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

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page m974
https://doi.org/10.1107/S1600536812028292

(2,2′-Bi­pyrimidine-κ2N1,N1′)di­iodidopalladium(II)

Kwang Haa*

aSchool of Applied Chemical Engineering, Research Institute of Catalysis, Chonnam National University, Gwangju 500-757, Republic of Korea
*Correspondence e-mail: hakwang@chonnam.ac.kr

(Received 17 June 2012; accepted 21 June 2012; online 30 June 2012)

In the title complex, [PdI2(C8H6N4)], the PdII ion is four-coordinated in a slightly distorted square-planar environment defined by two pyrimidine N atoms derived from a chelating 2,2′-bipyrimidine (bpym) ligand and two mutually cis iodide anions. The nearly planar bpym ligand [maximum deviation = 0.053 (3) Å] is slightly inclined to the least-squares plane of the PdI2N2 unit [maximum deviation = 0.055 (2) Å], making a dihedral angle of 3.9 (2)°. In the crystal, pairs of complex mol­ecules are assembled by inter­molecular C—H⋯N hydrogen bonds into dimers. Intra­molecular C—H⋯I hydrogen bonds are also observed.

Related literature

For the crystal structure of the related PtII complex [PtI2(bpym)], see: Ha (2010[Ha, K. (2010). Z. Kristallogr. New Cryst. Struct. 225, 661-662.]).

[Scheme 1]

Experimental

Crystal data

  • [PdI2(C8H6N4)]

  • Mr = 518.37

  • Monoclinic, C 2/c

  • a = 16.1967 (10) Å

  • b = 15.2274 (10) Å

  • c = 10.4686 (6) Å

  • β = 113.199 (1)°

  • V = 2373.1 (3) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 6.74 mm−1

  • T = 273 K

  • 0.34 × 0.16 × 0.14 mm
Data collection

  • Bruker SMART 1000 CCD diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.716, Tmax = 1.000

  • 7042 measured reflections

  • 2268 independent reflections

  • 1937 reflections with I > 2σ(I)

  • Rint = 0.024
Refinement

  • R[F2 > 2σ(F2)] = 0.021

  • wR(F2) = 0.053

  • S = 1.10

  • 2268 reflections

  • 136 parameters

  • H-atom parameters constrained

  • Δρmax = 0.64 e Å−3

  • Δρmin = −0.53 e Å−3

Table 1
Selected geometric parameters (Å, °)

Pd1—N1 2.082 (3)
Pd1—N4 2.082 (4)
Pd1—I1 2.5696 (4)
Pd1—I2 2.5746 (5)
N1—Pd1—N4 79.57 (13)
I1—Pd1—I2 89.215 (14)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C1—H1⋯I2 0.93 2.92 3.525 (4) 124
C8—H8⋯I1 0.93 2.91 3.522 (5) 124
C6—H6⋯N2i 0.93 2.60 3.523 (6) 173
Symmetry code: (i) -x, -y, -z+1.

Data collection: SMART (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812028292/zq2173sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812028292/zq2173Isup2.hkl

checkCIF report


Comment top

The title complex, [PdI2(bpym)] (bpym = 2,2'-bipyrimidine, C8H6N4), is a structural isomer of the previously reported PtII complex [PtI2(bpym)] (Ha, 2010).

The PdII ion is four-coordinated in a slightly distorted square-planar environment defined by two pyrimidine N atoms derived from a chelating bpym ligand and two mutually cis iodide anions (Fig. 1). The main contribution to the distortion is the tight N1—Pd1—N4 chelate angle of 79.57 (13)°, which results in non-linear trans axes [<I1—Pd1—N1 = 175.12 (10)° and <I2—Pd1—N4 = 173.70 (9)°]. The Pd—N and Pd—I bond lengths are almost equivalent, respectively (Table 1). The nearly planar bpym ligand [maximum deviation = 0.053 (3) Å] is slightly inclined to the least-squares plane of the PdI2N2 unit [maximum deviation = 0.055 (2) Å], making a dihedral angle of 3.9 (2)°. In the crystal, two complex molecules are assembled by intermolecular C—H···N hydrogen bonds with C···N = 3.523 (6) Å, forming a dimer-type species (Fig. 2, Table 2). Intramolecular C—H···I hydrogen bonds are also observed (Table 2). The molecules are stacked in columns along the a axis with Pd···Pd distances of 3.8061 (5) Å and 4.6600 (6) Å. In the columns, numerous intermolecular π-π interactions between adjacent pyrimidine rings are present, the shortest ring centroid-centroid distance being 3.560 (3) Å.

