#------------------------------------------------------------------------------ #$Date: 2024-03-21 17:39:32 +0200 (Thu, 21 Mar 2024) $ #$Revision: 290575 $ #$URL: file:///home/coder/svn-repositories/cod/cif/3/00/04/3000467.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/ # # All data on this site have been placed in the public domain by the # contributors. # data_3000467 loop_ _publ_author_name 'P\'erez-Romero, Antonio' 'Cano-Mu\~noz, Mario' 'L\'opez-Chamorro, Carmen' 'Conejero-Lara, Francisco' 'Palacios, Oscar' 'Dobado, Jos\'e A' 'Galindo, Miguel A' _publ_section_title ; Selective Formation of Pd-DNA Hybrids Using Tailored Palladium-Mediated Base Pairs: Towards Heteroleptic Pd-DNA Systems. ; _journal_issue 11 _journal_name_full 'Angewandte Chemie International Edition' _journal_page_first e202400261 _journal_paper_doi 10.1002/anie.202400261 _journal_volume 63 _journal_year 2024 _chemical_formula_moiety 'C12 H10 N4 O6 Pd, 3 (H2 O)' _chemical_formula_sum 'C12 H16 N4 O9 Pd' _chemical_formula_weight 466.69 _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 direct _atom_sites_solution_secondary difmap _audit_creation_method SHELXL-2019/3 _cell_angle_alpha 95.501(2) _cell_angle_beta 93.318(2) _cell_angle_gamma 107.373(2) _cell_formula_units_Z 2 _cell_length_a 6.7020(3) _cell_length_b 9.8320(5) _cell_length_c 13.1889(7) _cell_measurement_reflns_used 9989 _cell_measurement_temperature 100(2) _cell_measurement_theta_max 66.55 _cell_measurement_theta_min 3.38 _cell_volume 822.17(7) _computing_cell_refinement 'Bruker SAINT' _computing_data_collection 'Bruker APEX2' _computing_data_reduction 'Bruker SAINT' _computing_structure_refinement 'SHELXL-2019/2 (Sheldrick, 2019)' _computing_structure_solution 'SHELXS-97 (Sheldrick, 2008)' _diffrn_ambient_temperature 100(2) _diffrn_measured_fraction_theta_full 0.986 _diffrn_measured_fraction_theta_max 0.986 _diffrn_measurement_device_type 'Bruker D8 Venture' _diffrn_measurement_method '\f and \w scans' _diffrn_radiation_monochromator multilayer _diffrn_radiation_type CuK\a _diffrn_radiation_wavelength 1.54178 _diffrn_reflns_av_R_equivalents 0.0403 _diffrn_reflns_av_unetI/netI 0.0307 _diffrn_reflns_Laue_measured_fraction_full 0.986 _diffrn_reflns_Laue_measured_fraction_max 0.986 _diffrn_reflns_limit_h_max 7 _diffrn_reflns_limit_h_min -7 _diffrn_reflns_limit_k_max 11 _diffrn_reflns_limit_k_min -11 _diffrn_reflns_limit_l_max 15 _diffrn_reflns_limit_l_min -15 _diffrn_reflns_number 11629 _diffrn_reflns_point_group_measured_fraction_full 0.986 _diffrn_reflns_point_group_measured_fraction_max 