#------------------------------------------------------------------------------ #$Date: 2013-12-28 15:58:47 +0200 (Sat, 28 Dec 2013) $ #$Revision: 91933 $ #$URL: file:///home/coder/svn-repositories/cod/cif/2/01/46/2014652.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_2014652 loop_ _publ_author_name 'Yue Wang' 'Yu Mizubayashi' 'Mamiko Odoko' 'Nobuo Okabe' _publ_section_title ;(Di-2-pyridylamine-\k^2^N,N')(naphthalene-2,3-diolato-\k^2^O,O')palladium(II) monohydrate and (di-2-pyridylamine-\k^2^N,N')(3-oxidonaphthalene-2-carboxylato-\k^2^O,O')palladium(II) ; _journal_issue 2 _journal_name_full 'Acta Crystallographica Section C' _journal_page_first m67 _journal_page_last m70 _journal_volume 61 _journal_year 2005 _chemical_formula_iupac '[Pd (C11 H6 O3) (C10 H9 N3)]' _chemical_formula_moiety 'C21 H15 N3 O3 Pd' _chemical_formula_sum 'C21 H15 N3 O3 Pd' _chemical_formula_weight 463.76 _chemical_name_systematic ; (di-2-pyridylamine-\k^2^N,N')(2-oxidonaphthalene-3-carboxylato- \k^2^O,O')palladium(II) ; _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' _atom_sites_solution_hydrogens geom _atom_sites_solution_primary direct _atom_sites_solution_secondary difmap _audit_creation_method SHELXL-97 _cell_angle_alpha 90.00 _cell_angle_beta 94.94(3) _cell_angle_gamma 90.00 _cell_formula_units_Z 4 _cell_length_a 12.168(9) _cell_length_b 11.500(10) _cell_length_c 13.195(8) _cell_measurement_reflns_used 13283 _cell_measurement_temperature 296.1 _cell_measurement_theta_max 27.5 _cell_measurement_theta_min 3.1 _cell_volume 1840(2) _computing_cell_refinement RAPID-AUTO _computing_data_collection 'RAPID-AUTO (Rigaku, 2003)' _computing_data_reduction ; CrystalStructure (Rigaku/MSC, 2004) and CRYSTALS ( Watkin et al., 1996) ; _computing_molecular_graphics 'ORTEPIII (Farrugia, 1997)' _computing_publication_material CrystalStructure _computing_structure_refinement 'SHELXL97 (Sheldrick, 1997)' _computing_structure_solution ; SIR97 (Altomare et al., 1999) and DIRDIF99 (Beurskens et al., 1999) ; _diffrn_ambient_temperature 296.1 _diffrn_detector_area_resol_mean 10.00 _diffrn_measured_fraction_theta_full 0.983 _diffrn_measured_fraction_theta_max 0.983 _diffrn_measurement_device_type 'Rigaku R-AXIS RAPID' _diffrn_measurement_method \w _diffrn_radiation_monochromator graphite _diffrn_radiation_source 'fine-focus sealed tube' _diffrn_radiation_type MoK\a _diffrn_radiation_wavelength 0.71073 _diffrn_reflns_av_R_equivalents 0.0000 _diffrn_reflns_av_sigmaI/netI 0.0344 _diffrn_reflns_limit_h_max 15 _diffrn_reflns_limit_h_min -15 _diffrn_reflns_limit_k_max 14 _diffrn_reflns_limit_k_min 0 _diffrn_reflns_limit_l_max 17 _diffrn_reflns_limit_l_min 0 _diffrn_reflns_number 4149 _diffrn_reflns_theta_full 27.48 _diffrn_reflns_theta_max 27.48 _diffrn_reflns_theta_min 3.10 _diffrn_standards_number 18070 _exptl_absorpt_coefficient_mu 1.037 _exptl_absorpt_correction_T_max 0.901 _exptl_absorpt_correction_T_min 0.808 _exptl_absorpt_correction_type multi-scan _exptl_absorpt_process_details ; (ABSCOR; Higashi, 1995) ; _exptl_crystal_colour yellow _exptl_crystal_density_diffrn 1.675 _exptl_crystal_density_method 