#------------------------------------------------------------------------------ #$Date: 2025-08-19 11:43:10 +0100 (Tue, 19 Aug 2025) $ #$Revision: 301803 $ #$URL: svn://www.crystallography.net/cod/cif/2/20/25/2202505.cif $ #------------------------------------------------------------------------------ # # This file is available in the Crystallography Open Database (COD), # http://www.crystallography.net/. The original data for this entry # were provided by IUCr Journals, http://journals.iucr.org/. # # The file may be used within the scientific community so long as # proper attribution is given to the journal article from which the # data were obtained. # data_2202505 loop_ _publ_author_name 'Okabe, Nobuo ' 'Muranishi, Yasunori ' _publ_section_title ;(1,2-Benzenediolato-\k^2^O,O')(1,10-phenanthroline-\k^2^N,N')palladium(II) dihydrate ; _journal_issue 10 _journal_name_full 'Acta Crystallographica Section E' _journal_page_first m936 _journal_page_last m938 _journal_paper_doi 10.1107/S1600536803020166 _journal_volume 59 _journal_year 2003 _chemical_formula_iupac '[Pd (C6 H4 O2 )(C12 H8 N2 )] , 2H~2~O' _chemical_formula_moiety 'C18 H12 N2 O2 Pd, 2(H2 O)' _chemical_formula_sum 'C18 H16 N2 O4 Pd' _chemical_formula_weight 430.75 _space_group_IT_number 14 _symmetry_cell_setting monoclinic _symmetry_space_group_name_Hall '-P 2yn' _symmetry_space_group_name_H-M 'P 1 21/n 1' _cell_angle_alpha 90 _cell_angle_beta 94.700(10) _cell_angle_gamma 90 _cell_formula_units_Z 4 _cell_length_a 9.248(2) _cell_length_b 16.462(2) _cell_length_c 10.8020(10) _cell_measurement_reflns_used 25 _cell_measurement_temperature 296.2 _cell_measurement_theta_max 15.0 _cell_measurement_theta_min 14.7 _cell_volume 1639.0(4) _computing_cell_refinement 'MSC/AFC Diffractometer Control Software' _computing_data_collection ;MSC/AFC Diffractometer Control Software (Molecular Structure Corporation, 1992) ; _computing_data_reduction 'TEXSAN (Molecular Structure Corporation & Rigaku Corporation, 2000)' _computing_molecular_graphics 'ORTEPII (Johnson, 1976)' _computing_publication_material TEXSAN _computing_structure_refinement 'SHELXL97 (Sheldrick, 1997)' _computing_structure_solution 'SIR97 (Altomare et al., 1999)' _diffrn_measured_fraction_theta_full 1.000 _diffrn_measured_fraction_theta_max 1.000 _diffrn_measurement_device_type 'Rigaku AFC-5R' _diffrn_measurement_method \w-2\q _diffrn_radiation_type 'Mo K\a' _diffrn_radiation_wavelength 0.7107 _diffrn_reflns_av_R_equivalents 0.042 _diffrn_reflns_limit_h_max 12 _diffrn_reflns_limit_h_min 0 _diffrn_reflns_limit_k_max 21 _diffrn_reflns_limit_k_min 0 _diffrn_reflns_limit_l_max 13 _diffrn_reflns_limit_l_min -14 _diffrn_reflns_number 4127 _diffrn_reflns_theta_full 27.50 _diffrn_reflns_theta_max 27.50 _diffrn_standards_decay_% 0.74 _diffrn_standards_interval_count 150 _diffrn_standards_number 3 _exptl_absorpt_coefficient_mu 1.159 _exptl_absorpt_correction_T_max 0.793 _exptl_absorpt_correction_T_min 0.757 _exptl_absorpt_correction_type psi-scan _exptl_absorpt_process_details '(North et al., 1968)' _exptl_crystal_colour 'dark red' _exptl_crystal_density_diffrn 1.746 _exptl_crystal_density_method 'not measured' _exptl_crystal_description plate _exptl_crystal_F_000 864.0 _exptl_crystal_size_max 0.50 _exptl_crystal_size_mid 0.20 _exptl_crystal_size_min 0.20 _refine_diff_density_max 0.37 _refine_diff_density_min -0.66 _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 1.129 _refine_ls_hydrogen_treatment mixed _refine_ls_number_parameters 226 _refine_ls_number_reflns 3760 _refine_ls_R_factor_gt 0.0258 _refine_ls_shift/su_max 0.0030 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'w = 1/[\s^2^(Fo^2^) + (0.0340P)^2^] where P = (Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_ref 0.0714 _reflns_number_gt 3021 _reflns_number_total 3760 _reflns_threshold_expression 'I > 2.0\s(I)' _cod_data_source_file ci6273.cif _cod_data_source_block I _cod_original_sg_symbol_H-M 'P 21/n' _cod_original_formula_sum 'C18 H16 N2 O4 Pd ' _cod_database_code 2202505 _cod_database_fobs_code 2202505 loop_ _symmetry_equiv_pos_as_xyz x,y,z 1/2-x,1/2+y,1/2-z -x,-y,-z 1/2+x,1/2-y,1/2+z loop_ _atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv _atom_site_adp_type _atom_site_calc_flag _atom_site_refinement_flags _atom_site_occupancy _atom_site_disorder_assembly _atom_site_disorder_group _atom_site_type_symbol Pd1 -0.06586(2) 0.972270(10) 0.68957(2) 0.03041(7) Uani d . 1.00 . . Pd O1 -0.2289(2) 0.96720(10) 0.5578(2) 0.0392(4) Uani d . 1.00 . . O O2 0.0017(2) 0.87110(10) 0.6135(2) 0.0420(4) Uani d . 1.00 . . O O3 0.2951(2) 0.88690(10) 0.5620(2) 0.0514(5) Uani d . 1.00 . . O O4 0.5476(2) 0.9208(2) 0.7183(2) 0.0752(7) Uani d . 1.00 . . O N1 -0.1230(2) 1.07720(10) 0.7691(2) 0.0336(4) Uani d . 1.00 . . N N2 0.0970(2) 0.97870(10) 0.8233(2) 0.0316(4) Uani d . 1.00 . . N C1 -0.2389(3) 1.1246(2) 0.7425(2) 0.0414(6) Uani d . 