Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure.
Zwolenik, A.; Tchoń, D; Makal, A.; IUCrJ 11 (2024) –; doi:10.1107/S2052252524003634

data_1571603
_publ_section_title
;
 Evolution of structure and spectroscopic properties of a new
 1,3-diacetylpyrene polymorph with temperature and pressure.
;
_journal_issue                   4
_journal_name_full               IUCrJ
_journal_paper_doi               10.1107/S2052252524003634
_journal_volume                  11
_journal_year                    2024
_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
_audit_creation_date             2024-02-18
_audit_creation_method
;
Olex2 1.5-alpha
(compiled 2023.11.24 svn.r209d9fb for OlexSys, GUI svn.r6869)
;
_cell_angle_alpha                90
_cell_angle_beta                 100.735(12)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   6.8196(10)
_cell_length_b                   10.5519(14)
_cell_length_c                   17.3617(17)
_cell_measurement_reflns_used    1931
_cell_measurement_temperature    298
_cell_measurement_theta_max      20.0810
_cell_measurement_theta_min      1.7870
_cell_volume                     1227.5(3)
_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-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'olex2.refine 1.5-alpha (Bourhis et al., 2015)'
_computing_structure_solution    'SHELXS  (Sheldrick, 2008)'
_diffrn_ambient_temperature      571.15
_diffrn_crystal_treatment
'pressurized rapidly in silicone oil as a hydrostatic medium'
_diffrn_measured_fraction_theta_full 0.8973
_diffrn_measured_fraction_theta_max 0.8741
_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    -49.00  49.00   1.00    1.00    --    0.00   0.00   0.00   98
  2  \w    -49.00  49.00   1.00    5.00    --    0.00   0.00   0.00   98
  3  \w    -49.00  49.00   1.00    5.00    --    0.00  25.00   0.00   98
  4  \w    -49.00  49.00   1.00    5.00    --    0.00  45.00   0.00   98
;
_diffrn_measurement_device       'abstract diffractometer'
_diffrn_measurement_device_type
'esperanto-CrysAlisPro-abstract goniometer imported esperanto images'
_diffrn_measurement_method       '\w scans'
_diffrn_measurement_specimen_support
'Diamond Anvil Cell, effective opening angle of 52 deg.'
_diffrn_radiation_type           synchrotron
_diffrn_radiation_wavelength     0.41618
_diffrn_reflns_av_R_equivalents  0.1546
_diffrn_reflns_av_unetI/netI     0.0974
_diffrn_reflns_Laue_measured_fraction_full 0.8973
_diffrn_reflns_Laue_measured_fraction_max 0.8741
_diffrn_reflns_limit_h_max       9
_diffrn_reflns_limit_h_min       -11
_diffrn_reflns_limit_k_max       15
_diffrn_reflns_limit_k_min       -15
_diffrn_reflns_limit_l_max       27
_diffrn_reflns_limit_l_min       -26
_diffrn_reflns_number            26835
_diffrn_reflns_point_group_measured_fraction_full 0.8973
_diffrn_reflns_point_group_measured_fraction_max 0.8741
_diffrn_reflns_theta_full        14.4602
_diffrn_reflns_theta_max         17.29
_diffrn_reflns_theta_min         1.80
_exptl_absorpt_coefficient_mu    0.043
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.66598
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.43d (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear dark orange'
_exptl_crystal_colour_lustre     clear
_exptl_crystal_colour_modifier   dark
_exptl_crystal_colour_primary    orange
_exptl_crystal_density_diffrn    1.549
_exptl_crystal_description       irregular
_exptl_crystal_F_000             600.009
_exptl_crystal_preparation
'Mounted in a Diamond-Anvil Cell using silicone oil as pressure medium.'
_exptl_crystal_pressure_history  'Pressurized to 1.7 GPa.'
_exptl_crystal_size_max          0.2
_exptl_crystal_size_mid          0.15
_exptl_crystal_size_min          0.1
_refine_diff_density_max         0.4758
_refine_diff_density_min         -0.4787
_refine_diff_density_rms         0.1153
_refine_ls_d_res_high            0.7001
_refine_ls_d_res_low             6.6331
_refine_ls_extinction_coef       0.05(4)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_goodness_of_fit_ref   1.1178
_refine_ls_hydrogen_treatment    refall
_refine_ls_matrix_type           full
_refine_ls_number_constraints    0
_refine_ls_number_parameters     326
_refine_ls_number_reflns         3269
_refine_ls_number_restraints     186
_refine_ls_restrained_S_all      1.0840
_refine_ls_R_factor_all          0.1533
_refine_ls_R_factor_gt           0.0990
_refine_ls_shift/su_max          0.0009
_refine_ls_shift/su_mean         0.0001
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.2P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.2757
_refine_ls_wR_factor_ref         0.3359
_reflns_Friedel_coverage         0.0
_reflns_limit_h_max              9
_reflns_limit_h_min              -9
_reflns_limit_k_max              14
_reflns_limit_k_min              0
_reflns_limit_l_max              24
_reflns_limit_l_min              0
_reflns_number_gt                1875
_reflns_number_total             3269
_reflns_threshold_expression     I>=2u(I)
_cod_data_source_file            yc5047.cif
_cod_data_source_block           2oAPb_1p7GPa_HAR
_cod_database_code               1571603
_olex2_refinement_description
;
1. Restrained distances
 C18-H18b \\sim C18-H18c \\sim C18-H18a \\sim C20-H20a \\sim C20-H20c \\sim
C20-H20b
 with sigma of 0.02
2. Uiso/Uaniso restraints and constraints
C18 \\sim H18b \\sim H18c \\sim H18a: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 2A
C20 \\sim H20c \\sim H20a \\sim H20b: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 2A
Uanis(H20c) \\sim Ueq, Uanis(H20a) \\sim Ueq, Uanis(H18c) \\sim Ueq,
Uanis(H18a) \\sim Ueq, Uanis(H18b) \\sim Ueq: with sigma of 0.04 and sigma for
terminal atoms of 0.08
Uanis(H20b) \\sim Ueq: with sigma of 0.02 and sigma for terminal atoms of 0.04
Uanis(H14) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
3. Rigid body (RIGU) restrains
 C3, H3, C4, H4, C5, C6, H6, C7, H7, C8, H8, C9, C10, H10, C11, H11
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
;
_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:           2024-02-18_14-51-03
;
_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
;