Structure-directing synthesis of two germanate cages featuring odd-member ring windows.
Li, Hao; Xu, Yanan; Zhang, Shiyue; Gu, Pengliang; Hu, Qing; Zhang, Yu; Wang, Wenkai; Shi, Zhan; Fu, Xinyi; Du, Hongbin; Dalton transactions (Cambridge, England : 2003) 54 (2025) 13775–13782; doi:10.1039/d5dt01561h

data_7719301
_publ_section_title
;
 Structure-directing synthesis of two germanate cages featuring odd-member
 ring windows.
;
_journal_issue                   36
_journal_name_full
'Dalton transactions (Cambridge, England : 2003)'
_journal_page_first              13775
_journal_page_last               13782
_journal_paper_doi               10.1039/d5dt01561h
_journal_volume                  54
_journal_year                    2025
_chemical_formula_moiety
'8(C20 H30 N8), F36 Ge84 O168, 8(H2 O), 4(C2 H8 N)'
_chemical_formula_sum            'C168 H288 F36 Ge84 N68 O176'
_chemical_formula_weight         12858.21
_space_group_crystal_system      tetragonal
_space_group_IT_number           87
_space_group_name_Hall           '-I 4'
_space_group_name_H-M_alt        'I 4/m'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     iterative
_audit_block_doi                 10.5517/ccdc.csd.cc2nwqdp
_audit_creation_date             2024-01-05
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2025-07-03 deposited with the CCDC.	2025-08-22 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   24.0248(6)
_cell_length_b                   24.0248(6)
_cell_length_c                   35.8100(12)
_cell_measurement_reflns_used    9869
_cell_measurement_temperature    299.00
_cell_measurement_theta_max      53.876
_cell_measurement_theta_min      3.119
_cell_volume                     20669.2(10)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve 1.5 (Bourhis et al., 2015)'
_diffrn_ambient_temperature      299.00
_diffrn_measured_fraction_theta_full 0.995
_diffrn_measured_fraction_theta_max 0.995
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_type           GaK\a
_diffrn_radiation_wavelength     1.34139
_diffrn_reflns_av_R_equivalents  0.0403
_diffrn_reflns_av_unetI/netI     0.0297
_diffrn_reflns_Laue_measured_fraction_full 0.995
_diffrn_reflns_Laue_measured_fraction_max 0.995
_diffrn_reflns_limit_h_max       28
_diffrn_reflns_limit_h_min       -28
_diffrn_reflns_limit_k_max       22
_diffrn_reflns_limit_k_min       -28
_diffrn_reflns_limit_l_max       41
_diffrn_reflns_limit_l_min       -43
_diffrn_reflns_number            51199
_diffrn_reflns_point_group_measured_fraction_full 0.995
_diffrn_reflns_point_group_measured_fraction_max 0.995
_diffrn_reflns_theta_full        53.594
_diffrn_reflns_theta_max         53.962
_diffrn_reflns_theta_min         1.926
_diffrn_source_current           2.23
_diffrn_source_power             0.1554533
_diffrn_source_voltage           69.71
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    5.036
_exptl_absorpt_correction_T_max  0.3012
_exptl_absorpt_correction_T_min  0.2128
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0892 before and 0.0572 after correction.
The Ratio of minimum to maximum transmission is 0.7065.
The \l/2 correction factor is Not present.
;
_exptl_crystal_density_diffrn    2.066
_exptl_crystal_description       block
_exptl_crystal_F_000             12384
_exptl_crystal_size_max          0.13
_exptl_crystal_size_mid          0.12
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.774
_refine_diff_density_min         -0.785
_refine_diff_density_rms         0.131
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.061
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     799
_refine_ls_number_reflns         9598
_refine_ls_number_restraints     764
_refine_ls_restrained_S_all      1.035
_refine_ls_R_factor_all          0.0573
_refine_ls_R_factor_gt           0.0521
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0554P)^2^+301.2077P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1398
_refine_ls_wR_factor_ref         0.1430
_reflns_Friedel_coverage         0.000
_reflns_number_gt                8468
_reflns_number_total             9598
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5dt01561h2.cif
_cod_data_source_block           9944_0m
_cod_depositor_comments
'Adding full bibliography for 7719300--7719301.cif.'
