supplementary materials


lx2203 scheme

Acta Cryst. (2012). E68, m91    [ doi:10.1107/S160053681105481X ]

catena-Poly[[bis(acetato-[kappa]O)aquacopper(II)]-[mu]-5-(pyridin-3-yl)pyrimidine-[kappa]2N1:N5]

J.-F. Sun, G.-G. Hou and X.-P. Dai

Abstract top

In the title compound, [Cu(CH3CO2)2(C9H7N3)(H2O)]n, the CuII ion is pentacoordinated in a square-pyramidal geometry. The N atoms of the two chelating symmetry-related 5-(pyridin-3-yl)pyrimidine ligands and the O atoms of the two monodentate acetate anions are nearly coplanar, with a mean deviation from the least-squares plane of 0.157 (2) Å and the CuII ion is displaced by 0.050 (3) Å from this plane towards the apical water O atom. Bridging through the bis-monodentate 5-(pyridin-3-yl)pyrimidine ligand forms a one-dimensional coordination polymer extending parallel to [010]. In the crystal, O-H...O hydrogen bonds link the molecules into a two-dimensional supramolecular structure parallel to (100). The crystal studied was an inversion twin with a 0.57 (3):0.43 (3) domain ratio.

Comment top

Asymmetric organic ligands with various topologies and coordination natures, are widely used in the construction of coordination polymers and supramolecular complexes by chemists. Some of them exhibit encouraging potential for application in magnetic (He et al., 2006), luminescent property (Allendorf et al., 2009; Hou et al., 2010) and nonlinear optical materials (Evans et al., 2002). Among these strategies, the geometry of organic ligands is one of the most important factors in determining the structure of the framework. Pyrimidine derivatives have been widely used in supramolecular chemistry and many coordination polymers with versatile structures and potential properties have been reported (Thébault, et al., 2006; Fujita, et al., 2005). For example, Champness and co-workers have reported a highly unusual three-dimensional polymer, [Cu3I3(5-(4-Pyridyl)pyrimidine)]n, in which the 5-(4-Pyridyl)pyrimidine ligand bridges two-dimensional brick-wall (CuI)n sheets (Thébault, et al., 2006). In this work, we employed 5-(pyridin-3-yl)pyrimidine and acetate as ligands.

The crystal studied of the title compound was an inversion twin with a 0.57 (3):0.43 (3) domain ratio. In the title complex, the Cu2+ ion is pentacoordinated, with two different N atoms of the chelating 5-(pyridin-3-yl)pyrimidine ligand and two O atoms of two acetate ligands in the basal plane and the O atom of water molecule completing the square-pyramidal geometry from the apical site (Fig. 1). The pyrimidine and pyridine rings in the asymmetric ligand are seriously twisted. The corresponding dihedral angle is about 47.1 (1)°, which is distinctly larger than the reported value of 34.0 (1)° in [Cu3I3(5-(4-pyridyl)pyrimidine)]n (Thébault, et al., 2006). The atoms N1i, N2, O1 and O3i [Symmetry code: (i)x - 1, -y + 1, z - 1/2] are on the nearly coplanar, with a mean deviation from the least-squares plane of 0.157 (2) Å and the Cu atom is displaced by 0.050 (3) Å from this plane towards the apical O atom. Further coordination via the bidentate 5-(pyridin-3-yl)pyrimidine ligand forms a one-dimensional coordination polymer extending parallel to [010]. In the crystal structure (Fig. 2), intermolecular O–H···O hydrogen bonds link the molecules into a 2D supramolecular structure (Table 1).

Related literature top

For background to the network topologies and applications of coordination polymers, see: Allendorf et al. (2009); Evans & Lin (2002); Fujita et al. (2005); He et al. (2006); Hou et al. (2010). For complexes with 5-(4-pyridyl)pyrimidine, see: Thébault et al. (2006).

