Design and Assembly of Chiral Coordination Cages for Asymmetric Sequential Reactions.
Jiao, Jingjing; Tan, Chunxia; Li, Zijian; Liu, Yan; Han, Xing; Cui, Yong; Journal of the American Chemical Society  (2018) –; doi:10.1021/jacs.7b11679

data_4127129
_publ_section_title
;
 Design and Assembly of Chiral Coordination Cages for Asymmetric
 Sequential Reactions.
;
_journal_name_full               'Journal of the American Chemical Society'
_journal_paper_doi               10.1021/jacs.7b11679
_journal_year                    2018
_chemical_absolute_configuration ad
_chemical_formula_moiety         '2(C240 H264 Cr6 N12 O52 Zr12), 12(Cl), 1(O)'
_chemical_formula_sum            'C480 H528 Cl12 Cr12 N24 O105 Zr24'
_chemical_formula_weight         11539.82
_space_group_crystal_system      trigonal
_space_group_IT_number           155
_space_group_name_Hall           'R 3 2"'
_space_group_name_H-M_alt        'R 3 2'
_symmetry_space_group_name_Hall  'R 3 2"'
_symmetry_space_group_name_H-M   'R 3 2 :H'
_atom_sites_solution_hydrogens   geom
_audit_creation_date             2017-12-23
_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                120
_cell_formula_units_Z            3
_cell_length_a                   34.2265(14)
_cell_length_b                   34.2265(14)
_cell_length_c                   83.822(4)
_cell_measurement_reflns_used    9960
_cell_measurement_temperature    100.15
_cell_measurement_theta_max      43.78
_cell_measurement_theta_min      2.62
_cell_volume                     85038(6)
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.15
_diffrn_measured_fraction_theta_full 0.977
_diffrn_measured_fraction_theta_max 0.976
_diffrn_measurement_device_type  'Bruker D8 VENTURE CMOS photon'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54178
_diffrn_reflns_av_R_equivalents  0.1091
_diffrn_reflns_av_unetI/netI     0.0905
_diffrn_reflns_Laue_measured_fraction_full 0.977
_diffrn_reflns_Laue_measured_fraction_max 0.976
_diffrn_reflns_limit_h_max       30
_diffrn_reflns_limit_h_min       -29
_diffrn_reflns_limit_k_max       30
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       74
_diffrn_reflns_limit_l_min       -75
_diffrn_reflns_number            57462
_diffrn_reflns_point_group_measured_fraction_full 0.974
_diffrn_reflns_point_group_measured_fraction_max 0.974
_diffrn_reflns_theta_full        44.082
_diffrn_reflns_theta_max         44.082
_diffrn_reflns_theta_min         2.582
_exptl_absorpt_coefficient_mu    3.165
_exptl_absorpt_correction_T_max  0.7
_exptl_absorpt_correction_T_min  0.6
_exptl_absorpt_correction_type   multi-scan
_exptl_crystal_colour            'clear brownish brown'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   brownish
_exptl_crystal_colour_primary    brown
_exptl_crystal_density_diffrn    0.676
_exptl_crystal_description       block
_exptl_crystal_F_000             17568
_exptl_crystal_size_max          0.12
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.08
_refine_diff_density_max         1.106
_refine_diff_density_min         -0.386
_refine_diff_density_rms         0.080
_refine_ls_abs_structure_details
;
 Flack x determined using 1949 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.505(12)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.056
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     910
_refine_ls_number_reflns         14230
_refine_ls_number_restraints     2189
_refine_ls_restrained_S_all      1.046
_refine_ls_R_factor_all          0.1963
_refine_ls_R_factor_gt           0.0965
_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          0.2490
_refine_ls_wR_factor_ref         0.3501
_reflns_Friedel_coverage         0.861
_reflns_Friedel_fraction_full    0.972
_reflns_Friedel_fraction_max     0.972
_reflns_number_gt                6114
_reflns_number_total             14230
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja7b11679_si_003.cif
_cod_data_source_block           cr-1_sq
_cod_original_cell_volume        85038(8)
_cod_database_code               4127129
_shelx_shelxl_version_number     2014/7
_olex2_refinement_description
;

Single Crystal X-ray Crystallography 

    Single-crystal XRD data for 1-Cr was collected on a Bruker D8 VENTURE CMOS 
photon 100 diffractometer with helios mx multilayer monochromator Cu K&#x00A6;&#x00C1; 
radiation (&#x00A6;&#x00CB; = 1.54178 A) at 100 K in the Instrumental Analysis Center 
of Shanghai Jiao Tong University, People&#x00A1;&#x00AF;s Republic of China. The empirical 
absorption correction was applied by using the SADABS program (G. M. Sheldrick, 
SADABS, program for empirical absorption correction of area detector data; 
University of G?ttingen, G?ttingen, Germany, 1996). The structure was solved 
by direct methods with SHELXS-2014 and refined with SHELXL-2014 (Sheldrick,
 G. M. SHELXT-2014, 2013) using OLEX 2-1.2 (J. Appl.Crystallogr. 2009, 42, 339-341). 
    Though many attempts have been made to grow good single-crystals of the cage,
the resolution of the diffraction point is only up to 1.00 A and the intensity
of diffraction point is not very strong, especially at higher Bragg angles,
even with a very long exposure time up to 60 seconds. Fortunately, the
positions of the framework atoms including zirconium atoms, two Cr(salen) 
units except one chiral cyclohexyl, cyclopentadiene, three guest chlorine 
atoms and one water molecule were clearly located from these initial maps 
after choosing R32 as the space group. After these atoms were located, the 
benzene ring atoms and the cyclopentadiene ring atoms were geometrically
restrained to fit idealized six and five membered rings, respectively. 
Several weak Q peaks were assigned to cyclohexyl and many restrainments
were used to make the unit chemically reasonable. Then, all the atoms
were refined anisotropically by full-matri program. Because of the 
relatively high anisotropic atomic displacement parameter, one chlorine
atom was satisfactorily modeled with the positional disorder and was 
treated with FVAR. All of the disordered parts and other atoms were
restrained using AFIX, FLAT, SADI, DFIX, DANG, RIGU, and SIMU instructions
to make the displacement parameters more reasonable.  Due to the lack of 
the hydrogen bonding interactions and no obvious Fourier Q peaks can be 
assigned to hydrogen atoms for the guest and coordinated water molecules, 
these molecules were only refined anisotropically without adding H-atoms.
 For the other atoms, the hydrogen atoms were fixed at their calculated
 positions.
    Because of high voids in  the cage, many diffused electron
densities resulting from these residual and disordered solvent molecules
were removed from the data set using the SQUEEZE routine of PLATON was
applied, followed by more cycles of refinement. The final R1 = 0.0965, 
wR2 = 0.2490, GOOF =1.056 for [I>2sigma(I)] was achieved. We think the 
possible reasons for the high flack parameter may be the disorder of 
the chiral Cr(salen), which weakens the anomalous scattering, leading 
to the determination of the absolute configuration inaccuracy. In fact,
 we can not find any obvious Q peaks of one chiral cyclohexyl when solving 
the crystal structure, further indicating the highly disorder of the chiral
units. Thus the disorder of the chiral units may result in the high flack value. 
    In addition, co-crystallization of different possible diasteromeric cages,
in one crystal may also contribute to the high R(int) values and other final structural 
parameters.
 

Explanation For The Alert A and B

Alert level A

THETM01_ALERT_3_A The value of sine(theta_max)/wavelength is less than 0.550 Calculated sin(theta_max)/wavelength = 0.4512

Discussion: A full set of data was collected, however&#x00A3;&#x00AC; the very high angle data was dominated by noise and was omitted. This
arbitrary theta limit is inappropriate for highly disordered structures. It would rule out all macromolecular structures.
A limit on data / parameter ratio&#x00A1;&#x00AF;s that properly takes into account the number of restraints / constraints and the 
redundancy of the measurements would be more appropriate. Unfortunately the cifcheck routine does not do this. Short 
contacts between disordered fragments are to be expected.