1.00 . . C C2 -0.2577(3) 1.1975(2) 0.8045(3) 0.0483(7) Uani d . 1.00 . . C C3 -0.1560(3) 1.2233(2) 0.8946(3) 0.0459(7) Uani d . 1.00 . . C C4 -0.0335(3) 1.1746(2) 0.9267(2) 0.0386(6) Uani d . 1.00 . . C C5 -0.0230(3) 1.10190(10) 0.8613(2) 0.0325(5) Uani d . 1.00 . . C C6 0.0956(3) 1.0481(2) 0.8918(2) 0.0317(5) Uani d . 1.00 . . C C7 0.2003(3) 1.0662(2) 0.9879(2) 0.0362(5) Uani d . 1.00 . . C C8 0.3104(3) 1.0083(2) 1.0147(3) 0.0422(6) Uani d . 1.00 . . C C9 0.3105(3) 0.9392(2) 0.9457(3) 0.0449(6) Uani d . 1.00 . . C C10 0.2024(3) 0.9248(2) 0.8508(3) 0.0391(6) Uani d . 1.00 . . C C11 0.1886(3) 1.1421(2) 1.0528(3) 0.0443(6) Uani d . 1.00 . . C C12 0.0784(3) 1.1936(2) 1.0219(3) 0.0473(7) Uani d . 1.00 . . C C13 -0.2049(3) 0.9047(2) 0.4790(2) 0.0387(6) Uani d . 1.00 . . C C14 -0.2975(4) 0.8891(2) 0.3744(3) 0.0508(7) Uani d . 1.00 . . C C15 -0.2686(4) 0.8236(2) 0.2975(3) 0.0615(9) Uani d . 1.00 . . C C16 -0.1487(4) 0.7754(2) 0.3253(3) 0.0598(9) Uani d . 1.00 . . C C17 -0.0558(4) 0.7903(2) 0.4307(3) 0.0505(7) Uani d . 1.00 . . C C18 -0.0829(3) 0.8551(2) 0.5091(2) 0.0390(6) Uani d . 1.00 . . C H1 -0.3089 1.1083 0.6808 0.0497 Uiso calc . 1.00 . . H H2 -0.3401 1.2288 0.7845 0.0579 Uiso calc . 1.00 . . H H3 -0.1676 1.2726 0.9345 0.0551 Uiso calc . 1.00 . . H H3A 0.2175 0.8744 0.5746 0.0618 Uiso d . 1.00 . . H H3B 0.2815 0.9307 0.5433 0.0618 Uiso d . 1.00 . . H H4A 0.4794 0.9139 0.6757 0.0895 Uiso d . 1.00 . . H H4B 0.6033 0.9306 0.6722 0.0895 Uiso d . 1.00 . . H H8 0.3822 1.0172 1.0787 0.0506 Uiso calc . 1.00 . . H H9 0.3836 0.9010 0.9622 0.0539 Uiso calc . 1.00 . . H H10 0.2038 0.8767 0.8057 0.0470 Uiso calc . 1.00 . . H H11 0.2580 1.1557 1.1167 0.0532 Uiso calc . 1.00 . . H H12 0.0748 1.2428 1.0637 0.0568 Uiso calc . 1.00 . . H H14 -0.3782 0.9218 0.3554 0.0610 Uiso calc . 1.00 . . H H15 -0.3307 0.8126 0.2274 0.0738 Uiso calc . 1.00 . . H H16 -0.1296 0.7324 0.2731 0.0717 Uiso calc . 1.00 . . H H17 0.0245 0.7571 0.4490 0.0606 Uiso calc . 1.00 . . H loop_ _atom_site_aniso_label _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Pd1 0.03220(10) 0.02870(10) 0.03060(10) -0.00060(7) 0.00398(7) -0.00222(7) O1 0.0410(10) 0.0390(10) 0.0369(10) -0.0008(8) -0.0017(8) -0.0043(8) O2 0.0410(10) 0.0351(10) 0.0510(10) 0.0014(8) 0.0048(8) -0.0110(8) O3 0.0440(10) 0.0570(10) 0.0530(10) 0.0020(9) -0.0006(9) 0.0060(10) O4 0.0480(10) 0.128(2) 0.0490(10) -0.0150(10) 0.0000(10) -0.0070(10) N1 0.0370(10) 0.0350(10) 0.0290(10) 0.0033(9) 0.0048(8) 0.0015(8) N2 