Anisotropic Contraction of a Polyaromatic Capsule and Its Cavity-Induced Compression Effect.
Kishida, Natsuki; Matsumoto, Kyosuke; Tanaka, Yuya; Akita, Munetaka; Sakurai, Hidehiro; Yoshizawa, Michito; Journal of the American Chemical Society 142 (2020) 9599–9603; doi:10.1021/jacs.0c02932

data_4134970
_publ_contact_author             'Michito Yoshizawa'
_publ_section_title
;
 Anisotropic Contraction of a Polyaromatic Capsule and Its Cavity-Induced
 Compression Effect.
;
_journal_issue                   21
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              9599
_journal_page_last               9603
_journal_paper_doi               10.1021/jacs.0c02932
_journal_volume                  142
_journal_year                    2020
_chemical_formula_moiety
'C200 H160 N8 O16 Pd2, B C24 F20, C18 H12, 2(N O3)'
_chemical_formula_sum            'C242 H172 B F20 N10 O22 Pd2'
_chemical_formula_weight         4175.52
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2020-03-13
_audit_creation_method
;
Olex2 1.2
(compiled May 18 2018 14:05:52 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                74.7610(10)
_cell_angle_beta                 85.2890(10)
_cell_angle_gamma                73.4320(10)
_cell_formula_units_Z            2
_cell_length_a                   16.6921(2)
_cell_length_b                   24.5705(4)
_cell_length_c                   30.8870(4)
_cell_measurement_reflns_used    83771
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      75.5080
_cell_measurement_theta_min      3.6880
_cell_volume                     11714.6(3)
_computing_cell_refinement       'CrysAlisPro 1.171.40.72a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.40.72a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.40.72a (Rigaku OD, 2020)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve (Bourhis et al., 2015)'
_diffrn_ambient_temperature      293(2)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.966
_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    -22.00  28.00   0.50   15.00    --  -46.20  19.00 -30.00  100
  2  \w    -12.00  17.00   0.50   15.00    --  -46.20  19.00 -60.00   58
  3  \w    -64.00  16.00   0.50   15.00    --  -46.20  99.00 -33.00  160
  4  \w    -18.00  76.00   0.50   15.00    --   46.20 -99.00-139.00  188
  5  \w     79.00 106.00   0.50   12.00    --  104.61 -99.00-139.00   54
  6  \w     77.00 108.00   0.50   12.00    --  104.61-107.00 -59.00   62
  7  \w     55.00  95.00   0.50   12.00    --  104.61 -94.00 -90.00   80
  8  \w     46.00 111.00   0.50   12.00    --  104.61-125.00-180.00  130
  9  \w     48.00 104.00   0.50   12.00    --  104.61 -77.00-180.00  112
 10  \w    104.00 131.00   0.50   12.00    --  104.61  15.00-120.00   54
 11  \w    145.00 177.00   0.50   12.00    --  104.61  15.00-120.00   64
 12  \w    101.00 148.00   0.50   12.00    --  104.61  99.00 -33.00   94
 13  \w     92.00 161.00   0.50   12.00    --  104.61  45.00 120.00  138
 14  \w     41.00  69.00   0.50   15.00    --   46.20-125.00 120.00   56
 15  \w     39.00  69.00   0.50   12.00    --  104.61 -61.00   0.00   60
 16  \w     34.00  59.00   0.50   12.00    --  104.61 -61.00  60.00   50
