zn34 \\sim I408-Zn34
 with sigma of 0.02
 I307-Zn34 \\sim I407-Zn34
 with sigma of 0.02
 I505-Zn53 \\sim I405-Zn43
 with sigma of 0.02
 I506-Zn53 \\sim I406-Zn43
 with sigma of 0.02
 I318-Zn39 \\sim I418-Zn49
 with sigma of 0.02
 I317-Zn39 \\sim I417-Zn49
 with sigma of 0.02
 Zn39-N331 \\sim Zn49-N331
 with sigma of 0.02
 Zn39-N330 \\sim Zn49-N330
 with sigma of 0.02
 I318-I317 \\sim I418-I417
 with sigma of 0.04
 I318-N331 \\sim I418-N331
 with sigma of 0.04
 I318-N330 \\sim I418-N330
 with sigma of 0.04
 I317-N331 \\sim I417-N331
 with sigma of 0.04
 I317-N330 \\sim I417-N330
 with sigma of 0.04
 N329-C483 \\sim N329-C383
 with sigma of 0.02
 C381-C482 \\sim C381-C382
 with sigma of 0.02
 C483-C482 \\sim C383-C382
 with sigma of 0.02
 N329-C482 \\sim N329-C382
 with sigma of 0.04
 C381-C483 \\sim C381-C383
 with sigma of 0.04
 N306-C318 \\sim N306-C418
 with sigma of 0.02
 C316-C317 \\sim C316-C417
 with sigma of 0.02
 C318-C317 \\sim C418-C417
 with sigma of 0.02
 N306-C317 \\sim N306-C417
 with sigma of 0.04
 C316-C318 \\sim C316-C418
 with sigma of 0.04
3. Uiso/Uaniso restraints and constraints
C7A \\sim O3A \\sim C12A \\sim C15A \\sim C11A \\sim C10A \\sim C4A \\sim C8A
\\sim C9A \\sim C5A \\sim C3A \\sim O2A \\sim C6A \\sim C13A \\sim C2A \\sim
C14A \\sim C1A \\sim O1A: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08 within 2A
Uanis(Zn36) = Uanis(Zn46)
Uanis(C382) = Uanis(C482) = Uanis(C383) = Uanis(C483)
Uanis(C318) = Uanis(C317) = Uanis(C417) = Uanis(C418)
Uanis(Zn35) = Uanis(Zn45)
4. Rigid body (RIGU) restrains
 Zn45, Zn35, I310, I410, I309, I409
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(I416)=Sof(Zn48)=Sof(I415)=1-FVAR(1)
 Sof(I315)=Sof(I316)=Sof(Zn38)=FVAR(1)
 Sof(Zn47)=Sof(I413)=Sof(I414)=1-FVAR(2)
 Sof(I313)=Sof(I314)=Sof(Zn37)=FVAR(2)
 Sof(Zn42)=Sof(I403)=Sof(I404)=1-FVAR(3)
 Sof(I303)=Sof(I304)=Sof(Zn32)=FVAR(3)
 Sof(I402)=Sof(I401)=1-FVAR(4)
 Sof(I302)=Sof(I301)=FVAR(4)
 Sof(I407)=Sof(I408)=1-FVAR(5)
 Sof(I308)=Sof(I307)=FVAR(5)
 Sof(C383)=Sof(H383)=Sof(C382)=Sof(H382)=1-FVAR(6)
 Sof(C483)=Sof(H483)=Sof(C482)=Sof(H482)=FVAR(6)
 Sof(C417)=Sof(H417)=Sof(C418)=Sof(H418)=1-FVAR(7)
 Sof(C318)=Sof(H318)=Sof(C317)=Sof(H317)=FVAR(7)
 Fixed Sof: I309(0.51454) I305(0.54936) I310(0.51454) I318(0.6091)
 I306(0.54936) I312(0.56781) I317(0.6091) I311(0.56781) Zn35(0.51454)
 Zn36(0.56781) Zn39(0.6091) Zn33(0.54936) I409(0.45455) Zn45(0.45455)
 I410(0.45455) I411(0.43219) Zn46(0.43219) I412(0.43219) O3A(0.77146)
 C1A(0.77146) H1A(0.77146) O2A(0.77146) O1A(0.77146) H1AA(0.77146)
 C12A(0.77146) C9A(0.77146) H9A(0.77146) C6A(0.77146) H6A(0.77146) C5A(0.77146)
 C14A(0.77146) H14A(0.77146) H14B(0.77146) H14C(0.77146) C4A(0.77146)
 C8A(0.77146) C11A(0.77146) H11A(0.77146) C15A(0.77146) H15A(0.77146)
 H15B(0.77146) H15C(0.77146) C7A(0.77146) C2A(0.77146) H2A(0.77146)
 C13A(0.77146) H13A(0.77146) H13B(0.77146) I509(0.03092) I510(0.03092)
 Zn55(0.03092) I406(0.4192) Zn43(0.4192) I405(0.4192) I506(0.03144)
 Zn53(0.03144) I505(0.03144) C3A(0.77146) H3A(0.77146) C10A(0.77146)
 H10A(0.77146) Zn49(0.35582) I418(0.35582) I417(0.35582) I518(0.0351)
 I517(0.0351) Zn59(0.0351)
 Fixed Uiso: I509(0.08) I510(0.08) Zn55(0.08) I506(0.08) Zn53(0.08) I505(0.08)
 I402(0.08) I401(0.08) I518(0.08) I517(0.08) Zn59(0.08)
6.a Secondary CH2 refined with riding coordinates:
 C13A(H13A,H13B)
6.b Aromatic/amide H refined with riding coordinates:
 C348(H348), C340(H340), C331(H331), C356(H356), C330(H330), C341(H341),
 C319(H319), C355(H355), C353(H353), C350(H350), C337(H337), C305(H305),
 C365(H365), C315(H315), C351(H351), C301(H301), C320(H320), C354(H354),
 C329(H329), C349(H349), C338(H338), C304(H304), C364(H364), C312(H312),
 C333(H333), C328(H328), C390(H390), C314(H314), C302(H302), C359(H359),
 C385(H385), C402(H402), C310(H310), C313(H313), C336(H336), C346(H346),
 C332(H332), C335(H335), C391(H391), C387(H387), C389(H389), C358(H358),
 C384(H384), C377(H377), C392(H392), C311(H311), C374(H374), C376(H376),
 C373(H373), C318(H318), C400(H400), C322(H322), C386(H386), C404(H404),
 C408(H408), C317(H317), C347(H347), C323(H323), C368(H368), C407(H407),
 C372(H372), C367(H367), C369(H369), C366(H366), C483(H483), C482(H482),
 C403(H403), C1A(H1A), C9A(H9A), C6A(H6A), C11A(H11A), C2A(H2A), C371(H371),
 C3A(H3A), C401(H401), C405(H405), C10A(H10A), C395(H395), C394(H394),
 C383(H383), C382(H382), C417(H417), C418(H418)
6.c Idealised Me refined as rotating group:
 C14A(H14A,H14B,H14C), C15A(H15A,H15B,H15C)
6.d Idealised tetrahedral OH refined as rotating group:
 O1A(H1AA)
;
_shelx_res_checksum              47830
_shelx_hkl_checksum              21772
_olex2_date_sample_data_collection 2022-03-01
_olex2_date_sample_submission    2022-03-01
_olex2_submission_original_sample_id 25_1_96a
_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 3.246
_oxdiff_exptl_absorpt_empirical_full_min 0.417