metal-organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

Poly[hexa­aqua­tri-μ-malonato-didysprosium(III)]

aSchool of Chemistry and Environment, South China Normal University, Guangzhou 510006, People's Republic of China
*Correspondence e-mail: zhqfang77@yahoo.com.cn

(Received 24 April 2008; accepted 27 May 2008; online 7 June 2008)

The title compound, [Dy2(C3H2O4)3(H2O)6]n, forms a coordination polymeric structure comprising hydrated dysprosium ions and malonate ligands. In the asymmetric unit, there are one dysprosium ion, one and a half malonate ligands, and three water mol­ecules. Each DyIII atom is coordinated by six O atoms from four malonate ligands and by three water mol­ecules, and displays a tricapped trigonal–prismatic coordination geometry. The malonate ligands adopt two types of coordination mode, linking dysprosium centres to form a three-dimensional coordination polymer. The extensive network of hydrogen bonds in this polymer enhances the structural stability.

Related literature

For related literature, see: Iglesias et al. (2003[Iglesias, S., Castillo, O., Luque, A. & Romaan, P. (2003). Inorg. Chim. Acta, 349, 273-278.]); Kim et al. (2003[Kim, J. C., Jo, H., Lough, A. J., Cho, J., Lee, U. & Pyun, S. Y. (2003). Inorg. Chem. Commun. 6, 474-477.]); Moulton & Zaworotko (2001[Moulton, B. & Zaworotko, M. J. (2001). Chem. Rev. 101, 1629-1658.]).

[Scheme 1]

Experimental

Crystal data
  • [Dy2(C3H2O4)3(H2O)6]

  • Mr = 739.23

  • Monoclinic, C 2/c

  • a = 17.1805 (2) Å

  • b = 12.3124 (1) Å

  • c = 11.1541 (1) Å

  • β = 127.52 (2)°

  • V = 1871.4 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 8.02 mm−1

  • T = 296 (2) K

  • 0.11 × 0.10 × 0.08 mm

Data collection
  • Bruker APEXII area-detector diffractometer

  • Absorption correction: multi-scan (APEX2; Bruker, 2004[Bruker (2004). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.435, Tmax = 0.529

  • 10051 measured reflections

  • 2136 independent reflections

  • 2001 reflections with I > 2σ(I)

  • Rint = 0.023

Refinement
  • R[F2 > 2σ(F2)] = 0.019

  • wR(F2) = 0.053

  • S = 1.07

  • 2136 reflections

  • 132 parameters

  • 10 restraints

  • H-atom parameters constrained

  • Δρmax = 0.91 e Å−3

  • Δρmin = −0.51 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1W—H1W⋯O5i 0.82 2.04 2.854 (4) 172
O1W—H2W⋯O3ii 0.81 1.94 2.729 (4) 165
O2W—H3W⋯O3iii 0.82 1.95 2.761 (4) 170
O3W—H6W⋯O4iii 0.81 2.02 2.802 (4) 160
O3W—H6W⋯O3iii 0.81 2.59 3.291 (4) 144
O3W—H5W⋯O2iv 0.81 1.96 2.738 (4) 161
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]; (ii) [-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z]; (iii) [x, -y, z+{\script{1\over 2}}]; (iv) [-x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1].

Data collection: APEX2 (Bruker, 2004[Bruker (2004). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: APEX2; data reduction: APEX2; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: PLATON (Spek, 2003[Spek, A. L. (2003). J. Appl. Cryst. 36, 7-13.]) and SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXL97.

Supporting information


Comment top

Molecular self-assembly of supramolecular architectures has received much attention during recent decades (Kim et al., 2003; Iglesias et al., 2003; Moulton & Zaworotko, 2001). The structures and properties of such systems depend on the coordination and geometric preferences of both the central metals ions and bridging building blocks as well as the influence of weaker non-covalent interactions, such as hydrogen bonds and π-π stacking interactions. Recently, we obtained the title compound, (I), by the hydrothermal reaction of Dy(NO3)3 with malonic acid in alkaline aqueous solution.

