Site-specific sulfur-for-metal replacement in silver nanocluster
Wu, Ya-Ge; Huang, Jia-Hong; Zhang, Chong; Dong, Xi-Yan; Guo, Xiang-Kun; Wu, Weina; Zang, Shuang-Quan; Chemical Communications  (2022) –; doi:10.1039/D2CC00794K

data_7130161
_publ_section_title
;
 Site-specific sulfur-for-metal replacement in silver nanocluster
;
_journal_name_full               'Chemical Communications'
_journal_paper_doi               10.1039/D2CC00794K
_journal_year                    2022
_chemical_formula_moiety
'C194 H184 Ag34.99 F30 N4 O24 P2 Pd S18, 2(H2 O), 8(C3 H7 N O), 2(C3 N O)'
_chemical_formula_sum            'C224 H258 Ag35 F30 N14 O36 P2 Pd S18'
_chemical_formula_weight         8813.30
_space_group_crystal_system      monoclinic
_space_group_IT_number           15
_space_group_name_Hall           '-C 2yc'
_space_group_name_H-M_alt        'C 1 2/c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     iterative
_audit_creation_date             2022-05-27
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_audit_update_record
;
2022-05-28 deposited with the CCDC.	2022-05-31 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 98.3850(10)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   41.1371(3)
_cell_length_b                   30.7832(2)
_cell_length_c                   21.93730(10)
_cell_measurement_reflns_used    39869
_cell_measurement_temperature    199.99(10)
_cell_measurement_theta_max      73.8190
_cell_measurement_theta_min      3.0330
_cell_volume                     27482.9(3)
_computing_cell_refinement       'CrysAlisPro 1.171.39.27b (Rigaku OD, 2015)'
_computing_data_collection       'CrysAlisPro 1.171.39.27b (Rigaku OD, 2015)'
_computing_data_reduction        'CrysAlisPro 1.171.39.27b (Rigaku OD, 2015)'
_computing_molecular_graphics    'Olex2 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 (Dolomanov et al., 2009)'
_computing_structure_refinement  'ShelXL (Sheldrick, 2015)'
_computing_structure_solution    'olex2.solve (Bourhis et al., 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      199.99(10)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.967
_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    -28.00  23.00   0.50    1.34    --    0.00 -57.00  90.00  102
  2  \w    -18.00  27.00   0.50    1.34    --    0.00  38.00 -30.00   90
  3  \w     48.00  75.00   0.50    1.34    --    0.00  36.00 132.00   54
  4  \w     47.00  89.00   0.50    1.34    --    0.00  38.00 -30.00   84
  5  \w    -66.00 -37.00   0.50    1.34    --    0.00 -57.00  90.00   58
  6  \w    129.00 177.00   0.50    5.35    --   95.20  77.00-150.00   96
  7  \w      8.00 114.00   0.50    5.35    --   95.20 -30.00-180.00  212
  8  \w     85.00 185.00   0.50    5.35    --   95.20  30.00 150.00  200
  9  \w      7.00  90.00   0.50    5.35    --   95.20 -15.00   0.00  166
 10  \w     70.00 114.00   0.50    5.35    --   95.20 -45.00-150.00   88
 11  \w     31.00  94.00   0.50    5.35    --   95.20 -45.00-180.00  126
 12  \w      8.00  34.00   0.50    5.35    --   95.20 -61.00  30.00   52
 13  \w     11.00 118.00   0.50    5.35    --   95.20 -61.00-180.00  214
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB AFC12 (RINC): Kappa single'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0302556000
_diffrn_orient_matrix_UB_12      0.0136185000
_diffrn_orient_matrix_UB_13      0.0458853000
_diffrn_orient_matrix_UB_21      -0.0227134000
_diffrn_orient_matrix_UB_22      0.0187437000
_diffrn_orient_matrix_UB_23      0.0433499000
_diffrn_orient_matrix_UB_31      -0.0003480000
_diffrn_orient_matrix_UB_32      -0.0443987000
_diffrn_orient_matrix_UB_33      0.0324481000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0636
_diffrn_reflns_av_unetI/netI     0.0545
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.967
