Evaluation of the Binding Mode of a Cytotoxic Dinuclear Nickel Complex to two Neighboring Phosphates of the DNA Backbone
Simon, Jasmin; Horstmann, Claudia; Mix, Andreas; Stammler, Anja; Oldengott, Jan; Bögge, Hartmut; Glaser, Thorsten; Dalton Transactions  (2022) –; doi:10.1039/D1DT03813C

data_7709348
_publ_section_title
;
 Evaluation of the Binding Mode of a Cytotoxic Dinuclear Nickel Complex to
 two Neighboring Phosphates of the DNA Backbone
;
_journal_name_full               'Dalton Transactions'
_journal_paper_doi               10.1039/D1DT03813C
_journal_year                    2022
_chemical_absolute_configuration ad
_chemical_formula_moiety
'C43 H53 N6 Ni2 O8 P, 2(Cl O4), 0.75(C4 H10 O)'
_chemical_formula_sum            'C46 H60.5 Cl2 N6 Ni2 O16.75 P'
_chemical_formula_weight         1184.79
_space_group_crystal_system      monoclinic
_space_group_IT_number           9
_space_group_name_Hall           'C -2yc'
_space_group_name_H-M_alt        'C 1 c 1'
_atom_sites_solution_hydrogens   mixed
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary   difmap
_audit_creation_date             2020-11-02
_audit_creation_method
;
Olex2 1.3-alpha
(compiled 2020.04.02 svn.r1fbe7b6f for OlexSys, GUI svn.r6076)
;
_audit_update_record
;
2021-04-23 deposited with the CCDC.	2022-01-24 downloaded from the CCDC.
;
_cell_angle_alpha                90
_cell_angle_beta                 93.002(5)
_cell_angle_gamma                90
_cell_formula_units_Z            4
_cell_length_a                   15.0590(16)
_cell_length_b                   15.3717(16)
_cell_length_c                   22.448(2)
_cell_measurement_reflns_used    9862
_cell_measurement_temperature    100(2)
_cell_measurement_theta_max      29.688
_cell_measurement_theta_min      2.709
_cell_volume                     5189.2(9)
_computing_cell_refinement       'SAINT v8.27A (Bruker, 2012)'
_computing_data_collection       'APEX2 v2012.12-0 (Bruker AXS, 2012)'
_computing_data_reduction        'SAINT v8.27A (Bruker, 2012)'
_computing_molecular_graphics    'Olex2 1.3-alpha (Dolomanov et al., 2009)'
_computing_publication_material  'Olex2 1.3-alpha (Dolomanov et al., 2009)'
_computing_structure_refinement  'SHELXL 2018/3 (Sheldrick, 2015)'
_computing_structure_solution    'SHELXS (Sheldrick, 2008)'
_diffrn_ambient_temperature      100(2)
_diffrn_detector_area_resol_mean 7.9
_diffrn_detector_type            'Bruker APEX II area detector'
_diffrn_measured_fraction_theta_full 0.998
_diffrn_measured_fraction_theta_max 0.993
_diffrn_measurement_device       '\k-geometry diffractometer'
_diffrn_measurement_device_type  'Bruker APEX-II CCD'
_diffrn_measurement_method       '\f and \w scans'
_diffrn_radiation_monochromator  graphite
_diffrn_radiation_type           MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_reflns_av_R_equivalents  0.0266
_diffrn_reflns_av_unetI/netI     0.0397
_diffrn_reflns_Laue_measured_fraction_full 0.998
_diffrn_reflns_Laue_measured_fraction_max 0.993
_diffrn_reflns_limit_h_max       21
_diffrn_reflns_limit_h_min       -21
_diffrn_reflns_limit_k_max       21
_diffrn_reflns_limit_k_min       -21
_diffrn_reflns_limit_l_max       31
_diffrn_reflns_limit_l_min       -31
_diffrn_reflns_number            55058
_diffrn_reflns_point_group_measured_fraction_full 0.984
_diffrn_reflns_point_group_measured_fraction_max 0.920
_diffrn_reflns_theta_full        25.242
_diffrn_reflns_theta_max         30.150
_diffrn_reflns_theta_min         3.214
_diffrn_source_current           30.0
_diffrn_source_power             1.5
_diffrn_source_voltage           50.0
_diffrn_standards_number         0
_exptl_absorpt_coefficient_mu    0.935
_exptl_absorpt_correction_T_max  0.7460
_exptl_absorpt_correction_T_min  0.6733
_exptl_absorpt_correction_type   multi-scan
_exptl_absorpt_process_details
;
SADABS-2012/1 (Bruker,2012) was used for absorption correction.
wR2(int) was 0.0776 before and 0.0555 after correction.
The Ratio of minimum to maximum transmission is 0.9025.
The \l/2 correction factor is 0.0015.
