The use of effective core potentials in Hirshfeld atom refinement: making quantum crystallography faster in NoSpherA2
Kleemiss, Florian; Meurer, Florian; Shenderovich, Ilya G.; Bodensteiner, Michael; Journal of Applied Crystallography 58 (2025) –; doi:10.1107/S1600576725000901

data_2300757
_publ_section_title
;
 The use of effective core potentials in Hirshfeld atom refinement: making
 quantum crystallography faster in NoSpherA2
;
_journal_coeditor_code           WOZ5004SUP1
_journal_issue                   2
_journal_name_full               'Journal of Applied Crystallography'
_journal_paper_doi               10.1107/S1600576725000901
_journal_volume                  58
_journal_year                    2025
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C52 H48 Hg P4, 2(F6 P)'
_chemical_formula_sum            'C52 H48 F12 Hg P6'
_chemical_formula_weight         1287.385
_space_group_crystal_system      triclinic
_space_group_IT_number           1
_space_group_name_Hall           'P 1'
_space_group_name_H-M_alt        'P 1'
_symmetry_Int_Tables_number      1
_audit_creation_date             2024-09-24
_audit_creation_method
;
Olex2 1.5-dev
(compiled 2024.09.02 svn.r9ddf420b for OlexSys, GUI svn.r7016)
;
_cell_angle_alpha                102.495(1)
_cell_angle_beta                 107.125(1)
_cell_angle_gamma                96.849(1)
_cell_formula_units_Z            1
_cell_length_a                   9.9613(1)
_cell_length_b                   11.6741(2)
_cell_length_c                   11.9272(2)
_cell_measurement_reflns_used    52349
_cell_measurement_temperature    100.00(10)
_cell_measurement_theta_max      52.7540
_cell_measurement_theta_min      2.1540
_cell_volume                     1268.99(3)
_computing_cell_refinement       'CrysAlisPro 1.171.43.93a (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 42.51a 64-bit (release 28-03-2022))'
_computing_data_reduction        'CrysAlisPro 1.171.43.93a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5-dev (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-dev (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5-dev (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_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-Arc 150'
_diffrn_measured_fraction_theta_full 0.9996
_diffrn_measured_fraction_theta_max 0.9791
_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    -43.00  11.00   0.50    1.92    --  -42.25  52.00-118.00  108
  2  \w    -96.00 -42.00   0.50    1.92    --  -42.25 -52.00  96.00  108
  3  \w    -11.00  43.00   0.50    1.92    --   42.58 -52.00  96.00  108
  4  \w     42.00  96.00   0.50    1.92    --   42.58  52.00-118.00  108
  5  \w     -6.00  48.00   0.50    1.92    --   47.37 -52.00  96.00  108
  6  \w     47.00 101.00   0.50    1.92    --   47.37  52.00-118.00  108
  7  \w   -101.00 -47.00   0.50    1.92    --  -47.70 -52.00  96.00  108
  8  \w    -48.00   6.00   0.50    1.92    --  -47.70  52.00-118.00  108
  9  \w    -39.00 -11.00   0.50    1.92    --    0.00 123.00 132.22   56
 10  \w    -42.00  -1.00   0.50    1.92    --  -12.00 109.00  13.51   82
 11  \w    -13.00  14.00   0.50    1.92    --   12.00 102.00  25.01   54
 12  \w     -4.00  22.00   0.50    1.92    --   20.00 100.00-161.74   52
 13  \w     14.00  41.00   0.50    1.92    --   32.00  92.00 -98.76   54
 14  \w     14.00  41.00   0.50    1.92    --   32.00  92.00  32.16   54
