Molecular Recognition and Cocrystallization of Methylated and Halogenated Fragments of Danicalipin A by Enantiopure Alleno-Acetylenic Cage Receptors.
Gropp, Cornelius; Fischer, Stefan; Husch, Tamara; Trapp, Nils; Carreira, Erick M.; Diederich, François; Journal of the American Chemical Society 142 (2020) 4749–4755; doi:10.1021/jacs.9b13217

data_4134292
_publ_section_title
;
 Molecular Recognition and Cocrystallization of Methylated and Halogenated
 Fragments of Danicalipin A by Enantiopure Alleno-Acetylenic Cage
 Receptors.
;
_journal_issue                   10
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              4749
_journal_page_last               4755
_journal_paper_doi               10.1021/jacs.9b13217
_journal_volume                  142
_journal_year                    2020
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C128 H168 O12, C5 H10 Br2 O'
_chemical_formula_sum            'C133 H178 Br2 O13'
_chemical_formula_weight         2144.56
_space_group_crystal_system      orthorhombic
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2018-02-05
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   15.60920(10)
_cell_length_b                   18.73600(10)
_cell_length_c                   44.0628(3)
_cell_measurement_reflns_used    136895
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      79.5640
_cell_measurement_theta_min      3.0950
_cell_volume                     12886.34(14)
_computing_cell_refinement       'CrysAlisPro 1.171.39.28d (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.39.28d (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.39.28d (Rigaku OD, 2015)'
_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    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.0(1)
_diffrn_detector                 'CCD plate'
_diffrn_detector_type            'Pilatus 300K'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.991
_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    -26.00  55.00   0.50    0.88    --   49.37 -19.00  60.00  162
  2  \w     78.00 116.00   0.50    0.88    --   49.37  77.00 120.00   76
  3  \w     78.00 116.00   0.50    0.88    --   49.37  77.00   0.00   76
  4  \w     94.00 123.00   0.50    3.51    --  110.00 -19.00  60.00   58
  5  \w     94.00 123.00   0.50    3.51    --  110.00 -19.00 120.00   58
  6  \w     94.00 123.00   0.50    3.51    --  110.00 -19.00 150.00   58
  7  \w     97.00 171.00   0.50    3.51    --  110.00  19.00 150.00  148
  8  \w     97.00 123.00   0.50    3.51    --  110.00 -19.00  30.00   52
  9  \w    153.00 178.00   0.50    3.51    --  110.00  57.00 -60.00   50
 10  \w    108.00 177.00   0.50    3.51    --  110.00  57.00 -90.00  138
 11  \w     94.00 123.00   0.50    3.51    --  110.00 -19.00-120.00   58
 12  \w     94.00 123.00   0.50    3.51    --  110.00 -19.00-180.00   58
 13  \w     97.00 175.00   0.50    3.51    --  110.00  57.00-150.00  156
 14  \w     94.00 120.00   0.50    3.51    --  110.00 -19.00 -90.00   52
 15  \w    101.00 178.00   0.50    3.51    --  110.00  57.00-120.00  154
 16  \w     95.00 138.00   0.50    3.51    --  110.00  57.00 -60.00   86
 17  \w     38.00  84.00   0.50    3.51    --  110.00 -57.00 -30.00   92
 18  \w     53.00 106.00   0.50    3.51    --  110.00 -99.00 -60.00  106
 19  \w     40.00 110.00   0.50    3.51    --  110.00 -99.00   0.00  140
 20  \w     55.00 106.00   0.50    3.51    --  110.00 -99.00  90.00  102
 21  \w     64.00  94.00   0.50    3.51    --  110.00 -77.00  90.00   60
 22  \w     39.00 122.00   0.50    3.51    --  110.00-125.00  90.00  166
 23  \w     39.00  65.00   0.50    3.51    --  110.00 -57.00   0.00   52
 24  \w     38.00  84.00   0.50    3.51    --  110.00 -57.00  30.00   92
 25  \w     40.00  73.00   0.50    3.51    --  110.00 -57.00 120.00   66
 26  \w     38.00  82.00   0.50    3.51    --  110.00 -57.00  60.00   88
