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Acta Crystallogr Sect E Struct Rep Online. 2008 January 1; 64(Pt 1): m7.
Published online 2007 December 6. doi:  10.1107/S1600536807060977
PMCID: PMC2914890

Bis(pyrimidine-2-carboxyl­ato-κ2 N,O)copper(II)

Abstract

The title compound, [Cu(C5H3N2O2)2], was prepared in a water–ethanol solution containing 2-cyano­pyrimidine, malonic acid and copper(II) nitrate trihydrate. The CuII ion, located on an inversion center, is chelated by two pyrimidine-2-carboxyl­ate anions in a CuO2N2 square-planar geometry. The uncoordinated carboxyl­ate O atom and pyrimidine N atoms are linked to adjacent pyrimidine rings via weak C—H(...)O and C—H(...)N hydrogen bonding. π–π Stacking is observed between nearly parallel pyrimidine rings, the centroid-to-centroid separation being 3.8605 (13) Å.

Related literature

For general background, see: Cheng et al. (2000 [triangle]); Xu et al. (1996 [triangle]). For related structures, see: Antolić et al. (2000 [triangle] Rodriquez-Dieguez et al. (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-000m7-scheme1.jpg

Experimental

Crystal data

  • [Cu(C5H3N2O2)2]
  • M r = 309.73
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-000m7-efi1.jpg
  • a = 5.1408 (8) Å
  • b = 13.2624 (12) Å
  • c = 7.6735 (11) Å
  • β = 94.025 (15)°
  • V = 521.88 (12) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 2.11 mm−1
  • T = 291 (2) K
  • 0.32 × 0.20 × 0.16 mm

Data collection

  • Rigaku R-AXIS RAPID IP diffractometer
  • Absorption correction: multi-scan (ABSCOR; Higashi, 1995 [triangle]) T min = 0.545, T max = 0.722
  • 3167 measured reflections
  • 1196 independent reflections
  • 1068 reflections with I > 2σ(I)
  • R int = 0.016

Refinement

  • R[F 2 > 2σ(F 2)] = 0.025
  • wR(F 2) = 0.072
  • S = 1.07
  • 1196 reflections
  • 88 parameters
  • H-atom parameters constrained
  • Δρmax = 0.25 e Å−3
  • Δρmin = −0.42 e Å−3

Data collection: PROCESS-AUTO (Rigaku, 1998 [triangle]); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SIR92 (Altomare et al., 1993 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Selected geometric parameters (Å, °)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536807060977/xu2383sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536807060977/xu2383Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

The work was supported by the ZIJIN project of Zhejiang University, China.

supplementary crystallographic information

Comment

As part of our ongoing investigation on the nature of π-π stacking in metal complexes (Cheng et al., 2000; Xu et al., 1996), the title CuII compound has recently been prepared and its crystal structure is presented here.

The molecular structure of the title complex is shown in Fig. 1. The CuII is located an inversion center and chelated by two pyrimidine-2-carboxylate anions in a CuO2N2 square-planar coordination geometry (Table 1). The pyridine-2-carboxylate anion does not play a role of bridging ligand, this is different from the situation found in pyrimidine-2-carboxylate complex of cobalt(II) and pyrimidine-2-carboxylate complex of iron(II) (Rodriquez-Dieguez et al., 2007), but similar to that found in pyrimidine-2-carboxylate complex of cobalt(III) (Antolić et al., 2000). In the title crystal, two carboxylate-O atoms from adjacent molecules occupy at the axial direction of the CuII ion (Fig. 1), but the rather longer separation of 2.7300 (15) Å indicates un-coordination. In the title complex, the uncoordinated carboxylate-O atom and uncoordinated pyrimidine-N atom link with the adjacent pyrimidine ring via C—H···O and C—H···N hydrogen bonding (Table 2).