 15  \w     16.00  43.00   0.50    1.92    --   32.00  89.00-163.86   54
 16  \w     17.00  43.00   0.50    1.92    --   32.00  88.00   7.62   52
 17  \w     14.00  41.00   0.50    1.92    --   32.00  92.00  92.31   54
 18  \w     14.00  41.00   0.50    1.92    --   32.00  92.00 -59.31   54
 19  \w     14.00  41.00   0.50    1.92    --   32.00  92.00 128.77   54
 20  \w    -81.00 -29.00   0.50    1.92    --  -36.00 -75.00 -41.52  104
 21  \w    -41.00  14.00   0.50    1.92    --  -42.25  38.00  30.00  110
 22  \w    -27.00  15.00   0.50    1.92    --  -42.25  19.00-120.00   84
 23  \w    -91.00   7.00   0.50    1.92    --  -42.25   0.00-150.00  196
 24  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00-180.00  106
 25  \w    -27.00  15.00   0.50    1.92    --  -42.25  19.00  90.00   84
 26  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00-120.00  106
 27  \w    -27.00  15.00   0.50    1.92    --  -42.25  19.00-150.00   84
 28  \w    -27.00  15.00   0.50    1.92    --  -42.25  19.00 -30.00   84
 29  \w    -27.00  15.00   0.50    1.92    --  -42.25  19.00 -60.00   84
 30  \w    -14.00  33.00   0.50    1.92    --   42.58 -19.00 -90.00   94
 31  \w     35.00  87.00   0.50    1.92    --   42.58  77.00  60.00  104
 32  \w     35.00  87.00   0.50    1.92    --   42.58  77.00  30.00  104
 33  \w     19.00  83.00   0.50    1.92    --   42.58-125.00-120.00  128
 34  \w     35.00  87.00   0.50    1.92    --   42.58  77.00 150.00  104
 35  \w     19.00  83.00   0.50    1.92    --   42.58-125.00 150.00  128
 36  \w     19.00  83.00   0.50    1.92    --   42.58-125.00 -30.00  128
 37  \w    -89.00 -36.00   0.50    1.92    --  -44.00 -76.00-133.95  106
 38  \w    -89.00 -36.00   0.50    1.92    --  -44.00 -76.00 -60.14  106
 39  \w    -90.00 -38.00   0.50    1.92    --  -44.00 -74.00 177.55  104
 40  \w    -83.00 -10.00   0.50    1.92    --  -44.98 121.00 -22.62  146
 41  \w     37.00  90.00   0.50    1.92    --   44.98  76.00  85.09  106
 42  \w    -92.00 -39.00   0.50    1.92    --  -47.70 -77.00 -90.00  106
 43  \w    -27.00  10.00   0.50    1.92    --  -47.70  19.00  60.00   74
 44  \w    -88.00 -13.00   0.50    1.92    --  -47.70 125.00  90.00  150
 45  \w    -92.00 -39.00   0.50    1.92    --  -47.70 -77.00  90.00  106
 46  \w    -88.00 -13.00   0.50    1.92    --  -47.70 125.00   0.00  150
 47  \w    -27.00  10.00   0.50    1.92    --  -47.70  19.00  30.00   74
 48  \w    -88.00 -13.00   0.50    1.92    --  -47.70 125.00 150.00  150
 49  \w   -104.00 -47.00   0.50    1.92    --  -47.70 -38.00 -30.00  114
 50  \w    -88.00 -13.00   0.50    1.92    --  -47.70 125.00 -90.00  150
 51  \w   -104.00 -47.00   0.50    1.92    --  -47.70 -38.00   0.00  114
 52  \w    -92.00 -39.00   0.50    1.92    --  -47.70 -77.00 150.00  106
 53  \w    -97.00   1.00   0.50    1.92    --  -47.70   0.00-180.00  196
 54  \w    -97.00   1.00   0.50    1.92    --  -47.70   0.00   0.00  196
 55  \w    -88.00 -13.00   0.50    1.92    --  -47.70 125.00  30.00  150
 56  \w    -27.00  10.00   0.50    1.92    --  -47.70  19.00   0.00   74
 57  \w    -88.00 -13.00   0.50    1.92    --  -47.70 125.00-150.00  150
 58  \w    -38.00 -10.00   0.50    1.92    --    0.00 121.00-155.26   56
 59  \w    -32.00  31.00   0.50    1.92    --  -12.00  95.00  76.89  126
 60  \w    -39.00   3.00   0.50    1.92    --  -12.00 104.00-126.08   84
