Acta Cryst. (2008). E64, m7 [ doi:10.1107/S1600536807060977 ]
![[kappa]](/logos/entities/kappa_rmgif.gif)
2N,O)copper(II)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-HN hydrogen bonding. ![[pi]](/logos/entities/pi_rmgif.gif)
- Stacking is observed between nearly parallel pyrimidine rings, the centroid-to-centroid separation being 3.8605 (13) Å.
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.
H atoms were placed in calculated positions with C—H = 0.93 Å and refined in riding mode with Uiso(H) = 1.2Ueq(C).
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).
![[Figure 1]](./xu2383fig1thm.gif)
| 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]](./xu2383fig2thm.gif)
| Fig. 2. π-π stacking between nearly parallel pyrimidine rings [symmetry code: (iv) x, 1.5 - y, 1/2 + z]. |
| [Cu(C5H3N2O2)2] | F000 = 310 |
| Mr = 309.73 | Dx = 1.971 Mg m−3 |
| Monoclinic, P21/c | Mo Kα radiation λ = 0.71073 Å |
| Hall symbol: -P 2ybc | Cell parameters from 2068 reflections |
| a = 5.1408 (8) Å | θ = 3.5–25.0º |
| b = 13.2624 (12) Å | µ = 2.11 mm−1 |
| c = 7.6735 (11) Å | T = 291 (2) K |
| β = 94.025 (15)º | Prism, blue |
| V = 521.88 (12) Å3 | 0.32 × 0.20 × 0.16 mm |
| Z = 2 |
| Rigaku R-AXIS RAPID IP diffractometer | 1196 independent reflections |
| Radiation source: fine-focus sealed tube | 1068 reflections with I > 2σ(I) |
| Monochromator: graphite | Rint = 0.016 |
| Detector resolution: 10.0 pixels mm-1 | θmax = 27.5º |
| T = 291(2) K | θmin = 3.1º |
| ω scans | h = −6→6 |
| Absorption correction: multi-scan (ABSCOR; Higashi, 1995) | k = −9→17 |
| Tmin = 0.545, Tmax = 0.722 | l = −9→9 |
| 3167 measured reflections |
| Refinement on F2 | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
| R[F2 > 2σ(F2)] = 0.025 | H-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 reflections | Δρmax = 0.25 e Å−3 |
| 88 parameters | Δρmin = −0.42 e Å−3 |
| Primary atom site location: structure-invariant direct methods | Extinction correction: none |
| [Cu(C5H3N2O2)2] | V = 521.88 (12) Å3 |
| Mr = 309.73 | Z = 2 |
| Monoclinic, P21/c | Mo Kα |
| a = 5.1408 (8) Å | µ = 2.11 mm−1 |
| b = 13.2624 (12) Å | T = 291 (2) K |
| c = 7.6735 (11) Å | 0.32 × 0.20 × 0.16 mm |
| β = 94.025 (15)º |
| 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 = 0.722 | Rint = 0.016 |
| 3167 measured reflections |
| R[F2 > 2σ(F2)] = 0.025 | 88 parameters |
| wR(F2) = 0.072 | H-atom parameters constrained |
| S = 1.07 | Δρmax = 0.25 e Å−3 |
| 1196 reflections | Δρmin = −0.42 e Å−3 |
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. |
| x | y | z | Uiso*/Ueq | ||
| Cu | 0.5000 | 0.5000 | 0.5000 | 0.02825 (13) | |
| N1 | 0.6118 (3) | 0.64215 (11) | 0.51341 (19) | 0.0256 (3) | |
| N2 | 0.9563 (3) | 0.74012 (12) | 0.6465 (2) | 0.0305 (3) | |
| O1 | 0.8109 (3) | 0.47785 (10) | 0.6527 (2) | 0.0326 (3) | |
| O2 | 1.1774 (3) | 0.55441 (11) | 0.7517 (2) | 0.0405 (4) | |
