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

data_1573201
_publ_section_title
;
 Tracking anharmonic oscillations in the structure of
 &#x3b2;-1,3-diacetylpyrene.
;
_journal_coeditor_code           PEN5002
_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     direct
_audit_creation_date             2024-08-09
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_cell_angle_alpha                90
_cell_angle_beta                 102.584(3)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   7.14940(18)
_cell_length_b                   10.9139(3)
_cell_length_c                   17.7592(5)
_cell_measurement_reflns_used    5835
_cell_measurement_temperature    109.99(12)
_cell_measurement_theta_max      77.0810
_cell_measurement_theta_min      4.7730
_cell_volume                     1352.42(7)
_computing_cell_refinement       'CrysAlisPro 1.171.39.43d (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.43d (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.43d (Rigaku OD, 2018)'
_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    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      109.99(12)
_diffrn_detector                 'CCD plate'
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.9992
_diffrn_measured_fraction_theta_max 0.9916
_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    -22.00  32.00   0.50    0.10    --    0.00  52.00 -16.00  108
  2  \w     39.00  65.00   0.50    0.10    --    0.00  52.00 -16.00   52
  3  \w     -1.00  25.00   0.50    0.30    --   66.60 -52.00-161.00   52
  4  \w     29.00 124.00   0.50    0.30    --   66.60  52.00 -16.00  190
  5  \w     61.00  94.00   0.50    0.30    --   66.60 -52.00-161.00   66
  6  \w     45.00  74.00   0.50    0.30    --  121.75 -52.00-161.00   58
  7  \w    -43.00  20.00   0.50    0.10    --    0.00  77.00-180.00  126
  8  \w    -37.00  40.00   0.50    0.10    --    0.00 -77.00 -30.00  154
  9  \w    -77.00 -45.00   0.50    0.10    --    0.00 -77.00 -30.00   64
 10  \w     -8.00  33.00   0.50    0.10    --    0.00 -52.00-161.00   82
 11  \w      0.00  54.00   0.50    0.10    --    0.00 -99.00-180.00  108
 12  \w    -78.00 -21.00   0.50    0.10    --    0.00 -52.00-161.00  114
 13  \w     11.00  53.00   0.50    0.10    --    0.00 -99.00-120.00   84
 14  \w     24.00 149.00   0.50    0.30    --   66.60  77.00  60.00  250
 15  \w     24.00 150.00   0.50    0.30    --   66.60  77.00-150.00  252
 16  \w     34.00 109.00   0.50    0.30    --   66.60-125.00 -90.00  150
 17  \w    115.00 141.00   0.50    0.30    --   66.60  77.00 114.06   52
 18  \w     25.00  79.00   0.50    0.30    --   66.60  77.00-180.00  108
 19  \w     97.00 150.00   0.50    0.30    --   66.60 125.00 -90.00  106
 20  \w    118.00 150.00   0.50    0.30    --   66.60 125.00-180.00   64
 21  \w    108.00 152.00   0.50    0.30    --   66.60  77.00 -30.00   88
 22  \w     24.00 150.00   0.50    0.30    --   66.60  77.00 150.00  252
 23  \w     24.00  59.00   0.50    0.30    --   66.60  77.00 -60.00   70
 24  \w     81.00 141.00   0.50    0.30    --   66.60  77.00  30.00  120
 25  \w     97.00 148.00   0.50    0.30    --   66.60 125.00 120.00  102
 26  \w     24.00  69.00   0.50    0.30    --   66.60  77.00   0.00   90
 27  \w    107.00 146.00   0.50    0.30    --   66.60  77.00-180.00   78
 28  \w     24.00  69.00   0.50    0.30    --   66.60  77.00 114.06   90
 29  \w     25.00  78.00   0.50    0.30    --   66.60  77.00  30.00  106
 30  \w     26.00  70.00   0.50    0.30    --   66.60  77.00 -90.00   88
 31  \w     24.00  60.00   0.50    0.30    --   66.60  77.00  90.00   72
 32  \w     24.00  57.00   0.50    0.30    --   66.60  77.00 -30.00   66
 33  \w     24.00  71.00   0.50    0.30    --   66.60  77.00-120.00   94
 34  \w     88.00 152.00   0.50    0.30    --   66.60  77.00-120.00  128
 35  \w     66.00 108.00   0.50    0.30    --   66.60-125.00 150.00   84
 36  \w     88.00 146.00   0.50    0.30    --   66.60  77.00  90.00  116
 37  \w    112.00 138.00   0.50    0.30    --   66.60  77.00 -90.00   52
 38  \w     84.00 152.00   0.50    0.30    --   66.60  77.00 -60.00  136
 39  \w     79.00 105.00   0.50    0.30    --  121.75  76.00 -66.31   52
 40  \w     83.00 113.00   0.50    0.30    --  121.75  68.00  55.50   60
 41  \w     84.00 113.00   0.50    0.30    --  121.75  67.00 173.08   58
 42  \w    138.00 178.00   0.50    0.30    --  121.75  63.00 150.00   80
 43  \w     85.00 110.00   0.50    0.30    --  121.75  63.00 150.00   50
 44  \w     53.00 108.00   0.50    0.30    --  121.75-111.00 -60.00  110
 45  \w     32.00  83.00   0.50    0.30    --  121.75 -91.00-150.00  102
 46  \w    145.00 176.00   0.50    0.30    --  121.75  77.00 -60.00   62
 47  \w     85.00 175.00   0.50    0.30    --  121.75  63.00   0.00  180
 48  \w     79.00 139.00   0.50    0.30    --  121.75  77.00 -60.00  120
 49  \w    145.00 178.00   0.50    0.30    --  121.75  63.00-120.00   66