 61  \w      5.00  34.00   0.50    1.92    --   24.00  94.00 179.22   58
 62  \w    -81.00 -28.00   0.50    1.92    --  -36.00 -76.00 -83.02  106
 63  \w    -80.00 -28.00   0.50    1.92    --  -36.00 -77.00 161.69  104
 64  \w     29.00  82.00   0.50    1.92    --   36.00  75.00-108.82  106
 65  \w     29.00  82.00   0.50    1.92    --   36.00  75.00-139.51  106
 66  \w     28.00  81.00   0.50    1.92    --   36.00  77.00-172.95  106
 67  \w    -86.00 -34.00   0.50    1.92    --  -40.00 -74.00 126.83  104
 68  \w     32.00  85.00   0.50    1.92    --   40.00  77.00 -95.48  106
 69  \w    -27.00  15.00   0.50    1.92    --  -42.25  19.00  30.00   84
 70  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00 -90.00  106
 71  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00 150.00  106
 72  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00  90.00  106
 73  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00   0.00  106
 74  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00  30.00  106
 75  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00  60.00  106
 76  \w    -87.00 -34.00   0.50    1.92    --  -42.25 -77.00-150.00  106
 77  \w     19.00  83.00   0.50    1.92    --   42.58-125.00  60.00  128
 78  \w    -14.00  33.00   0.50    1.92    --   42.58 -19.00 -30.00   94
 79  \w     19.00  83.00   0.50    1.92    --   42.58-125.00   0.00  128
 80  \w     35.00  87.00   0.50    1.92    --   42.58  77.00 -60.00  104
 81  \w     35.00  87.00   0.50    1.92    --   42.58  77.00 120.00  104
 82  \w     35.00  87.00   0.50    1.92    --   42.58  77.00 -30.00  104
 83  \w     35.00  87.00   0.50    1.92    --   42.58  77.00  90.00  104
 84  \w     35.00  87.00   0.50    1.92    --   42.58  77.00-120.00  104
 85  \w     35.00  87.00   0.50    1.92    --   42.58  77.00-180.00  104
 86  \w    -88.00 -36.00   0.50    1.92    --  -44.00 -77.00 -30.55  104
 87  \w    -88.00 -36.00   0.50    1.92    --  -44.00 -77.00  69.36  104
 88  \w     38.00  90.00   0.50    1.92    --   44.98  75.00-100.95  104
 89  \w     39.00  92.00   0.50    1.92    --   47.37  77.00 150.00  106
 90  \w      5.00 105.00   0.50    1.92    --   47.37  19.00 -60.00  200
 91  \w      5.00 105.00   0.50    1.92    --   47.37  19.00-120.00  200
 92  \w      5.00 105.00   0.50    1.92    --   47.37  19.00-150.00  200
 93  \w      5.00 105.00   0.50    1.92    --   47.37  19.00-180.00  200
 94  \w     39.00  92.00   0.50    1.92    --   47.37  77.00  60.00  106
 95  \w     39.00  89.00   0.50    1.92    --   47.37  77.00 -60.00  100
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy R, DW system, HyPix-Arc 150'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0677428000
_diffrn_orient_matrix_UB_12      0.0391419000
_diffrn_orient_matrix_UB_13      0.0222648000
_diffrn_orient_matrix_UB_21      0.0011423000
_diffrn_orient_matrix_UB_22      -0.0078407000
_diffrn_orient_matrix_UB_23      -0.0603448000
_diffrn_orient_matrix_UB_31      -0.0343968000
_diffrn_orient_matrix_UB_32      0.0493370000
_diffrn_orient_matrix_UB_33      -0.0052536000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0000
_diffrn_reflns_av_unetI/netI     0.0405
_diffrn_reflns_Laue_measured_fraction_full 0.9996
_diffrn_reflns_Laue_measured_fraction_max 0.9791
_diffrn_reflns_limit_h_max       22
_diffrn_reflns_limit_h_min       -22
