Combinatorial Identification of Hydrides in a Ligated Ag<sub>40</sub> Nanocluster with Noncompact Metal Core.
Yuan, Xiting; Sun, Cunfa; Li, Xihua; Malola, Sami; Teo, Boon K.; Häkkinen, Hannu; Zheng, Lan-Sun; Zheng, Nanfeng; Journal of the American Chemical Society 141 (2019) 11905–11911; doi:10.1021/jacs.9b03009

data_4128561
_publ_section_title
;
 Combinatorial Identification of Hydrides in a Ligated Ag<sub>40</sub>
 Nanocluster with Noncompact Metal Core.
;
_journal_issue                   30
_journal_name_full               'Journal of the American Chemical Society'
_journal_page_first              11905
_journal_page_last               11911
_journal_paper_doi               10.1021/jacs.9b03009
_journal_volume                  141
_journal_year                    2019
_chemical_formula_moiety         'C336 H348 Ag40 P8 S24'
_chemical_formula_sum            'C336 H348 Ag40 P8 S24'
_chemical_formula_weight         9718.12
_space_group_crystal_system      tetragonal
_space_group_IT_number           104
_space_group_name_Hall           'P 4 -2n'
_space_group_name_H-M_alt        'P 4 n c'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_audit_creation_date             2019-03-19
_audit_creation_method
;
Olex2 1.2
(compiled 2018.05.29 svn.r3508 for OlexSys, GUI svn.r5506)
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   29.9757(4)
_cell_length_b                   29.9757(4)
_cell_length_c                   25.6092(5)
_cell_measurement_reflns_used    25743
_cell_measurement_temperature    100.01(10)
_cell_measurement_theta_max      25.3720
_cell_measurement_theta_min      3.5430
_cell_volume                     23011.0(6)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46e (Rigaku OD, 2018)'
_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    'ShelXS (Sheldrick, 2008)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      100.01(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.4741
_diffrn_detector_type            Atlas
_diffrn_measured_fraction_theta_full 0.997
_diffrn_measured_fraction_theta_max 0.998
_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     13.00  80.00   1.00  150.00    --   11.59  37.00-120.00   67
  2  \w     14.00  83.00   1.00  150.00    --   11.59  37.00-180.00   69
  3  \w     46.00  89.00   1.00  150.00    --   11.59  19.00 120.00   43
  4  \w     46.00  74.00   1.00  150.00    --   11.59 178.00  30.00   28
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, Atlas'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0156851000
_diffrn_orient_matrix_UB_12      0.0175445000
_diffrn_orient_matrix_UB_13      0.0026975000
_diffrn_orient_matrix_UB_21      0.0139666000
_diffrn_orient_matrix_UB_22      0.0141998000
_diffrn_orient_matrix_UB_23      -0.0150083000
_diffrn_orient_matrix_UB_31      -0.0108708000
_diffrn_orient_matrix_UB_32      -0.0071210000
_diffrn_orient_matrix_UB_33      -0.0231341000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0973
_diffrn_reflns_av_unetI/netI     0.0671
_diffrn_reflns_Laue_measured_fraction_full 0.997
_diffrn_reflns_Laue_measured_fraction_max 0.998
_diffrn_reflns_limit_h_max       31
_diffrn_reflns_limit_h_min       -38
_diffrn_reflns_limit_k_max       38
_diffrn_reflns_limit_k_min       -37
_diffrn_reflns_limit_l_max       33
_diffrn_reflns_limit_l_min       -24
_diffrn_reflns_number            130794
_diffrn_reflns_point_group_measured_fraction_full 0.862
_diffrn_reflns_point_group_measured_fraction_max 0.826
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.483
_diffrn_reflns_theta_min         3.293
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    1.830
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.03980
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46e (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear dark black'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    black
_exptl_crystal_density_diffrn    1.403
_exptl_crystal_description       block
_exptl_crystal_F_000             9496
_exptl_crystal_size_max          0.431
_exptl_crystal_size_mid          0.216
_exptl_crystal_size_min          0.178
_refine_diff_density_max         3.796
_refine_diff_density_min         -1.525
_refine_diff_density_rms         0.250
_refine_ls_abs_structure_details
;
 Flack x determined using 4185 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons and Flack (2004), Acta Cryst. A60, s61).
