A switch-on luminescent europium(iii) probe for selective and time-resolved detection of adenosine diphosphate (ADP).
Bodman, Samantha E.; Stachelek, Patrycja; Rehman, Umatur; Plasser, Felix; Pal, Robert; Butler, Stephen J.; Chemical science 16 (2025) 5602–5612; doi:10.1039/d4sc07188c

data_1573929
_publ_section_title
;
 A switch-on luminescent europium(iii) probe for selective and
 time-resolved detection of adenosine diphosphate (ADP).
;
_journal_issue                   13
_journal_name_full               'Chemical science'
_journal_page_first              5602
_journal_page_last               5612
_journal_paper_doi               10.1039/d4sc07188c
_journal_volume                  16
_journal_year                    2025
_chemical_formula_moiety         'C46 H50 Gd N6 O7, C F3 O3 S, 10[H2O]'
_chemical_formula_sum            'C47 H70 F3 Gd N6 O20 S'
_chemical_formula_weight         1265.24
_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             2025-01-23
_audit_creation_method
;
Olex2 1.5
(compiled 2024.02.16 svn.r378c4104 for OlexSys, GUI svn.r6928)
;
_audit_update_record
;
2025-01-31 deposited with the CCDC.	2025-02-05 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 94.300(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   16.8352(3)
_cell_length_b                   17.2648(2)
_cell_length_c                   18.6772(3)
_cell_measurement_reflns_used    32669
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      32.6410
_cell_measurement_theta_min      2.1720
_cell_volume                     5413.37(14)
_computing_cell_refinement       'CrysAlisPro 1.171.43.143a (Rigaku OD, 2024)'
_computing_data_collection
'CrysAlisPro system (CCD 42.100a 64-bit (release 16-08-2023))'
_computing_data_reduction        'CrysAlisPro 1.171.43.143a (Rigaku OD, 2024)'
_computing_molecular_graphics    'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.5 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_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 1.000
_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    -25.00  58.00   0.50  150.00    --  -15.70  52.00 -35.00  166
  2  \w    -89.00  -6.00   0.50  150.00    --  -15.70 -52.00 179.00  166
  3  \w     16.00  63.00   0.50  150.00    --  -15.70  19.00  90.00   94
  4  \w    -61.00 -22.00   0.50  150.00    --   15.85 -19.00-120.00   78
  5  \w     -6.00  46.00   0.50  150.00    --   15.85 -99.00  60.00  104
  6  \w    -61.00 -22.00   0.50  150.00    --   15.85 -19.00 -90.00   78
  7  \w      5.00  56.00   0.50  150.00    --   15.85  57.00 150.00  102
  8  \w     -6.00  19.00   0.50  150.00    --   15.85 -99.00-150.00   50
  9  \w     10.00  91.00   0.50  150.00    --   15.85  38.00  30.00  162
 10  \w    -72.00 -47.00   0.50  150.00    --  -15.70 -52.00 179.00   50
 11  \w     16.00  63.00   0.50  150.00    --  -15.70  19.00 120.00   94
 12  \w    -35.00  18.00   0.50  150.00    --  -15.70  77.00-120.00  106
 13  \w    -35.00  18.00   0.50  150.00    --  -15.70  77.00 150.00  106
