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_4134291
_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 Br2 O'
_chemical_formula_sum            'C132 H176 Br2 O13'
_chemical_formula_weight         2130.54
_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                   15.60580(10)
_cell_length_b                   18.73660(10)
_cell_length_c                   43.8709(3)
_cell_measurement_reflns_used    105389
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      79.1870
_cell_measurement_theta_min      3.4730
_cell_volume                     12827.84(14)
_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 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   -123.00 -36.00   0.50    1.10    --  -49.37 -46.00  99.00  174
  2  \w    -83.00   6.00   0.50    3.30    --  -70.00  38.00 -30.00  178
  3  \w    -62.00  25.00   0.50    1.10    --  -49.37  46.00-110.00  174
  4  \w    -73.00  17.00   0.50    1.10    --  -49.37  77.00  30.00  180
  5  \w    -94.00  -3.00   0.50    3.30    --  -70.00  77.00   0.00  182
  6  \w   -116.00 -78.00   0.50    1.10    --  -49.37 -77.00   0.00   76
  7  \w   -116.00 -78.00   0.50    1.10    --  -49.37 -77.00 -60.00   76
  8  \w   -116.00 -78.00   0.50    1.10    --  -49.37 -77.00-120.00   76
  9  \w   -116.00 -78.00   0.50    1.10    --  -49.37 -77.00-150.00   76
 10  \w   -140.00 -84.00   0.50    3.30    --  -70.00 -99.00-150.00  112
 11  \w   -137.00 -78.00   0.50    3.30    --  -70.00 -77.00 -60.00  118
 12  \w   -141.00 -75.00   0.50    3.30    --  -70.00-125.00  30.00  132
 13  \w   -116.00 -78.00   0.50    1.10    --  -49.37 -77.00 150.00   76
 14  \w     57.00 122.00   0.50    1.10    --   49.37-178.00  90.00  130
 15  \w     62.00 102.00   0.50    3.30    --  110.00 -99.00   0.00   80
 16  \w     73.00 121.00   0.50    3.30    --  110.00-125.00   0.00   96
 17  \w     60.00  86.00   0.50    3.30    --  110.00 -99.00  30.00   52
 18  \w     48.00  74.00   0.50    3.30    --  110.00 -57.00  60.00   52
 19  \w     95.00 123.00   0.50    3.30    --  110.00 -19.00  60.00   56
 20  \w    123.00 168.00   0.50    3.30    --  110.00  19.00  90.00   90
 21  \w    134.00 161.00   0.50    3.30    --  110.00  38.00 120.00   54
 22  \w     94.00 178.00   0.50    3.30    --  110.00  57.00   0.00  168
 23  \w    131.00 172.00   0.50    3.30    --  110.00  57.00 -60.00   82
 24  \w    113.00 138.00   0.50    3.30    --  110.00 125.00 -30.00   50
 25  \w     97.00 123.00   0.50    3.30    --  110.00  57.00 -60.00   52
 26  \w     95.00 176.00   0.50    3.30    --  110.00  57.00  30.00  162
 27  \w     98.00 171.00   0.50    3.30    --  110.00  57.00 120.00  146
 28  \w    101.00 178.00   0.50    3.30    --  110.00  57.00  60.00  154
 29  \w     96.00 123.00   0.50    3.30    --  110.00 -19.00   0.00   54
 30  \w     41.00 110.00   0.50    3.30    --  110.00 -97.00-117.00  138
 31  \w     94.00 123.00   0.50    3.30    --  110.00 -19.00-180.00   58
 32  \w     40.00 110.00   0.50    3.30    --  110.00 -99.00 -90.00  140
 33  \w     44.00 109.00   0.50    3.30    --  110.00 -99.00-180.00  130
 34  \w     47.00 119.00   0.50    3.30    --  110.00-125.00-180.00  144
 35  \w     38.00  84.00   0.50    3.30    --  110.00 -57.00-120.00   92
 36  \w     44.00  82.00   0.50    3.30    --  110.00 -57.00 -90.00   76
 37  \w     38.00  74.00   0.50    3.30    --  110.00 -57.00 -30.00   72
 38  \w     38.00  84.00   0.50    3.30    --  110.00 -57.00   0.00   92
 39  \w     43.00  69.00   0.50    3.30    --  110.00-125.00   0.00   52
 40  \w     39.00 108.00   0.50    3.30    --  110.00-125.00 120.00  138
 41  \w     38.00  84.00   0.50    3.30    --  110.00 -57.00 150.00   92
 42  \w     44.00  73.00   0.50    3.30    --  110.00 -99.00-150.00   58
;
_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      0.0699105000
_diffrn_orient_matrix_UB_12      -0.0467838000
_diffrn_orient_matrix_UB_13      -0.0147092000
_diffrn_orient_matrix_UB_21      0.0531379000
_diffrn_orient_matrix_UB_22      0.0042354000
_diffrn_orient_matrix_UB_23      0.0295378000
_diffrn_orient_matrix_UB_31      -0.0450776000
_diffrn_orient_matrix_UB_32      -0.0674929000
_diffrn_orient_matrix_UB_33      0.0120108000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0481
_diffrn_reflns_av_unetI/netI     0.0256
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -19
_diffrn_reflns_limit_k_max       22
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       55
_diffrn_reflns_limit_l_min       -55
_diffrn_reflns_number            210855
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.808
_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    1.233
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.591
_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    1.103
_exptl_crystal_description       block
_exptl_crystal_F_000             4568
_exptl_crystal_size_max          0.226
_exptl_crystal_size_mid          0.111
_exptl_crystal_size_min          0.075
_refine_diff_density_max         2.766
_refine_diff_density_min         -2.228
_refine_diff_density_rms         0.120
_refine_ls_abs_structure_details
;
 Flack x determined using 10633 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.014(4)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1453
_refine_ls_number_reflns         27662
_refine_ls_number_restraints     287
_refine_ls_restrained_S_all      1.040
_refine_ls_R_factor_all          0.0865
_refine_ls_R_factor_gt           0.0821
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1989P)^2^+6.3994P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2409
_refine_ls_wR_factor_ref         0.2481
_reflns_Friedel_coverage         0.842
_reflns_Friedel_fraction_full    1.000
_reflns_Friedel_fraction_max     0.985
_reflns_number_gt                25334
_reflns_number_total             27662
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            CCDC-1914841.cif
_cod_data_source_block           d160815_44_24
_cod_depositor_comments
'Adding full bibliography for 4134283--4134298.cif.'