 27  \w     46.00 112.00   0.50    3.51    --  110.00-125.00 -60.00  132
 28  \w     53.00 108.00   0.50    3.51    --  110.00 -99.00-180.00  110
 29  \w     38.00  84.00   0.50    3.51    --  110.00 -57.00-180.00   92
 30  \w     40.00 102.00   0.50    3.51    --  110.00-125.00-120.00  124
 31  \w     40.00  66.00   0.50    3.51    --  110.00 -57.00 -90.00   52
 32  \w    -65.00  22.00   0.50    0.88    --  -49.37  57.00 150.00  174
 33  \w    -63.00  26.00   0.50    0.88    --  -49.37  38.00  30.00  178
 34  \w    -86.00   2.00   0.50    3.51    --  -70.00  57.00  60.00  176
 35  \w    -83.00   6.00   0.50    3.51    --  -70.00  38.00-150.00  178
 36  \w    -94.00  -3.00   0.50    3.51    --  -70.00  77.00 -90.00  182
 37  \w   -116.00 -78.00   0.50    0.88    --  -49.37 -77.00 -90.00   76
 38  \w   -116.00 -78.00   0.50    0.88    --  -49.37 -77.00  30.00   76
 39  \w   -116.00 -78.00   0.50    0.88    --  -49.37 -77.00  90.00   76
 40  \w   -142.00 -54.00   0.50    3.51    --  -70.00 -57.00 -90.00  176
 41  \w   -141.00 -75.00   0.50    3.51    --  -70.00-125.00-180.00  132
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, Pilatus 300K'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0204854000
_diffrn_orient_matrix_UB_12      0.0559369000
_diffrn_orient_matrix_UB_13      -0.0245658000
_diffrn_orient_matrix_UB_21      0.0499743000
_diffrn_orient_matrix_UB_22      0.0443621000
_diffrn_orient_matrix_UB_23      0.0235090000
_diffrn_orient_matrix_UB_31      0.0826061000
_diffrn_orient_matrix_UB_32      -0.0407921000
_diffrn_orient_matrix_UB_33      -0.0081394000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_unetI/netI     0.0206
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.991
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -16
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       55
_diffrn_reflns_limit_l_min       -55
_diffrn_reflns_number            44246
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.985
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         80.143
_diffrn_reflns_theta_min         3.096
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.230
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.69134
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.28d (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.105
_exptl_crystal_description       irregular
_exptl_crystal_F_000             4600
_exptl_crystal_size_max          0.254
_exptl_crystal_size_mid          0.155
_exptl_crystal_size_min          0.102
_refine_diff_density_max         0.688
_refine_diff_density_min         -1.191
_refine_diff_density_rms         0.095
_refine_ls_abs_structure_details
;
 Flack x determined using 11498 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   -0.024(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.024
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1461
_refine_ls_number_reflns         44246
_refine_ls_number_restraints     315
_refine_ls_restrained_S_all      1.034
_refine_ls_R_factor_all          0.0679
_refine_ls_R_factor_gt           0.0653
_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^)+(0.1373P)^2^+8.8337P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1875
_refine_ls_wR_factor_ref         0.1912
_reflns_Friedel_coverage         0.840
_reflns_Friedel_fraction_full    0.999
_reflns_Friedel_fraction_max     0.978
_reflns_number_gt                42127
_reflns_number_total             44246
_reflns_threshold_expression     'I > 2\s(I)'
_twin_special_details
;
Component 2 rotated by 175.8636\% 
 around [1.00 0.00 -0.00] (reciprocal) or [1.00 -0.00 -0.00] (direct)
;
_cod_data_source_file            CCDC-1914856.cif
_cod_data_source_block           d160815_44_38_twin1_hklf4
_cod_depositor_comments
'Adding full bibliography for 4134283--4134298.cif.'
