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Acta Crystallogr Sect E Struct Rep Online. 2008 May 1; 64(Pt 5): m649–m650.
Published online 2008 April 10. doi:  10.1107/S1600536808009380
PMCID: PMC2961229

Poly[aqua­(μ2-oxalato)(4-oxidopyri­din­ium)erbium(II)]

Abstract

The title complex, [Er(C5H5NO)(C2O4)(H2O)]n, is a new erbium polymer based on oxalate and 4-oxidopyridinium ligands. The ErII center is coordinated by six O atoms from three oxalate ligands, one O atom from a 4-oxidopyridinium ligand and one water mol­ecule, and displays a distorted square-anti­prismatic coordination geometry. The oxalate ligands are both chelating and bridging, and link ErII ions, forming Er–oxalate layers in which the attached water and 4-oxidopyridinium units point alternately up and down. A mirror plane passes through the Er atom, one C, the oxide O and two oxalate O atoms. The layers are assembled into a three-dimensional supra­molecular network via inter­molecular hydrogen bonding and π–π stacking inter­actions [centroid–centroid distances of 3.587 (2) Å between parallel pyridinium rings]. Both the water mol­ecule and the 4-oxidopyridinium ligand are disordered over two sites in a 1:1 ratio.

Related literature

For related literature, see: Yaghi et al. (1998 [triangle], 2003 [triangle]); Serre et al. (2004 [triangle]); James (2003 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0m649-scheme1.jpg

Experimental

Crystal data

  • [Er(C5H5NO)(C2O4)(H2O)]
  • M r = 412.41
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m649-efi1.jpg
  • a = 16.8649 (2) Å
  • b = 11.1863 (2) Å
  • c = 6.5152 (1) Å
  • β = 112.213 (1)°
  • V = 1137.91 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 7.41 mm−1
  • T = 296 (2) K
  • 0.21 × 0.19 × 0.13 mm

Data collection

  • Bruker APEXII area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.241, T max = 0.392
  • 7274 measured reflections
  • 1365 independent reflections
  • 1341 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.014
  • wR(F 2) = 0.036
  • S = 1.16
  • 1365 reflections
  • 105 parameters
  • 39 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.53 e Å−3
  • Δρmin = −0.88 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT (Bruker, 2004 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808009380/zl2097sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808009380/zl2097Isup2.hkl

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

Acknowledgments

The authors thank Guang Dong Ocean University for supporting this study.

supplementary crystallographic information

Comment

The use of multifunctional organic linker molecules to polymerize metal centers into open-framework materials has led to the development of a rich field of chemistry (Yaghi et al., 1998, 2003; Serre et al., 2004; James, 2003) owing to the potential applications of these materials in catalysis, separation, gas storage and molecular recognition. Among such novel open-framework materials, lanthanide oxalates are particularly noteworthy. The wide variety of coordination modes of the oxalate anion permits the use of metal-oxalate units as excellent building blocks to construct a great diversity of frameworks ranging from discrete oligomeric entities to one-, two- and three-dimensional networks. Recently, we obtained the title erbium polymer (I), and its crystal structure is reported here.

The ErII centre in the title compound exhibits a distorted square-antiprismatic coordination geometry, defined by six O atoms from three oxalate ligands, one O atom from the 4-oxidopyridinium ligand and one water molecule (Fig. 1). The oxalate ligands exhibit bidentate O atoms and link to the ErII ions in a bridging mode to adjacent metal centres with Er—Er distances of 6.153 (2) Å and 6.112 (3) Å, respectively, thus forming Er-oxalate layers with the attached water and the 4-oxidopyridinium units that are alternatingly pointing up and down (Fig. 2). The layers are assembled into a three-dimensional supramolecular network via intermolecular O—H···O and N—H···O hydrogen bonding interactions (Table 1) involving the coordinated water molecules, N-protonated 4-hydroxypyridine, the hydroxy O atoms and the oxalate O atoms. They are also stabilized by π-π stacking interactions with centroid to centroid distances of 3.587 (2)A% between parallel pyridinium rings of neighboring complexes (at -x, y, 1 -z). The coordinated water molecule and the 4-oxidopyridinium ligands are located close to a mirror plane perpendicular to the b-axis of the unit cell and are disordered across this plane in a one to one ratio. As stated above the water molecules are engaged in hydrogen bonding to the hydroxide O atom O1 and to oxalate atom O2 (Table 1), and the orientation of the hydrogen O—H···O bond is equivalent but opposite for the two different disordered moieties, thus causing the disorder observed for the water molecule. The hydrogen bond formed by the 4-oxidopyridinium moiety is directed to either of the two symmetry equivalent oxalate oxygen atoms O4 (Table 1), and formation of either of the two H bonds is again responsible for the presence of the disorder observed.