Experimental top

A solution of Cu(CH3COO)2 (10.0 mg, 0.050 mmol) in CH3CN (2 ml) was layered into a solution of 5-(pyridin-3-yl)pyrimidine (7.8 mg, 0.050 mmol) in CH2Cl2 (2 ml) solvent. The solutions were left for about three weeks at room temperature, and blue crystals were obtained. Yield, 73%.

Refinement top

The reported Flack parameter was obtained by TWIN/BASF procedure in SHELXL (Sheldrick, 2008). Hydrogen atoms on the water molecule were located in the difference Fourier map and refined as riding in their as-found relative positions. Uiso(H) = 1.5Ueq(O). Other H atoms were placed in idealized positions and treated as riding, with C–H = 0.93 Å (CH) or 0.96 (CH3) and, Uiso(H) = 1.2 Ueq(CH) and Uiso(H) = 1.5 Ueq(CH3).

Computing details top

Data collection: SMART (Bruker, 2003); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as small spheres of arbitrary radius. [Symmetry codes: (i) x - 1, -y + 1, z - 1/2.]
[Figure 2] Fig. 2. Two dimensional hydrogenbond interactions in the title compound. H atoms non-participating in hydrogen-bonding were omitted for clarity. [symmetry code: (iii) x, -y + 1, z - 1/2]
catena-Poly[[bis(acetato-κO)aquacopper(II)]-µ- 5-(pyridin-3-yl)pyrimidine-κ2N1:N5] top
Crystal data top
[Cu(C2H3O2)2(C9H7N3)(H2O)]F(000) = 366
Mr = 356.82Dx = 1.591 Mg m3
Monoclinic, PcMo Kα radiation, λ = 0.71073 Å
Hall symbol: P -2ycCell parameters from 1345 reflections
a = 9.154 (2) Åθ = 2.3–23.5°
b = 7.9940 (19) ŵ = 1.49 mm1
c = 10.590 (2) ÅT = 298 K
β = 106.040 (3)°Block, blue
V = 744.8 (3) Å30.12 × 0.10 × 0.10 mm
Z = 2
Data collection top
Bruker SMART APEX CCD
diffractometer
2305 independent reflections
Radiation source: fine-focus sealed tube2226 reflections with I > 2σ(I)
graphiteRint = 0.028
φ and ω scansθmax = 25.5°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2003)
h = 117
Tmin = 0.841, Tmax = 0.865k = 99
3778 measured reflectionsl = 1212
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.050H-atom parameters constrained
wR(F2) = 0.118 w = 1/[σ2(Fo2) + (0.0642P)2 + 0.3262P]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
2305 reflectionsΔρmax = 1.20 e Å3
203 parametersΔρmin = 0.57 e Å3
2 restraintsAbsolute structure: Flack (1983), 912 Friedel pairs
Primary atom site location: structure-invariant direct methodsFlack parameter: 0.43 (3)