0.0310(10) 0.0320(10) 0.0320(10) 0.0004(8) 0.0048(8) -0.0007(8) C1 0.0460(10) 0.047(2) 0.0320(10) 0.0120(10) 0.0010(10) 0.0040(10) C2 0.058(2) 0.045(2) 0.043(2) 0.0210(10) 0.0090(10) 0.0080(10) C3 0.064(2) 0.0350(10) 0.0400(10) 0.0100(10) 0.0150(10) -0.0030(10) C4 0.050(2) 0.0320(10) 0.0350(10) 0.0000(10) 0.0110(10) -0.0010(10) C5 0.0360(10) 0.0330(10) 0.0300(10) -0.0020(10) 0.0089(10) 0.0013(9) C6 0.0320(10) 0.0310(10) 0.0330(10) -0.0046(10) 0.0084(10) 0.0017(10) C7 0.0350(10) 0.0430(10) 0.0320(10) -0.0090(10) 0.0070(10) 0.0020(10) C8 0.0300(10) 0.058(2) 0.0390(10) -0.0060(10) 0.0030(10) 0.0030(10) C9 0.0350(10) 0.055(2) 0.045(2) 0.0090(10) 0.0060(10) 0.0060(10) C10 0.0380(10) 0.0380(10) 0.0420(10) 0.0070(10) 0.0080(10) 0.0020(10) C11 0.0440(10) 0.050(2) 0.0380(10) -0.0100(10) 0.0010(10) -0.0090(10) C12 0.065(2) 0.0390(10) 0.0390(10) -0.0090(10) 0.0090(10) -0.0120(10) C13 0.0450(10) 0.0370(10) 0.0340(10) -0.0140(10) 0.0080(10) -0.0010(10) C14 0.059(2) 0.054(2) 0.039(2) -0.0180(10) 0.0010(10) 0.0030(10) C15 0.080(2) 0.066(2) 0.038(2) -0.037(2) 0.006(2) -0.0070(10) C16 0.087(2) 0.049(2) 0.046(2) -0.029(2) 0.028(2) -0.0160(10) C17 0.062(2) 0.0360(10) 0.057(2) -0.0130(10) 0.0240(10) -0.0100(10) C18 0.0460(10) 0.0330(10) 0.0390(10) -0.0130(10) 0.0150(10) -0.0040(10) loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.003 0.002 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.4) ; H H 0.000 0.000 ;International Tables for Crystallography (1992, Vol. C, Table 6.1.1.4) ; O O 0.011 0.006 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.4) ; N N 0.006 0.003 ;International Tables for Crystallography (1992, Vol. C, Tables 4.2.6.8 and 6.1.1.4) ; Pd Pd -0.999 1.007 ;International Tables for Crystallography (1992, 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_publ_flag O1 PD1 O2 85.09(7) yes O1 PD1 N1 97.51(7) yes O1 PD1 N2 179.19(8) yes O2 PD1 N1 176.80(8) yes O2 PD1 N2 95.72(8) yes N1 PD1 N2 81.69(8) yes PD1 O1 C13 109.00(10) no PD1 O2 C18 109.30(10) no H3A O3 H3B 99.5 no H4A O4 H4B 102.0 no PD1 N1 C1 129.8(2) no PD1 N1 C5 112.3(2) no C1 N1 C5 117.8(2) no PD1 N2 C6 113.3(2) no PD1 N2 C10 128.2(2) no C6 N2 C10 118.5(2) no N1 C1 C2 121.9(2) no N1 C1 H1 119.0 no C2 C1 H1 119.0 no C1 C2 C3 120.3(3) no C1 C2 H2 119.8 no C3 C2 H2 119.8 no C2 C3 C4 119.5(3) no C2 C3 H3 120.2 no C4 C3 H3 120.2 no C3 C4 C5 116.8(2) no C3 C4 C12 124.9(2) no C5 C4 C12 118.2(2) no N1 C5 C4 123.6(2) no N1 C5 C6 116.5(2) no