Covalency between the uranyl ion and dithiophosphinate by sulfur <i>K</i>-edge X-ray absorption spectroscopy and density functional theory
Zhang, Yusheng; Duan, Wuhua; Wang, Qiang; Zheng, Lei; Wang, Jianchen; Chen, Jing; Sun, Taoxiang; Journal of Synchrotron Radiation 29 (2022) 11–20; doi:10.1107/S160057752101198X

data_1565720
_publ_section_title
;
 Covalency between the uranyl ion and dithiophosphinate by sulfur
 <i>K</i>-edge X-ray absorption spectroscopy and density functional theory
;
_journal_issue                   1
_journal_name_full               'Journal of Synchrotron Radiation'
_journal_page_first              11
_journal_page_last               20
_journal_paper_doi               10.1107/S160057752101198X
_journal_volume                  29
_journal_year                    2022
_chemical_absolute_configuration ad
_chemical_formula_moiety         'C30 H22 F12 O3 P2 S4 U, C2 H6 O'
_chemical_formula_sum            'C32 H28 F12 O4 P2 S4 U'
_chemical_formula_weight         1132.75
_space_group_crystal_system      orthorhombic
_space_group_IT_number           29
_space_group_name_Hall           'P 2c -2ac'
_space_group_name_H-M_alt        'P c a 21'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2019-03-06
_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            8
_cell_length_a                   16.5607(6)
_cell_length_b                   8.1303(3)
_cell_length_c                   59.7044(13)
_cell_measurement_reflns_used    4125
_cell_measurement_temperature    173.00(10)
_cell_measurement_theta_max      70.7010
_cell_measurement_theta_min      5.3930
_cell_volume                     8038.8(5)
_computing_cell_refinement       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.46 (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.46 (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    'ShelXT (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      173.00(10)
_diffrn_detector                 'CCD plate'
_diffrn_detector_area_resol_mean 10.4273
_diffrn_detector_type            AtlasS2
_diffrn_measured_fraction_theta_full 0.994
_diffrn_measured_fraction_theta_max 0.974
_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    -89.00 -55.00   1.00    2.00    --  -40.81 -38.00 -30.00   34
  2  \w    -92.00  -3.00   1.00    2.00    --  -40.81 125.00-150.00   89
  3  \w     26.00  64.00   1.00    2.00    --   40.81-125.00  90.00   38
  4  \w    110.00 169.00   1.00    7.00    --  100.91 125.00-120.00   59
  5  \w     44.00 121.00   1.00    7.00    --  100.91 -45.00-150.00   77
  6  \w     57.00 130.00   1.00    7.00    --  100.91 -61.00  90.00   73
  7  \w     98.00 144.00   1.00    7.00    --  100.91  45.00 -60.00   46
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, AtlasS2'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0064878000
_diffrn_orient_matrix_UB_12      0.1167562000
_diffrn_orient_matrix_UB_13      0.0202921000
_diffrn_orient_matrix_UB_21      -0.0603441000
_diffrn_orient_matrix_UB_22      0.1184981000
_diffrn_orient_matrix_UB_23      -0.0111690000
_diffrn_orient_matrix_UB_31      -0.0703694000
_diffrn_orient_matrix_UB_32      -0.0907803000
_diffrn_orient_matrix_UB_33      0.0114271000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           CuK\a
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0607
_diffrn_reflns_av_unetI/netI     0.0822
_diffrn_reflns_Laue_measured_fraction_full 0.994
_diffrn_reflns_Laue_measured_fraction_max 0.974
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       7
_diffrn_reflns_limit_k_min       -9
_diffrn_reflns_limit_l_max       72
_diffrn_reflns_limit_l_min       -68
_diffrn_reflns_number            19109
_diffrn_reflns_point_group_measured_fraction_full 0.784
_diffrn_reflns_point_group_measured_fraction_max 0.755
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         71.570
_diffrn_reflns_theta_min         4.443
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    14.900
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.67454
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.46 (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear yellow'
_exptl_crystal_density_diffrn    1.872
_exptl_crystal_description       plate
_exptl_crystal_F_000             4368
_exptl_crystal_size_max          0.16
_exptl_crystal_size_mid          0.1
_exptl_crystal_size_min          0.02
_refine_diff_density_max         6.197
_refine_diff_density_min         -2.112
_refine_diff_density_rms         0.210
_refine_ls_abs_structure_details
;
 Flack x determined using 2747 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.147(10)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1018
_refine_ls_number_reflns         11827
_refine_ls_number_restraints     238
_refine_ls_restrained_S_all      1.030
_refine_ls_R_factor_all          0.0791
_refine_ls_R_factor_gt           0.0672
_refine_ls_shift/su_max          0.014
_refine_ls_shift/su_mean         0.001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0900P)^2^+51.5220P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1675
_refine_ls_wR_factor_ref         0.1779
_reflns_Friedel_coverage         0.535
_reflns_Friedel_fraction_full    0.569
_reflns_Friedel_fraction_max     0.532
_reflns_number_gt                9865
_reflns_number_total             11827
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            yw5001sup1.cif
_cod_data_source_block           IV
_cod_depositor_comments
'Adding full bibliography for 1565717--1565720.cif.'
