Poly[bis­(μ2-pyrimidine-2-carboxyl­ato-κ4O,N:O′,N′)calcium]

Zhang, B.-Y.; Nie, J.-J.; Xu, D.-J.

doi:10.1107/S1600536809025537

metal-organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Pages m878-m879

doi:10.1107/S1600536809025537

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Poly[bis(μ₂-pyrimidine-2-carboxylato-κ⁴O,N:O′,N′)calcium]

Bing-Yu Zhang,^a Jing-Jing Nie ^a and Duan-Jun Xu ^a ^*

^aDepartment of Chemistry, Zhejiang University, People's Republic of China
^*Correspondence e-mail: xudj@mail.hz.zj.cn

(Received 26 June 2009; accepted 1 July 2009; online 8 July 2009)

In the crystal structure of the title polymeric complex, [Ca(C₅H₃N₂O₂)₂]_n, the Ca^II cation has site symmetry $[\overline{4}]$ 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, I 4₁ /a m d
a = 6.5312 (12) Å
c = 25.734 (3) Å
V = 1097.7 (3) Å³
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[F² > 2σ(F²)] = 0.025
wR(F²) = 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

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) $[y+{\script{1\over 4}}, -x+{\script{5\over 4}}, z-{\script{1\over 4}}]$ .

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 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536809025537/hk2721sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536809025537/hk2721Isup2.hkl

checkCIF report

Comment top

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).

Related literature top

For general background, see: Deisenhofer & Michel (1989); Pan & Xu (2004); Li et al. (2005). For polymeric structures of pyrimidine-2-carboxylate complexes of metals, 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 top

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.

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, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top

	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.

Poly[bis(µ₂-pyrimidine-2-carboxylato- κ⁴O,N:O',N')calcium] top

Crystal data top

[Ca(C₅H₃N₂O₂)₂]	D_x = 1.732 Mg m⁻³
M_r = 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 top

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

Refinement top

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(F_o²) + (0.0407P)² + 0.7773P] where P = (F_o² + 2F_c²)/3
S = 1.13	(Δ/σ)_max < 0.001
375 reflections	Δρ_max = 0.22 e Å⁻³
34 parameters	Δρ_min = −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)

Crystal data top

[Ca(C₅H₃N₂O₂)₂]	Z = 4
M_r = 286.27	Mo Kα radiation
Tetragonal, I4₁/amd	µ = 0.59 mm⁻¹
a = 6.5312 (12) Å	T = 294 K
c = 25.734 (3) Å	0.22 × 0.20 × 0.14 mm
V = 1097.7 (3) Å³

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	375 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	364 reflections with I > 2σ(I)
T_min = 0.85, T_max = 0.92	R_int = 0.016
3191 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.025	0 restraints
wR(F²) = 0.068	H-atom parameters constrained
S = 1.13	Δρ_max = 0.22 e Å⁻³
375 reflections	Δρ_min = −0.17 e Å⁻³
34 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

	x	y	z	U_iso*/U_eq
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 (Å²) top

	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, º) top

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—O1^iv	1.2447 (15)
Ca—O1ⁱⁱⁱ	2.3644 (12)	C1—C2	1.528 (3)
Ca—N1ⁱⁱⁱ	2.6923 (14)	C2—N1^iv	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—C3^iv	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—O1^iv	126.2 (2)
O1ⁱⁱ—Ca—N1	164.58 (4)	O1—C1—C2	116.91 (10)
O1—Ca—N1	63.93 (4)	O1^iv—C1—C2	116.91 (10)
O1ⁱⁱⁱ—Ca—N1	74.796 (18)	N1^iv—C2—N1	126.74 (19)
N1ⁱⁱⁱ—Ca—N1	114.05 (3)	N1^iv—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—C3^iv	117.9 (2)
N1—Ca—N1ⁱⁱ	100.65 (5)	C3—C4—H4	121.1
O1ⁱ—Ca—N1ⁱ	63.93 (4)	C3^iv—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, º) top

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O1^v	0.93	2.57	3.3689 (19)	144

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

Experimental details

Crystal data
Chemical formula	[Ca(C₅H₃N₂O₂)₂]
M_r	286.27
Crystal system, space group	Tetragonal, I4₁/amd
Temperature (K)	294
a, c (Å)	6.5312 (12), 25.734 (3)
V (Å³)	1097.7 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.59
Crystal size (mm)	0.22 × 0.20 × 0.14

Data collection
Diffractometer	Rigaku R-AXIS RAPID IP diffractometer
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.85, 0.92
No. of measured, independent and observed [I > 2σ(I)] reflections	3191, 375, 364
R_int	0.016
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.025, 0.068, 1.13
No. of reflections	375
No. of parameters	34
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.22, −0.17

Computer programs: PROCESS-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), SIR92 (Altomare et al., 1993), SHELXL97 (Sheldrick, 2008), ORTEP-3 for Windows (Farrugia, 1997), WinGX (Farrugia, 1999).

Selected bond lengths (Å) top

Ca—O1

2.3644 (11)

Ca—N1

2.6923 (13)

Hydrogen-bond geometry (Å, º) top

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) y+1/4, −x+5/4, z−1/4.

Acknowledgements

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

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