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_7251614
_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 H16 N2 O'
_chemical_formula_sum            'C32 H16 N2 O'
_chemical_formula_weight         444.47
_space_group_crystal_system      monoclinic
_space_group_IT_number           7
_space_group_name_Hall           'P -2yac'
_space_group_name_H-M_alt        'P 1 n 1'
_atom_sites_solution_hydrogens   geom
_atom_sites_solution_primary     dual
_audit_creation_date             2022-03-09
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6408)
;
_audit_update_record
;
2023-04-13 deposited with the CCDC.	2026-01-26 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 96.658(2)
_cell_angle_gamma                90
_cell_formula_units_Z            2
_cell_length_a                   3.95070(10)
_cell_length_b                   17.9552(4)
_cell_length_c                   13.8102(4)
_cell_measurement_reflns_used    6963
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      73.8080
_cell_measurement_theta_min      4.0440
_cell_volume                     973.03(4)
_computing_cell_refinement       'CrysAlisPro 1.171.41.123a (Rigaku OD, 2022)'
_computing_data_collection       'CrysAlisPro 1.171.41.123a (Rigaku OD, 2022)'
_computing_data_reduction        'CrysAlisPro 1.171.41.123a (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      100(2)
_diffrn_detector                 'Hybrid Pixel Array Detector'
_diffrn_detector_area_resol_mean 10.0000
_diffrn_detector_type            HyPix
_diffrn_measured_fraction_theta_full 1.000
_diffrn_measured_fraction_theta_max 0.980
_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   -120.00 -38.00   0.50    5.00    --  -48.31 -42.00  -7.00  164
  2  \w    -40.00  23.00   0.50    5.00    --  -48.31  42.00 144.00  126
  3  \w    -23.00  54.00   0.50    5.00    --   48.31 -42.00  -7.00  154
  4  \w     38.00 120.00   0.50    5.00    --   48.31  42.00 144.00  164
  5  \w   -161.00 -79.00   0.50   35.00    --  -90.00 -42.00  -7.00  164
  6  \w    101.00 178.00   0.50   35.00    --  111.50  42.00 144.00  154
  7  \w   -119.00 -34.00   0.50    5.00    --  -48.31 -57.00-120.00  170
  8  \w   -120.00 -38.00   0.50    5.00    --  -48.31 -40.00 -93.77  164
  9  \w   -119.00 -73.00   0.50    5.00    --  -48.31-125.00  60.00   92
 10  \w   -119.00 -27.00   0.50    5.00    --  -48.31 -77.00-150.00  184
 11  \w     38.00 121.00   0.50    5.00    --   48.31  37.00-120.00  166
 12  \w     34.00  95.00   0.50    5.00    --   48.31-125.00-120.00  122
 13  \w   -161.00 -72.00   0.50   35.00    --  -90.00 -68.00-138.68  178
 14  \w   -161.00 -69.00   0.50   35.00    --  -90.00 -74.00 -53.28  184
 15  \w   -161.00 -69.00   0.50   35.00    --  -90.00 -74.00 -81.43  184
 16  \w   -161.00 -68.00   0.50   35.00    --  -90.00 -77.00 -60.00  186
 17  \w   -161.00 -70.00   0.50   35.00    --  -90.00 -72.00 -78.48  182
 18  \w   -161.00 -70.00   0.50   35.00    --  -90.00 -73.00-117.10  182
 19  \w   -161.00 -71.00   0.50   35.00    --  -90.00 -69.00-109.81  180
 20  \w    -65.00 -18.00   0.50   35.00    --  -90.00  61.00 -30.00   94
 21  \w   -161.00 -69.00   0.50   35.00    --  -90.00 -74.00-106.89  184
 22  \w   -130.00 -71.00   0.50   35.00    --  -90.00 -72.00-104.05  118
 23  \w   -104.00 -78.00   0.50   35.00    --  -90.00 -65.00-158.95   52
