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_4134285
_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 syn
_chemical_formula_moiety         'C128 H168 O12, C7 H16 O'
_chemical_formula_sum            'C135 H184 O13'
_chemical_formula_weight         2014.81
_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             2017-10-18
_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                   15.5129(4)
_cell_length_b                   18.7006(6)
_cell_length_c                   44.5116(19)
_cell_measurement_reflns_used    17420
_cell_measurement_temperature    100.00(1)
_cell_measurement_theta_max      78.4580
_cell_measurement_theta_min      3.0700
_cell_volume                     12912.8(8)
_computing_cell_refinement       'CrysAlisPro 1.171.39.23a (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.39.23a (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.39.23a (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'XL (Sheldrick, 2008)'
_computing_structure_solution    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(1)
_diffrn_detector                 'CCD plate'
_diffrn_detector_type            'Pilatus 300K'
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.979
_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    7.00    --  -49.37 -77.00  30.00   76
  2  \w   -116.00 -78.00   0.50    7.00    --  -49.37 -77.00 -30.00   76
  3  \w   -116.00 -78.00   0.50    7.00    --  -49.37 -77.00   0.00   76
  4  \w   -136.00 -83.00   0.50   20.00    --  -70.00 -77.00 -60.00  106
  5  \w   -125.00 -36.00   0.50    7.00    --  -49.37 -38.00-150.00  178
  6  \w    -95.00 -56.00   0.50   20.00    --  -70.00 -57.00-150.00   78
  7  \w   -116.00 -78.00   0.50    7.00    --  -49.37 -77.00-150.00   76
  8  \w   -142.00-110.00   0.50   20.00    --  -70.00 -57.00-150.00   64
  9  \w   -120.00 -38.00   0.50    7.00    --  -49.37-178.00  30.00  164
 10  \w   -116.00 -78.00   0.50    7.00    --  -49.37 -77.00 150.00   76
 11  \w    -22.00  65.00   0.50    7.00    --   49.37 -57.00 120.00  174
 12  \w     94.00 119.00   0.50   20.00    --  110.00 -19.00  90.00   50
 13  \w     94.00 119.00   0.50   20.00    --  110.00 -19.00  60.00   50
 14  \w     74.00 107.00   0.50   20.00    --  110.00 -99.00 150.00   66
 15  \w     40.00  76.00   0.50   20.00    --  110.00 -57.00 120.00   72
 16  \w     45.00  73.00   0.50   20.00    --  110.00 -57.00 150.00   56
 17  \w     40.00  95.00   0.50   20.00    --  110.00 -99.00 120.00  110
 18  \w     42.00 121.00   0.50   20.00    --  110.00-125.00  30.00  158
 19  \w     64.00  92.00   0.50   20.00    --  110.00 -99.00 -60.00   56
 20  \w     62.00  88.00   0.50   20.00    --  110.00 -99.00 -90.00   52
 21  \w     47.00  72.00   0.50   20.00    --  110.00 -57.00-120.00   50
 22  \w     94.00 123.00   0.50   20.00    --  110.00 -19.00-180.00   58
 23  \w     96.00 123.00   0.50   20.00    --  110.00 -19.00-150.00   54
 24  \w     94.00 121.00   0.50   20.00    --  110.00 -19.00 -90.00   54
 25  \w     79.00 175.00   0.50   20.00    --  110.00   0.00-150.00  192
 26  \w    108.00 176.00   0.50   20.00    --  110.00  38.00-120.00  136
 27  \w    113.00 154.00   0.50   20.00    --  110.00 125.00-150.00   82
 28  \w    105.00 166.00   0.50   20.00    --  110.00 124.00-174.00  122
 29  \w    115.00 173.00   0.50   20.00    --  110.00  57.00 -60.00  116
 30  \w     95.00 177.00   0.50   20.00    --  110.00  57.00 -90.00  164
 31  \w     63.00 116.00   0.50    7.00    --   49.37 178.00  60.00  106
 32  \w     35.00  65.00   0.50    7.00    --   49.37  57.00-180.00   60
 33  \w     40.00  66.00   0.50   20.00    --  110.00   0.00-150.00   52
 34  \w     50.00  79.00   0.50   20.00    --  110.00 -57.00-180.00   58
 35  \w     47.00 109.00   0.50   20.00    --  110.00 -99.00-150.00  124
