A Molecular Trefoil Knot From a Trimeric Circular Helicate.
Zhang, Liang; August, David; Zhong, Jiankang; Whitehead, George F. S.; Vitorica-Yrezabal, Inigo J; Leigh, David A.; Journal of the American Chemical Society  (2018) –; doi:10.1021/jacs.8b00738

data_4127217
_publ_section_title
;
 A Molecular Trefoil Knot From a Trimeric Circular Helicate.
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_paper_doi               10.1021/jacs.8b00738
_journal_year                    2018
_chemical_formula_moiety         'C84 H96 N18 O6 Zn3, 6(B F4), 6(C2 H3 N), H2 O'
_chemical_formula_sum            'C96 H116 B6 F24 N24 O7 Zn3'
_chemical_formula_weight         2435.09
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_symmetry_space_group_name_Hall  '-P 2ybc'
_symmetry_space_group_name_H-M   'P 1 21/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2017-12-21
_audit_creation_method
;
Olex2 1.2
(compiled 2017.08.10 svn.r3458 for OlexSys, GUI svn.r5381)
;
_cell_angle_alpha                90
_cell_angle_beta                 105.355(5)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.5521(8)
_cell_length_b                   18.7147(9)
_cell_length_c                   32.1206(16)
_cell_measurement_reflns_used    20702
_cell_measurement_temperature    150.05(10)
_cell_measurement_theta_max      70.1830
_cell_measurement_theta_min      2.7270
_cell_volume                     11333.8(10)
_computing_cell_refinement       'CrysAlisPro 1.171.39.30c (Rigaku OD, 2017)'
_computing_data_collection       'CrysAlisPro 1.171.39.30c (Rigaku OD, 2017)'
_computing_data_reduction        'CrysAlisPro 1.171.39.30c (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      150.05(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.976
_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      0.00  88.00   1.00    5.00    --    0.00  43.00-120.00   88
  2  \w    -87.00 -14.00   1.00    5.00    --    0.00  43.00-120.00   73
  3  \w    -50.00   4.00   1.00    5.00    --    0.00  60.00  30.00   54
  4  \w     42.00  67.00   1.00    5.00    --    0.00  60.00  30.00   25
  5  \w    -33.00 114.00   1.00   15.00    --   55.00  60.00-150.00  147
  6  \w    -21.00  74.00   1.00   15.00    --   55.00  60.00 150.00   95
  7  \w      4.00 143.00   1.00   15.00    --   55.00  60.00  90.00  139
  8  \w     34.00 144.00   1.00   15.00    --   55.00   0.00 -60.00  110
  9  \w     78.00 135.00   1.00   15.00    --   55.00  60.00 150.00   57
 10  \w    -32.00  -6.00   1.00   15.00    --   55.00  60.00  30.00   26
 11  \w    108.00 141.00   1.00   15.00    --   55.00  60.00 -60.00   33
 12  \w    -34.00 137.00   1.00   15.00    --   55.00  60.00  60.00  171
 13  \w    103.00 140.00   1.00   15.00    --   55.00  60.00-120.00   37
 14  \w     35.00  61.00   1.00   15.00    --  110.00  60.00-150.00   26
 15  \w    142.00 179.00   1.00   15.00    --  110.00  60.00  30.00   37
 16  \w     51.00 133.00   1.00   15.00    --  110.00  38.00-150.00   82
 17  \w     21.00 199.00   1.00   15.00    --  110.00  60.00-120.00  178
 18  \w     26.00 196.00   1.00   15.00    --  110.00  19.00  90.00  170
 19  \w    115.00 197.00   1.00   15.00    --  110.00  60.00 -30.00   82
 20  \w    150.00 196.00   1.00   15.00    --  110.00  60.00 120.00   46
 21  \w     76.00 102.00   1.00   15.00    --  110.00  60.00 120.00   26
 22  \w    131.00 198.00   1.00   15.00    --  110.00  60.00  60.00   67
 23  \w     22.00 194.00   1.00   15.00    --  110.00  60.00 -60.00  172
