Applicability of transferable multipole pseudo-atoms for restoring inner-crystal electronic force density fields. Chemical bonding and binding features in the crystal and dimer of 1,3-bis(2-hydroxyethyl)-6-methyluracil
Saifina, Alina F.; Kartashov, Sergey V.; Saifina, Liliya F.; Fayzullin, Robert R.; IUCrJ 10 (2023) 584–602; doi:10.1107/S2052252523007108

data_1569763
_publ_section_title
;
 Applicability of transferable multipole pseudo-atoms for restoring
 inner-crystal electronic force density fields. Chemical bonding and
 binding features in the crystal and dimer of
 1,3-bis(2-hydroxyethyl)-6-methyluracil
;
_journal_coeditor_code           LT5061
_journal_issue                   5
_journal_name_full               IUCrJ
_journal_page_first              584
_journal_page_last               602
_journal_paper_doi               10.1107/S2052252523007108
_journal_volume                  10
_journal_year                    2023
_chemical_formula_moiety         'C9 H14 N2 O4'
_chemical_formula_sum            'C9 H14 N2 O4'
_chemical_formula_weight         214.22
_chemical_melting_point          384
_chemical_name_systematic
1,3-bis(2-hydroxyethyl)-6-methylpyrimidine-2,4(1H,3H)-dione
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2yn'
_space_group_name_H-M_alt        'P 1 21/n 1'
_atom_sites_solution_hydrogens   difmap
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_method           MoPro
_cell_angle_alpha                90
_cell_angle_beta                 94.4437(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.8840(3)
_cell_length_b                   7.2121(3)
_cell_length_c                   16.7362(6)
_cell_measurement_reflns_used    97902
_cell_measurement_temperature    100.0(2)
_cell_measurement_theta_max      78.46
_cell_measurement_theta_min      2.59
_cell_volume                     948.76(6)
_computing_cell_refinement       'APEX4 v2021.10-0 (Bruker AXS)'
_computing_data_collection       'APEX4 v2021.10-0 (Bruker AXS)'
_computing_data_reduction        'APEX4 v2021.10-0 (Bruker AXS)'
_computing_molecular_graphics
;
MoProViewer (Jelsch et al., 2005, 10.1107/S0021889804025518); 
WinXPRO, 3DPlot, TrajPlot (Stash & Tsirelson, 2022, 10.1107/S1600576722002321); 
WinGX, ORTEP (Farrugia, 2012) 
;
_computing_publication_material
;
WinXPRO (Stash & Tsirelson, 2022, 10.1107/S1600576722002321); 
VMoPro (Jelsch et al., 2005, 10.1107/S0021889804025518)
;
_computing_structure_refinement
'MoPro (Jelsch et al., 2005, 10.1107/S0021889804025518)'
_computing_structure_solution
'SHELXT-2018/2 (Sheldrick, 2015, 10.1107/S2053273314026370)'
_diffrn_ambient_temperature      100.0(2)
_diffrn_detector                 'PHOTON III'
_diffrn_measured_fraction_theta_max 0.988
_diffrn_measurement_device_type  'Bruker D8 QUEST'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  'multilayer optics'
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0357
_diffrn_reflns_av_unetI/netI     0.0107
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       19
_diffrn_reflns_limit_k_min       -19
_diffrn_reflns_limit_l_max       41
_diffrn_reflns_limit_l_min       -44
_diffrn_reflns_number            580996
_diffrn_reflns_point_group_measured_fraction_max 0.988
_diffrn_reflns_theta_max         78.721
_diffrn_reflns_theta_min         2.778
_diffrn_source                   'microfocus Mo X-ray tube'
_diffrn_source_type              'I\mS DIAMOND'
_exptl_absorpt_coefficient_mu    0.119
_exptl_absorpt_correction_T_max  0.9253
_exptl_absorpt_correction_T_min  0.8642
_exptl_absorpt_correction_type   numerical
_exptl_absorpt_process_details
;
SADABS-2016/2 (Krause et al., 2015, 10.1107/S1600576714022985)

 Equivalent reflections defined by point group 2/m for scaling and error model
 Mean and maximum errors in direction cosine check function =   0.000   0.004
 Restraint esd for equal adjacent scale factors =  0.0050
 Maximum odd and even orders for spherical harmonics =   1   4
 509697 reflections employed for parameter determination
 Effective data to parameter ratio =   20.44
 wR2(int) =  0.1115 (selected reflections only, before parameter refinement)
 wR2(int) =  0.0569 (selected reflections only, after parameter refinement)

  597067 total and  21411 unique reflections assuming Friedel's law
 plus   8840 total and  1437 unique reflections in fast scans
 Reflections rejected for which |I-<I>|/su >   4.00
 where:  su^2 = sigma(I)^2 + (  0.04000 <I>)^2  (sigma(I) from SAINT)