C4 C5 C6 119.9(2) no N2 C6 C5 115.9(2) no N2 C6 C7 123.2(2) no C5 C6 C7 120.9(2) no C6 C7 C8 117.1(2) no C6 C7 C11 118.2(2) no C8 C7 C11 124.6(2) no C7 C8 C9 119.1(2) no C7 C8 H8 120.5 no C9 C8 H8 120.5 no C8 C9 C10 120.9(3) no C8 C9 H9 119.5 no C10 C9 H9 119.5 no N2 C10 C9 121.2(2) no N2 C10 H10 119.4 no C9 C10 H10 119.4 no C7 C11 C12 120.6(2) no C7 C11 H11 119.7 no C12 C11 H11 119.7 no C4 C12 C11 121.9(3) no C4 C12 H12 119.0 no C11 C12 H12 119.0 no O1 C13 C14 121.9(2) no O1 C13 C18 117.4(2) no C14 C13 C18 120.7(3) no C13 C14 C15 119.5(3) no C13 C14 H14 120.2 no C15 C14 H14 120.2 no C14 C15 C16 120.2(3) no C14 C15 H15 119.9 no C16 C15 H15 119.9 no C15 C16 C17 120.6(3) no C15 C16 H16 119.7 no C17 C16 H16 119.7 no C16 C17 C18 120.1(3) no C16 C17 H17 119.9 no C18 C17 H17 119.9 no O2 C18 C13 118.7(2) no O2 C18 C17 122.5(2) no C13 C18 C17 118.8(2) no loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_1 _geom_bond_site_symmetry_2 _geom_bond_distance _geom_bond_publ_flag PD1 O1 . . 1.989(2) yes PD1 O2 . . 1.981(2) yes PD1 N1 . . 2.019(2) yes PD1 N2 . . 2.003(2) yes O1 C13 . . 1.365(3) yes O2 C18 . . 1.344(3) yes O3 H3A . . 0.77 no O3 H3B . . 0.76 no O4 H4A . . 0.76 no O4 H4B . . 0.76 no N1 C1 . . 1.337(3) no N1 C5 . . 1.365(3) no N2 C6 . . 1.362(3) no N2 C10 . . 1.333(3) no C1 C2 . . 1.393(4) no C1 H1 . . 0.93 no C2 C3 . . 1.364(4) no C2 H2 . . 0.93 no C3 C4 . . 1.408(4) no C3 H3 . . 0.93 no C4 C5 . . 1.398(4) no C4 C12 . . 1.433(4) no C5 C6 . . 1.427(3) no C6 C7 . . 1.392(3) no C7 C8 . . 1.408(4) no C7 C11 . . 1.442(4) no C8 C9 . . 1.360(4) no C8 H8 . . 0.93 no C9 C10 . . 1.392(4) no C9 H9 . . 0.93 no C10 H10 . . 0.93 no C11 C12 . . 1.346(4) no C11 H11 . . 0.93 no C12 H12 . . 0.93 no C13 C14 . . 1.385(4) no C13 C18 . . 1.409(4) no C14 C15 . . 1.400(5) no C14 H14 . . 0.93 no C15 C16 . . 1.377(5) no C15 H15 . . 0.93 no C16 C17 . . 1.390(4) no C16 H16 . . 0.93 no C17 C18 . . 1.398(4) no C17 H17 . . 0.93 no loop_ _geom_contact_atom_site_label_1 _geom_contact_atom_site_label_2 _geom_contact_distance _geom_contact_site_symmetry_2 O1 O3 2.772(3) 3_576 O1 O4 2.907(3) 1_455 O3 C1 3.293(3) 3_576 O3 C12 3.535(4) 2_546 O3 C13 3.549(3) 3_576 O4 C8 3.284(4) 3_677 O4 C11 3.485(4) 3_677 O4 C13 3.600(4) 1_655 N1 C8 3.332(4) 3_577 N1 C17 3.568(4) 3_576 C1 C8 3.520(4) 3_577 C2 C9 3.577(4) 3_577 C3 C18 3.469(4) 2_456 C3 C9 3.546(4) 3_577 C3 C17 3.565(4) 2_456 C3 C13 3.568(4) 2_456 C4 C10 3.393(4) 3_577 C4 C16 3.417(4) 3_576 