 17  \w     36.00  73.00   0.50   12.00    --  104.61 -61.00  30.00   74
 18  \w     33.00 103.00   0.50   12.00    --  104.61 -94.00 -30.00  140
 19  \w     33.00  98.00   0.50   12.00    --  104.61-125.00  60.00  130
 20  \w     32.00  67.00   0.50   12.00    --  104.61-107.00 -59.00   70
 21  \w      8.00  61.00   0.50   15.00    --   46.20 -57.00 -90.00  106
 22  \w     32.00 100.00   0.50   12.00    --  104.61 -94.00-180.00  136
 23  \w    -24.00  17.00   0.50   15.00    --   46.20 -19.00  60.00   82
 24  \w    -28.00  26.00   0.50   15.00    --   46.20 -19.00 150.00  108
 25  \w     35.00  61.00   0.50   12.00    --  104.61 -61.00  90.00   52
 26  \w    -27.00  20.00   0.50   15.00    --   46.20 -19.00 -60.00   94
 27  \w   -104.00 -60.00   0.50   12.00    -- -102.00  99.00 -33.00   88
 28  \w    -68.00 -35.00   0.50   12.00    -- -102.00  61.00 -60.00   66
 29  \w    -63.00 -38.00   0.50   12.00    -- -102.00  61.00-120.00   50
 30  \w    -59.00 -29.00   0.50   12.00    -- -102.00  61.00-180.00   60
 31  \w   -130.00-104.00   0.50   12.00    -- -102.00 -45.00 -30.00   52
 32  \w   -157.00 -98.00   0.50   12.00    -- -102.00 -99.00-139.00  118
 33  \w   -152.00 -85.00   0.50   12.00    -- -102.00 -94.00 -90.00  134
 34  \w   -165.00 -97.00   0.50   12.00    -- -102.00 -30.00-180.00  136
 35  \w   -173.00 -90.00   0.50   12.00    -- -102.00 -45.00 -60.00  166
 36  \w   -173.00-146.00   0.50   12.00    -- -102.00 -45.00 -30.00   54
 37  \w   -149.00 -75.00   0.50   12.00    -- -102.00-125.00 120.00  148
 38  \w   -108.00 -51.00   0.50   12.00    -- -102.00 112.00  82.89  114
 39  \w   -107.00 -48.00   0.50   12.00    -- -102.00 108.00  38.87  118
 40  \w     24.00  61.00   0.50   15.00    --   46.20  77.00 150.00   74
 41  \w   -119.00 -36.00   0.50   15.00    --  -46.20 -37.00-150.00  166
 42  \w   -102.00 -34.00   0.50   15.00    --  -46.20 -37.00 -30.00  136
 43  \w    -97.00 -35.00   0.50   15.00    --  -46.20 -37.00 -90.00  124
 44  \w    -66.00 -34.00   0.50   15.00    --  -46.20 -41.00  36.10   64
 45  \w    -78.00 -35.00   0.50   15.00    --  -46.20 -37.00  90.00   86
 46  \w    -79.00 -34.00   0.50   15.00    --  -46.20 -37.00 150.00   90
 47  \w     24.00  58.00   0.50   15.00    --   46.20  77.00  90.00   68
 48  \w     24.00  90.00   0.50   15.00    --   46.20  77.00 -30.00  132
 49  \w     24.00  58.00   0.50   15.00    --   46.20  77.00  60.00   68
 50  \w     24.00  60.00   0.50   15.00    --   46.20  77.00-180.00   72
 51  \w     24.00  63.00   0.50   15.00    --   46.20  77.00 -90.00   78
 52  \w     91.00 118.00   0.50   15.00    --   46.20  77.00 150.00   54
 53  \w     24.00  61.00   0.50   15.00    --   46.20  77.00  30.00   74
 54  \w     24.00  88.00   0.50   15.00    --   46.20  77.00-120.00  128
 55  \w     24.00  59.00   0.50   15.00    --   46.20  77.00   0.00   70
 56  \w     25.00  64.00   0.50   15.00    --   46.20  77.00-150.00   78
 57  \w     24.00  62.00   0.50   15.00    --   46.20  77.00 120.00   76
 58  \w     24.00  62.00   0.50   15.00    --   46.20  77.00 -60.00   76
 59  \w   -107.00 -81.00   0.50   12.00    -- -102.00 -72.00  81.64   52
 60  \w   -124.00 -79.00   0.50   12.00    -- -102.00 -76.00-155.24   90
