Fluorescent molecular probe for in vivo and in vitro targeting and imaging of an intracellular bacterial infection
Koirala, Shailendra; Gaspar, Miguel A.; Wijesundara, Yalini H.; Li, Dong-Hao; Gadhvi, Jashkaran G.; Ehrman, Ryanne N.; Cornelius, Samuel A.; Mariasoosai, Charles; Nguyen, Thien-Quang N.; Trashi, Orikeda; Trashi, Ikeda; Kumari, Sneha; Hagge, Laurel M.; Howlett, Thomas S.; Torabifard, Hedieh; Smith, Bradley D.; De Nisco, Nicole J.; Gassensmith, Jeremiah J.; Chemical Science 16 (2025) 7902–7911; doi:10.1039/D4SC05680A

data_1574206
_publ_section_title
;
 Fluorescent molecular probe for in vivo and in vitro targeting and
 imaging of an intracellular bacterial infection
;
_journal_issue                   18
_journal_name_full               'Chemical Science'
_journal_page_first              7902
_journal_page_last               7911
_journal_paper_doi               10.1039/D4SC05680A
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C38 H37 F6 N7 O5 Zn2, 2(N O3)'
_chemical_formula_sum            'C38 H37 F6 N9 O11 Zn2'
_chemical_formula_weight         1040.50
_space_group_crystal_system      triclinic
_space_group_IT_number           2
_space_group_name_Hall           '-P 1'
_space_group_name_H-M_alt        'P -1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     dual
_audit_creation_date             2024-06-19
_audit_creation_method
;
Olex2 1.5-ac6-020
(compiled 2024.02.14 svn.r2f8d729c for Rigaku Oxford Diffraction, GUI svn.r6966)
;
_audit_update_record
;
2025-01-16 deposited with the CCDC.	2025-03-17 downloaded from the CCDC.
;
_cell_angle_alpha                100.082(3)
_cell_angle_beta                 101.234(3)
_cell_angle_gamma                94.294(3)
_cell_formula_units_Z            2
_cell_length_a                   10.1650(3)
_cell_length_b                   10.5732(4)
_cell_length_c                   20.3723(8)
_cell_measurement_reflns_used    23701
_cell_measurement_temperature    149.99(13)
_cell_measurement_theta_max      80.0090
_cell_measurement_theta_min      4.2700
_cell_volume                     2100.92(14)
_computing_cell_refinement       'CrysAlisPro 1.171.43.126a (Rigaku OD, 2024)'
_computing_data_collection       'CrysAlisPro 1.171.43.126a (Rigaku OD, 2024)'
_computing_data_reduction        'CrysAlisPro 1.171.43.126a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5-ac6-020 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5-ac6-020 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT  (Sheldrick, 2015)'
_diffrn_ambient_environment      N~2~
_diffrn_ambient_temperature      149.99(13)
_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 0.975
_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     96.00 148.00   0.50    0.50    --  113.25 125.00-150.00  104
  2  \w     -3.00  26.00   0.50    0.50    --  -47.16  19.00-150.00   58
  3  \w     -8.00  26.00   0.50    0.50    --  -47.16  66.00 -72.00   68
  4  \w    -54.00 -14.00   0.50    0.50    --  -47.16  66.00 -72.00   80
  5  \w    -28.00  14.00   0.50    0.50    --   47.16 -19.00-180.00   84
  6  \w    -23.00  16.00   0.50    0.50    --   47.16 -19.00-150.00   78
  7  \w    -17.00  66.00   0.50    0.50    --   47.16 -66.00 152.00  166
  8  \w     43.00  74.00   0.50    0.50    --  113.25 -77.00  30.00   62
  9  \w     45.00  90.00   0.50    0.50    --  113.25 -77.00  60.00   90
 10  \w     42.00  69.00   0.50    0.50    --  113.25 -66.00 152.00   54