_cod_original_cell_volume        20669.2(12)
_cod_database_code               7719301
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.633
_shelx_estimated_absorpt_t_min   0.561
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H,H) groups, All N(H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 N9-C1B
 1.47 with sigma of 0.02
 N4A-N4A_$1
 2 with sigma of 0.02
 N9-C1A
 1.48 with sigma of 0.02
 C7-N3 \\sim C7-N3A
 with sigma of 0.02
 N4-C21 \\sim N4A-C21
 with sigma of 0.02
 N3A-C7A \\sim N3-C7
 with sigma of 0.02
 N9-C1A \\sim N9-C1B
 with sigma of 0.02
 N7-C17 \\sim N7A-C17A
 with sigma of 0.02
 N7-C18 \\sim N7A-C18A
 with sigma of 0.04
 N5-C11 \\sim N5A-C11A
 with sigma of 0.02
 N5-C12 \\sim N5A-C12A
 with sigma of 0.02
 N5-C14 \\sim N5A-C14A
 with sigma of 0.02
 N6-C13 \\sim N6A-C13A
 with sigma of 0.02
 N6-C14 \\sim N6A-C14A
 with sigma of 0.02
 N6-C15 \\sim N6A-C15A
 with sigma of 0.02
 C12-C13 \\sim C12A-C13A
 with sigma of 0.02
 C15-C16 \\sim C15A-C16A
 with sigma of 0.02
 C19-N8 \\sim C19A-N8A
 with sigma of 0.02
 N5-N6 \\sim N5A-N6A
 with sigma of 0.04
 N5-C13 \\sim N5A-C13A
 with sigma of 0.04
 N6-C12 \\sim N6A-C12A
 with sigma of 0.04
 N6-C16 \\sim N6A-C16A
 with sigma of 0.04
 N7-C16 \\sim N7A-C16A
 with sigma of 0.04
 C14-C12A \\sim C13-C12
 with sigma of 0.02
 N5A-C14A \\sim N6-C13
 with sigma of 0.02
3. Restrained planarity
 C7A, N3A, C8A, C9A, N4A, C10A, C5A, C6A
 with sigma of 0.1
 C8, C7, C6, C5, C10, C21, N4, N3
 with sigma of 0.1
4. Uiso/Uaniso restraints and constraints
C8 \\sim C21 \\sim C10 \\sim C5 \\sim C6 \\sim C7 \\sim N4 \\sim N4A \\sim C8A
\\sim C9A \\sim C10A \\sim C5A \\sim C6A \\sim C7A \\sim N3 \\sim N3A: within
2A with sigma of 0.01 and sigma for terminal atoms of 0.02 within 2A
C16 \\sim N5 \\sim C11 \\sim C12 \\sim C14 \\sim C13 \\sim N6 \\sim C15 \\sim
C20 \\sim C17 \\sim C19 \\sim C18 \\sim N7 \\sim N8 \\sim C20A \\sim C16A \\sim
C15A \\sim C17A \\sim N6A \\sim C18A \\sim N7A \\sim C14A \\sim C13A \\sim C19A
\\sim N5A \\sim C12A \\sim N8A \\sim C11A: within 2A with sigma of 0.01 and
sigma for terminal atoms of 0.02 within 2A
N9 \\sim C1A \\sim C1B: within 2A with sigma of 0.01 and sigma for terminal
atoms of 0.02 within 2A
Uanis(C5) \\sim Ueq, Uanis(C5A) \\sim Ueq, Uanis(C10A) \\sim Ueq, Uanis(C10)
