Surface defects in atom-precise copper nanoclusters and their different catalytic efficiencies.
Ge, Xin; Chen, Ruihang; Deng, Hongwen; Fang, Lei; Pan, Kunyi; Shan, Bochen; Gu, Bangde; Sun, Xin; Zheng, Yun; Teo, Boon K.; Sun, Cunfa; Nanoscale 17 (2025) 25490–25494; doi:10.1039/d5nr03643g

data_1576128
_publ_section_title
;
 Surface defects in atom-precise copper nanoclusters and their different
 catalytic efficiencies.
;
_journal_issue                   44
_journal_name_full               Nanoscale
_journal_page_first              25490
_journal_page_last               25494
_journal_paper_doi               10.1039/d5nr03643g
_journal_volume                  17
_journal_year                    2025
_chemical_formula_moiety         'C207 H222 Cu20 P3 S19'
_chemical_formula_sum            'C207 H222 Cu20 P3 S19'
_chemical_formula_weight         4682.68
_space_group_crystal_system      trigonal
_space_group_IT_number           146
_space_group_name_Hall           'R 3'
_space_group_name_H-M_alt        'R 3 :H'
_atom_sites_solution_hydrogens   geom
_audit_block_doi                 10.5517/ccdc.csd.cc2krvnv
_audit_creation_date             2024-08-08
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2024-08-08 deposited with the CCDC.	2025-10-22 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                120
_cell_formula_units_Z            3
_cell_length_a                   33.2347(3)
_cell_length_b                   33.2347(3)
_cell_length_c                   17.02607(19)
_cell_measurement_reflns_used    54025
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      76.7580
_cell_measurement_theta_min      3.9920
_cell_volume                     16286.5(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.92a (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 43.92a 64-bit (release 05-10-2023))'
_computing_data_reduction        'CrysAlisPro 1.171.43.92a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2013/2 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.941
_diffrn_measured_fraction_theta_max 1.000
_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    -58.00 -33.00   0.50    0.24    --  -99.00  57.00 -60.00   50
  2  \w    -63.00 -34.00   0.50    0.24    --  -99.00  57.00   0.00   58
  3  \w    -61.00 -36.00   0.50    0.24    --  -99.00  55.00  28.00   50
  4  \w    -57.00 -30.00   0.50    0.24    --  -99.00  54.00  57.00   54
  5  \w     -3.00  27.00   0.50    0.06    --  -47.84  19.00 -60.00   60
  6  \w    -75.00 -49.00   0.50    0.24    --  -99.00  65.00  82.00   52
  7  \w   -119.00 -54.00   0.50    0.06    --  -47.84 -67.00  86.00  130
  8  \w     36.00  65.00   0.50    0.24    --  105.22 -57.00-120.00   58
  9  \w     36.00  94.00   0.50    0.24    --  105.22-107.00-152.00  116
 10  \w     33.00  58.00   0.50    0.24    --  105.22 -57.00 -90.00   50
 11  \w     -9.00  28.00   0.50    0.06    --   47.84 -19.00  90.00   74
 12  \w     84.00 176.00   0.50    0.24    --  105.22  77.00   0.00  184
 13  \w     92.00 167.00   0.50    0.24    --  105.22  54.00  57.00  150
 14  \w     86.00 128.00   0.50    0.24    --  105.22  81.00  95.00   84
 15  \w    -22.00  21.00   0.50    0.06    --  -47.84  19.00-120.00   86
 16  \w    -21.00  26.00   0.50    0.06    --  -47.84  19.00   0.00   94
 17  \w    -22.00   4.00   0.50    0.06    --   47.84 -19.00-180.00   52
 18  \w     20.00  71.00   0.50    0.06    --   47.84-125.00 -60.00  102
 19  \w     20.00  81.00   0.50    0.06    --   47.84-125.00 120.00  122
 20  \w    -11.00  39.00   0.50    0.06    --   47.84 -38.00-150.00  100
 21  \w    -18.00  79.00   0.50    0.06    --   47.84 -99.00-180.00  194
 22  \w   -106.00 -78.00   0.50    0.24    --  -99.00 -77.00 -30.00   56
 23  \w   -128.00 -95.00   0.50    0.24    --  -99.00 -57.00 -60.00   66
 24  \w    -53.00 -27.00   0.50    0.24    --  -99.00  57.00 -90.00   52
 25  \w   -120.00 -87.00   0.50    0.24    --  -99.00 136.00 -52.34   66
 26  \w   -121.00 -74.00   0.50    0.24    --  -99.00 138.00 155.98   94
 27  \w    -57.00 -31.00   0.50    0.24    --  -99.00 125.00 -30.00   52
