Self-Sorting Assembly of Molecular Trefoil Knots of Single Handedness.
Zhong, Jiankang; Zhang, Liang; August, David P.; Whitehead, George F. S.; Leigh, David A.; Journal of the American Chemical Society 141 (2019) 14249–14256; doi:10.1021/jacs.9b06127

data_4128813
_publ_section_title
;
 Self-Sorting Assembly of Molecular Trefoil Knots of Single Handedness.
;
_journal_issue                   36
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              14249
_journal_page_last               14256
_journal_paper_doi               10.1021/jacs.9b06127
_journal_volume                  141
_journal_year                    2019
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C84 H96 N18 O6 Zn3, 6(B F4), 8(C2 H3 N)'
_chemical_formula_sum            'C100 H120 B6 F24 N26 O6 Zn3'
_chemical_formula_weight         2499.18
_space_group_crystal_system      orthorhombic
_space_group_IT_number           18
_space_group_name_Hall           'P 2 2ab'
_space_group_name_H-M_alt        'P 21 21 2'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2019-02-15
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            6
_cell_length_a                   52.6707(6)
_cell_length_b                   18.7850(2)
_cell_length_c                   17.85193(18)
_cell_measurement_reflns_used    47240
_cell_measurement_temperature    150.00(10)
_cell_measurement_theta_max      74.0250
_cell_measurement_theta_min      2.8760
_cell_volume                     17663.0(3)
_computing_cell_refinement       'CrysAlisPro 1.171.40.14a (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.40.14a (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.40.14a (Rigaku OD, 2018)'
_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      150.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.999
_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    -85.00  21.00   0.50    0.50    --  -58.90  57.00 -30.00  212
  2  \w    -87.00  18.00   0.50    0.50    --  -58.90  76.00  60.00  210
  3  \w    -84.00  21.00   0.50    0.50    --  -58.90  57.00-150.00  210
  4  \w   -178.00-152.00   0.50    2.00    -- -110.00 -48.00  19.00   52
  5  \w     -6.00  34.00   0.50    2.00    --    5.00  57.00 -60.00   80
  6  \w    -10.00  44.00   0.50    2.00    --  -45.00  57.00  60.00  108
  7  \w    -75.00 -18.00   0.50    2.00    --  -45.00  57.00  60.00  114
  8  \w   -111.00 -21.00   0.50    2.00    -- -110.00  76.00 150.00  180
  9  \w   -145.00-104.00   0.50    2.00    -- -110.00 -57.00 120.00   82
 10  \w   -183.00-157.00   0.50    2.00    -- -110.00 -57.00 120.00   52
 11  \w    -79.00 -22.00   0.50    2.00    -- -110.00  76.00-180.00  114
 12  \w   -149.00-107.00   0.50    2.00    -- -110.00  76.00-180.00   84
 13  \w   -142.00 -21.00   0.50    2.00    -- -110.00  57.00  30.00  242
 14  \w   -150.00-121.00   0.50    2.00    -- -110.00  76.00 150.00   58
 15  \w   -157.00-131.00   0.50    2.00    -- -110.00 -57.00  90.00   52
 16  \w   -129.00-104.00   0.50    2.00    -- -110.00 -57.00  90.00   50
 17  \w   -126.00 -21.00   0.50    2.00    -- -110.00  38.00  30.00  210
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC11 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0100989000
_diffrn_orient_matrix_UB_12      -0.0768746000
_diffrn_orient_matrix_UB_13      0.0038061000
_diffrn_orient_matrix_UB_21      0.0225099000
_diffrn_orient_matrix_UB_22      0.0209128000
