Pyridinium modification of a hexaazaphenalene skeleton: structure and spectroelectrochemical analysis
Deekamwong, Krittanun; Usov, Pavel M.; Ohtsu, Hiroyoshi; Kawano, Masaki; CrystEngComm  (2020) –; doi:10.1039/D0CE00850H

data_7240990
_publ_section_title
;
 Pyridinium modification of a hexaazaphenalene skeleton: structure and
 spectroelectrochemical analysis
;
_journal_name_full               CrystEngComm
_journal_paper_doi               10.1039/D0CE00850H
_journal_year                    2020
_chemical_formula_moiety
'2(C22 H12 N9), 1.983(C16 H36 N), 11.894(H2 O), 2.106(O), 0.277(C H2)'
_chemical_formula_sum            'C76 H119.79 N20 O14'
_chemical_formula_weight         1537.70
_chemical_name_systematic        TBATPHAP
_chemical_properties_physical    Hygroscopic,Photo-sensitive
_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'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2020-04-09
_audit_creation_method
;
Olex2 1.3
(compiled 2020.02.04 svn.rd84adfe8 for OlexSys, GUI svn.r6032)
;
_audit_update_record
;
2020-06-05 deposited with the CCDC.	2020-08-04 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90.527(4)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   18.7617(8)
_cell_length_b                   21.4672(9)
_cell_length_c                   20.4528(8)
_cell_measurement_reflns_used    18855
_cell_measurement_temperature    123(2)
_cell_measurement_theta_max      30.2550
_cell_measurement_theta_min      2.4200
_cell_volume                     8237.2(6)
_computing_cell_refinement       'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_data_collection       'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_data_reduction        'CrysAlisPro 1.171.39.43c (Rigaku OD, 2018)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2014/5 (Sheldrick, 2014)'
_diffrn_ambient_temperature      123(2)
_diffrn_detector                 'CCD plate'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.994
_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   -115.00  65.00   0.50    8.00    --  -25.00  45.00   0.00  360
  2  \w   -115.00  65.00   0.50    8.00    --  -25.00  45.00  90.00  360
  3  \w   -115.00  65.00   0.50    8.00    --  -25.00  45.00 180.00  360
  4  \w   -115.00  65.00   0.50    8.00    --  -25.00  45.00 240.00  360
;
_diffrn_measurement_device       'abstract diffractometer'
_diffrn_measurement_device_type
'dtrek-CrysAlisPro-abstract goniometer imported rigaku-d*trek images'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      -0.0003884000
_diffrn_orient_matrix_UB_12      -0.0330232000
_diffrn_orient_matrix_UB_13      -0.0011317000
_diffrn_orient_matrix_UB_21      0.0153721000
_diffrn_orient_matrix_UB_22      -0.0011156000
_diffrn_orient_matrix_UB_23      0.0317930000
_diffrn_orient_matrix_UB_31      -0.0345413000
_diffrn_orient_matrix_UB_32      -0.0001153000
_diffrn_orient_matrix_UB_33      0.0138029000
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.2004
_diffrn_reflns_av_unetI/netI     0.1485
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.994
_diffrn_reflns_limit_h_max       24
_diffrn_reflns_limit_h_min       -24
_diffrn_reflns_limit_k_max       27
_diffrn_reflns_limit_k_min       -27
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -26
_diffrn_reflns_number            114625
_diffrn_reflns_point_group_measured_fraction_full 0.998
_diffrn_reflns_point_group_measured_fraction_max 0.994
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         27.559
_diffrn_reflns_theta_min         2.578
_diffrn_source                   'fine-focus sealed X-ray tube'
_diffrn_source_type              'Enhance (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    0.087
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.89585
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.39.43c (Rigaku Oxford Diffraction, 2018)
