Bis(pyrimidine-2-carboxyl­ato-κ²N,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 Cu^II 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.

Key indicators

• Single-crystal X-ray study
• T = 291 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.025
• wR factor = 0.072
• Data-to-parameter ratio = 13.6

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT232_ALERT_2_C Hirshfeld Test Diff (M-X)  Cu     -   N1      ..       5.70 su
PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor ....       2.10

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   2 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   0 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. 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 Cu^II 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 Cu^II 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 Cu^II 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 N1^iv-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

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).

S2. 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.

S3. Refinement

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

Computing details

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

	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].

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

Crystal data

[Cu(C5H3N2O2)2]	F(000) = 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 = 3.5–25.0°
b = 13.2624 (12) Å	µ = 2.11 mm^−1
c = 7.6735 (11) Å	T = 291 K
β = 94.025 (15)°	Prism, blue
V = 521.88 (12) Å^3	0.32 × 0.20 × 0.16 mm
Z = 2

Data collection

Rigaku R-AXIS RAPID IP diffractometer	1196 independent reflections
Radiation source: fine-focus sealed tube	1068 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.016
Detector resolution: 10.0 pixels mm^-1	θmax = 27.5°, θmin = 3.1°
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

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.025	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.072	H-atom parameters constrained
S = 1.07	w = 1/[σ^2(Fo^2) + (0.0413P)^2 + 0.1691P] where P = (Fo^2 + 2Fc^2)/3
1196 reflections	(Δ/σ)max < 0.001
88 parameters	Δρmax = 0.25 e Å^−3
0 restraints	Δρmin = −0.42 e Å^−3

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 (Ų)

	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)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

Geometric parameters (Å, º)

Cu—O1	1.9367 (14)	O1—C5	1.281 (2)
Cu—O1^i	1.9367 (14)	O2—C5	1.224 (2)
Cu—N1^i	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—O1^i	180.0	C2—C1—H1	119.8
O1—Cu—N1^i	96.41 (6)	C1—C2—C3	117.70 (18)
O1^i—Cu—N1^i	83.59 (6)	C1—C2—H2	121.1
O1—Cu—N1	83.59 (6)	C3—C2—H2	121.1
O1^i—Cu—N1	96.41 (6)	N2—C3—C2	122.61 (17)
N1^i—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 code: (i) −x+1, −y+1, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C1—H1···N2^ii	0.93	2.62	3.511 (3)	160
C2—H2···O2^ii	0.93	2.39	3.193 (3)	145
C3—H3···O1^iii	0.93	2.57	3.336 (3)	140
C3—H3···O2^iii	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.