;
_refine_ls_abs_structure_Flack   0.439(19)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.056
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     799
_refine_ls_number_reflns         21810
_refine_ls_number_restraints     896
_refine_ls_restrained_S_all      1.055
_refine_ls_R_factor_all          0.1729
_refine_ls_R_factor_gt           0.1055
_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^)+(0.1303P)^2^+511.3882P]
 where P=(Fo^2^+2Fc^2^)/3
;
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2655
_refine_ls_wR_factor_ref         0.3327
_reflns_Friedel_coverage         0.618
_reflns_Friedel_fraction_full    0.720
_reflns_Friedel_fraction_max     0.646
_reflns_number_gt                12958
_reflns_number_total             21810
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            ja9b03009_si_002.cif
_cod_data_source_block           Ag40
_cod_original_cell_volume        23011.0(7)
_cod_database_code               4128561
_shelxl_version_number           2013-2
_chemical_oxdiff_formula         Ag40S24P8C336h348
_reflns_odcompleteness_completeness 99.67
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     27.42
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 C280-C281
 1.5 with sigma of 0.01
 C314-C315
 1.5 with sigma of 0.01
 C330-C331
 1.5 with sigma of 0.01
 C322-C323
 1.5 with sigma of 0.01
 HB_$1-Ag29_$2
 2.074 with sigma of 0.01
 HB_$1-Ag6_$1
 1.69 with sigma of 0.01
 HB_$1-Ag30_$2
 1.88 with sigma of 0.01
 Ag6_$2-HB_$1
 1.92 with sigma of 0.01
 C291-C292
 1.5 with sigma of 0.01
 C281-C282
 2.54 with sigma of 0.01
 C279-C281
 2.5 with sigma of 0.01
3. Restrained planarity
 C283, C285, C286, C279, S24, C280, C282, C281, C284
 with sigma of 0.1
 S13, C329, C330, C332, C333, C334, C336, C331, C335
 with sigma of 0.1
 C318, S15, C313, C320, C319
 with sigma of 0.1
 S15, C313, C317, C318, C319, C320
 with sigma of 0.1
 S14, C321, C322, C323, C324, C325, C326, C327, C328
 with sigma of 0.1
 C314, C316, C317, C318, C319, C320, C313, S15
 with sigma of 0.1
 C292, C291, C290, C288, C289, C287, S23, C294, C293
 with sigma of 0.1
 S22, C271, C272, C273, C274, C275, C278, C277, C276
 with sigma of 0.1
 S24, C279, C286, C285, C283, C284, C282, C280, C281
 with sigma of 0.1
 C331, C330, C332, C333, C329, C336, C335, C334
 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
C309 \\sim C308 \\sim C310: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08
C319 \\sim C320 \\sim C318 \\sim C313: within 1.7A with sigma of 0.04 and sigma
for terminal atoms of 0.08
C254 \\sim C255 \\sim C256 \\sim C257 \\sim C253 \\sim C258: within 1.7A with
sigma of 0.04 and sigma for terminal atoms of 0.08
C303 \\sim C304 \\sim C305 \\sim C306 \\sim C301 \\sim C302: within 1.7A with
sigma of 0.04 and sigma for terminal atoms of 0.08
C263 \\sim C264 \\sim C259 \\sim C260 \\sim C261 \\sim C262: within 1.7A with
sigma of 0.04 and sigma for terminal atoms of 0.08
Ag8 \\sim Ag32 \\sim Ag23: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08
C318 \\sim C319 \\sim C313 \\sim C320 \\sim S15: within 1.7A with sigma of 0.04
and sigma for terminal atoms of 0.08
C317 \\sim C318 \\sim C319 \\sim C320 \\sim C313: within 1.7A with sigma of
0.04 and sigma for terminal atoms of 0.08
Ag23 \\sim Ag24 \\sim Ag8 \\sim Ag31 \\sim Ag6 \\sim Ag29 \\sim Ag30: within
1.7A with sigma of 0.04 and sigma for terminal atoms of 0.08
Ag31 \\sim Ag6 \\sim Ag23 \\sim Ag8 \\sim Ag24: within 1.7A with sigma of 0.04
and sigma for terminal atoms of 0.08
Ag6 \\sim Ag31 \\sim Ag30: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08
Ag31 \\sim Ag6 \\sim Ag30: within 1.7A with sigma of 0.04 and sigma for
terminal atoms of 0.08
Ag29 \\sim Ag6 \\sim Ag6 \\sim Ag30: within 1.7A with sigma of 0.04 and sigma
for terminal atoms of 0.08
Ag23 \\sim Ag8 \\sim Ag24 \\sim Ag31 \\sim Ag6: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08
Ag6 \\sim Ag31: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08
Ag30 \\sim Ag6 \\sim Ag6: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
C313 \\sim C320: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08
Ag6: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
C315 \\sim C316 \\sim C314: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
Ag24 \\sim Ag23 \\sim Ag8: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
C292 \\sim C291: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08
C314 \\sim C315 \\sim C313: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
C288 \\sim C289: within 2A with sigma of 0.01 and sigma for terminal atoms of
