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_4134286
_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, 0.49(C4 H8 Cl2 O)'
_chemical_formula_sum            'C129.98 H171.96 Cl0.99 O12.5'
_chemical_formula_weight         1969.44
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2017-10-30
_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                   15.60340(10)
_cell_length_b                   18.7470(2)
_cell_length_c                   43.6221(4)
_cell_measurement_reflns_used    70958
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      78.9690
_cell_measurement_theta_min      3.4830
_cell_volume                     12760.2(2)
_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  'XL (Sheldrick, 2008)'
_computing_structure_solution    'XT (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 0.995
_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    -65.00  22.00   0.50    5.00    --  -49.37  57.00-180.00  174
  2  \w    -63.00  26.00   0.50    5.00    --  -49.37  38.00   0.00  178
  3  \w    -26.00  49.00   0.50    5.00    --   49.37 -38.00 -60.00  150
  4  \w     94.00 178.00   0.50   15.00    --  110.00  57.00-180.00  168
  5  \w     97.00 178.00   0.50   15.00    --  110.00  19.00 -60.00  162
  6  \w     95.00 121.00   0.50   15.00    --  110.00 -19.00  60.00   52
  7  \w     95.00 120.00   0.50   15.00    --  110.00 -19.00   0.00   50
  8  \w     99.00 161.00   0.50   15.00    --  110.00  38.00  60.00  124
  9  \w    129.00 178.00   0.50   15.00    --  110.00  57.00 150.00   98
 10  \w    148.00 174.00   0.50   15.00    --  110.00 125.00  60.00   52
 11  \w    106.00 133.00   0.50   15.00    --  110.00 125.00  60.00   54
 12  \w     91.00 178.00   0.50   15.00    --  110.00 125.00  90.00  174
 13  \w     97.00 143.00   0.50   15.00    --  110.00  57.00 -30.00   92
 14  \w     78.00 116.00   0.50    5.00    --   49.37  77.00  60.00   76
 15  \w     94.00 123.00   0.50   15.00    --  110.00 -19.00 150.00   58
 16  \w     40.00 110.00   0.50   15.00    --  110.00 -99.00 150.00  140
 17  \w     40.00 110.00   0.50   15.00    --  110.00 -99.00  90.00  140
 18  \w     41.00  94.00   0.50   15.00    --  110.00 -99.00   0.00  106
 19  \w     38.00  84.00   0.50   15.00    --  110.00 -57.00 -30.00   92
 20  \w     38.00  63.00   0.50   15.00    --  110.00 -57.00 -90.00   50
 21  \w     55.00  81.00   0.50   15.00    --  110.00 -99.00-120.00   52
 22  \w     53.00  81.00   0.50   15.00    --  110.00 -57.00-150.00   56
 23  \w     48.00 106.00   0.50   15.00    --  110.00-125.00 -90.00  116
 24  \w     43.00 119.00   0.50   15.00    --  110.00-125.00 -30.00  152
 25  \w     51.00 117.00   0.50   15.00    --  110.00-125.00  90.00  132
 26  \w     50.00  79.00   0.50   15.00    --  110.00 -57.00 150.00   58
 27  \w     38.00  84.00   0.50   15.00    --  110.00 -57.00 120.00   92
 28  \w     47.00  73.00   0.50   15.00    --  110.00 -57.00  60.00   52
 29  \w     94.00 175.00   0.50   15.00    --  110.00  57.00-150.00  162
 30  \w     42.00 101.00   0.50   15.00    --  110.00-125.00-180.00  118
 31  \w    -83.00   6.00   0.50   15.00    --  -70.00  38.00 150.00  178
 32  \w    -86.00   2.00   0.50   15.00    --  -70.00  57.00  30.00  176
 33  \w    -86.00   2.00   0.50   15.00    --  -70.00  57.00-120.00  176
 34  \w   -116.00 -78.00   0.50    5.00    --  -49.37 -77.00-150.00   76
