Selective and Benign Alkylation of Sulfido-Oxo Stannate Clusters with Propyl, Pentyl, or Hexyl Substituents
Stuhrmann, Gina; Schneider, Jannik; Schmidt, Kilian; Dehnen, Stefanie Susanne; Chemical Communications  (2023) –; doi:10.1039/D3CC03525E

data_7132203
_publ_section_title
;
 Selective and Benign Alkylation of Sulfido-Oxo Stannate Clusters with
 Propyl, Pentyl, or Hexyl Substituents
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D3CC03525E
_journal_year                    2023
_chemical_formula_moiety
'C9.50 H10.33 O4 S20 Sn10, C16 H27 N2, C14 H24 N2, C10 H10 N2'
_chemical_formula_sum            'C68.5 H97.34 N8 O4 S20 Sn10'
_chemical_formula_weight         2924.97
_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   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2023-08-29
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2023-10-05 deposited with the CCDC.	2023-10-09 downloaded from the CCDC.
;
_cell_angle_alpha                99.505(7)
_cell_angle_beta                 115.794(7)
_cell_angle_gamma                110.290(7)
_cell_formula_units_Z            2
_cell_length_a                   18.7606(17)
_cell_length_b                   20.0088(19)
_cell_length_c                   21.1091(19)
_cell_measurement_reflns_used    10994
_cell_measurement_temperature    100
_cell_measurement_theta_max      30.00
_cell_measurement_theta_min      2.57
_cell_volume                     6205.5(13)
_computing_cell_refinement       'X-Area Recipe 1.34.0.0 (STOE, 2019)'
_computing_data_collection       'X-Area Pilatus3_SV 1.31.154.0 (STOE, 2019)'
_computing_data_reduction
;
X-Area Integrate 1.77.0.0 (STOE, 2019)
X-Area LANA 1.77.1.0 (STOE, 2019)
;
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2016/6 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      100.00
_diffrn_detector                 Pilatus300K
_diffrn_detector_area_resol_mean 5.81
_diffrn_detector_type            'DECTRIS PILATUS 300K'
_diffrn_measured_fraction_theta_full 0.990
_diffrn_measured_fraction_theta_max 0.969
_diffrn_measurement_details      '4288 frames, detector distance = 60 mm'
_diffrn_measurement_device       'Eulerian 4-circle diffractometer'
_diffrn_measurement_device_type  'STOE STADIVARI'
_diffrn_measurement_method       'rotation method, \w scans'
_diffrn_radiation_monochromator  'Graded multilayer mirror'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54186
_diffrn_reflns_av_R_equivalents  0.0539
_diffrn_reflns_av_unetI/netI     0.0624
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.969
_diffrn_reflns_limit_h_max       19
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       25
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -26
_diffrn_reflns_number            125372
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.969
_diffrn_reflns_theta_full        67.686
_diffrn_reflns_theta_max         76.606
_diffrn_reflns_theta_min         2.823
_diffrn_source                   'GeniX 3D HF Cu'
_diffrn_source_target            Mo
_exptl_absorpt_coefficient_mu    19.152
_exptl_absorpt_correction_T_max  0.9123
_exptl_absorpt_correction_T_min  0.3189
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
STOE LANA, absorption correction by scaling of reflection intensities.
J. Koziskova, F. Hahn, J. Richter, J. Kozisek, "Comparison of different
absorption corrections on the model structure of tetrakis(\m~2~-acetato)-
diaqua-di-copper(II)", Acta Chimica Slovaca, vol. 9, no. 2, 2016, pp. 136 - 140.
Afterwards a spherical absorption correction was performed within STOE LANA.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.565
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       plate
_exptl_crystal_F_000             2833
_exptl_crystal_size_max          0.023
_exptl_crystal_size_mid          0.02
_exptl_crystal_size_min          0.01
_exptl_crystal_size_rad          0.0559
_refine_diff_density_max         0.965
_refine_diff_density_min         -0.798
_refine_diff_density_rms         0.110
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.842
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     902
_refine_ls_number_reflns         25303
_refine_ls_number_restraints     68
_refine_ls_restrained_S_all      0.844
_refine_ls_R_factor_all          0.0822
_refine_ls_R_factor_gt           0.0456
_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^)+(0.0705P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1230
_refine_ls_wR_factor_ref         0.1346
_reflns_Friedel_coverage         0.000
_reflns_number_gt                13000
_reflns_number_total             25303
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3cc03525e2.cif
_cod_data_source_block           ks009
_cod_original_cell_volume        6205.5(11)
_cod_original_formula_sum        'C68.50 H97.34 N8 O4 S20 Sn10'
_cod_database_code               7132203
_shelx_shelxl_version_number     2016/6
_shelx_estimated_absorpt_t_max   0.832
_shelx_estimated_absorpt_t_min   0.667
_olex2_refinement_description
;
'Main problem: Owing to (even) high(er) conformational freedom 
of the hexyl groups, the electron density of some of the C atoms 
is "smeared" in space in a way that makes it impossible to localize 
them on the difference Fourier map. For the same reason, some of 
the C atoms that can be localized still have a high displacement 
tendency, so they cannot be reasonably refined using anisotropic 
displacement parameters (without producing "npd", results), nor 
does modelling of disorder help in these cases to improve the R 
values or the reasonability of the model. Here, we outline what 
we did to optimize the crystallographic data and refinement:
X-ray measurement:
We tried several ways of setting up the X-ray diffraction measurement 
for crystals of compound 3:
1. STOE StadiVari diffractometer, Cu-K\^I+- radiation (lambda = 1.54186 A), 
immediate cooling from room temperature (r.t.) to 100 K upon mounting
the crystal.
