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In the title complexes, [Pd(C10H6O2)(C10H9N3)]·H2O, (I), and [Pd(C11H6O3)(C10H9N3)], (II), the PdII centers have a dis­torted cis-square-planar geometry. In (I), the PdII atom is coordinated to two N atoms of the di-2-pyridyl­amine (DPA) ligand and two O atoms of the naphthalene-2,3-diolate (ND) dianion. In (II), the PdII atom is coordinated to two N atoms of the DPA ligand, one carboxyl­ate O atom and one oxide O atom from the 3-oxido­naphthalene-2-carboxyl­ate (NC) ligand. The dihedral angle between the planes of the two pyridine rings of DPA in (I) is 16.20 (12)° and that in (II) is 29.45 (10)°. In (I), the mol­ecules are linked by N—H...O and O—H...O hydrogen bonds to generate centrosymmetric dimers. In (II), mol­ecules are linked by N—H...O and C—H...O hydrogen bonds to generate spirals.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S010827010403197X/fg1798sup1.cif
Contains datablocks I, II, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S010827010403197X/fg1798Isup2.hkl
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S010827010403197X/fg1798IIsup3.hkl
Contains datablock 7911

CCDC references: 264778; 264779

Comment top

2,2'-Dipyridylamine (DPA) is an aromatic amine, similar to bipyridine. DPA has three possible conformations when coordinating to metal centers, viz. trans–trans, cis–trans and cis–cis, in which the orientations of the pyridyl N atoms are opposite, the reverse of one another and on the same side relative to the orientation of the N—H bond at the central linking N atom (Du et al., 2003). The two pyridine rings of the DPA molecule are bridged by the NH group; the molecule is flexible and the two rings can adopt either coplanar or non-planar conformations in the coordination to metal centers (Bolm et al., 2004; Youngme et al., 2003; Du et al., 2003; Romeo et al., 1998).

Many PtII and PdII complexes with various kinds of ligands have been widely studied in relation to their cytotoxic activity, because they are usually isostructural (Barnham et al., 1995). PtII and PdII complexes of DPA bind to DNA and also have cytotoxic activity. The mode of binding between the complexes and DNA seems to be non-covalent groove binding or intercalation, and the NH group of DPA seems to have an important role for the interactions (Tu et al., 2003; Paul et al., 1993). DNA intercalation has been considered as an important mode of non-covalent interaction of heterocyclic compounds with DNA (Lerman, 1961), and the intercalation of homologous square-planar PdII and PtII complexes with bipyridine or biquinoline has been suggested (Cusumano & Giannetto 1997). Although the molecular structures of a few PtII complexes of DPA have been reported (Romeo et al., 1998; Paul et al., 1993; Tu et al., 2004), little is known about the PdII complex of DPA.

In this study, we have prepared two cis-coordinated ternary PdII complexes with DPA and other planar ligands, 2,3-naphthalenediolate (ND), [Pd(DPA)(ND)]H20, (I), and 2-naphthol-3-carboxylate (NC), [Pd(DPA)(NC)], (II), and determined their structures. The present study is the first determination of the crystal structures of PdII complexes with DPA.

The structure of complex (I) is shown in Fig. 1. Selected geometrical parameters are listed in Table 1. DPA adopts a trans–trans conformation. The coordination around the PdII ion is distorted cis-square-planar and the PdII ion is coordinated by two N atoms from the bidentate DPA ligand and two O atoms from the bidentate ND ligand. In the square-planar coordination, atoms Pd1, O1, O2, N1 and N2 deviate by 0.0001 (2), 0.0242 (15), −0.0306 (16), 0.0332 (18) and −0.0407 (18) Å, respectively, from the mean plane through these five atoms. The Pd—O distances are slightly longer than the analogous ternary PdII complexes with the heterocyclic 2,2'-bipyridine (BPY) and NC ligands, [Pd(BPY)(NC)] [1.981 (3)–1.984 (2) Å] or with biquinoline (BQ) and NC, [Pd(BQ)(NC)] [1.982 (4)–1.992 (4) Å; Okabe et al., 2004].

In the coordination sphere, the largest anglular deviation is that for O1—Pd1—O2, in the five-membered chelate ring, Pd1/O1/C2/C3/O2, and others are similar.?? The dihedral angle between the two pyridyl rings of DPA is 16.20 (12)°, indicating that the two DPA pyridine rings are nearly coplanar. A six-membered chelate ring, Pd1/N1/C12/N3/C22/N2, and a five-membered ring, Pd1/O1/C2/C3/O2, are formed between the PdII ion and the DPA ligand, and between the PdII ion and the ND ligand, respectively. The six-membered chelate ring adopts a boat conformation, in which atoms Pd1 and N3 are displaced 0.304 (3) and 0.138 (3) Å from the mean plane through atoms N1, N2, C12 and C22, respectively. The angles between the mean ND plane and two pyridine rings containing atoms N1 and N2 are 11.57 (11) and 4.63 (12)°, respectively, indicating that the ND ligand is nearly coplanar with the DPA ligand.

