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

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 Dy^III 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.

Key indicators

• Single-crystal X-ray study
• T = 296 K
• Mean [sigma](C-C) = 0.006 Å
• R factor = 0.020
• wR factor = 0.053
• Data-to-parameter ratio = 16.2

checkCIF/PLATON results

No syntax errors found



Alert level B
PLAT222_ALERT_3_B Large Non-Solvent    H     Ueq(max)/Ueq(min) ...       4.06 Ratio

Alert level C
PLAT220_ALERT_2_C Large Non-Solvent    O     Ueq(max)/Ueq(min) ...       3.05 Ratio
PLAT417_ALERT_2_C Short Inter D-H..H-D       H4W    ..  H4W     ..       2.10 Ang.
PLAT142_ALERT_4_C su on b - Axis Small or Missing (x 100000) .....         10 Ang.
PLAT143_ALERT_4_C su on c - Axis Small or Missing (x 100000) .....         10 Ang.

Alert level G
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......         10

   0 ALERT level A = In general: serious problem
   1 ALERT level B = Potentially serious problem
   4 ALERT level C = Check and explain
   1 ALERT level G = General alerts; check

   0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   2 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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S1. Comment

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 Dy^III 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 Dy^III ions; one uses three carboxyl O atoms to coordinate to two Dy^III 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

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

S2. Experimental

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.

S3. Refinement

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 U_iso(H) = 1.5 U_eq(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 U_iso(H) = 1.2 U_eq(C).

Computing details

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

	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]
	Fig. 2. The molecular packing showing the intra/intermolecular hydrogen bonding interactions as broken lines.

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

Crystal data

[Dy2(C3H2O4)3(H2O)6]	F(000) = 1392
Mr = 739.23	Dx = 2.624 Mg m^−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 6377 reflections
a = 17.1805 (2) Å	θ = 1.7–28.0°
b = 12.3124 (1) Å	µ = 8.02 mm^−1
c = 11.1541 (1) Å	T = 296 K
β = 127.52 (2)°	Block, colorless
V = 1871.4 (5) Å^3	0.11 × 0.10 × 0.08 mm
Z = 4

Data collection

Bruker APEXII area-detector diffractometer	2136 independent reflections
Radiation source: fine-focus sealed tube	2001 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
ϕ and ω scans	θmax = 27.5°, θmin = 2.2°
Absorption correction: multi-scan (APEX2; Bruker, 2004)	h = −22→20
Tmin = 0.435, Tmax = 0.529	k = −15→15
10051 measured reflections	l = −12→14

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.020	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.053	H-atom parameters constrained
S = 1.07	w = 1/[σ^2(Fo^2) + (0.0241P)^2 + 12.727P] where P = (Fo^2 + 2Fc^2)/3
2136 reflections	(Δ/σ)max = 0.001
132 parameters	Δρmax = 0.91 e Å^−3
10 restraints	Δρmin = −0.51 e Å^−3

