Comparing organic and metallo-organic hydrazone molecular cages as potential carriers for doxorubicin delivery
Montà-González, Giovanni; Bastante-Rodríguez, David; García-Fernández, Alba; Lusby, Paul J.; Martínez-Máñez, Ramón; Martí-Centelles, Vicente; Chemical Science 15 (2024) 10010–10017; doi:10.1039/D4SC02294G

data_1571802
_publ_section_title
;
 Comparing organic and metallo-organic hydrazone molecular cages as
 potential carriers for doxorubicin delivery
;
_journal_issue                   26
_journal_name_full               'Chemical Science'
_journal_page_first              10010
_journal_page_last               10017
_journal_paper_doi               10.1039/D4SC02294G
_journal_volume                  15
_journal_year                    2024
_chemical_formula_moiety
'0.5(C104 H81 N24 O12 Pd2), 2(C2 H6 O S), 0.5(N O3), 0.5(N1 O1.667)'
_chemical_formula_sum            'C56 H52.5 N13 O10.5 Pd S2'
_chemical_formula_weight         1246.13
_space_group_crystal_system      monoclinic
_space_group_IT_number           4
_space_group_name_Hall           'P 2yb'
_space_group_name_H-M_alt        'P 1 21 1'
_atom_sites_solution_hydrogens   mixed
_audit_creation_date             2023-07-14
_audit_creation_method
;
Olex2 1.3
(compiled 2020.11.12 svn.r5f609507 for OlexSys, GUI svn.r6272)
;
_audit_update_record
;
2023-09-18 deposited with the CCDC.	2024-06-07 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 113.508(2)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   19.6620(13)
_cell_length_b                   23.7645(17)
_cell_length_c                   19.8456(14)
_cell_measurement_reflns_used    9255
_cell_measurement_temperature    120.0
_cell_measurement_theta_max      24.200
_cell_measurement_theta_min      2.237
_cell_volume                     8503.4(10)
_computing_cell_refinement       'SAINT V8.40B (?, 2016)'
_computing_data_reduction        'SAINT V8.40B (?, 2016)'
_computing_molecular_graphics    'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3 (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2019/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXT 2018/2 (Sheldrick, 2018)'
_diffrn_ambient_temperature      120.0
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.997
_diffrn_measurement_device_type  'Bruker D8 Venture Diffractometer'
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0595
_diffrn_reflns_av_unetI/netI     0.0565
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.997
_diffrn_reflns_limit_h_max       23
_diffrn_reflns_limit_h_min       -23
_diffrn_reflns_limit_k_max       28
_diffrn_reflns_limit_k_min       -28
_diffrn_reflns_limit_l_max       23
_diffrn_reflns_limit_l_min       -23
_diffrn_reflns_number            113633
_diffrn_reflns_point_group_measured_fraction_full 0.993
_diffrn_reflns_point_group_measured_fraction_max 0.992
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         25.391
_diffrn_reflns_theta_min         2.066
_diffrn_source_current           1.4
_diffrn_source_power             0.07
_diffrn_source_voltage           50.0
_exptl_absorpt_coefficient_mu    0.315
_exptl_absorpt_correction_T_max  0.7452
_exptl_absorpt_correction_T_min  0.6464
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2016/2 (Bruker,2016/2) was used for absorption correction.
wR2(int) was 0.0819 before and 0.0599 after correction.
The Ratio of minimum to maximum transmission is 0.8674.
The \l/2 correction factor is Not present.
;
_exptl_crystal_colour            colourless
_exptl_crystal_colour_primary    colourless
_exptl_crystal_density_diffrn    0.973
_exptl_crystal_description       Hexagonal
_exptl_crystal_F_000             2566
_exptl_crystal_recrystallization_method 'Vapour deposition'
_exptl_crystal_size_max          0.201
_exptl_crystal_size_mid          0.164
_exptl_crystal_size_min          0.056
_refine_diff_density_max         0.651
_refine_diff_density_min         -0.327
_refine_diff_density_rms         0.051
_refine_ls_abs_structure_details
;
 Refined as an inversion twin.