;
_exptl_crystal_colour            green
_exptl_crystal_colour_primary    green
_exptl_crystal_density_diffrn    1.517
_exptl_crystal_description       plate
_exptl_crystal_F_000             2470
_exptl_crystal_size_max          0.42
_exptl_crystal_size_mid          0.14
_exptl_crystal_size_min          0.12
_refine_diff_density_max         0.780
_refine_diff_density_min         -0.420
_refine_diff_density_rms         0.070
_refine_ls_abs_structure_details
;
 Flack x determined using 5171 quotients [(I+)-(I-)]/[(I+)+(I-)]
 (Parsons, Flack and Wagner, Acta Cryst. B69 (2013) 249-259).
;
_refine_ls_abs_structure_Flack   0.012(3)
_refine_ls_extinction_method     none
_refine_ls_goodness_of_fit_ref   1.022
_refine_ls_hydrogen_treatment    mixed
_refine_ls_matrix_type           full
_refine_ls_number_parameters     726
_refine_ls_number_reflns         14130
_refine_ls_number_restraints     59
_refine_ls_restrained_S_all      1.030
_refine_ls_R_factor_all          0.0426
_refine_ls_R_factor_gt           0.0351
_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^)+(0.0593P)^2^] where P=(Fo^2^+2Fc^2^)/3'
_refine_ls_weighting_scheme      calc
_refine_ls_wR_factor_gt          0.0888
_refine_ls_wR_factor_ref         0.0921
_reflns_Friedel_coverage         0.852
_reflns_Friedel_fraction_full    0.970
_reflns_Friedel_fraction_max     0.848
_reflns_number_gt                12535
_reflns_number_total             14130
_reflns_threshold_expression     'I > 2\s(I)'
_cod_data_source_file            d1dt03813c2.cif
_cod_data_source_block           g2330
_cod_original_cell_volume        5189.3(10)
_cod_original_formula_sum        'C46 H60.50 Cl2 N6 Ni2 O16.75 P'
_cod_database_code               7709348
_shelx_shelxl_version_number     2018/3
_shelx_estimated_absorpt_t_max   0.896
_shelx_estimated_absorpt_t_min   0.695
_olex2_refinement_description
;
1. Fixed Uiso
 At 1.2 times of:
  All C(H) groups, All C(H,H) groups
 At 1.5 times of:
  All C(H,H,H) groups
2. Restrained distances
 O66-H66
 0.87 with sigma of 0.02
 O65-H65A = O65-H65B
 0.88 with sigma of 0.02
3. Uiso/Uaniso restraints and constraints
Uanis(O1S) \\sim Ueq, Uanis(C3S) \\sim Ueq, Uanis(C4S) \\sim Ueq, Uanis(C2S)
\\sim Ueq, Uanis(C1S) \\sim Ueq: with sigma of 0.01 and sigma for terminal
atoms of 0.02
Uanis(O21) \\sim Ueq, Uanis(O21B) \\sim Ueq, Uanis(O23B) \\sim Ueq, Uanis(O24B)
\\sim Ueq: with sigma of 0.005 and sigma for terminal atoms of 0.01
4. Others
 Fixed Sof: O21(0.7) O21B(0.3) O23(0.7) O23B(0.3) O24(0.7) O24B(0.3) O1S(0.75)
 C1S(0.75) H1SA(0.75) H1SB(0.75) H1SC(0.75) C2S(0.75) H2SA(0.75) H2SB(0.75)
 C3S(0.75) H3SA(0.75) H3SB(0.75) C4S(0.75) H4SA(0.75) H4SB(0.75) H4SC(0.75)
5.a Secondary CH2 refined with riding coordinates:
 C11(H11A,H11B), C12(H12A,H12B), C22(H22A,H22B), C31(H31A,H31B), C32(H32A,
 H32B), C42(H42A,H42B), C2S(H2SA,H2SB), C3S(H3SA,H3SB)
5.b Me refined with riding coordinates:
 C1S(H1SA,H1SB,H1SC), C4S(H4SA,H4SB,H4SC)
5.c Aromatic/amide H refined with riding coordinates:
 C3(H3), C4(H4), C9(H9), C10(H10), C14(H14), C15(H15), C16(H16), C24(H24),
 C25(H25), C26(H26), C34(H34), C35(H35), C36(H36), C44(H44), C45(H45), C46(H46)
5.d Idealised Me refined as rotating group:
 C18(H18A,H18B,H18C), C28(H28A,H28B,H28C), C38(H38A,H38B,H38C), C48(H48A,H48B,
 H48C), C66(H66A,H66B,H66C), C101(H10A,H10B,H10C), C107(H10D,H10E,H10F)
;
_shelx_res_checksum              42066
_shelx_hkl_checksum              50462
_olex2_submission_special_instructions 'No special instructions were received'