 11  \w     42.00  93.00   0.50    0.50    --  113.25 -77.00 -90.00  102
 12  \w     41.00  66.00   0.50    0.50    --  113.25 -77.00-150.00   50
 13  \w     66.00  91.00   0.50    0.50    --  113.25 -77.00 -60.00   50
 14  \w     42.00  67.00   0.50    0.50    --  113.25 -94.00   0.00   50
 15  \w     47.00  72.00   0.50    0.50    --  113.25-133.00  68.31   50
 16  \w     46.00  76.00   0.50    0.50    --  113.25-125.00  90.00   60
 17  \w     81.00 112.00   0.50    0.50    --  113.25-125.00  90.00   62
 18  \w     87.00 118.00   0.50    0.50    --  113.25-133.00  68.31   62
 19  \w     47.00  74.00   0.50    0.50    --  113.25-125.00 150.00   54
 20  \w     87.00 112.00   0.50    0.50    --  113.25-125.00 150.00   50
 21  \w     86.00 111.00   0.50    0.50    --  113.25-125.00 120.00   50
 22  \w     45.00  71.00   0.50    0.50    --  113.25-125.00 120.00   52
 23  \w     47.00 112.00   0.50    0.50    --  113.25-125.00  30.00  130
 24  \w     84.00 112.00   0.50    0.50    --  113.25-125.00 -60.00   56
 25  \w     66.00 112.00   0.50    0.50    --  113.25-125.00 -90.00   92
 26  \w     49.00 112.00   0.50    0.50    --  113.25-125.00-150.00  126
 27  \w     63.00 104.00   0.50    0.50    --  113.25-125.00-180.00   82
 28  \w     43.00 110.00   0.50    0.50    --  113.25-125.00-120.00  134
 29  \w     42.00 105.00   0.50    0.50    --  113.25 -94.00 -90.00  126
 30  \w     45.00  71.00   0.50    0.50    --  113.25 -94.00 -30.00   52
 31  \w     71.00 105.00   0.50    0.50    --  113.25 -94.00   0.00   68
 32  \w     65.00 107.00   0.50    0.50    --  113.25 -94.00  60.00   84
 33  \w     43.00  76.00   0.50    0.50    --  113.25 -94.00 120.00   66
 34  \w    136.00 173.00   0.50    0.50    --  113.25  15.00  30.00   74
 35  \w    116.00 169.00   0.50    0.50    --  113.25  77.00 150.00  106
 36  \w     95.00 120.00   0.50    0.50    --  113.25  77.00 120.00   50
 37  \w     95.00 176.00   0.50    0.50    --  113.25  66.00 -72.00  162
 38  \w    127.00 168.00   0.50    0.50    --  113.25  61.00 -90.00   82
 39  \w    102.00 172.00   0.50    0.50    --  113.25  30.00 -90.00  140
 40  \w     98.00 170.00   0.50    0.50    --  113.25  61.00-150.00  144
 41  \w    100.00 152.00   0.50    0.50    --  113.25  45.00-180.00  104
 42  \w    100.00 150.00   0.50    0.50    --  113.25  15.00   0.00  100
 43  \w     28.00 118.00   0.50    0.50    --   47.16  66.00 -72.00  180
 44  \w    -87.00 -16.00   0.50    0.50    --  -47.16 125.00  30.00  142
 45  \w    -73.00 -35.00   0.50    0.50    --  -47.16 -66.00 152.00   76
 46  \w   -109.00 -76.00   0.50    0.50    --  -47.16 -66.00 152.00   66
 47  \w   -144.00-118.00   0.50    0.50    --  -91.75 -66.00 152.00   52
 48  \w    -98.00 -59.00   0.50    0.50    --  -47.16 -57.00  90.00   78
 49  \w    -45.00 -16.00   0.50    0.50    --  -91.75  30.00 -60.00   58
 50  \w    -58.00 -32.00   0.50    0.50    --  -91.75  66.00 -72.00   52
 51  \w    -78.00 -35.00   0.50    0.50    --  -91.75  61.00  90.00   86
 52  \w    -45.00 -20.00   0.50    0.50    --  -91.75  30.00 150.00   50
 53  \w   -124.00 -96.00   0.50    0.50    --  -91.75 -94.00-120.00   56
 54  \w   -153.00-127.00   0.50    0.50    --  -91.75 -94.00-120.00   52
;
_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      0.0240219000
_diffrn_orient_matrix_UB_12      0.1357589000
_diffrn_orient_matrix_UB_13      0.0455754000
_diffrn_orient_matrix_UB_21      -0.1080822000
