Climbing Jacob’s Ladder of Structural Refinement: Introduction of a Localized Molecular Orbital-Based Embedding for Accurate X-ray Determinations of Hydrogen Atom Positions
Wieduwilt, Erna K.; Macetti, Giovanni; Genoni, Alessandro; The Journal of Physical Chemistry Letters  (2020) 463–471; doi:10.1021/acs.jpclett.0c03421

data_8000469
_publ_contact_author
;
    Dr. Alessandro Genoni
;
_publ_section_title
;
 Climbing Jacob&#x2019;s Ladder of Structural Refinement: Introduction of
 a Localized Molecular Orbital-Based Embedding for Accurate X-ray
 Determinations of Hydrogen Atom Positions
;
_journal_name_full               'The Journal of Physical Chemistry Letters'
_journal_page_first              463
_journal_page_last               471
_journal_paper_doi               10.1021/acs.jpclett.0c03421
_journal_year                    2020
_chemical_absolute_configuration unk
_chemical_formula_moiety         'C5 H12 O5'
_chemical_formula_sum            'C5 H12 O5'
_chemical_formula_weight         152.1484
_chemical_name_common            xylitol
_space_group_IT_number           19
_space_group_name_Hall           'P 2ac 2ab'
_space_group_name_H-M_alt        'P 21 21 21'
_symmetry_cell_setting           orthorhombic
_symmetry_Int_Tables_number      19
_symmetry_space_group_name_Hall  'P 2ac 2ab'
_symmetry_space_group_name_H-M   'P 21 21 21'
_atom_sites_solution_hydrogens   HAR
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   direct
_audit_creation_date             2020-7-28
_audit_creation_method           'Tonto 19.12.17 github v. dd352d58'
_cell_angle_alpha                90.000000(0)
_cell_angle_beta                 90.000000(0)
_cell_angle_gamma                90.000000(0)
_cell_formula_units_Z            4
_cell_length_a                   8.264(4)
_cell_length_b                   8.901(2)
_cell_length_c                   8.9223(14)
_cell_measurement_reflns_used    20
_cell_measurement_temperature    122.4(5)
_cell_volume                     656.3(4)
_diffrn_ambient_temperature      122.4(5)
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 1.000
_diffrn_measurement_device_type  'Enraf Nonius CAD4'
_diffrn_measurement_method       '\w 2\q scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0171
_diffrn_reflns_av_unetI/netI     0.0235
_diffrn_reflns_number            33102
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         59.940
_diffrn_reflns_theta_min         3.233
_exptl_absorpt_coefficient_mu    0.139
_exptl_absorpt_correction_type   none
_exptl_crystal_colour            colourless
_exptl_crystal_density_diffrn    1.540
_exptl_crystal_density_method    'not measured'
_exptl_crystal_description       prism
_exptl_crystal_F_000             328
_exptl_crystal_size_max          0.37
_exptl_crystal_size_mid          0.32
_exptl_crystal_size_min          0.26
_refine_diff_density_max         0.1280
_refine_diff_density_min         -0.1292
_refine_diff_density_rms         0.0307
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_all   0.8238
_refine_ls_goodness_of_fit_gt    0.8238
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_constraints    0
_refine_ls_number_parameters     199
_refine_ls_number_reflns         5407
_refine_ls_number_restraints     0
_refine_ls_R_factor_all          0.0180
_refine_ls_R_factor_gt           0.0180
_refine_ls_R_Fsqd_factor         0.0327
_refine_ls_shift/su_max          0.0000
_refine_ls_structure_factor_coef F
_refine_ls_weighting_details     w=1/\s(F)
_refine_ls_weighting_scheme      sigma
_refine_ls_wR_factor_all         0.0130
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_reflns_d_resolution_high        6.301475
_reflns_d_resolution_low         0.410587
_reflns_Friedel_coverage         0.000
_reflns_Friedel_fraction_full    0.000
_reflns_Friedel_fraction_max     0.000
_reflns_limit_h_max              20
_reflns_limit_h_min              0
_reflns_limit_k_max              21
_reflns_limit_k_min              0
_reflns_limit_l_max              21
_reflns_limit_l_min              0
_reflns_number_gt                5407
_reflns_number_total             5407
_reflns_threshold_expression     'F>0 & |F_calc|>10^-3'
_cod_data_source_file            xylitol_B3LYP-cc-pVDZ_ELMO4A.cif
_cod_data_source_block           xylitol_B3LYP-cc-pVDZ_ELMO4A
_cod_depositor_comments
;
The following automatic conversions were performed:

data item '_symmetry_cell_setting' value 'Orthorhombic' was changed
to 'orthorhombic' in accordance with the
/home/data/users/saulius/crontab/automatic-downloads/rss-feeds/ACS/lib/dictionaries/cif_core.dic
dictionary named 'cif_core.dic' version 2.4.2 last updated on
2011-04-26.

Automatic conversion script
Id: cif_fix_values 7556 2019-12-06 15:28:31Z antanas 
;
_cod_original_sg_symbol_Hall     'p 2ac 2ab'
_cod_original_sg_symbol_H-M      'p 21 21 21'
_cod_database_code               8000469
_qcr_software                    Tonto
_qcr_software_version            '19.12.17 v. dd352d58 modified'
_qcr_software_platform           Linux-4.15.0-72-generic
_qcr_software_build_date         '2019-12-17 16:54'
_qcr_software_website            https://github.com/dylan-jayatilaka/tonto
_qcr_calc_method                 'B3LYP/ELMO R=4.0 A'
_qcr_calc_gaussian_basis_set     cc-pVDZ
_qcr_calc_gaussian_basis_set_kind cartesian
_qcr_calc_unit_spin_multiplicity 1
_qcr_calc_unit_n_electrons       1394
_qcr_calc_unit_n_alpha_electrons 697
_qcr_calc_unit_n_beta_electrons  697
_refine_ls_kind                  'Hirshfeld atom refinement (HAR)'
_refine_ls_method_description
;
   S.C. Capelli, H.-B. Burgi, B. Dittrich, S.Grabowsky
   and Dylan Jayatilaka, IUCrJ (2014). 1, 361-379
;
_refine_qcr_psi_constraint       none
_refine_ls_svd_threshold         0.1E-02
_refine_ls_coordinate_system     cartesian
_refine_ls_shift/su_conv_tol     0.0150
_refine_ls_shift/su_max_mean     0.0000
_refine_ls_shift/su_max_par
;
;
_shelx_f_calc_maximum            79.320720