Related literature top

For the crystal structure of the related PtII complex [PtI2(bpym)], see: Ha (2010).

Experimental top

To a solution of Na2PdCl4 (0.1472 g, 0.500 mmol) and KI (0.8381 g, 5.049 mmol) in H2O (20 ml) was added 2,2'-bipyrimidine (0.0792 g, 0.501 mmol), and the mixture was stirred for 3 h at room temperature. The precipitate was then separated by filtration, washed with H2O and acetone, and dried at 323 K, to give a redbrown powder (0.2003 g). Crystals suitable for X-ray analysis were obtained by slow evaporation from a CH3CN solution at room temperature.

Refinement top

H atoms were included in calculated positions and treated as riding atoms: C—H = 0.93 Å with Uiso(H) = 1.2Ueq(C). The highest peak (0.64 e Å-3) and the deepest hole (-0.53 e Å-3) in the difference Fourier map are located 1.10 Å and 0.93 Å, respectively, from the atoms I1 and Pd1.

Structure description top

The title complex, [PdI2(bpym)] (bpym = 2,2'-bipyrimidine, C8H6N4), is a structural isomer of the previously reported PtII complex [PtI2(bpym)] (Ha, 2010).

The PdII ion is four-coordinated in a slightly distorted square-planar environment defined by two pyrimidine N atoms derived from a chelating bpym ligand and two mutually cis iodide anions (Fig. 1). The main contribution to the distortion is the tight N1—Pd1—N4 chelate angle of 79.57 (13)°, which results in non-linear trans axes [<I1—Pd1—N1 = 175.12 (10)° and <I2—Pd1—N4 = 173.70 (9)°]. The Pd—N and Pd—I bond lengths are almost equivalent, respectively (Table 1). The nearly planar bpym ligand [maximum deviation = 0.053 (3) Å] is slightly inclined to the least-squares plane of the PdI2N2 unit [maximum deviation = 0.055 (2) Å], making a dihedral angle of 3.9 (2)°. In the crystal, two complex molecules are assembled by intermolecular C—H···N hydrogen bonds with C···N = 3.523 (6) Å, forming a dimer-type species (Fig. 2, Table 2). Intramolecular C—H···I hydrogen bonds are also observed (Table 2). The molecules are stacked in columns along the a axis with Pd···Pd distances of 3.8061 (5) Å and 4.6600 (6) Å. In the columns, numerous intermolecular π-π interactions between adjacent pyrimidine rings are present, the shortest ring centroid-centroid distance being 3.560 (3) Å.

For the crystal structure of the related PtII complex [PtI2(bpym)], see: Ha (2010).

