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Acta Cryst. (2012). E68, m1429    [ doi:10.1107/S160053681204411X ]

Tetraaquabis[2-(pyridin-4-yl-[kappa]N)pyrimidine-5-carboxylato]zinc

R. Sen, D. Mal, P. Brandao and Z. Lin

Abstract top

In the title complex, [Zn(C10H6N3O2)2(H2O)4], the ZnII ion lies on an inversion center and is coordinated in a slightly distorted octahedral geometry by two N atoms from two 2-(pyridin-4-yl)pyrimidine-5-carboxylate ligands and four water molecules. In the symmetry-unique part of the molecule, the pyridine and pyrimidine rings form a dihedral angle of 7.0 (1)°. In the crystal, the coordinating water molecules act as donor groups and carboxylate O atoms act as acceptors in O-H...O hydrogen bonds, forming a three-dimensional network.

Comment top

The aim of designing coordination frameworks is now been motivated through the field of supramolecular chemistry (Collet et al., 1996) and crystal engineering (Sen et al., 2012) from the viewpoints of the development of novel multi-functional MOFs. Fabricating MOFs with the desired properties are now the present day challenges of the chemist. N-Heterocyclic carboxylic acids share a major role in developing MOFs based material synthesis (Sen et al., 2012, Saha et al. 2012). Herein, we wish to report a new compound having an N-heterocyclic carboxylate ligand (2-pyridin-4-ylpyrimidine-5-carboxylato).

The molecular structure of the title compound is shown in Fig. 1. The ZnII ion lies on an inversion center and is coordinated in a slightly distorted octahedral geometry by two N atoms from two 2-pyridin-4-ylpyrimidine-5-carboxylato ligands and four water molecules. The equatorial plane is formed by the four water molecule and the two axial sites are occupied by the N-donor sites of the ligand. In the crystal, O—H···O hydrogen bonds form a three-dimensional network (Fig. 2). The related structure, tetraaquabis[4-(4H-1,2,4-triazol-4-yl)benzoato- κN1]manganese(II) decahydrate, has been published (Piao & Xuan, 2011).

Related literature top

For a general background to supramolecular chemistry, see: Collet et al. (1996). For general syntheses and applications of MOFs, see: Sen et al. (2012); Saha et al. (2012). For a related structure, see: Piao & Xuan (2011).

Experimental top

To prepare the complex we followed a routine hydrothermal process. Zn(NO3)2 hydrate and 2-pyridin-4-ylpyrimidine-5-carboxylic acid were mixed in a 1:1 ratio, and kept in a reaction bomb at 433 K for 2 days in autogenously created pressure. After cooling to room temperature colourless block-shaped crystals were obtained. Yield ca. 45% (based on metal). The crystals were collected by filtration, washed thoroughly with water and dried in ambient conditions.

Refinement top

The hydrogen atoms of the C—H bonds were placed at calculated positions and refined as riding atoms, with C—H = 0.95 Å with Uiso(H) =1.2Ueq(C) of the atom to which they are attached. The positions of the hydrogen atoms of the water molecules were discernible in difference Fourier maps and they were included in the structure refinement with individual isotropic thermal parameters and refined with an O—H distance restraint of 0.83 (2) Å.