_diffrn_orient_matrix_UB_23      -0.0504862000
_diffrn_orient_matrix_UB_31      0.0157317000
_diffrn_orient_matrix_UB_32      0.0193214000
_diffrn_orient_matrix_UB_33      0.0698837000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0383
_diffrn_reflns_av_unetI/netI     0.0334
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.979
_diffrn_reflns_limit_h_max       66
_diffrn_reflns_limit_h_min       -63
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -14
_diffrn_reflns_number            119580
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.962
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         77.292
_diffrn_reflns_theta_min         2.475
_diffrn_source                   'Rotating-anode X-ray tube (dual wavelength)'
_diffrn_source_type              'Rigaku (Cu) X-ray DW Source'
_exptl_absorpt_coefficient_mu    1.578
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.69478
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.40.14a (Rigaku Oxford Diffraction, 2018)
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    1.410
_exptl_crystal_description       block
_exptl_crystal_F_000             7716
_exptl_crystal_size_max          0.442
_exptl_crystal_size_mid          0.33
_exptl_crystal_size_min          0.241
_refine_diff_density_max         1.226
_refine_diff_density_min         -0.579
_refine_diff_density_rms         0.082
_refine_ls_abs_structure_details
;
 Flack x determined using 12585 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.009(7)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.050
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     2346
_refine_ls_number_reflns         36053
_refine_ls_number_restraints     1858
_refine_ls_restrained_S_all      1.061
_refine_ls_R_factor_all          0.0767
_refine_ls_R_factor_gt           0.0708
_refine_ls_shift/su_max          0.003
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1303P)^2^+9.2801P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2005
_refine_ls_wR_factor_ref         0.2070
_reflns_Friedel_coverage         0.827
_reflns_Friedel_fraction_full    0.997
_reflns_Friedel_fraction_max     0.941
_reflns_number_gt                31882
_reflns_number_total             36053
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja9b06127_si_002.cif
_cod_data_source_block           wit_rdl28
_cod_database_code               4128813
_shelx_shelxl_version_number     2018/1
_chemical_oxdiff_formula         C14H4N2O8Zn1
_shelx_estimated_absorpt_t_max   0.702
_shelx_estimated_absorpt_t_min   0.542
_reflns_odcompleteness_completeness 99.92
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     68.13
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C25A-C23A = C24A-C26A
 2.3 with sigma of 0.02
 C27A-C28A = C27A-C26A = C24A-C25A = C24A-C23A
 1.54 with sigma of 0.02
 C26A-C25A
 1.25 with sigma of 0.02
 C26B-C24B = C25B-C27B
 2.3 with sigma of 0.02
 O1A-C24B = C23B-C25B = C26B-C28B = C27B-O2A
 2.4 with sigma of 0.02
 C27B-C28B = C27B-C26B = C24B-C23B = C24B-C25B
 1.54 with sigma of 0.02
 C26B-C25B
 1.25 with sigma of 0.02
 C23A-C25A = C26A-C28A = C27A-O2A = O1A-C24A
 2.4 with sigma of 0.02
 O1A-C23B = O1A-C23A = O2A-C28B = O2A-C28A
 1.4 with sigma of 0.02
 C1_10-C2_10
 C1_11-C2_11
 C1_12-C2_12
 C1_13-C2_13
 C1_14-C2_14
 C1_15-C2_15
 C1_16-C2_16
 C1_17-C2_17
 C1_19-C2_19
 C1_21-C2_21
 C1_22-C2_22