 61  \w   -115.00 -79.00   0.50   12.00    -- -102.00 -77.00-120.00   72
 62  \w   -164.00-138.00   0.50   12.00    -- -102.00 -76.00-155.24   52
 63  \w   -106.00 -79.00   0.50   12.00    -- -102.00 -77.00-105.07   54
 64  \w   -141.00 -84.00   0.50   12.00    -- -102.00 -65.00 -35.96  114
 65  \w   -166.00-127.00   0.50   12.00    -- -102.00 -67.00 154.78   78
 66  \w   -109.00 -83.00   0.50   12.00    -- -102.00 -67.00 154.78   52
 67  \w   -106.00 -80.00   0.50   12.00    -- -102.00 -75.00-141.62   52
 68  \w   -174.00-148.00   0.50   12.00    -- -102.00 -69.00 107.60   52
 69  \w   -108.00 -82.00   0.50   12.00    -- -102.00 -69.00 107.60   52
 70  \w   -171.00-144.00   0.50   12.00    -- -102.00 -72.00  31.16   54
 71  \w   -145.00-109.00   0.50   12.00    -- -102.00 -77.00-105.07   72
 72  \w   -130.00 -82.00   0.50   12.00    -- -102.00 -69.00 -97.61   96
 73  \w   -168.00-143.00   0.50   12.00    -- -102.00 -77.00-120.00   50
 74  \w   -106.00 -79.00   0.50   12.00    -- -102.00 -77.00 141.30   54
 75  \w   -140.00 -83.00   0.50   12.00    -- -102.00 -67.00  85.80  114
 76  \w   -106.00 -80.00   0.50   12.00    -- -102.00 -74.00-136.43   52
 77  \w   -107.00 -79.00   0.50   12.00    -- -102.00 -78.00 -10.02   56
 78  \w   -111.00 -82.00   0.50   12.00    -- -102.00 -69.00 -49.71   58
 79  \w   -105.00 -78.00   0.50   12.00    -- -102.00 -80.00  70.00   54
 80  \w   -174.00-147.00   0.50   12.00    -- -102.00 -78.00 -10.02   54
 81  \w   -106.00 -80.00   0.50   12.00    -- -102.00 -74.00-149.10   52
 82  \w   -108.00 -83.00   0.50   12.00    -- -102.00 -67.00 169.49   50
 83  \w   -119.00 -79.00   0.50   12.00    -- -102.00 -77.00   0.00   80
 84  \w   -105.00 -79.00   0.50   12.00    -- -102.00 -77.00 -60.00   52
 85  \w   -166.00-123.00   0.50   12.00    -- -102.00 -77.00   0.00   86
 86  \w   -175.00-146.00   0.50   12.00    -- -102.00 -65.00 -35.96   58
 87  \w   -111.00 -81.00   0.50   12.00    -- -102.00 -72.00  40.30   60
 88  \w   -118.00 -78.00   0.50   12.00    -- -102.00 -79.00 131.99   80
 89  \w   -105.00 -79.00   0.50   12.00    -- -102.00 -76.00 104.10   52
 90  \w   -110.00 -84.00   0.50   12.00    -- -102.00 -65.00 159.83   52
 91  \w   -114.00 -85.00   0.50   12.00    -- -102.00 -61.00-180.00   58
 92  \w   -107.00 -81.00   0.50   12.00    -- -102.00 -73.00-104.58   52
 93  \w   -172.00 -79.00   0.50   12.00    -- -102.00 -77.00  77.84  186
 94  \w   -106.00 -80.00   0.50   12.00    -- -102.00 -74.00 155.37   52
 95  \w   -105.00 -80.00   0.50   12.00    -- -102.00 -74.00 -34.78   50
 96  \w   -171.00-124.00   0.50   12.00    -- -102.00 -79.00 131.99   94
 97  \w   -167.00-126.00   0.50   12.00    -- -102.00 -78.00  24.67   82
 98  \w   -165.00-139.00   0.50   12.00    -- -102.00 -74.00 -34.78   52
 99  \w   -117.00 -81.00   0.50   12.00    -- -102.00 -72.00  27.43   72
100  \w   -106.00 -80.00   0.50   12.00    -- -102.00 -74.00  67.22   52
101  \w   -105.00 -79.00   0.50   12.00    -- -102.00 -76.00 -77.17   52
102  \w   -106.00 -79.00   0.50   12.00    -- -102.00 -77.00-124.38   54
103  \w   -107.00 -81.00   0.50   12.00    -- -102.00 -72.00 -70.13   52
104  \w   -114.00 -82.00   0.50   12.00    -- -102.00 -69.00 142.38   64