As illustrated in Fig. 1, in the asymmetric unit of complex (I), each DyIII centre is coordinated by six carboxyl O atoms from four malonate ligands, and three water molecules. The two unique malonate ligands act as two types of chelating and bridging modes: one lies on an inversion centre and uses each carboxylate group to bond to two DyIII ions; one uses three carboxyl O atoms to coordinate to two DyIII ions involving a six-membered chelate ring. The adjacent Dy···Dy separations are 4.303 (3), 6.600 (1) and 6.982 (2) Å respectively. The ligands link dysprosium centres to form a three-dimensional coordination polymer which is also stabilized by the extensive network of hydrogen bonding interactions (Fig. 2; Table 1).

Related literature top

For related literature, see: Iglesias et al. (2003); Kim et al. (2003); Moulton & Zaworotko (2001).

Experimental top

A mixture of Dy(NO3)3 (0.1 mmol), malonato acid (0.15 mmol), NaOH (0.1 mmol), water (10 ml) was stirred vigorously for 20 min and then sealed in a Teflon-lined stainless-steel autoclave (20 ml, capacity). The autoclave was heated to and maintained at 433 K for 7 days, and then cooled to room temperature at 5 K h-1 to obtain the colorless block crystals.

Refinement top

Water H atoms were tentatively located in difference Fourier maps and were refined with distance restraints of O–H = 0.82 Å and H···H = 1.30 Å, and with Uiso(H) = 1.5 Ueq(O), and then were treated as riding mode. Carbon-bound H atoms were placed at calculated positions and were treated as riding on the parent C atoms with C—H = 0.97 Å, and with Uiso(H) = 1.2 Ueq(C).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: APEX2 (Bruker, 2004); data reduction: APEX2 (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003) and SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top
[Figure 1] Fig. 1. The molecular structure showing the atomic-numbering scheme. Displacement ellipsoids drawn at the 30% probability level. H atoms have been omitted for clarity. [Symmetry codes: (i) 1-x, y, 3/2-y; (ii) 1/2-x, y-1/2, 1/2-z; (iii) 1/2-x, 1/2-y, 1-z]
[Figure 2] Fig. 2. The molecular packing showing the intra/intermolecular hydrogen bonding interactions as broken lines.
Poly[hexaaquatri-µ-malonato-didysprosium(III)] top
Crystal data top
[Dy2(C3H2O4)3(H2O)6]F(000) = 1392
Mr = 739.23Dx = 2.624 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 6377 reflections
a = 17.1805 (2) Åθ = 1.7–28.0°
b = 12.3124 (1) ŵ = 8.02 mm1
c = 11.1541 (1) ÅT = 296 K
β = 127.52 (2)°Block, colorless
V = 1871.4 (5) Å30.11 × 0.10 × 0.08 mm
Z = 4
Data collection top
Bruker APEXII area-detector
diffractometer
2136 independent reflections
Radiation source: fine-focus sealed tube2001 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.023
