Tunable structural rearrangement in Cu cluster assemblies through linker and solvent alterations.
Das, Saikat; Sakai, Jin; Nakatani, Riki; Kondo, Ayumu; Tomioka, Rina; Das, Subhabrata; Takahashi, Shuntaro; Kawawaki, Tokuhisa; Biswas, Sourav; Negishi, Yuichi; Chemical science 16 (2025) 2600–2608; doi:10.1039/d4sc07730j

data_1573735
_publ_section_title
;
 Tunable structural rearrangement in Cu cluster assemblies through linker
 and solvent alterations.
;
_journal_issue                   6
_journal_name_full               'Chemical science'
_journal_page_first              2600
_journal_page_last               2608
_journal_paper_doi               10.1039/d4sc07730j
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety
'C59 H66 Cu6 F6 N5 O3 S4, C H2 Cl2, 1[CF3COO], 2[C4H9NO]'
_chemical_formula_sum            'C70 H86 Cl2 Cu6 F9 N7 O7 S4'
_chemical_formula_weight         1888.83
_space_group_crystal_system      orthorhombic
_space_group_IT_number           62
_space_group_name_Hall           '-P 2ac 2n'
_space_group_name_H-M_alt        'P n m a'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2024-10-02
_audit_creation_method
;
Olex2 1.5
(compiled 2023.08.24 svn.re1ec1418 for OlexSys, GUI svn.r6817)
;
_audit_update_record
;
2024-11-05 deposited with the CCDC.	2025-01-22 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   36.1356(2)
_cell_length_b                   16.4719(2)
_cell_length_c                   28.0985(3)
_cell_measurement_reflns_used    14051
_cell_measurement_temperature    293(2)
_cell_measurement_theta_max      69.2450
_cell_measurement_theta_min      1.9850
_cell_volume                     16724.8(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.107a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 43.107a 64-bit (release 07-02-2024))'
_computing_data_reduction        'CrysAlisPro 1.171.43.107a (Rigaku OD, 2024)'
_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      293(2)
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.994
_diffrn_measured_fraction_theta_max 0.973
_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   -144.00-103.00   0.50    3.37    --  -54.83-107.00 152.00   82
  2  \w   -142.00 -82.00   0.50    3.37    --  -54.83-112.00-111.00  120
  3  \w    -25.00  28.00   0.50    3.37    --  -54.83  23.00 144.00  106
  4  \w     16.00  72.00   0.50    3.37    --   54.83-112.00-111.00  112
  5  \w   -154.00-120.00   0.50    3.37    -- -104.00 -23.00 -20.00   68
  6  \w   -149.00-110.00   0.50    3.37    -- -104.00-112.00-111.00   78
  7  \w     23.00  96.00   0.50    3.37    --  109.67-112.00-111.00  146
  8  \w     20.00 106.00   0.50    3.37    --  109.67-107.00 152.00  172
  9  \w     -8.00  45.00   0.50    0.84    --    0.00 -99.00   0.00  106
 10  \w    -93.00 -40.00   0.50    0.84    --    0.00 178.00 -60.00  106
 11  \w    -23.00   9.00   0.50    3.37    --  -54.83  15.00-150.00   64
 12  \w     -5.00  21.00   0.50    3.37    --  -54.83  15.00 -90.00   52
 13  \w    -48.00 -22.00   0.50    3.37    -- -104.00  50.00   0.00   52
 14  \w     25.00  55.00   0.50    3.37    --  109.67 -50.00  30.00   60
 15  \w     21.00  47.00   0.50    3.37    --  109.67 -37.00 120.00   52
 16  \w     25.00  71.00   0.50    3.37    --  109.67 -63.00 150.00   92