105  \w   -114.00 -81.00   0.50   12.00    -- -102.00 -72.00  31.16   66
106  \w   -106.00 -79.00   0.50   12.00    -- -102.00 -78.00  24.67   54
107  \w   -105.00 -79.00   0.50   12.00    -- -102.00 -76.00   6.20   52
108  \w   -108.00 -82.00   0.50   12.00    -- -102.00 -70.00 -90.82   52
109  \w   -171.00 -85.00   0.50   12.00    -- -102.00 -62.00  38.02  172
110  \w   -113.00 -83.00   0.50   12.00    -- -102.00 -68.00 -57.70   60
111  \w   -173.00-146.00   0.50   12.00    -- -102.00 -76.00 104.10   54
112  \w   -113.00 -87.00   0.50   12.00    -- -102.00 -55.00 165.17   52
113  \w   -112.00 -84.00   0.50   12.00    -- -102.00 -65.00   2.46   56
114  \w   -175.00-128.00   0.50   12.00    -- -102.00 -67.00 169.49   94
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0162493000
_diffrn_orient_matrix_UB_12      0.0637997000
_diffrn_orient_matrix_UB_13      0.0031368000
_diffrn_orient_matrix_UB_21      0.0303411000
_diffrn_orient_matrix_UB_22      0.0172179000
_diffrn_orient_matrix_UB_23      -0.0488518000
_diffrn_orient_matrix_UB_31      -0.0899326000
_diffrn_orient_matrix_UB_32      0.0141130000
_diffrn_orient_matrix_UB_33      -0.0166189000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0777
_diffrn_reflns_av_unetI/netI     0.0307
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.966
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       31
_diffrn_reflns_limit_k_min       -31
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            364706
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.966
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         76.656
_diffrn_reflns_theta_min         3.487
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.890
_exptl_absorpt_correction_T_max  0.797
_exptl_absorpt_correction_T_min  0.745
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.72a (Rigaku Oxford Diffraction, 2020)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.184
_exptl_crystal_description       block
_exptl_crystal_F_000             4294
_exptl_crystal_size_max          0.21
_exptl_crystal_size_mid          0.13
_exptl_crystal_size_min          0.12
_refine_diff_density_max         2.130
_refine_diff_density_min         -0.933
_refine_diff_density_rms         0.144
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.819
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2648
_refine_ls_number_reflns         49254
_refine_ls_number_restraints     3802
_refine_ls_restrained_S_all      1.834
_refine_ls_R_factor_all          0.1638
_refine_ls_R_factor_gt           0.1442
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4296
_refine_ls_wR_factor_ref         0.4471
_reflns_Friedel_coverage         0.000
_reflns_number_gt                32707
_reflns_number_total             49254
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja0c02932_si_002.cif
_cod_data_source_block           NKS267
_cod_depositor_comments          'Adding full bibliography for 4134970.cif.'
_cod_database_code               4134970
_shelx_shelxl_version_number     2018/3
_diffrn_oxdiff_digest_frames
;
014b8f46b1e31517368c73de2db0cccb1f000257633
;
_diffrn_oxdiff_digest_hkl
;
01aae51d7fd29c648422b7e2d9f9e5ffb704d2
;
_reflns_odcompleteness_completeness 99.92