C4 C9 3.543(4) 3_577 C5 C16 3.345(4) 3_576 C5 C15 3.533(4) 3_576 C5 C8 3.569(4) 3_577 C5 C9 3.575(4) 3_577 C6 C15 3.426(4) 3_576 C6 C6 3.431(5) 3_577 C8 C8 3.557(5) 3_677 C10 C16 3.591(4) 4_565 loop_ _geom_hbond_atom_site_label_D _geom_hbond_atom_site_label_H _geom_hbond_atom_site_label_A _geom_hbond_site_symmetry_A _geom_hbond_distance_DH _geom_hbond_distance_HA _geom_hbond_distance_DA _geom_hbond_angle_DHA O3 H3A O2 . 0.77 2.07 2.826(3) 166 O3 H3B O1 3_576 0.76 2.04 2.772(3) 163 O4 H4B O1 1_655 0.76 2.15 2.907(3) 174 O4 H4A O3 . 0.76 2.07 2.823(3) 176 loop_ _geom_torsion_atom_site_label_1 _geom_torsion_atom_site_label_2 _geom_torsion_atom_site_label_3 _geom_torsion_atom_site_label_4 _geom_torsion _geom_torsion_publ_flag PD1 O1 C13 C14 -176.8(2) no PD1 O1 C13 C18 4.4(3) no PD1 O2 C18 C13 -5.5(3) no PD1 O2 C18 C17 175.7(2) no PD1 N1 C1 C2 -177.2(2) no PD1 N1 C5 C4 176.8(2) no PD1 N1 C5 C6 -4.6(3) no PD1 N2 C6 C5 2.7(3) no PD1 N2 C6 C7 -178.6(2) no PD1 N2 C10 C9 178.6(2) no O1 PD1 O2 C18 6.1(2) no O1 PD1 N1 C1 2.8(2) no O1 PD1 N1 C5 -175.4(2) no O1 C13 C14 C15 -179.2(3) no O1 C13 C18 O2 0.8(4) no O1 C13 C18 C17 179.6(2) no O2 PD1 O1 C13 -5.7(2) no O2 PD1 N2 C6 174.1(2) no O2 PD1 N2 C10 -5.6(2) no O2 C18 C13 C14 -178.1(3) no O2 C18 C17 C16 178.5(3) no N1 PD1 O1 C13 172.4(2) no N1 PD1 N2 C6 -4.0(2) no N1 PD1 N2 C10 176.3(2) no N1 C1 C2 C3 0.7(4) no N1 C5 C4 C3 0.8(4) no N1 C5 C4 C12 179.8(2) no N1 C5 C6 N2 1.3(3) no N1 C5 C6 C7 -177.4(2) no N2 PD1 O2 C18 -174.0(2) no N2 PD1 N1 C1 -177.1(2) no N2 PD1 N1 C5 4.7(2) no N2 C6 C5 C4 -180.0(2) no N2 C6 C7 C8 -1.0(4) no N2 C6 C7 C11 179.1(2) no N2 C10 C9 C8 1.0(4) no C1 N1 C5 C4 -1.7(4) no C1 N1 C5 C6 176.9(2) no C1 C2 C3 C4 -1.6(4) no C2 C1 N1 C5 0.9(4) no C2 C3 C4 C5 0.9(4) no C2 C3 C4 C12 -178.0(3) no C3 C4 C5 C6 -177.8(2) no C3 C4 C12 C11 176.1(3) no C4 C5 C6 C7 1.2(4) no C4 C12 C11 C7 1.8(4) no C5 C4 C12 C11 -2.7(4) no C5 C6 N2 C10 -177.6(2) no C5 C6 C7 C8 177.7(2) no C5 C6 C7 C11 -2.2(4) no C6 N2 C10 C9 -1.1(4) no C6 C5 C4 C12 1.2(4) no C6 C7 C8 C9 0.9(4) no C6 C7 C11 C12 0.7(4) no C7 C6 N2 C10 1.2(4) no C7 C8 C9 C10 -0.9(4) no C8 C7 C11 C12 -179.1(3) no C9 C8 C7 C11 -179.3(3) no C13 C14 C15 C16 -0.3(5) no C13 C18 C17 C16 -0.3(4) no C14 C13 C18 C17 0.8(4) no C14 C15 C16 C17 0.8(5) no C15 C14 C13 C18 -0.5(4) no C15 C16 C17 C18 -0.5(5) no C15 C16 C17 C18 -0.5(5) no loop_ _cod_related_entry_id _cod_related_entry_database _cod_related_entry_code 1 PubChem 139066065