 24  \w     46.00 136.00   1.00   15.00    --  110.00  57.00   0.00   90
 25  \w    169.00 195.00   1.00   15.00    --  110.00  60.00-180.00   26
 26  \w     27.00  53.00   1.00   15.00    --  110.00  60.00  60.00   26
 27  \w     94.00 165.00   1.00   15.00    --  110.00  60.00-180.00   71
 28  \w     66.00  91.00   1.00   15.00    --  110.00   0.00-150.00   25
 29  \w     22.00  65.00   1.00   15.00    --  110.00  60.00-180.00   43
 30  \w    138.00 166.00   1.00   15.00    --  110.00  60.00-150.00   28
 31  \w     25.00  50.00   1.00   15.00    --  110.00   0.00-150.00   25
 32  \w    126.00 199.00   1.00   15.00    --  110.00  60.00  90.00   73
 33  \w     75.00 101.00   1.00   15.00    --  110.00  60.00  90.00   26
 34  \w     47.00 199.00   1.00   15.00    --  110.00  29.00  60.00  152
 35  \w    170.00 195.00   1.00   15.00    --  110.00  38.00-150.00   25
 36  \w    164.00 190.00   1.00   15.00    --  110.00   0.00-150.00   26
 37  \w     33.00  67.00   1.00   15.00    --  110.00  60.00 -30.00   34
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC11 (RINC): quarter-chi single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0151127000
_diffrn_orient_matrix_UB_12      -0.0807614000
_diffrn_orient_matrix_UB_13      0.0053713000
_diffrn_orient_matrix_UB_21      0.0222038000
_diffrn_orient_matrix_UB_22      -0.0006648000
_diffrn_orient_matrix_UB_23      -0.0425510000
_diffrn_orient_matrix_UB_31      0.0771999000
_diffrn_orient_matrix_UB_32      0.0160357000
_diffrn_orient_matrix_UB_33      0.0251269000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0916
_diffrn_reflns_av_unetI/netI     0.0611
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.976
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       22
_diffrn_reflns_limit_k_min       -23
_diffrn_reflns_limit_l_max       39
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            112675
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.976
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         71.634
_diffrn_reflns_theta_min         2.343
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    1.625
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.17196
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.30c (Rigaku Oxford Diffraction, 2017)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear brown'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    brown
_exptl_crystal_density_diffrn    1.427
_exptl_crystal_description       plate
_exptl_crystal_F_000             5008
_exptl_crystal_size_max          0.146
_exptl_crystal_size_mid          0.07
_exptl_crystal_size_min          0.02
_refine_diff_density_max         0.835
_refine_diff_density_min         -1.187
_refine_diff_density_rms         0.083
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.101
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1515
_refine_ls_number_reflns         21604
_refine_ls_number_restraints     488
_refine_ls_restrained_S_all      1.114
_refine_ls_R_factor_all          0.1018
_refine_ls_R_factor_gt           0.0722
_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^)+(0.1181P)^2^+9.4694P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1969
_refine_ls_wR_factor_ref         0.2297
_reflns_Friedel_coverage         0.000
_reflns_number_gt                14882
_reflns_number_total             21604
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja8b00738_si_002.cif