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title complex, with atom numbering. Displacement ellipsoids are drawn at the 50% probability level for non-H atoms.
[Figure 2] Fig. 2. A view of the crystal packing of the title complex. Intermolecular C—H···N hydrogen-bonds are shown as dashed lines.
(2,2'-Bipyrimidine-κ2N1,N1')diiodidopalladium(II) top
Crystal data top
[PdI2(C8H6N4)]F(000) = 1872
Mr = 518.37Dx = 2.902 Mg m−3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 4768 reflections
a = 16.1967 (10) Åθ = 2.4–26.0°
b = 15.2274 (10) ŵ = 6.74 mm−1
c = 10.4686 (6) ÅT = 273 K
β = 113.199 (1)°Block, brown
V = 2373.1 (3) Å30.34 × 0.16 × 0.14 mm
Z = 8
Data collection top
Bruker SMART 1000 CCD
diffractometer		2268 independent reflections
Radiation source: fine-focus sealed tube1937 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
φ and ω scansθmax = 26.0°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −19→19
Tmin = 0.716, Tmax = 1.000k = −18→14
7042 measured reflectionsl = −12→12
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)] = 0.021Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.053H-atom parameters constrained
S = 1.10 w = 1/[σ2(Fo2) + (0.0213P)2 + 1.3937P]
where P = (Fo2 + 2Fc2)/3
2268 reflections(Δ/σ)max < 0.001
136 parametersΔρmax = 0.64 e Å−3
0 restraintsΔρmin = −0.53 e Å−3
Crystal data top
[PdI2(C8H6N4)]V = 2373.1 (3) Å3
Mr = 518.37Z = 8
Monoclinic, C2/cMo Kα radiation
a = 16.1967 (10) ŵ = 6.74 mm−1
b = 15.2274 (10) ÅT = 273 K
c = 10.4686 (6) Å0.34 × 0.16 × 0.14 mm
β = 113.199 (1)°
Data collection top
Bruker SMART 1000 CCD
diffractometer		2268 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		1937 reflections with I > 2σ(I)
Tmin = 0.716, Tmax = 1.000Rint = 0.024
7042 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0210 restraints
wR(F2) = 0.053H-atom parameters constrained
S = 1.10Δρmax = 0.64 e Å−3
2268 reflectionsΔρmin = −0.53 e Å−3
136 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
Pd10.15635 (2)0.29183 (2)0.33518 (3)0.02688 (10)
I10.254992 (19)0.26771 (2)0.19695 (3)0.03728 (10)
I20.16606 (2)0.45868 (2)0.30377 (3)0.04108 (11)
N10.0758 (2)0.2998 (2)0.4483 (3)0.0281 (8)
N2−0.0087 (2)0.2101 (2)0.5372 (3)0.0319 (8)
N30.0566 (3)0.0658 (3)0.4549 (4)0.0406 (9)
N40.1337 (2)0.1591 (2)0.3566 (3)0.0290 (8)
C10.0498 (3)0.3714 (3)0.4974 (4)0.0365 (11)
H10.07020.42640.48460.044*
C2−0.0068 (3)0.3644 (3)0.5664 (4)0.0372 (11)
H2−0.02410.41370.60200.045*
C3−0.0364 (3)0.2830 (3)0.5807 (4)0.0359 (11)
H3−0.07750.27770.62220.043*
C40.0465 (3)0.2224 (3)0.4733 (4)0.0279 (9)
C50.0804 (3)0.1433 (3)0.4274 (4)0.0308 (10)
C60.0876 (3)−0.0035 (3)0.4089 (5)0.0458 (12)
H60.0726−0.05960.42760.055*
C70.1411 (3)0.0054 (3)0.3348 (5)0.0474 (13)
H70.1613−0.04340.30210.057*
C80.1636 (3)0.0892 (3)0.3112 (4)0.0360 (11)
H80.20030.09720.26260.043*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Pd10.02714 (18)0.0290 (2)0.02898 (18)0.00127 (14)0.01582 (14)0.00223 (14)
I10.03387 (18)0.0462 (2)0.04086 (18)0.00306 (14)0.02450 (14)0.00367 (14)
I20.0467 (2)0.03180 (19)0.0551 (2)0.00018 (14)0.03117 (16)0.00690 (14)
N10.0290 (18)0.028 (2)0.0278 (18)0.0023 (16)0.0118 (15)0.0021 (16)
N20.0286 (19)0.036 (2)0.037 (2)−0.0042 (17)0.0197 (16)−0.0057 (17)
N30.045 (2)0.031 (2)0.058 (2)−0.0066 (18)0.034 (2)−0.0061 (19)
N40.0284 (18)0.029 (2)0.0338 (18)0.0016 (16)0.0174 (15)−0.0006 (16)
C10.046 (3)0.029 (3)0.039 (2)0.000 (2)0.022 (2)0.000 (2)
C20.040 (3)0.036 (3)0.040 (3)0.009 (2)0.020 (2)−0.003 (2)
C30.031 (2)0.047 (3)0.037 (2)0.002 (2)0.021 (2)−0.003 (2)
C40.026 (2)0.032 (3)0.028 (2)−0.0003 (19)0.0129 (18)−0.0017 (19)
C50.028 (2)0.034 (3)0.032 (2)0.000 (2)0.0140 (18)−0.001 (2)
C60.050 (3)0.024 (3)0.074 (3)−0.003 (2)0.037 (3)−0.006 (3)
C70.053 (3)0.036 (3)0.065 (3)0.000 (2)0.035 (3)−0.011 (3)
C80.035 (2)0.036 (3)0.044 (3)0.002 (2)0.024 (2)0.001 (2)
Geometric parameters (Å, º) top
Pd1—N12.082 (3)C1—C21.376 (6)
Pd1—N42.082 (4)C1—H10.9300
Pd1—I12.5696 (4)C2—C31.358 (6)
Pd1—I22.5746 (5)C2—H20.9300
N1—C41.335 (5)C3—H30.9300
N1—C11.342 (5)C4—C51.479 (6)
N2—C41.325 (5)C6—C71.379 (6)
N2—C31.343 (6)C6—H60.9300
N3—C51.309 (6)C7—C81.376 (7)
N3—C61.338 (6)C7—H70.9300
N4—C81.332 (6)C8—H80.9300
N4—C51.363 (5)
N1—Pd1—N479.57 (13)C1—C2—H2121.1
N1—Pd1—I1175.12 (10)N2—C3—C2122.5 (4)
N4—Pd1—I195.56 (9)N2—C3—H3118.7
N1—Pd1—I295.66 (10)C2—C3—H3118.7
N4—Pd1—I2173.70 (9)N2—C4—N1126.0 (4)
I1—Pd1—I289.215 (14)N2—C4—C5117.3 (4)
C4—N1—C1116.9 (3)N1—C4—C5116.7 (3)
C4—N1—Pd1114.3 (3)N3—C5—N4125.7 (4)
C1—N1—Pd1128.8 (3)N3—C5—C4118.9 (4)
C4—N2—C3115.9 (4)N4—C5—C4115.4 (4)
C5—N3—C6116.6 (4)N3—C6—C7122.3 (5)
C8—N4—C5116.8 (4)N3—C6—H6118.9
C8—N4—Pd1129.3 (3)C7—C6—H6118.9
C5—N4—Pd1113.9 (3)C8—C7—C6117.5 (5)
N1—C1—C2120.9 (4)C8—C7—H7121.3
N1—C1—H1119.6C6—C7—H7121.3
C2—C1—H1119.6N4—C8—C7121.2 (4)
C3—C2—C1117.8 (4)N4—C8—H8119.4
C3—C2—H2121.1C7—C8—H8119.4
N4—Pd1—N1—C4−2.9 (3)C1—N1—C4—C5−176.0 (3)
I2—Pd1—N1—C4173.0 (3)Pd1—N1—C4—C54.5 (5)
N4—Pd1—N1—C1177.6 (4)C6—N3—C5—N40.0 (7)
I2—Pd1—N1—C1−6.5 (4)C6—N3—C5—C4178.8 (4)
N1—Pd1—N4—C8−179.4 (4)C8—N4—C5—N30.3 (6)
I1—Pd1—N4—C80.4 (4)Pd1—N4—C5—N3−179.8 (4)
N1—Pd1—N4—C50.7 (3)C8—N4—C5—C4−178.5 (4)
I1—Pd1—N4—C5−179.5 (3)Pd1—N4—C5—C41.4 (4)
C4—N1—C1—C2−1.9 (6)N2—C4—C5—N3−1.8 (6)
Pd1—N1—C1—C2177.6 (3)N1—C4—C5—N3177.1 (4)
N1—C1—C2—C3−1.2 (7)N2—C4—C5—N4177.2 (4)
C4—N2—C3—C2−3.0 (6)N1—C4—C5—N4−3.9 (6)
C1—C2—C3—N23.8 (7)C5—N3—C6—C7−0.7 (7)
C3—N2—C4—N1−0.4 (6)N3—C6—C7—C81.2 (8)
C3—N2—C4—C5178.4 (4)C5—N4—C8—C70.2 (6)
C1—N1—C4—N22.8 (6)Pd1—N4—C8—C7−179.7 (3)
Pd1—N1—C4—N2−176.7 (3)C6—C7—C8—N4−0.9 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···I20.932.923.525 (4)124
C8—H8···I10.932.913.522 (5)124
C6—H6···N2i0.932.603.523 (6)173
Symmetry code: (i) −x, −y, −z+1.