 28  \w   -108.00 -64.00   0.50    0.24    --  -99.00 111.00  -3.24   88
 29  \w   -163.00-121.00   0.50    0.24    --  -99.00 -77.00 -30.00   84
 30  \w     40.00 112.00   0.50    0.24    --  105.22-125.00-180.00  144
 31  \w     80.00 105.00   0.50    0.24    --  105.22 -99.00 -90.00   50
 32  \w     94.00 178.00   0.50    0.24    --  105.22  19.00-180.00  168
 33  \w     44.00  70.00   0.50    0.24    --  105.22 -99.00 -90.00   52
 34  \w     47.00 104.00   0.50    0.24    --  105.22 -99.00-120.00  114
 35  \w     36.00  89.00   0.50    0.24    --  105.22 -99.00  90.00  106
 36  \w     60.00 112.00   0.50    0.24    --  105.22-125.00 150.00  104
 37  \w     51.00 105.00   0.50    0.24    --  105.22 -99.00-180.00  108
 38  \w     47.00 111.00   0.50    0.24    --  105.22-125.00  90.00  128
 39  \w     41.00  67.00   0.50    0.24    --  105.22 -57.00 -90.00   52
 40  \w     97.00 168.00   0.50    0.24    --  105.22  57.00  30.00  142
 41  \w     38.00 102.00   0.50    0.24    --  105.22 -99.00   0.00  128
 42  \w     35.00  65.00   0.50    0.24    --  105.22 -57.00  60.00   60
 43  \w    117.00 177.00   0.50    0.24    --  105.22  19.00 150.00  120
 44  \w     34.00  66.00   0.50    0.24    --  105.22 -57.00-180.00   64
 45  \w     40.00  66.00   0.50    0.24    --  105.22 -57.00 120.00   52
 46  \w    134.00 174.00   0.50    0.24    --  105.22  81.00  95.00   80
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0117713000
_diffrn_orient_matrix_UB_12      -0.0266470000
_diffrn_orient_matrix_UB_13      0.0613216000
_diffrn_orient_matrix_UB_21      0.0506042000
_diffrn_orient_matrix_UB_22      0.0244418000
_diffrn_orient_matrix_UB_23      -0.0295817000
_diffrn_orient_matrix_UB_31      0.0129538000
_diffrn_orient_matrix_UB_32      0.0394830000
_diffrn_orient_matrix_UB_33      0.0595535000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0596
_diffrn_reflns_av_unetI/netI     0.0450
_diffrn_reflns_Laue_measured_fraction_full 0.941
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       36
_diffrn_reflns_limit_h_min       -39
_diffrn_reflns_limit_k_max       39
_diffrn_reflns_limit_k_min       -35
_diffrn_reflns_limit_l_max       20
_diffrn_reflns_limit_l_min       -20
_diffrn_reflns_number            72599
_diffrn_reflns_point_group_measured_fraction_full 0.941
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         64.998
_diffrn_reflns_theta_min         4.022
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    4.314
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.32626
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.92a (Rigaku Oxford Diffraction, 2023)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.432
_exptl_crystal_description       block
_exptl_crystal_F_000             7179
_exptl_crystal_size_max          0.25
_exptl_crystal_size_mid          0.2
_exptl_crystal_size_min          0.15
_refine_diff_density_max         0.984
_refine_diff_density_min         -1.086
_refine_diff_density_rms         0.126
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.61(8)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.048
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     659
_refine_ls_number_reflns         11649
_refine_ls_number_restraints     2848
_refine_ls_restrained_S_all      0.962
_refine_ls_R_factor_all          0.1099
_refine_ls_R_factor_gt           0.1022
_refine_ls_shift/su_max          0.058
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
;
 w=1/[\s^2^(Fo^2^)+(0.0969P)^2^+549.0135P]
 where P=(Fo^2^+2Fc^2^)/3
;
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2606
_refine_ls_wR_factor_ref         0.2646
_reflns_Friedel_coverage         1.000
_reflns_Friedel_fraction_full    0.941
_reflns_Friedel_fraction_max     1.000
_reflns_number_gt                11186
_reflns_number_total             11649
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5nr03643g2.cif
_cod_data_source_block           exp_7813_auto
_cod_depositor_comments          'Adding full bibliography for 1576128.cif.'