\\sim Ueq, Uanis(C9A) \\sim Ueq, Uanis(C21) \\sim Ueq, Uanis(C8A) \\sim Ueq,
Uanis(C8) \\sim Ueq, Uanis(C7A) \\sim Ueq, Uanis(C7) \\sim Ueq, Uanis(C6A)
\\sim Ueq, Uanis(C6) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms
of 0.02
5. Others
 Sof(C14)=Sof(H14)=Sof(C15)=Sof(C16A)=Sof(H16A)=Sof(C17A)=Sof(C18A)=Sof(H18A)=
 Sof(C19A)=Sof(C20A)=Sof(H20A)=Sof(N4A)=Sof(H4AA)=Sof(H4AB)=Sof(H4AC)=Sof(C8A)=
 Sof(H8A)=Sof(C9A)=Sof(C10A)=Sof(H10A)=Sof(C5A)=Sof(C6A)=Sof(H6A)=Sof(C7A)=
 Sof(N3A)=Sof(H3AA)=Sof(H3AB)=Sof(H3AC)=Sof(N5A)=Sof(C11A)=Sof(H11D)=Sof(H11E)=
 Sof(H11F)=Sof(C12A)=Sof(H12A)=Sof(C14A)=Sof(H14A)=Sof(N6A)=Sof(N7A)=Sof(H7AA)=
 Sof(H7AB)=Sof(H7AC)=Sof(N8A)=Sof(H8AA)=Sof(H8AB)=Sof(H8AC)=1-FVAR(1)
 Sof(N5)=Sof(N6)=Sof(N7)=Sof(H7A)=Sof(H7B)=Sof(H7C)=Sof(C8)=Sof(H8)=Sof(C21)=
 Sof(C10)=Sof(H10)=Sof(C5)=Sof(C6)=Sof(H6)=Sof(C7)=Sof(C11)=Sof(H11A)=Sof(H11B)=
 Sof(H11C)=Sof(C12)=Sof(H12)=Sof(C13)=Sof(H13)=Sof(C16)=Sof(H16)=Sof(C17)=
 Sof(C18)=Sof(H18)=Sof(C19)=Sof(C20)=Sof(H20)=Sof(N4)=Sof(H4A)=Sof(H4B)=
 Sof(H4C)=Sof(N8)=Sof(H8B)=Sof(H8C)=Sof(H8D)=Sof(N3)=Sof(H3A)=Sof(H3B)=Sof(H3C)=
 Sof(C13A)=Sof(H13A)=Sof(C15A)=FVAR(1)
 Fixed Sof: N9(0.5) H9A(0.5) H9B(0.5) C1A(0.5) H1AA(0.5) H1AB(0.5) H1AC(0.5)
 C1B(0.5) H1BA(0.5) H1BB(0.5) H1BC(0.5)
6.a Everything fixed:
 H4AA, H4AB, H4AC, H3AA, H3AB, H3AC
6.b Free rotating group:
 O29(H29A,H29B)
6.c Secondary CH2 refined with riding coordinates:
 N9(H9A,H9B)
6.d Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), C4(H4), C8(H8), C10(H10), C6(H6), C12(H12), C13(H13),
 C14(H14), C16A(H16A), C18A(H18A), C20A(H20A), C16(H16), C18(H18), C20(H20),
 C8A(H8A), C10A(H10A), C6A(H6A), C12A(H12A), C14A(H14A), C13A(H13A)
6.e Fitted hexagon refined as free rotating group:
 C8(C21,C10,C5,C6,C7), C15(C16A,C17A,C18A,C19A,C20A), C8A(C9A,C10A,C5A,C6A,C7A)
6.f Idealised Me refined as rotating group:
 C1(H1A,H1B,H1C), N7(H7A,H7B,H7C), C11(H11A,H11B,H11C), N4(H4A,H4B,H4C),
 N8(H8B,H8C,H8D), N3(H3A,H3B,H3C), C11A(H11D,H11E,H11F), N7A(H7AA,H7AB,H7AC),
 N8A(H8AA,H8AB,H8AC), C1A(H1AA,H1AB,H1AC), C1B(H1BA,H1BB,H1BC)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              6404
_shelx_hkl_checksum              9347
_shelx_fab_checksum              7522
_olex2_submission_special_instructions 'No special instructions were received'