0.986 _diffrn_reflns_theta_full 66.557 _diffrn_reflns_theta_max 66.557 _diffrn_reflns_theta_min 3.380 _diffrn_source 'high brilliance microfocus sealed tube' _exptl_absorpt_coefficient_mu 9.662 _exptl_absorpt_correction_T_max 0.7528 _exptl_absorpt_correction_T_min 0.4324 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details 'Bruker SADABS-2014/5 (Bruker, 2014)' _exptl_crystal_colour yellow _exptl_crystal_density_diffrn 1.885 _exptl_crystal_description plate _exptl_crystal_F_000 468 _exptl_crystal_size_max 0.120 _exptl_crystal_size_mid 0.120 _exptl_crystal_size_min 0.080 _refine_diff_density_max 0.782 _refine_diff_density_min -1.832 _refine_diff_density_rms 0.100 _refine_ls_extinction_coef . _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 1.148 _refine_ls_hydrogen_treatment mixed _refine_ls_matrix_type full _refine_ls_number_parameters 267 _refine_ls_number_reflns 2848 _refine_ls_number_restraints 4 _refine_ls_restrained_S_all 1.147 _refine_ls_R_factor_all 0.0425 _refine_ls_R_factor_gt 0.0395 _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^)+(0.0400P)^2^+2.0000P] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.0984 _refine_ls_wR_factor_ref 0.1025 _reflns_Friedel_coverage 0.000 _reflns_Friedel_fraction_full . _reflns_Friedel_fraction_max . _reflns_number_gt 2683 _reflns_number_total 2848 _reflns_threshold_expression 'I > 2\s(I)' _cod_data_source_file mag31_x.cif _cod_data_source_block mag31 _cod_depositor_comments 'Releasing structure 3000467 into public domain as published material.' _cod_database_code 3000467 _cod_database_fobs_code 3000467 _shelx_shelxl_version_number 2019/3 _shelx_space_group_comment ; The symmetry employed for this shelxl refinement is uniquely defined by the following loop, which should always be used as a source of symmetry information in preference to the above space-group names. They are only intended as comments. ; _shelx_estimated_absorpt_t_min 0.390 _shelx_estimated_absorpt_t_max 0.512 loop_ _space_group_symop_id _space_group_symop_operation_xyz 1 'x, y, z' 2 '-x, -y, -z' loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_occupancy _atom_site_site_symmetry_order _atom_site_calc_flag _atom_site_refinement_flags_posn _atom_site_refinement_flags_adp _atom_site_refinement_flags_occupancy _atom_site_disorder_assembly _atom_site_disorder_group Pd1 Pd 0.17024(5) 0.34936(4) 0.23601(2) 0.04892(16) Uani 1 1 d . . . . . N1 N 0.1723(6) 0.3988(5) 0.5586(3) 0.0513(11) Uani 1 1 d . . . . . C2 C 0.1445(8) 0.3465(7) 0.4560(4) 0.0559(15) Uani 1 1 d . . . . . O2 