metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2414-3146

(2,2′-Bi­pyridine-κ2N,N′)(pyridine-2,6-di­carboxyl­ato-κ2N,O)palladium(II) monohydrate

aChonnam National University, School of Chemical Engineering, Research Institute of Catalysis, Gwangju, Republic of Korea
*Correspondence e-mail: hakwang@chonnam.ac.kr

Edited by J. Simpson, University of Otago, New Zealand (Received 29 November 2019; accepted 3 December 2019; online 6 December 2019)

In the title compound, [Pd(C7H3NO4)(C10H8N2)]·H2O, the PdII cation is four-coordinated in a distorted square-planar coordination geometry defined by the two N atoms of the 2,2′-bi­pyridine ligand, one O atom and one N atom from the pyridine-2,6-di­carboxyl­ate anion. The complex and solvent water mol­ecule are linked by inter­molecular hydrogen bonds. In the crystal, the complex mol­ecules are stacked in columns along the a axis.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

With reference to the title compound, [Pd(dipic)(bipy)]·H2O (dipic = pyridine-2,6-di­carboxyl­ate; bipy = 2,2′-bi­pyridine), the crystal structures of related PdII complexes [Pd(dipic)(phen)]·4H2O and [Pd(dipic23)(bipy)]·3H2O (phen = 1,10-phenanthroline; dipic23 = pyridine-2,3-di­carboxyl­ate) have been determined previously (Wang & Okabe, 2005[Wang, Y. & Okabe, N. (2005). Chem. Pharm. Bull. 53, 366-373.]).

In the title complex, the central PdII cation is four-coordinated in a distorted square-planar coordination geometry defined by the N1 and N2 atoms of the bidentate bipy ligand, the O3 and N3 atoms of the di-anionic dipic ligand. An intra­molecular C10—H10⋯·O3 hydrogen bond further stabilizes the complex (Fig. 1[link], Table 1[link]). The tight O—Pd—N and N—Pd—N chelating angles of <O3—Pd1—N3 = 81.07 (10)° and <N1—Pd1—N2 = 80.21 (12)°, and the steric inter­actions between the non-coordinating carboxyl­ate group and the (N1–C5) pyridyl ring contribute to the distortion of the square plane. The Pd—N and Pd—O bonds are almost equal [1.992 (3)-2.038 (3) Å] and the nearly planar pyridyl rings of the bipy ligand are slightly twisted with a dihedral angle of 12.6 (1)° between them. The dihedral angle between the least-squares plane [maximum deviation = 0.176 (2) Å] of the bipy ligand and the pyridyl ring of the dipic ligand is 30.6 (1)°.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O5—H5A⋯O1i 0.84 1.96 2.792 (4) 174
O5—H5B⋯O2ii 0.84 1.99 2.790 (4) 160
C2—H2⋯O5iii 0.94 2.59 3.460 (5) 154
C3—H3⋯O2iv 0.94 2.31 3.245 (4) 173
C4—H4⋯O1v 0.94 2.35 3.261 (4) 162
C8—H8⋯O5v 0.94 2.47 2.997 (5) 116
C10—H10⋯O3 0.94 2.55 3.083 (4) 117
C13—H13⋯O4vi 0.94 2.43 3.336 (5) 161
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) [x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (iii) x, y, z+1; (iv) -x+1, -y+1, -z+2; (v) [x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (vi) [-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}].
[Figure 1]
Figure 1
The mol­ecular structure of the title compound showing the atom labelling and displacement ellipsoids drawn at the 50% probability level for non-H atoms. The intra­molecular hydrogen bond is drawn as a double-dashed line.

In the crystal structure (Fig. 2[link]), the complex and solvent mol­ecules form inter­molecular O—H⋯O and C—H⋯O hydrogen bonds (Table 1[link]). The complex mol­ecules are stacked in columns along the a axis. In the columns, numerous inter­molecular ππ inter­actions between adjacent pyridyl rings are present. For Cg1 (the centroid of ring N1–C5) and Cg2i [the centroid of ring N2—C10; symmetry code: (i) x, [{3\over 2}] − y, [{1\over 2}] + z], the centroid–centroid distance is 3.657 (2) Å and the dihedral angle between the ring planes is 12.4 (2)°.