The structure of complex (II) is shown in Fig. 2. Selected geometric parameters are listed in Table 3. The DPA molecule adopts a distorted trans–trans conformation. The PdII atom has distorted cis-square-planar coordination, and it is bonded to two N atoms of the DPA molecule, one naphthol O atom and one carboxylate O atom of the NC ligand. In the coordination sphere, the largest angular deviation is for N2—Pd1—O1. In the square-planar coordination, atoms Pd1, O1, O2, N1 and N2 deviate by −0.0257 (6), 0.0392 (8), −0.0245 (8), 0.0379 (8) and −0.0269 (9) Å, respectively, from the mean plane through these five atoms. The Pd II atom and DPA forms a six-membered chelate ring with a boat conformation, in which atoms Pd1 and N3 are displaced 0.688 (3) and 0.268 (3) Å, respectively, from the mean plane through atoms N1, N2, C12 and C22. This boat deformation is larger than that found in (I).

The two pyridine rings of the DPA ligand adopt a non-planar conformation, with a dihedral angle between the pyridine rings of 29.45 (10)°, significantly larger than that found in (I). A similarly large distortion of the DPA group was also observed in [Cu(DPA)2(N3)2] [dihedral angle 40.9 (2)°; Du et al., 2003] and [PtMe(DPA)(Me2SO)]CF3SO3 [dihedral angle 46.4 (1)°].

The distorted conformation of the DPA ligand in (II) may be explained by intramolecular steric hindrance between the N2-containing pyridine ring of the DPA ligand and the NC ligand, because the NC ligand with different substituents at the 2- and 3-positions moves closer?? to the N2-containing pyridine ring by coordinating to the PdII atom. The O1···H26 and O2···H16 separations in (II) are 2.40 and 2.46 Å, respectively. These values are significantly longer than the corresponding values in (I) (O1—H26 = 2.23 Å and O2—H16 = 2.27 Å). These differences arise from the slightly different conformations of the DPA ligands in (I) and (II), which are presumably a direct result of the different modes of N—H···O hydrogen bonding and packing in (I) and (II).

In the crystal structure of (I), centrosymmetric dimers are formed by N—H···O and O—H···O intermolecular hydrogen bonds (Table 2 and Fig. 3). Between the dimers there is a further weak C—H···π interaction involving C8—H8 and the centroid Cg1# of the C1–C4/C9/C10 ring [at (1/2 + x,1/2 − y,z)] with a H8···Cg# distance of 2.86 Å and a C8—H8···Cg1# angle of 136°. This leads to the formation of sheets in the [100] plane. The crystal of (II) is also stabilized by an N—H···O hydrogen bond, which with an associated C—H···O hydrogen bond generates spirals by the operation of a 21 screw axis along the b direction (Fig. 4 and Table 4).

Experimental top

Red prismatic crystals of (I) were obtained by slow evaporation of a dimethylformamide solution of a mixture of 2,3-naphthalenediol, 2,2'-bipyridylamine and Pd(CH3COO)2 (molar ratio 1:1:1) at room temperature. Yellow needle-shaped crystals of (II) were obtained by slow evaporation of a dimethylformamide solution of a mixture of 2-naphthol-3-carboxylic acid, 2,2'-bipyridylamine and Pd(CH3COO)2 (molar ratio 1:1:1) at room temperature.

Refinement top

All H atoms, including water H atoms, were located from difference Fourier maps and were then treated as riding, with C—H distances of 0.93 Å, an N—H distance of 0.86 Å, and O—H distances of 0.09 and 0.91 Å, and with Uiso(H) values of 1.2Ueq(C,N). [Treatment for water Uiso(H)s?] The weighting scheme was optimized.

Computing details top

For both compounds, data collection: RAPID-AUTO (Rigaku, 2003); cell refinement: RAPID-AUTO. Data reduction: CrystalStructure (Rigaku/MSC, 2004) and CRYSTALS (Watkin et al., 1996) for (I); CrystalStructure (Rigaku/MSC, 2004) and CRYSTALS ( Watkin et al., 1996) for (II). For both compounds, program(s) used to solve structure: SIR97 (Altomare et al., 1999) and DIRDIF99 (Beurskens et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Farrugia, 1997); software used to prepare material for publication: CrystalStructure.