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
C1	0.3116 (3)	0.3839 (3)	0.2419 (4)	0.0139 (7)
C2	0.3805 (3)	0.3285 (3)	0.2198 (5)	0.0174 (7)
H2A	0.4462	0.3325	0.3148	0.021*
H2B	0.3808	0.3704	0.1464	0.021*
C3	0.3607 (3)	0.2110 (3)	0.1686 (4)	0.0137 (7)
C4	0.4246 (2)	0.2993 (3)	0.6243 (4)	0.0119 (7)
C5	0.5000	0.3747 (4)	0.7500	0.0135 (10)
H5A	0.4703	0.4205	0.7829	0.016*	0.50
H5B	0.5297	0.4205	0.7171	0.016*	0.50
Dy1	0.283235 (12)	0.148077 (13)	0.379865 (19)	0.01461 (7)
O1	0.2989 (2)	0.4832 (2)	0.2144 (4)	0.0268 (6)
O2	0.2741 (2)	0.3315 (2)	0.2918 (3)	0.0165 (5)
O3	0.3717 (2)	0.1844 (2)	0.0723 (3)	0.0256 (6)
O4	0.3355 (2)	0.14437 (19)	0.2259 (3)	0.0200 (6)
O5	0.44917 (18)	0.2424 (2)	0.5591 (3)	0.0192 (5)
O6	0.34060 (17)	0.2909 (2)	0.5918 (3)	0.0144 (5)
O1W	0.1257 (2)	0.1789 (2)	0.1179 (3)	0.0226 (6)
H1W	0.0785	0.2029	0.1100	0.034*
H2W	0.1369	0.2230	0.0756	0.034*
O2W	0.4141 (3)	0.0048 (3)	0.4897 (5)	0.0435 (10)
H3W	0.4088	−0.0512	0.5238	0.065*
H4W	0.4700	0.0253	0.5538	0.065*
O3W	0.3194 (2)	0.0640 (2)	0.6116 (4)	0.0322 (7)
H6W	0.3294	−0.0003	0.6333	0.048*
H5W	0.3019	0.0889	0.6593	0.048*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0179 (17)	0.0087 (15)	0.0121 (17)	0.0002 (13)	0.0077 (15)	−0.0012 (13)
C2	0.0267 (19)	0.0119 (16)	0.024 (2)	−0.0038 (14)	0.0211 (18)	−0.0010 (14)
C3	0.0166 (17)	0.0121 (16)	0.0163 (18)	−0.0007 (13)	0.0119 (15)	−0.0004 (13)
C4	0.0099 (15)	0.0139 (16)	0.0082 (16)	−0.0002 (12)	0.0037 (14)	0.0026 (13)
C5	0.010 (2)	0.011 (2)	0.014 (2)	0.000	0.005 (2)	0.000
Dy1	0.01901 (10)	0.01230 (10)	0.01759 (11)	−0.00036 (6)	0.01376 (8)	−0.00016 (6)
O1	0.0366 (17)	0.0102 (12)	0.0372 (18)	0.0042 (11)	0.0244 (15)	0.0062 (12)
O2	0.0249 (14)	0.0116 (12)	0.0203 (14)	0.0034 (10)	0.0175 (12)	0.0027 (10)
O3	0.0474 (18)	0.0187 (14)	0.0288 (16)	−0.0005 (13)	0.0326 (16)	−0.0014 (12)
O4	0.0366 (16)	0.0100 (12)	0.0276 (16)	−0.0013 (10)	0.0270 (14)	−0.0012 (10)
O5	0.0137 (12)	0.0264 (14)	0.0183 (13)	−0.0008 (10)	0.0102 (11)	−0.0068 (11)
O6	0.0104 (11)	0.0196 (13)	0.0131 (12)	−0.0015 (9)	0.0072 (10)	−0.0016 (10)
O1W	0.0206 (14)	0.0300 (15)	0.0198 (15)	−0.0003 (12)	0.0137 (12)	0.0065 (12)
O2W	0.0431 (19)	0.0277 (17)	0.085 (3)	0.0166 (15)	0.052 (2)	0.0281 (18)
O3W	0.063 (2)	0.0176 (14)	0.0415 (19)	0.0177 (14)	0.0450 (18)	0.0154 (13)

Geometric parameters (Å, º)