[Figure 2]
Figure 2
The packing in the crystal structure of the title compound, viewed approximately along the a axis. Hydrogen-bonding inter­actions are drawn as dashed lines.

Synthesis and crystallization

To a solution of Pd(CH3CO2)2 (0.2036 g, 0.907 mmol) in acetone (25 ml) and MeOH (5 ml) were added pyridine-2,6-di­carb­oxy­lic acid (0.1520 g, 0.910 mmol) and 2,2′-bi­pyridine (0.1423 g, 0.911 mmol), and stirred for 2 h at room temperature. The precipitate that formed was separated by filtration, washed with acetone, and dried at 333 K, to give a yellow powder (0.3605 g). Yellow crystals suitable for X-ray analysis were obtained by slow evaporation from an ethanol solution at room temperature.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula [Pd(C7H3NO4)(C10H8N2)]·H2O
Mr 445.70
Crystal system, space group Monoclinic, P21/c
Temperature (K) 223
a, b, c (Å) 12.9031 (10), 12.1751 (10), 10.4256 (7)
β (°) 106.246 (2)
V3) 1572.4 (2)
Z 4
Radiation type Mo Kα
μ (mm−1) 1.22
Crystal size (mm) 0.17 × 0.11 × 0.06
 
Data collection
Diffractometer PHOTON 100 CMOS detector
Absorption correction Multi-scan (SADABS; Bruker, 2016[Bruker (2016). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.683, 0.745
No. of measured, independent and observed [I > 2σ(I)] reflections 40118, 3110, 2325
Rint 0.110
(sin θ/λ)max−1) 0.619
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.061, 1.06
No. of reflections 3110
No. of parameters 235
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.69, −0.71
Computer programs: APEX2 and SAINT (Bruker, 2016[Bruker (2016). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]), ORTEP-3 for Windows (Farrugia, 2012[Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849-854.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Structural data


Computing details top

Data collection: APEX2 (Bruker, 2016); cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXL2014 (Sheldrick, 2015); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015).

(2,2'-Bipyridine-κ2N,N')(pyridine-2,6-dicarboxylato-κ2N,O)palladium(II) monohydrate top
Crystal data top
[Pd(C7H3NO4)(C10H8N2)]·H2OF(000) = 888
Mr = 445.70Dx = 1.883 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 12.9031 (10) ÅCell parameters from 8336 reflections
b = 12.1751 (10) Åθ = 2.4–26.0°
c = 10.4256 (7) ŵ = 1.22 mm1
β = 106.246 (2)°T = 223 K
V = 1572.4 (2) Å3Rod, yellow
Z = 40.17 × 0.11 × 0.06 mm
Data collection top
PHOTON 100 CMOS detector
diffractometer
2325 reflections with I > 2σ(I)
Radiation source: sealed tubeRint = 0.110
φ and ω scansθmax = 26.1°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Bruker, 2016)
h = 1515
Tmin = 0.683, Tmax = 0.745k = 1515
40118 measured reflectionsl = 1212
3110 independent 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)] = 0.030Hydrogen site location: mixed
wR(F2) = 0.061H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.0181P)2 + 2.4725P]
where P = (Fo2 + 2Fc2)/3
3110 reflections(Δ/σ)max < 0.001
235 parametersΔρmax = 0.69 e Å3
0 restraintsΔρmin = 0.71 e Å3
Special details top