;
_refine_ls_abs_structure_Flack   0.487(17)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.037
_refine_ls_hydrogen_treatment    constr
_refine_ls_matrix_type           full
_refine_ls_number_parameters     1522
_refine_ls_number_reflns         31019
_refine_ls_number_restraints     346
_refine_ls_restrained_S_all      1.049
_refine_ls_R_factor_all          0.0628
_refine_ls_R_factor_gt           0.0449
_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^)+(0.0636P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.1073
_refine_ls_wR_factor_ref         0.1162
_reflns_Friedel_coverage         0.938
_reflns_Friedel_fraction_full    0.988
_reflns_Friedel_fraction_max     0.986
_reflns_number_gt                24654
_reflns_number_total             31019
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d4sc02294g2.cif
_cod_data_source_block           mo_gm2560bis_0m_a_july2023
_cod_depositor_comments          'Adding full bibliography for 1571802.cif.'
_cod_original_formula_sum        'C56 H52.50 N13 O10.50 Pd S2'
_cod_database_code               1571802
_shelx_shelxl_version_number     2019/3
_shelx_estimated_absorpt_t_max   0.983
_shelx_estimated_absorpt_t_min   0.939
_olex2_refinement_description
;
1. Twinned data refinement
 Scales: 0.513(17)
 0.487(17)
2. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All N(H) groups
 At 1.5 times of:
  All C(H,H,H) groups
3. Restrained distances
 C01N-C01F
 1.4 with sigma of 0.005
 C03I-C01N
 1.4 with sigma of 0.005
 C03V-C03D
 1.4 with sigma of 0.005
 C03W-C03V
 1.4 with sigma of 0.005
 C03W-C03I
 1.4 with sigma of 0.005
 C03D-C01F
 1.4 with sigma of 0.005
 C23-C04D
 1.4 with sigma of 0.01
 C04J-C03N
 1.4 with sigma of 0.01
 C23-C050
 1.4 with sigma of 0.01
 C04Y-C04D
 1.4 with sigma of 0.01
 C04Y-C03N
 1.4 with sigma of 0.01
 C050-C04J
 1.4 with sigma of 0.01
 C02F-C01O
 1.4 with sigma of 0.01
 C032-C02F
 1.4 with sigma of 0.01
 C032-C01Y
 1.4 with sigma of 0.01
 C01V-C01O
 1.4 with sigma of 0.01
 O5-N7
 1.25 with sigma of 0.01
 N7-O10
 1.25 with sigma of 0.01
 N7-O5
 1.25 with sigma of 0.01
 O10-N7 = N7-O5
 1.25 with sigma of 0.01
 O10-O5
 2.165 with sigma of 0.02
4. Rigid bond restraints
 C014, C01X, C01S, C018, C012, C02W
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C03A, C044, C04P, C03B, C01T
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C01T, C03A, C044, C04P, C03B
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C02W, C014, C01X, C01S, C018, C012
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C02E, C01Q, C011, C03R, C039, C03C
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C039, C03R, C011, C01Q, C02E, C03C
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C01F, C03D, C03V, C03W, C03I, C01N
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C01R, C01I, C02S, C02A, C047
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C036, C042, C01L, C01E, C028
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C043, C04B, C03G, C02Q, C02I, C02L
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C03V, C03D, C01F, C01N, C03I, C03W
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C04Y, C04D, C23, C050, C04J, C03N
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C012, C02W, C014, C01X, C01S, C018
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C046, C03E, C02P, C03M, C02X, C03P
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C02L, C043, C04B, C03G, C02Q, C02I
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C033, C030, C021, C01M, C02M
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C03W, C03V, C03D, C01F, C01N, C03I
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C04D, C04Y, C03N, C04J, C050, C23
 with sigma for 1-2 distances of 0.005 and sigma for 1-3 distances of 0.005
 C022, C02U, C038, C023, C00P
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C33, C31, C29, C22, C35, C27
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C03G, C04B, C043, C02L, C02I, C02Q
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C04B, C03G, C02Q, C02I, C02L, C043
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
 C04J, C050, C23, C04D, C04Y, C03N
