Fusion of pyrene and phenanthrene through 5<i>H</i>-imidazo[1,2-<i>a</i>]azepine scaffolds: structural tuning for fluorescence labeling and bacterial imaging.
Qiu, Nicholas P.; Eradeh, Ramin; Britt, Liam H.; Zhao, Yuming; Physical chemistry chemical physics : PCCP 28 (2026) 5880–5893; doi:10.1039/d5cp02942b

data_7251612
_publ_section_title
;
 Fusion of pyrene and phenanthrene through
 5<i>H</i>-imidazo[1,2-<i>a</i>]azepine scaffolds: structural tuning for
 fluorescence labeling and bacterial imaging.
;
_journal_issue                   9
_journal_name_full               'Physical chemistry chemical physics : PCCP'
_journal_page_first              5880
_journal_page_last               5893
_journal_paper_doi               10.1039/d5cp02942b
_journal_volume                  28
_journal_year                    2026
_chemical_formula_moiety         'C32 H18 N2 O'
_chemical_formula_sum            'C32 H18 N2 O'
_chemical_formula_weight         446.48
_space_group_crystal_system      orthorhombic
_space_group_IT_number           61
_space_group_name_Hall           '-P 2ac 2ab'
_space_group_name_H-M_alt        'P b c a'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_block_doi                 10.5517/ccdc.csd.cc2mkxmr
_audit_creation_date             2022-05-24
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6408)
;
_audit_update_record
;
2025-03-10 deposited with the CCDC.	2026-01-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_formula_units_Z            8
_cell_length_a                   12.4359(3)
_cell_length_b                   15.9420(6)
_cell_length_c                   21.1245(4)
_cell_measurement_reflns_used    5444
_cell_measurement_temperature    110(2)
_cell_measurement_theta_max      76.6280
_cell_measurement_theta_min      4.1890
_cell_volume                     4188.0(2)
_computing_cell_refinement       'CrysAlisPro 1.171.42.55a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.42.55a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.42.55a (Rigaku OD, 2022)'
_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 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      110(2)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 0.999
_diffrn_measured_fraction_theta_max 0.977
_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    -14.00  19.00   0.50   35.00    --  -48.45  16.00 100.00   66
  2  \w    -23.00  19.00   0.50   35.00    --   48.45 -16.00 -69.00   84
  3  \w   -151.00-110.00   0.50  100.00    --  -90.00-126.00  84.00   82
  4  \w     41.00 104.00   0.50  100.00    --  111.50-111.00 167.00  126
  5  \w    104.00 152.00   0.50  100.00    --  111.50  16.00 100.00   96
  6  \w    -13.00  26.00   0.50   35.00    --  -48.45  19.00-120.00   78
  7  \w    -34.00  12.00   0.50   35.00    --  -48.45  37.00-180.00   92
  8  \w    -67.00 -20.00   0.50   35.00    --  -48.45 125.00 -60.00   94
  9  \w    108.00 178.00   0.50  100.00    --  111.50  45.00-180.00  140
 10  \w     45.00 102.00   0.50  100.00    --  111.50-125.00 -90.00  114
 11  \w     55.00 107.00   0.50  100.00    --  111.50-125.00   0.00  104
 12  \w     40.00  77.00   0.50  100.00    --  111.50 -61.00  90.00   74
 13  \w     91.00 124.00   0.50  100.00    --  111.50-144.00 -83.00   66
 14  \w     40.00  68.00   0.50  100.00    --  111.50 -61.00  30.00   56
 15  \w    128.00 174.00   0.50  100.00    --  111.50  45.00  90.00   92
 16  \w     40.00  76.00   0.50  100.00    --  111.50 -61.00  60.00   72
 17  \w     52.00  77.00   0.50  100.00    --  111.50-126.00  84.00   50
 18  \w    -77.00 -52.00   0.50  100.00    --  -90.00 126.00 161.00   50
 19  \w   -119.00 -54.00   0.50   50.00    --  -48.32 -57.00 -60.00  130
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'XtaLAB Synergy, Dualflex, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0680075000
_diffrn_orient_matrix_UB_12      -0.0782322000
_diffrn_orient_matrix_UB_13      0.0147262000
_diffrn_orient_matrix_UB_21      -0.1032908000
_diffrn_orient_matrix_UB_22      -0.0533079000
_diffrn_orient_matrix_UB_23      0.0040242000
_diffrn_orient_matrix_UB_31      0.0080661000
_diffrn_orient_matrix_UB_32      -0.0190315000
_diffrn_orient_matrix_UB_33      -0.0713377000
_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  0.0828
_diffrn_reflns_av_unetI/netI     0.0627
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.977
_diffrn_reflns_limit_h_max       15
_diffrn_reflns_limit_h_min       -15
_diffrn_reflns_limit_k_max       19
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       19
_diffrn_reflns_limit_l_min       -26
_diffrn_reflns_number            21301
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.977
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.189
_diffrn_reflns_theta_min         4.186
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.676
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.58670
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.42.55a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    1.416
_exptl_crystal_description       prism
_exptl_crystal_F_000             1856
_exptl_crystal_size_max          0.128
_exptl_crystal_size_mid          0.092
_exptl_crystal_size_min          0.019
_refine_diff_density_max         0.337
_refine_diff_density_min         -0.317
_refine_diff_density_rms         0.098
_refine_ls_extinction_coef       0.00119(15)
_refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
_refine_ls_extinction_method     'SHELXL-2018/3 (Sheldrick 2018)'
_refine_ls_goodness_of_fit_ref   1.037
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     320
_refine_ls_number_reflns         4433
_refine_ls_number_restraints     1
_refine_ls_restrained_S_all      1.038
_refine_ls_R_factor_all          0.0890
_refine_ls_R_factor_gt           0.0565
_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^)+(0.0708P)^2^+1.9554P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1329
_refine_ls_wR_factor_ref         0.1500
_reflns_Friedel_coverage         0.000
_reflns_number_gt                3071
_reflns_number_total             4433
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cp02942b2.cif
_cod_data_source_block           nq01
_cod_depositor_comments
'Adding full bibliography for 7251612--7251614.cif.'
_cod_database_code               7251612
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C32H20N2O
_shelx_estimated_absorpt_t_max   0.987
_shelx_estimated_absorpt_t_min   0.918
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  H5 of C5, H1A of C1, H8 of C8, H12 of C12, H13 of C13, H4 of C4, H20 of C20,
   H11 of C11, H9 of C9, H6 of C6, H21 of C21, H27 of C27, H29 of C29, H25 of
  C25, H28 of C28, H22 of C22, H24 of C24
 At 1.5 times of:
  H1 of C24
2. Restrained distances
 O1-H1
 0.84 with sigma of 0.02
3.a Ternary CH refined with riding coordinates:
 C1(H1A)
3.b Aromatic/amide H refined with riding coordinates:
 C4(H4), C5(H5), C6(H6), C8(H8), C9(H9), C11(H11), C12(H12), C13(H13),
 C20(H20), C21(H21), C22(H22), C24(H24), C25(H25), C27(H27), C28(H28), C29(H29)
;
_shelx_res_checksum              75210
_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 2.098
_oxdiff_exptl_absorpt_empirical_full_min 0.385