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

data_1573206
_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             2024-08-04
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_cell_angle_alpha                90
_cell_angle_beta                 104.385(7)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.2522(5)
_cell_length_b                   11.4389(8)
_cell_length_c                   17.7050(13)
_cell_measurement_reflns_used    3034
_cell_measurement_temperature    350.00(10)
_cell_measurement_theta_max      79.1690
_cell_measurement_theta_min      4.6270
_cell_volume                     1422.71(18)
_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      air
_diffrn_ambient_temperature      350.00(10)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.9852
_diffrn_measured_fraction_theta_max 0.9687
_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      -0.0485165578
_diffrn_orient_matrix_UB_12      0.0933634007
_diffrn_orient_matrix_UB_13      0.0547165287
_diffrn_orient_matrix_UB_21      0.1932976920
_diffrn_orient_matrix_UB_22      -0.0215031390
_diffrn_orient_matrix_UB_23      0.0584964782
_diffrn_orient_matrix_UB_31      0.0914647225
_diffrn_orient_matrix_UB_32      0.0945475498
_diffrn_orient_matrix_UB_33      -0.0408438935
_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  0.0309
_diffrn_reflns_av_unetI/netI     0.0303
_diffrn_reflns_Laue_measured_fraction_full 0.9852
_diffrn_reflns_Laue_measured_fraction_max 0.9687
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -7
_diffrn_reflns_limit_k_max       14
_diffrn_reflns_limit_k_min       -14
_diffrn_reflns_limit_l_max       21
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            9254
_diffrn_reflns_point_group_measured_fraction_full 0.9852
_diffrn_reflns_point_group_measured_fraction_max 0.9687
_diffrn_reflns_theta_full        67.6840
_diffrn_reflns_theta_max         79.33
_diffrn_reflns_theta_min         4.65
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.679
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.817
_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    1.337
_exptl_crystal_description       irregular
_exptl_crystal_F_000             601.956
_exptl_crystal_size_max          0.183
_exptl_crystal_size_mid          0.129
_exptl_crystal_size_min          0.107
_refine_diff_density_max         0.1500
_refine_diff_density_min         -0.1970
_refine_diff_density_rms         0.0368
_refine_ls_d_res_high            0.7845
_refine_ls_d_res_low             9.5163
_refine_ls_goodness_of_fit_ref   1.0112
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_constraints    0
_refine_ls_number_parameters     305
_refine_ls_number_reflns         3002
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.0112
_refine_ls_R_factor_all          0.0785
_refine_ls_R_factor_gt           0.0418
_refine_ls_shift/su_max          0.0005
_refine_ls_shift/su_mean         0.0001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0447P)^2^+0.1797P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1036
_refine_ls_wR_factor_ref         0.1345
_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                1685
_reflns_number_total             3002
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            pen5002.cif
_cod_data_source_block           350K
_cod_database_code               1573206
_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:           2024-03-29_16-39-36
;
_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 1.621
_oxdiff_exptl_absorpt_empirical_full_min 0.650