 17  \w     25.00  50.00   0.50    3.37    --  109.67 -50.00-150.00   50
 18  \w     20.00  48.00   0.50    3.37    --  109.67 -37.00  60.00   56
 19  \w     20.00  46.00   0.50    3.37    --  109.67 -37.00   0.00   52
 20  \w     22.00  48.00   0.50    3.37    --  109.67 -37.00 -30.00   52
 21  \w     20.00  45.00   0.50    3.37    --  109.67 -37.00-150.00   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0322
_diffrn_reflns_av_unetI/netI     0.0332
_diffrn_reflns_Laue_measured_fraction_full 0.994
_diffrn_reflns_Laue_measured_fraction_max 0.973
_diffrn_reflns_limit_h_max       16
_diffrn_reflns_limit_h_min       -44
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       34
_diffrn_reflns_limit_l_min       -33
_diffrn_reflns_number            51292
_diffrn_reflns_point_group_measured_fraction_full 0.994
_diffrn_reflns_point_group_measured_fraction_max 0.973
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         71.217
_diffrn_reflns_theta_min         3.342
_exptl_absorpt_coefficient_mu    3.796
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.62414
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.107a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            Yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.500
_exptl_crystal_description       block
_exptl_crystal_F_000             7712
_exptl_crystal_size_max          0.15
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.15
_refine_diff_density_max         2.483
_refine_diff_density_min         -1.483
_refine_diff_density_rms         0.147
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.055
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     771
_refine_ls_number_reflns         16378
_refine_ls_number_restraints     964
_refine_ls_restrained_S_all      1.083
_refine_ls_R_factor_all          0.1215
_refine_ls_R_factor_gt           0.1032
_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^)+(0.1822P)^2^+79.5385P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.3038
_refine_ls_wR_factor_ref         0.3217
_reflns_Friedel_coverage         0.000
_reflns_number_gt                12404
_reflns_number_total             16378
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc07730j2.cif
_cod_data_source_block           Cu6-dpb
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_exptl_crystal_colour_primary' value 'Yellow' was changed
to 'yellow' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/RSC/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 8170 2020-07-09 18:12:32Z antanas 

 Adding full bibliography for 1573735--1573741.cif.
;
_cod_database_code               1573735
_shelx_shelxl_version_number     2019/2
_shelx_estimated_absorpt_t_max   0.600
_shelx_estimated_absorpt_t_min   0.600
_olex2_refinement_description
;
1. 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
2. Restrained distances
 N5-C2_$1 = C65-C2 = C65_$1-C29 = C65-C29 = C65-C2 = N5-C2
 1.39 with sigma of 0.01
 C2_$1-C29
 2.39 with sigma of 0.01
 C65-C65_$1
 2.39 with sigma of 0.01
 C29-C2
 2.39 with sigma of 0.01
 C2-C2_$1
 2.39 with sigma of 0.01
 C65-N5
 2.39 with sigma of 0.01
 N5-C65_$1
 2.39 with sigma of 0.01
 C67-C7 = C17-C67 = C17-C27 = C17_$1-C27 = C17-C67 = C67_$1-C7
 1.39 with sigma of 0.01
 C7-C17
 2.39 with sigma of 0.01
 C67-C27
 2.39 with sigma of 0.01