_cod_original_cell_volume        16286.5(4)
_cod_original_sg_symbol_H-M      'R 3'
_cod_database_code               1576128
_shelxl_version_number           2013-2
_chemical_oxdiff_usercomment     'Pd C P N O'
_shelx_estimated_absorpt_t_max   0.564
_shelx_estimated_absorpt_t_min   0.412
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.39(8)
 0.61(8)
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. Restrained distances
 C66-C23 = C23-C31
 1.55 with sigma of 0.001
 C28-C3 = C3-C45
 1.55 with sigma of 0.001
 C49-C55 = C55-C63
 1.55 with sigma of 0.001
 C61-C67 = C67-C33
 1.55 with sigma of 0.001
 C48-C64 = C64-C62
 1.55 with sigma of 0.001
 C52-C2 = C2-C65
 1.55 with sigma of 0.001
 C31-C23 = C23-C66
 1.55 with sigma of 0.001
 C31-C23
 1.55 with sigma of 0.00001
 C66-C23
 1.55 with sigma of 0.00001
 C8-C47
 1.55 with sigma of 0.00001
 C41-C17
 1.55 with sigma of 0.00001
 C14-C11
 1.55 with sigma of 0.00001
 C3-C28
 1.55 with sigma of 0.00001
 C45-C3
 1.55 with sigma of 0.00001
 C67-C61
 1.55 with sigma of 0.00001
 C67-C33
 1.55 with sigma of 0.00001
 C52-C2
 1.55 with sigma of 0.00001
 C65-C2
 1.55 with sigma of 0.00001
 C55-C49
 1.55 with sigma of 0.00001
 C63-C55
 1.55 with sigma of 0.00001
 C64-C48
 1.55 with sigma of 0.00001
 C64-C62
 1.55 with sigma of 0.00001
 S4-C31
 1.75 with sigma of 0.02
 C66-C31
 2.532 with sigma of 0.002
 C28-C45
 2.532 with sigma of 0.002
 C49-C63
 2.532 with sigma of 0.002
 C61-C33
 2.532 with sigma of 0.002
 C48-C62
 2.532 with sigma of 0.002
 C52-C65
 2.532 with sigma of 0.002
 C31-C66
 2.532 with sigma of 0.002
4. Rigid bond restraints
 C1, P1, C20, C19
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.002
 S3, C65
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.02
 S4, C31
 with sigma for 1-2 distances of 0.001 and sigma for 1-3 distances of 0.002
5. Uiso/Uaniso restraints and constraints
C1 \\sim C4 \\sim C6 \\sim C8 \\sim C10 \\sim C12 \\sim C2 \\sim C3 \\sim C7
\\sim C57 \\sim C29 \\sim C59 \\sim C15 \\sim C61 \\sim C11 \\sim C14 \\sim C16
\\sim C18 \\sim C20 \\sim C22 \\sim C24 \\sim C17 \\sim C19 \\sim C39 \\sim C5
\\sim C41 \\sim C21 \\sim C43 \\sim C23 \\sim C26 \\sim C28 \\sim C30 \\sim C32
\\sim C34 \\sim C36 \\sim C31 \\sim C33 \\sim C38 \\sim C40 \\sim C42 \\sim C44
\\sim C46 \\sim C48 \\sim C45 \\sim C47 \\sim C49 \\sim C25 \\sim C51 \\sim C13
\\sim C53 \\sim C27 \\sim C50 \\sim C52 \\sim C54 \\sim C56 \\sim C58 \\sim C60
\\sim C55 \\sim C62 \\sim C63 \\sim C64 \\sim C65 \\sim C66 \\sim C68 \\sim C69
\\sim C35 \\sim C9 \\sim C37 \\sim C67: within 5A with sigma of 0.01 and sigma
for terminal atoms of 0.02 within 5A
Uanis(C64) \\sim Ueq, Uanis(C62) \\sim Ueq, Uanis(C48) \\sim Ueq, Uanis(C46)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C64) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(C7) \\sim Ueq, Uanis(C35) \\sim Ueq, Uanis(C37) \\sim Ueq, Uanis(C68)
\\sim Ueq, Uanis(C66) \\sim Ueq, Uanis(C23) \\sim Ueq, Uanis(C31) \\sim Ueq:
with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(S3) \\sim Ueq, Uanis(S4) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(S3) \\sim Ueq, Uanis(C65) \\sim Ueq: with sigma of 0.1 and sigma for
terminal atoms of 0.2
6. Others
 Fixed Sof: Cu9(0.638) Cu7(0.362) Cu6(0.333333)
7.a Secondary CH2 refined with riding coordinates:
 C2(H2A,H2B), C3(H3A,H3B), C23(H23A,H23B), C31(H31A,H31B), C33(H33A,H33B),
 C45(H45A,H45B), C55(H55A,H55B), C62(H62A,H62B), C63(H63A,H63B), C64(H64A,H64B),
  C65(H65A,H65B), C67(H67A,H67B)
7.b Aromatic/amide H refined with riding coordinates:
 C4(H4), C6(H6), C10(H10), C12(H12), C7(H7), C57(H57), C29(H29), C59(H59),
 C16(H16), C18(H18), C22(H22), C24(H24), C39(H39), C5(H5), C21(H21), C43(H43),
 C26(H26), C30(H30), C32(H32), C34(H34), C36(H36), C38(H38), C40(H40), C42(H42),
  C44(H44), C46(H46), C25(H25), C51(H51), C13(H13), C53(H53), C27(H27),
 C50(H50), C54(H54), C56(H56), C58(H58), C60(H60), C68(H68), C69(H69), C35(H35),
  C9(H9), C37(H37)
7.c Fitted hexagon refined as free rotating group:
 C1(C4,C6,C8,C10,C12), C7(C57,C29,C59,C15,C61), C14(C16,C18,C20,C22,C24),
 C19(C39,C5,C41,C21,C43), C26(C28,C30,C32,C34,C36), C38(C40,C42,C44,C46,C48),
 C49(C25,C51,C13,C53,C27), C50(C52,C54,C56,C58,C60), C66(C68,C69,C35,C9,C37)
7.d Idealised Me refined as rotating group:
 C11(H11A,H11B,H11C), C17(H17A,H17B,H17C), C47(H47A,H47B,H47C)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              20821
_shelx_fab_checksum              38976
_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 3.161
_oxdiff_exptl_absorpt_empirical_full_min 0.534