Computing details top

Data collection: SMART (Bruker, 2008); cell refinement: SAINT (Bruker, 2008); data reduction: SAINT (Bruker, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound. Displacement ellipsoids are drawn at the 30% probability level [Symmetry code: (i) -x,-y, -z].
[Figure 2] Fig. 2. Part of the crystal structure showing the three-dimensional hydrogen-bonded network.
Tetraaquabis[2-(pyridin-4-yl-κN)pyrimidine-5-carboxylato]zinc top
Crystal data top
[Zn(C10H6N3O2)2(H2O)4]Z = 1
Mr = 537.79F(000) = 276
Triclinic, P1Dx = 1.781 Mg m−3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.2764 (7) ÅCell parameters from 246 reflections
b = 6.9208 (7) Åθ = 2.6–27.6°
c = 12.7810 (17) ŵ = 1.29 mm−1
α = 99.676 (7)°T = 150 K
β = 92.638 (7)°Block, colourless
γ = 112.639 (5)°0.26 × 0.20 × 0.04 mm
V = 501.36 (10) Å3
Data collection top
Bruker SMART CCD
diffractometer		2184 independent reflections
Radiation source: fine-focus sealed tube2030 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
fine–focus sealed tube scansθmax = 27.4°, θmin = 3.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		h = −8→8
Tmin = 0.730, Tmax = 0.950k = −8→8
8143 measured reflectionsl = −16→16
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.033Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.089H atoms treated by a mixture of independent and constrained refinement
S = 1.14 w = 1/[σ2(Fo2) + (0.0522P)2 + 0.1478P]
where P = (Fo2 + 2Fc2)/3
2184 reflections(Δ/σ)max < 0.001
176 parametersΔρmax = 1.05 e Å−3
4 restraintsΔρmin = −0.61 e Å−3
Crystal data top
[Zn(C10H6N3O2)2(H2O)4]γ = 112.639 (5)°
Mr = 537.79V = 501.36 (10) Å3
Triclinic, P1Z = 1
a = 6.2764 (7) ÅMo Kα radiation
b = 6.9208 (7) ŵ = 1.29 mm−1
c = 12.7810 (17) ÅT = 150 K
α = 99.676 (7)°0.26 × 0.20 × 0.04 mm
β = 92.638 (7)°
Data collection top
Bruker SMART CCD
diffractometer		2184 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2008)		2030 reflections with I > 2σ(I)
Tmin = 0.730, Tmax = 0.950Rint = 0.032
8143 measured reflectionsθmax = 27.4°
Refinement top
R[F2 > 2σ(F2)] = 0.033H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.089Δρmax = 1.05 e Å−3
S = 1.14Δρmin = −0.61 e Å−3
2184 reflectionsAbsolute structure: ?
176 parametersFlack parameter: ?
4 restraintsRogers parameter: ?
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
xyzUiso*/Ueq
Zn0.00000.00000.00000.01467 (13)
O10.1899 (3)−0.1897 (2)−0.03156 (12)0.0170 (3)
H1A0.129 (5)−0.303 (3)−0.0767 (17)0.028 (7)*
H1B0.238 (6)−0.227 (6)0.0190 (19)0.051 (10)*
O20.2499 (3)0.2665 (3)−0.05357 (13)0.0196 (3)
H2A0.184 (5)0.334 (5)−0.080 (2)0.044 (9)*
H2B0.365 (4)0.265 (5)−0.082 (2)0.046 (10)*
N30.1681 (3)0.1214 (3)0.16096 (14)0.0152 (4)
C40.0418 (4)0.1047 (3)0.24398 (17)0.0165 (4)
H4−0.12160.06100.22960.020*
C50.1386 (4)0.1481 (3)0.34911 (16)0.0159 (4)
H50.04300.13340.40530.019*
C60.3782 (4)0.2137 (3)0.37137 (16)0.0138 (4)
C70.5107 (4)0.2394 (3)0.28616 (17)0.0167 (4)
H70.67510.28900.29850.020*
C80.3995 (4)0.1916 (3)0.18334 (17)0.0173 (4)
H80.49140.20940.12590.021*
C90.4895 (4)0.2521 (3)0.48227 (16)0.0148 (4)
N100.3511 (3)0.2432 (3)0.56043 (14)0.0167 (4)
C110.4536 (4)0.2753 (3)0.65945 (17)0.0169 (4)
H110.36200.26850.71690.020*
C120.6871 (4)0.3180 (3)0.68231 (16)0.0146 (4)
C130.8139 (4)0.3264 (4)0.59538 (17)0.0179 (4)
H130.97510.35710.60780.022*
N140.7165 (3)0.2928 (3)0.49487 (14)0.0179 (4)
C150.7950 (4)0.3495 (3)0.79525 (16)0.0166 (4)
O161.0133 (3)0.4300 (3)0.81382 (12)0.0203 (3)
O170.6557 (3)0.2901 (3)0.86250 (12)0.0214 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Zn0.01318 (19)0.0201 (2)0.01366 (19)0.00978 (14)0.00064 (12)0.00383 (13)
O10.0168 (7)0.0215 (8)0.0163 (8)0.0118 (7)−0.0000 (6)0.0033 (6)
O20.0167 (8)0.0232 (9)0.0225 (8)0.0101 (7)0.0040 (6)0.0086 (6)
N30.0151 (8)0.0197 (9)0.0140 (8)0.0103 (7)0.0014 (7)0.0033 (7)