_diffrn_reflns_limit_h_max       51
_diffrn_reflns_limit_h_min       -46
_diffrn_reflns_limit_k_max       23
_diffrn_reflns_limit_k_min       -37
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            75567
_diffrn_reflns_point_group_measured_fraction_full 0.997
_diffrn_reflns_point_group_measured_fraction_max 0.967
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         74.145
_diffrn_reflns_theta_min         2.171
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    22.094
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.09786
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.27b (Rigaku Oxford Diffraction, 2015)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            black
_exptl_crystal_colour_primary    black
_exptl_crystal_density_diffrn    2.130
_exptl_crystal_description       block
_exptl_crystal_F_000             17068
_exptl_crystal_size_max          0.3
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.2
_refine_diff_density_max         2.530
_refine_diff_density_min         -3.272
_refine_diff_density_rms         0.550
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.060
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1687
_refine_ls_number_reflns         27045
_refine_ls_number_restraints     446
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.0906
_refine_ls_R_factor_gt           0.0722
_refine_ls_shift/su_max          0.006
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.1101P)^2^+615.2066P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1877
_refine_ls_wR_factor_ref         0.2066
_reflns_Friedel_coverage         0.000
_reflns_number_gt                21320
_reflns_number_total             27045
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d2cc00794k2.cif
_cod_data_source_block           pd@ag35
_cod_database_code               7130161
_shelx_shelxl_version_number     2016/6
_chemical_oxdiff_formula         'C H O N S Cu'
_chemical_oxdiff_usercomment     ' '
_shelx_estimated_absorpt_t_max   0.096
_shelx_estimated_absorpt_t_min   0.058
_reflns_odcompleteness_completeness 99.66
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     66.97
_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, All O(H,H) groups
2. Restrained distances
 C66-C65
 1.51 with sigma of 0.02
 N7-C119 = N7-C117 = N7-C114
 1.5 with sigma of 0.02
 C116-N7
 1.5 with sigma of 0.02
 C72-C71
 1.5 with sigma of 0.02
 O6-C71
 1.2 with sigma of 0.02
 F10-C72 = F11-C72
 1.35 with sigma of 0.01
 O16-C110
 1.2 with sigma of 0.02
 O18-C118 = O17-C113
 1.2 with sigma of 0.02
 F2-F1 \\sim F2-F3 \\sim F1-F3
 with sigma of 0.02
 F3-C66 \\sim F1-C66 \\sim F2-C66
 with sigma of 0.02
 F8A-C70 \\sim F8-C70 \\sim F9-C70 \\sim F9A-C70 \\sim F7-C70 \\sim F7A-C70
 with sigma of 0.02
3. Restrained planarity
 F1, F1_$1, F2, F2_$1, F3, F3_$1
 with sigma of 0.1
4. Rigid bond restraints
 O13, N3, C101, C102, C103
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C37, C38, C39, C40, C41, C42
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 F7, C70, F8A, F8, F7A, F9, F9A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
F15 \\sim F16 \\sim F17: within 2A with sigma of 0.02 and sigma for terminal
atoms of 0.04
C36 \\sim C37 \\sim C38 \\sim C39 \\sim C40 \\sim C41 \\sim C42: within 2A with
sigma of 0.02 and sigma for terminal atoms of 0.04
Uanis(C56) \\sim Ueq, Uanis(C51) \\sim Ueq, Uanis(C52) \\sim Ueq, Uanis(C53)
\\sim Ueq, Uanis(C54) \\sim Ueq, Uanis(C55) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(C53) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(F8) \\sim Ueq, Uanis(F7) \\sim Ueq, Uanis(F9) \\sim Ueq, Uanis(F15) \\sim
Ueq, Uanis(F16) \\sim Ueq, Uanis(F8) \\sim Ueq, Uanis(F7) \\sim Ueq, Uanis(F9)
