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_7132990
_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 H113 N6 O10, 18[C4H8O2]'
_chemical_formula_sum            'C198 H251 N6 O46'
_chemical_formula_weight         3451.03
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 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                 90.916(4)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   22.4005(12)
_cell_length_b                   26.9673(7)
_cell_length_c                   32.2242(12)
_cell_measurement_reflns_used    16148
_cell_measurement_temperature    100.02(11)
_cell_measurement_theta_max      22.5210
_cell_measurement_theta_min      2.0940
_cell_volume                     19463.5(14)
_computing_cell_refinement       'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_data_collection       'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_computing_data_reduction        'CrysAlisPro 1.171.41.93a (Rigaku OD, 2020)'
_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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      100.15
_diffrn_detector_area_resol_mean 10.0000
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.999
_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    -98.00  80.00   0.50   80.00    --   -8.90  -5.00 -95.00  356
  2  \w    -98.00  26.00   0.50   80.00    --   -8.90 -57.00 120.00  248
  3  \w    -46.00  32.00   0.50   80.00    --   -8.90  68.00  60.00  156
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RCD3): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0658
_diffrn_reflns_av_unetI/netI     0.0447
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.999
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       28
_diffrn_reflns_limit_k_min       -28
_diffrn_reflns_limit_l_max       33
_diffrn_reflns_limit_l_min       -33
_diffrn_reflns_number            145511
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.999
_diffrn_reflns_theta_full        21.967
_diffrn_reflns_theta_max         21.967
_diffrn_reflns_theta_min         1.720
_exptl_absorpt_coefficient_mu    0.083
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.85972
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.93a (Rigaku Oxford Diffraction, 2020)
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    1.178
_exptl_crystal_description       needle
_exptl_crystal_F_000             7396
_exptl_crystal_size_max          0.1
_exptl_crystal_size_mid          0.025
_exptl_crystal_size_min          0.007
_refine_diff_density_max         0.789
_refine_diff_density_min         -0.460
_refine_diff_density_rms         0.079
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.474
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1281
_refine_ls_number_reflns         23765
_refine_ls_number_restraints     257
_refine_ls_restrained_S_all      1.501
_refine_ls_R_factor_all          0.1475
_refine_ls_R_factor_gt           0.1175
_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          0.3649
_refine_ls_wR_factor_ref         0.3900
_reflns_Friedel_coverage         0.000
_reflns_number_gt                15077
_reflns_number_total             23765
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4cc01407c3.cif
_cod_data_source_block           exp_390
_cod_depositor_comments
'Adding full bibliography for 7132990--7132997.cif.'
_cod_database_code               7132990
_shelx_shelxl_version_number     2019/2
_shelx_estimated_absorpt_t_max   0.999
_shelx_estimated_absorpt_t_min   0.992
_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
 C5-C6
 2.52 with sigma of 0.04
 C25-C22 \\sim C25-C26 \\sim C25-C27 \\sim C25-C28
 with sigma of 0.02
 C22-C26 \\sim C22-C27 \\sim C22-C28 \\sim C26-C27 \\sim C26-C28 \\sim C27-C28
 with sigma of 0.04
 C80-C84 \\sim C80-C83 \\sim C80-C82 \\sim C84-C83 \\sim C84-C82 \\sim C83-C82
 with sigma of 0.04
 C7-C4 \\sim C7-C8 \\sim C7-C5
 with sigma of 0.01
 C81-C80 \\sim C81-C84 \\sim C81-C83 \\sim C81-C82
 with sigma of 0.02
 C4-C8 \\sim C4-C6 \\sim C4-C5 \\sim C8-C6 \\sim C8-C5
 with sigma of 0.001
 C52-C56 \\sim C52-C54 \\sim C52-C55 \\sim C56-C54 \\sim C56-C55 \\sim C54-C55
 with sigma of 0.04
 C53-C52 \\sim C53-C56 \\sim C53-C54 \\sim C53-C55
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O1) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
Uanis(C43) \\sim Ueq, Uanis(C41) \\sim Ueq, Uanis(C44) \\sim Ueq, Uanis(C42)
\\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
Uanis(C28) \\sim Ueq, Uanis(C27) \\sim Ueq, Uanis(C26) \\sim Ueq, Uanis(C25)
\\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.05
Uanis(C5) \\sim Ueq, Uanis(C6) \\sim Ueq, Uanis(C8) \\sim Ueq, Uanis(C7) \\sim
Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C13) \\sim Ueq, Uanis(C15) \\sim Ueq, Uanis(C14) \\sim Ueq, Uanis(C16)
\\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(C70) \\sim Ueq, Uanis(C72) \\sim Ueq, Uanis(C69) \\sim Ueq, Uanis(C71)
\\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(O4) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(O6) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(O7) \\sim Ueq, Uanis(O8) \\sim Ueq: with sigma of 0.1 and sigma for
terminal atoms of 0.2
Uanis(C55) \\sim Ueq, Uanis(C56) \\sim Ueq, Uanis(C53) \\sim Ueq, Uanis(C54)
\\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(C82) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
4.a Ternary CH refined with riding coordinates:
 C91(H91), C112(H112)
4.b Secondary CH2 refined with riding coordinates:
 C43(H43A,H43B)
4.c Me refined with riding coordinates:
 C34(H34A,H34B,H34C), C35(H35A,H35B,H35C), C36(H36A,H36B,H36C), C54(H54A,H54B,
 H54C), C55(H55A,H55B,H55C), C56(H56A,H56B,H56C), C62(H62A,H62B,H62C), C63(H63A,
 H63B,H63C), C64(H64A,H64B,H64C), C82(H82A,H82B,H82C), C83(H83A,H83B,H83C),
 C84(H84A,H84B,H84C), C26(H26A,H26B,H26C), C8(H8A,H8B,H8C), C6(H6A,H6B,H6C),
 C27(H27A,H27B,H27C), C5(H5A,H5B,H5C), C28(H28A,H28B,H28C)
4.d Aromatic/amide H refined with riding coordinates:
 N2(H2), N3(H3), N4(H4), N5(H5), N6(H6), C3(H3A), C9(H9), C10(H10A), C13(H13),
 C14(H14), C15(H15), C16(H16), C19(H19), C20(H20), C23(H23), C31(H31), C37(H37),
  C38(H38), C41(H41), C42(H42), C44(H44), C47(H47), C48(H48), C51(H51),
 C59(H59), C65(H65), C66(H66), C69(H69), C70(H70), C71(H71), C72(H72), C75(H75),
  C76(H76), C79(H79), C86(H86), C87(H87), C88(H88), C96(H96), C97(H97),
 C99(H99), C102(H102), C103(H103), C105(H105), C107(H107), C108(H108),
 C109(H109), C117(H117), C118(H118), C119(H119), C123(H123), C124(H124),
 C125(H125), N1(H1)
4.e Idealised tetrahedral OH refined as rotating group:
 O8(H8), O10(H10)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              76929
_shelx_hkl_checksum              50863
_shelx_fab_checksum              779
_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
;