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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 64| Part 1| January 2008| Page m7
https://doi.org/10.1107/S1600536807060977

Bis(pyrimidine-2-carboxyl­ato-κ2N,O)copper(II)

Bing-Yu Zhang,a Qian Yanga and Jing-Jing Niea*

aDepartment of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
*Correspondence e-mail: niejj@zju.edu.cn

(Received 19 November 2007; accepted 20 November 2007; online 6 December 2007)

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[Cheng, D.-P., Zheng, Y., Lin, J., Xu, D. & Xu, Y. (2000). Acta Cryst. C56, 523-524.]); Xu et al. (1996[Xu, D.-J., Xie, A.-L., Xu, Y.-Z., Zhang, C.-G. & Chen, W.-G. (1996). J. Coord. Chem. 39, 273-280.]). For related structures, see: Antolić et al. (2000[Antolić, S., Kojić-Prodić, B. & Lovrić, J. (2000). Acta Cryst. C56, e51-e52.] Rodriquez-Dieguez et al. (2007[Rodriquez-Dieguez, A., Cano, J., Kivekas, R., Debdoudi, A. & Colacio, E. (2007). Inorg. Chem. 46, 2503-2510.]).

[Scheme 1]

Experimental

Crystal data

  • [Cu(C5H3N2O2)2]

  • Mr = 309.73

  • Monoclinic, P 21 /c

  • 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[Higashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.545, Tmax = 0.722

  • 3167 measured reflections

  • 1196 independent reflections

  • 1068 reflections with I > 2σ(I)

  • Rint = 0.016
Refinement

  • R[F2 > 2σ(F2)] = 0.025

  • wR(F2) = 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

Table 1
Selected geometric parameters (Å, °)

Cu—O1 1.9367 (14)
Cu—N1 1.9714 (15)
O1—Cu—N1 83.59 (6)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C1—H1⋯N2i 0.93 2.62 3.511 (3) 160
C2—H2⋯O2i 0.93 2.39 3.193 (3) 145
C3—H3⋯O1ii 0.93 2.57 3.336 (3) 140
C3—H3⋯O2ii 0.93 2.53 3.317 (2) 142
Symmetry codes: (i) [x-1, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]; (ii) [-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: PROCESS-AUTO (Rigaku, 1998[Rigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan.]); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002[Rigaku/MSC (2002). CrystalStructure. Version 3.00. Rigaku/MSC, The Woodlands, Texas, USA.]); program(s) used to solve structure: SIR92 (Altomare et al., 1993[Altomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst. 26, 343-350.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536807060977/xu2383Isup2.hkl

checkCIF report


Comment top

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)°.

Related literature top

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

Experimental top

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 top

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

Structure description top

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)°.

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

Computing details top

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

Figures top
[Figure 1] 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].
[Figure 2] Fig. 2. π-π stacking between nearly parallel pyrimidine rings [symmetry code: (iv) x, 1.5 - y, 1/2 + z].
Bis(pyrimidine-2-carboxylato-κ2N,O)copper(II) top
Crystal data top
[Cu(C5H3N2O2)2]F(000) = 310
Mr = 309.73Dx = 1.971 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 2068 reflections
a = 5.1408 (8) Åθ = 3.5–25.0°
b = 13.2624 (12) ŵ = 2.11 mm−1
c = 7.6735 (11) ÅT = 291 K
β = 94.025 (15)°Prism, blue
V = 521.88 (12) Å30.32 × 0.20 × 0.16 mm
Z = 2
Data collection top
Rigaku R-AXIS RAPID IP
diffractometer		1196 independent reflections
Radiation source: fine-focus sealed tube1068 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
Detector resolution: 10.0 pixels mm-1θmax = 27.5°, θmin = 3.1°
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 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)] = 0.025Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.072H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0413P)2 + 0.1691P]
where P = (Fo2 + 2Fc2)/3
1196 reflections(Δ/σ)max < 0.001
88 parametersΔρmax = 0.25 e Å−3
0 restraintsΔρmin = −0.42 e Å−3
Crystal data top
[Cu(C5H3N2O2)2]V = 521.88 (12) Å3
Mr = 309.73Z = 2
Monoclinic, P21/cMo Kα radiation
a = 5.1408 (8) ŵ = 2.11 mm−1
b = 13.2624 (12) ÅT = 291 K
c = 7.6735 (11) Å0.32 × 0.20 × 0.16 mm
β = 94.025 (15)°
Data collection top
Rigaku R-AXIS RAPID IP
diffractometer		1196 independent reflections
Absorption correction: multi-scan
(ABSCOR; Higashi, 1995)		1068 reflections with I > 2σ(I)
Tmin = 0.545, Tmax = 0.722Rint = 0.016
3167 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0250 restraints
wR(F2) = 0.072H-atom parameters constrained
S = 1.07Δρmax = 0.25 e Å−3
1196 reflectionsΔρmin = −0.42 e Å−3
88 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
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) top
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, º) top
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 code: (i) −x+1, −y+1, −z+1.
Hydrogen-bond geometry (Å, º) top
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.