Alert level B

PLAT306_ALERT_2_B Isolated Oxygen Atom (H-atoms Missing ?) ....... O19 Check

Discussion: Due to the lack of the hydrogen bonding interactions, hydrogen atoms can not be added automatically. 
And no obvious Fourier Q peaks can be found near this isolated O19 atom.

PLAT342_ALERT_3_B Low Bond Precision on C-C Bonds ............... 0.05337 Ang. 

Discussion: Weak diffractions and poor crystal data reduced low standard uncertainty.

PLAT987_ALERT_1_B The Flack x is >> 0 - Do a BASF/TWIN Refinement Please Check

Discussion: We try to refine the structure with twin law to decrease the flack value, but failed. 
The possible reasons maybe the disorder of cyclohexyl groups of chiral Cr(salen) units over two 
positions, which is very serious and cannot be modeled and so a number of restraints such as DFIX, 
SIMU and RIGU were applied to control the refinement. This disorder can weaken the anomalous 
scattering, leading to the determination of the absolute configuration inaccuracy. In addition, 
co-crystallization of different possible diasteromeric cages in one crystal may also contribute
 to the high R(int) value and other final structural parameters.

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
 C42-C45
 1.53 with sigma of 0.02
 C45-C48
 1.53 with sigma of 0.02
 C45-C47
 1.53 with sigma of 0.02
 C45-C46
 1.53 with sigma of 0.02
 C38-C37
 1.4 with sigma of 0.02
 C39-C37
 2.5 with sigma of 0.02
 C44-C40
 1.4 with sigma of 0.02
 C57-C54
 1.53 with sigma of 0.02
 C57-C59
 1.53 with sigma of 0.02
 C57-C54 = C57-C60 = C57-C59 = C57-C58
 1.53 with sigma of 0.02
 C48-C47 = C47-C46 = C48-C46
 2.5 with sigma of 0.02
 C47-C42
 2.5 with sigma of 0.02
 C48-C42
 2.5 with sigma of 0.02
 C46-C42
 2.5 with sigma of 0.02
 C54-C58
 2.5 with sigma of 0.02
 C59-C54
 2.5 with sigma of 0.02
 C60-C54
 2.5 with sigma of 0.02
 C52-C56
 1.45 with sigma of 0.02
 C35-C36
 1.53 with sigma of 0.02
 C35-C34
 1.53 with sigma of 0.02
 C36-C35
 1.524 with sigma of 0.02
 C36-C34
 2.517 with sigma of 0.02
 N4-C37
 1.25 with sigma of 0.02
 C49-C50
 1.53 with sigma of 0.02
 N3-C49
 1.3 with sigma of 0.02
 C27-C29 = C27-C30 = C27-C28
 1.53 with sigma of 0.02
 C27-C24
 1.53 with sigma of 0.02
 C29-C30 = C29-C28
 2.5 with sigma of 0.02
 C30-C28
 2.5 with sigma of 0.02
 C16-C17 = C18-C16
 2.6 with sigma of 0.02
 C17-C18
 2.6 with sigma of 0.02
 C28-C24
 2.6 with sigma of 0.02
 C24-C30
 2.6 with sigma of 0.02
 C29-C24
 2.6 with sigma of 0.02
 C19-C20
 1.38 with sigma of 0.02