 C17-C17_$1
 2.39 with sigma of 0.01
 C27-C67_$1
 2.39 with sigma of 0.01
 C17_$1-C7
 2.39 with sigma of 0.01
 C67_$1-C67
 2.39 with sigma of 0.01
 Cu7-O5
 2.4 with sigma of 0.02
 F2-C35 = F3-C35
 1.34 with sigma of 0.02
 F5-C35
 1.33 with sigma of 0.02
 O3-C69
 1.25 with sigma of 0.02
 O2-C69
 1.24 with sigma of 0.02
 C69-C35
 1.55 with sigma of 0.02
 C7-C29
 1.53 with sigma of 0.01
 F2-F5 = F5-F3
 2.16 with sigma of 0.04
 F2-F3
 2.15 with sigma of 0.04
 F2-C69
 2.37 with sigma of 0.04
 F5-C69
 2.42 with sigma of 0.04
 F3-C69
 2.39 with sigma of 0.04
 O3-O2
 2.25 with sigma of 0.04
 O3-C35
 2.38 with sigma of 0.04
 O2-C35
 2.35 with sigma of 0.04
 C35-F2 \\sim C35-F5 \\sim C35-F3
 with sigma of 0.02
 C69-F2 \\sim C69-F5 \\sim C69-F3
 with sigma of 0.04
 F2-F5 \\sim F5-F3 \\sim F3-F2
 with sigma of 0.04
 C69-O2 \\sim C69-O3
 with sigma of 0.02
3. Restrained planarity
 N5, C2, C2_$1, C29, C65_$1, C65
 with sigma of 0.1
 C7, C17, C17_$1, C27, C67_$1, C67
 with sigma of 0.1
 O2, O3, C35, C69
 with sigma of 0.1
4. Rigid bond restraints
 All non-hydrogen atoms
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
All non-hydrogen atoms have similar U: within 2A with sigma of 0.01 and sigma
for terminal atoms of 0.02 within 2A
F2 \\sim F3 \\sim F5 \\sim O2 \\sim O3 \\sim C35 \\sim C69: within 2A with
sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
Uanis(C27) \\sim Ueq, Uanis(C17) \\sim Ueq, Uanis(C67) \\sim Ueq, Uanis(C7)
\\sim Ueq, Uanis(C29) \\sim Ueq, Uanis(C65) \\sim Ueq, Uanis(C2) \\sim Ueq:
with sigma of 0.01 and sigma for terminal atoms of 0.02
6. Rigid body (RIGU) restrains
 F2, F3, F5, O2, O3, C35, C69
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
7. Others
 Fixed Sof: H5A(0.5) H5B(0.5) H5C(0.5) H11A(0.5) H11B(0.5) H11C(0.5) H33A(0.5)
 H33B(0.5) H33C(0.5) H58A(0.5) H58B(0.5) H58C(0.5)
8.a Riding coordinates:
 C63(H63A,H63B,H63C)
8.b Secondary CH2 refined with riding coordinates:
 C61(H61A,H61B)
8.c Me refined with riding coordinates:
 C33(H33A,H33B,H33C), C58(H58A,H58B,H58C)
8.d Aromatic/amide H refined with riding coordinates:
 C1(H1), C4(H4), C8(H8), C10(H10), C32(H32), C34(H34), C38(H38), C40(H40),
 C12(H12), C14(H14), C18(H18), C20(H20), C22(H22), C24(H24), C28(H28), C30(H30),
  C2(H2), C13(H13), C17(H17), C25(H25), C44(H44), C46(H46), C50(H50), C52(H52),
 C47(H47), C51(H51), C65(H65), C67(H67), C70(H70), C71(H71), C37(H37), C19(H19)
8.e Fitted hexagon refined as free rotating group:
 N1(C1,C4,C6,C8,C10), N3(C32,C34,C36,C38,C40), N4(C12,C14,C16,C18,C20), N6(C22,
 C24,C26,C28,C30), C42(C44,C46,C48,C50,C52), C68(C70,C71,C9,C37,C19)
8.f Idealised Me refined as rotating group:
 C5(H5A,H5B,H5C), C11(H11A,H11B,H11C), C31(H31A,H31B,H31C), C39(H39A,H39B,
 H39C), C43(H43A,H43B,H43C), C49(H49A,H49B,H49C), C53(H53A,H53B,H53C), C55(H55A,
 H55B,H55C), C57(H57A,H57B,H57C), C59(H59A,H59B,H59C), C60(H60A,H60B,H60C)
;
_smtbx_masks_special_details
;
A solvent mask was calculated and 1136 electrons were 
found in a volume of 4932\%A^3^ in 1 void per unit cell. 
This is consistent with the presence of 
3[C4H9NO] per formula unit 
which account for 1152 electrons 
per unit cell.
;
_shelx_res_checksum              16022
_shelx_fab_checksum              95152
_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
;