Experimental details

Crystal data
Chemical formula[Cu(C5H3N2O2)2]
Mr309.73
Crystal system, space groupMonoclinic, P21/c
Temperature (K)291
a, b, c (Å)5.1408 (8), 13.2624 (12), 7.6735 (11)
β (°) 94.025 (15)
V (Å3)521.88 (12)
Z2
Radiation typeMo Kα
µ (mm−1)2.11
Crystal size (mm)0.32 × 0.20 × 0.16
Data collection
DiffractometerRigaku R-AXIS RAPID IP
Absorption correctionMulti-scan
(ABSCOR; Higashi, 1995)
Tmin, Tmax0.545, 0.722
No. of measured, independent and
observed [I > 2σ(I)] reflections		3167, 1196, 1068
Rint0.016
(sin θ/λ)max (Å−1)0.649
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.025, 0.072, 1.07
No. of reflections1196
No. of parameters88
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.25, −0.42

Computer programs: PROCESS-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Selected geometric parameters (Å, º) top
Cu—O11.9367 (14)Cu—N11.9714 (15)
O1—Cu—N183.59 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1···N2i0.932.623.511 (3)160
C2—H2···O2i0.932.393.193 (3)145
C3—H3···O1ii0.932.573.336 (3)140
C3—H3···O2ii0.932.533.317 (2)142
Symmetry codes: (i) x−1, −y+3/2, z−1/2; (ii) −x+2, y+1/2, −z+3/2.
 

Acknowledgements

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

References

First citationAltomare, A., Cascarano, G., Giacovazzo, C. & Guagliardi, A. (1993). J. Appl. Cryst. 26, 343–350.  CrossRef Web of Science IUCr Journals Google Scholar
 First citationAntolić, S., Kojić-Prodić, B. & Lovrić, J. (2000). Acta Cryst. C56, e51–e52.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationCheng, D.-P., Zheng, Y., Lin, J., Xu, D. & Xu, Y. (2000). Acta Cryst. C56, 523–524.  CrossRef CAS IUCr Journals Google Scholar
 First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
 First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
 First citationHigashi, T. (1995). ABSCOR. Rigaku Corporation, Tokyo, Japan.  Google Scholar
 First citationRigaku (1998). PROCESS-AUTO. Rigaku Corporation, Tokyo, Japan.  Google Scholar
 First citationRigaku/MSC (2002). CrystalStructure. Version 3.00. Rigaku/MSC, The Woodlands, Texas, USA.  Google Scholar
 First citationRodriquez-Dieguez, A., Cano, J., Kivekas, R., Debdoudi, A. & Colacio, E. (2007). Inorg. Chem. 46, 2503–2510.  Web of Science CSD CrossRef PubMed Google Scholar
 First citationSheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.  Google Scholar
 First citationXu, D.-J., Xie, A.-L., Xu, Y.-Z., Zhang, C.-G. & Chen, W.-G. (1996). J. Coord. Chem. 39, 273–280.  CrossRef CAS Web of Science 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 64| Part 1| January 2008| Page m7
https://doi.org/10.1107/S1600536807060977
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