Lithium metal atoms fill vacancies in the germanium network of a type-I clathrate: Synthesis and structural characterization of Ba8Li5Ge41
Ghosh, Kowsik; Ovchinnikov, Alexander; Baitinger, Michael; Krnel, Mitja; Burkhardt, Ulrich; Grin, Yuri; Bobev, Svilen; Dalton Transactions  (2023) –; doi:10.1039/D3DT01168B

data_7713072
_publ_section_title
;
 Lithium metal atoms fill vacancies in the germanium network of a type-I
 clathrate: Synthesis and structural characterization of Ba8Li5Ge41
;
_journal_name_full               'Dalton Transactions'
_journal_paper_doi               10.1039/D3DT01168B
_journal_year                    2023
_chemical_formula_moiety
'2(C36 H38 N4 O2 Zn), 0.5(C6 H14), 1.5(C H2 Cl2)'
_chemical_formula_sum            'C76.5 H86 Cl3 N8 O4 Zn2'
_chemical_formula_weight         1418.62
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-06-24
_audit_creation_method
;
Olex2 1.5
(compiled 2022.04.07 svn.rca3783a0 for OlexSys, GUI svn.r6498)
;
_audit_update_record
;
2022-06-27 deposited with the CCDC.	2023-05-17 downloaded from the CCDC.
;
_cell_angle_alpha                89.305(3)
_cell_angle_beta                 80.720(4)
_cell_angle_gamma                82.276(4)
_cell_formula_units_Z            1
_cell_length_a                   8.2841(6)
_cell_length_b                   10.5138(8)
_cell_length_c                   19.9849(15)
_cell_measurement_reflns_used    9989
_cell_measurement_temperature    100.0(1)
_cell_measurement_theta_max      66.79
_cell_measurement_theta_min      4.82
_cell_volume                     1702.2(2)
_computing_cell_refinement       'SAINT V8.40B (Bruker, 2016)'
_computing_data_collection       'APEX4 (Bruker, 2021)'
_computing_data_reduction        'SAINT V8.40B (Bruker, 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    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_temperature      100.0(1)
_diffrn_detector                 CMOS
_diffrn_detector_area_resol_mean '1024 x 1024'
_diffrn_detector_type            'Photon 100'
_diffrn_measured_fraction_theta_full 0.981
_diffrn_measured_fraction_theta_max 0.982
_diffrn_measurement_device       '\k-geometry diffractometer'
_diffrn_measurement_device_type  'Bruker D8 VENTURE'
_diffrn_measurement_method       '\f and \w scans''
_diffrn_radiation_collimation    'focusing mirrors'
_diffrn_radiation_monochromator  'QUAZAR MX multilayer optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a~1~'
_diffrn_radiation_wavelength     1.54178
_diffrn_radiation_xray_symbol    K-L~3~
_diffrn_reflns_av_unetI/netI     0.0332
_diffrn_reflns_Laue_measured_fraction_full 0.981
_diffrn_reflns_Laue_measured_fraction_max 0.982
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       12
_diffrn_reflns_limit_k_min       -12
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       0
_diffrn_reflns_number            10719
_diffrn_reflns_point_group_measured_fraction_full 0.981
_diffrn_reflns_point_group_measured_fraction_max 0.982
_diffrn_reflns_theta_full        66.897
_diffrn_reflns_theta_max         66.897
_diffrn_reflns_theta_min         4.781
_diffrn_source                   'sealed X-ray tube'
_diffrn_source_current           1.0
_diffrn_source_power             0.05
_diffrn_source_target            Cu
_diffrn_source_type              'high brilliance microfocus sealed tube, Cu'
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    2.399
_exptl_absorpt_correction_T_max  0.71
_exptl_absorpt_correction_T_min  0.57
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
 TWINABS-2012/1 (Bruker,2012) was used for absorption correction.
 
For component 1:
 wR2(int) was 0.1178 before and 0.0638 after correction.
 