 with sigma for 1-2 distances of 0.01 and sigma for 1-3 distances of 0.01
5. Uiso/Uaniso restraints and constraints
Uanis(N1) \\sim Ueq, Uanis(C029) \\sim Ueq, Uanis(C01M) \\sim Ueq: with sigma
of 0.01 and sigma for terminal atoms of 0.02
Uanis(N1) \\sim Ueq, Uanis(C01M) \\sim Ueq, Uanis(C02W) \\sim Ueq, Uanis(C012)
\\sim Ueq, Uanis(O009) \\sim Ueq: with sigma of 0.005 and sigma for terminal
atoms of 0.01
Uanis(C01T) \\sim Ueq, Uanis(C04P) \\sim Ueq, Uanis(C03A) \\sim Ueq: with sigma
of 0.005 and sigma for terminal atoms of 0.01
Uanis(N00T) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C055) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C012) \\sim Ueq, Uanis(C02W) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.01
Uanis(C03C) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C03S) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C033) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C02W) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(N01K) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C048) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C03K) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C03V) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(C04Y) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(N1) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(C012) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(N02H) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(N02J) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(N00J) \\sim Ueq: with sigma of 0.001 and sigma for terminal atoms of 0.002
Uanis(O009) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(C02U) \\sim Ueq: with sigma of 0.05 and sigma for terminal atoms of 0.1
Uanis(O04T) \\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
Uanis(O10) \\sim Ueq, Uanis(N29) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.01
Uanis(N7) \\sim Ueq, Uanis(N51) \\sim Ueq: with sigma of 0.005 and sigma for
terminal atoms of 0.01
Uanis(O10) \\sim Ueq, Uanis(O5) \\sim Ueq: with sigma of 0.001 and sigma for
terminal atoms of 0.002
Uanis(C39) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C56) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C38) \\sim Ueq, Uanis(C03K) \\sim Ueq: with sigma of 0.01 and sigma for
terminal atoms of 0.02
Uanis(O51) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(N00Y) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
Uanis(C38) \\sim Ueq: with sigma of 0.01 and sigma for terminal atoms of 0.02
6. Others
 Fixed Sof: N51(0.33333) N7(0.33333) O10(0.33333) N29(0.33333) O5(0.33333)
7.a Riding coordinates:
 N027(H027)
7.b Aromatic/amide H refined with riding coordinates:
 N00D(H00D), N00H(H00H), N00I(H00I), N00J(H00J), C00P(H00P), C010(H010),
 C011(H011), C014(H014), C018(H018), N01A(H01A), C01D(H01D), C01H(H01H),
 C01J(H01J), C01L(H01L), C01N(H01N), C01O(H01O), C01P(H01P), C01Q(H01Q),
 C01R(H01R), C01S(H01S), C01T(H01T), C01U(H01U), C01V(H01V), N01W(H01W),
 C01Y(H01Y), C020(H020), C021(H021), C022(H022), N026(H026), C028(H028),
 C029(H029), C02A(H02A), C02C(H02C), C02F(H02F), C02G(H02G), N02H(H02H),
 C02I(H02I), C02M(H02M), C02O(H02O), C02Q(H02Q), C02S(H02S), C02U(H02U),
 C02W(H02W), C02X(H02X), C02Z(H02Z), C030(H030), C031(H031), C033(H033),
 C036(H036), C038(H038), C039(H039), C03A(H03A), C03C(H03C), C03D(H03D),
 C03E(H03E), C03H(H03H), C03I(H03I), C03L(H03L), C03M(H03M), C03N(H03N),
 C03O(H03O), C03V(H03V), C040(H040), C041(H041), C042(H042), C043(H043),
 C044(H044), C046(H046), C047(H047), C04A(H04A), C04B(H04B), C04P(H04P),
 C04Q(H04Q), C04Y(H04Y), C050(H050), C23(H23), C29(H29), C31(H31), C35(H35),
 C27(H27)
7.c Idealised Me refined as rotating group:
 C03K(H03B,H03F,H03G), C04F(H04C,H04D,H04E), C055(H05A,H05B,H05C), C38(H38A,
 H38B,H38C), C41(H41A,H41B,H41C), C39(H39A,H39B,H39C), C65(H65A,H65B,H65C),
 C56(H56A,H56B,H56C)
;
_smtbx_masks_void_probe_radius   1.2
_smtbx_masks_void_truncation_radius 1.2
_shelx_res_checksum              88485
_shelx_hkl_checksum              35378
_shelx_fab_checksum              17779
_olex2_submission_special_instructions 'No special instructions were received'