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_7132204
_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
'C8 H8 O4 S20 Sn10, C12 H18 N2, C11 H13 N2, C9.46 H12.24 N2, C5.8063 H4.81608 N2'
_chemical_formula_sum            'C49.67 H56.06 N8 O4 S20 Sn10'
_chemical_formula_weight         2657.16
_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             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                99.744(2)
_cell_angle_beta                 112.258(2)
_cell_angle_gamma                110.568(2)
_cell_formula_units_Z            2
_cell_length_a                   19.5954(4)
_cell_length_b                   19.2861(5)
_cell_length_c                   19.7915(5)
_cell_measurement_reflns_used    15936
_cell_measurement_temperature    100
_cell_measurement_theta_max      30.03
_cell_measurement_theta_min      2.71
_cell_volume                     6073.7(3)
_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 X-Red32 1.65.0.0 (STOE, 2018)
;
_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  (Sheldrick, 2015)'
_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 0.990
_diffrn_measurement_details
;
 5293 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  0.0604
_diffrn_reflns_av_unetI/netI     0.0469
_diffrn_reflns_Laue_measured_fraction_full 0.990
_diffrn_reflns_Laue_measured_fraction_max 0.990
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            135107
_diffrn_reflns_point_group_measured_fraction_full 0.990
_diffrn_reflns_point_group_measured_fraction_max 0.990
_diffrn_reflns_theta_full        67.500
_diffrn_reflns_theta_max         67.500
_diffrn_reflns_theta_min         2.793
_diffrn_source                   'GeniX 3D HF Cu'
_diffrn_source_target            Mo
_exptl_absorpt_coefficient_mu    19.510
_exptl_absorpt_correction_T_max  0.7942
_exptl_absorpt_correction_T_min  0.0868
_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.
;
_exptl_crystal_colour            'clear colourless'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.453
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       plate
_exptl_crystal_F_000             2524
_exptl_crystal_size_max          0.24
_exptl_crystal_size_mid          0.18
_exptl_crystal_size_min          0.01
_exptl_crystal_size_rad          0.0541
_refine_diff_density_max         0.805
_refine_diff_density_min         -0.863
_refine_diff_density_rms         0.102
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   0.824
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     741
_refine_ls_number_reflns         21685
_refine_ls_number_restraints     233
_refine_ls_restrained_S_all      0.826
_refine_ls_R_factor_all          0.0938
_refine_ls_R_factor_gt           0.0524
_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^)+(0.1007P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1507
_refine_ls_wR_factor_ref         0.1632
_reflns_Friedel_coverage         0.000
_reflns_number_gt                10196
_reflns_number_total             21685
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d3cc03525e2.cif
_cod_data_source_block           bp149b
_cod_database_code               7132204
_shelx_shelxl_version_number     2016/6
_shelx_estimated_absorpt_t_max   0.829
_shelx_estimated_absorpt_t_min   0.089
_olex2_refinement_description
;
'Main problem: Owing to high conformational freedom of the pentyl 
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 2:
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
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-position of the chain if the 
atoms in 5-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: In one of the imidazole rings, N atoms cannot be refined using 
anisotropic displacement parameters (hence, produces npd results), owing to the 
uncertainty of the C atoms attached. None of the known SHELX commands helps, so we 
decided to refine these atoms using isotropic displacement parameters, which is 
often found in the literature (in many cases also for entire organic groups).
Problem 4: Some of the C atoms have large displacement parameters, owing to the 
inherent mobility of the pentyl 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 
increased residual electron density peak.'
1. Restrained distances
 C6_6-C7_6 = C7_6-C8_6 = C8_6-C9_6 = C9_6-C10_6
 1.52 with sigma of 0.02
 C6_7-C7_7 = C7_7-C8_7 = C8_7-C9_7 = C9_7-C10_7
 1.52 with sigma of 0.02
 C6_8-C7_8 = C7_8-C8_8 = C8_8-C9_8 = C9_8-C10_8
 1.52 with sigma of 0.02
 C6_9-C7_9
 1.52 with sigma of 0.02
 C6_10-C7_10 = C7_10-C8_10 = C8_10-C9_10 = C9_10-C10_10
 1.52 with sigma of 0.02
 C4_11-C5_11
 1.52 with sigma of 0.02
 C6_6-C8_6 = C7_6-C9_6 = C8_6-C10_6
 2.54 with sigma of 0.04
 C6_7-C8_7 = C7_7-C9_7 = C8_7-C10_7
 2.54 with sigma of 0.04
 C6_8-C8_8 = C7_8-C9_8 = C8_8-C10_8
 2.54 with sigma of 0.04
 C6_10-C8_10 = C7_10-C9_10 = C8_10-C10_10
 2.54 with sigma of 0.04
2. Restrained planarity
 with sigma of 0.1
 N1A, N2A, C1A, C2A, C3A
 with sigma of 0.1
3. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 1A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 1A
Uanis(N2_2) \\sim Ueq: with sigma of 0.008 and sigma for terminal atoms of 0.016
Uanis(C7_10) \\sim Ueq, Uanis(C8_10) \\sim Ueq, Uanis(C9_10) \\sim Ueq: with
sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C7_10) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of
0.002
4. Rigid body (RIGU) restrains
 N1_1, N2_1, C1_1, C2_1, C3_1
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N1_2, N2_2, C1_2, C2_2, C3_2
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 N1_4, N2_4, C1_4, C2_4, C3_4
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C6_5, C7_5, C8_5, C9_5, C10_5
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C6_6, C7_6, C8_6, C9_6, C10_6
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C6_7, C7_7, C8_7, C9_7, C10_7
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C6_8, C7_8, C8_8, C9_8, C10_8
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C6_9, C7_9
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C4_11, C5_11
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C6_10, C7_10, C8_10, C9_10, C10_10
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(H1)=1-FVAR(1)
 Sof(C6)=Sof(H6A)=Sof(H6B)=Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(C8)=Sof(H8A)=Sof(H8B)=
 Sof(C9)=Sof(H9A)=Sof(H9B)=Sof(C10)=FVAR(1)
 Sof(C1A)=Sof(C2A)=Sof(C3A)=1-FVAR(2)
 Sof(C6)=Sof(H6A)=Sof(H6B)=Sof(C7)=Sof(H7A)=Sof(H7B)=Sof(C8)=Sof(H8A)=Sof(H8B)=
 Sof(C9)=Sof(H9A)=Sof(H9B)=Sof(C10)=FVAR(2)
6.a Secondary CH2 refined with riding coordinates:
 C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B), C6(H6A,H6B), C7(H7A,H7B),
 C8(H8A,H8B), C9(H9A,H9B), C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B),
 C6(H6A,H6B), C7(H7A,H7B), C8(H8A,H8B), C9(H9A,H9B), C6(H6A,H6B), C7(H7A,H7B),
 C8(H8A,H8B), C9(H9A,H9B), C10(H10A,H10B)
6.b Aromatic/amide H refined with riding coordinates:
 C2(H2), C3(H3), N1(H1), C2(H2), C3(H3), C2(H2), C3(H3)
6.c Idealised Me refined as rotating group:
 C01M(H01D,H01E,H01F), C01B(H01A,H01B,H01C), C01O(H01G,H01H,H01I), C10(H10A,
 H10B,H10C)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 297 electrons were 
found in a volume of 1972\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
3[C6H14] per Asymmetric Unit 
which account for 300 electrons 
per unit cell.
;
_shelx_res_checksum              94442
_shelx_hkl_checksum              15327
_shelx_fab_checksum              87308
_olex2_submission_special_instructions 'No special instructions were received'