_cod_database_code               1565720
_cod_database_fobs_code          1565720
_shelx_shelxl_version_number     2014/7
_shelx_estimated_absorpt_t_max   0.755
_shelx_estimated_absorpt_t_min   0.199
_reflns_odcompleteness_completeness 99.43
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     64.99
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H) groups
2. Restrained distances
 O3-H3
 0.85 with sigma of 0.01
 C30-C29
 1.54 with sigma of 0.02
 O7-H7
 0.85 with sigma of 0.01
 C62A-C61
 1.54 with sigma of 0.02
 C62A-C61 = C62B-C61
 1.54 with sigma of 0.02
 U1-H3
 2.891388 with sigma of 0.02
 C29-H3
 1.940519 with sigma of 0.02
 U2-H7
 2.860598 with sigma of 0.02
 C61-H7
 1.876164 with sigma of 0.02
 O7-C62A
 2.42 with sigma of 0.04
 O7-C62B
 2.42 with sigma of 0.04
 F6A-C14A \\sim F5A-C14A \\sim F5B-C14B \\sim F4A-C14A \\sim F4B-C14B \\sim
F6B-C14B
 with sigma of 0.02
 C14A-C13 \\sim C14B-C13
 with sigma of 0.02
 F6A-F5A \\sim F5B-F6B
 with sigma of 0.02
 F6A-F4A \\sim F4B-F6B
 with sigma of 0.02
 F4A-F5A \\sim F4B-F5B
 with sigma of 0.02
3. Rigid bond restraints
 C8, F4A, C13, F5A, F6A, C12, C14A, C9, C10, C11, F6B, C14B, F5B, F4B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C15, F7, F9, F8, C20, C17, C21, C16, C18, C19
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 F19, F21, F20, C51, C52, C53, C50, C48, C49, C47
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 F23, C55, F22, F24, C59, C58, C54, C60, C56, C57
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 F16, F18, C45, C41, F17, C40, C43, C42, C44, C46
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 F15, F14, F13, C33, C39, C38, C34, C37, C36, C35
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 O3, C29, C30
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 O7, C61, C62A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C62B, C61, O7, C62A
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
Uanis(F18) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(F6A) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O5) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(C15) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(F4B) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C42) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C62B) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
5. Others
 Sof(F6B)=Sof(C14B)=Sof(F4B)=Sof(F5B)=1-FVAR(1)
 Sof(F4A)=Sof(F5A)=Sof(F6A)=Sof(C14A)=FVAR(1)
 Sof(H61C)=Sof(H61D)=Sof(C62B)=Sof(H62D)=Sof(H62E)=Sof(H62F)=1-FVAR(2)
 Sof(H61A)=Sof(H61B)=Sof(C62A)=Sof(H62A)=Sof(H62B)=Sof(H62C)=FVAR(2)
6.a Secondary CH2 refined with riding coordinates:
 C31(H31A,H31B), C29(H29A,H29B), C61(H61A,H61B), C61(H61C,H61D), C63(H63A,H63B)
6.b Aromatic/amide H refined with riding coordinates:
 C9(H9), C10(H10), C11(H11), C12(H12), C3(H3A), C55(H55), C24(H24), C25(H25),
 C51(H51), C4(H4), C2(H2), C17(H17), C58(H58), C5(H5), C23(H23), C16(H16),
 C50(H50), C48(H48), C18(H18), C26(H26), C49(H49), C19(H19), C34(H34), C44(H44),
  C43(H43), C42(H42), C41(H41), C56(H56), C37(H37), C36(H36), C57(H57), C35(H35)
6.c Fitted hexagon refined as free rotating group:
 C8(C9,C10,C11,C12,C13), C40(C45,C44,C43,C42,C41)
6.d Tetrahedral OH refined with riding coordinates:
 O4(H4A), O8(H8)
6.e Idealised Me refined with riding coordinates:
 C62B(H62D,H62E,H62F)
6.f Idealised Me refined as rotating group:
 C64(H64A,H64B,H64C), C30(H30A,H30B,H30C), C32(H32A,H32B,H32C), C62A(H62A,H62B,
 H62C)
6.g Idealised tetrahedral OH refined with riding coordinates:
 O7(H7), O3(H3)
;
_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 1.540
_oxdiff_exptl_absorpt_empirical_full_min 0.725