Empirical absorption correction using spherical harmonics,
 implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            Yellow
_exptl_crystal_density_diffrn    1.240
_exptl_crystal_description       Plate
_exptl_crystal_F_000             3311
_exptl_crystal_recrystallization_method
'Re-crystallisation from solvent: DMSO/H2O'
_exptl_crystal_size_max          0.077
_exptl_crystal_size_mid          0.067
_exptl_crystal_size_min          0.022
_refine_diff_density_max         0.501
_refine_diff_density_min         -0.416
_refine_diff_density_rms         0.067
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.015
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1055
_refine_ls_number_reflns         18933
_refine_ls_number_restraints     47
_refine_ls_restrained_S_all      1.015
_refine_ls_R_factor_all          0.2122
_refine_ls_R_factor_gt           0.0896
_refine_ls_shift/su_max          0.000
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0831P)^2^+0.6230P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1741
_refine_ls_wR_factor_ref         0.2239
_reflns_Friedel_coverage         0.000
_reflns_number_gt                8166
_reflns_number_total             18933
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d0ce00850h2.cif
_cod_data_source_block           TBATPHAP
_cod_database_code               7240990
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C22H12N9
_reflns_odcompleteness_completeness 99.32
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     27.50
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 C3-H3F
 0.97 with sigma of 0.02
 C3-H3E
 0.97 with sigma of 0.02
 H3F-H3E
 1.57 with sigma of 0.04
3. Rigid bond restraints
 C18E, C17E, C16E, C15E
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C17E, C3
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
4. Uiso/Uaniso restraints and constraints
C18E \\sim C17E \\sim C16E \\sim C15E: within 2A with sigma of 0.04 and sigma
for terminal atoms of 0.08 within 2A
C3 \\sim C17E: within 2A with sigma of 0.04 and sigma for terminal atoms of
0.08 within 2A
Uanis(O15) = Uanis(O10)
5. Rigid body (RIGU) restrains
 C18E, C17E, C16E, C15E
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C17E, C3
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
6. Others
 Sof(C3)=Sof(H3E)=Sof(H3F)=1-FVAR(1)
 Sof(C17E)=Sof(H17D)=Sof(H17E)=FVAR(1)
 Sof(O15)=1-FVAR(2)
 Sof(O10)=Sof(H10E)=Sof(H10F)=FVAR(2)
7.a Free rotating group:
 O5(H5C,H5D), O2(H2C,H2D), O1(H1A,H1B), O4(H4A,H4B), O6(H6C,H6D), O14(H14C,
 H14D), O13(H13G,H13H), O3(H3C,H3D), O9(H9A,H9B), O7(H7A,H7B), O8(H8A,H8B),
 O10(H10E,H10F)
7.b Secondary CH2 refined with riding coordinates:
 C2C(H2CA,H2CB), C3C(H3CA,H3CB), C4C(H4CA,H4CB), C6C(H6CA,H6CB), C7C(H7CA,
 H7CB), C8C(H8CA,H8CB), C10C(H10A,H10B), C11C(H11A,H11B), C12C(H12A,H12B),
 C14C(H14A,H14B), C15C(H15A,H15B), C16C(H16A,H16B), C2D(H2DA,H2DB), C3D(H3DA,
 H3DB), C4D(H4DA,H4DB), C6D(H6DA,H6DB), C7D(H7DA,H7DB), C8D(H8DA,H8DB),
 C10D(H10C,H10D), C11D(H11C,H11D), C12D(H12C,H12D), C15E(H15C,H15D), C16E(H16C,
 H16D), C17E(H17D,H17E)
7.c Aromatic/amide H refined with riding coordinates:
 C2B(H2B), C3B(H3B), C5B(H5B), C6B(H6B), C21B(H21B), C22B(H22B), C24B(H24B),
 C25B(H25B), C27B(H27B), C28B(H28B), C30B(H30B), C31B(H31B), C2A(H2A), C3A(H3A),
  C5A(H5A), C6A(H6A), C21A(H21A), C22A(H22A), C24A(H24A), C25A(H25A),
 C27A(H27A), C28A(H28A), C30A(H30A), C31A(H31A)
7.d Idealised Me refined as rotating group:
 C5C(H5CA,H5CB,H5CC), C9C(H9CA,H9CB,H9CC), C13C(H13A,H13B,H13C), C17C(H17A,
 H17B,H17C), C5D(H5DA,H5DB,H5DC), C9D(H9DA,H9DB,H9DC), C13D(H13D,H13E,H13F),
 C18E(H18A,H18B,H18C)
;
_shelx_res_checksum              6926
_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
- Detector area scaling
;
_oxdiff_exptl_absorpt_empirical_full_max 1.116
_oxdiff_exptl_absorpt_empirical_full_min 0.923