Tracking anharmonic oscillations in the structure of β-1,3-diacetylpyrene.
Zwolenik, A.; Makal, A.; IUCrJ 12 (2025) –; doi:10.1107/S2052252524010443

data_1573204
_publ_section_title
;
 Tracking anharmonic oscillations in the structure of
 &#x3b2;-1,3-diacetylpyrene.
;
_journal_issue                   1
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252524010443
_journal_volume                  12
_journal_year                    2025
_chemical_formula_moiety         'C20 H14 O2'
_chemical_formula_sum            'C20 H14 O2'
_chemical_formula_weight         286.333
_space_group_crystal_system      monoclinic
_space_group_IT_number           14
_space_group_name_Hall           '-P 2ybc'
_space_group_name_H-M_alt        'P 1 21/c 1'
_symmetry_Int_Tables_number      14
_atom_sites_solution_primary     dual
_audit_creation_date             2024-08-02
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_cell_angle_alpha                90
_cell_angle_beta                 103.161(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.2211(2)
_cell_length_b                   11.0779(3)
_cell_length_c                   17.7769(5)
_cell_measurement_reflns_used    4768
_cell_measurement_temperature    250.00(10)
_cell_measurement_theta_max      78.8980
_cell_measurement_theta_min      4.7240
_cell_volume                     1384.70(7)
_computing_cell_refinement       'CrysAlisPro 1.171.43.104a (Rigaku OD, 2023)'
_computing_data_collection
'CrysAlisPro system (CCD 42.70a 64-bit (release 22-09-2022))'
_computing_data_reduction        'CrysAlisPro 1.171.43.104a (Rigaku OD, 2023)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5 (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      250.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.9968
_diffrn_measured_fraction_theta_max 0.9873
_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    -96.00   3.00   0.50    0.40    --  -38.96 -60.00 100.00  198
  2  \w     84.00 141.00   0.50    1.60    --   84.48  60.00-120.00  114
  3  \w      7.00 124.00   0.50    1.60    --   84.48 -60.00 100.00  234
  4  \w    126.00 168.00   0.50    3.20    --  130.00 -60.00 100.00   84
  5  \w     42.00 109.00   0.50    3.20    --  130.00 -60.00 100.00  134
  6  \w    149.00 178.00   0.50    3.20    --  130.00  60.00-120.00   58
  7  \w   -129.00 -88.00   0.50    0.40    --  -38.96 -99.00-120.00   82
  8  \w   -103.00 -74.00   0.50    0.40    --  -38.96-125.00-180.00   58
  9  \w    -39.00  42.00   0.50    0.40    --  -38.96  60.00-120.00  162
 10  \w     41.00 111.00   0.50    0.40    --   38.96-125.00   0.00  140
 11  \w    110.00 169.00   0.50    1.60    --   84.48 111.00  30.00  118
 12  \w    103.00 132.00   0.50    1.60    --   84.48  63.00-180.00   58
 13  \w    108.00 148.00   0.50    1.60    --   84.48 111.00-150.00   80
 14  \w    145.00 171.00   0.50    1.60    --   84.48  63.00-180.00   52
 15  \w    120.00 145.00   0.50    1.60    --   84.48 178.00  30.00   50
 16  \w     63.00 118.00   0.50    1.60    --   84.48 178.00  90.00  110
 17  \w     75.00 108.00   0.50    1.60    --   84.48 178.00 150.00   66
 18  \w     24.00 107.00   0.50    1.60    --   84.48-111.00 120.00  166
 19  \w     24.00 108.00   0.50    1.60    --   84.48-111.00  60.00  168
 20  \w     54.00 101.00   0.50    3.20    --  130.00-104.00-180.00   94
 21  \w    142.00 177.00   0.50    3.20    --  130.00 104.00 120.00   70
 22  \w    151.00 176.00   0.50    3.20    --  130.00  63.00-180.00   50
 23  \w     63.00 102.00   0.50    3.20    --  130.00 -50.00 -30.00   78
 24  \w    117.00 165.00   0.50    3.20    --  130.00  50.00-150.00   96
 25  \w    102.00 134.00   0.50    3.20    --  130.00  63.00-180.00   64
 26  \w     37.00 107.00   0.50    3.20    --  130.00-104.00  90.00  140
 27  \w    136.00 173.00   0.50    3.20    --  130.00   0.00  90.00   74
 28  \w     36.00 105.00   0.50    3.20    --  130.00   0.00  90.00  138
 29  \w     31.00  77.00   0.50    3.20    --  130.00 -91.00  30.00   92
 30  \w     36.00  87.00   0.50    3.20    --  130.00-104.00-150.00  102
 31  \w     33.00 104.00   0.50    3.20    --  130.00 -91.00  90.00  142
 32  \w    130.00 155.00   0.50    3.20    --  130.00 -50.00 -30.00   50
 33  \w     91.00 167.00   0.50    3.20    --  130.00 138.00 -30.00  152
 34  \w     89.00 122.00   0.50    3.20    --  130.00  77.00 -60.00   66
 35  \w    121.00 173.00   0.50    3.20    --  130.00 104.00 -60.00  104
 36  \w     48.00  73.00   0.50    3.20    --  130.00 -91.00   0.00   50
 37  \w     42.00  72.00   0.50    3.20    --  130.00-104.00 150.00   60
 38  \w     36.00  67.00   0.50    3.20    --  130.00-104.00  30.00   62