C1—O1	1.247 (4)	Dy1—O4	2.375 (3)
C1—O2	1.256 (4)	Dy1—O2	2.430 (2)
C1—C2	1.512 (5)	Dy1—O6^iii	2.452 (2)
C2—C3	1.516 (5)	Dy1—O3W	2.487 (3)
C2—H2A	0.9700	Dy1—O2W	2.513 (3)
C2—H2B	0.9700	Dy1—O1W	2.524 (3)
C3—O3	1.243 (4)	Dy1—O5	2.555 (3)
C3—O4	1.266 (4)	Dy1—O6	2.610 (2)
C4—O5	1.254 (4)	O1W—H1W	0.8155
C4—O6	1.260 (4)	O1W—H2W	0.8146
C4—C5	1.514 (4)	O2W—H3W	0.8184
C5—C4^i	1.514 (4)	O2W—H4W	0.8133
C5—H5A	0.9700	O3W—H6W	0.8149
C5—H5B	0.9700	O3W—H5W	0.8144
Dy1—O1^ii	2.326 (3)
O1—C1—O2	123.5 (3)	O4—Dy1—O1W	77.10 (10)
O1—C1—C2	116.0 (3)	O2—Dy1—O1W	68.42 (9)
O2—C1—C2	120.4 (3)	O6^iii—Dy1—O1W	72.58 (9)
C1—C2—C3	118.3 (3)	O3W—Dy1—O1W	132.74 (10)
C1—C2—H2A	107.7	O2W—Dy1—O1W	132.85 (12)
C3—C2—H2A	107.7	O1^ii—Dy1—O5	146.20 (10)
C1—C2—H2B	107.7	O4—Dy1—O5	80.87 (9)
C3—C2—H2B	107.7	O2—Dy1—O5	70.15 (9)
H2A—C2—H2B	107.1	O6^iii—Dy1—O5	113.70 (8)
O3—C3—O4	123.0 (3)	O3W—Dy1—O5	85.58 (10)
O3—C3—C2	117.3 (3)	O2W—Dy1—O5	72.37 (10)
O4—C3—C2	119.7 (3)	O1W—Dy1—O5	137.36 (9)
O5—C4—O6	121.2 (3)	O1^ii—Dy1—O6	141.99 (9)
O5—C4—C5	118.7 (3)	O4—Dy1—O6	124.57 (8)
O6—C4—C5	120.1 (3)	O2—Dy1—O6	68.62 (8)
C4—C5—C4^i	104.4 (4)	O6^iii—Dy1—O6	63.60 (9)
C4—C5—H5A	110.9	O3W—Dy1—O6	67.78 (9)
C4^i—C5—H5A	110.9	O2W—Dy1—O6	107.42 (11)
C4—C5—H5B	110.9	O1W—Dy1—O6	119.61 (9)
C4^i—C5—H5B	110.9	O5—Dy1—O6	50.15 (8)
H5A—C5—H5B	108.9	C1—O1—Dy1^iv	159.0 (3)
O1^ii—Dy1—O4	92.80 (10)	C1—O2—Dy1	137.0 (2)
O1^ii—Dy1—O2	139.15 (10)	C3—O4—Dy1	138.4 (2)
O4—Dy1—O2	71.67 (8)	C4—O5—Dy1	95.7 (2)
O1^ii—Dy1—O6^iii	89.46 (9)	C4—O6—Dy1^iii	150.4 (2)
O4—Dy1—O6^iii	147.09 (9)	C4—O6—Dy1	92.9 (2)
O2—Dy1—O6^iii	85.38 (8)	Dy1^iii—O6—Dy1	116.40 (9)
O1^ii—Dy1—O3W	78.76 (11)	Dy1—O1W—H1W	118.3
O4—Dy1—O3W	141.16 (9)	Dy1—O1W—H2W	107.9
O2—Dy1—O3W	136.14 (9)	H1W—O1W—H2W	105.4
O6^iii—Dy1—O3W	71.36 (9)	Dy1—O2W—H3W	119.8
O1^ii—Dy1—O2W	73.98 (11)	Dy1—O2W—H4W	115.9
O4—Dy1—O2W	73.66 (10)	H3W—O2W—H4W	105.1
O2—Dy1—O2W	131.94 (9)	Dy1—O3W—H6W	126.0
O6^iii—Dy1—O2W	137.86 (9)	Dy1—O3W—H5W	124.4
O3W—Dy1—O2W	67.55 (10)	H6W—O3W—H5W	105.5
O1^ii—Dy1—O1W	71.37 (10)

Symmetry codes: (i) −x+1, y, −z+3/2; (ii) −x+1/2, y−1/2, −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)

D—H···A	D—H	H···A	D···A	D—H···A
O1W—H1W···O5^v	0.82	2.04	2.854 (4)	172
O1W—H2W···O3^vi	0.81	1.94	2.729 (4)	165
O2W—H3W···O3^vii	0.82	1.95	2.761 (4)	170
O3W—H6W···O4^vii	0.81	2.02	2.802 (4)	160
O3W—H6W···O3^vii	0.81	2.59	3.291 (4)	144
O3W—H5W···O2^iii	0.81	1.96	2.738 (4)	161

Symmetry codes: (iii) −x+1/2, −y+1/2, −z+1; (v) x−1/2, −y+1/2, z−1/2; (vi) −x+1/2, −y+1/2, −z; (vii) x, −y, z+1/2.