'not measured' _exptl_crystal_description needle _exptl_crystal_F_000 928 _exptl_crystal_size_max 0.20 _exptl_crystal_size_mid 0.20 _exptl_crystal_size_min 0.10 _refine_diff_density_max 0.307 _refine_diff_density_min -0.313 _refine_ls_extinction_method none _refine_ls_goodness_of_fit_ref 0.899 _refine_ls_hydrogen_treatment constr _refine_ls_matrix_type full _refine_ls_number_parameters 253 _refine_ls_number_reflns 4149 _refine_ls_number_restraints 0 _refine_ls_restrained_S_all 0.899 _refine_ls_R_factor_all 0.0329 _refine_ls_R_factor_gt 0.0218 _refine_ls_shift/su_max 0.002 _refine_ls_shift/su_mean 0.000 _refine_ls_structure_factor_coef Fsqd _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.0273P)^2^] where P=(Fo^2^+2Fc^2^)/3' _refine_ls_weighting_scheme calc _refine_ls_wR_factor_gt 0.0480 _refine_ls_wR_factor_ref 0.0489 _reflns_number_gt 3016 _reflns_number_total 4149 _reflns_threshold_expression I>2\s(I) _[local]_cod_data_source_file fg1798.cif _[local]_cod_data_source_block II _[local]_cod_cif_authors_sg_H-M 'P 21/n' _[local]_cod_cif_authors_sg_Hall -p_2yn _cod_database_code 2014652 loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x+1/2, y+1/2, -z+1/2' '-x, -y, -z' 'x-1/2, -y-1/2, z-1/2' 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 0.115867(13) 0.125471(14) 0.673166(10) 0.03125(6) Uani d . 1 . . Pd O1 0.03908(13) 0.19139(13) 0.54965(10) 0.0424(4) Uani d . 1 . . O O2 0.19859(12) 0.01124(13) 0.59521(10) 0.0396(4) Uani d . 1 . . O O3 0.23466(13) -0.09666(13) 0.46524(10) 0.0431(4) Uani d . 1 . . O N1 0.19704(14) 0.07313(15) 0.80496(12) 0.0335(4) Uani d . 1 . . N N2 0.03220(14) 0.24079(15) 0.75112(12) 0.0347(4) Uani d . 1 . . N N3 0.17842(15) 0.25870(14) 0.87884(12) 0.0371(4) Uani d . 1 . . N H3 0.2202 0.3106 0.9091 0.044 Uiso calc R 1 . . H C1 0.00333(19) 0.23125(19) 0.37928(16) 0.0409(5) Uani d . 1 . . C H1 -0.0338 0.2975 0.3980 0.049 Uiso calc R 1 . . H C2 0.05458(17) 0.16168(18) 0.45490(15) 0.0338(5) Uani d . 1 . . C C3 0.11826(17) 0.06436(18) 0.42658(14) 0.0323(5) Uani d . 1 . . C C4 0.11931(18) 0.03922(19) 0.32344(14) 0.0360(5) Uani d . 1 . . C H4 0.1593 -0.0250 0.3046 0.043 Uiso calc R 1 . . H C5 0.0635(2) 0.0788(2) 0.14106(16) 0.0507(6) Uani d . 1 . . C H5 0.1017 0.0138 0.1211 0.061 Uiso calc R 1 . . H C6 0.0084(2) 0.1472(3) 0.06933(17) 0.0602(7) Uani d . 1 . . C H6 0.0090 0.1283 0.0008 0.072 Uiso calc R 1 . . H C7 -0.0491(2) 0.2456(2) 0.09800(18) 0.0600(7) Uani d . 1 . . C H7 -0.0864 0.2915 0.0482 0.072 Uiso calc R 1 . . H C8 -0.0510(2) 0.2749(2) 0.19756(17) 0.0539(7) Uani d . 1 . . C H8 -0.0894 0.3408 0.2153 0.065 Uiso calc R 1 . . H C9 0.00523(18) 0.2055(2) 0.27509(15) 0.0400(5) Uani d . 1 . . C C10 0.06307(18) 0.10589(19) 0.24673(15) 0.0379(5) Uani d . 1 . . C C12 0.21851(17) 0.14723(17) 0.88317(15) 0.0333(5) Uani d . 1 . . C C13 0.28289(19) 0.1136(2) 0.97084(16) 0.0429(5) Uani d . 1 . . C H13 0.2976 0.1658 1.0241 0.051 Uiso calc R 1 . . H C14 0.3240(2) 0.0031(2) 0.97755(18) 0.0526(6) Uani d . 1 . . C H14 0.3676 -0.0203 1.0353 0.063 Uiso calc R 1 . . H C15 0.3006(2) -0.0735(2) 0.89812(17) 0.0535(7) Uani d . 1 . . C H15 0.3275 -0.1492 0.9018 0.064 Uiso calc R 1 . . H C16 0.2373(2) -0.03631(19) 0.81426(16) 0.0442(6) Uani d . 1 . . C H16 0.2210 -0.0884 0.7611 0.053 Uiso calc R 1 . . H C22 0.07996(18) 0.29809(18) 0.83233(15) 0.0345(5) Uani d . 1 . . C C23 0.0306(2) 0.39648(19) 0.87102(16) 0.0458(6) Uani d . 1 . . C H23 0.0666 0.4385 0.9242 0.055 Uiso calc R 1 . . H C24 -0.0708(2) 0.4300(2) 0.82984(18) 0.0559(7) Uani d . 1 . . C H24 -0.1048 0.4954 0.8545 0.067 Uiso calc R 1 . . H C25 -0.1232(2) 0.3657(2) 0.75058(17) 0.0547(7) Uani d . 1 . . C H25 -0.1939 0.3853 0.7236 0.066 Uiso calc R 1 . . H C26 -0.06961(18) 0.2741(2) 0.71324(16) 0.0433(6) Uani d . 1 . . C H26 -0.1044 0.2323 0.6593 0.052 Uiso calc R 1 . . H C31 0.18620(17) -0.01180(18) 0.49915(15) 0.0333(5) Uani d . 1 . . C 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 0.03628(9) 0.02982(8) 0.02671(8) 0.00007(8) -0.00274(6) -0.00262(7) O1 0.0512(10) 0.0461(9) 0.0287(7) 0.0125(8) -0.0034(7) -0.0024(7) O2 0.0489(10) 0.0394(9) 0.0292(7) 0.0101(7) -0.0042(7) -0.0031(6) O3 0.0584(10) 0.0383(9) 0.0318(8) 0.0151(7) -0.0018(7) -0.0035(6) N1 0.0389(10) 0.0302(9) 0.0306(9) -0.0007(8) -0.0010(7) -0.0008(7) N2 0.0377(10) 0.0365(10) 0.0289(9) 0.0026(8) -0.0019(7) -0.0030(7) N3 0.0423(11) 0.0298(10) 0.0369(9) -0.0037(8) -0.0093(8) -0.0051(7) C1 0.0445(14) 0.0385(13) 0.0389(12) 0.0069(11) -0.0009(10) 0.0007(10) C2 0.0336(12) 0.0367(12) 0.0302(10) -0.0038(9) -0.0025(9) -0.0009(8) C3 0.0344(12) 0.0307(11) 0.0312(11) -0.0054(9) -0.0002(8) 0.0000(9) C4 0.0385(12) 0.0349(12) 0.0344(11) -0.0028(10) 0.0016(9) -0.0015(9) C5 0.0562(16) 0.0614(16) 0.0343(12) -0.0024(13) 0.0024(11) -0.0025(11) C6 0.0680(18) 0.082(2) 0.0299(12) -0.0073(16) -0.0002(12) 0.0050(12) C7 0.0697(18) 0.0697(19) 0.0391(13) 0.0017(15) -0.0036(12) 0.0198(12) C8 0.0640(17) 0.0535(16) 0.0430(13) 0.0084(13) -0.0031(12) 0.0131(12) C9 0.0426(13) 0.0444(13) 0.0324(11) -0.0039(11) 0.0001(9) 0.0067(10) C10 0.0389(12) 0.0426(14) 0.0320(11) -0.0070(10) 0.0013(9) 0.0010(9) C12 0.0329(11) 0.0340(13) 0.0327(11) -0.0020(9) 0.0010(8) -0.0003(8) C13 0.0482(14) 0.0457(14) 0.0329(11) 0.0018(12) -0.0065(9) -0.0021(10) C14 0.0591(17) 0.0575(16) 0.0390(13) 0.0121(13) -0.0090(11) 0.0055(11) C15 0.0715(18) 0.0417(14) 0.0461(14) 0.0172(13) -0.0019(12) 0.0041(11) C16 0.0577(15) 0.0336(12) 0.0408(12) 0.0062(11) 0.0009(11) -0.0035(10) C22 0.0391(12) 0.0339(12) 0.0302(10) -0.0016(10) 0.0017(9) 0.0000(9) C23 0.0581(15) 0.0406(15) 0.0377(12) 0.0069(11) -0.0013(11) -0.0084(10) C24 0.0648(17) 0.0535(16) 0.0489(15) 0.0212(14) 0.0027(13) -0.0088(12) C25 0.0484(15) 0.0702(18) 0.0445(13) 0.0232(14) -0.0028(11) -0.0060(13) C26 0.0387(13) 0.0567(15) 0.0332(11) 0.0066(11) -0.0041(10) -0.0041(10) C31 0.0340(12) 0.0321(12) 0.0337(11) -0.0041(9) 0.0015(9) 0.0002(9) loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_site_symmetry_2 _geom_bond_distance _geom_bond_publ_flag Pd1 O1 . 1.9600(16) yes Pd1 O2 . 1.9938(17) yes Pd1 N2 . 2.0084(19) yes Pd1 N1 . 2.0165(19) yes O1 C2 . 1.325(2) no O2 C31 . 1.291(2) no O3 C31 . 1.243(2) no N1 C12 . 1.346(3) no N1 C16 . 1.352(3) no N2 C22 . 1.346(3) no N2 C26 . 