Crystal data top
[Cu(C2H3O2)2(C9H7N3)(H2O)]V = 744.8 (3) Å3
Mr = 356.82Z = 2
Monoclinic, PcMo Kα radiation
a = 9.154 (2) ŵ = 1.49 mm1
b = 7.9940 (19) ÅT = 298 K
c = 10.590 (2) Å0.12 × 0.10 × 0.10 mm
β = 106.040 (3)°
Data collection top
Bruker SMART APEX CCD
diffractometer
2305 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2003)
2226 reflections with I > 2σ(I)
Tmin = 0.841, Tmax = 0.865Rint = 0.028
3778 measured reflectionsθmax = 25.5°
Refinement top
R[F2 > 2σ(F2)] = 0.050H-atom parameters constrained
wR(F2) = 0.118Δρmax = 1.20 e Å3
S = 1.10Δρmin = 0.57 e Å3
2305 reflectionsAbsolute structure: Flack (1983), 912 Friedel pairs
203 parametersFlack parameter: 0.43 (3)
2 restraints
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
Cu10.61030 (11)0.52089 (7)0.66628 (10)0.0291 (2)
N10.1787 (6)0.3833 (6)0.1934 (5)0.0305 (12)
N20.4051 (5)0.4089 (6)0.6244 (4)0.0268 (11)
N30.2208 (7)0.2714 (9)0.7028 (5)0.0482 (16)
O10.5280 (5)0.7024 (5)0.5469 (4)0.0314 (10)
O20.4417 (8)0.8581 (8)0.6826 (5)0.0735 (19)
O30.7014 (5)0.3218 (5)0.7628 (4)0.0334 (10)
O40.7659 (6)0.2455 (7)0.5853 (4)0.0545 (14)
O50.5716 (6)0.6364 (6)0.8582 (4)0.0468 (12)
H5A0.65200.63620.91660.070*
H5B0.51930.72020.83420.070*
C10.1278 (8)0.3318 (7)0.0925 (6)0.0324 (14)
H10.19420.32950.00840.039*
C20.0175 (9)0.2835 (9)0.1108 (6)0.0374 (16)
H20.04870.24760.03880.045*
C30.1209 (9)0.2859 (8)0.2328 (6)0.0370 (16)
H30.22190.25580.24420.044*
C40.0683 (7)0.3352 (7)0.3387 (6)0.0266 (13)
C50.0823 (7)0.3815 (7)0.3133 (6)0.0268 (13)
H50.11840.41310.38380.032*
C60.3104 (7)0.4091 (7)0.5014 (6)0.0277 (13)
H60.34160.45890.43380.033*
C70.1690 (7)0.3374 (7)0.4744 (6)0.0264 (12)
C80.1251 (8)0.2725 (8)0.5788 (6)0.0377 (15)
H80.02780.22840.56430.045*
C90.3576 (8)0.3358 (8)0.7159 (6)0.0348 (15)
H90.42670.32810.79870.042*
C100.4699 (8)0.8334 (8)0.5766 (5)0.0347 (15)
C110.4311 (13)0.9693 (10)0.4751 (9)0.070 (3)
H11A0.40481.06930.51400.105*
H11B0.34650.93460.40400.105*
H11C0.51720.99090.44240.105*
C120.7641 (8)0.2209 (9)0.6993 (6)0.0362 (14)
C130.8361 (11)0.0699 (10)0.7730 (8)0.063 (2)
H13A0.93960.09460.81940.095*
H13B0.83370.02020.71250.095*
H13C0.78140.03790.83450.095*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cu10.0200 (3)0.0287 (3)0.0328 (3)0.0013 (5)0.0025 (2)0.0095 (5)
N10.025 (3)0.032 (3)0.029 (3)0.001 (2)0.003 (2)0.003 (2)
