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Acta Crystallogr Sect E Struct Rep Online. 2009 August 1; 65(Pt 8): m878–m879.
Published online 2009 July 8. doi:  10.1107/S1600536809025537
PMCID: PMC2977290

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 CaII cation has site symmetry An external file that holds a picture, illustration, etc.
Object name is e-65-0m878-efi9.jpg 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 CaII 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 [triangle]); Pan & Xu (2004 [triangle]); Li et al. (2005 [triangle]). For polymeric structures of metal complexes with the pyrimidine-2-carboxyl­ate ligand, see: Rodríguez-Diéguez et al. (2007 [triangle], 2008 [triangle]); Zhang et al. (2008a [triangle],b [triangle]); Sava et al. (2008 [triangle]). For mononuclear metal complexes of pyrimidine-2-carboxyl­ate, see: Antolić et al. (2000 [triangle]); Zhang et al. (2008 [triangle]); Xu et al. (2008 [triangle]). For Ca—N and Ca—O bond distances in N,O-chelated complexes, see: Starosta & Leciejewicz (2004 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0m878-scheme1.jpg

Experimental

Crystal data

  • [Ca(C5H3N2O2)2]
  • M r = 286.27
  • Tetragonal, An external file that holds a picture, illustration, etc.
Object name is e-65-0m878-efi10.jpg
  • 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 [triangle]) 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
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.17 e Å−3

Data collection: PROCESS-AUTO (Rigaku, 1998 [triangle]); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 [triangle]); program(s) used to solve structure: SIR92 (Altomare et al., 1993 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 [triangle]); software used to prepare material for publication: WinGX (Farrugia, 1999 [triangle]).

Table 1
Selected bond lengths (Å)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

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

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

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

Acknowledgments

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

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 CaII 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 CaII 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 CaII 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 Uiso(H) = 1.2Ueq(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 ...
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 m3
Mr = 286.27Mo Kα radiation, λ = 0.71073 Å
Tetragonal, I41/amdCell parameters from 1086 reflections
Hall symbol: -I 4bd 2θ = 3.2–25.0°
a = 6.5312 (12) ŵ = 0.59 mm1
c = 25.734 (3) ÅT = 294 K
V = 1097.7 (3) Å3Block, colorless
Z = 40.22 × 0.20 × 0.14 mm
F(000) = 584

Data collection

Rigaku R-AXIS RAPID IP diffractometer375 independent reflections
Radiation source: fine-focus sealed tube364 reflections with I > 2σ(I)
graphiteRint = 0.016
ω scansθmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)h = −8→8
Tmin = 0.85, Tmax = 0.92k = −7→8
3191 measured reflectionsl = −14→33

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.025H-atom parameters constrained
wR(F2) = 0.068w = 1/[σ2(Fo2) + (0.0407P)2 + 0.7773P] where P = (Fo2 + 2Fc2)/3
S = 1.13(Δ/σ)max < 0.001
375 reflectionsΔρmax = 0.22 e Å3
34 parametersΔρmin = −0.17 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction 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 (Å2)

xyzUiso*/Ueq
Ca0.50000.75000.37500.0164 (3)
N10.50000.4327 (2)0.30820 (5)0.0226 (4)
O10.50000.41994 (18)0.41274 (4)0.0292 (4)
C10.50000.25000.39085 (8)0.0197 (5)
C20.50000.25000.33146 (8)0.0188 (5)
C30.50000.4306 (3)0.25605 (6)0.0299 (4)
H30.50000.55420.23810.036*
C40.50000.25000.22845 (10)0.0319 (6)
H40.50000.25000.19230.038*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Ca0.0152 (3)0.0152 (3)0.0189 (4)0.0000.0000.000
N10.0254 (7)0.0209 (7)0.0215 (7)0.0000.0000.0026 (5)
O10.0499 (8)0.0169 (6)0.0209 (6)0.0000.000−0.0015 (4)
C10.0224 (10)0.0181 (10)0.0186 (10)0.0000.0000.000
C20.0170 (9)0.0201 (10)0.0193 (10)0.0000.0000.000
C30.0345 (9)0.0326 (9)0.0226 (8)0.0000.0000.0072 (7)
C40.0337 (13)0.0438 (15)0.0184 (10)0.0000.0000.000

Geometric parameters (Å, °)

Ca—O1i2.3644 (12)N1—C31.342 (2)
Ca—O1ii2.3644 (11)O1—C11.2447 (15)
Ca—O12.3644 (11)C1—O1iv1.2447 (15)
Ca—O1iii2.3644 (12)C1—C21.528 (3)
Ca—N1iii2.6923 (14)C2—N1iv1.3350 (16)
Ca—N12.6923 (13)C3—C41.377 (2)
Ca—N1ii2.6923 (13)C3—H30.9300
Ca—N1i2.6923 (14)C4—C3iv1.377 (2)
N1—C21.3350 (16)C4—H40.9300
O1i—Ca—O1ii99.72 (2)O1ii—Ca—N1i74.795 (18)
O1i—Ca—O199.72 (2)O1—Ca—N1i74.795 (18)
O1ii—Ca—O1131.49 (5)O1iii—Ca—N1i164.58 (4)
O1i—Ca—O1iii131.49 (5)N1iii—Ca—N1i100.65 (6)
O1ii—Ca—O1iii99.72 (2)N1—Ca—N1i114.05 (3)
O1—Ca—O1iii99.72 (2)N1ii—Ca—N1i114.05 (3)
O1i—Ca—N1iii164.58 (4)C2—N1—C3116.03 (15)
O1ii—Ca—N1iii74.795 (18)C2—N1—Ca113.69 (10)
O1—Ca—N1iii74.795 (18)C3—N1—Ca130.28 (11)
O1iii—Ca—N1iii63.93 (4)C1—O1—Ca128.83 (11)
O1i—Ca—N174.796 (18)O1—C1—O1iv126.2 (2)
O1ii—Ca—N1164.58 (4)O1—C1—C2116.91 (10)
O1—Ca—N163.93 (4)O1iv—C1—C2116.91 (10)
O1iii—Ca—N174.796 (18)N1iv—C2—N1126.74 (19)
N1iii—Ca—N1114.05 (3)N1iv—C2—C1116.63 (10)
O1i—Ca—N1ii74.796 (18)N1—C2—C1116.63 (10)
O1ii—Ca—N1ii63.93 (4)N1—C3—C4121.66 (16)
O1—Ca—N1ii164.58 (4)N1—C3—H3119.2
O1iii—Ca—N1ii74.796 (18)C4—C3—H3119.2
N1iii—Ca—N1ii114.05 (3)C3—C4—C3iv117.9 (2)
N1—Ca—N1ii100.65 (5)C3—C4—H4121.1
O1i—Ca—N1i63.93 (4)C3iv—C4—H4121.1

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···AD—HH···AD···AD—H···A
C3—H3···O1v0.932.573.3689 (19)144

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HK2721).

References

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