2. STOE StadiVari diffractometer, Cu-K\^I+- radiation, slow cooling from 
r.t. to 100 K up-on mounting the crystal (10 K per hour)
3. Bruker Quest diffractometer, Mo-K\^I+- radiation (lambda = 0.71073 A) 
radiation, immediate cooling from r.t. to 100 K upon mounting the 
crystal.
--> Measurement no. 1 produced the best data set. 
Refinement:
Problem 1: We cannot refine all C atoms of the alkyl chains, although 
we tried the following variations:
1. Model disorder of the alkyl chains at once 
--> The refinement did not converge with all-connected C atoms in the 
alkyl chains (except for two of the hexyl chains).
2. Refine C atoms stepwise on single or disordered positions to "build 
up" the chains atom by atom 
--> Works for some of the atoms, but not for the whole alkyl chains.
Problem 2: We cannot reasonably calculate H atoms to ride on the highly 
mobile C atoms. This applies especially to C atoms in 4- or 5-position 
of the chain if the atoms in (5- and) 6-position are missing. We tried 
all variations of HFIX together with a diversity of further SHELX commands 
in Olex to cope with the "open" connectivity of the 5th C atoms, but none 
of these refinements converged into a reasonable set of C-H bonds. The 
data is limited owing to the intrinsic problem mentioned above.
Problem 3: Some of the C atoms have large displacement parameters, owing 
to the inherent mobility of the hexyl groups. However, they are still 
connected to the alkyl chains, so we consider this kind of modelling better 
than just deleting the respective atom from the atom list, which would also 
cause a correspondingly in-creased residual electron density peak. To cope 
with this problem, we needed to reduce the s.o.f. of some of the C atoms 
below 1.0. This makes full sense, as the partially occupied site is only 
one of several disorder positions of the respective atom, with the other 
ones being non-localizable in the smeared residual electron density.'
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, {H6A,H6B,H12} of C6, All C(H,H) groups
 At 1.5 times of:
  {H48A,H48B,H48C} of C48, {H33A,H33B,H33C} of C33, {H63A,H63B,H63C} of C63,
  {H57A,H57B,H57C} of C57, {H29A,H29B,H29C} of C29, {H67E,H67F,H67G} of C67,
  {H17A,H17B,H17C} of C17
2. Restrained distances
 C2-C1
 1.5 with sigma of 0.02
 C22A-C23
 1.5 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
C9: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
Uanis(C6) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C8) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(C9) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C30) \\sim Ueq, Uanis(N01L) \\sim Ueq, Uanis(C32) \\sim Ueq, Uanis(N01V)
\\sim Ueq, Uanis(C31) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(C11) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C1) \\sim Ueq: with sigma of 0.1 and sigma for terminal atoms of 0.2
Uanis(C22A) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
4. Others
 Fixed Sof: C4(0.5) H12(0.333333) H21A(0.5) H21B(0.5) C22A(0.5) H22A(0.5)
 H22B(0.5) C22B(0.5) H22C(0.5) H22D(0.5) H66A(0.5) H66B(0.5) C67A(0.5)
 H67A(0.5) H67B(0.5) C67B(0.5) H67C(0.5) H67D(0.5) C68A(0.5) C68B(0.5)
5.a Secondary CH2 refined with riding coordinates:
 C1(H1A,H1B), C2(H2A,H2B), C5(H5A,H5B), C6(H6A,H6B), C12(H12A,H12B), C18(H18A,
 H18B), C19(H19A,H19B), C20(H20A,H20B), C21(H21A,H21B), C22A(H22A,H22B),
 C22B(H22C,H22D), C24(H24A,H24B), C25(H25A,H25B), C26(H26A,H26B), C27(H27A,
 H27B), C28(H28A,H28B), C22(H22E,H22F), C59(H59A,H59B), C60(H60A,H60B),
 C62(H62A,H62B), C64(H64A,H64B), C65(H65A,H65B), C66(H66A,H66B), C67A(H67A,
 H67B), C67B(H67C,H67D), C36(H36A,H36B), C37(H37A,H37B), C38(H38A,H38B),
 C43(H43A,H43B), C44(H44A,H44B), C45(H45A,H45B), C46(H46A,H46B), C47(H47A,H47B),
  C49(H49A,H49B), C50(H50A,H50B), C51(H51A,H51B), C52(H52A,H52B)
5.b Aromatic/amide H refined with riding coordinates:
 C14(H14), C15(H15), C54(H54), C55(H55), C58(H58), C31(H31), C40(H40), C41(H41)
5.c Idealised Me refined as rotating group:
 C17(H17A,H17B,H17C), C29(H29A,H29B,H29C), C57(H57A,H57B,H57C), C63(H63A,H63B,
 H63C), C33(H33A,H33B,H33C), C48(H48A,H48B,H48C), C67(H67E,H67F,H67G)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 83 electrons were 
found in a volume of 1007\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
1[C5H12] per Asymmetric Unit 
which account for 84 electrons 
per unit cell.
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              82743
_shelx_hkl_checksum              57797
_shelx_fab_checksum              33198
_olex2_submission_special_instructions 'No special instructions were received'