Exploration of the polymorphic solid-state landscape of an amide-linked organic cage using computation and automation.
Shields, C. E.; Fellowes, T.; Slater, A. G.; Cooper, A. I.; Andrews, K. G.; Szczypiński, F T; Chemical communications (Cambridge, England) 60 (2024) 6023–6026; doi:10.1039/d4cc01407c

data_7132992
_publ_section_title
;
 Exploration of the polymorphic solid-state landscape of an amide-linked
 organic cage using computation and automation.
;
_journal_issue                   47
_journal_name_full               'Chemical communications (Cambridge, England)'
_journal_page_first              6023
_journal_page_last               6026
_journal_paper_doi               10.1039/d4cc01407c
_journal_volume                  60
_journal_year                    2024
_chemical_formula_moiety         'C126 H112 N6 O10, 8(C4 H6 O3), 8[C4O3H6]'
_chemical_formula_sum            'C190 H208 N6 O58'
_chemical_formula_weight         3503.61
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2024-03-26
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-03-27 deposited with the CCDC.	2024-05-02 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 109.9980(9)
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   39.4383(4)
_cell_length_b                   27.5839(2)
_cell_length_c                   35.2015(4)
_cell_measurement_reflns_used    10815
_cell_measurement_temperature    100.15
_cell_measurement_theta_max      22.9016075084314
_cell_measurement_theta_min      1.0658047357595362
_cell_volume                     35985.4(6)
_computing_data_collection       'GDA - generic data acquisition software'
_computing_data_reduction
;
DIALS 3.12.1-2-g1c07bc2b3-release (Winter, G. et al., 2018)
dials.scale (Beilsten-Edmands, J. et al., 2020)
XIA2 3.12.0 (Winter, G., 2010)
;
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/2 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.15
_diffrn_detector_type            'Dectris PILATUS 2M'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.998
_diffrn_measurement_device       'Fixed \c 3-circle diffractometer'
_diffrn_measurement_device_type  'Fluid Film Devices'
_diffrn_measurement_method       'shutterless scans'
_diffrn_measurement_specimen_support 'MiTeGen MicroMount'
_diffrn_radiation_type           synchrotron
_diffrn_radiation_wavelength     0.6889
_diffrn_reflns_av_R_equivalents  0.0693
_diffrn_reflns_av_unetI/netI     0.0677
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       39
_diffrn_reflns_limit_h_min       -39
_diffrn_reflns_limit_k_max       27
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       35
_diffrn_reflns_limit_l_min       -35
_diffrn_reflns_number            62103
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.998
_diffrn_reflns_theta_full        20.148
_diffrn_reflns_theta_max         20.148
_diffrn_reflns_theta_min         1.065
_diffrn_source_details           'Allan et al. (2017)'
_exptl_absorpt_coefficient_mu    0.090
_exptl_absorpt_correction_T_max  1.0
_exptl_absorpt_correction_T_min  0.9005943081521229
_exptl_absorpt_correction_type   empirical
_exptl_absorpt_process_details
;
DIALS 3.12.1-2-g1c07bc2b3-release
Scaling & analysis of unmerged intensities, absorption correction using spherical harmonics
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.293
_exptl_crystal_description       needle
_exptl_crystal_F_000             14832
_exptl_crystal_size_max          0.299
_exptl_crystal_size_mid          0.034
_exptl_crystal_size_min          0.006
_refine_diff_density_max         1.483
_refine_diff_density_min         -0.871
_refine_diff_density_rms         0.120
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.085
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1703
_refine_ls_number_reflns         18806
_refine_ls_number_restraints     477
_refine_ls_restrained_S_all      1.107
_refine_ls_R_factor_all          0.1886
_refine_ls_R_factor_gt           0.1539
_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^)+(0.3670P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.4287
_refine_ls_wR_factor_ref         0.4705
_reflns_Friedel_coverage         0.000
_reflns_number_gt                11245
_reflns_number_total             18806
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4cc01407c3.cif
_cod_data_source_block           ka1_pc_diox
_cod_depositor_comments
'Adding full bibliography for 7132990--7132997.cif.'