 C1_23-C2_23
 C1_24-C2_24
 C1_25-C2_25
 C1_26-C2_26
 1.394 with sigma of 0.02
 N1_10-C1_10
 N1_11-C1_11
 N1_12-C1_12
 N1_13-C1_13
 N1_14-C1_14
 N1_15-C1_15
 N1_16-C1_16
 N1_17-C1_17
 N1_19-C1_19
 N1_21-C1_21
 N1_22-C1_22
 N1_23-C1_23
 N1_24-C1_24
 N1_25-C1_25
 N1_26-C1_26
 1.159 with sigma of 0.02
 N1_16-N1_24
 -3.1 with sigma of 0.02
 N1_10-C2_10
 N1_11-C2_11
 N1_12-C2_12
 N1_13-C2_13
 N1_14-C2_14
 N1_15-C2_15
 N1_16-C2_16
 N1_17-C2_17
 N1_19-C2_19
 N1_21-C2_21
 N1_22-C2_22
 N1_23-C2_23
 N1_24-C2_24
 N1_25-C2_25
 N1_26-C2_26
 2.55 with sigma of 0.04
3. Restrained planarity
 C27A, C26A, C25A, C24A
 with sigma of 0.1
 C24B, C25B, C26B, C27B
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
F1_1 \\sim F2_1 \\sim F3_1 \\sim F4_1 \\sim B1_1 \\sim F1_2 \\sim F2_2 \\sim
F3_2 \\sim F4_2 \\sim B1_2 \\sim F1_3 \\sim F2_3 \\sim F3_3 \\sim F4_3 \\sim
B1_3 \\sim F1_4 \\sim F2_4 \\sim F3_4 \\sim F4_4 \\sim B1_4 \\sim F1_5 \\sim
F2_5 \\sim F3_5 \\sim F4_5 \\sim B1_5 \\sim F1_6 \\sim F2_6 \\sim F3_6 \\sim
F4_6 \\sim B1_6 \\sim F1_7 \\sim F2_7 \\sim F3_7 \\sim F4_7 \\sim B1_7 \\sim
F1_8 \\sim F2_8 \\sim F3_8 \\sim F4_8 \\sim B1_8 \\sim F1_9 \\sim F2_9 \\sim
F3_9 \\sim F4_9 \\sim B1_9 \\sim F1_18 \\sim F2_18 \\sim F3_18 \\sim F4_18
\\sim B1_18: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
N1_10 \\sim C1_10 \\sim C2_10 \\sim N1_11 \\sim C1_11 \\sim C2_11 \\sim N1_12
\\sim C1_12 \\sim C2_12 \\sim N1_13 \\sim C1_13 \\sim C2_13 \\sim N1_14 \\sim
C1_14 \\sim C2_14 \\sim N1_15 \\sim C1_15 \\sim C2_15 \\sim N1_16 \\sim C1_16
\\sim C2_16 \\sim N1_17 \\sim C1_17 \\sim C2_17 \\sim N1_19 \\sim C1_19 \\sim
C2_19 \\sim N1_21 \\sim C1_21 \\sim C2_21 \\sim N1_22 \\sim C1_22 \\sim C2_22
\\sim N1_23 \\sim C1_23 \\sim C2_23 \\sim N1_24 \\sim C1_24 \\sim C2_24 \\sim
N1_25 \\sim C1_25 \\sim C2_25 \\sim N1_26 \\sim C1_26 \\sim C2_26: within 2A
with sigma of 0.005 and sigma for terminal atoms of 0.01
C23A \\sim C24A \\sim C27A \\sim C24B \\sim C25A \\sim C26B \\sim C28A \\sim
C28B \\sim C26A \\sim C23B \\sim C27B \\sim C25B \\sim O2A \\sim O1A: within 2A
with sigma of 0.04 and sigma for terminal atoms of 0.08
O5 \\sim C62 \\sim C63 \\sim C64 \\sim C65 \\sim C60 \\sim C66: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08
5. Rigid body (RIGU) restrains
 F1_1, F2_1, F3_1, F4_1, B1_1
 F1_2, F2_2, F3_2, F4_2, B1_2
 F1_3, F2_3, F3_3, F4_3, B1_3
 F1_4, F2_4, F3_4, F4_4, B1_4
 F1_5, F2_5, F3_5, F4_5, B1_5
 F1_6, F2_6, F3_6, F4_6, B1_6
 F1_7, F2_7, F3_7, F4_7, B1_7
 F1_8, F2_8, F3_8, F4_8, B1_8
 F1_9, F2_9, F3_9, F4_9, B1_9
 F1_18, F2_18, F3_18, F4_18, B1_18
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N1_10, C1_10, C2_10
 N1_11, C1_11, C2_11
 N1_12, C1_12, C2_12
 N1_13, C1_13, C2_13
 N1_14, C1_14, C2_14
 N1_15, C1_15, C2_15
 N1_16, C1_16, C2_16
 N1_17, C1_17, C2_17
 N1_19, C1_19, C2_19
 N1_21, C1_21, C2_21
 N1_22, C1_22, C2_22
 N1_23, C1_23, C2_23
 N1_24, C1_24, C2_24
 N1_25, C1_25, C2_25
 N1_26, C1_26, C2_26
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C23A, C24A, C27A, C24B, C25A, C26B, C28A, C28B, C26A, C23B, C27B, C25B, O2A,
 O1A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Same fragment restrains
{F1_2, F2_2, F3_2, F4_2, B1_2}
{F1_3, F2_3, F3_3, F4_3, B1_3}
{F1_4, F2_4, F3_4, F4_4, B1_4}
{F1_5, F2_5, F3_5, F4_5, B1_5}
{F1_6, F2_6, F3_6, F4_6, B1_6}
{F1_7, F2_7, F3_7, F4_7, B1_7}
{F1_8, F2_8, F3_8, F4_8, B1_8}