C40.0140 (10)0.0187 (11)0.0192 (10)0.0090 (8)0.0020 (8)0.0038 (8)
C50.0160 (10)0.0186 (11)0.0160 (10)0.0091 (9)0.0040 (8)0.0048 (8)
C60.0168 (10)0.0114 (10)0.0157 (10)0.0080 (8)0.0011 (8)0.0036 (7)
C70.0132 (10)0.0192 (11)0.0198 (11)0.0088 (9)0.0016 (8)0.0036 (8)
C80.0161 (10)0.0213 (11)0.0163 (10)0.0092 (9)0.0035 (8)0.0038 (8)
C90.0162 (10)0.0140 (10)0.0166 (10)0.0079 (8)0.0014 (8)0.0044 (8)
N100.0160 (9)0.0193 (9)0.0170 (9)0.0089 (7)0.0017 (7)0.0051 (7)
C110.0185 (10)0.0178 (11)0.0161 (10)0.0084 (9)0.0022 (8)0.0051 (8)
C120.0161 (10)0.0130 (10)0.0174 (10)0.0082 (8)0.0004 (8)0.0046 (8)
C130.0158 (10)0.0213 (11)0.0190 (11)0.0100 (9)0.0006 (8)0.0045 (8)
N140.0159 (9)0.0225 (10)0.0170 (9)0.0094 (8)0.0008 (7)0.0045 (7)
C150.0201 (10)0.0160 (11)0.0177 (10)0.0118 (9)0.0008 (8)0.0030 (8)
O160.0170 (7)0.0255 (8)0.0198 (8)0.0100 (7)−0.0008 (6)0.0053 (6)
O170.0199 (8)0.0330 (9)0.0179 (8)0.0156 (7)0.0040 (6)0.0096 (6)
Geometric parameters (Å, º) top
Zn—O12.0923 (15)C6—C71.394 (3)
Zn—O1i2.0923 (15)C6—C91.486 (3)
Zn—N3i2.1419 (17)C7—C81.384 (3)
Zn—N32.1420 (17)C7—H70.9500
Zn—O2i2.1512 (15)C8—H80.9500
Zn—O22.1512 (15)C9—N141.338 (3)
O1—H1A0.830 (10)C9—N101.348 (3)
O1—H1B0.822 (10)N10—C111.336 (3)
O2—H2A0.833 (10)C11—C121.385 (3)
O2—H2B0.827 (10)C11—H110.9500
N3—C81.341 (3)C12—C131.392 (3)
N3—C41.347 (3)C12—C151.510 (3)
C4—C51.383 (3)C13—N141.340 (3)
C4—H40.9500C13—H130.9500
C5—C61.393 (3)C15—O161.257 (3)
C5—H50.9500C15—O171.258 (3)
O1—Zn—O1i180.0C4—C5—H5120.5
O1—Zn—N3i88.59 (6)C6—C5—H5120.5
O1i—Zn—N3i91.41 (6)C5—C6—C7118.01 (19)
O1—Zn—N391.41 (6)C5—C6—C9121.15 (18)
O1i—Zn—N388.59 (6)C7—C6—C9120.83 (19)
N3i—Zn—N3180.0C8—C7—C6119.2 (2)
O1—Zn—O2i86.31 (6)C8—C7—H7120.4
O1i—Zn—O2i93.69 (6)C6—C7—H7120.4
N3i—Zn—O2i91.45 (6)N3—C8—C7123.13 (19)
N3—Zn—O2i88.55 (6)N3—C8—H8118.4
O1—Zn—O293.69 (6)C7—C8—H8118.4
O1i—Zn—O286.31 (6)N14—C9—N10126.45 (19)
N3i—Zn—O288.55 (6)N14—C9—C6117.08 (18)
N3—Zn—O291.45 (6)N10—C9—C6116.48 (19)
O2i—Zn—O2180.0C11—N10—C9115.59 (19)
Zn—O1—H1A118 (2)N10—C11—C12123.16 (19)
Zn—O1—H1B118 (2)N10—C11—H11118.4
H1A—O1—H1B103 (3)C12—C11—H11118.4
Zn—O2—H2A110 (2)C11—C12—C13116.22 (19)
Zn—O2—H2B125 (2)C11—C12—C15121.41 (18)
H2A—O2—H2B114 (3)C13—C12—C15122.36 (19)
C8—N3—C4117.43 (18)N14—C13—C12122.3 (2)
C8—N3—Zn121.52 (14)N14—C13—H13118.8
C4—N3—Zn120.54 (14)C12—C13—H13118.8
N3—C4—C5123.19 (19)C9—N14—C13116.28 (18)
N3—C4—H4118.4O16—C15—O17125.88 (19)
C5—C4—H4118.4O16—C15—C12117.94 (18)
C4—C5—C6118.99 (19)O17—C15—C12116.18 (19)
Symmetry code: (i) −x, −y, −z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O16ii0.83 (2)1.98 (2)2.805 (3)175 (3)
O1—H1B···O17iii0.82 (3)1.81 (3)2.631 (3)175 (4)
O2—H2A···O16iv0.83 (4)2.04 (4)2.840 (3)162 (4)
O2—H2B···O17v0.83 (3)1.94 (3)2.767 (3)173 (3)
Symmetry codes: (ii) x−1, y−1, z−1; (iii) −x+1, −y, −z+1; (iv) x−1, y, z−1; (v) x, y, z−1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H1A···O16i0.83 (2)1.98 (2)2.805 (3)175 (3)
O1—H1B···O17ii0.82 (3)1.81 (3)2.631 (3)175 (4)
O2—H2A···O16iii0.83 (4)2.04 (4)2.840 (3)162 (4)
O2—H2B···O17iv0.83 (3)1.94 (3)2.767 (3)173 (3)
Symmetry codes: (i) x−1, y−1, z−1; (ii) −x+1, −y, −z+1; (iii) x−1, y, z−1; (iv) x, y, z−1.
Acknowledgements top

RS wishes to thank FCT(SFRH/BPD/71798/2010) for a postdoctoral grant.

references
References top

Bruker (2008). SMART, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.

Collet, A. (1996). Comprehensive Supramolecular Chemistry, edited by J. L. Atwood, J. E. D. Davies, D. D. M. Nicol, F. Vögtle & J. M. Lehn, Vol. 6, pp. 281–303. Oxford: Pergamon.

Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453–457.

Piao, Y.-A. & Xuan, Z.-Y. (2011). Acta Cryst. E67, m1072.

Saha, D., Sen, R., Maity, T. & Koner, S. (2012). Dalton Trans. 41, 7399–7408.

Sen, R., Saha, D. & Koner, S. (2012). Chem. Eur. J. 18, 5979–5986.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.