Poly[bis­(μ₂-pyrimidine-2-carboxyl­ato-κ⁴ O,N:O′,N′)calcium]

Abstract

In the crystal structure of the title polymeric complex, [Ca(C₅H₃N₂O₂)₂]_n, the Ca^II cation has site symmetry m2 and is N,O-chelated by four pyrimidine-2-carboxyl­ate anions in a square-anti­prismatic geometry. The planar pyrimidine-2-carboxyl­ate anion is located on a crystallographic special position, three C atoms have site symmetry 2mm, while the carboxyl O atom, the pyrimidine N atom and the other C atom have site symmetry m. Each pyrimidine-2-­carboxyl­ate anion bridges two Ca^II cations, forming polymeric sheets extending parallel to (001). π–π stacking exists between parallel pyrimidine rings [centroid–centroid distance = 3.6436 (6) Å] of adjacent polymeric sheets. Weak C—H⋯O hydrogen bonding is also observed between these sheets.

Related literature

For general background, see: Deisenhofer & Michel (1989 ▶); Pan & Xu (2004 ▶); Li et al. (2005 ▶). For polymeric structures of metal complexes with the pyrimidine-2-carboxyl­ate ligand, see: Rodríguez-Diéguez et al. (2007 ▶, 2008 ▶); Zhang et al. (2008a ▶,b ▶); Sava et al. (2008 ▶). For mononuclear metal complexes of pyrimidine-2-carboxyl­ate, see: Antolić et al. (2000 ▶); Zhang et al. (2008 ▶); Xu et al. (2008 ▶). For Ca—N and Ca—O bond distances in N,O-chelated complexes, see: Starosta & Leciejewicz (2004 ▶).

Experimental

Crystal data

• [Ca(C₅H₃N₂O₂)₂]

• M _r = 286.27

• Tetragonal,

• a = 6.5312 (12) Å

• c = 25.734 (3) Å

• V = 1097.7 (3) ų

• Z = 4

• Mo Kα radiation

• μ = 0.59 mm⁻¹

• T = 294 K

• 0.22 × 0.20 × 0.14 mm

Data collection

• Rigaku R-AXIS RAPID IP diffractometer

• Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ▶) T _min = 0.85, T _max = 0.92

• 3191 measured reflections

• 375 independent reflections

• 364 reflections with I > 2σ(I)

• R _int = 0.016

Refinement

• R[F ² > 2σ(F ²)] = 0.025

• wR(F ²) = 0.068

• S = 1.13

• 375 reflections

• 34 parameters

• H-atom parameters constrained

• Δρ_max = 0.22 e Å⁻³

• Δρ_min = −0.17 e Å⁻³

Data collection: PROCESS-AUTO (Rigaku, 1998 ▶); cell refinement: PROCESS-AUTO; 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, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶).

Supplementary Material

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

Table 1. Selected bond lengths (Å).

Ca—O1	2.3644 (11)
Ca—N1	2.6923 (13)

Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
C3—H3⋯O1i	0.93	2.57	3.3689 (19)	144

Symmetry code: (i) .

supplementary crystallographic information

Comment

As π-π stacking between aromatic rings is correlated with the electron transfer process in some biological systems (Deisenhofer & Michel, 1989), a series metal complexes incorporating the aromatic compound has been prepared in our laboratory to investigate the nature of π-π stacking (Li et al., 2005; Pan & Xu, 2004). We report herein the crystal structure of the title compound of pyridinecarboxylate to show π-π stacking in the crystal structure.

A part of the polymeric structure of the title molecule is shown in Fig. 1. In the crystal structure, the Ca^II cation has site symmetry -4m2 and is N,O-chelated by four pyrimidinecarboxylate anions with the square-antiprism geometry. The Ca—N and Ca—O bond distances (Table 1) agree with those found in the N,O-chelated Ca^II complex (Starosta & Leciejewicz, 2004). The planar pyrimidinecarboxylate anion is located on the crystallographic special position, three C atoms have site symmetry 2 mm while the carboxyl O atom, the pirimidine N atom and the other C atom have site symmetry m. Each pyrimidinecarboxylate anion N,O-chelates two Ca^II cations (Antolić et al., 2000; Zhang et al., 2008; Xu et al., 2008), forming the two-dimensional polymeric sheets, similar to those found in reported compounds (Rodríguez-Diéguez et al., 2007, 2008; Zhang et al., 2008a,b; Sava et al. 2008). π-π stacking [centroid-centroid distance = 3.6436 (6) Å] exists between parallel pyrimidine rings of adjacent polymeric sheets (Fig. 2). Weak C—H···O hydrogen bonding is also observed between polymeric sheets (Table 2).

Experimental

2-Cyanopyrimidine (0.2 g, 2 mmol), NaOH (1.2 g, 30 mmol) and calcium chloride (0.1 g, 1 mmol) were dissolved in water (10 ml). The solution was refluxed for 3 h. After cooling to room temperature the solution was filtered. The single crystals were obtained from the filtrate after 5 d.

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).

Figures

Fig. 1.

A part of polymeric structure of the title compound with 30% probability displacement ellipsoids for non-H atoms (arbitrary spheres for H atoms) [symmetry codes: (i) 1 - x, 3/2 - y, z; (ii) 1 - x, 1/2 - y, z; (iii) 5/4 - y, 1/4 + x, 3/4 - z; (iv) -1/4 + y, 1/4 + x, 3/4 - z; (v) x, -1 + y, z].

Fig. 2.

A diagram showing π-π stacking between parallel pyrimidine rings of adjacent polymeric sheets.