  592439 total and  21410 unique reflections left after |I-<I>|/su test
 plus   8822 total and  1437 unique reflections in fast scans
 su^2 = [K*sigma(I)]^2 + [g<I>]^2  where sigma(I) is from SAINT

 Error model 5: refine all K and overall g

 Run 2theta R(int) Incid. factors Diffr. factors    K      g   I/s(lim) Total I>2sig(I)
   1f  0.0  0.0575  2.612 - 3.713  0.995 - 1.019  1.027  0.0321  31.1    4443    3175
   2f  0.0  0.0856  2.699 - 3.789  0.995 - 1.019  0.870  0.0321  31.1    4379    2900
   3   0.0  0.0617  2.456 - 3.985  0.995 - 1.016  0.903  0.0321  31.1    5233    3639
   4  21.9  0.0328  0.261 - 0.331  0.995 - 1.021  1.062  0.0321  31.1    6567    5389
   5  21.9  0.0337  0.283 - 0.409  0.995 - 1.020  0.995  0.0321  31.1    6542    5301
   6  21.9  0.0348  0.266 - 0.419  0.995 - 1.019  0.991  0.0321  31.1    6560    5303
   7  21.9  0.0335  0.246 - 0.335  0.995 - 1.022  1.096  0.0321  31.1    5168    4317
   8  21.9  0.0378  0.273 - 0.438  0.995 - 1.017  0.996  0.0321  31.1    6548    5278
   9  21.9  0.0369  0.263 - 0.427  0.995 - 1.022  1.120  0.0321  31.1    5562    4581
  10  21.9  0.0320  0.237 - 0.324  0.995 - 1.017  0.971  0.0321  31.1    6547    5387
  11  21.9  0.0343  0.235 - 0.421  0.995 - 1.016  1.000  0.0321  31.1    6570    5305
  12  31.2  0.0280  0.262 - 0.329  0.995 - 1.022  1.145  0.0321  31.1    7612    6824
  13  37.9  0.0289  0.239 - 0.314  0.995 - 1.020  1.095  0.0321  31.1    5456    4991
  14  37.9  0.0313  0.254 - 0.336  0.995 - 1.023  1.143  0.0321  31.1    5620    5069
  15  41.4  0.0336  0.249 - 0.438  0.995 - 1.023  1.105  0.0321  31.1   11473   10207
  16  46.2  0.0293  0.260 - 0.329  0.995 - 1.021  1.032  0.0321  31.1   10480    9133
  17  56.4  0.0295  0.239 - 0.435  0.995 - 1.023  1.020  0.0321  31.1   12425   11113
  18  61.2  0.0265  0.279 - 0.431  0.995 - 1.019  0.974  0.0321  31.1   12672   11128
  19  61.2  0.0261  0.267 - 0.435  0.995 - 1.018  0.991  0.0321  31.1   12599   10913
  20  71.4  0.0247  0.232 - 0.431  0.995 - 1.022  0.992  0.0321  31.1   14109   12576
  21  71.4  0.0267  0.279 - 0.428  0.995 - 1.020  0.948  0.0321  31.1   13804   11916
  22  71.4  0.0245  0.233 - 0.435  0.995 - 1.022  0.952  0.0321  31.1   14110   12622
  23  86.4  0.0278  0.279 - 0.429  0.995 - 1.020  0.917  0.0321  31.1   14458   12242
  24  86.4  0.0302  0.249 - 0.326  0.995 - 1.021  0.931  0.0321  31.1   14470   12275
  25  86.4  0.0247  0.232 - 0.415  0.995 - 1.023  0.921  0.0321  31.1   15259   13375
  26  86.4  0.0285  0.265 - 0.405  0.995 - 1.019  0.907  0.0321  31.1   14433   12100
  27  86.4  0.0258  0.234 - 0.292  0.995 - 1.018  0.933  0.0321  31.1    8876    7894
  28 101.4  0.0324  0.241 - 0.321  0.995 - 1.021  0.884  0.0321  31.1   13906   11511
  29 101.4  0.0301  0.260 - 0.395  0.995 - 1.022  0.893  0.0321  31.1    7811    6618
  30 101.4  0.0327  0.276 - 0.429  0.995 - 1.019  0.926  0.0321  31.1   13833   11298
  31 101.4  0.0339  0.265 - 0.392  0.995 - 1.018  0.915  0.0321  31.1   13912   11246
  32 101.4  0.0332  0.244 - 0.321  0.995 - 1.016  0.924  0.0321  31.1   13862   11483
  33 116.4  0.0397  0.233 - 0.311  0.995 - 1.020  0.912  0.0321  31.1   12105    9616
  34 116.4  0.0417  0.273 - 0.422  0.995 - 1.020  0.914  0.0321  31.1   12106    9652
  35 116.4  0.0397  0.220 - 0.268  0.995 - 1.019  0.915  0.0321  31.1   12144    9663
  36 116.4  0.0422  0.230 - 0.393  0.995 - 1.016  0.949  0.0321  31.1   12196    9684
  37 116.4  0.0393  0.244 - 0.411  0.995 - 1.016  0.924  0.0321  31.1   12072    9695
  38 116.4  0.0401  0.226 - 0.307  0.995 - 1.017  0.946  0.0321  31.1   12095    9583
  39 116.4  0.0430  0.256 - 0.402  0.995 - 1.020  0.951  0.0321  31.1   12264    9436
  40 116.4  0.0405  0.240 - 0.316  0.995 - 1.016  0.913  0.0321  31.1   12086    9779
  41 116.4  0.0994  0.439 - 0.654  0.995 - 1.020  2.071  0.0321  31.1   12881    8159
  42 116.4  0.0990  0.489 - 0.712  0.995 - 1.016  1.973  0.0321  31.1   12298    7720
  43 116.4  0.1074  0.439 - 0.705  0.995 - 1.022  1.938  0.0321  31.1   12493    7387
  44 116.4  0.0431  0.246 - 0.357  0.995 - 1.016  0.974  0.0321  31.1   12163    9818
  45 116.4  0.0973  0.487 - 0.679  0.995 - 1.021  2.001  0.0321  31.1   12900    8199
  46 116.4  0.0421  0.261 - 0.427  0.995 - 1.019  0.929  0.0321  31.1   12162    9677
  47 116.4  0.0399  0.248 - 0.334  0.995 - 1.016  0.940  0.0321  31.1   12152    9814
  48 116.4  0.0424  0.236 - 0.378  0.995 - 1.018  0.927  0.0321  31.1   12178    9708
  49 116.4  0.0385  0.209 - 0.276  0.995 - 1.020  0.932  0.0321  31.1    7051    5762
  50 116.4  0.0975  0.422 - 0.693  0.995 - 1.016  1.881  0.0321  31.1   12837    8444
  51 116.4  0.0416  0.251 - 0.387  0.995 - 1.020  0.922  0.0321  31.1   12192    9569
  52 116.4  0.0427  0.258 - 0.399  0.996 - 1.022  0.922  0.0321  31.1   12248    9418
  53 116.4  0.0396  0.249 - 0.423  0.995 - 1.017  0.892  0.0321  31.1   12096    9730
  54 116.4  0.0403  0.247 - 0.394  0.995 - 1.016  0.952  0.0321  31.1   12144    9817
  55 101.4  0.0286  0.232 - 0.398  0.995 - 1.023  0.878  0.0321  31.1   14833   12737
  56   0.0  0.0342  0.281 - 0.397  0.995 - 1.020  1.212  0.0321  31.1    5070    4356
  57  53.0  0.0339  0.322 - 0.367  0.995 - 1.015  1.188  0.0321  31.1     548     456
  58  89.0  0.0328  0.324 - 0.363  0.995 - 1.016  0.931  0.0321  31.1     648     518