 C22-C26
 1.38 with sigma of 0.02
 C20-C19
 1.48 with sigma of 0.02
 C25-C19
 2.6 with sigma of 0.02
 C3-C5
 2.517 with sigma of 0.02
 C2-C4
 2.517 with sigma of 0.02
 C2-C19
 2.4 with sigma of 0.02
 C1-C3
 2.517 with sigma of 0.02
 N2-C20
 2.4 with sigma of 0.02
 N2-C2
 1.46 with sigma of 0.02
 N2-C1
 2.4 with sigma of 0.02
 C35-C34 = C33-C34 = C33-C32 = C32-C31 = C31-C36
 1.524 with sigma of 0.02
 C31-C35
 2.517 with sigma of 0.02
 C35-C33
 2.517 with sigma of 0.02
 C34-C32
 2.517 with sigma of 0.02
 C33-C31
 2.517 with sigma of 0.02
 C32-C36
 2.517 with sigma of 0.02
 N3-C31
 1.45 with sigma of 0.02
 C32-N4
 1.45 with sigma of 0.02
 N3-C32
 2.4 with sigma of 0.02
 C31-N4
 2.4 with sigma of 0.02
 C1-C4
 2.95 with sigma of 0.02
 C2-C5
 2.95 with sigma of 0.02
 C38-O8
 2.5 with sigma of 0.02
 O8-C42
 2.5 with sigma of 0.02
 O9-C56
 1.2 with sigma of 0.02
 O8-C43
 1.2 with sigma of 0.02
 O7-C55
 1.2 with sigma of 0.02
 O7-C60
 2.6 with sigma of 0.02
 O7-C54
 2.4 with sigma of 0.02
 C50-O7
 2.4 with sigma of 0.02
 O7-Cr2
 2 with sigma of 0.02
 O8-Cr2
 2 with sigma of 0.02
 N3-Cr2
 2.3 with sigma of 0.02
 Cr2-C37
 3 with sigma of 0.02
 N4-Cr2
 2.3 with sigma of 0.02
 Cr2-C49
 3 with sigma of 0.02
 O11-C40
 2.3 with sigma of 0.02
 O12-C40
 2.3 with sigma of 0.02
 O4-C14 = O3-C14
 1.42 with sigma of 0.02
 O6-C22
 2.5 with sigma of 0.02
 O5-C22
 2.5 with sigma of 0.02
 N2-Cr1
 2 with sigma of 0.02
 C20-O2
 2.4 with sigma of 0.02
 C24-O2
 2.4 with sigma of 0.02
 O2-C30
 2.6 with sigma of 0.02
 O2-C28
 2.6 with sigma of 0.02
 Cr1-O2 = Cr1-O1
 1.95 with sigma of 0.02
 C12-C14
 1.38 with sigma of 0.02
 C17-C15 = C18-C15 = C16-C15 = C15-C10
 1.53 with sigma of 0.02
 C10-C18
 2.6 with sigma of 0.02
 C17-C10
 2.6 with sigma of 0.02
 C16-C10
 2.6 with sigma of 0.02
 C8-N1
 2.4 with sigma of 0.02
 N1-C1
 1.4 with sigma of 0.02
 N1-Cr1
 2 with sigma of 0.02
 O1-C9 = O2-C25
 1.4 with sigma of 0.02
 O1-C8
 2.4 with sigma of 0.02
 O1-C10
 2.4 with sigma of 0.02
 C4-C6
 2.517 with sigma of 0.02
 C6-C2
 2.517 with sigma of 0.02
 C5-C4 = C5-C6 = C4-C3 = C6-C1 = C1-C2 = C3-C2
 1.524 with sigma of 0.02
 C7-C1
 2.4 with sigma of 0.02
 C3-C6
 2.95 with sigma of 0.02
 C7-C8
 1.38 with sigma of 0.02
 C20-C19 = C7-C8
 1.38 with sigma of 0.02
 N2-C19 = N1-C7
 1.25 with sigma of 0.02
 H6A-H7
 1.95 with sigma of 0.01
 H7-H6B
 1.95 with sigma of 0.01
 H7-H6A
 1.95 with sigma of 0.01
 H6B-H7
 1.95 with sigma of 0.01
 C6-C7
 2.65 with sigma of 0.01
 C8-C7
 1.42 with sigma of 0.01