{F1_9, F2_9, F3_9, F4_9, B1_9}
{F1_18, F2_18, F3_18, F4_18, B1_18}
as
{F1_1, F2_1, F3_1, F4_1, B1_1} sigma for 1-2: 0.02 1-3: 0.04
{N1_11, C1_11, C2_11}
{N1_12, C1_12, C2_12}
{N1_13, C1_13, C2_13}
{N1_14, C1_14, C2_14}
{N1_15, C1_15, C2_15}
{N1_16, C1_16, C2_16}
{N1_17, C1_17, C2_17}
{N1_19, C1_19, C2_19}
{N1_21, C1_21, C2_21}
{N1_22, C1_22, C2_22}
{N1_23, C1_23, C2_23}
{N1_24, C1_24, C2_24}
{N1_25, C1_25, C2_25}
{N1_26, C1_26, C2_26}
as
{N1_10, C1_10, C2_10} sigma for 1-2: 0.02 1-3: 0.04
7. Others
 Sof(C24B)=Sof(H24C)=Sof(H24D)=Sof(C26B)=Sof(H26B)=Sof(C28B)=Sof(H28E)=
 Sof(H28F)=Sof(C23B)=Sof(H23C)=Sof(H23D)=Sof(C27B)=Sof(H27F)=Sof(H27G)=
 Sof(C25B)=Sof(H25B)=1-FVAR(1)
 Sof(C23A)=Sof(H23A)=Sof(H23B)=Sof(C24A)=Sof(H24A)=Sof(H24B)=Sof(C27A)=
 Sof(H27D)=Sof(H27E)=Sof(C25A)=Sof(H25A)=Sof(C28A)=Sof(H28C)=Sof(H28D)=
 Sof(C26A)=Sof(H26A)=FVAR(1)
 Sof(N1)=Sof(C1)=Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(H2C)=1-FVAR(2)
 Sof(N1)=Sof(C1)=Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(H2C)=FVAR(2)
 Sof(N1)=Sof(C1)=Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(H2C)=1-FVAR(3)
 Sof(N1)=Sof(C1)=Sof(C2)=Sof(H2A)=Sof(H2B)=Sof(H2C)=FVAR(3)
 Fixed Sof: F1(0.5) F2(0.5) F3(0.5) F4(0.5) B1(0.5) F1(0.5) F2(0.5) F3(0.5)
 F4(0.5) B1(0.5) N1(0.5) C1(0.5) C2(0.5) H2A(0.5) H2B(0.5) H2C(0.5) N1(0.5)
 C1(0.5) C2(0.5) H2A(0.5) H2B(0.5) H2C(0.5)
8.a Ternary CH refined with riding coordinates:
 C7A(H7AA), C35A(H35C), C15A(H15A), C46(H46), C74(H74), C82(H82), C26(H26),
 C18(H18), C54(H54)
8.b Secondary CH2 refined with riding coordinates:
 C17A(H17C,H17D), C84(H84A,H84B), C6A(H6AA,H6AB), C56(H56A,H56B), C34(H34A,
 H34B), C34A(H34C,H34D), C73(H73A,H73B), C28(H28A,H28B), C17(H17A,H17B),
 C45(H45A,H45B), C35(H35A,H35B), C10(H10A,H10B), C11(H11A,H11B), C7(H7A,H7B),
 C38(H38A,H38B), C39(H39A,H39B), C42A(H42A,H42B), C6(H6A,H6B), C23A(H23A,H23B),
 C63(H63A,H63B), C67(H67A,H67B), C66(H66A,H66B), C24A(H24A,H24B), C27A(H27D,
 H27E), C41A(H41A,H41B), C62(H62A,H62B), C24B(H24C,H24D), C28A(H28C,H28D),
 C28B(H28E,H28F), C23B(H23C,H23D), C27B(H27F,H27G)
8.c Aromatic/amide H refined with riding coordinates:
 C81(H81), C22(H22), C78(H78), C37A(H37A), C12A(H12A), C51(H51), C9A(H9A),
 C14A(H14A), C12(H12), C79(H79), C39A(H39C), C23(H23), C20(H20), C76(H76),
 C29A(H29A), C53(H53), C50(H50), C48(H48), C11A(H11C), C37(H37), C40(H40),
 C25(H25), C2(H2), C33(H33), C1A(H1A), C31A(H31A), C68(H68), C32A(H32A),
 C71(H71), C22A(H22A), C43(H43), C4A(H4A), C30(H30), C5(H5), C58(H58),
 C19A(H19D), C15(H15), C31(H31), C3(H3), C3A(H3A), C70(H70), C40A(H40A),
 C14(H14), C36(H36), C59(H59), C42(H42), C20A(H20A), C61(H61), C9(H9), C8(H8),
 C65(H65), C64(H64), C25A(H25A), C26B(H26B), C26A(H26A), C25B(H25B)
8.d Idealised Me refined with riding coordinates:
 C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,
 H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C),
 C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,H2C), C2(H2A,H2B,
 H2C), C2(H2A,H2B,H2C)
8.e Idealised Me refined as rotating group:
 C27(H27A,H27B,H27C), C83(H83A,H83B,H83C), C36A(H36A,H36B,H36C), C8A(H8AA,H8AB,
 H8AC), C75(H75A,H75B,H75C), C16A(H16A,H16B,H16C), C47(H47A,H47B,H47C),
 C55(H55A,H55B,H55C), C19(H19A,H19B,H19C)
;
_shelx_res_checksum              13149
_shelx_hkl_checksum              4906
_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 1.372
_oxdiff_exptl_absorpt_empirical_full_min 0.791