 36  \w     44.00  78.00   0.50   20.00    --  110.00 -57.00-150.00   68
 37  \w     44.00  78.00   0.50   20.00    --  110.00 -57.00 -90.00   68
 38  \w     39.00  74.00   0.50   20.00    --  110.00 -57.00 -30.00   70
 39  \w     68.00 110.00   0.50   20.00    --  110.00 -99.00  30.00   84
 40  \w     41.00  69.00   0.50   20.00    --  110.00 -99.00 150.00   56
 41  \w     38.00  79.00   0.50   20.00    --  110.00 -57.00   0.00   82
 42  \w    -90.00  -6.00   0.50   20.00    --  -70.00  77.00 -90.00  168
 43  \w    -91.00 -22.00   0.50   20.00    --  -70.00  77.00  90.00  138
;
_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      -0.0186706000
_diffrn_orient_matrix_UB_12      0.0456636000
_diffrn_orient_matrix_UB_13      -0.0281076000
_diffrn_orient_matrix_UB_21      -0.0105894000
_diffrn_orient_matrix_UB_22      0.0666725000
_diffrn_orient_matrix_UB_23      0.0198808000
_diffrn_orient_matrix_UB_31      0.0970090000
_diffrn_orient_matrix_UB_32      0.0160909000
_diffrn_orient_matrix_UB_33      -0.0032453000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_unetI/netI     0.1333
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.979
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -19
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       56
_diffrn_reflns_limit_l_min       -56
_diffrn_reflns_number            45980
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.969
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         81.503
_diffrn_reflns_theta_min         3.017
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.502
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.32770
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.23a (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    1.036
_exptl_crystal_description       plank
_exptl_crystal_F_000             4392
_exptl_crystal_size_max          0.124
_exptl_crystal_size_mid          0.072
_exptl_crystal_size_min          0.025
_refine_diff_density_max         0.453
_refine_diff_density_min         -0.447
_refine_diff_density_rms         0.081
_refine_ls_abs_structure_details
;
 Classical Flack method preferred over Parsons because s.u. lower.
;
_refine_ls_abs_structure_Flack   1.1(5)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.068
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1458
_refine_ls_number_reflns         45980
_refine_ls_number_restraints     361
_refine_ls_restrained_S_all      1.075
_refine_ls_R_factor_all          0.1758
_refine_ls_R_factor_gt           0.1270
_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^)+(0.2000P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3005
_refine_ls_wR_factor_ref         0.3375
_reflns_Friedel_coverage         0.834
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.958
_reflns_number_gt                28246
_reflns_number_total             45980
_reflns_threshold_expression     'I > 2\s(I)'
_twin_special_details
;
Component 2 rotated by -179.8713\% 
 around [0.00 -0.00 1.00] (reciprocal) or [-0.00 -0.01 1.00] (direct)
Component 3 rotated by -179.2993\% 
 around [1.00 0.00 0.00] (reciprocal) or [1.00 -0.00 -0.00] (direct)
Component 4 rotated by 179.7632\% 
 around [0.00 1.00 0.02] (reciprocal) or [-0.00 1.00 0.00] (direct)
;
_cod_data_source_file            CCDC-1914840.cif
_cod_data_source_block           d160815_44_23_twin1_hklf4
_cod_depositor_comments
'Adding full bibliography for 4134283--4134298.cif.'
_cod_database_code               4134285
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         C135H184O13
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.19(2)
 0.31(2) 0.167(8) 0.332(5)
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 C(H,H,H,H,H,H) groups, All O(H) groups
3. Restrained distances
 C2-C1 = C2A-C1A = C3-C2 = C4-C3 = C3A-C2A = C4A-C3A = C5-C4A = C5-C4 = C6-C5 =