_diffrn_reflns_limit_k_max       26
_diffrn_reflns_limit_k_min       -26
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -27
_diffrn_reflns_number            61739
_diffrn_reflns_point_group_measured_fraction_full 0.9996
_diffrn_reflns_point_group_measured_fraction_max 0.9630
_diffrn_reflns_theta_full        25.2417
_diffrn_reflns_theta_max         54.59
_diffrn_reflns_theta_min         2.18
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    3.303
_exptl_absorpt_correction_T_max  0.989
_exptl_absorpt_correction_T_min  0.702
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.93a (Rigaku Oxford Diffraction, 2023)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear yellow'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.685
_exptl_crystal_description       block
_exptl_crystal_F_000             637.301
_exptl_crystal_size_max          0.158
_exptl_crystal_size_mid          0.115
_exptl_crystal_size_min          0.082
_refine_diff_density_max         2.9488
_refine_diff_density_min         -4.6970
_refine_diff_density_rms         0.1816
_refine_ls_abs_structure_details
'Hooft, R.W.W., Straver, L.H., Spek, A.L. (2010). J. Appl. Cryst., 43, 665-668.'
_refine_ls_abs_structure_Flack   -0.0030(5)
_refine_ls_d_res_high            0.4360
_refine_ls_d_res_low             9.3348
_refine_ls_goodness_of_fit_ref   1.0033
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_constraints    92
_refine_ls_number_parameters     666
_refine_ls_number_reflns         61739
_refine_ls_number_restraints     3
_refine_ls_restrained_S_all      1.0033
_refine_ls_R_factor_all          0.0409
_refine_ls_R_factor_gt           0.0312
_refine_ls_shift/su_max          -0.0007
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0232P)^2^+0.2970P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0529
_refine_ls_wR_factor_ref         0.0558
_reflns_Friedel_coverage         0.947
_reflns_limit_h_max              22
_reflns_limit_h_min              -22
_reflns_limit_k_max              26
_reflns_limit_k_min              -26
_reflns_limit_l_max              27
_reflns_limit_l_min              -27
_reflns_number_gt                56135
_reflns_number_total             61739
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            woz5004.cif
_cod_data_source_block           dppe2HgPF62_IAM
_cod_original_cell_volume        1268.99(4)
_cod_original_sg_symbol_Hall     ' P 1'
_cod_database_code               2300757
_chemical_oxdiff_formula         C52H48F12HgP6
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.7299(10)
 0.2701(10)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
3.a Secondary CH2 refined with riding coordinates:
 C00I(H00a,H00b), C00L(H00c,H00d), C00P(H00e,H00f), C00R(H00g,H00h)
3.b Aromatic/amide H refined with riding coordinates:
 C00N(H00N), C00S(H00S), C00T(H00T), C00U(H00U), C00V(H00V), C00W(H00W),
 C010(H010), C012(H012), C014(H014), C015(H015), C016(H016), C01A(H01A),
 C01C(H01C), C01D(H01D), C01E(H01E), C01F(H01F), C01G(H01G), C01H(H01H),
 C01I(H01I), C01J(H01J), C01L(H01L), C01N(H01N), C01O(H01O), C01P(H01P),
 C01R(H01R), C01S(H01S), C01T(H01T), C01U(H01U), C01W(H01W), C01X(H01X),
 C01Y(H01Y), C01Z(H01Z), C022(H022), C024(H024), C025(H025), C027(H027),
 C029(H029), C02A(H02A), C3(H3), C4(H4)
;
_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 1.385
_oxdiff_exptl_absorpt_empirical_full_min 0.687