0.02
P6 \\sim C307 \\sim C308 \\sim C309 \\sim C310 \\sim C311 \\sim C312: within 2A
with sigma of 0.04 and sigma for terminal atoms of 0.08
P8 \\sim C259 \\sim C260 \\sim C261 \\sim C262 \\sim C263 \\sim C264: within 2A
with sigma of 0.04 and sigma for terminal atoms of 0.08
C285 \\sim C286 \\sim C279 \\sim S24 \\sim C280 \\sim C282 \\sim C283 \\sim
C284 \\sim C281: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08
C266 \\sim C265 \\sim C267: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
Ag24 \\sim Ag31 \\sim Ag6 \\sim Ag30 \\sim Ag29 \\sim Ag32 \\sim Ag8 \\sim
Ag23: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
Ag6 \\sim Ag31 \\sim Ag8 \\sim Ag24 \\sim Ag23: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08
Ag31 \\sim Ag6: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08
Ag6 \\sim Ag31 \\sim Ag24 \\sim Ag23 \\sim Ag8: within 2A with sigma of 0.04
and sigma for terminal atoms of 0.08
H \\sim Ag6 \\sim Ag31: within 2A with sigma of 0.04 and sigma for terminal
atoms of 0.08
HA \\sim Ag23 \\sim Ag8 \\sim Ag8: within 2A with sigma of 0.04 and sigma for
terminal atoms of 0.08
HB \\sim Ag6: within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08
C317 \\sim C318: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08
Uanis(C318) \\sim Ueq, Uanis(C319) \\sim Ueq, Uanis(C320) \\sim Ueq,
Uanis(C313) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C276) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C324) \\sim Ueq, Uanis(C327) \\sim Ueq, Uanis(C293) \\sim Ueq,
Uanis(C275) \\sim Ueq, Uanis(C277) \\sim Ueq, Uanis(C289) \\sim Ueq,
Uanis(C311) \\sim Ueq, Uanis(C331) \\sim Ueq, Uanis(C267) \\sim Ueq,
Uanis(C268) \\sim Ueq, Uanis(C273) \\sim Ueq, Uanis(C282) \\sim Ueq,
Uanis(C259) \\sim Ueq, Uanis(C263) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C278) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(Ag8) \\sim Ueq, Uanis(Ag8) \\sim Ueq, Uanis(Ag8) \\sim Ueq, Uanis(Ag8)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C274) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C254) \\sim Ueq, Uanis(C255) \\sim Ueq, Uanis(C253) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(C284) \\sim Ueq, Uanis(C316) \\sim Ueq, Uanis(C315) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(Ag6) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C326) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C292) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C330) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C280) \\sim Ueq, Uanis(C281) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(C301) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C307) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(Ag8) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C318) \\sim Ueq, Uanis(C326) \\sim Ueq, Uanis(C284) \\sim Ueq,
Uanis(C292) \\sim Ueq, Uanis(C334) \\sim Ueq, Uanis(C276) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(C334) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
6.a Aromatic/amide H refined with riding coordinates:
 C324(H324), C327(H327), C328(H328), C294(H294), C293(H293), C290(H290),
 C306(H306), C305(H305), C304(H304), C303(H303), C302(H302), C332(H332),
 C335(H335), C336(H336), C274(H274), C278(H278), C277(H277), C296(H296),
 C297(H297), C298(H298), C299(H299), C300(H300), C308(H308), C309(H309),
 C310(H310), C311(H311), C312(H312), C266(H266), C267(H267), C268(H268),
 C269(H269), C270(H270), C282(H282), C286(H286), C285(H285), C262(H262),
 C261(H261), C260(H260), C264(H264), C263(H263), C258(H258), C257(H257),
 C256(H256), C255(H255), C254(H254), C316(H316), C319(H319), C320(H320)
6.b Fitted hexagon refined as free rotating group:
 C321(C322,C324,C325,C327,C328), C287(C294,C293,C291,C290,C288), C301(C306,
 C305,C304,C303,C302), C329(C330,C332,C333,C335,C336), C275(C274,C272,C271,C278,
 C277), C295(C296,C297,C298,C299,C300), C307(C308,C309,C310,C311,C312),
 C265(C266,C267,C268,C269,C270), C283(C282,C280,C279,C286,C285), C262(C261,C260,
 C259,C264,C263), C253(C258,C257,C256,C255,C254), C314(C316,C317,C319,C320,C313)
6.c Idealised Me refined as rotating group:
 C326(H32A,H32B,H32C), C276(H27A,H27B,H27C), C289(H28A,H28B,H28C), C292(H29A,
 H29B,H29C), C334(H33A,H33B,H33C), C323(H32D,H32E,H32F), C331(H33D,H33E,H33F),
 C281(H28D,H28E,H28F), C273(H27D,H27E,H27F), C284(H28G,H28H,H28I), C318(H31A,
 H31B,H31C), C315(H31D,H31E,H31F)
;
_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
- Detector area scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 8.923
_oxdiff_exptl_absorpt_empirical_full_min 0.355