 39  \w    107.00 163.00   0.50    3.20    --  130.00 104.00-180.00  112
 40  \w    153.00 178.00   0.50    3.20    --  130.00  38.00  30.00   50
 41  \w     95.00 120.00   0.50    3.20    --  130.00 -38.00 120.00   50
 42  \w    149.00 178.00   0.50    3.20    --  130.00 -38.00 120.00   58
 43  \w     67.00  97.00   0.50    3.20    --  130.00  38.00  30.00   60
 44  \w    129.00 154.00   0.50    3.20    --  130.00  63.00 -90.00   50
 45  \w    119.00 144.00   0.50    3.20    --  130.00 104.00 150.00   50
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'SuperNova, Dual, Cu at home/near, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0550282363
_diffrn_orient_matrix_UB_12      0.0968070342
_diffrn_orient_matrix_UB_13      -0.0531951463
_diffrn_orient_matrix_UB_21      -0.1910358620
_diffrn_orient_matrix_UB_22      -0.0192090967
_diffrn_orient_matrix_UB_23      -0.0583781870
_diffrn_orient_matrix_UB_31      -0.0918746673
_diffrn_orient_matrix_UB_32      0.0979682638
_diffrn_orient_matrix_UB_33      0.0411236177
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Cu K\a'
_diffrn_radiation_wavelength     1.54184
_diffrn_reflns_av_R_equivalents  0.0248
_diffrn_reflns_av_unetI/netI     0.0282
_diffrn_reflns_Laue_measured_fraction_full 0.9968
_diffrn_reflns_Laue_measured_fraction_max 0.9873
_diffrn_reflns_limit_h_max       7
_diffrn_reflns_limit_h_min       -9
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -21
_diffrn_reflns_number            9298
_diffrn_reflns_point_group_measured_fraction_full 0.9968
_diffrn_reflns_point_group_measured_fraction_max 0.9873
_diffrn_reflns_theta_full        67.6840
_diffrn_reflns_theta_max         79.17
_diffrn_reflns_theta_min         4.74
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.698
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.836
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.104a (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    1.373
_exptl_crystal_description       irregular
_exptl_crystal_F_000             601.956
_exptl_crystal_size_max          0.18
_exptl_crystal_size_mid          0.13
_exptl_crystal_size_min          0.11
_refine_diff_density_max         0.1070
_refine_diff_density_min         -0.1198
_refine_diff_density_rms         0.0256
_refine_ls_d_res_high            0.7849
_refine_ls_d_res_low             9.3307
_refine_ls_goodness_of_fit_ref   1.0489
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_constraints    0
_refine_ls_number_parameters     375
_refine_ls_number_reflns         2964
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.0489
_refine_ls_R_factor_all          0.0319
_refine_ls_R_factor_gt           0.0245
_refine_ls_shift/su_max          0.0002
_refine_ls_shift/su_mean         0.0000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0087P)^2^+0.0475P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0524
_refine_ls_wR_factor_ref         0.0552
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              8
_reflns_limit_h_min              -9
_reflns_limit_k_max              14
_reflns_limit_k_min              0
_reflns_limit_l_max              22
_reflns_limit_l_min              0
_reflns_number_gt                2379
_reflns_number_total             2964
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            pen5002.cif
_cod_data_source_block           250K
_cod_database_code               1573204
_chemical_oxdiff_formula         'C20 H14 O2'
_olex2_refinement_description
;
;
_olex2_refine_details
;
Refinement using NoSpherA2, an implementation of
NOn-SPHERical Atom-form-factors in Olex2.
Please cite:
F. Kleemiss et al. Chem. Sci. DOI 10.1039/D0SC05526C - 2021
NoSpherA2 implementation of HAR makes use of
tailor-made aspherical atomic form factors calculated
on-the-fly from a Hirshfeld-partitioned electron density (ED) - not from
spherical-atom form factors.

The ED is calculated from a gaussian basis set single determinant SCF
wavefunction - either Hartree-Fock or DFT using selected funtionals
 - for a fragment of the crystal.
This fragment can be embedded in an electrostatic crystal field by employing cluster charges
or modelled using implicit solvation models, depending on the software used.
The following options were used:
   SOFTWARE:       ORCA 5.0
   PARTITIONING:   NoSpherA2
   INT ACCURACY:   Normal
   METHOD:         B3LYP
   BASIS SET:      6-31G(d,p)
   CHARGE:         0
   MULTIPLICITY:   1
   DATE:           2024-08-02_16-36-42
;
_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 1.113
_oxdiff_exptl_absorpt_empirical_full_min 0.868