 C8-C7 = C20-C19
 1.45 with sigma of 0.01
 C27-C23
 2.57 with sigma of 0.04
 C27-C25
 2.57 with sigma of 0.04
 C9-C15
 2.57 with sigma of 0.04
 C11-C15
 2.57 with sigma of 0.04
 C48-C47 \\sim C47-C46
 with sigma of 0.02
 C47-C46 \\sim C46-C48
 with sigma of 0.02
 C60-C58 \\sim C58-C59
 with sigma of 0.02
 C58-C59 \\sim C59-C60
 with sigma of 0.02
 C59-C54 \\sim C54-C60
 with sigma of 0.02
 C58-C54 \\sim C54-C60
 with sigma of 0.02
 C20-C10 \\sim C24-C8
 with sigma of 0.02
3. Restrained planarity
 C42, C43, C38, C39, C41, O8, O7
 with sigma of 0.1
 Cr2, C43, C38, O8, N4, C37
 with sigma of 0.1
 C25, C24, C23, C22, C21, C20, C10, C11, C12, C13, C8, C9
 with sigma of 0.1
 C25, C24, C22, C20, C10, C13, C8, C9, O1, O2
 with sigma of 0.1
 N1, N2, O1, O2
 with sigma of 0.1
 C25, C22, C21, C20, C13, C8, C9, C7, C19
 with sigma of 0.1
 C1, N1, C7, O1, C9, C8
 with sigma of 0.2
4. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08
5. Rigid body (RIGU) restrains
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(Cl1A)=0.5*(1-FVAR(2))
 Sof(Cl1)=0.5*FVAR(2)
7.a Ternary CH refined with riding coordinates:
 C31(H31), C32(H32), C2(H2), C1(H1)
7.b Secondary CH2 refined with riding coordinates:
 C35(H35A,H35B), C34(H34A,H34B), C33(H33A,H33B), C36(H36A,H36B), C3(H3A,H3B),
 C6(H6A,H6B), C4(H4A,H4B), C5(H5A,H5B)
7.c Me refined with riding coordinates:
 C48(H48A,H48B,H48C), C46(H46A,H46B,H46C), C47(H47A,H47B,H47C), C59(H59A,H59B,
 H59C), C58(H58A,H58B,H58C), C60(H60A,H60B,H60C), C28(H28A,H28B,H28C), C29(H29A,
 H29B,H29C), C30(H30A,H30B,H30C), C18(H18A,H18B,H18C), C17(H17A,H17B,H17C),
 C16(H16A,H16B,H16C)
7.d Aromatic/amide H refined with riding coordinates:
 C62(H62), C63(H63), C64(H64), C65(H65), C61(H61), C76(H76), C77(H77),
 C78(H78), C79(H79), C80(H80), C39(H39), C41(H41), C69(H69), C68(H68), C67(H67),
  C66(H66), C70(H70), C72(H72), C71(H71), C75(H75), C74(H74), C73(H73),
 C53(H53), C51(H51), C37(H37), C49(H49), C23(H23), C21(H21), C11(H11), C13(H13),
  C7(H7), C19(H19)
7.e Fitted pentagon refined as free rotating group:
 C62(C63,C64,C65,C61), C76(C77,C78,C79,C80), C69(C68,C67,C66,C70), C72(C71,C75,
 C74,C73)
7.f Fitted hexagon refined as free rotating group:
 C42(C43,C38,C39,C40,C41), C55(C54,C53,C52,C51,C50), C25(C24,C23,C22,C21,C20),
 C10(C11,C12,C13,C8,C9)
;
_shelx_res_checksum              85929
_shelx_hkl_checksum              9500
_shelx_fab_checksum              7667
_olex2_submission_special_instructions 'No special instructions were received'