Experimental details

Crystal data
Chemical formula[PdI2(C8H6N4)]
Mr518.37
Crystal system, space groupMonoclinic, C2/c
Temperature (K)273
a, b, c (Å)16.1967 (10), 15.2274 (10), 10.4686 (6)
β (°) 113.199 (1)
V (Å3)2373.1 (3)
Z8
Radiation typeMo Kα
µ (mm−1)6.74
Crystal size (mm)0.34 × 0.16 × 0.14
Data collection
DiffractometerBruker SMART 1000 CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.716, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections		7042, 2268, 1937
Rint0.024
(sin θ/λ)max (Å−1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.021, 0.053, 1.10
No. of reflections2268
No. of parameters136
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.64, −0.53

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997) and PLATON (Spek, 2009).

Selected geometric parameters (Å, º) top
Pd1—N12.082 (3)Pd1—I12.5696 (4)
Pd1—N42.082 (4)Pd1—I22.5746 (5)
N1—Pd1—N479.57 (13)I1—Pd1—I289.215 (14)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···I20.932.923.525 (4)123.7
C8—H8···I10.932.913.522 (5)124.4
C6—H6···N2i0.932.603.523 (6)172.5
Symmetry code: (i) −x, −y, −z+1.
 

Acknowledgements

This work was supported by the Priority Research Centers Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (grant No. 2011-0030747).

References

First citationBruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
 First citationHa, K. (2010). Z. Kristallogr. New Cryst. Struct. 225, 661–662.  CAS Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 68| Part 7| July 2012| Page m974
https://doi.org/10.1107/S1600536812028292
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