ϕ and ω scansθmax = 27.5°, θmin = 2.2°
Absorption correction: multi-scan
(APEX2; Bruker, 2004)
h = 2220
Tmin = 0.435, Tmax = 0.529k = 1515
10051 measured reflectionsl = 1214
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)] = 0.020Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.053H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0241P)2 + 12.727P]
where P = (Fo2 + 2Fc2)/3
2136 reflections(Δ/σ)max = 0.001
132 parametersΔρmax = 0.91 e Å3
10 restraintsΔρmin = 0.51 e Å3
Crystal data top
[Dy2(C3H2O4)3(H2O)6]V = 1871.4 (5) Å3
Mr = 739.23Z = 4
Monoclinic, C2/cMo Kα radiation
a = 17.1805 (2) ŵ = 8.02 mm1
b = 12.3124 (1) ÅT = 296 K
c = 11.1541 (1) Å0.11 × 0.10 × 0.08 mm
β = 127.52 (2)°
Data collection top
Bruker APEXII area-detector
diffractometer
2136 independent reflections
Absorption correction: multi-scan
(APEX2; Bruker, 2004)
2001 reflections with I > 2σ(I)
Tmin = 0.435, Tmax = 0.529Rint = 0.023
10051 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.02010 restraints
wR(F2) = 0.053H-atom parameters constrained
S = 1.07 w = 1/[σ2(Fo2) + (0.0241P)2 + 12.727P]
where P = (Fo2 + 2Fc2)/3
2136 reflectionsΔρmax = 0.91 e Å3
132 parametersΔρmin = 0.51 e Å3
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*/UeqOcc. (<1)
C10.3116 (3)0.3839 (3)0.2419 (4)0.0139 (7)
C20.3805 (3)0.3285 (3)0.2198 (5)0.0174 (7)
H2A0.44620.33250.31480.021*
H2B0.38080.37040.14640.021*
C30.3607 (3)0.2110 (3)0.1686 (4)0.0137 (7)
C40.4246 (2)0.2993 (3)0.6243 (4)0.0119 (7)
C50.50000.3747 (4)0.75000.0135 (10)
H5A0.47030.42050.78290.016*0.50
H5B0.52970.42050.71710.016*0.50
Dy10.283235 (12)0.148077 (13)0.379865 (19)0.01461 (7)
O10.2989 (2)0.4832 (2)0.2144 (4)0.0268 (6)
O20.2741 (2)0.3315 (2)0.2918 (3)0.0165 (5)
O30.3717 (2)0.1844 (2)0.0723 (3)0.0256 (6)
O40.3355 (2)0.14437 (19)0.2259 (3)0.0200 (6)
O50.44917 (18)0.2424 (2)0.5591 (3)0.0192 (5)
O60.34060 (17)0.2909 (2)0.5918 (3)0.0144 (5)
O1W0.1257 (2)0.1789 (2)0.1179 (3)0.0226 (6)
H1W0.07850.20290.11000.034*
H2W0.13690.22300.07560.034*
O2W0.4141 (3)0.0048 (3)0.4897 (5)0.0435 (10)
H3W0.40880.05120.52380.065*
H4W0.47000.02530.55380.065*
O3W0.3194 (2)0.0640 (2)0.6116 (4)0.0322 (7)
H6W0.32940.00030.63330.048*
H5W0.30190.08890.65930.048*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0179 (17)0.0087 (15)0.0121 (17)0.0002 (13)0.0077 (15)0.0012 (13)
C20.0267 (19)0.0119 (16)0.024 (2)0.0038 (14)0.0211 (18)0.0010 (14)
C30.0166 (17)0.0121 (16)0.0163 (18)0.0007 (13)0.0119 (15)0.0004 (13)
C40.0099 (15)0.0139 (16)0.0082 (16)0.0002 (12)0.0037 (14)0.0026 (13)
C50.010 (2)0.011 (2)0.014 (2)0.0000.005 (2)0.000
Dy10.01901 (10)0.01230 (10)0.01759 (11)0.00036 (6)0.01376 (8)0.00016 (6)
O10.0366 (17)0.0102 (12)0.0372 (18)0.0042 (11)0.0244 (15)0.0062 (12)
O20.0249 (14)0.0116 (12)0.0203 (14)0.0034 (10)0.0175 (12)0.0027 (10)