Experimental

A mixture of Er2O3 (0.5 mmol), oxalic acid (1 mmol), 4-hydroxypyridine (1 mmol) and H2O (10 ml) was placed in a 23 ml Teflon reactor, which was heated to 433 K for three days and then cooled to room temperature at a rate of 10 K h-1. The crystals obtained were washed with water and dryed in air.

Refinement

In the initial refinement with disorder not taken into account both the water molecule and the 4-oxidopyridinium moiety showed significantly elongated thermal ellipsoids indicating disorder, and they were thus refined as being disordered over two positions across a crystallographic mirror plane perpendicular to the b-axis. The ADPs of the disordered atoms were restrained to be close to isotropic and those of equivalent atoms were set to be identical. Carbon-bound H atoms were placed in calculated positions and were treated as riding on the parent C atoms with C—H = 0.93 Å, N—H = 0.86 Å and with Uiso(H) = 1.2 Ueq(C, N); Water H atoms were tentatively located in difference Fourier maps and were refined with distance restraints of O–H = 0.85 Å and H···H = 1.39 Å, each within a standard deviation of 0.01 Å, and with Uiso(H) = 1.5 Ueq(O).

Figures

Fig. 1.
The structure of the title compound, showing the atom-numbering scheme and displacement ellipsoids drawn at the 30% probability level.
Fig. 2.
A layer view of (I). Hydrogen bonds are depicted as broken lines.

Crystal data

[Er(C5H5NO)(C2O4)(H2O)]F000 = 776
Mr = 412.41Dx = 2.407 Mg m3
Monoclinic, C2/mMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2yCell parameters from 8000 reflections
a = 16.8649 (2) Åθ = 1.7–26.0º
b = 11.1863 (2) ŵ = 7.41 mm1
c = 6.51520 (10) ÅT = 296 (2) K
β = 112.2130 (10)ºBlock, white
V = 1137.91 (3) Å30.21 × 0.19 × 0.13 mm
Z = 4

Data collection

Bruker APEXII area-detector diffractometer1365 independent reflections
Radiation source: fine-focus sealed tube1341 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.022
T = 296(2) Kθmax = 27.5º
[var phi] and ω scansθmin = 2.2º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −21→18
Tmin = 0.241, Tmax = 0.392k = −14→14
7274 measured reflectionsl = −8→8

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.014H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.036  w = 1/[σ2(Fo2) + (0.019P)2 + 1.5595P] where P = (Fo2 + 2Fc2)/3
S = 1.16(Δ/σ)max = 0.001
1365 reflectionsΔρmax = 0.53 e Å3
105 parametersΔρmin = −0.87 e Å3
39 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods

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*/UeqOcc. (<1)
N1−0.02721 (14)0.4755 (4)0.2392 (5)0.0325 (18)0.50
H6−0.08150.47010.20560.039*0.50
C10.0218 (3)0.3724 (4)0.2667 (9)0.0358 (13)0.50
H1−0.00410.29770.24870.043*0.50
C20.1096 (3)0.3811 (8)0.3210 (9)0.0381 (10)0.50
H20.14250.31210.33940.046*0.50
C30.14844 (16)0.4927 (10)0.3478 (5)0.0326 (13)0.50
C40.0994 (4)0.5958 (8)0.3203 (9)0.0381 (10)0.50
H40.12540.67050.33830.046*0.50
C50.0116 (4)0.5871 (4)0.2660 (9)0.0358 (13)0.50
H5−0.02120.65610.24760.043*0.50
O1W0.3241 (2)0.4753 (8)−0.1619 (6)0.040 (3)0.50
H1W0.358 (4)0.438 (6)−0.200 (10)0.060*0.50
H2W0.291 (4)0.506 (8)−0.276 (7)0.060*0.50
C60.20541 (15)0.2749 (2)−0.0746 (4)0.0252 (5)
C70.4856 (2)0.50000.5987 (5)0.0212 (6)
Er10.311393 (8)0.50000.17883 (2)0.01752 (6)
O10.23010 (16)0.50000.3883 (4)0.0347 (6)
O20.40635 (16)0.50000.5514 (4)0.0313 (6)
O30.54305 (16)0.50000.7871 (4)0.0324 (6)
O40.19303 (11)0.38280 (16)−0.0507 (3)0.0313 (4)
O50.15399 (12)0.20337 (17)−0.2053 (3)0.0338 (4)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0174 (18)0.056 (6)0.0245 (17)−0.0017 (19)0.0082 (14)−0.0025 (18)
C10.0264 (18)0.052 (4)0.0305 (15)−0.0077 (17)0.0121 (13)−0.0001 (17)
C20.0235 (17)0.059 (3)0.0322 (15)−0.011 (2)0.0107 (13)0.005 (2)
C30.0204 (19)0.062 (4)0.0147 (15)0.008 (5)0.0055 (14)−0.008 (5)
C40.0235 (17)0.059 (3)0.0322 (15)−0.011 (2)0.0107 (13)0.005 (2)
C50.0264 (18)0.052 (4)0.0305 (15)−0.0077 (17)0.0121 (13)−0.0001 (17)
O1W0.0155 (15)0.089 (9)0.0155 (13)0.001 (2)0.0049 (11)0.002 (2)
C60.0150 (12)0.0301 (11)0.0257 (12)0.0024 (9)0.0021 (10)−0.0033 (9)
C70.0120 (15)0.0322 (16)0.0177 (14)0.0000.0036 (12)0.000
Er10.00977 (9)0.02597 (9)0.01457 (8)0.0000.00206 (6)0.000
O10.0134 (12)0.0683 (19)0.0206 (12)0.0000.0044 (10)0.000
O20.0111 (11)0.0639 (18)0.0177 (11)0.0000.0041 (9)0.000
O30.0122 (12)0.0645 (18)0.0186 (12)0.0000.0038 (10)0.000
O40.0161 (9)0.0284 (8)0.0392 (10)0.0039 (7)−0.0011 (8)−0.0073 (7)
O50.0187 (9)0.0307 (9)0.0374 (10)0.0035 (8)−0.0058 (7)−0.0064 (8)

Geometric parameters (Å, °)

