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_4134287
_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, C4 H8 Cl2 O'
_chemical_formula_sum            'C132 H176 Cl2 O13'
_chemical_formula_weight         2041.62
_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             2017-11-01
_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                   15.61350(10)
_cell_length_b                   18.75150(10)
_cell_length_c                   43.6512(2)
_cell_measurement_reflns_used    108975
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      79.3190
_cell_measurement_theta_min      3.1090
_cell_volume                     12780.05(12)
_computing_cell_refinement       'CrysAlisPro 1.171.39.31d (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.31d (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.31d (Rigaku OD, 2017)'
_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 1.000
_diffrn_measured_fraction_theta_max 0.997
_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   -116.00 -78.00   0.50    1.30    --  -49.37 -77.00-180.00   76
  2  \w   -137.00 -78.00   0.50    5.00    --  -70.00 -77.00-150.00  118
  3  \w   -116.00 -78.00   0.50    1.30    --  -49.37 -77.00 -30.00   76
  4  \w   -116.00 -78.00   0.50    1.30    --  -49.37 -77.00   0.00   76
  5  \w   -116.00 -78.00   0.50    1.30    --  -49.37 -77.00  60.00   76
  6  \w   -116.00 -78.00   0.50    1.30    --  -49.37 -77.00 120.00   76
  7  \w   -137.00 -78.00   0.50    5.00    --  -70.00 -77.00  90.00  118
  8  \w   -137.00 -78.00   0.50    5.00    --  -70.00 -77.00 -90.00  118
  9  \w    -65.00  22.00   0.50    1.30    --  -49.37  57.00  90.00  174
 10  \w    -73.00  17.00   0.50    1.30    --  -49.37  77.00  90.00  180
 11  \w     78.00 116.00   0.50    1.30    --   49.37  77.00 -30.00   76
 12  \w     78.00 116.00   0.50    1.30    --   49.37  77.00-120.00   76
 13  \w     94.00 178.00   0.50    5.00    --  110.00  57.00   0.00  168
 14  \w    150.00 176.00   0.50    5.00    --  110.00  57.00 120.00   52
 15  \w     94.00 178.00   0.50    5.00    --  110.00  57.00  60.00  168
 16  \w     97.00 126.00   0.50    5.00    --  110.00  57.00 120.00   58
 17  \w     95.00 174.00   0.50    5.00    --  110.00  57.00  30.00  158
 18  \w     78.00 116.00   0.50    1.30    --   49.37  77.00 120.00   76
 19  \w     38.00  84.00   0.50    5.00    --  110.00 -57.00  30.00   92
 20  \w     74.00 100.00   0.50    5.00    --  110.00 -99.00  60.00   52
 21  \w     47.00 122.00   0.50    5.00    --  110.00-125.00 150.00  150
 22  \w     39.00 122.00   0.50    5.00    --  110.00-125.00   0.00  166
 23  \w     92.00 134.00   0.50    5.00    --  110.00 -77.00 -90.00   84
 24  \w     95.00 122.00   0.50    5.00    --  110.00 -19.00-180.00   54
 25  \w     86.00 177.00   0.50    5.00    --  110.00  77.00-180.00  182
 26  \w     46.00 108.00   0.50    5.00    --  110.00 -95.00-134.00  124
 27  \w     52.00  78.00   0.50    5.00    --  110.00 -77.00 -90.00   52
 28  \w     38.00  84.00   0.50    5.00    --  110.00 -57.00-120.00   92
 29  \w     40.00 100.00   0.50    5.00    --  110.00 -99.00-180.00  120
 30  \w     38.00  84.00   0.50    5.00    --  110.00 -57.00-150.00   92
 31  \w     52.00 168.00   0.50    5.00    --  110.00   0.00-180.00  232
 32  \w     38.00  84.00   0.50    5.00    --  110.00 -57.00  60.00   92
 33  \w     41.00 103.00   0.50    5.00    --  110.00 -99.00  30.00  124
 34  \w     38.00  84.00   0.50    5.00    --  110.00 -57.00 -60.00   92
 35  \w     38.00  75.00   0.50    5.00    --  110.00 -57.00   0.00   74