 35  \w   -116.00 -78.00   0.50    5.00    --  -49.37 -77.00-180.00   76
 36  \w   -116.00 -78.00   0.50    5.00    --  -49.37 -77.00-120.00   76
 37  \w   -140.00 -84.00   0.50   15.00    --  -70.00 -99.00-150.00  112
 38  \w   -116.00 -78.00   0.50    5.00    --  -49.37 -77.00  30.00   76
 39  \w   -125.00 -36.00   0.50    5.00    --  -49.37 -38.00  60.00  178
 40  \w   -140.00 -84.00   0.50   15.00    --  -70.00 -99.00 120.00  112
;
_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      -0.0009602000
_diffrn_orient_matrix_UB_12      0.0189761000
_diffrn_orient_matrix_UB_13      0.0343503000
_diffrn_orient_matrix_UB_21      0.0649146000
_diffrn_orient_matrix_UB_22      0.0604449000
_diffrn_orient_matrix_UB_23      -0.0059235000
_diffrn_orient_matrix_UB_31      -0.0744127000
_diffrn_orient_matrix_UB_32      0.0523448000
_diffrn_orient_matrix_UB_33      -0.0056173000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0678
_diffrn_reflns_av_unetI/netI     0.0368
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       17
_diffrn_reflns_limit_h_min       -19
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       55
_diffrn_reflns_limit_l_min       -55
_diffrn_reflns_number            210282
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         80.021
_diffrn_reflns_theta_min         3.008
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.683
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.798
_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    1.025
_exptl_crystal_description       plate
_exptl_crystal_F_000             4275
_exptl_crystal_size_max          0.122
_exptl_crystal_size_mid          0.11
_exptl_crystal_size_min          0.044
_refine_diff_density_max         1.241
_refine_diff_density_min         -0.440
_refine_diff_density_rms         0.061
_refine_ls_abs_structure_details
;
 Flack x determined using 8662 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.029(8)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1419
_refine_ls_number_reflns         27516
_refine_ls_number_restraints     263
_refine_ls_restrained_S_all      1.075
_refine_ls_R_factor_all          0.0837
_refine_ls_R_factor_gt           0.0713
_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^)+(0.1313P)^2^+3.5868P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1983
_refine_ls_wR_factor_ref         0.2112
_reflns_Friedel_coverage         0.840
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.981
_reflns_number_gt                22771
_reflns_number_total             27516
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            CCDC-1914852.cif
_cod_data_source_block           d160815_44_27
_cod_depositor_comments
'Adding full bibliography for 4134283--4134298.cif.'
_cod_original_formula_sum        'C129.98 H171.96 Cl0.99 O12.50'
_cod_database_code               4134286
_shelx_shelxl_version_number     2014/7
_chemical_oxdiff_formula         C132H176Cl2O13
_shelx_estimated_absorpt_t_max   0.971
_shelx_estimated_absorpt_t_min   0.921
_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, All O(H,H) groups
2. Restrained distances
 C27A-C26 = C26-C25 = C26-C25A = C27-C26
 1.52 with sigma of 0.005
 C25-C27 = C25A-C27A
 2.55 with sigma of 0.01
 H2-O3
 2 with sigma of 0.02
 H1-O2
 2 with sigma of 0.02
 O1A-C26 = O1-C26
 1.43 with sigma of 0.005
 O1A-C27A = O1A-C25A = O1-C27 = O1-C25
 2.36 with sigma of 0.01
 H1AA-O2