| C1 | 0.4897 (3) | 0.72551 (15) | 0.4523 (3) | 0.0299 (4) | |
| H1 | 0.3330 | 0.7201 | 0.3847 | 0.036* | |
| C2 | 0.5948 (4) | 0.81889 (15) | 0.4891 (3) | 0.0340 (4) | |
| H2 | 0.5094 | 0.8774 | 0.4505 | 0.041* | |
| C3 | 0.8314 (4) | 0.82293 (14) | 0.5852 (3) | 0.0352 (4) | |
| H3 | 0.9074 | 0.8856 | 0.6084 | 0.042* | |
| C4 | 0.8391 (3) | 0.65348 (13) | 0.6096 (2) | 0.0247 (4) | |
| C5 | 0.9575 (3) | 0.55522 (14) | 0.6793 (2) | 0.0281 (4) |
| U11 | U22 | U33 | U12 | U13 | U23 | |
| Cu | 0.02102 (19) | 0.02422 (19) | 0.0376 (2) | −0.00481 (11) | −0.01119 (13) | 0.00144 (12) |
| N1 | 0.0194 (6) | 0.0268 (7) | 0.0296 (7) | −0.0016 (6) | −0.0045 (5) | −0.0006 (6) |
| N2 | 0.0276 (7) | 0.0265 (8) | 0.0361 (8) | −0.0041 (6) | −0.0069 (6) | −0.0030 (6) |
| O1 | 0.0252 (7) | 0.0260 (6) | 0.0445 (8) | −0.0032 (5) | −0.0132 (6) | 0.0037 (6) |
| O2 | 0.0279 (7) | 0.0349 (8) | 0.0554 (9) | −0.0024 (6) | −0.0201 (6) | 0.0024 (7) |
| C1 | 0.0232 (8) | 0.0328 (10) | 0.0326 (9) | 0.0030 (7) | −0.0047 (7) | 0.0020 (8) |
| C2 | 0.0337 (9) | 0.0282 (9) | 0.0395 (10) | 0.0048 (8) | −0.0027 (8) | 0.0030 (8) |
| C3 | 0.0403 (10) | 0.0250 (9) | 0.0395 (10) | −0.0038 (8) | −0.0037 (8) | −0.0029 (8) |
| C4 | 0.0194 (7) | 0.0270 (9) | 0.0270 (8) | −0.0008 (6) | −0.0032 (6) | −0.0026 (6) |
| C5 | 0.0244 (8) | 0.0281 (9) | 0.0308 (9) | −0.0009 (7) | −0.0061 (7) | −0.0013 (7) |
| Cu—O1 | 1.9367 (14) | O1—C5 | 1.281 (2) |
| Cu—O1i | 1.9367 (14) | O2—C5 | 1.224 (2) |
| Cu—N1i | 1.9714 (15) | C1—C2 | 1.373 (3) |
| Cu—N1 | 1.9714 (15) | C1—H1 | 0.9300 |
| N1—C1 | 1.339 (2) | C2—C3 | 1.378 (3) |
| N1—C4 | 1.346 (2) | C2—H2 | 0.9300 |
| N2—C4 | 1.319 (2) | C3—H3 | 0.9300 |
| N2—C3 | 1.341 (2) | C4—C5 | 1.520 (2) |
| O1—Cu—O1i | 180.0 | C2—C1—H1 | 119.8 |
| O1—Cu—N1i | 96.41 (6) | C1—C2—C3 | 117.70 (18) |
| O1i—Cu—N1i | 83.59 (6) | C1—C2—H2 | 121.1 |
| O1—Cu—N1 | 83.59 (6) | C3—C2—H2 | 121.1 |
| O1i—Cu—N1 | 96.41 (6) | N2—C3—C2 | 122.61 (17) |
| N1i—Cu—N1 | 180.0 | N2—C3—H3 | 118.7 |
| C1—N1—C4 | 117.84 (16) | C2—C3—H3 | 118.7 |
| C1—N1—Cu | 130.04 (13) | N2—C4—N1 | 125.53 (16) |
| C4—N1—Cu | 111.96 (12) | N2—C4—C5 | 120.37 (15) |
| C4—N2—C3 | 115.95 (15) | N1—C4—C5 | 114.10 (15) |
| C5—O1—Cu | 115.23 (12) | O2—C5—O1 | 125.42 (17) |
| N1—C1—C2 | 120.31 (17) | O2—C5—C4 | 120.11 (16) |
| N1—C1—H1 | 119.8 | O1—C5—C4 | 114.46 (15) |
| Symmetry codes: (i) −x+1, −y+1, −z+1. |
| D—H···A | D—H | H···A | D···A | D—H···A |
| C1—H1···N2ii | 0.93 | 2.62 | 3.511 (3) | 160 |
| C2—H2···O2ii | 0.93 | 2.39 | 3.193 (3) | 145 |
| C3—H3···O1iii | 0.93 | 2.57 | 3.336 (3) | 140 |
| C3—H3···O2iii | 0.93 | 2.53 | 3.317 (2) | 142 |
| Symmetry codes: (ii) x−1, −y+3/2, z−1/2; (iii) −x+2, y+1/2, −z+3/2. |
| 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+3/2, z−1/2; (ii) −x+2, y+1/2, −z+3/2. |
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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)°.