 14  \w      5.00  43.00   0.50  150.00    --   15.85  57.00  60.00   76
 15  \w    -61.00 -22.00   0.50  150.00    --   15.85 -19.00-150.00   78
;
_diffrn_measurement_device       'four-circle diffractometer'
_diffrn_measurement_device_type  'ROD, Synergy Custom system, HyPix'
_diffrn_measurement_method       '\w scans'
_diffrn_orient_matrix_type
'CrysAlisPro convention (1999,Acta A55,543-557)'
_diffrn_orient_matrix_UB_11      0.0341809000
_diffrn_orient_matrix_UB_12      0.0081267000
_diffrn_orient_matrix_UB_13      0.0233301000
_diffrn_orient_matrix_UB_21      0.0146865000
_diffrn_orient_matrix_UB_22      0.0246001000
_diffrn_orient_matrix_UB_23      -0.0264116000
_diffrn_orient_matrix_UB_31      -0.0200013000
_diffrn_orient_matrix_UB_32      0.0318941000
_diffrn_orient_matrix_UB_33      0.0144519000
_diffrn_radiation_monochromator  mirror
_diffrn_radiation_probe          x-ray
_diffrn_radiation_type           'Mo K\a'
_diffrn_radiation_wavelength     0.71075
_diffrn_reflns_av_R_equivalents  0.0639
_diffrn_reflns_av_unetI/netI     0.0321
_diffrn_reflns_Laue_measured_fraction_full 1.000
_diffrn_reflns_Laue_measured_fraction_max 1.000
_diffrn_reflns_limit_h_max       20
_diffrn_reflns_limit_h_min       -20
_diffrn_reflns_limit_k_max       20
_diffrn_reflns_limit_k_min       -20
_diffrn_reflns_limit_l_max       22
_diffrn_reflns_limit_l_min       -22
_diffrn_reflns_number            83075
_diffrn_reflns_point_group_measured_fraction_full 1.000
_diffrn_reflns_point_group_measured_fraction_max 1.000
_diffrn_reflns_theta_full        25.028
_diffrn_reflns_theta_max         25.028
_diffrn_reflns_theta_min         1.965
_diffrn_source                   'Rotating-anode X-ray tube'
_diffrn_source_type              'Rigaku (Mo) X-ray Source'
_exptl_absorpt_coefficient_mu    1.354
_exptl_absorpt_correction_T_max  1.000
_exptl_absorpt_correction_T_min  0.682
_exptl_absorpt_correction_type   gaussian
_exptl_absorpt_process_details
;
CrysAlisPro 1.171.43.143a (Rigaku Oxford Diffraction, 2024)
Numerical absorption correction based on gaussian integration over
a multifaceted crystal model
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    1.552
_exptl_crystal_description       plate
_exptl_crystal_F_000             2564
_exptl_crystal_size_max          0.153
_exptl_crystal_size_mid          0.091
_exptl_crystal_size_min          0.017
_refine_diff_density_max         3.554
_refine_diff_density_min         -1.101
_refine_diff_density_rms         0.144
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.058
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     834
_refine_ls_number_reflns         9558
_refine_ls_number_restraints     400
_refine_ls_restrained_S_all      1.063
_refine_ls_R_factor_all          0.0929
_refine_ls_R_factor_gt           0.0642
_refine_ls_shift/su_max          0.001
_refine_ls_shift/su_mean         0.000
_refine_ls_structure_factor_coef Fsqd
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0724P)^2^+48.8184P] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1602
_refine_ls_wR_factor_ref         0.1864