_cod_database_code               7132992
_shelx_shelxl_version_number     2019/2
_shelx_estimated_absorpt_t_max   0.999
_shelx_estimated_absorpt_t_min   0.974
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 C1_8-O1_8
 C1_9-O1_9
 C1_10-O1_10
 C1_11-O1_11
 C1_12-O1_12
 C1_13-O1_13
 C1_14-O1_14
 C1_15-O1_15
 1.22 with sigma of 0.02
 C1_8-O2_8 = C1_8-O3_8 = O2_8-C2_8 = O3_8-C3_8
 C1_9-O2_9 = C1_9-O3_9 = O2_9-C2_9 = O3_9-C3_9
 C1_10-O2_10 = C1_10-O3_10 = O2_10-C2_10 = O3_10-C3_10
 C1_11-O2_11 = C1_11-O3_11 = O2_11-C2_11 = O3_11-C3_11
 C1_12-O2_12 = C1_12-O3_12 = O2_12-C2_12 = O3_12-C3_12
 C1_13-O2_13 = C1_13-O3_13 = O2_13-C2_13 = O3_13-C3_13
 C1_14-O2_14 = C1_14-O3_14 = O2_14-C2_14 = O3_14-C3_14
 C1_15-O2_15 = C1_15-O3_15 = O2_15-C2_15 = O3_15-C3_15
 1.34 with sigma of 0.02
 C2_8-C3_8 = C2_8-C4_8
 C2_9-C3_9 = C2_9-C4_9
 C2_10-C3_10 = C2_10-C4_10
 C2_11-C3_11 = C2_11-C4_11
 C2_12-C3_12 = C2_12-C4_12
 C2_13-C3_13 = C2_13-C4_13
 C2_14-C3_14 = C2_14-C4_14
 C2_15-C3_15 = C2_15-C4_15
 1.54 with sigma of 0.02
 H7_1-O1_8
 1.83 with sigma of 0.02
 C1_8-C2_8 = C1_8-C3_8
 C1_9-C2_9 = C1_9-C3_9
 C1_10-C2_10 = C1_10-C3_10
 C1_11-C2_11 = C1_11-C3_11
 C1_12-C2_12 = C1_12-C3_12
 C1_13-C2_13 = C1_13-C3_13
 C1_14-C2_14 = C1_14-C3_14
 C1_15-C2_15 = C1_15-C3_15
 2.2 with sigma of 0.04
 O2_8-C3_8 = O3_8-C2_8
 O2_9-C3_9 = O3_9-C2_9
 O2_10-C3_10 = O3_10-C2_10
 O2_11-C3_11 = O3_11-C2_11
 O2_12-C3_12 = O3_12-C2_12
 O2_13-C3_13 = O3_13-C2_13
 O2_14-C3_14 = O3_14-C2_14
 O2_15-C3_15 = O3_15-C2_15
 2.31 with sigma of 0.04
 C3_8-C4_8
 C3_9-C4_9
 C3_10-C4_10
 C3_11-C4_11
 C3_12-C4_12
 C3_13-C4_13
 C3_14-C4_14
 C3_15-C4_15
 2.56 with sigma of 0.01
 O2_8-C4_8
 O2_9-C4_9
 O2_10-C4_10
 O2_11-C4_11
 O2_12-C4_12
 O2_13-C4_13
 O2_14-C4_14
 O2_15-C4_15
 2.39 with sigma of 0.01
 C32_1-C36_1 \\sim C32_1-C35_1 \\sim C32_1-C34_1 \\sim C36_1-C35_1 \\sim
C36_1-C34_1 \\sim C35_1-
 C34_1
 with sigma of 0.04
 C33_1-C32_1 \\sim C33_1-C36_1 \\sim C33_1-C35_1 \\sim C33_1-C34_1
 with sigma of 0.02
 C60_1-C63_1 \\sim C60_1-C64_1 \\sim C60_1-C62_1 \\sim C63_1-C64_1 \\sim
C63_1-C62_1 \\sim C64_1-
 C62_1
 with sigma of 0.04
 C61_1-C60_1 \\sim C61_1-C63_1 \\sim C61_1-C64_1 \\sim C61_1-C62_1
 with sigma of 0.02
3. Restrained planarity
 O1_8, C1_8, O2_8, O3_8, C2_8, C3_8
 O1_9, C1_9, O2_9, O3_9, C2_9, C3_9
 O1_10, C1_10, O2_10, O3_10, C2_10, C3_10
 O1_11, C1_11, O2_11, O3_11, C2_11, C3_11
 O1_12, C1_12, O2_12, O3_12, C2_12, C3_12
 O1_13, C1_13, O2_13, O3_13, C2_13, C3_13
 O1_14, C1_14, O2_14, O3_14, C2_14, C3_14
 O1_15, C1_15, O2_15, O3_15, C2_15, C3_15
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C2_13) \\sim Ueq, Uanis(C3_13) \\sim Ueq, Uanis(C4_13) \\sim Ueq: with