N20.018 (3)0.031 (2)0.030 (3)0.003 (2)0.005 (2)0.001 (2)
N30.029 (4)0.075 (4)0.039 (3)0.011 (3)0.006 (3)0.008 (3)
O10.034 (3)0.032 (2)0.025 (2)0.0038 (18)0.0027 (18)0.0034 (17)
O20.083 (5)0.091 (5)0.049 (3)0.036 (4)0.023 (3)0.002 (3)
O30.028 (3)0.036 (2)0.033 (2)0.0060 (18)0.0029 (19)0.0076 (18)
O40.057 (4)0.072 (3)0.032 (3)0.004 (3)0.009 (2)0.002 (2)
O50.048 (3)0.052 (3)0.044 (3)0.004 (2)0.019 (2)0.012 (2)
C10.037 (4)0.040 (3)0.020 (3)0.005 (3)0.006 (3)0.006 (2)
C20.031 (4)0.056 (4)0.029 (3)0.003 (3)0.015 (3)0.007 (3)
C30.034 (4)0.047 (4)0.035 (3)0.003 (3)0.019 (3)0.003 (3)
C40.017 (3)0.026 (3)0.033 (3)0.002 (2)0.002 (2)0.002 (2)
C50.026 (3)0.028 (3)0.025 (3)0.004 (2)0.005 (2)0.007 (2)
C60.022 (3)0.033 (3)0.026 (3)0.000 (2)0.003 (2)0.002 (2)
C70.021 (3)0.031 (3)0.026 (3)0.004 (2)0.005 (2)0.002 (2)
C80.017 (3)0.055 (4)0.038 (3)0.005 (3)0.003 (3)0.002 (3)
C90.031 (4)0.042 (4)0.028 (3)0.000 (3)0.003 (3)0.000 (3)
C100.035 (4)0.044 (3)0.023 (3)0.000 (3)0.005 (3)0.006 (2)
C110.084 (7)0.041 (4)0.073 (6)0.009 (4)0.002 (5)0.012 (4)
C120.023 (3)0.053 (4)0.028 (3)0.004 (3)0.001 (3)0.003 (3)
C130.074 (6)0.046 (4)0.063 (5)0.022 (4)0.008 (4)0.004 (4)
Geometric parameters (Å, °) top
Cu1—O11.935 (4)C2—C31.375 (9)
Cu1—O31.950 (4)C2—H20.9300
Cu1—N22.016 (5)C3—C41.395 (9)
Cu1—N1i2.023 (5)C3—H30.9300
Cu1—O52.347 (4)C4—C51.380 (8)
N1—C51.332 (7)C4—C71.478 (7)
N1—C11.343 (8)C5—H50.9300
N1—Cu1ii2.023 (5)C6—C71.372 (8)
N2—C91.306 (8)C6—H60.9300
N2—C61.350 (7)C7—C81.378 (9)
N3—C91.325 (9)C8—H80.9300
N3—C81.362 (8)C9—H90.9300
O1—C101.253 (7)C10—C111.500 (10)
O2—C101.236 (8)C11—H11A0.9600
O3—C121.283 (8)C11—H11B0.9600
O4—C121.228 (8)C11—H11C0.9600
O5—H5A0.8200C12—C131.488 (10)
O5—H5B0.8218C13—H13A0.9600
C1—C21.346 (10)C13—H13B0.9600
C1—H10.9300C13—H13C0.9600
O1—Cu1—O3170.9 (2)N1—C5—C4123.5 (6)
O1—Cu1—N291.05 (19)N1—C5—H5118.3
O3—Cu1—N289.44 (19)C4—C5—H5118.3
O1—Cu1—N1i89.60 (19)N2—C6—C7121.2 (6)
O3—Cu1—N1i88.9 (2)N2—C6—H6119.4
N2—Cu1—N1i173.7 (2)C7—C6—H6119.4
O1—Cu1—O598.41 (17)C6—C7—C8117.3 (5)
O3—Cu1—O590.70 (18)C6—C7—C4120.4 (5)
N2—Cu1—O590.64 (19)C8—C7—C4122.3 (5)
N1i—Cu1—O595.44 (19)N3—C8—C7121.5 (6)
C5—N1—C1118.1 (5)N3—C8—H8119.2
C5—N1—Cu1ii119.6 (4)C7—C8—H8119.2
C1—N1—Cu1ii122.1 (4)N2—C9—N3126.5 (6)
C9—N2—C6117.4 (5)N2—C9—H9116.8
C9—N2—Cu1121.1 (4)N3—C9—H9116.8