_cod_database_code               4134292
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         C133H178Br2O13
_shelx_estimated_absorpt_t_max   0.885
_shelx_estimated_absorpt_t_min   0.745
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.9449(9)
 0.0551(9)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
3. Restrained distances
 C5-C4 = C5-C4A = C4-C3 = C4A-C3A = C3-C2 = C3A-C2A = C2-C1 = C6-C5
 1.51 with sigma of 0.01
 C3C-C2C \\sim C3D-C2D
 with sigma of 0.02
 C2C-C1C \\sim C2D-C1C
 with sigma of 0.02
 C5C-C2C \\sim C4D-C2D
 with sigma of 0.02
 C5D-C3D \\sim C4C-C3C
 with sigma of 0.02
 Br2C-C3D \\sim Br2C-C3C
 with sigma of 0.02
 Br1C-C2D \\sim Br1C-C2C
 with sigma of 0.02
 C9-C10 \\sim C9-C8 \\sim C9-C8A \\sim C8-C7 \\sim C8A-C7A
 with sigma of 0.02
 C7-C9 \\sim C7A-C9 \\sim C8-C10 \\sim C8A-C10
 with sigma of 0.02
 C6-C5 \\sim C5-C4 \\sim C5-C4A \\sim C4-C3 \\sim C4A-C3A \\sim C3-C2 \\sim
C3A-C2A \\sim C2-C1 \\sim C2A-C1A
 with sigma of 0.02
 C1-C3 \\sim C1A-C3A \\sim C2-C4 \\sim C2A-C4A \\sim C3-C5 \\sim C3A-C5
 with sigma of 0.02
4. Uiso/Uaniso restraints and constraints
Uanis(C1) \\sim Ueq, Uanis(C2A) \\sim Ueq, Uanis(C2) \\sim Ueq, Uanis(C3) \\sim
Ueq, Uanis(C3A) \\sim Ueq, Uanis(C4A) \\sim Ueq, Uanis(C5) \\sim Ueq, Uanis(C4)
\\sim Ueq, Uanis(C1A) \\sim Ueq: with sigma of 0.005 and sigma for terminal
atoms of 0.01
Uanis(C7) = Uanis(C7A)
Uanis(C1) = Uanis(C1A)
5. Rigid body (RIGU) restrains
 Br1C, Br2C, C1C, O00O, C2C, C3C, C4C, C5C, C2D, C3D, C4D, C5D
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C7, C8, C9, C7A, C8A, C10, C11
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C1, C2, C3, C4, C5, C6, C4A, C3A, C2A, C1A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(H1CC)=Sof(H1CD)=Sof(C2D)=Sof(C3D)=Sof(H3D)=Sof(C4D)=Sof(H4DA)=Sof(H4DB)=
 Sof(H4DC)=Sof(C5D)=Sof(H5DA)=Sof(H5DB)=Sof(H5DC)=1-FVAR(1)
 Sof(H1CA)=Sof(H1CB)=Sof(C2C)=Sof(C3C)=Sof(H3C)=Sof(C4C)=Sof(H4CA)=Sof(H4CB)=
 Sof(H4CC)=Sof(C5C)=Sof(H5CA)=Sof(H5CB)=Sof(H5CC)=FVAR(1)
 Sof(H5BC)=Sof(H5BD)=Sof(H9BC)=Sof(H9BD)=Sof(C4A)=Sof(H4AA)=Sof(H4AB)=Sof(C3A)=
 Sof(H3AA)=Sof(H3AB)=Sof(C2A)=Sof(H2AA)=Sof(H2AB)=Sof(C7A)=Sof(H7AA)=Sof(H7AB)=
 Sof(H7AC)=Sof(C8A)=Sof(H8AA)=Sof(H8AB)=Sof(C1A)=Sof(H1AA)=Sof(H1AB)=Sof(H1AC)=
 1-FVAR(2)
 Sof(C1)=Sof(H1A)=Sof(H1B)=Sof(H1C)=Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(C3)=Sof(H3A)=