N1—C11.3900C6—O51.249 (3)
N1—C51.3900C6—C6i1.553 (5)
N1—H60.8600C7—O31.243 (4)
C1—C21.3900C7—O21.253 (4)
C1—H10.9300C7—C7ii1.537 (6)
C2—C31.3900Er1—O12.271 (3)
C2—H20.9300Er1—O1Wiii2.326 (3)
C3—O11.303 (3)Er1—O5i2.3388 (19)
C3—C41.3900Er1—O5iv2.3388 (19)
C4—C51.3900Er1—O22.349 (2)
C4—H40.9300Er1—O3ii2.380 (2)
C5—H50.9300Er1—O42.3839 (17)
O1W—Er12.326 (3)Er1—O4iii2.3839 (17)
O1W—H1W0.818 (10)O1—C3iii1.303 (4)
O1W—H2W0.818 (10)O3—Er1ii2.380 (2)
C6—O41.245 (3)O5—Er1i2.3388 (19)
C1—N1—C5120.0O1W—Er1—O5iv94.3 (2)
C1—N1—H6120.0O5i—Er1—O5iv153.17 (9)
C5—N1—H6120.0O1—Er1—O273.12 (9)
C2—C1—N1120.0O1Wiii—Er1—O2135.51 (11)
C2—C1—H1120.0O1W—Er1—O2135.51 (11)
N1—C1—H1120.0O5i—Er1—O282.54 (5)
C1—C2—C3120.0O5iv—Er1—O282.54 (5)
C1—C2—H2120.0O1—Er1—O3ii141.24 (9)
C3—C2—H2120.0O1Wiii—Er1—O3ii67.96 (11)
O1—C3—C4120.4 (7)O1W—Er1—O3ii67.96 (11)
O1—C3—C2119.5 (7)O5i—Er1—O3ii76.89 (5)
C4—C3—C2120.0O5iv—Er1—O3ii76.89 (5)
C5—C4—C3120.0O2—Er1—O3ii68.12 (8)
C5—C4—H4120.0O1—Er1—O479.89 (7)
C3—C4—H4120.0O1Wiii—Er1—O479.87 (16)
C4—C5—N1120.0O1W—Er1—O472.16 (15)
C4—C5—H5120.0O5i—Er1—O468.77 (6)
N1—C5—H5120.0O5iv—Er1—O4135.04 (6)
Er1—O1W—H1W133 (5)O2—Er1—O4136.92 (6)
Er1—O1W—H2W123 (4)O3ii—Er1—O4130.40 (6)
H1W—O1W—H2W104.2 (17)O1—Er1—O4iii79.89 (7)
O4—C6—O5126.9 (2)O1Wiii—Er1—O4iii72.16 (15)
O4—C6—C6i116.0 (3)O1W—Er1—O4iii79.87 (16)
O5—C6—C6i117.1 (3)O5i—Er1—O4iii135.04 (6)
O3—C7—O2127.1 (3)O5iv—Er1—O4iii68.77 (6)
O3—C7—C7ii116.8 (4)O2—Er1—O4iii136.92 (6)
O2—C7—C7ii116.0 (4)O3ii—Er1—O4iii130.40 (6)
O1—Er1—O1Wiii150.24 (12)O4—Er1—O4iii66.72 (8)
O1—Er1—O1W150.24 (12)C3—O1—Er1135.2 (2)
O1Wiii—Er1—O1W13.6 (5)C3iii—O1—Er1135.2 (2)
O1—Er1—O5i98.41 (5)C7—O2—Er1120.1 (2)
O1Wiii—Er1—O5i94.3 (2)C7—O3—Er1ii118.9 (2)
O1W—Er1—O5i81.0 (2)C6—O4—Er1118.12 (15)
O1—Er1—O5iv98.41 (5)C6—O5—Er1i118.91 (16)
O1Wiii—Er1—O5iv81.0 (2)

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

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1W—H2W···O1v0.818 (10)2.03 (4)2.769 (4)149 (8)
O1W—H1W···O2v0.818 (10)2.18 (6)2.729 (4)124 (6)
N1—H6···O4vi0.862.413.041 (3)130
N1—H6···O4vii0.862.022.794 (3)150

Symmetry codes: (v) x, y, z−1; (vi) −x, −y+1, −z; (vii) −x, y, −z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: ZL2097).

References

  • Bruker (2004). APEX2 and SAINT Bruker AXS Inc, Madison, Wisconsin, USA.
  • James, S. L. (2003). Chem. Soc. Rev.32, 276–288. [PubMed]
  • Serre, C., Millange, F., Thouvenot, C., Gardant, N., Pelle, F. & Ferey, G. (2004). J. Mater. Chem.14, 1540–1543.
  • Sheldrick, G. M. (1996). SADABS University of Göttingen, Germany.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Yaghi, O. M., Li, H. L., Davis, C., Richardson, D. & Groy, T. L. (1998). Acc. Chem. Res.31, 474–484.
  • Yaghi, O. M., O’Keeffe, M., Ockwig, N. W., Chae, H. K., Eddaoudi, M. & Kim, J. (2003). Nature (London), 423, 705–714. [PubMed]

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