Crystal data

[Ca(C5H3N2O2)2]	Dx = 1.732 Mg m−3
Mr = 286.27	Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I41/amd	Cell parameters from 1086 reflections
Hall symbol: -I 4bd 2	θ = 3.2–25.0°
a = 6.5312 (12) Å	µ = 0.59 mm−1
c = 25.734 (3) Å	T = 294 K
V = 1097.7 (3) Å3	Block, colorless
Z = 4	0.22 × 0.20 × 0.14 mm
F(000) = 584

Data collection

Rigaku R-AXIS RAPID IP diffractometer	375 independent reflections
Radiation source: fine-focus sealed tube	364 reflections with I > 2σ(I)
graphite	Rint = 0.016
ω scans	θmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −8→8
Tmin = 0.85, Tmax = 0.92	k = −7→8
3191 measured reflections	l = −14→33

Refinement

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) = 0.068	w = 1/[σ2(Fo2) + (0.0407P)2 + 0.7773P] where P = (Fo2 + 2Fc2)/3
S = 1.13	(Δ/σ)max < 0.001
375 reflections	Δρmax = 0.22 e Å−3
34 parameters	Δρmin = −0.17 e Å−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.071 (5)

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
Ca	0.5000	0.7500	0.3750	0.0164 (3)
N1	0.5000	0.4327 (2)	0.30820 (5)	0.0226 (4)
O1	0.5000	0.41994 (18)	0.41274 (4)	0.0292 (4)
C1	0.5000	0.2500	0.39085 (8)	0.0197 (5)
C2	0.5000	0.2500	0.33146 (8)	0.0188 (5)
C3	0.5000	0.4306 (3)	0.25605 (6)	0.0299 (4)
H3	0.5000	0.5542	0.2381	0.036*
C4	0.5000	0.2500	0.22845 (10)	0.0319 (6)
H4	0.5000	0.2500	0.1923	0.038*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Ca	0.0152 (3)	0.0152 (3)	0.0189 (4)	0.000	0.000	0.000
N1	0.0254 (7)	0.0209 (7)	0.0215 (7)	0.000	0.000	0.0026 (5)
O1	0.0499 (8)	0.0169 (6)	0.0209 (6)	0.000	0.000	−0.0015 (4)
C1	0.0224 (10)	0.0181 (10)	0.0186 (10)	0.000	0.000	0.000
C2	0.0170 (9)	0.0201 (10)	0.0193 (10)	0.000	0.000	0.000
C3	0.0345 (9)	0.0326 (9)	0.0226 (8)	0.000	0.000	0.0072 (7)
C4	0.0337 (13)	0.0438 (15)	0.0184 (10)	0.000	0.000	0.000

Geometric parameters (Å, °)

Ca—O1i	2.3644 (12)	N1—C3	1.342 (2)
Ca—O1ii	2.3644 (11)	O1—C1	1.2447 (15)
Ca—O1	2.3644 (11)	C1—O1iv	1.2447 (15)
Ca—O1iii	2.3644 (12)	C1—C2	1.528 (3)
Ca—N1iii	2.6923 (14)	C2—N1iv	1.3350 (16)
Ca—N1	2.6923 (13)	C3—C4	1.377 (2)
Ca—N1ii	2.6923 (13)	C3—H3	0.9300
Ca—N1i	2.6923 (14)	C4—C3iv	1.377 (2)
N1—C2	1.3350 (16)	C4—H4	0.9300
O1i—Ca—O1ii	99.72 (2)	O1ii—Ca—N1i	74.795 (18)
O1i—Ca—O1	99.72 (2)	O1—Ca—N1i	74.795 (18)
O1ii—Ca—O1	131.49 (5)	O1iii—Ca—N1i	164.58 (4)
O1i—Ca—O1iii	131.49 (5)	N1iii—Ca—N1i	100.65 (6)
O1ii—Ca—O1iii	99.72 (2)	N1—Ca—N1i	114.05 (3)
O1—Ca—O1iii	99.72 (2)	N1ii—Ca—N1i	114.05 (3)
O1i—Ca—N1iii	164.58 (4)	C2—N1—C3	116.03 (15)
O1ii—Ca—N1iii	74.795 (18)	C2—N1—Ca	113.69 (10)
O1—Ca—N1iii	74.795 (18)	C3—N1—Ca	130.28 (11)
O1iii—Ca—N1iii	63.93 (4)	C1—O1—Ca	128.83 (11)
O1i—Ca—N1	74.796 (18)	O1—C1—O1iv	126.2 (2)
O1ii—Ca—N1	164.58 (4)	O1—C1—C2	116.91 (10)
O1—Ca—N1	63.93 (4)	O1iv—C1—C2	116.91 (10)
O1iii—Ca—N1	74.796 (18)	N1iv—C2—N1	126.74 (19)
N1iii—Ca—N1	114.05 (3)	N1iv—C2—C1	116.63 (10)
O1i—Ca—N1ii	74.796 (18)	N1—C2—C1	116.63 (10)
O1ii—Ca—N1ii	63.93 (4)	N1—C3—C4	121.66 (16)
O1—Ca—N1ii	164.58 (4)	N1—C3—H3	119.2
O1iii—Ca—N1ii	74.796 (18)	C4—C3—H3	119.2
N1iii—Ca—N1ii	114.05 (3)	C3—C4—C3iv	117.9 (2)
N1—Ca—N1ii	100.65 (5)	C3—C4—H4	121.1
O1i—Ca—N1i	63.93 (4)	C3iv—C4—H4	121.1

Symmetry codes: (i) y−1/4, x+1/4, −z+3/4; (ii) −x+1, −y+3/2, z; (iii) −y+5/4, x+1/4, −z+3/4; (iv) −x+1, −y+1/2, z.

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O1v	0.93	2.57	3.3689 (19)	144

Symmetry codes: (v) y+1/4, −x+5/4, z−1/4.