 24  \w   -100.00 -69.00   0.50   35.00    --  -90.00 -77.00 -90.00   62
 25  \w     40.00  97.00   0.50   35.00    --  111.50-125.00 -30.00  114
 26  \w     91.00 173.00   0.50   35.00    --  111.50  77.00 -60.00  164
 27  \w    135.00 161.00   0.50   35.00    --  111.50  30.00-150.00   52
 28  \w    105.00 134.00   0.50   35.00    --  111.50  30.00-150.00   58
 29  \w    153.00 178.00   0.50   35.00    --  111.50 125.00  30.00   50
 30  \w     96.00 145.00   0.50   35.00    --  111.50 125.00  30.00   98
 31  \w    105.00 161.00   0.50   35.00    --  111.50  45.00-120.00  112
 32  \w     91.00 116.00   0.50   35.00    --  111.50  77.00-120.00   50
 33  \w     49.00  74.00   0.50   35.00    --  111.50 -61.00   0.00   50
 34  \w     44.00  73.00   0.50   35.00    --  111.50 -61.00 150.00   58
 35  \w    142.00 169.00   0.50   35.00    --  111.50  15.00  30.00   54
 36  \w    103.00 148.00   0.50   35.00    --  111.50  30.00 120.00   90
 37  \w    101.00 137.00   0.50   35.00    --  111.50  15.00  30.00   72
 38  \w     94.00 123.00   0.50   35.00    --  111.50  77.00-180.00   58
 39  \w     40.00  84.00   0.50   35.00    --  111.50-125.00 -60.00   88
 40  \w    145.00 174.00   0.50   35.00    --  111.50  45.00-180.00   58
 41  \w     40.00  65.00   0.50   35.00    --  111.50 -61.00 -30.00   50
 42  \w     97.00 122.00   0.50   35.00    --  111.50  61.00-150.00   50
 43  \w    101.00 135.00   0.50   35.00    --  111.50  61.00-120.00   68
 44  \w    153.00 178.00   0.50   35.00    --  111.50  61.00-120.00   50
 45  \w     96.00 123.00   0.50   35.00    --  111.50  61.00 -90.00   54
 46  \w     70.00  96.00   0.50   35.00    --  111.50 -94.00  60.00   52
 47  \w    102.00 142.00   0.50   35.00    --  111.50  45.00 120.00   80
 48  \w     93.00 174.00   0.50   35.00    --  111.50  77.00 -90.00  162
 49  \w     79.00 105.00   0.50   35.00    --  111.50 -94.00   0.00   52
 50  \w     45.00  71.00   0.50   35.00    --  111.50 -94.00   0.00   52
 51  \w     40.00  65.00   0.50   35.00    --  111.50 -61.00-120.00   50
 52  \w     40.00  87.00   0.50   35.00    --  111.50 -94.00 120.00   94
 53  \w     49.00  78.00   0.50   35.00    --  111.50 -61.00-180.00   58
;
_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      -0.1947850000
_diffrn_orient_matrix_UB_12      -0.0166041000
_diffrn_orient_matrix_UB_13      -0.1009226000
_diffrn_orient_matrix_UB_21      -0.2724015000
_diffrn_orient_matrix_UB_22      -0.0427428000
_diffrn_orient_matrix_UB_23      0.0489925000
_diffrn_orient_matrix_UB_31      -0.2046131000
_diffrn_orient_matrix_UB_32      0.0725432000
_diffrn_orient_matrix_UB_33      0.0057797000
_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  0.0506
_diffrn_reflns_av_unetI/netI     0.0386
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 0.980
_diffrn_reflns_limit_h_max       4
_diffrn_reflns_limit_h_min       -4
_diffrn_reflns_limit_k_max       22
_diffrn_reflns_limit_k_min       -22
_diffrn_reflns_limit_l_max       17
_diffrn_reflns_limit_l_min       -17
_diffrn_reflns_number            19374
_diffrn_reflns_point_group_measured_fraction_full 0.931
_diffrn_reflns_point_group_measured_fraction_max 0.895
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         79.388
_diffrn_reflns_theta_min         2.461