O30.0474 (18)0.0187 (14)0.0288 (16)0.0005 (13)0.0326 (16)0.0014 (12)
O40.0366 (16)0.0100 (12)0.0276 (16)0.0013 (10)0.0270 (14)0.0012 (10)
O50.0137 (12)0.0264 (14)0.0183 (13)0.0008 (10)0.0102 (11)0.0068 (11)
O60.0104 (11)0.0196 (13)0.0131 (12)0.0015 (9)0.0072 (10)0.0016 (10)
O1W0.0206 (14)0.0300 (15)0.0198 (15)0.0003 (12)0.0137 (12)0.0065 (12)
O2W0.0431 (19)0.0277 (17)0.085 (3)0.0166 (15)0.052 (2)0.0281 (18)
O3W0.063 (2)0.0176 (14)0.0415 (19)0.0177 (14)0.0450 (18)0.0154 (13)
Geometric parameters (Å, º) top
C1—O11.247 (4)Dy1—O42.375 (3)
C1—O21.256 (4)Dy1—O22.430 (2)
C1—C21.512 (5)Dy1—O6iii2.452 (2)
C2—C31.516 (5)Dy1—O3W2.487 (3)
C2—H2A0.9700Dy1—O2W2.513 (3)
C2—H2B0.9700Dy1—O1W2.524 (3)
C3—O31.243 (4)Dy1—O52.555 (3)
C3—O41.266 (4)Dy1—O62.610 (2)
C4—O51.254 (4)O1W—H1W0.8155
C4—O61.260 (4)O1W—H2W0.8146
C4—C51.514 (4)O2W—H3W0.8184
C5—C4i1.514 (4)O2W—H4W0.8133
C5—H5A0.9700O3W—H6W0.8149
C5—H5B0.9700O3W—H5W0.8144
Dy1—O1ii2.326 (3)
O1—C1—O2123.5 (3)O4—Dy1—O1W77.10 (10)
O1—C1—C2116.0 (3)O2—Dy1—O1W68.42 (9)
O2—C1—C2120.4 (3)O6iii—Dy1—O1W72.58 (9)
C1—C2—C3118.3 (3)O3W—Dy1—O1W132.74 (10)
C1—C2—H2A107.7O2W—Dy1—O1W132.85 (12)
C3—C2—H2A107.7O1ii—Dy1—O5146.20 (10)
C1—C2—H2B107.7O4—Dy1—O580.87 (9)
C3—C2—H2B107.7O2—Dy1—O570.15 (9)
H2A—C2—H2B107.1O6iii—Dy1—O5113.70 (8)
O3—C3—O4123.0 (3)O3W—Dy1—O585.58 (10)
O3—C3—C2117.3 (3)O2W—Dy1—O572.37 (10)
O4—C3—C2119.7 (3)O1W—Dy1—O5137.36 (9)
O5—C4—O6121.2 (3)O1ii—Dy1—O6141.99 (9)
O5—C4—C5118.7 (3)O4—Dy1—O6124.57 (8)
O6—C4—C5120.1 (3)O2—Dy1—O668.62 (8)
C4—C5—C4i104.4 (4)O6iii—Dy1—O663.60 (9)
C4—C5—H5A110.9O3W—Dy1—O667.78 (9)
C4i—C5—H5A110.9O2W—Dy1—O6107.42 (11)
C4—C5—H5B110.9O1W—Dy1—O6119.61 (9)
C4i—C5—H5B110.9O5—Dy1—O650.15 (8)
H5A—C5—H5B108.9C1—O1—Dy1iv159.0 (3)
O1ii—Dy1—O492.80 (10)C1—O2—Dy1137.0 (2)
O1ii—Dy1—O2139.15 (10)C3—O4—Dy1138.4 (2)
O4—Dy1—O271.67 (8)C4—O5—Dy195.7 (2)
O1ii—Dy1—O6iii89.46 (9)C4—O6—Dy1iii150.4 (2)
O4—Dy1—O6iii147.09 (9)C4—O6—Dy192.9 (2)
O2—Dy1—O6iii85.38 (8)Dy1iii—O6—Dy1116.40 (9)
O1ii—Dy1—O3W78.76 (11)Dy1—O1W—H1W118.3
O4—Dy1—O3W141.16 (9)Dy1—O1W—H2W107.9
O2—Dy1—O3W136.14 (9)H1W—O1W—H2W105.4
O6iii—Dy1—O3W71.36 (9)Dy1—O2W—H3W119.8
O1ii—Dy1—O2W73.98 (11)Dy1—O2W—H4W115.9
O4—Dy1—O2W73.66 (10)H3W—O2W—H4W105.1
O2—Dy1—O2W131.94 (9)Dy1—O3W—H6W126.0
O6iii—Dy1—O2W137.86 (9)Dy1—O3W—H5W124.4
O3W—Dy1—O2W67.55 (10)H6W—O3W—H5W105.5
O1ii—Dy1—O1W71.37 (10)
Symmetry codes: (i) x+1, y, z+3/2; (ii) x+1/2, y1/2, z+1/2; (iii) x+1/2, y+1/2, z+1; (iv) x+1/2, y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1W···O5v0.822.042.854 (4)172
O1W—H2W···O3vi0.811.942.729 (4)165
O2W—H3W···O3vii0.821.952.761 (4)170
O3W—H6W···O4vii0.812.022.802 (4)160
O3W—H6W···O3vii0.812.593.291 (4)144
O3W—H5W···O2iii0.811.962.738 (4)161
Symmetry codes: (iii) x+1/2, y+1/2, z+1; (v) x1/2, y+1/2, z1/2; (vi) x+1/2, y+1/2, z; (vii) x, y, z+1/2.