π-π stacking is observed between nearly parallel N1-pyrimidine and N1iv-pyrimidine rings [symmetry code: (iv) x, 1.5 - y, 1/2 + z] of adjacent complex molecules (Fig. 2). The centroid-to-centroid separation between is 3.8605 (13)°, the dihedral angle is 6.40 (9)°.

Experimental

2-Cyanopyrimidine (0.19 g, 1.8 mmol), copper nitrate trihydrate (0.24 g, 1 mmol) and malonic acid (0.10 g, 1 mmol) were dissolved in a mixture solution of water (15 ml) and ethanol (5 ml). The solution was refluxed for 5 h and then filtered. Single crystals of the title compound were obtained from the filtrate after 8 d.

Refinement

H atoms were placed in calculated positions with C—H = 0.93 Å and refined in riding mode with Uiso(H) = 1.2Ueq(C).

Figures

Fig. 1.
The molecular structure of the title compound with 30% probability displacement (arbitrary spheres for H atoms) [symmetry codes: (ii) x - 1,y,z; (iii) 1 - x,1/2 + y,1.5 - z].
Fig. 2.
π-π stacking between nearly parallel pyrimidine rings [symmetry code: (iv) x, 1.5 - y, 1/2 + z].

Crystal data

[Cu(C5H3N2O2)2]F000 = 310
Mr = 309.73Dx = 1.971 Mg m3
Monoclinic, P21/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2068 reflections
a = 5.1408 (8) Åθ = 3.5–25.0º
b = 13.2624 (12) ŵ = 2.11 mm1
c = 7.6735 (11) ÅT = 291 (2) K
β = 94.025 (15)ºPrism, blue
V = 521.88 (12) Å30.32 × 0.20 × 0.16 mm
Z = 2

Data collection

Rigaku R-AXIS RAPID IP diffractometer1196 independent reflections
Radiation source: fine-focus sealed tube1068 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.016
Detector resolution: 10.0 pixels mm-1θmax = 27.5º
T = 291(2) Kθmin = 3.1º
ω scansh = −6→6
Absorption correction: multi-scan(ABSCOR; Higashi, 1995)k = −9→17
Tmin = 0.545, Tmax = 0.722l = −9→9
3167 measured reflections

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.072  w = 1/[σ2(Fo2) + (0.0413P)2 + 0.1691P] where P = (Fo2 + 2Fc2)/3
S = 1.07(Δ/σ)max < 0.001
1196 reflectionsΔρmax = 0.25 e Å3
88 parametersΔρmin = −0.42 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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)

xyzUiso*/Ueq
Cu0.50000.50000.50000.02825 (13)
N10.6118 (3)0.64215 (11)0.51341 (19)0.0256 (3)
N20.9563 (3)0.74012 (12)0.6465 (2)0.0305 (3)
O10.8109 (3)0.47785 (10)0.6527 (2)0.0326 (3)
O21.1774 (3)0.55441 (11)0.7517 (2)0.0405 (4)
C10.4897 (3)0.72551 (15)0.4523 (3)0.0299 (4)
H10.33300.72010.38470.036*
C20.5948 (4)0.81889 (15)0.4891 (3)0.0340 (4)
H20.50940.87740.45050.041*
C30.8314 (4)0.82293 (14)0.5852 (3)0.0352 (4)
H30.90740.88560.60840.042*
C40.8391 (3)0.65348 (13)0.6096 (2)0.0247 (4)
C50.9575 (3)0.55522 (14)0.6793 (2)0.0281 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Cu0.02102 (19)0.02422 (19)0.0376 (2)−0.00481 (11)−0.01119 (13)0.00144 (12)
N10.0194 (6)0.0268 (7)0.0296 (7)−0.0016 (6)−0.0045 (5)−0.0006 (6)
N20.0276 (7)0.0265 (8)0.0361 (8)−0.0041 (6)−0.0069 (6)−0.0030 (6)
O10.0252 (7)0.0260 (6)0.0445 (8)−0.0032 (5)−0.0132 (6)0.0037 (6)
O20.0279 (7)0.0349 (8)0.0554 (9)−0.0024 (6)−0.0201 (6)0.0024 (7)
C10.0232 (8)0.0328 (10)0.0326 (9)0.0030 (7)−0.0047 (7)0.0020 (8)
C20.0337 (9)0.0282 (9)0.0395 (10)0.0048 (8)−0.0027 (8)0.0030 (8)
C30.0403 (10)0.0250 (9)0.0395 (10)−0.0038 (8)−0.0037 (8)−0.0029 (8)
C40.0194 (7)0.0270 (9)0.0270 (8)−0.0008 (6)−0.0032 (6)−0.0026 (6)
C50.0244 (8)0.0281 (9)0.0308 (9)−0.0009 (7)−0.0061 (7)−0.0013 (7)

Geometric parameters (Å, °)

Cu—O11.9367 (14)O1—C51.281 (2)
Cu—O1i1.9367 (14)O2—C51.224 (2)
Cu—N1i1.9714 (15)C1—C21.373 (3)
Cu—N11.9714 (15)C1—H10.9300
N1—C11.339 (2)C2—C31.378 (3)
N1—C41.346 (2)C2—H20.9300
N2—C41.319 (2)C3—H30.9300
N2—C31.341 (2)C4—C51.520 (2)
O1—Cu—O1i180.0C2—C1—H1119.8
O1—Cu—N1i96.41 (6)C1—C2—C3117.70 (18)
O1i—Cu—N1i83.59 (6)C1—C2—H2121.1
O1—Cu—N183.59 (6)C3—C2—H2121.1
O1i—Cu—N196.41 (6)N2—C3—C2122.61 (17)
N1i—Cu—N1180.0N2—C3—H3118.7
C1—N1—C4117.84 (16)C2—C3—H3118.7
C1—N1—Cu130.04 (13)N2—C4—N1125.53 (16)
C4—N1—Cu111.96 (12)N2—C4—C5120.37 (15)
C4—N2—C3115.95 (15)N1—C4—C5114.10 (15)
C5—O1—Cu115.23 (12)O2—C5—O1125.42 (17)
N1—C1—C2120.31 (17)O2—C5—C4120.11 (16)
N1—C1—H1119.8O1—C5—C4114.46 (15)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
C1—H1···N2ii0.932.623.511 (3)160
C2—H2···O2ii0.932.393.193 (3)145
C3—H3···O1iii0.932.573.336 (3)140
C3—H3···O2iii0.932.533.317 (2)142

Symmetry codes: (ii) x−1, −y+3/2, z−1/2; (iii) −x+2, y+1/2, −z+3/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2383).

References

  • Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst.26, 343–350.
  • Antolić, S., Kojić-Prodić, B. & Lovrić, J. (2000). Acta Cryst. C56, e51–e52.
  • Cheng, D.-P., Zheng, Y., Lin, J., Xu, D. & Xu, Y. (2000). Acta Cryst. C56, 523–524. [PubMed]
  • Farrugia, L. J. (1997). J. Appl. Cryst.30, 565.
  • Farrugia, L. J. (1999). J. Appl. Cryst.32, 837–838.
  • Higashi, T. (1995). ABSCOR Rigaku Corporation, Tokyo, Japan.
  • Rigaku (1998). PROCESS-AUTO Rigaku Corporation, Tokyo, Japan.
  • Rigaku/MSC (2002). CrystalStructure Version 3.00. Rigaku/MSC, The Woodlands, Texas, USA.
  • Rodriquez-Dieguez, A., Cano, J., Kivekas, R., Debdoudi, A. & Colacio, E. (2007). Inorg. Chem.46, 2503–2510. [PubMed]
  • Sheldrick, G. M. (1997). SHELXL97 University of Göttingen, Germany. [PubMed]
  • Xu, D.-J., Xie, A.-L., Xu, Y.-Z., Zhang, C.-G. & Chen, W.-G. (1996). J. Coord. Chem.39, 273–280.

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