1.351(3) no N3 C12 . 1.371(3) no N3 C22 . 1.375(3) no N3 H3 . 0.8600 no C1 C9 . 1.408(3) no C1 H1 . 0.9300 no C2 C1 . 1.385(3) no C3 C4 . 1.393(3) no C3 C2 . 1.429(3) no C3 C31 . 1.494(3) no C4 H4 . 0.9300 no C5 C10 . 1.429(3) no C5 H5 . 0.9300 no C6 C5 . 1.362(3) no C6 H6 . 0.9300 no C7 C6 . 1.400(4) no C7 H7 . 0.9300 no C8 C7 . 1.358(3) no C8 H8 . 0.9300 no C9 C10 . 1.412(3) no C9 C8 . 1.425(3) no C10 C4 . 1.400(3) no C12 C13 . 1.395(3) no C13 C14 . 1.366(3) no C13 H13 . 0.9300 no C14 C15 . 1.380(3) no C14 H14 . 0.9300 no C15 C16 . 1.362(3) no C15 H15 . 0.9300 no C16 H16 . 0.9300 no C22 C23 . 1.398(3) no C23 C24 . 1.360(3) no C23 H23 . 0.9300 no C24 C25 . 1.390(3) no C24 H24 . 0.9300 no C25 C26 . 1.354(3) no C25 H25 . 0.9300 no C26 H26 . 0.9300 no loop_ _atom_type_symbol _atom_type_description _atom_type_scat_dispersion_real _atom_type_scat_dispersion_imag _atom_type_scat_source C C 0.0033 0.0016 '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 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0106 0.0060 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' Pd Pd -0.9988 1.0072 '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_publ_flag O1 Pd1 O2 92.95(7) yes O1 Pd1 N2 86.80(8) yes O2 Pd1 N2 179.75(6) yes O1 Pd1 N1 174.61(6) yes O2 Pd1 N1 90.96(7) yes N2 Pd1 N1 89.29(8) yes C2 O1 Pd1 126.05(14) no C31 O2 Pd1 128.34(13) no C12 N1 C16 118.34(18) no C12 N1 Pd1 121.36(15) no C16 N1 Pd1 120.18(14) no C22 N2 C26 118.37(18) no C22 N2 Pd1 121.85(15) no C26 N2 Pd1 119.12(14) no C12 N3 C22 128.30(18) no C12 N3 H3 115.8 no C22 N3 H3 115.8 no C4 C3 C2 117.96(18) no C4 C3 C31 116.98(19) no C2 C3 C31 125.04(18) no O1 C2 C1 116.0(2) no O1 C2 C3 124.96(18) no C1 C2 C3 119.00(19) no C2 C1 C9 122.5(2) no C2 C1 H1 118.7 no C9 C1 H1 118.7 no C1 C9 C10 118.65(19) no C1 C9 C8 122.4(2) no C10 C9 C8 118.9(2) no C7 C8 C9 120.5(3) no C7 C8 H8 119.7 no C9 C8 H8 119.7 no C8 C7 C6 120.9(2) no C8 C7 H7 119.6 no C6 C7 H7 119.6 no C5 C6 C7 120.4(2) no C5 C6 H6 119.8 no C7 C6 H6 119.8 no C6 C5 C10 120.6(2) no C6 C5 H5 119.7 no C10 C5 H5 119.7 no C4 C10 C9 118.45(19) no C4 C10 C5 122.9(2) no C9 C10 C5 118.6(2) no C3 C4 C10 123.2(2) no C3 C4 H4 118.4 no C10 C4 H4 118.4 no O3 C31 O2 119.71(19) no O3 C31 C3 118.88(18) no O2 C31 C3 121.36(19) no N1 C12 N3 120.99(18) no N1 C12 C13 121.2(2) no N3 C12 C13 117.78(18) no C14 C13 C12 119.2(2) no C14 C13 H13 120.4 no C12 C13 H13 120.4 no C13 C14 C15 119.6(2) no C13 C14 H14 120.2 no C15 C14 H14 120.2 no C16 C15 C14 118.8(2) no C16 C15 H15 120.6 no C14 C15 H15 120.6 no N1 C16 C15 122.8(2) no N1 C16 H16 118.6 no C15 C16 H16 118.6 no N2 C22 N3 119.59(19) no N2 C22 C23 121.1(2) no N3 C22 C23 119.26(19) no C24 C23 C22 119.1(2) no C24 C23 H23 120.4 no C22 C23 H23 120.4 no C23 C24 C25 119.4(2) no C23 C24 H24 120.3 no C25 C24 H24 120.3 no C26 C25 C24 118.9(2) no C26 C25 H25 120.5 no C24 C25 H25 120.5 no N2 C26 C25 122.7(2) no N2 C26 H26 118.6 no C25 C26 H26 118.6 no 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 N3 H3 O3 2_556 0.86 2.01 2.783(2) 149 C15 H15 O1 2_546 0.93 2.50 3.371(4) 157 _journal_paper_doi 10.1107/S010827010403197X