 36  \w     38.00  84.00   0.50    5.00    --  110.00 -57.00 150.00   92
 37  \w     40.00 110.00   0.50    5.00    --  110.00 -99.00 150.00  140
 38  \w    -94.00  -3.00   0.50    5.00    --  -70.00  77.00   0.00  182
 39  \w    -94.00  -3.00   0.50    5.00    --  -70.00  77.00-150.00  182
;
_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      0.0107032000
_diffrn_orient_matrix_UB_12      0.0140589000
_diffrn_orient_matrix_UB_13      0.0345596000
_diffrn_orient_matrix_UB_21      -0.0347939000
_diffrn_orient_matrix_UB_22      -0.0751216000
_diffrn_orient_matrix_UB_23      0.0070252000
_diffrn_orient_matrix_UB_31      0.0917045000
_diffrn_orient_matrix_UB_32      -0.0301526000
_diffrn_orient_matrix_UB_33      -0.0013644000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0432
_diffrn_reflns_av_unetI/netI     0.0227
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -15
_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            210898
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.738
_diffrn_reflns_theta_min         3.006
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.889
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.809
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.31d (Rigaku Oxford Diffraction, 2017)
Numerical absorption correction based on gaussian integration over
			a multifaceted crystal model
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    1.061
_exptl_crystal_description       block
_exptl_crystal_F_000             4424
_exptl_crystal_size_max          0.154
_exptl_crystal_size_mid          0.112
_exptl_crystal_size_min          0.076
_refine_diff_density_max         1.102
_refine_diff_density_min         -1.375
_refine_diff_density_rms         0.074
_refine_ls_abs_structure_details
;
 Flack x determined using 10731 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.066(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.028
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1442
_refine_ls_number_reflns         27582
_refine_ls_number_restraints     366
_refine_ls_restrained_S_all      1.049
_refine_ls_R_factor_all          0.0757
_refine_ls_R_factor_gt           0.0718
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1549P)^2^+5.6809P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2119
_refine_ls_wR_factor_ref         0.2171
_reflns_Friedel_coverage         0.842
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.986
_reflns_number_gt                25595
_reflns_number_total             27582
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            CCDC-1914858.cif
_cod_data_source_block           d160815_44_30
_cod_depositor_comments
'Adding full bibliography for 4134283--4134298.cif.'
_cod_database_code               4134287
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         C132H176Cl2O13
_reflns_odcompleteness_completeness 99.96
_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, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 C5-C4A = C6-C5 = C5-C4 = C4A-C3A = C4-C3 = C3-C2A = C3A-C2A = C2A-C1 = C2A-
 C1A = C6-C57
 1.5 with sigma of 0.01
 H1-O2
 2 with sigma of 0.01
 Cl2C-C3C \\sim Cl2C-C3D
 with sigma of 0.02
 C4C-C3C \\sim C4D-C3D
 with sigma of 0.02
 C3C-C2C \\sim C3D-C2D
 with sigma of 0.02
 C2D-C1C \\sim C2C-C1C
 with sigma of 0.01
 Cl1C-C2D \\sim Cl1C-C2C
 with sigma of 0.02
 C9-C10 \\sim C9-C8A \\sim C9-C8 \\sim C8A-C7A \\sim C8-C7
 with sigma of 0.02
 C7-C9 \\sim C7A-C9 \\sim C8-C10 \\sim C8A-C10
 with sigma of 0.02
 C1-C3 \\sim C1A-C3A \\sim C2A-C4A \\sim C3-C5 \\sim C3A-C5 \\sim C4-C6 \\sim