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    0.727
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.86908
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.41.123a (Rigaku Oxford Diffraction, 2022)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            yellow
_exptl_crystal_colour_primary    yellow
_exptl_crystal_density_diffrn    1.517
_exptl_crystal_description       needle
_exptl_crystal_F_000             460
_exptl_crystal_size_max          0.287
_exptl_crystal_size_mid          0.044
_exptl_crystal_size_min          0.032
_refine_diff_density_max         0.286
_refine_diff_density_min         -0.209
_refine_diff_density_rms         0.040
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.036
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     429
_refine_ls_number_reflns         3747
_refine_ls_number_restraints     44
_refine_ls_restrained_S_all      1.036
_refine_ls_R_factor_all          0.0619
_refine_ls_R_factor_gt           0.0517
_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^)+(0.0734P)^2^+0.3173P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1337
_refine_ls_wR_factor_ref         0.1424
_reflns_Friedel_coverage         0.817
_reflns_Friedel_fraction_full    0.862
_reflns_Friedel_fraction_max     0.809
_reflns_number_gt                3173
_reflns_number_total             3747
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d5cp02942b2.cif
_cod_data_source_block           re50-2
_cod_depositor_comments
'Adding full bibliography for 7251612--7251614.cif.'
_cod_database_code               7251614
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         C32H16N2O
_shelx_estimated_absorpt_t_max   0.977
_shelx_estimated_absorpt_t_min   0.818
_reflns_odcompleteness_completeness 99.85
_reflns_odcompleteness_iscentric 1
_reflns_odcompleteness_theta     74.33
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.9(9)
 0.1(9)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups
3. Uiso/Uaniso restraints and constraints
Uanis(C16A) \\sim Ueq, Uanis(C17A) \\sim Ueq, Uanis(C14A) \\sim Ueq,
Uanis(C12A) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C19A) \\sim Ueq, Uanis(C20A) \\sim Ueq, Uanis(C21A) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(C21) = Uanis(C11A)
Uanis(C15A) = Uanis(C32)
4. Others
 Sof(O1A)=Sof(N1A)=Sof(C17A)=Sof(C16A)=Sof(N2A)=Sof(C14A)=Sof(C1A)=Sof(C15A)=
 Sof(C13A)=Sof(C12A)=Sof(H12A)=Sof(C11A)=Sof(H11A)=Sof(C10A)=Sof(H10A)=
 Sof(C18A)=Sof(C19A)=Sof(H19A)=Sof(C20A)=Sof(H20A)=Sof(C21A)=Sof(H21A)=1-FVAR(1)
 Sof(O1)=Sof(N1)=Sof(N2)=Sof(C1)=Sof(C10)=Sof(H10)=Sof(C11)=Sof(H11)=Sof(C12)=
 Sof(H12)=Sof(C13)=Sof(C14)=Sof(C17)=Sof(C18)=Sof(C19)=Sof(C20)=Sof(H20)=
 Sof(C21)=Sof(H21)=Sof(C22)=Sof(H22)=Sof(C32)=FVAR(1)
5.a Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C5(H5), C7(H7), C8(H8), C12A(H12A), C11A(H11A), C10A(H10A),
 C19A(H19A), C20A(H20A), C21A(H21A), C24(H24), C25(H25), C27(H27), C28(H28),
 C29(H29), C10(H10), C11(H11), C12(H12), C20(H20), C21(H21), C22(H22)
5.b Fitted pentagon refined as free rotating group:
 N1A(C17A,C16A,N2A,C14A)
5.c Fitted hexagon refined as free rotating group:
 C15A(C13A,C12A,C11A,C10A,C23)
;
_shelx_res_checksum              64741
_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 2.298
_oxdiff_exptl_absorpt_empirical_full_min 0.408