_reflns_Friedel_coverage         0.000
_reflns_number_gt                6603
_reflns_number_total             9558
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc07188c2.cif
_cod_data_source_block           2023ncs0541f
_cod_depositor_comments          'Adding full bibliography for 1573929.cif.'
_cod_database_code               1573929
_shelx_shelxl_version_number     2019/3
_chemical_oxdiff_formula         'C47 H48 F3 Gd N6 O9 S'
_chemical_oxdiff_usercomment     'SEB-Gd6PhOMe_attempt2 (vial1)'
_shelx_estimated_absorpt_t_max   0.977
_shelx_estimated_absorpt_t_min   0.820
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups, All C(H,H,H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups, All O(H,H) groups
2. Restrained distances
 C47-F1 = C47-F3 = C47-F2
 1.33 with sigma of 0.02
 S1-O9 = S1-O10 = S1-O8A
 1.44 with sigma of 0.02
 C47A-F1A = C47A-F3A = C47A-F2A
 1.33 with sigma of 0.02
 C47A-S1A
 1.82 with sigma of 0.02
 S1A-O8 = S1A-O9A = S1A-O10A
 1.44 with sigma of 0.02
 C47-O9
 2.58 with sigma of 0.04
 C47-O10
 2.56 with sigma of 0.04
 C47-O8A
 2.57 with sigma of 0.04
 C47A-O8
 2.58 with sigma of 0.04
 C47A-O9A
 2.56 with sigma of 0.04
 C47A-O10A
 2.57 with sigma of 0.04
 N6-C35 \\sim C35-N6A
 with sigma of 0.02
 N3-C10 \\sim C10-N3A
 with sigma of 0.02
 N4-C37 \\sim C37-N4A
 with sigma of 0.02
 N5-C27 \\sim C27-N5A
 with sigma of 0.02
 C47-F1 \\sim C47-F3 \\sim C47-F2
 with sigma of 0.02
 F1-F3 \\sim F3-F2 \\sim F2-F1
 with sigma of 0.04
 S1-F1 \\sim S1-F3 \\sim S1-F2
 with sigma of 0.04
 S1-O9 \\sim S1-O10 \\sim S1-O8A
 with sigma of 0.02
 O9-O10 \\sim O10-O8A \\sim O9-O8A
 with sigma of 0.04
 C47-O9 \\sim C47-O10 \\sim C47-O8A
 with sigma of 0.04
 C47A-F1A \\sim C47A-F3A \\sim C47A-F2A
 with sigma of 0.02
 F1A-F3A \\sim F3A-F2A \\sim F2A-F1A
 with sigma of 0.04
 S1A-F1A \\sim S1A-F3A \\sim S1A-F2A
 with sigma of 0.04
 S1A-O8 \\sim S1A-O9A \\sim S1A-O10A
 with sigma of 0.02
 O8-O9A \\sim O9A-O10A \\sim O8-O10A
 with sigma of 0.04
 C47A-O8 \\sim C47A-O9A \\sim C47A-O10A
 with sigma of 0.04
 O10-O10A \\sim O9A-O9 \\sim O8-O8A
 with sigma of 0.04
 Gd1-H7A \\sim Gd1-H7B
 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
C47 \\sim F1 \\sim F3 \\sim F2 \\sim S1 \\sim O9 \\sim O10 \\sim O8A: within 2A
with sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
C47A \\sim F1A \\sim F3A \\sim F2A \\sim S1A \\sim O8 \\sim O9A \\sim O10A:
within 2A with sigma of 0.04 and sigma for terminal atoms of 0.08 within 2A
Uanis(O15) \\sim Ueq, Uanis(O15A) \\sim Ueq, Uanis(O16A) \\sim Ueq, Uanis(O16)
\\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(O12) \\sim Ueq, Uanis(O11A) \\sim Ueq, Uanis(O11) \\sim Ueq, Uanis(O12A)
\\sim Ueq, Uanis(O14) \\sim Ueq, Uanis(O14A) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(O18) \\sim Ueq, Uanis(O18A) \\sim Ueq, Uanis(O19) \\sim Ueq, Uanis(O19A)
\\sim Ueq, Uanis(O20) \\sim Ueq, Uanis(O20A) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(S1A) \\sim Ueq, Uanis(C47A) \\sim Ueq, Uanis(C47) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(O8) \\sim Ueq, Uanis(O8A) \\sim Ueq, Uanis(O10A) \\sim Ueq, Uanis(O10)