_cod_data_source_block           ldl5
_cod_original_cell_volume        11333.7(9)
_cod_database_code               4127217
_shelx_shelxl_version_number     2017/1
_chemical_oxdiff_formula         'Zn C H N'
_shelx_estimated_absorpt_t_max   0.968
_shelx_estimated_absorpt_t_min   0.797
_reflns_odcompleteness_completeness 99.92
_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,H) groups
2. Shared sites
{B6A, B6}
3. Restrained distances
 F22A-F24A \\sim F24-F22 \\sim F21A-F24A \\sim F24-F21 \\sim F24-F23 \\sim
F21-F23 \\sim F21A-F22A ~
 F22A-F23A \\sim F21A-F23A \\sim F23A-F24A \\sim F23-F22 \\sim F21-F22
 with sigma of 0.02
 F22-B6 \\sim F24-B6 \\sim F24A-B6A \\sim F23-B6 \\sim F23A-B6A \\sim F21A-B6A
\\sim F21-B6 \\sim F22A-B6A
 with sigma of 0.02
 C10-C105 \\sim C10-C14 \\sim C107-C106 \\sim C106-C105 \\sim C71-C70 \\sim
C70-C69 \\sim C3-C4 \\sim C3-
 C2 \\sim C40-C39 \\sim C38-C39 \\sim C34-C33 \\sim C35-C34 \\sim C75-C74 \\sim
C75-C76
 with sigma of 0.02
 C36-C35 \\sim C73-C74 \\sim C37-C38 \\sim C1-C2 \\sim C71-C72 \\sim C14-C108
\\sim C107-C5
 with sigma of 0.02
4. Uiso/Uaniso restraints and constraints
B6 \\sim F22 \\sim F21 \\sim F23 \\sim F24 \\sim F22A \\sim F24A \\sim B6A
\\sim F21A \\sim F23A: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
C105 \\sim C106 \\sim C10 \\sim C14 \\sim C107 \\sim C5: within 2A with sigma
of 0.04 and sigma for terminal atoms of 0.08
Uanis(B6A) = Uanis(B6)
5. Rigid body (RIGU) restrains
 B6, F22, F21, F24, F23, B6A, F24A, F23A, F22A, F21A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C108, C106, C5, C107, C10, C14
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(F22)=Sof(F21)=Sof(F24)=Sof(F23)=Sof(B6)=1-FVAR(1)
 Sof(F24A)=Sof(F23A)=Sof(F22A)=Sof(B6A)=Sof(F21A)=FVAR(1)
 Sof(H10C)=Sof(H10D)=Sof(C106)=Sof(H10G)=Sof(H10H)=Sof(C5)=Sof(H5A)=Sof(H5B)=
 Sof(C107)=Sof(H107)=1-FVAR(2)
 Sof(H10A)=Sof(H10B)=Sof(C108)=Sof(H10E)=Sof(H10F)=Sof(C10)=Sof(H10I)=
 Sof(H10J)=Sof(C14)=Sof(H14)=FVAR(2)
7.a Free rotating group:
 O049(H04A,H04B)
7.b Secondary CH2 refined with riding coordinates:
 C60(H60A,H60B), C24(H24A,H24B), C49(H49A,H49B), C12(H12A,H12B), C84(H84A,
 H84B), C96(H96A,H96B), C61(H61A,H61B), C25(H25A,H25B), C85(H85A,H85B),
 C13(H13A,H13B), C48(H48A,H48B), C97(H97A,H97B), C69(H69A,H69B), C76(H76A,H76B),
  C4(H4A,H4B), C33(H33A,H33B), C70(H70A,H70B), C75(H75A,H75B), C3(H3A,H3B),
 C34(H34A,H34B), C105(H10C,H10D), C105(H10A,H10B), C39(H39A,H39B), C40(H40A,
 H40B), C106(H10G,H10H), C10(H10I,H10J)
7.c Aromatic/amide H refined with riding coordinates:
 C92(H92), C15(H15), C87(H87), C89(H89), C94(H94), C11(H11), C22(H22),
 C53(H53), C30(H30), C51(H51), C66(H66), C27(H27), C58(H58), C56(H56),
 C102(H102), C17(H17), C28(H28), C20(H20), C47(H47), C83(H83), C63(H63),
 C80(H80), C8(H8), C79(H79), C64(H64), C7(H7), C99(H99), C44(H44), C100(H100),
 C43(H43), C74(H74), C2(H2), C71(H71), C35(H35), C38(H38), C107(H107), C14(H14)
7.d X=CH2 refined with riding coordinates:
 C72(H72A,H72B), C108(H10E,H10F), C1(H1A,H1B), C73(H73A,H73B), C37(H37A,H37B),
 C36(H36A,H36B), C5(H5A,H5B)
7.e Idealised Me refined as rotating group:
 C21B(H21A,H21B,H21C), C30B(H30A,H30B,H30C), C24B(H24C,H24D,H24E), C33B(H33C,
 H33D,H33E), C36B(H36C,H36D,H36E), C27B(H27A,H27B,H27C)
;
_shelx_res_checksum              27047
_shelx_hkl_checksum              48775
_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 4.479
_oxdiff_exptl_absorpt_empirical_full_min 0.408