_diffrn_orient_matrix_UB_22      -0.0403114000
_diffrn_orient_matrix_UB_23      0.0382451000
_diffrn_orient_matrix_UB_31      0.1092197000
_diffrn_orient_matrix_UB_32      -0.0458700000
_diffrn_orient_matrix_UB_33      0.0514550000
_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  0.0260
_diffrn_reflns_av_unetI/netI     0.0233
_diffrn_reflns_Laue_measured_fraction_full 0.999
_diffrn_reflns_Laue_measured_fraction_max 0.975
_diffrn_reflns_limit_h_max       12
_diffrn_reflns_limit_h_min       -12
_diffrn_reflns_limit_k_max       13
_diffrn_reflns_limit_k_min       -13
_diffrn_reflns_limit_l_max       26
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            31444
_diffrn_reflns_point_group_measured_fraction_full 0.999
_diffrn_reflns_point_group_measured_fraction_max 0.975
_diffrn_reflns_theta_full        67.684
_diffrn_reflns_theta_max         80.347
_diffrn_reflns_theta_min         4.274
_diffrn_source                   'micro-focus sealed X-ray tube'
_diffrn_source_type              'PhotonJet (Cu) X-ray Source'
_exptl_absorpt_coefficient_mu    2.276
_exptl_absorpt_correction_T_max  1.00000
_exptl_absorpt_correction_T_min  0.84251
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.126a (Rigaku Oxford Diffraction, 2024)
Empirical absorption correction using spherical harmonics,
implemented in SCALE3 ABSPACK scaling algorithm.
;
_exptl_crystal_colour            'clear light colourless'
_exptl_crystal_density_diffrn    1.645
_exptl_crystal_description       block
_exptl_crystal_F_000             1060
_exptl_crystal_size_max          0.07
_exptl_crystal_size_mid          0.06
_exptl_crystal_size_min          0.05
_refine_diff_density_max         0.763
_refine_diff_density_min         -0.501
_refine_diff_density_rms         0.064
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.069
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     607
_refine_ls_number_reflns         8958
_refine_ls_number_restraints     0
_refine_ls_restrained_S_all      1.069
_refine_ls_R_factor_all          0.0373
_refine_ls_R_factor_gt           0.0349
_refine_ls_shift/su_max          0.002
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0462P)^2^+1.7283P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0948
_refine_ls_wR_factor_ref         0.0964
_reflns_Friedel_coverage         0.000
_reflns_number_gt                8298
_reflns_number_total             8958
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc05680a20.cif
_cod_data_source_block           str1482lt150kcu34mm_auto
_cod_depositor_comments
'Adding full bibliography for 1574205--1574206.cif.'
_cod_original_cell_volume        2100.92(13)
_cod_database_code               1574206
_shelx_shelxl_version_number     2018/3
_chemical_oxdiff_formula         'C45 H40 N6 O Zn2'
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
2.a Secondary CH2 refined with riding coordinates:
 C7(H7D,H7E), C8(H8A,H8B), C9(H9A,H9B), C10(H10A,H10B), C11(H11A,H11B),
 C17(H17A,H17B), C27(H27A,H27B), C33(H33A,H33B)
2.b Aromatic/amide H refined with riding coordinates:
 C3(H3), C5(H5), C13(H13), C14(H14), C15(H15), C16(H16), C19(H19), C20(H20),
 C21(H21), C22(H22), C29(H29), C30(H30), C31(H31), C32(H32), C35(H35), C36(H36),
  C37(H37), C38(H38)
;
_shelx_res_checksum              50091
_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 1.500
_oxdiff_exptl_absorpt_empirical_full_min 0.767