C6—N2—Cu1121.5 (4)O2—C10—O1124.8 (6)
C9—N3—C8115.9 (6)O2—C10—C11117.9 (7)
C10—O1—Cu1125.3 (4)O1—C10—C11117.3 (6)
C12—O3—Cu1115.3 (4)C10—C11—H11A109.5
Cu1—O5—H5A109.5C10—C11—H11B109.5
Cu1—O5—H5B105.5H11A—C11—H11B109.5
H5A—O5—H5B124.0C10—C11—H11C109.5
N1—C1—C2121.3 (6)H11A—C11—H11C109.5
N1—C1—H1119.3H11B—C11—H11C109.5
C2—C1—H1119.3O4—C12—O3123.0 (6)
C1—C2—C3121.8 (7)O4—C12—C13121.4 (7)
C1—C2—H2119.1O3—C12—C13115.6 (6)
C3—C2—H2119.1C12—C13—H13A109.5
C2—C3—C4117.3 (7)C12—C13—H13B109.5
C2—C3—H3121.4H13A—C13—H13B109.5
C4—C3—H3121.4C12—C13—H13C109.5
C5—C4—C3117.9 (5)H13A—C13—H13C109.5
C5—C4—C7120.5 (5)H13B—C13—H13C109.5
C3—C4—C7121.6 (5)
O1—Cu1—N2—C9140.6 (5)C1—N1—C5—C42.4 (8)
O3—Cu1—N2—C948.5 (5)Cu1ii—N1—C5—C4172.9 (4)
N1i—Cu1—N2—C9123.5 (18)C3—C4—C5—N10.8 (9)
O5—Cu1—N2—C942.2 (5)C7—C4—C5—N1179.5 (5)
O1—Cu1—N2—C638.1 (4)C9—N2—C6—C70.9 (8)
O3—Cu1—N2—C6132.8 (4)Cu1—N2—C6—C7177.9 (4)
N1i—Cu1—N2—C658 (2)N2—C6—C7—C83.0 (8)
O5—Cu1—N2—C6136.5 (4)N2—C6—C7—C4178.5 (5)
O3—Cu1—O1—C10178.3 (11)C5—C4—C7—C6132.9 (6)
N2—Cu1—O1—C1088.7 (5)C3—C4—C7—C647.5 (8)
N1i—Cu1—O1—C1097.5 (5)C5—C4—C7—C845.5 (8)
O5—Cu1—O1—C102.1 (5)C3—C4—C7—C8134.1 (6)
O1—Cu1—O3—C125.4 (16)C9—N3—C8—C70.2 (10)
N2—Cu1—O3—C1298.5 (5)C6—C7—C8—N33.4 (9)
N1i—Cu1—O3—C1275.4 (5)C4—C7—C8—N3178.2 (6)
O5—Cu1—O3—C12170.9 (4)C6—N2—C9—N35.1 (10)
C5—N1—C1—C21.7 (9)Cu1—N2—C9—N3173.6 (6)
Cu1ii—N1—C1—C2173.5 (5)C8—N3—C9—N24.8 (10)
N1—C1—C2—C30.6 (11)Cu1—O1—C10—O28.3 (10)
C1—C2—C3—C42.1 (11)Cu1—O1—C10—C11172.2 (5)
C2—C3—C4—C51.4 (9)Cu1—O3—C12—O40.8 (9)
C2—C3—C4—C7178.2 (6)Cu1—O3—C12—C13179.0 (5)
Symmetry codes: (i) x+1, −y+1, z+1/2; (ii) x−1, −y+1, z−1/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
O5—H5A···O4iii0.822.042.734 (7)143.
O5—H5B···O20.821.922.606 (7)141.
Symmetry codes: (iii) x, −y+1, z+1/2.
Table 1
Hydrogen-bond geometry (Å, °)
top
D—H···AD—HH···AD···AD—H···A
O5—H5A···O4i0.822.042.734 (7)143.
O5—H5B···O20.821.922.606 (7)141.
Symmetry codes: (i) x, −y+1, z+1/2.
Acknowledgements top

We are grateful for financial support from the National Natural Science Foundation of China (grant No. 30970298), and we are also thankful for financial support from the Foundation of Shandong province (No. J11LF27) and the Foundation of Yantai City (No. 2011076).

references
References top

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