Experimental details

Crystal data
Chemical formula[Dy2(C3H2O4)3(H2O)6]
Mr739.23
Crystal system, space groupMonoclinic, C2/c
Temperature (K)296
a, b, c (Å)17.1805 (2), 12.3124 (1), 11.1541 (1)
β (°) 127.52 (2)
V3)1871.4 (5)
Z4
Radiation typeMo Kα
µ (mm1)8.02
Crystal size (mm)0.11 × 0.10 × 0.08
Data collection
DiffractometerBruker APEXII area-detector
diffractometer
Absorption correctionMulti-scan
(APEX2; Bruker, 2004)
Tmin, Tmax0.435, 0.529
No. of measured, independent and
observed [I > 2σ(I)] reflections
10051, 2136, 2001
Rint0.023
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.020, 0.053, 1.07
No. of reflections2136
No. of parameters132
No. of restraints10
H-atom treatmentH-atom parameters constrained
w = 1/[σ2(Fo2) + (0.0241P)2 + 12.727P]
where P = (Fo2 + 2Fc2)/3
Δρmax, Δρmin (e Å3)0.91, 0.51

Computer programs: APEX2 (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2003) and SHELXTL (Sheldrick, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1W···O5i0.822.042.854 (4)172.1
O1W—H2W···O3ii0.811.942.729 (4)164.5
O2W—H3W···O3iii0.821.952.761 (4)169.7
O3W—H6W···O4iii0.812.022.802 (4)160.0
O3W—H6W···O3iii0.812.593.291 (4)144.4
O3W—H5W···O2iv0.811.962.738 (4)161.0
Symmetry codes: (i) x1/2, y+1/2, z1/2; (ii) x+1/2, y+1/2, z; (iii) x, y, z+1/2; (iv) x+1/2, y+1/2, z+1.
 

Acknowledgements

The authors acknowledge South China Normal University for supporting this work.

References

First citationBruker (2004). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationIglesias, S., Castillo, O., Luque, A. & Romaan, P. (2003). Inorg. Chim. Acta, 349, 273–278.  Web of Science CSD CrossRef CAS Google Scholar
First citationKim, J. C., Jo, H., Lough, A. J., Cho, J., Lee, U. & Pyun, S. Y. (2003). Inorg. Chem. Commun. 6, 474–477.  Web of Science CSD CrossRef CAS Google Scholar
First citationMoulton, B. & Zaworotko, M. J. (2001). Chem. Rev. 101, 1629–1658.  Web of Science CrossRef PubMed CAS Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2003). J. Appl. Cryst. 36, 7–13.  Web of Science CrossRef CAS IUCr Journals Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds