Reversible mechanical protection: building a 3D “suit” around a T-shaped benzimidazole axle
Zhu, Kelong; Baggi, Giorgio; Vukotic, V. Nicholas; Loeb, Stephen J.; Chem. Sci. 8 (2017) 3898–; doi:10.1039/C7SC00790F

data_1545990
_publ_section_title
;
 Reversible mechanical protection: building a 3D &#x201C;suit&#x201D;
 around a T-shaped benzimidazole axle
;
_journal_issue                   5
_journal_name_full               'Chem. Sci.'
_journal_page_first              3898
_journal_paper_doi               10.1039/C7SC00790F
_journal_volume                  8
_journal_year                    2017
_chemical_formula_moiety         'C34 H50 O10, C25 H18 N2, C2 H3 N'
_chemical_formula_sum            'C61 H71 N3 O10'
_chemical_formula_weight         1006.20
_space_group_crystal_system      orthorhombic
_space_group_IT_number           61
_space_group_name_Hall           '-P 2ac 2ab'
_space_group_name_H-M_alt        'P b c a'
_symmetry_space_group_name_Hall  '-P 2ac 2ab'
_symmetry_space_group_name_H-M   'P b c a'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     direct
_audit_creation_date             2017-02-16
_audit_creation_method
;
Olex2 1.2
(compiled 2017.01.04 svn.r3372 for OlexSys, GUI svn.r5292)
;
_audit_update_record
;
2017-02-17 deposited with the CCDC.
2017-03-15 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   17.819(3)
_cell_length_b                   17.457(3)
_cell_length_c                   34.337(5)
_cell_measurement_reflns_used    9925
_cell_measurement_temperature    173(2)
_cell_measurement_theta_max      26.38
_cell_measurement_theta_min      2.37
_cell_volume                     10681(3)
_computing_cell_refinement       'SAINT v7.60A (Bruker, 2009)'
_computing_data_collection       'SMART V5.631 (?, 2016)'
_computing_data_reduction        'SAINT v7.60A (Bruker, 2009)'
_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    'XS (Sheldrick, 2008)'
_diffrn_ambient_temperature      173
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 1.000
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  Parallel,graphite
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.1488
_diffrn_reflns_av_unetI/netI     0.0705
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -19
_diffrn_reflns_limit_k_max       19
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       38
_diffrn_reflns_limit_l_min       -38
_diffrn_reflns_number            80139
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        23.256
_diffrn_reflns_theta_max         23.256
_diffrn_reflns_theta_min         2.018
_diffrn_source_current           30.0
_diffrn_source_power             1.5
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.085
_exptl_absorpt_correction_T_max  0.7411
_exptl_absorpt_correction_T_min  0.5036
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details
;
SADABS-2014/5 (Bruker,2014/5) was used for absorption correction.
wR2(int) was 0.1450 before and 0.0994 after correction.
The Ratio of minimum to maximum transmission is 0.6795.
The \l/2 correction factor is 0.00150.