 50  \w     86.00 142.00   0.50    0.30    --  121.75  63.00-120.00  112
 51  \w     82.00 108.00   0.50    0.30    --  121.75  70.00-107.63   52
 52  \w     46.00 106.00   0.50    0.30    --  121.75-111.00  30.00  120
 53  \w     79.00 132.00   0.50    0.30    --  121.75  77.00  30.00  106
 54  \w    133.00 159.00   0.50    0.30    --  121.75  77.00   0.00   52
 55  \w     80.00 177.00   0.50    0.30    --  121.75  77.00  60.00  194
 56  \w     79.00 174.00   0.50    0.30    --  121.75  77.00 120.00  190
 57  \w     34.00  95.00   0.50    0.30    --  121.75 -91.00 150.00  122
 58  \w     79.00 115.00   0.50    0.30    --  121.75  77.00   0.00   72
 59  \w     79.00 114.00   0.50    0.30    --  121.75  77.00  90.00   70
 60  \w    118.00 147.00   0.50    0.30    --  121.75  77.00  90.00   58
 61  \w    121.00 178.00   0.50    0.30    --  121.75  72.00-140.82  114
 62  \w     80.00 113.00   0.50    0.30    --  121.75  72.00-140.82   66
 63  \w    119.00 145.00   0.50    0.30    --  121.75  77.00 -30.00   52
 64  \w     85.00 163.00   0.50    0.30    --  121.75  63.00-150.00  156
 65  \w     49.00 108.00   0.50    0.30    --  121.75-111.00  90.00  118
 66  \w    132.00 172.00   0.50    0.30    --  121.75  68.00  55.50   80
 67  \w     80.00 109.00   0.50    0.30    --  121.75  77.00 -30.00   58
 68  \w    115.00 158.00   0.50    0.30    --  121.75  76.00 -66.31   86
 69  \w     44.00 108.00   0.50    0.30    --  121.75-111.00-150.00  128
 70  \w     38.00  86.00   0.50    0.30    --  121.75 -91.00 120.00   96
 71  \w    141.00 172.00   0.50    0.30    --  121.75  77.00 -90.00   62
 72  \w    144.00 177.00   0.50    0.30    --  121.75  77.00 100.66   66
 73  \w     86.00 170.00   0.50    0.30    --  121.75  60.00  26.94  168
 74  \w     79.00 116.00   0.50    0.30    --  121.75  77.00 -90.00   74
 75  \w     79.00 139.00   0.50    0.30    --  121.75  77.00 100.66  120
;
_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      -0.0759220706
_diffrn_orient_matrix_UB_12      -0.1321599966
_diffrn_orient_matrix_UB_13      -0.0005440199
_diffrn_orient_matrix_UB_21      0.1871087465
_diffrn_orient_matrix_UB_22      -0.0391624315
_diffrn_orient_matrix_UB_23      0.0556416354
_diffrn_orient_matrix_UB_31      -0.0890548812
_diffrn_orient_matrix_UB_32      0.0305439480
_diffrn_orient_matrix_UB_33      0.0693389950
_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  0.0403
_diffrn_reflns_av_unetI/netI     0.0230
_diffrn_reflns_Laue_measured_fraction_full 0.9992
_diffrn_reflns_Laue_measured_fraction_max 0.9916
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -8
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -21
_diffrn_reflns_number            20709
_diffrn_reflns_point_group_measured_fraction_full 0.9992
_diffrn_reflns_point_group_measured_fraction_max 0.9916
_diffrn_reflns_theta_full        67.6840
_diffrn_reflns_theta_max         77.51
_diffrn_reflns_theta_min         4.79
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'SuperNova (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.714
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.731
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.43d (Rigaku Oxford Diffraction, 2018)
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    1.406
_exptl_crystal_description       irregular
_exptl_crystal_F_000             601.956
_exptl_crystal_size_max          0.175
_exptl_crystal_size_mid          0.135
_exptl_crystal_size_min          0.093
_refine_diff_density_max         0.1301
_refine_diff_density_min         -0.1126
_refine_diff_density_rms         0.0302
_refine_ls_d_res_high            0.7896
_refine_ls_d_res_low             9.2355
_refine_ls_goodness_of_fit_ref   1.0543
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_constraints    0
_refine_ls_number_parameters     325
_refine_ls_number_reflns         2847
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.0543
_refine_ls_R_factor_all          0.0287
_refine_ls_R_factor_gt           0.0229
_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^)+(0.0210P)^2^+0.0993P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0543
_refine_ls_wR_factor_ref         0.0567
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              8
_reflns_limit_h_min              -9
_reflns_limit_k_max              13
_reflns_limit_k_min              0
_reflns_limit_l_max              22
_reflns_limit_l_min              0
_reflns_number_gt                2431
_reflns_number_total             2847
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            pen5002.cif
_cod_data_source_block           110K
_cod_original_cell_volume        1352.42(6)
_cod_database_code               1573201
_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_15-02-08
;
_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 1.202
_oxdiff_exptl_absorpt_empirical_full_min 0.895