\\sim Ueq, Uanis(F13) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(C62) \\sim Ueq, Uanis(C61) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C61) \\sim Ueq, Uanis(C62) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C100) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(F2) \\sim Ueq, Uanis(F3) \\sim Ueq, Uanis(C66) \\sim Ueq, Uanis(F1) \\sim
Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C72) \\sim Ueq, Uanis(C71) \\sim Ueq, Uanis(O6) \\sim Ueq, Uanis(F10)
\\sim Ueq, Uanis(F11) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(F5) \\sim Ueq, Uanis(F13) \\sim Ueq, Uanis(F15) \\sim Ueq, Uanis(F9)
\\sim Ueq, Uanis(C63) \\sim Ueq, Uanis(C109) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(C102) \\sim Ueq, Uanis(O13) \\sim Ueq, Uanis(C101) \\sim Ueq, Uanis(N3)
\\sim Ueq, Uanis(C103) \\sim Ueq, Uanis(C111) \\sim Ueq, Uanis(N6) \\sim Ueq,
Uanis(C110) \\sim Ueq, Uanis(C112) \\sim Ueq, Uanis(O16) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(O14) \\sim Ueq, Uanis(N4) \\sim Ueq, Uanis(C105) \\sim Ueq, Uanis(C104)
\\sim Ueq, Uanis(C106) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(C38) \\sim Ueq, Uanis(C40) \\sim Ueq, Uanis(C41) \\sim Ueq, Uanis(C42)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(F9) \\sim Ueq, Uanis(F13) \\sim Ueq, Uanis(F15) \\sim Ueq: with sigma of
0.01 and sigma for terminal atoms of 0.02
Uanis(F8A) \\sim Ueq, Uanis(F9A) \\sim Ueq, Uanis(F7A) \\sim Ueq, Uanis(F9)
\\sim Ueq, Uanis(C70) \\sim Ueq, Uanis(F7) \\sim Ueq, Uanis(F8) \\sim Ueq: with
sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(F8A) \\sim Ueq, Uanis(C70) \\sim Ueq, Uanis(F9) \\sim Ueq, Uanis(F9A)
\\sim Ueq, Uanis(F7A) \\sim Ueq, Uanis(F7) \\sim Ueq, Uanis(F8) \\sim Ueq: with
sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(Ag0A) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(Ag17) \\sim Ueq, Uanis(Ag1) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(Ag20) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
6. Others
 Sof(F7A)=Sof(F8A)=Sof(F9A)=1-FVAR(1)
 Sof(F7)=Sof(F8)=Sof(F9)=FVAR(1)
 Sof(Ag1)=1-FVAR(2)
 Sof(Ag17)=FVAR(2)
 Sof(O18)=Sof(C114)=Sof(C118)=Sof(C119)=1-FVAR(3)
 Sof(O17)=Sof(C113)=Sof(C116)=Sof(C117)=FVAR(3)
 Fixed Sof: F1(0.5) F2(0.5) F3(0.5) F10(0.5) C72(0.5)
7.a Riding coordinates:
 O1W(H1Wa,H1Wb)
7.b Secondary CH2 refined with riding coordinates:
 C1(H1a,H1b), C8(H8a,H8b), C15(H15a,H15b), C22(H22a,H22b), C29(H29a,H29b),
 C36(H36a,H36b), C43(H43a,H43b), C50(H50a,H50b), C57(H57a,H57b)
7.c Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5), C6(H6), C7(H7), C10(H10), C11(H11), C12(H12),
 C13(H13), C14(H14), C17(H17), C18(H18), C19(H19), C20(H20), C21(H21), C23(H23),
  C25(H25), C26(H26), C27(H27), C28(H28), C31(H31), C32(H32), C33(H33),
 C34(H34), C35(H35), C38(H38), C39(H39), C40(H40), C41(H41), C42(H42), C45(H45),
  C46(H46), C47(H47), C48(H48), C49(H49), C56(H56), C55(H55), C54(H54),
 C53(H53), C52(H52), C60(H60), C61(H61), C62(H62), C63(H63), C64(H64), C78(H78),
  C79(H79), C80(H80), C81(H81), C82(H82), C84(H84), C85(H85), C86(H86),
 C87(H87), C88(H88), C90(H90), C91(H91), C92(H92), C93(H93), C94(H94), C95(H95),
  C98(H98), C101(H101), C104(H104), C107(H107), C110(H110)
7.d Fitted hexagon refined as free rotating group:
 C56(C55,C54,C53,C52,C51)
7.e Idealised Me refined as rotating group:
 C96(H96a,H96b,H96c), C97(H97a,H97b,H97c), C99(H99a,H99b,H99c), C100(H10a,H10b,
 H10c), C102(H10d,H10e,H10f), C103(H10g,H10h,H10i), C105(H10j,H10k,H10l),
 C106(H10m,H10n,H10o), C108(H10p,H10q,H10r), C109(H10s,H10t,H10u), C111(H11a,
 H11b,H11c), C112(H11d,H11e,H11f)
;
_shelx_res_checksum              81775
_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
;
_oxdiff_exptl_absorpt_empirical_full_max 5.777
_oxdiff_exptl_absorpt_empirical_full_min 0.410