C4A-C6
 with sigma of 0.02
 C5-C4A \\sim C6-C5 \\sim C5-C4 \\sim C4A-C3A \\sim C4-C3 \\sim C3-C2A \\sim
C3A-C2A \\sim C2A-C1 \\sim C2A-
 C1A \\sim C6-C57
 with sigma of 0.02
3. Rigid bond restraints
 C7, C8, C9, C10, C11, C8A, C7A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C1, C3, C4, C5, C6, C4A, C3A, C1A, C2A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
Uanis(C10) \\sim Ueq, Uanis(C9) \\sim Ueq, Uanis(C8A) \\sim Ueq, Uanis(C8)
\\sim Ueq, Uanis(C7A) \\sim Ueq, Uanis(C7) \\sim Ueq: with sigma of 0.005 and
sigma for terminal atoms of 0.01
Uanis(C1) \\sim Ueq, Uanis(C3) \\sim Ueq, Uanis(C4) \\sim Ueq, Uanis(C5) \\sim
Ueq, Uanis(C4A) \\sim Ueq, Uanis(C3A) \\sim Ueq, Uanis(C1A) \\sim Ueq,
Uanis(C2A) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
5. Rigid body (RIGU) restrains
 O4, Cl1C, Cl2C, C1C, C2C, C3C, C4C, C2D, C3D, C4D
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C7, C8, C9, C10, C11, C8A, C7A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C1, C3, C4, C5, C6, C4A, C3A, C1A, C2A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(H9BC)=Sof(H9BD)=Sof(H1CC)=Sof(H1CD)=Sof(C2D)=Sof(H2D)=Sof(C3D)=Sof(H3D)=
 Sof(C4D)=Sof(H4DA)=Sof(H4DB)=Sof(H4DC)=Sof(C8A)=Sof(H8AA)=Sof(H8AB)=Sof(C7A)=
 Sof(H7AA)=Sof(H7AB)=Sof(H7AC)=1-FVAR(1)
 Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(H7C)=Sof(C8)=Sof(H8A)=Sof(H8B)=Sof(H9AA)=
 Sof(H9AB)=Sof(H1CA)=Sof(H1CB)=Sof(C2C)=Sof(H2C)=Sof(C3C)=Sof(H3C)=Sof(C4C)=
 Sof(H4CA)=Sof(H4CB)=Sof(H4CC)=FVAR(1)
 Sof(H5BC)=Sof(H5BD)=Sof(C4A)=Sof(H4AA)=Sof(H4AB)=Sof(C3A)=Sof(H3AA)=Sof(H3AB)=
 Sof(C1A)=Sof(H1AA)=Sof(H1AB)=Sof(H1AC)=Sof(H2AC)=Sof(H2AD)=1-FVAR(2)
 Sof(C1)=Sof(H1A)=Sof(H1B)=Sof(H1C)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(C4)=Sof(H4A)=
 Sof(H4B)=Sof(H5AA)=Sof(H5AB)=Sof(H2AA)=Sof(H2AB)=FVAR(2)
7.a Ternary CH refined with riding coordinates:
 C38(H38), C46(H46), C57(H57), C60(H60), C2C(H2C), C3C(H3C), C2D(H2D), C3D(H3D)
7.b Secondary CH2 refined with riding coordinates:
 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), C50(H50A,H50B), C65(H65A,H65B), C71(H71A,H71B), C78(H78A,
 H78B), C1C(H1CA,H1CB), C1C(H1CC,H1CD), C4A(H4AA,H4AB), C3A(H3AA,H3AB),
 C2A(H2AA,H2AB), C2A(H2AC,H2AD), C8A(H8AA,H8AB)
7.c Me refined with riding coordinates:
 C128(H12Z,HE,HF)
7.d Aromatic/amide H refined with riding coordinates:
 C25(H25), C43(H43), C52(H52), C56(H56)
7.e Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C7(H7A,H7B,H7C), C13(H13A,H13B,H13C), C19(H19A,H19B,H19C),
 C88(H88A,H88B,H88C), C89(H89A,H89B,H89C), C90(H90A,H90B,H90C), C93(H93A,H93B,
 H93C), C95(H95A,H95B,H95C), C99(H99A,H99B,H99C), C100(H10C,H10D,H10E),
 C101(H10F,H10G,H10H), C102(H10I,H10J,H10K), C103(H10L,H10M,H10N), C104(H10O,
 H10P,H10Q), C105(H10R,H10S,H10T), C106(H10U,H10V,H10W), C109(H10X,H10Y,H),
 C110(H11C,H11D,H11E), C111(H11F,H11G,H11H), C113(H11I,H11J,H11K), C114(H11L,
 H11M,H11N), C115(H11O,H11P,H11Q), C116(H11R,H11S,H11T), C117(H11U,H11V,H11W),
 C118(H11X,H11Y,HA), C119(H11Z,HB,HC), 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,HD), C4C(H4CA,H4CB,
 H4CC), C4D(H4DA,H4DB,H4DC), C1A(H1AA,H1AB,H1AC), C7A(H7AA,H7AB,H7AC)
7.f Idealised tetrahedral OH refined as rotating group:
 O1(H1), O2(H2), O3(H3), O00B(H00B), O4(H4)
;
_shelx_res_checksum              19649
_shelx_hkl_checksum              54696
_olex2_date_sample_data_collection 2017-10-24
_olex2_date_sample_submission    2017-10-24
_olex2_submission_original_sample_id d160815_44_30
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 1.402
_oxdiff_exptl_absorpt_empirical_full_min 0.871