       1 Overloads replaced by fast scan measurements
  592440 Corrected reflections written to file hkl
 Estimated minimum and maximum transmission:  0.8642  0.9253
 Additional spherical absorption correction applied with mu*r =  0.0480
 3lambda correction factor = 0.00150
;
_exptl_crystal_colour            colorless
_exptl_crystal_density_diffrn    1.500
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             456
_exptl_crystal_size_max          0.457
_exptl_crystal_size_mid          0.402
_exptl_crystal_size_min          0.340
_refine_diff_density_max         0.154
_refine_diff_density_min         -0.312
_refine_diff_density_rms         0.052
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.005
_refine_ls_hydrogen_treatment    refxyz
_refine_ls_matrix_type           full
_refine_ls_number_parameters     436
_refine_ls_number_reflns         19363
_refine_ls_number_restraints     34
_refine_ls_restrained_S_all      2.144
_refine_ls_R_factor_all          0.0182
_refine_ls_R_factor_gt           0.0182
_refine_ls_shift/su_max          -0.007
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef F
_refine_ls_weighting_details     'calc w =1/[4.3924*\s^2^(Fo^2^)]'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0286
_refine_ls_wR_factor_ref         0.0286
_reflns_Friedel_coverage         0.000
_reflns_number_gt                19363
_reflns_number_total             20648
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            lt5061.cif
_cod_data_source_block           I
_cod_original_sg_symbol_H-M      'P 21/n'
_cod_database_code               1569763