 Sof(H3B)=Sof(C4)=Sof(H4A)=Sof(H4B)=Sof(H5AA)=Sof(H5AB)=Sof(C7)=Sof(H7A)=
 Sof(H7B)=Sof(H7C)=Sof(C8)=Sof(H8A)=Sof(H8B)=Sof(H9AA)=Sof(H9AB)=FVAR(2)
7.a Ternary CH refined with riding coordinates:
 C38(H38), C55(H55), C56(H56), C57(H57), C3C(H3C), C3D(H3D)
7.b Secondary CH2 refined with riding coordinates:
 C2(H2A,H2B), C3(H3A,H3B), C4(H4A,H4B), C5(H5AA,H5AB), C5(H5BC,H5BD), C6(H6A,
 H6B), C8(H8A,H8B), C9(H9AA,H9AB), C9(H9BC,H9BD), C10(H10A,H10B), C11(H11A,
 H11B), C12(H12A,H12B), C14(H14A,H14B), C15(H15A,H15B), C16(H16A,H16B),
 C17(H17A,H17B), C18(H18A,H18B), C20(H20A,H20B), C21(H21A,H21B), C22(H22A,H22B),
  C23(H23A,H23B), C24(H24A,H24B), C45(H45A,H45B), C51(H51A,H51B), C62(H62A,
 H62B), C75(H75A,H75B), C1C(H1CA,H1CB), C1C(H1CC,H1CD), C4A(H4AA,H4AB),
 C3A(H3AA,H3AB), C2A(H2AA,H2AB), C8A(H8AA,H8AB)
7.c Aromatic/amide H refined with riding coordinates:
 C25(H25), C30(H30), C37(H37), C48(H48)
7.d Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C7(H7A,H7B,H7C), C13(H13A,H13B,H13C), C19(H19A,H19B,H19C),
 C92(H92A,H92B,H92C), C95(H95A,H95B,H95C), C97(H97A,H97B,H97C), C99(H99A,H99B,
 H99C), C100(H10C,H10D,H10E), C101(H10F,H10G,H10H), C103(H10I,H10J,H10K),
 C104(H10L,H10M,H10N), C105(H10O,H10P,H10Q), C106(H10R,H10S,H10T), C107(H10U,
 H10V,H10W), C108(H10X,H10Y,H), C109(H10Z,HA,HB), C110(H11C,H11D,H11E),
 C111(H11F,H11G,H11H), C112(H11I,H11J,H11K), C113(H11L,H11M,H11N), C114(H11O,
 H11P,H11Q), C115(H11R,H11S,H11T), C116(H11U,H11V,H11W), C117(H11X,H11Y,HC),
 C118(H11Z,HD,HE), C119(H11,HF,HG), C120(H12C,H12D,H12E), C121(H12F,H12G,H12H),
 C122(H12I,H12J,H12K), C123(H12L,H12M,H12N), C124(H12O,H12P,H12Q), C125(H12R,
 H12S,H12T), C126(H12U,H12V,H12W), C127(H12X,H12Y,HH), C128(H12Z,HI,HJ),
 C4C(H4CA,H4CB,H4CC), C5C(H5CA,H5CB,H5CC), C4D(H4DA,H4DB,H4DC), C5D(H5DA,H5DB,
 H5DC), C7A(H7AA,H7AB,H7AC), C1A(H1AA,H1AB,H1AC)
7.e Idealised tetrahedral OH refined as rotating group:
 O1(H1), O2(H2), O3(H3), O4(H4), O00O(H00O)
;
_shelx_res_checksum              30273
_shelx_hkl_checksum              31578
_olex2_date_sample_data_collection 2018-02-02
_olex2_date_sample_submission    2018-02-02
_olex2_submission_original_sample_id d160815_44_38
_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 2.350
_oxdiff_exptl_absorpt_empirical_full_min 0.436
_oxdiff_twin_integration_method  simultaneous
_oxdiff_twin_items               2