 2 with sigma of 0.02
 H3-O4
 2 with sigma of 0.02
 H4B-O1A
 2.17 with sigma of 0.001
 O4-H4B
 0.93 with sigma of 0.001
 O1C-C1C
 1.44 with sigma of 0.001
 C26-C25A \\sim C26-C25 \\sim C27A-C26 \\sim C27-C26
 with sigma of 0.02
 C25-C27 \\sim C25A-C27A
 with sigma of 0.02
 C6-C123 \\sim C6-C5 \\sim C5-C4 \\sim C5-C4A \\sim C4-C3 \\sim C4A-C3A \\sim
C3-C2 \\sim C3A-C2 \\sim C2-C1
 with sigma of 0.02
 C1-C3 \\sim C1-C3A \\sim C2-C4 \\sim C2-C4A \\sim C3-C5 \\sim C3A-C5 \\sim
C4-C6 \\sim C4A-C6
 with sigma of 0.02
 O1-C26 \\sim O1A-C26
 with sigma of 0.02
 O1A-C27A \\sim O1A-C25A \\sim O1-C27 \\sim O1-C25
 with sigma of 0.02
3. Rigid bond restraints
 C1, C2, C3, C4, C5, C6, C4A, C3A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Rigid body (RIGU) restrains
 Cl1C, Cl2C, O1C, C1C, C2C, C3C, C4C
 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
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 O1, C25, C26, C28, C25A, C27, O1A, C27A, C29
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(H4B)=Sof(O1A)=Sof(H1AA)=Sof(C25A)=Sof(H25D)=Sof(H25E)=Sof(H25F)=Sof(C27A)=
 Sof(H27D)=Sof(H27E)=Sof(H27F)=1-FVAR(1)
 Sof(O1)=Sof(H1)=Sof(H4A)=Sof(C25)=Sof(H25A)=Sof(H25B)=Sof(H25C)=Sof(C27)=
 Sof(H27A)=Sof(H27B)=Sof(H27C)=Sof(Cl1C)=Sof(Cl2C)=Sof(O1C)=Sof(H1CA)=Sof(C1C)=
 Sof(H1CB)=Sof(H1CC)=Sof(C2C)=Sof(H2C)=Sof(C3C)=Sof(H3C)=Sof(C4C)=Sof(H4CA)=
 Sof(H4CB)=Sof(H4CC)=FVAR(1)
 Sof(H2BC)=Sof(H2BD)=Sof(H5BC)=Sof(H5BD)=Sof(C4A)=Sof(H4AA)=Sof(H4AB)=Sof(C3A)=
 Sof(H3AA)=Sof(H3AB)=1-FVAR(2)
 Sof(H2AA)=Sof(H2AB)=Sof(C3)=Sof(H3A)=Sof(H3B)=Sof(C4)=Sof(H4C)=Sof(H4D)=
 Sof(H5AA)=Sof(H5AB)=FVAR(2)
6.a Ternary CH refined with riding coordinates:
 C55(H55), C67(H67), C120(H120), C123(H123), C2C(H2C), C3C(H3C)
6.b Secondary CH2 refined with riding coordinates:
 C2(H2AA,H2AB), C2(H2BC,H2BD), C3(H3A,H3B), C4(H4C,H4D), 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), C57(H57A,H57B), C77(H77A,H77B), C122(H12C,
 H12D), C127(H12E,H12F), C1C(H1CB,H1CC), C4A(H4AA,H4AB), C3A(H3AA,H3AB)
6.c Aromatic/amide H refined with riding coordinates:
 C49(H49), C58(H58), C61(H61), C121(H121)
6.d Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), C7(H7A,H7B,H7C), C13(H13A,H13B,H13C), C19(H19A,H19B,H19C),
 C25(H25A,H25B,H25C), C27(H27A,H27B,H27C), C32(H32A,H32B,H32C), C33(H33A,H33B,
 H33C), C34(H34A,H34B,H34C), C38(H38A,H38B,H38C), C39(H39A,H39B,H39C), C40(H40A,
 H40B,H40C), C78(H78A,H78B,H78C), C86(H86A,H86B,H86C), C87(H87A,H87B,H87C),
 C88(H88A,H88B,H88C), C89(H89A,H89B,H89C), C90(H90A,H90B,H90C), C91(H91A,H91B,
 H91C), C92(H92A,H92B,H92C), C93(H93A,H93B,H93C), C94(H94A,H94B,H94C), C95(H95A,
 H95B,H95C), C96(H96A,H96B,H96C), C97(H97A,H97B,H97C), C98(H98A,H98B,H98C),
 C99(H99A,H99B,H99C), C100(H10C,H10D,H10E), C105(H10F,H10G,H10H), C107(H10I,
 H10J,H10K), C108(H10L,H10M,H10N), C109(H10O,H10P,H10Q), C110(H11C,H11D,H11E),
 C112(H11F,H11G,H11H), C113(H11I,H11J,H11K), C114(H11L,H11M,H11N), C4C(H4CA,
 H4CB,H4CC), C25A(H25D,H25E,H25F), C27A(H27D,H27E,H27F)
6.e Idealised tetrahedral OH refined as rotating group:
 O1(H1), O2(H2), O3(H3), O4(H4A), O1C(H1CA), O1A(H1AA)
;
_shelx_res_checksum              2367
_shelx_hkl_checksum              47291
_olex2_date_sample_data_collection 2017-10-19
_olex2_date_sample_submission    2017-10-19
_olex2_submission_original_sample_id d160815_44_27
_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 1.846
_oxdiff_exptl_absorpt_empirical_full_min 0.786