\\sim Ueq, Uanis(O9A) \\sim Ueq, Uanis(O9) \\sim Ueq: with sigma of 0.01 and
sigma for terminal atoms of 0.02
Uanis(N6) = Uanis(N6A)
Uanis(N5) = Uanis(N5A)
Uanis(N4) = Uanis(N4A)
Uanis(N3) = Uanis(N3A)
Uanis(C39A) = Uanis(C40A) = Uanis(C41A) = Uanis(C42A) = Uanis(C43A) =
Uanis(C44A) = Uanis(C45A) = Uanis(C46A)
Uanis(F3A) = Uanis(F3) = Uanis(F2) = Uanis(F2A) = Uanis(F1) = Uanis(F1A)
Uanis(O9A) = Uanis(O9) = Uanis(O8) = Uanis(O8A) = Uanis(O10A) = Uanis(O10) =
Uanis(S1A) = Uanis(S1)
Uanis(C47A) = Uanis(C47)
4. Rigid body (RIGU) restrains
 C47, F1, F3, F2, S1, O9, O10, O8A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
 C47A, F1A, F3A, F2A, S1A, O8, O9A, O10A
 with sigma for 1-2 distances of 0.004 and sigma for 1-3 distances of 0.004
5. Others
 Sof(C47A)=Sof(F1A)=Sof(F3A)=Sof(F2A)=Sof(S1A)=Sof(O8)=Sof(O9A)=Sof(O10A)=1-
 FVAR(1)
 Sof(C47)=Sof(F1)=Sof(F3)=Sof(F2)=Sof(S1)=Sof(O9)=Sof(O10)=Sof(O8A)=FVAR(1)
 Sof(O11)=1-FVAR(2)
 Sof(O11A)=FVAR(2)
 Sof(O13A)=1-FVAR(3)
 Sof(O13)=FVAR(3)
 Sof(O12)=1-FVAR(4)
 Sof(O12A)=FVAR(4)
 Sof(O20A)=1-FVAR(5)
 Sof(O20)=FVAR(5)
 Sof(O18)=1-FVAR(6)
 Sof(O18A)=FVAR(6)
 Sof(O19A)=Sof(O15A)=1-FVAR(7)
 Sof(O19)=Sof(O15)=FVAR(7)
 Sof(O14A)=1-FVAR(8)
 Sof(O14)=FVAR(8)
 Sof(O16A)=1-FVAR(9)
 Sof(O16)=FVAR(9)
 Fixed Sof: N3(0.7) N4(0.7) H35A(0.7) H35B(0.7) H35C(0.3) H35D(0.3) N5(0.7)
 N6(0.7) H27A(0.7) H27B(0.7) H27C(0.3) H27D(0.3) H37A(0.7) H37B(0.7) H37C(0.3)
 H37D(0.3) H10A(0.7) H10B(0.7) H10C(0.3) H10D(0.3) C43(0.7) H43A(0.7) H43B(0.7)
 C45(0.7) H45A(0.7) H45B(0.7) C46(0.7) H46A(0.7) H46B(0.7) C40(0.7) H40A(0.7)
 H40B(0.7) C39(0.7) H39A(0.7) H39B(0.7) C41(0.7) H41A(0.7) H41B(0.7) C44(0.7)
 H44A(0.7) H44B(0.7) C42(0.7) H42A(0.7) H42B(0.7) C39A(0.3) H39C(0.3) H39D(0.3)
 C43A(0.3) H43C(0.3) H43D(0.3) C41A(0.3) H41C(0.3) H41D(0.3) C45A(0.3)
 H45C(0.3) H45D(0.3) C44A(0.3) H44C(0.3) H44D(0.3) C40A(0.3) H40C(0.3)
 H40D(0.3) C46A(0.3) H46C(0.3) H46D(0.3) C42A(0.3) H42C(0.3) H42D(0.3) N3A(0.3)
 N6A(0.3) N5A(0.3) N4A(0.3)
6.a Free rotating group:
 O7(H7A,H7B)
6.b Secondary CH2 refined with riding coordinates:
 C35(H35A,H35B), C35(H35C,H35D), C27(H27A,H27B), C27(H27C,H27D), C37(H37A,
 H37B), C37(H37C,H37D), C10(H10A,H10B), C10(H10C,H10D), C43(H43A,H43B),
 C45(H45A,H45B), C46(H46A,H46B), C40(H40A,H40B), C39(H39A,H39B), C41(H41A,H41B),
  C44(H44A,H44B), C42(H42A,H42B), C39A(H39C,H39D), C43A(H43C,H43D), C41A(H41C,
 H41D), C45A(H45C,H45D), C44A(H44C,H44D), C40A(H40C,H40D), C46A(H46C,H46D),
 C42A(H42C,H42D)
6.c Aromatic/amide H refined with riding coordinates:
 C25(H25), C19(H19), C7(H7), C16(H16), C33(H33), C24(H24), C8(H8), C22(H22),
 C3(H3), C20(H20), C2(H2), C12(H12), C15(H15), C5(H5), C32(H32), C30(H30),
 C29(H29), C13(H13)
6.d Idealised Me refined as rotating group:
 C17(H17A,H17B,H17C), C34(H34A,H34B,H34C)
;
_shelx_res_checksum              9516
_olex2_submission_original_sample_id SBF09
_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 1.551
_oxdiff_exptl_absorpt_empirical_full_min 0.713