_cod_database_code               4134291
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         C132H176Br2O13
_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
 C6-C5 \\sim C6-C5A \\sim C5-C4 \\sim C5A-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-C5A \\sim
C4-C6 \\sim C4A-C6
 with sigma of 0.02
 C2C-C1B \\sim C2B-C1B
 with sigma of 0.02
 C4C-C3C \\sim C4B-C3B
 with sigma of 0.02
 Br2B-C3C \\sim Br2B-C3B
 with sigma of 0.02
 Br1B-C2B \\sim Br1B-C2C
 with sigma of 0.02
 C3C-C2C \\sim C3B-C2B
 with sigma of 0.02
 C9-C8A \\sim C9-C8 \\sim C8A-C7A \\sim C8-C7 \\sim C9-C10 \\sim C11-C10
 with sigma of 0.02
 C7A-C9 \\sim C7-C9 \\sim C8A-C10 \\sim C8-C10
 with sigma of 0.02
3. Rigid bond restraints
 C6, C1, C2, C3, C4, C5, C1A, C2A, C3A, C4A, C5A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C9, C10, C11, C7, C8, C7A, C8A
 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(C4B) = Uanis(C4C)
5. Rigid body (RIGU) restrains
 C6, C1, C2, C3, C4, C5, C1A, C2A, C3A, C4A, C5A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 Br1B, Br2B, O1B, C1B, C2B, C3B, C4B, C2C, C3C, C4C
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C9, C10, C11, C7, C8, C7A, C8A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(H6BC)=Sof(H6BD)=Sof(H9BC)=Sof(H9BD)=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)=Sof(C5A)=Sof(H5AA)=Sof(H5AB)=Sof(C7A)=Sof(H7AA)=Sof(H7AB)=
 Sof(H7AC)=Sof(C8A)=Sof(H8AA)=Sof(H8AB)=1-FVAR(1)
 Sof(H6AA)=Sof(H6AB)=Sof(H9AA)=Sof(H9AB)=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(C5)=Sof(H5A)=Sof(H5B)=Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(H7C)=Sof(C8)=Sof(H8A)=
 Sof(H8B)=FVAR(1)
 Sof(H1BD)=Sof(H1BE)=Sof(C2C)=Sof(H2C)=Sof(C3C)=Sof(H3C)=Sof(C4C)=Sof(H4CA)=
 Sof(H4CB)=Sof(H4CC)=1-FVAR(2)
 Sof(H1BB)=Sof(H1BC)=Sof(C2B)=Sof(H2BA)=Sof(C3B)=Sof(H3BA)=Sof(C4B)=Sof(H4BA)=
 Sof(H4BB)=Sof(H4BC)=FVAR(2)
7.a Ternary CH refined with riding coordinates:
 C39(H39), C45(H45), C57(H57), C58(H58), C2B(H2BA), C3B(H3BA), C2C(H2C),
 C3C(H3C)
7.b Secondary CH2 refined with riding coordinates:
 C6(H6AA,H6AB), C6(H6BC,H6BD), C9(H9BC,H9BD), C9(H9AA,H9AB), 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), C54(H54A,H54B), C61(H61A,H61B),
 C73(H73A,H73B), C80(H80A,H80B), C2(H2A,H2B), C3(H3A,H3B), C4(H4A,H4B), C5(H5A,
 H5B), C8(H8A,H8B), C2A(H2AA,H2AB), C3A(H3AA,H3AB), C4A(H4AA,H4AB), C5A(H5AA,
 H5AB), C8A(H8AA,H8AB), C1B(H1BB,H1BC), C1B(H1BD,H1BE)
7.c Me refined with riding coordinates:
 C7(H7A,H7B,H7C), C7A(H7AA,H7AB,H7AC)
7.d Aromatic/amide H refined with riding coordinates:
 C27(H27), C37(H37), C46(H46), C50(H50)
7.e Idealised Me refined as rotating group:
 C13(H13A,H13B,H13C), C19(H19A,H19B,H19C), C91(H91A,H91B,H91C), C94(H94A,H94B,
 H94C), C95(H95A,H95B,H95C), 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), C107(H,H10X,H10Y), C108(H10Z,HA,HB),
 C109(H10,HC,HD), 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,HE), C118(H11Z,HF,HG), C119(H11,HH,HI),
 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,HJ), C128(H12Z,HK,HL), C1(H1A,H1B,H1C), C1A(H1AA,H1AB,H1AC),
 C4B(H4BA,H4BB,H4BC), C4C(H4CA,H4CB,H4CC)
7.f Idealised tetrahedral OH refined as rotating group:
 O1(H1), O2(H2), O3(H3), O4(H4), O1B(H1BA)
;
_shelx_res_checksum              9545
_shelx_hkl_checksum              13998
_olex2_date_sample_data_collection 2017-10-16
_olex2_date_sample_submission    2017-10-16
_olex2_submission_original_sample_id d160815_44_24
_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 1.243
_oxdiff_exptl_absorpt_empirical_full_min 0.837