For component 2:
 wR2(int) was 0.1014 before and 0.0772 after correction.
 The Ratio of minimum to maximum transmission is 0.80.

Final HKLF 4 output contains 44641 reflections, Rint = 0.0510
 (34520 with I > 3sig(I), Rint = 0.0474)
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   light
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.384
_exptl_crystal_description       prism
_exptl_crystal_F_000             744
_exptl_crystal_recrystallization_method
'The material was recrystallised from a mixture of DCM and hexane  by slow evaporation'
_exptl_crystal_size_max          0.248
_exptl_crystal_size_mid          0.128
_exptl_crystal_size_min          0.086
_refine_diff_density_max         0.895
_refine_diff_density_min         -1.007
_refine_diff_density_rms         0.100
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.078
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     432
_refine_ls_number_reflns         10719
_refine_ls_number_restraints     5
_refine_ls_restrained_S_all      1.080
_refine_ls_R_factor_all          0.0716
_refine_ls_R_factor_gt           0.0625
_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^)+(0.0631P)^2^+3.7441P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1573
_refine_ls_wR_factor_ref         0.1636
_reflns_Friedel_coverage         0.000
_reflns_number_gt                9531
_reflns_number_total             10719
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3dt01168b2.cif
_cod_data_source_block           compound_4d
_cod_original_formula_sum        'C76.50 H86 Cl3 N8 O4 Zn2'
_cod_database_code               7713072
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.820
_shelx_estimated_absorpt_t_min   0.588
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.8060(9)
 0.1940(9)
2. 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
3. Uiso/Uaniso restraints and constraints
C13 \\sim C14 \\sim C15 \\sim C16 \\sim C17 \\sim C18: within 1.7A with sigma
of 0.004 and sigma for terminal atoms of 0.004 within 1.7A
Cl1 \\sim Cl2 \\sim C12: within 1.7A with sigma of 0.004 and sigma for terminal
atoms of 0.004 within 1.7A
4. Others
 Fixed Sof: Cl1(0.75) Cl2(0.75) C12(0.75) H12A(0.75) H12B(0.75) C18(0.25)
 H18A(0.25) H18B(0.25) H18C(0.25) C13(0.25) H13A(0.25) H13B(0.25) H13C(0.25)
 C14(0.25) H14A(0.25) H14B(0.25) C15(0.25) H15A(0.25) H15B(0.25) C16(0.25)
 H16A(0.25) H16B(0.25) C17(0.25) H17A(0.25) H17B(0.25)
5.a Free rotating group:
 C18(C13,C14,C15,C16,C17)
5.b Secondary CH2 refined with riding coordinates:
 C8(H8A,H8B), C8A(H8AA,H8AB), C9(H9A,H9B), C9A(H9AA,H9AB), C10(H10A,H10B),
 C10A(H10C,H10D), C11(H11A,H11B), C11A(H11C,H11D), C12(H12A,H12B), C14(H14A,
 H14B), C15(H15A,H15B), C16(H16A,H16B), C17(H17A,H17B)
5.c Aromatic/amide H refined with riding coordinates:
 C3(H3), C3'(H3'), C3'A(H3'A), C3A(H3A), C4(H4), C4'(H4'), C4'A(H4'A),
 C4A(H4A), C5(H5), C5'(H5'), C5'A(H5'A), C5A(H5A), C6(H6), C6'(H6'), C6'A(H6'A),
  C6A(H6A)
5.d Idealised Me refined as rotating group:
 C7'(H7'A,H7'B,H7'C), C7'A(H7'D,H7'E,H7'F), C18(H18A,H18B,H18C), C13(H13A,H13B,
 H13C)
;
_shelx_res_checksum              45927
_shelx_hkl_checksum              28286
_olex2_exptl_crystal_mounting_method
'The crystal was mounted on a MITIGEN holder oil'
_olex2_submission_special_instructions 'No special instructions were received'