  C6-C00K
 1.52 with sigma of 0.01
 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 \\sim
C4-C6 \\sim C4A-C6
 with sigma of 0.02
 C6B-C3B \\sim C7B-C2B \\sim C5B-C2B \\sim C4B-C3B
 with sigma of 0.02
 C5B-C2B \\sim C2C-C5B
 with sigma of 0.02
 C2C-C1B \\sim C2B-C1B
 with sigma of 0.02
 C7B-C2B \\sim C7C-C2C
 with sigma of 0.02
 C3C-C2C \\sim C3B-C2B
 with sigma of 0.02
 C6C-C3C \\sim C6B-C3B
 with sigma of 0.02
 C4B-C3C \\sim C4B-C3B
 with sigma of 0.02
4. Rigid bond restraints
 C5, C6, C1, C2, C3, C4, C1A, C2A, C3A, C4A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
Uanis(C5) \\sim Ueq, Uanis(C6) \\sim Ueq, Uanis(C4) \\sim Ueq, Uanis(C4A) \\sim
Ueq, Uanis(C3) \\sim Ueq, Uanis(C3A) \\sim Ueq, Uanis(C2A) \\sim Ueq, Uanis(C2)
\\sim Ueq, Uanis(C1) \\sim Ueq, Uanis(C1A) \\sim Ueq, Uanis(C8) \\sim Ueq,
Uanis(C7) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.04
6. Rigid body (RIGU) restrains
 C5, C6, C1, C2, C3, C4, C1A, C2A, C3A, C4A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C7, C8, C9, C10, C11
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O1B, C1B, C4B, C5B, C2B, C3B, C6B, C7B, C2C, C3C, C6C, C7C
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
7. Others
 Sof(H1BD)=Sof(H1BE)=Sof(H4BD)=Sof(H4BE)=Sof(H4BF)=Sof(H5BF)=Sof(H5BG)=
 Sof(H5BH)=Sof(C2C)=Sof(C3C)=Sof(H3C)=Sof(C6C)=Sof(H6CA)=Sof(H6CB)=Sof(H6CC)=
 Sof(C7C)=Sof(H7CA)=Sof(H7CB)=Sof(H7CC)=1-FVAR(1)
 Sof(H1BB)=Sof(H1BC)=Sof(H4BA)=Sof(H4BB)=Sof(H4BC)=Sof(H5BA)=Sof(H5BB)=
 Sof(H5BE)=Sof(C2B)=Sof(C3B)=Sof(H3BA)=Sof(C6B)=Sof(H6BA)=Sof(H6BB)=Sof(H6BC)=
 Sof(C7B)=Sof(H7BA)=Sof(H7BB)=Sof(H7BC)=FVAR(1)
 Sof(H5BC)=Sof(H5BD)=Sof(C1A)=Sof(H1AA)=Sof(H1AB)=Sof(H1AC)=Sof(C2A)=Sof(H2AA)=
 Sof(H2AB)=Sof(C3A)=Sof(H3AA)=Sof(H3AB)=Sof(C4A)=Sof(H4AA)=Sof(H4AB)=1-FVAR(2)
 Sof(H5AA)=Sof(H5AB)=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)=FVAR(2)
8.a Ternary CH refined with riding coordinates:
 C012(H012), C33(H33), C53(H53), C00K(H00K), C3B(H3BA), C3C(H3C)
8.b Secondary CH2 refined with riding coordinates:
 C5(H5AA,H5AB), C5(H5BC,H5BD), C6(H6A,H6B), C8(H8A,H8B), C9(H9A,H9B), 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), C27(H27A,H27B), C48(H48A,
 H48B), C50(H50A,H50B), C69(H69A,H69B), C2(H2A,H2B), C3(H3A,H3B), C4(H4A,H4B),
 C2A(H2AA,H2AB), C3A(H3AA,H3AB), C4A(H4AA,H4AB), C1B(H1BB,H1BC), C1B(H1BD,H1BE)
8.c Aromatic/amide H refined with riding coordinates:
 C021(H021), C41(H41), C83(H83), C89(H89)
8.d Idealised Me refined as rotating group:
 C7(H7A,H7B,H7C), C13(H13A,H13B,H13C), C19(H19A,H19B,H19C), C47(H47A,H47B,
 H47C), C55(H55A,H55B,H55C), C66(H66A,H66B,H66C), C74(H74A,H74B,H74C), C77(H77A,
 H77B,H77C), C82(H82A,H82B,H82C), C85(H85A,H85B,H85C), C86(H86A,H86B,H86C),
 C87(H87A,H87B,H87C), C88(H88A,H88B,H88C), C90(H90A,H90B,H90C), C91(H91A,H91B,
 H91C), C96(H96A,H96B,H96C), C101(H10C,H10D,H10E), C103(H10F,H10G,H10H),
 C104(H10I,H10J,H10K), C105(H10L,H10M,H10N), C106(H10O,H10P,H10Q), C108(H10R,
 H10S,H10T), C109(H10U,H10V,H10W), C111(H11C,H11D,H11E), C113(H11F,H11G,H11H),
 C114(H11I,H11J,H11K), C116(H11L,H11M,H11N), C117(H11O,H11P,H11Q), C118(H11R,
 H11S,H11T), C119(H11U,H11V,H11W), C120(H12C,H12D,H12E), C122(H12F,H12G,H12H),
 C123(H12I,H12J,H12K), C124(H12L,H12M,H12N), C125(H12O,H12P,H12Q), C1(H1A,H1B,
 H1C), C1A(H1AA,H1AB,H1AC), C4B(H4BA,H4BB,H4BC), C4B(H4BD,H4BE,H4BF), C5B(H5BA,
 H5BB,H5BE), C5B(H5BF,H5BG,H5BH), C6B(H6BA,H6BB,H6BC), C7B(H7BA,H7BB,H7BC),
 C6C(H6CA,H6CB,H6CC), C7C(H7CA,H7CB,H7CC)
8.e Idealised tetrahedral OH refined as rotating group:
 O1(H1), O2(H2), O3(H3), O4(H4), O1B(H1BA)
;
_shelx_res_checksum              8211
_shelx_hkl_checksum              539
_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 3.088
_oxdiff_exptl_absorpt_empirical_full_min 0.327
_oxdiff_twin_integration_method  simultaneous
_oxdiff_twin_items               4