sigma of 0.01 and sigma for terminal atoms of 0.02
5. Rigid body (RIGU) restrains
 O1_8, O2_8, O3_8, C1_8, C2_8, C3_8, C4_8
 O1_9, O2_9, O3_9, C1_9, C2_9, C3_9, C4_9
 O1_10, O2_10, O3_10, C1_10, C2_10, C3_10, C4_10
 O1_11, O2_11, O3_11, C1_11, C2_11, C3_11, C4_11
 O1_12, O2_12, O3_12, C1_12, C2_12, C3_12, C4_12
 O1_13, O2_13, O3_13, C1_13, C2_13, C3_13, C4_13
 O1_14, O2_14, O3_14, C1_14, C2_14, C3_14, C4_14
 O1_15, O2_15, O3_15, C1_15, C2_15, C3_15, C4_15
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Uiso(O3)=Uiso(O1)=Uiso(C1)=Uiso(O2)=Uiso(C3)=Uiso(C2)=Uiso(C4)=FVAR(1)
 Uiso(C2)=Uiso(C4)=Uiso(C3)=Uiso(O2)=Uiso(O3)=Uiso(C1)=Uiso(O1)=FVAR(2)
7.a Ternary CH refined with riding coordinates:
 C91(H91), C124(H124), C2(H2), C2(H2), C2(H2), C2(H2), C2(H2), C2(H2), C2(H2),
 C2(H2)
7.b Secondary CH2 refined with riding coordinates:
 C3(H3A,H3B), C3(H3A,H3B), C3(H3A,H3B), C3(H3A,H3B), C3(H3A,H3B), C3(H3A,H3B),
 C3(H3A,H3B), C3(H3A,H3B)
7.c Me refined with riding coordinates:
 C26(H26A,H26B,H26C), C8(H8A,H8B,H8C), C84(H84A,H84B,H84C), C83(H83A,H83B,
 H83C), C28(H28A,H28B,H28C), C55(H55A,H55B,H55C), C82(H82A,H82B,H82C), C27(H27A,
 H27B,H27C), C63(H63A,H63B,H63C), C6(H6A,H6B,H6C), C64(H64A,H64B,H64C),
 C54(H54A,H54B,H54C), C62(H62A,H62B,H62C), C56(H56A,H56B,H56C), C7(H7A,H7B,H7C),
  C36(H36A,H36B,H36C), C35(H35A,H35B,H35C), C34(H34A,H34B,H34C), C4(H4A,H4B,
 H4C), C4(H4A,H4B,H4C), C4(H4A,H4B,H4C), C4(H4A,H4B,H4C), C4(H4A,H4B,H4C),
 C4(H4A,H4B,H4C), C4(H4A,H4B,H4C), C4(H4A,H4B,H4C)
7.d Aromatic/amide H refined with riding coordinates:
 N3(H3), N1(H1), N6(H6), N2(H2), C98(H98), C96(H96), N5(H5), C87(H87),
 C97(H97), C114(H114), C104(H104), C103(H103), N4(H4), C115(H115), C88(H88),
 C121(H121), C102(H102), C41(H41), C42(H42), C43(H43), C117(H117), C11(H11),
 C47(H47), C13(H13), C86(H86), C19(H19), C20(H20), C120(H120), C38(H38),
 C15(H15), C44(H44), C122(H122), C37(H37), C79(H79), C23(H23), C16(H16), C9(H9),
  C14(H14), C48(H48), C110(H110), C31(H31), C3(H3B), C107(H107), C75(H75),
 C52(H52), C108(H108), C59(H59), C76(H76), C65(H65), C66(H66), C72(H72),
 C70(H70), C69(H69), C71(H71)
7.e Idealised tetrahedral OH refined as rotating group:
 O7(H7), O3(H3A)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 3613 electrons were 
found in a volume of 11454\%A^3^ in 2 voids per unit cell. 
This is consistent with the presence of 
8[C4O3H6] per Formula Unit 
which account for 3456 electrons 
per unit cell.
;
_shelx_res_checksum              53076
_shelx_hkl_checksum              97490
_shelx_fab_checksum              82825
_olex2_submission_special_instructions 'No special instructions were received'