Figures top
[Figure 1] Fig. 1. ORTEP-3 (Farrugia, 1997) drawing of (I), with the atomic numbering scheme. Displacement ellipsoids for non-H atoms are shown at the 50% probability level.
[Figure 2] Fig. 2. ORTEP-3 (Farrugia, 1997) drawing of (II), with the atomic numbering scheme. Displacement ellipsoids for non-H atoms are shown at the 50% probability level.
[Figure 3] Fig. 3. Packing of (I), showing centrosymmetric dimers and the weak C—H···π interaction. [Symmetry codes: (*) −x, −y, 1 − z; (#) 1/2 + x, 1/2 − y, z.]
[Figure 4] Fig. 4. Packing of (II), with hydrogen bonds indicated by broken lines. [Symmetry codes: (*) 1/2 − x, 1/2 + y, 3/2 − z; (#) 1/2 − x, −1/2 + y, 3/2 − z.]
(I) (Di-2-pyridylamine-κ2N,N')(naphthalene-2,3-diolato-κ2O,O')palladium(II) monohydrate top
Crystal data top
[Pd(C10H6O2)(C10H9N3)]·H2OF(000) = 912
Mr = 453.77Dx = 1.726 Mg m3
Monoclinic, P21/aMo Kα radiation, λ = 0.71075 Å
Hall symbol: -p 2yabCell parameters from 15210 reflections
a = 9.202 (9) Åθ = 3.0–27.5°
b = 17.136 (16) ŵ = 1.09 mm1
c = 11.087 (9) ÅT = 296 K
β = 92.53 (3)°Prism, red
V = 1747 (3) Å30.20 × 0.10 × 0.05 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer
3988 independent reflections
Radiation source: fine-focus sealed tube3516 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.021
Detector resolution: 10.00 pixels mm-1θmax = 27.5°, θmin = 3.0°
ω scansh = 1111
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
k = 2222
Tmin = 0.792, Tmax = 0.947l = 1414
16994 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.019Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.054H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0325P)2 + 0.2332P]
where P = (Fo2 + 2Fc2)/3
3988 reflections(Δ/σ)max < 0.001
245 parametersΔρmax = 0.32 e Å3
4 restraintsΔρmin = 0.39 e Å3
Crystal data top
[Pd(C10H6O2)(C10H9N3)]·H2OV = 1747 (3) Å3
Mr = 453.77Z = 4
Monoclinic, P21/aMo Kα radiation
a = 9.202 (9) ŵ = 1.09 mm1
b = 17.136 (16) ÅT = 296 K
c = 11.087 (9) Å0.20 × 0.10 × 0.05 mm
β = 92.53 (3)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
3988 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
3516 reflections with I > 2σ(I)
Tmin = 0.792, Tmax = 0.947Rint = 0.021
16994 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0194 restraints
wR(F2) = 0.054H-atom parameters constrained
S = 1.05Δρmax = 0.32 e Å3
3988 reflectionsΔρmin = 0.39 e Å3
245 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd10.337797 (13)0.046596 (7)0.470329 (10)0.03023 (5)
O10.47521 (13)0.13529 (7)0.45557 (10)0.0384 (3)
O20.36955 (14)0.03273 (7)0.29405 (11)0.0367 (3)
O30.10851 (17)0.05749 (11)0.17438 (15)0.0671 (5)
N10.20547 (16)0.04658 (8)0.47417 (13)0.0336 (3)
N20.30958 (16)0.06978 (9)0.64627 (13)0.0350 (3)
N30.10834 (16)0.01507 (10)0.66266 (13)0.0397 (3)
H30.03120.02120.70270.048*
C10.64962 (19)0.18122 (9)0.31903 (15)0.0341 (3)
H10.68440.21820.37450.041*
C20.53717 (17)0.13337 (9)0.34836 (14)0.0312 (3)
C30.48087 (18)0.07817 (10)0.26085 (15)0.0311 (3)
C40.53921 (19)0.07292 (10)0.14990 (15)0.0353 (4)
H40.49970.03780.09350.042*
C50.7279 (2)0.11222 (12)0.00832 (17)0.0461 (4)
H50.69280.07620.04850.055*
C60.8459 (2)0.15704 (14)0.01655 (17)0.0544 (6)
H60.89060.15100.08960.065*
C70.8994 (2)0.21184 (13)0.06732 (19)0.0541 (5)
H70.97950.24230.04980.065*
C80.8344 (2)0.22095 (12)0.17544 (18)0.0465 (4)
H80.87060.25810.23010.056*
C90.71372 (18)0.17514 (10)0.20549 (15)0.0348 (4)
C100.65823 (19)0.11976 (10)0.11929 (15)0.0350 (4)
C120.11425 (19)0.06231 (10)0.56317 (16)0.0345 (4)
C130.0216 (2)0.12661 (11)0.55648 (17)0.0418 (4)
H130.04360.13510.61690.050*
C140.0263 (2)0.17692 (12)0.46194 (18)0.0482 (5)
H140.03460.22030.45750.058*
C150.1241 (2)0.16250 (11)0.37133 (18)0.0483 (5)
H150.13100.19650.30650.058*
C160.2084 (2)0.09779 (11)0.38043 (16)0.0409 (4)
H160.27180.08780.31930.049*
C220.2025 (2)0.04023 (10)0.71041 (16)0.0369 (4)
C230.1810 (2)0.06526 (13)0.82945 (18)0.0487 (5)
H230.10400.04560.87180.058*
C240.2733 (3)0.11824 (13)0.88182 (18)0.0563 (5)
H240.26020.13530.96020.068*
C250.3884 (3)0.14691 (13)0.81672 (18)0.0538 (5)
H250.45440.18230.85150.065*
C260.4016 (2)0.12190 (11)0.70099 (16)0.0436 (4)
H260.47760.14160.65740.052*
H310.20200.04810.20200.052*
H320.09710.10760.15000.052*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02971 (8)0.03066 (8)0.03039 (8)0.00150 (5)0.00217 (5)0.00064 (5)
O10.0434 (7)0.0359 (6)0.0363 (6)0.0056 (5)0.0063 (5)0.0071 (5)
O20.0368 (6)0.0395 (7)0.0340 (6)0.0111 (5)0.0050 (5)0.0033 (5)
O30.0437 (8)0.1000 (14)0.0581 (9)0.0031 (8)0.0059 (7)0.0179 (9)
N10.0325 (7)0.0339 (7)0.0344 (7)0.0015 (6)0.0020 (6)0.0027 (5)
N20.0360 (7)0.0363 (7)0.0329 (7)0.0064 (6)0.0022 (6)0.0010 (6)
N30.0332 (8)0.0497 (9)0.0369 (8)0.0015 (7)0.0086 (6)0.0015 (7)
C10.0356 (9)0.0283 (8)0.0377 (8)0.0018 (7)0.0065 (7)0.0018 (7)
C20.0329 (8)0.0277 (8)0.0325 (8)0.0037 (6)0.0029 (6)0.0000 (6)
C30.0303 (8)0.0280 (8)0.0347 (8)0.0005 (6)0.0021 (7)0.0018 (6)
C40.0374 (9)0.0346 (8)0.0336 (8)0.0081 (7)0.0008 (7)0.0037 (7)
C50.0501 (11)0.0519 (11)0.0364 (9)0.0110 (9)0.0034 (8)0.0015 (8)
C60.0540 (12)0.0697 (15)0.0403 (10)0.0139 (10)0.0098 (9)0.0125 (9)
C70.0467 (11)0.0639 (13)0.0516 (11)0.0219 (10)0.0013 (9)0.0195 (10)
C80.0462 (11)0.0445 (10)0.0478 (10)0.0160 (9)0.0089 (8)0.0100 (8)
C90.0336 (9)0.0316 (8)0.0385 (8)0.0022 (7)0.0066 (7)0.0076 (7)
C100.0357 (8)0.0349 (9)0.0341 (8)0.0034 (7)0.0012 (7)0.0050 (7)
C120.0303 (8)0.0380 (9)0.0351 (8)0.0043 (7)0.0004 (7)0.0077 (7)
C130.0376 (9)0.0467 (11)0.0413 (9)0.0037 (8)0.0031 (8)0.0122 (8)
C140.0530 (12)0.0406 (10)0.0510 (10)0.0123 (9)0.0015 (9)0.0069 (9)
C150.0599 (12)0.0393 (10)0.0461 (10)0.0077 (9)0.0055 (9)0.0038 (8)
C160.0440 (10)0.0395 (9)0.0399 (9)0.0027 (8)0.0090 (8)0.0001 (7)
C220.0367 (9)0.0397 (9)0.0344 (8)0.0090 (7)0.0015 (7)0.0022 (7)
C230.0507 (12)0.0580 (12)0.0384 (10)0.0068 (10)0.0108 (9)0.0010 (9)
C240.0721 (15)0.0626 (14)0.0348 (9)0.0057 (11)0.0068 (10)0.0095 (9)
C250.0638 (13)0.0555 (12)0.0419 (10)0.0060 (11)0.0007 (9)0.0108 (9)
C260.0471 (10)0.0436 (10)0.0402 (9)0.0027 (8)0.0017 (8)0.0047 (8)
Geometric parameters (Å, º) top
Pd1—O11.9885 (18)C5—H50.9300
Pd1—O22.0030 (19)C6—C71.396 (3)
Pd1—N12.010 (2)C6—H60.9300
Pd1—N22.019 (2)C7—C81.372 (3)
O1—C21.341 (2)C7—H70.9300
O2—C31.351 (2)C8—C91.412 (3)
O3—H310.91C8—H80.9300
O3—H320.90C9—C101.425 (3)
N1—C121.351 (3)C12—C131.393 (3)
N1—C161.361 (2)C13—C141.359 (3)
N2—C221.340 (3)C13—H130.9300
N2—C261.356 (2)C14—C151.400 (3)
N3—C121.371 (2)C14—H140.9300
N3—C221.374 (3)C15—C161.355 (3)