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.251
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       block
_exptl_crystal_F_000             4304
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: acetonitrile'
_refine_diff_density_max         0.499
_refine_diff_density_min         -0.309
_refine_diff_density_rms         0.058
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.166
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     760
_refine_ls_number_reflns         7663
_refine_ls_number_restraints     292
_refine_ls_restrained_S_all      1.167
_refine_ls_R_factor_all          0.1513
_refine_ls_R_factor_gt           0.1148
_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^)+(0.0493P)^2^+32.7204P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2232
_refine_ls_wR_factor_ref         0.2406
_reflns_Friedel_coverage         0.000
_reflns_number_gt                5437
_reflns_number_total             7663
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            c7sc00790f2.cif
_cod_data_source_block           kz74a
_cod_original_cell_volume        10682(3)
_cod_database_code               1545990
_shelx_shelxl_version_number     2016/4
_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, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Uiso/Uaniso restraints and constraints
C57 \\sim C55 \\sim C56 \\sim O8 \\sim C55A \\sim C56A \\sim O8A: within 2A
with sigma of 0.04 and sigma for terminal atoms of 0.08
C40 \\sim C45 \\sim C46 \\sim C41 \\sim C43 \\sim C44 \\sim C42 \\sim C40A
\\sim C45A \\sim C46A \\sim C41A \\sim C43A \\sim C44A \\sim C42A: within 2A
with sigma of 0.04 and sigma for terminal atoms of 0.08
3. Same fragment restrains
{C54, C57, C55A, C56A, O8A} sigma for 1-2: 0.02, 1-3: 0.02
as
{C54, C57, C55, C56, O8}
{C39, C40A, C45A, C46A, C41A, C43A, C44A, C42A, O2} sigma for 1-2: 0.02, 1-3:
0.02
as
{C39, C40, C45, C46, C41, C43, C44, C42, O2}
4. Others
 Sof(H54C)=Sof(H54D)=Sof(H57C)=Sof(H57D)=Sof(C55A)=Sof(H55C)=Sof(H55D)=
 Sof(C56A)=Sof(H56C)=Sof(H56D)=Sof(O8A)=1-FVAR(1)
 Sof(H54A)=Sof(H54B)=Sof(H57A)=Sof(H57B)=Sof(C55)=Sof(H55A)=Sof(H55B)=Sof(C56)=
 Sof(H56A)=Sof(H56B)=Sof(O8)=FVAR(1)
 Sof(H39C)=Sof(H39D)=Sof(C40A)=Sof(H40C)=Sof(H40D)=Sof(C45A)=Sof(H45C)=
 Sof(H45D)=Sof(C46A)=Sof(H46C)=Sof(H46D)=Sof(C41A)=Sof(H41C)=Sof(H41D)=
 Sof(C43A)=Sof(H43C)=Sof(H43D)=Sof(C44A)=Sof(H44C)=Sof(H44D)=Sof(C42A)=
 Sof(H42C)=Sof(H42D)=1-FVAR(2)
 Sof(H39A)=Sof(H39B)=Sof(C40)=Sof(H40A)=Sof(H40B)=Sof(C45)=Sof(H45A)=Sof(H45B)=
 Sof(C46)=Sof(H46A)=Sof(H46B)=Sof(C41)=Sof(H41A)=Sof(H41B)=Sof(C43)=Sof(H43A)=
 Sof(H43B)=Sof(C44)=Sof(H44A)=Sof(H44B)=Sof(C42)=Sof(H42A)=Sof(H42B)=FVAR(2)
5.a Secondary CH2 refined with riding coordinates:
 C54(H54A,H54B), C54(H54C,H54D), C57(H57A,H57B), C57(H57C,H57D), C55(H55A,
 H55B), C56(H56A,H56B), C48(H48A,H48B), C49(H49A,H49B), C51(H51A,H51B),
 C53(H53A,H53B), C50(H50A,H50B), C52(H52A,H52B), C38(H38A,H38B), C47(H47A,H47B),
  C59(H59A,H59B), C58(H58A,H58B), C39(H39A,H39B), C39(H39C,H39D), C40(H40A,
 H40B), C45(H45A,H45B), C46(H46A,H46B), C41(H41A,H41B), C43(H43A,H43B),
 C44(H44A,H44B), C42(H42A,H42B), C40A(H40C,H40D), C45A(H45C,H45D), C46A(H46C,
 H46D), C41A(H41C,H41D), C43A(H43C,H43D), C44A(H44C,H44D), C42A(H42C,H42D),
 C55A(H55C,H55D), C56A(H56C,H56D)
5.b Aromatic/amide H refined with riding coordinates:
 C35(H35), C29(H29), C31(H31), C37(H37), C27(H27), C33(H33), C11(H11),
 C15(H15), C19(H19), C17(H17), C18(H18), C10(H10), C16(H16), C3(H3), C25(H25),
 C23(H23), C7(H7), C6(H6), C4(H4), C5(H5), C21(H21), C24(H24), C22(H22), N1(H1)
5.c Idealised Me refined as rotating group:
 C2S(H2SA,H2SB,H2SC)
;
_olex2_submission_special_instructions 'No special instructions were received'