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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Pd10.18480 (2)0.62619 (2)0.56502 (2)0.01608 (8)
O10.40895 (19)0.5298 (2)0.5905 (2)0.0247 (6)
O20.4447 (2)0.3619 (2)0.6786 (2)0.0345 (7)
O30.06841 (19)0.6372 (2)0.3919 (2)0.0229 (6)
O40.0568 (2)0.5284 (2)0.2619 (2)0.0313 (7)
N10.2794 (2)0.6223 (3)0.7542 (2)0.0179 (6)
N20.1816 (2)0.7845 (2)0.6120 (3)0.0172 (6)
N30.1930 (2)0.4707 (2)0.4962 (2)0.0169 (6)
C10.3089 (3)0.5325 (3)0.8287 (3)0.0201 (8)
H10.28610.46330.79140.024*
C20.3721 (3)0.5389 (3)0.9590 (3)0.0240 (9)
H20.39060.47481.01070.029*
C30.4080 (3)0.6398 (3)1.0131 (3)0.0239 (8)
H30.45410.64481.10040.029*
C40.3758 (3)0.7334 (3)0.9383 (3)0.0220 (8)
H40.39840.80300.97440.026*
C50.3094 (3)0.7229 (3)0.8088 (3)0.0170 (8)
C60.2582 (3)0.8153 (3)0.7249 (3)0.0165 (8)
C70.2802 (3)0.9246 (3)0.7548 (3)0.0215 (8)
H70.33490.94510.83140.026*
C80.2205 (3)1.0037 (3)0.6703 (3)0.0247 (8)
H80.23351.07870.68970.030*
C90.1419 (3)0.9715 (3)0.5575 (4)0.0246 (8)
H90.10021.02420.49960.030*
C100.1252 (3)0.8617 (3)0.5306 (3)0.0240 (8)
H100.07250.84000.45270.029*
C110.2729 (3)0.3955 (3)0.5297 (3)0.0195 (8)
C120.2544 (3)0.2891 (3)0.4812 (3)0.0291 (9)
H120.30950.23630.50690.035*
C130.1559 (3)0.2602 (3)0.3956 (4)0.0308 (9)
H130.14190.18740.36600.037*
C140.0777 (3)0.3407 (3)0.3540 (3)0.0246 (9)
H140.01110.32410.29240.029*
C150.0991 (3)0.4453 (3)0.4042 (3)0.0187 (8)
C160.3866 (3)0.4333 (3)0.6088 (3)0.0194 (8)
C170.0287 (3)0.5420 (3)0.3484 (3)0.0215 (8)
O50.4222 (2)0.3608 (3)0.2280 (3)0.0690 (11)
H5A0.47440.38910.28540.104*
H5B0.42810.29210.23250.104*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.01601 (14)0.01669 (13)0.01266 (12)0.00058 (13)0.00074 (9)0.00092 (12)
O10.0225 (14)0.0201 (14)0.0276 (13)0.0024 (11)0.0008 (11)0.0002 (11)
O20.0296 (15)0.0246 (15)0.0370 (15)0.0053 (13)0.0113 (12)0.0063 (13)
O30.0223 (13)0.0220 (14)0.0182 (12)0.0034 (12)0.0045 (10)0.0004 (11)
O40.0222 (15)0.0333 (16)0.0290 (14)0.0037 (12)0.0083 (12)0.0014 (12)
N10.0173 (15)0.0217 (15)0.0152 (13)0.0002 (14)0.0055 (11)0.0002 (13)
N20.0152 (15)0.0223 (16)0.0143 (14)0.0021 (13)0.0042 (12)0.0014 (12)
N30.0203 (17)0.0166 (16)0.0118 (14)0.0040 (13)0.0011 (12)0.0024 (12)
C10.021 (2)0.019 (2)0.0208 (18)0.0001 (16)0.0075 (16)0.0022 (15)
C20.020 (2)0.035 (2)0.0174 (18)0.0067 (18)0.0061 (15)0.0068 (16)
C30.0214 (19)0.036 (2)0.0111 (15)0.0022 (18)0.0005 (14)0.0025 (16)
C40.018 (2)0.029 (2)0.0185 (18)0.0009 (16)0.0035 (15)0.0071 (16)
C50.0150 (18)0.023 (2)0.0145 (16)0.0006 (16)0.0067 (14)0.0040 (14)
C60.0160 (19)0.0203 (19)0.0155 (17)0.0001 (15)0.0083 (14)0.0019 (14)
C70.022 (2)0.025 (2)0.0183 (18)0.0005 (16)0.0067 (15)0.0053 (15)
C80.030 (2)0.0188 (19)0.030 (2)0.0003 (17)0.0165 (17)0.0036 (16)
C90.022 (2)0.024 (2)0.028 (2)0.0058 (17)0.0067 (16)0.0059 (16)
C100.0209 (19)0.027 (2)0.0217 (17)0.0026 (17)0.0024 (15)0.0017 (17)
C110.0224 (19)0.018 (2)0.0155 (16)0.0002 (15)0.0013 (14)0.0025 (14)
C120.035 (2)0.018 (2)0.027 (2)0.0040 (18)0.0033 (18)0.0004 (16)
C130.038 (2)0.019 (2)0.030 (2)0.0077 (18)0.0003 (18)0.0021 (16)
C140.027 (2)0.026 (2)0.0161 (17)0.0120 (16)0.0017 (15)0.0018 (15)
C150.0164 (19)0.026 (2)0.0117 (16)0.0042 (16)0.0008 (14)0.0025 (14)
C160.020 (2)0.022 (2)0.0138 (17)0.0006 (16)0.0008 (15)0.0029 (15)
C170.017 (2)0.030 (2)0.0168 (18)0.0010 (17)0.0034 (16)0.0009 (16)
O50.043 (2)0.037 (2)0.099 (3)0.0097 (16)0.0277 (18)0.0245 (19)
Geometric parameters (Å, º) top
Pd1—N21.992 (3)C4—H40.9400
Pd1—O32.004 (2)C5—C61.465 (5)
Pd1—N12.009 (2)C6—C71.378 (5)
Pd1—N32.038 (3)C7—C81.385 (5)
O1—C161.238 (4)C7—H70.9400
O2—C161.242 (4)C8—C91.378 (5)
O3—C171.296 (4)C8—H80.9400
O4—C171.225 (4)C9—C101.371 (5)
N1—C11.334 (4)C9—H90.9400
N1—C51.361 (4)C10—H100.9400
N2—C101.337 (4)C11—C121.387 (5)
N2—C61.361 (4)C11—C161.538 (5)
N3—C111.350 (4)C12—C131.379 (5)
N3—C151.354 (4)C12—H120.9400
C1—C21.378 (5)C13—C141.386 (5)
C1—H10.9400C13—H130.9400
C2—C31.376 (5)C14—C151.375 (5)
C2—H20.9400C14—H140.9400
C3—C41.377 (5)C15—C171.501 (5)
C3—H30.9400O5—H5A0.8400
C4—C51.388 (4)O5—H5B0.8400
N2—Pd1—O395.44 (10)C6—C7—C8119.0 (3)
N2—Pd1—N180.21 (12)C6—C7—H7120.5
O3—Pd1—N1169.28 (10)C8—C7—H7120.5
N2—Pd1—N3172.85 (11)C9—C8—C7119.4 (3)
O3—Pd1—N381.07 (10)C9—C8—H8120.3
N1—Pd1—N3104.28 (11)C7—C8—H8120.3
C17—O3—Pd1112.2 (2)C10—C9—C8119.2 (3)
C1—N1—C5119.5 (3)C10—C9—H9120.4
C1—N1—Pd1125.9 (2)C8—C9—H9120.4
C5—N1—Pd1114.4 (2)N2—C10—C9122.0 (3)
C10—N2—C6119.3 (3)N2—C10—H10119.0
C10—N2—Pd1124.7 (2)C9—C10—H10119.0
C6—N2—Pd1114.8 (2)N3—C11—C12119.9 (3)
C11—N3—C15119.7 (3)N3—C11—C16118.7 (3)
C11—N3—Pd1130.6 (2)C12—C11—C16121.0 (3)
C15—N3—Pd1109.7 (2)C13—C12—C11120.5 (4)
N1—C1—C2121.4 (3)C13—C12—H12119.8
N1—C1—H1119.3C11—C12—H12119.8
C2—C1—H1119.3C12—C13—C14118.7 (3)
C3—C2—C1119.5 (3)C12—C13—H13120.6
C3—C2—H2120.2C14—C13—H13120.6
C1—C2—H2120.2C15—C14—C13119.0 (3)
C2—C3—C4119.6 (3)C15—C14—H14120.5
C2—C3—H3120.2C13—C14—H14120.5
C4—C3—H3120.2N3—C15—C14121.7 (3)
C3—C4—C5118.7 (3)N3—C15—C17114.9 (3)
C3—C4—H4120.6C14—C15—C17122.9 (3)
C5—C4—H4120.6O1—C16—O2128.8 (3)
N1—C5—C4121.0 (3)O1—C16—C11115.4 (3)
N1—C5—C6114.4 (3)O2—C16—C11115.7 (3)
C4—C5—C6124.3 (3)O4—C17—O3124.4 (3)
N2—C6—C7121.1 (3)O4—C17—C15120.1 (3)
N2—C6—C5113.7 (3)O3—C17—C15115.4 (3)
C7—C6—C5125.2 (3)H5A—O5—H5B109.1
C5—N1—C1—C22.0 (5)C8—C9—C10—N21.2 (5)
Pd1—N1—C1—C2178.4 (3)C15—N3—C11—C127.2 (5)
N1—C1—C2—C31.6 (5)Pd1—N3—C11—C12171.6 (3)
C1—C2—C3—C43.2 (5)C15—N3—C11—C16166.2 (3)
C2—C3—C4—C51.3 (5)Pd1—N3—C11—C1615.0 (4)
C1—N1—C5—C44.0 (5)N3—C11—C12—C132.0 (6)
Pd1—N1—C5—C4179.3 (3)C16—C11—C12—C13171.2 (3)
C1—N1—C5—C6170.6 (3)C11—C12—C13—C143.1 (6)
Pd1—N1—C5—C66.1 (4)C12—C13—C14—C153.0 (6)
C3—C4—C5—N12.4 (5)C11—N3—C15—C147.3 (5)
C3—C4—C5—C6171.7 (3)Pd1—N3—C15—C14171.6 (3)
C10—N2—C6—C71.6 (5)C11—N3—C15—C17164.5 (3)
Pd1—N2—C6—C7166.6 (3)Pd1—N3—C15—C1716.5 (3)
C10—N2—C6—C5176.6 (3)C13—C14—C15—N32.2 (5)
Pd1—N2—C6—C515.2 (4)C13—C14—C15—C17169.0 (3)
N1—C5—C6—N25.9 (4)N3—C11—C16—O128.4 (4)
C4—C5—C6—N2168.6 (3)C12—C11—C16—O1144.9 (3)
N1—C5—C6—C7176.0 (3)N3—C11—C16—O2154.0 (3)
C4—C5—C6—C79.6 (6)C12—C11—C16—O232.6 (5)
N2—C6—C7—C82.2 (5)Pd1—O3—C17—O4163.9 (3)
C5—C6—C7—C8175.8 (3)Pd1—O3—C17—C1520.6 (4)
C6—C7—C8—C91.0 (5)N3—C15—C17—O4178.1 (3)
C7—C8—C9—C100.6 (5)C14—C15—C17—O46.3 (5)
C6—N2—C10—C90.1 (5)N3—C15—C17—O32.4 (4)
Pd1—N2—C10—C9167.0 (3)C14—C15—C17—O3169.4 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O5—H5A···O1i0.841.962.792 (4)174
O5—H5B···O2ii0.841.992.790 (4)160
C2—H2···O5iii0.942.593.460 (5)154
C3—H3···O2iv0.942.313.245 (4)173
C4—H4···O1v0.942.353.261 (4)162
C8—H8···O5v0.942.472.997 (5)116
C10—H10···O30.942.553.083 (4)117
C13—H13···O4vi0.942.433.336 (5)161
Symmetry codes: (i) x+1, y+1, z+1; (ii) x, y+1/2, z1/2; (iii) x, y, z+1; (iv) x+1, y+1, z+2; (v) x, y+3/2, z+1/2; (vi) x, y1/2, z+1/2.
 

Acknowledgements

The author thanks the KBSI, Seoul Center, for the X-ray data collection.

Funding information

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (grant No. 2018R1D1A1B07050550).

References

First citationBruker (2016). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationFarrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2015). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWang, Y. & Okabe, N. (2005). Chem. Pharm. Bull. 53, 366–373.  Web of Science CSD CrossRef PubMed CAS Google Scholar

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