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_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
2. Restrained distances
 C3C-O2C
 1.5 with sigma of 0.02
 O3C-C4C
 1.43 with sigma of 0.02
 O1C-C1C
 1.43 with sigma of 0.02
 C2C-O2C
 1.43 with sigma of 0.02
 O2C-C3C
 1.43 with sigma of 0.02
 C1D-C2D
 1.54 with sigma of 0.02
 C2D-O2D
 1.43 with sigma of 0.02
 O2D-C3D
 1.43 with sigma of 0.02
 C2A-C3A = C2C-C3C
 2.3 with sigma of 0.04
 O2C-C1C
 2.4 with sigma of 0.04
 O1C-C2C
 2.4 with sigma of 0.04
 O3C-C5C
 2.4 with sigma of 0.04
 O2C-C1AA
 1.43 with sigma of 0.04
 C1AA-C2C
 2.3 with sigma of 0.04
 O2C-C3C \\sim O2C-C1AA
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.01 and sigma
for terminal atoms of 0.02
All non-hydrogen atoms restrained to be isotropic: with sigma of 0.01 and sigma
for terminal atoms of 0.02
4. Others
 Sof(C1AA)=Sof(H1AC)=Sof(H1AD)=Sof(H1AE)=1-FVAR(1)
 Sof(C3C)=Sof(H3CA)=Sof(H3CB)=Sof(H3CC)=FVAR(1)
5.a Secondary CH2 refined with riding coordinates:
 C5D(H5DA,H5DB), C5B(H5BA,H5BB), C4D(H4DA,H4DB), C2A(H2AA,H2AB), C1A(H1AA,
 H1AB), C4B(H4BA,H4BB), C4A(H4AA,H4AB), C1B(H1BA,H1BB), C2D(H2DA,H2DB),
 C5A(H5AA,H5AB), C1D(H1DA,H1DB), C4C(H4CA,H4CB), C5C(H5CA,H5CB), C2B(H2BA,H2BB),
  C1C(H1CA,H1CB), C2C(H2CA,H2CB)
5.b Me refined with riding coordinates:
 C3A(H3AA,H3AB,H3AC), C6D(H6DA,H6DB,H6DC), C6B(H6BA,H6BB,H6BC), C3B(H3BA,H3BB,
 H3BC), C3D(H3DA,H3DB,H3DC), C6A(H6AA,H6AB,H6AC), C3C(H3CA,H3CB,H3CC),
 C1AA(H1AC,H1AD,H1AE), C6C(H6CA,H6CB,H6CC)
5.c Aromatic/amide H refined with riding coordinates:
 C130(H130), C135(H135), C108(H108), C110(H110), C119(H119), C113(H113),
 C109(H109), C126(H126), C123(H123), C120(H120), C98(H98), C100(H100),
 C101(H101), C127(H127), C122(H122), C102(H102), C134(H134), C118(H118),
 C121(H121), C96(H96), C107(H107), C117(H117), C112(H112), C115(H115),
 C139(H139), C137(H137), C114(H114), C116(H116), C95(H95), C104(H104),
 C105(H105), C053(H053), C07S(H07S), C08F(H08F), C07M(H07M), C97(H97),
 C02X(H02X), C02Y(H02Y), C033(H033), C036(H036), C037(H037), C039(H039),
 C03B(H03B), C03C(H03C), C03E(H03E), C03G(H03G), C03I(H03I), C03N(H03N),
 C03O(H03O), C03P(H03P), C03S(H03S), C03T(H03T), C03V(H03V), C03X(H03X),
 C040(H040), C041(H041), C042(H042), C044(H044), C045(H045), C046(H046),
 C048(H048), C049(H049), C04B(H04B), C04C(H04C), C04E(H04E), C04I(H04I),
 C04K(H04K), C04L(H04L), C04O(H04O), C04Q(H04Q), C04R(H04R), C04S(H04S),
 C04X(H04X), C050(H050), C052(H052), C054(H054), C07W(H07W), C08N(H08N),
 C07N(H07N), C05U(H05U), C057(H057), C058(H058), C05B(H05B), C05C(H05C),
 C05D(H05D), C05F(H05F), C05J(H05J), C05M(H05M), C05N(H05N), C05T(H05T),
 C05V(H05V), C05W(H05W), C05Y(H05Y), C060(H060), C061(H061), C062(H062),
 C063(H063), C069(H069), C06C(H06C), C06D(H06D), C06E(H06E), C06J(H06J),
 C06N(H06N), C06O(H06O), C06S(H06S), C06V(H06V), C071(H071), C077(H077),
 C07E(H07E), C07J(H07J), C07O(H07O), C07R(H07R), C140(H140), C05Z(H05Z),
 C05S(H05S), C07X(H07X)
5.d Fitted hexagon refined as free rotating group:
 C90(C053,C07S,C08F,C07M,C065), C056(C07W,C08N,C07N,C05U,C03F), C07R(C140,C05Z,
 C03Q,C91,C05S)
;
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 2.052
_oxdiff_exptl_absorpt_empirical_full_min 0.560