O 0.0525(7) 0.2192(5) 0.4285(3) 0.0706(12) Uani 1 1 d . . . . . N3 N 0.2183(7) 0.4376(6) 0.3869(3) 0.0564(13) Uani 1 1 d . . . . . C4 C 0.3166(8) 0.5771(7) 0.4163(4) 0.0547(14) Uani 1 1 d . . . . . N4 N 0.3908(8) 0.6618(6) 0.3467(4) 0.0663(14) Uani 1 1 d . . . . . H4A H 0.375623 0.626504 0.281844 0.080 Uiso 1 1 calc R U . . . H4B H 0.455701 0.753583 0.365102 0.080 Uiso 1 1 calc R U . . . C5 C 0.3413(8) 0.6321(7) 0.5225(4) 0.0530(13) Uani 1 1 d . . . . . H5 H 0.407386 0.731146 0.544589 0.064 Uiso 1 1 calc R U . . . C6 C 0.2687(7) 0.5397(6) 0.5892(4) 0.0497(13) Uani 1 1 d . . . . . H6 H 0.284985 0.573660 0.659993 0.060 Uiso 1 1 calc R U . . . C7 C 0.0978(9) 0.2955(7) 0.6349(4) 0.0613(14) Uani 1 1 d . . . . . H7A H 0.110568 0.348747 0.702943 0.092 Uiso 1 1 calc R U . . . H7B H 0.183506 0.230376 0.636217 0.092 Uiso 1 1 calc R U . . . H7C H -0.049450 0.239692 0.615570 0.092 Uiso 1 1 calc R U . . . N1C N 0.1198(5) 0.2656(4) 0.0963(3) 0.0361(8) Uani 1 1 d . . . . . C2C C -0.0334(6) 0.2887(4) 0.0375(3) 0.0330(9) Uani 1 1 d . . . . . C3C C -0.0741(6) 0.2292(4) -0.0625(3) 0.0332(9) Uani 1 1 d . . . . . H3C H -0.182997 0.244069 -0.105130 0.040 Uiso 1 1 calc R U . . . C4C C 0.0481(6) 0.1455(4) -0.1008(3) 0.0319(9) Uani 1 1 d . . . . . O4C O -0.0006(5) 0.0874(4) -0.1973(2) 0.0455(8) Uani 1 1 d . . . . . H4C H 0.088174 0.046954 -0.214990 0.068 Uiso 1 1 calc R U . . . C5C C 0.2093(6) 0.1256(4) -0.0372(3) 0.0306(8) Uani 1 1 d . . . . . H5C H 0.295066 0.071038 -0.062595 0.037 Uiso 1 1 calc R U . . . C6C C 0.2405(6) 0.1869(4) 0.0628(3) 0.0325(9) Uani 1 1 d . . . . . C7C C 0.3999(7) 0.1792(5) 0.1463(3) 0.0407(10) Uani 1 1 d . . . . . O7C O 0.3945(5) 0.2477(4) 0.2352(2) 0.0519(9) Uani 1 1 d . . . . . O7C' O 0.5209(5) 0.1093(4) 0.1279(2) 0.0462(8) Uani 1 1 d . . . . . C8C C -0.1378(7) 0.3854(5) 0.0949(3) 0.0389(10) Uani 1 1 d . . . . . O8C O -0.0686(5) 0.4258(4) 0.1907(2) 0.0475(8) Uani 1 1 d . . . . . O8C' O -0.2761(5) 0.4231(4) 0.0517(2) 0.0431(7) Uani 1 1 d . . . . . O1W O 0.4937(5) 0.6003(4) 0.1425(2) 0.0462(8) Uani 1 1 d D . . . . H1WA H 0.425(8) 0.597(7) 0.087(3) 0.069 Uiso 1 1 d D U . . . H1WB H 0.574(8) 0.552(6) 0.128(5) 0.069 Uiso 1 1 d D U . . . O2W O -0.2357(7) 0.0516(6) 0.2745(3) 0.0717(13) Uani 1 1 d D . . . . H2WA H -0.367(2) 0.034(9) 0.266(7) 0.108 Uiso 1 1 d D U . . . H2WB H -0.164(11) 0.115(7) 0.321(4) 0.108 Uiso 1 1 d D U . . . O31W O 0.5442(14) 0.9344(8) 0.4170(6) 0.053(2) Uani 0.43 1 d . . P A -1 O32W O 0.2437(16) 1.0401(11) 0.4866(8) 0.056(3) Uani 0.35 1 d . . P B -1 O33W O 0.676(3) 1.0257(16) 0.6126(13) 0.062(5) Uani 0.22 1 d . . P C -1 loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_23 _atom_site_aniso_U_13 _atom_site_aniso_U_12 Pd1 0.0445(2) 0.0839(3) 0.0262(2) -0.02445(16) -0.01128(14) 0.04382(19) N1 0.037(2) 0.086(3) 0.034(2) -0.024(2) -0.0080(16) 0.035(2) C2 0.048(3) 0.095(4) 0.034(3) -0.024(3) -0.011(2) 0.048(3) O2 0.073(3) 0.098(3) 0.046(2) -0.035(2) -0.0196(19) 0.053(2) N3 0.046(2) 0.100(4) 0.034(2) -0.030(2) -0.0149(18) 0.053(2) C4 0.042(3) 0.101(4) 0.033(3) -0.014(3) -0.002(2) 0.048(3) N4 0.062(3) 0.104(4) 0.043(3) -0.018(3) 0.000(2) 0.049(3) C5 0.038(2) 0.083(4) 0.040(3) -0.023(3) -0.006(2) 0.032(2) C6 0.030(2) 0.088(4) 0.031(2) -0.023(2) -0.0047(19) 0.030(2) C7 0.053(3) 0.078(4) 0.054(3) -0.007(3) 0.002(3) 0.026(3) N1C 0.0308(18) 0.054(2) 0.0260(17) -0.0112(15) -0.0037(14) 0.0234(16) C2C 0.029(2) 0.042(2) 0.028(2) -0.0062(17) -0.0007(16) 0.0147(17) C3C 0.032(2) 0.041(2) 0.025(2) -0.0022(17) -0.0017(16) 0.0124(17) C4C 0.033(2) 0.036(2) 0.0228(19) -0.0039(16) 0.0018(16) 0.0078(16) O4C 0.0531(19) 0.062(2) 0.0246(15) -0.0145(14) -0.0064(13) 0.0306(16) C5C 0.029(2) 0.034(2) 0.0262(19) -0.0067(16) 0.0044(16) 0.0088(16) C6C 0.0266(19) 0.041(2) 0.029(2) -0.0074(17) 0.0009(16) 0.0117(17) C7C 0.035(2) 0.058(3) 0.030(2) -0.0132(19) -0.0046(18) 0.023(2) O7C 0.0486(19) 0.084(2) 0.0312(16) -0.0257(16) -0.0134(14) 0.0452(18) O7C' 0.0426(17) 0.068(2) 0.0336(16) -0.0187(14) -0.0067(13) 0.0353(16) C8C 0.035(2) 0.054(3) 0.030(2) -0.0094(19) -0.0011(18) 0.022(2) O8C 0.0443(18) 0.077(2) 0.0300(16) -0.0168(15) -0.0059(13) 0.0401(16) O8C' 0.0426(17) 0.0624(19) 0.0317(16) -0.0063(14) -0.0040(13) 0.0320(15) O1W 0.0443(19) 0.066(2) 0.0331(17) -0.0049(15) 0.0017(14) 0.0280(16) O2W 0.074(3) 0.118(4) 0.036(2) -0.028(2) -0.0130(19) 0.064(3) O31W 0.068(5) 0.042(4) 0.050(5) 0.008(4) 0.022(4) 0.014(4) O32W 0.054(6) 0.063(6) 0.064(7) 0.031(5) 0.014(5) 0.030(5) O33W 0.099(14) 0.037(8) 0.046(9) 0.011(7) -0.010(9) 0.015(8) loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0181 0.0091 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' Pd Pd 0.1215 3.9337 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' loop_ _geom_angle_atom_site_label_1 _geom_angle_atom_site_label_2 _geom_angle_atom_site_label_3 _geom_angle _geom_angle_site_symmetry_1 _geom_angle_site_symmetry_3 N1C Pd1 O7C 81.33(13) . . N1C Pd1 O8C 81.05(13) . . O7C Pd1 O8C 162.36(12) . . N1C Pd1 N3 178.84(17) . . O7C Pd1 N3 99.33(13) . . O8C Pd1 N3 98.31(13) . . C6 N1 C2 120.5(5) . . C6 N1 C7 120.9(4) . . C2 N1 C7 118.6(5) . . O2 C2 N3 120.7(5) . . O2 C2 N1 120.2(6) . . N3 C2 N1 119.1(5) . . C4 N3 C2 121.1(4) . . C4 N3 Pd1 122.7(4) . . C2 N3 Pd1 116.2(4) . . N4 C4 N3 119.2(5) . . N4 C4 C5 120.9(6) . . N3 C4 C5 119.9(6) . . C4 N4 H4A 120.0 . . C4 N4 H4B 120.0 . . H4A N4 H4B 120.0 . . C6 C5 C4 117.8(5) . . C6 C5 H5 121.1 . . C4 C5 H5 121.1 . . C5 C6 N1 121.7(4) . . C5 C6 H6 119.2 . . N1 C6 H6 119.2 . . N1 C7 H7A 109.5 . . N1 C7 H7B 109.5 . . H7A C7 H7B 109.5 . . N1 C7 H7C 109.5 . . H7A C7 H7C 109.5 . . H7B C7 H7C 109.5 . . C2C N1C C6C 123.7(4) . . C2C N1C Pd1 118.3(3) . . C6C N1C Pd1 118.0(3) . . N1C C2C C3C 119.6(4) . . N1C C2C C8C 111.9(3) . . C3C C2C C8C 128.5(4) . . C2C C3C C4C 118.7(4) . . C2C C3C H3C 120.7 . . C4C C3C H3C 120.7 . . O4C C4C C5C 123.6(4) . . O4C C4C C3C 116.5(4) . . C5C C4C C3C 120.0(4) . . C4C O4C H4C 109.5 . . C6C C5C C4C 118.4(4) . . C6C C5C H5C 120.8 . . C4C C5C H5C 120.8 . . N1C C6C C5C 119.6(4) . . N1C C6C C7C 111.9(3) . . C5C C6C C7C 128.5(4) . . O7C' C7C O7C 124.6(4) . . O7C' C7C C6C 119.8(4) . . O7C C7C C6C 115.6(4) . . C7C O7C Pd1 113.1(3) . . O8C' C8C O8C 123.6(4) . . O8C' C8C C2C 120.9(4) . . O8C C8C C2C 115.5(4) . . C8C O8C Pd1 113.2(3) . . H1WA O1W H1WB 104(6) . . H2WA O2W H2WB 120(8) . . loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_2 Pd1 N1C 1.913(3) . Pd1 O7C 2.038(3) . Pd1 O8C 2.044(3) . Pd1 N3 2.061(4) . N1 C6 1.352(7) . N1 C2 1.382(6) . N1 C7 1.499(7) . C2 O2 1.227(7) . C2 N3 1.349(8) . N3 C4 1.339(8) . C4 N4 1.317(8) . C4 C5 1.434(7) . N4 H4A 0.8800 . N4 H4B 0.8800 . C5 C6 1.332(8) . C5 H5 0.9500 . C6 H6 0.9500 . C7 H7A 0.9800 . C7 H7B 0.9800 . C7 H7C 0.9800 . N1C C2C 1.337(5) . N1C C6C 1.340(5) . C2C C3C 1.368(6) . C2C C8C 1.512(6) . C3C C4C 1.405(6) . C3C H3C 0.9500 . C4C O4C 1.324(5) . C4C C5C 1.401(6) . O4C H4C 0.8400 . C5C C6C 1.374(5) . C5C H5C 0.9500 . C6C C7C 1.512(6) . C7C O7C' 1.230(5) . C7C O7C 1.302(5) . C8C O8C' 1.227(5) . C8C O8C 1.302(5) . O1W H1WA 0.840(10) . O1W H1WB 0.840(10) . O2W H2WA 0.841(10) . O2W H2WB 0.840(10) . loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA _geom_hbond_site_symmetry_A _geom_hbond_publ_flag N4 H4A O1W 0.88 2.07 2.872(6) 151.7 . yes N4 H4B O31W 0.88 1.75 2.621(9) 168.7 . yes O4C H4C O2W 0.84 1.75 2.574(5) 168.0 2 yes O1W H1WA O8C' 0.840(10) 1.990(13) 2.827(4) 174(6) 2_565 yes O1W H1WB O8C' 0.840(10) 2.06(2) 2.876(4) 164(6) 1_655 yes O2W H2WA O7C' 0.841(10) 2.21(8) 2.668(5) 114(7) 1_455 yes O2W H2WB O2 0.840(10) 1.94(3) 2.752(6) 162(8) . yes O31W . O32W . . 2.695(13) . . yes O31W . O2W . . 2.599(9) . 1_665 yes O31W . O33W . . 2.658(19) . . yes O32W . O2 . . 2.613(10) . 1_565 yes