N3—H30.8600C15—H150.9300
C1—C21.371 (2)C16—H160.9300
C1—C91.417 (3)C22—C231.410 (3)
C1—H10.9300C23—C241.356 (3)
C2—C31.435 (2)C23—H230.9300
C3—C41.367 (2)C24—C251.396 (3)
C4—C101.411 (2)C24—H240.9300
C4—H40.9300C25—C261.363 (3)
C5—C61.368 (3)C25—H250.9300
C5—C101.418 (3)C26—H260.9300
O1—Pd1—O283.66 (5)C7—C8—C9121.40 (19)
O1—Pd1—N1175.67 (5)C7—C8—H8119.3
O2—Pd1—N192.35 (6)C9—C8—H8119.3
O1—Pd1—N292.21 (6)C8—C9—C1122.09 (17)
O2—Pd1—N2175.38 (5)C8—C9—C10118.30 (17)
N1—Pd1—N291.83 (7)C1—C9—C10119.58 (15)
C2—O1—Pd1110.54 (10)C4—C10—C5122.84 (16)
C3—O2—Pd1110.03 (10)C4—C10—C9118.44 (16)
H31—O3—H32111.2C5—C10—C9118.68 (16)
C12—N1—C16117.59 (16)N1—C12—N3121.19 (17)
C12—N1—Pd1124.80 (12)N1—C12—C13121.16 (17)
C16—N1—Pd1117.61 (12)N3—C12—C13117.64 (16)
C22—N2—C26118.11 (16)C14—C13—C12120.18 (17)
C22—N2—Pd1124.58 (13)C14—C13—H13119.9
C26—N2—Pd1117.23 (13)C12—C13—H13119.9
C12—N3—C22132.08 (16)C13—C14—C15118.98 (18)
C12—N3—H3114.0C13—C14—H14120.5
C22—N3—H3114.0C15—C14—H14120.5
C2—C1—C9120.99 (15)C16—C15—C14118.38 (18)
C2—C1—H1119.5C16—C15—H15120.8
C9—C1—H1119.5C14—C15—H15120.8
O1—C2—C1123.40 (15)C15—C16—N1123.63 (17)
O1—C2—C3117.42 (15)C15—C16—H16118.2
C1—C2—C3119.18 (15)N1—C16—H16118.2
O2—C3—C4122.69 (15)N2—C22—N3121.48 (17)
O2—C3—C2116.82 (15)N2—C22—C23121.27 (18)
C4—C3—C2120.49 (16)N3—C22—C23117.25 (17)
C3—C4—C10121.26 (16)C24—C23—C22119.5 (2)
C3—C4—H4119.4C24—C23—H23120.2
C10—C4—H4119.4C22—C23—H23120.2
C6—C5—C10121.14 (19)C23—C24—C25119.28 (19)
C6—C5—H5119.4C23—C24—H24120.4
C10—C5—H5119.4C25—C24—H24120.4
C5—C6—C7120.22 (19)C26—C25—C24118.5 (2)
C5—C6—H6119.9C26—C25—H25120.7
C7—C6—H6119.9C24—C25—H25120.7
C8—C7—C6120.25 (18)N2—C26—C25123.23 (19)
C8—C7—H7119.9N2—C26—H26118.4
C6—C7—H7119.9C25—C26—H26118.4
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O3i0.862.012.845 (4)163
O3—H31···O20.911.832.726 (3)165
Symmetry code: (i) x, y, z+1.
(II) (di-2-pyridylamine-κ2N,N')(2-oxidonaphthalene-3-carboxylato- κ2O,O')palladium(II) top
Crystal data top
[Pd(C11H6O3)(C10H9N3)]F(000) = 928
Mr = 463.76Dx = 1.675 Mg m3
Monoclinic, p_1_21/n_1Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -p_2ynCell parameters from 13283 reflections
a = 12.168 (9) Åθ = 3.1–27.5°
b = 11.50 (1) ŵ = 1.04 mm1
c = 13.195 (8) ÅT = 296 K
β = 94.94 (3)°Needle, yellow
V = 1840 (2) Å30.20 × 0.20 × 0.10 mm
Z = 4
Data collection top
Rigaku R-AXIS RAPID
diffractometer
4149 independent reflections
Radiation source: fine-focus sealed tube3016 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.000
Detector resolution: 10.00 pixels mm-1θmax = 27.5°, θmin = 3.1°
ω scansh = 1515
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
k = 014
Tmin = 0.808, Tmax = 0.901l = 017
4149 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.022Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.049H-atom parameters constrained
S = 0.90 w = 1/[σ2(Fo2) + (0.0273P)2]
where P = (Fo2 + 2Fc2)/3
4149 reflections(Δ/σ)max = 0.002
253 parametersΔρmax = 0.31 e Å3
0 restraintsΔρmin = 0.31 e Å3
Crystal data top
[Pd(C11H6O3)(C10H9N3)]V = 1840 (2) Å3
Mr = 463.76Z = 4
Monoclinic, p_1_21/n_1Mo Kα radiation
a = 12.168 (9) ŵ = 1.04 mm1
b = 11.50 (1) ÅT = 296 K
c = 13.195 (8) Å0.20 × 0.20 × 0.10 mm
β = 94.94 (3)°
Data collection top
Rigaku R-AXIS RAPID
diffractometer
4149 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)
3016 reflections with I > 2σ(I)
Tmin = 0.808, Tmax = 0.901Rint = 0.000
4149 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0220 restraints
wR(F2) = 0.049H-atom parameters constrained
S = 0.90Δρmax = 0.31 e Å3
4149 reflectionsΔρmin = 0.31 e Å3
253 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd10.115867 (13)0.125471 (14)0.673166 (10)0.03125 (6)
O10.03908 (13)0.19139 (13)0.54965 (10)0.0424 (4)
O20.19859 (12)0.01124 (13)0.59521 (10)0.0396 (4)
O30.23466 (13)0.09666 (13)0.46524 (10)0.0431 (4)
N10.19704 (14)0.07313 (15)0.80496 (12)0.0335 (4)
N20.03220 (14)0.24079 (15)0.75112 (12)0.0347 (4)
N30.17842 (15)0.25870 (14)0.87884 (12)0.0371 (4)
H30.22020.31060.90910.044*
C10.00333 (19)0.23125 (19)0.37928 (16)0.0409 (5)
H10.03380.29750.39800.049*
C20.05458 (17)0.16168 (18)0.45490 (15)0.0338 (5)
C30.11826 (17)0.06436 (18)0.42658 (14)0.0323 (5)
C40.11931 (18)0.03922 (19)0.32344 (14)0.0360 (5)
H40.15930.02500.30460.043*
C50.0635 (2)0.0788 (2)0.14106 (16)0.0507 (6)
H50.10170.01380.12110.061*
C60.0084 (2)0.1472 (3)0.06933 (17)0.0602 (7)
H60.00900.12830.00080.072*
C70.0491 (2)0.2456 (2)0.09800 (18)0.0600 (7)
H70.08640.29150.04820.072*
C80.0510 (2)0.2749 (2)0.19756 (17)0.0539 (7)
H80.08940.34080.21530.065*
C90.00523 (18)0.2055 (2)0.27509 (15)0.0400 (5)
C100.06307 (18)0.10589 (19)0.24673 (15)0.0379 (5)
C120.21851 (17)0.14723 (17)0.88317 (15)0.0333 (5)
C130.28289 (19)0.1136 (2)0.97084 (16)0.0429 (5)
H130.29760.16581.02410.051*
C140.3240 (2)0.0031 (2)0.97755 (18)0.0526 (6)
H140.36760.02031.03530.063*
C150.3006 (2)0.0735 (2)0.89812 (17)0.0535 (7)
H150.32750.14920.90180.064*
C160.2373 (2)0.03631 (19)0.81426 (16)0.0442 (6)
H160.22100.08840.76110.053*
C220.07996 (18)0.29809 (18)0.83233 (15)0.0345 (5)
C230.0306 (2)0.39648 (19)0.87102 (16)0.0458 (6)
H230.06660.43850.92420.055*
C240.0708 (2)0.4300 (2)0.82984 (18)0.0559 (7)
H240.10480.49540.85450.067*
C250.1232 (2)0.3657 (2)0.75058 (17)0.0547 (7)
H250.19390.38530.72360.066*
C260.06961 (18)0.2741 (2)0.71324 (16)0.0433 (6)
H260.10440.23230.65930.052*
C310.18620 (17)0.01180 (18)0.49915 (15)0.0333 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.03628 (9)0.02982 (8)0.02671 (8)0.00007 (8)0.00274 (6)0.00262 (7)
O10.0512 (10)0.0461 (9)0.0287 (7)0.0125 (8)0.0034 (7)0.0024 (7)
O20.0489 (10)0.0394 (9)0.0292 (7)0.0101 (7)0.0042 (7)0.0031 (6)
O30.0584 (10)0.0383 (9)0.0318 (8)0.0151 (7)0.0018 (7)0.0035 (6)
N10.0389 (10)0.0302 (9)0.0306 (9)0.0007 (8)0.0010 (7)0.0008 (7)
N20.0377 (10)0.0365 (10)0.0289 (9)0.0026 (8)0.0019 (7)0.0030 (7)
N30.0423 (11)0.0298 (10)0.0369 (9)0.0037 (8)0.0093 (8)0.0051 (7)
C10.0445 (14)0.0385 (13)0.0389 (12)0.0069 (11)0.0009 (10)0.0007 (10)
C20.0336 (12)0.0367 (12)0.0302 (10)0.0038 (9)0.0025 (9)0.0009 (8)
C30.0344 (12)0.0307 (11)0.0312 (11)0.0054 (9)0.0002 (8)0.0000 (9)
C40.0385 (12)0.0349 (12)0.0344 (11)0.0028 (10)0.0016 (9)0.0015 (9)
C50.0562 (16)0.0614 (16)0.0343 (12)0.0024 (13)0.0024 (11)0.0025 (11)
C60.0680 (18)0.082 (2)0.0299 (12)0.0073 (16)0.0002 (12)0.0050 (12)
C70.0697 (18)0.0697 (19)0.0391 (13)0.0017 (15)0.0036 (12)0.0198 (12)
C80.0640 (17)0.0535 (16)0.0430 (13)0.0084 (13)0.0031 (12)0.0131 (12)
C90.0426 (13)0.0444 (13)0.0324 (11)0.0039 (11)0.0001 (9)0.0067 (10)
C100.0389 (12)0.0426 (14)0.0320 (11)0.0070 (10)0.0013 (9)0.0010 (9)
C120.0329 (11)0.0340 (13)0.0327 (11)0.0020 (9)0.0010 (8)0.0003 (8)
C130.0482 (14)0.0457 (14)0.0329 (11)0.0018 (12)0.0065 (9)0.0021 (10)
C140.0591 (17)0.0575 (16)0.0390 (13)0.0121 (13)0.0090 (11)0.0055 (11)
C150.0715 (18)0.0417 (14)0.0461 (14)0.0172 (13)0.0019 (12)0.0041 (11)
C160.0577 (15)0.0336 (12)0.0408 (12)0.0062 (11)0.0009 (11)0.0035 (10)
C220.0391 (12)0.0339 (12)0.0302 (10)0.0016 (10)0.0017 (9)0.0000 (9)
C230.0581 (15)0.0406 (15)0.0377 (12)0.0069 (11)0.0013 (11)0.0084 (10)
C240.0648 (17)0.0535 (16)0.0489 (15)0.0212 (14)0.0027 (13)0.0088 (12)
C250.0484 (15)0.0702 (18)0.0445 (13)0.0232 (14)0.0028 (11)0.0060 (13)
C260.0387 (13)0.0567 (15)0.0332 (11)0.0066 (11)0.0041 (10)0.0041 (10)
C310.0340 (12)0.0321 (12)0.0337 (11)0.0041 (9)0.0015 (9)0.0002 (9)
Geometric parameters (Å, º) top
Pd1—O11.9600 (16)C6—H60.9300
Pd1—O21.9938 (17)C7—C61.400 (4)
Pd1—N22.0084 (19)C7—H70.9300
Pd1—N12.0165 (19)C8—C71.358 (3)
O1—C21.325 (2)C8—H80.9300
O2—C311.291 (2)C9—C101.412 (3)
O3—C311.243 (2)C9—C81.425 (3)
N1—C121.346 (3)C10—C41.400 (3)
N1—C161.352 (3)C12—C131.395 (3)
N2—C221.346 (3)C13—C141.366 (3)
N2—C261.351 (3)C13—H130.9300
N3—C121.371 (3)C14—C151.380 (3)
N3—C221.375 (3)C14—H140.9300
N3—H30.8600C15—C161.362 (3)
C1—C91.408 (3)C15—H150.9300
C1—H10.9300C16—H160.9300
C2—C11.385 (3)C22—C231.398 (3)
C3—C41.393 (3)C23—C241.360 (3)
C3—C21.429 (3)C23—H230.9300
C3—C311.494 (3)C24—C251.390 (3)
C4—H40.9300C24—H240.9300
C5—C101.429 (3)C25—C261.354 (3)
C5—H50.9300C25—H250.9300
C6—C51.362 (3)C26—H260.9300
O1—Pd1—O292.95 (7)C10—C5—H5119.7
O1—Pd1—N286.80 (8)C4—C10—C9118.45 (19)
O2—Pd1—N2179.75 (6)C4—C10—C5122.9 (2)
O1—Pd1—N1174.61 (6)C9—C10—C5118.6 (2)
O2—Pd1—N190.96 (7)C3—C4—C10123.2 (2)
N2—Pd1—N189.29 (8)C3—C4—H4118.4
C2—O1—Pd1126.05 (14)C10—C4—H4118.4
C31—O2—Pd1128.34 (13)O3—C31—O2119.71 (19)
C12—N1—C16118.34 (18)O3—C31—C3118.88 (18)
C12—N1—Pd1121.36 (15)O2—C31—C3121.36 (19)
C16—N1—Pd1120.18 (14)N1—C12—N3120.99 (18)
C22—N2—C26118.37 (18)N1—C12—C13121.2 (2)
C22—N2—Pd1121.85 (15)N3—C12—C13117.78 (18)
C26—N2—Pd1119.12 (14)C14—C13—C12119.2 (2)
C12—N3—C22128.30 (18)C14—C13—H13120.4
C12—N3—H3115.8C12—C13—H13120.4
C22—N3—H3115.8C13—C14—C15119.6 (2)
C4—C3—C2117.96 (18)C13—C14—H14120.2
C4—C3—C31116.98 (19)C15—C14—H14120.2
C2—C3—C31125.04 (18)C16—C15—C14118.8 (2)
O1—C2—C1116.0 (2)C16—C15—H15120.6
O1—C2—C3124.96 (18)C14—C15—H15120.6
C1—C2—C3119.00 (19)N1—C16—C15122.8 (2)
C2—C1—C9122.5 (2)N1—C16—H16118.6
C2—C1—H1118.7C15—C16—H16118.6
C9—C1—H1118.7N2—C22—N3119.59 (19)
C1—C9—C10118.65 (19)N2—C22—C23121.1 (2)
C1—C9—C8122.4 (2)N3—C22—C23119.26 (19)
C10—C9—C8118.9 (2)C24—C23—C22119.1 (2)
C7—C8—C9120.5 (3)C24—C23—H23120.4
C7—C8—H8119.7C22—C23—H23120.4
C9—C8—H8119.7C23—C24—C25119.4 (2)
C8—C7—C6120.9 (2)C23—C24—H24120.3
C8—C7—H7119.6C25—C24—H24120.3
C6—C7—H7119.6C26—C25—C24118.9 (2)
C5—C6—C7120.4 (2)C26—C25—H25120.5
C5—C6—H6119.8C24—C25—H25120.5
C7—C6—H6119.8N2—C26—C25122.7 (2)
C6—C5—C10120.6 (2)N2—C26—H26118.6
C6—C5—H5119.7C25—C26—H26118.6
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O3i0.862.012.783 (2)149
C15—H15···O1ii0.932.503.371 (4)157
Symmetry codes: (i) x+1/2, y+1/2, z+3/2; (ii) x+1/2, y1/2, z+3/2.

Experimental details

(I)(II)
Crystal data
Chemical formula[Pd(C10H6O2)(C10H9N3)]·H2O[Pd(C11H6O3)(C10H9N3)]
Mr453.77463.76
Crystal system, space groupMonoclinic, P21/aMonoclinic, p_1_21/n_1
Temperature (K)296296
a, b, c (Å)9.202 (9), 17.136 (16), 11.087 (9)12.168 (9), 11.50 (1), 13.195 (8)
β (°) 92.53 (3) 94.94 (3)
V3)1747 (3)1840 (2)
Z44
Radiation typeMo KαMo Kα
µ (mm1)1.091.04
Crystal size (mm)0.20 × 0.10 × 0.050.20 × 0.20 × 0.10
Data collection
DiffractometerRigaku R-AXIS RAPID
diffractometer
Rigaku R-AXIS RAPID
diffractometer
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Multi-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.792, 0.9470.808, 0.901
No. of measured, independent and
observed [I > 2σ(I)] reflections
16994, 3988, 3516 4149, 4149, 3016
Rint0.0210.000
(sin θ/λ)max1)0.6490.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.019, 0.054, 1.05 0.022, 0.049, 0.90
No. of reflections39884149
No. of parameters245253
No. of restraints40
H-atom treatmentH-atom parameters constrainedH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.32, 0.390.31, 0.31

Computer programs: RAPID-AUTO (Rigaku, 2003), RAPID-AUTO, CrystalStructure (Rigaku/MSC, 2004) and CRYSTALS (Watkin et al., 1996), CrystalStructure (Rigaku/MSC, 2004) and CRYSTALS ( Watkin et al., 1996), SIR97 (Altomare et al., 1999) and DIRDIF99 (Beurskens et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEPIII (Farrugia, 1997), CrystalStructure.

Selected geometric parameters (Å, º) for (I) top
Pd1—O11.9885 (18)Pd1—N12.010 (2)
Pd1—O22.0030 (19)Pd1—N22.019 (2)
O1—Pd1—O283.66 (5)O1—Pd1—N292.21 (6)
O1—Pd1—N1175.67 (5)O2—Pd1—N2175.38 (5)
O2—Pd1—N192.35 (6)N1—Pd1—N291.83 (7)
Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O3i0.862.012.845 (4)163
O3—H31···O20.911.832.726 (3)165
Symmetry code: (i) x, y, z+1.
Selected geometric parameters (Å, º) for (II) top
Pd1—O11.9600 (16)Pd1—N22.0084 (19)
Pd1—O21.9938 (17)Pd1—N12.0165 (19)
O1—Pd1—O292.95 (7)O1—Pd1—N1174.61 (6)
O1—Pd1—N286.80 (8)O2—Pd1—N190.96 (7)
O2—Pd1—N2179.75 (6)N2—Pd1—N189.29 (8)
Hydrogen-bond geometry (Å, º) for (II) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O3i0.862.012.783 (2)149
C15—H15···O1ii0.932.503.371 (4)157
Symmetry codes: (i) x+1/2, y+1/2, z+3/2; (ii) x+1/2, y1/2, z+3/2.
 

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