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The Cd atom in the rhombohedral modification of aqua(malonato)­cadmium(II) hydrate, [Cd(C3H2O4)(H2O)].H2O, shows pentagonal bipyramidal coordination. The malonate group chelates to the water-coordinated Cd atom; its two carboxyl groups also chelate adjacent Cd atoms.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536800018833/cf6007sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536800018833/cf6007Isup2.hkl
Contains datablock I

CCDC reference: 155836

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C) = 0.007 Å
  • R factor = 0.030
  • wR factor = 0.088
  • Data-to-parameter ratio = 13.4

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


Yellow Alert Alert Level C:
ABSTM_02 Alert C The ratio of expected to reported Tmax/Tmin(RR) is > 1.10 Tmin and Tmax reported: 0.458 0.535 Tmin and Tmax expected: 0.405 0.535 RR = 1.130 Please check that your absorption correction is appropriate. PLAT_601 Alert C Structure contains solvent accessible VOIDS of 73.00 A   3
0 Alert Level A = Potentially serious problem
0 Alert Level B = Potential problem
2 Alert Level C = Please check

Comment top

The malonate derivatives of divalent metals provide the framework for supramolecular crystal engineering (Li et al., 1997; Ruiz-Pérez et al., 2000; Shen et al., 2000; Zhang et al., 2000) when ligands such as 2,2'-bipyridine and 4,4'-bipyridine are used as spacers. The structural diversity of divalent metal malonates arises from the low point-group symmetry of the compounds, which leads to the formation of polymorphs. The cadmium malonates are suitable models for examining the coordination of metalloproteins in saccharide-specific lectin concanavalin A (Bailey et al., 1978) and parvalbumin (Drakenberg et al., 1978; Cave et al., 1979). The mode of coordination of the carboxyl entity in the models can be established by 113Cd NMR spectroscopy (Chung et al., 1995). The starting material, cadium malonate, exists as a monohydrate (Post & Trotter, 1974) whose Cd atom is seven-coordinate, and as a dihydrate (Chung et al., 1995), in which six- and eight-coordinated atoms are present. In the title dihydrate, (I), the Cd atom is seven-coordinate; the atom is chelated by the O atoms of two carboxyl entities, as well as by one malonate dianion through its two carboxyl ends. The seventh coordination site is occupied by a water molecule.

As shown in Fig. 2, the malonate dianion links the water-coordinated cadmium ions into a three-dimensional network structure. The coordinated water molecule is hydrogen bonded to the uncoordinated water molecule [O···O = 2.669 (5) Å] and also to an adjacent carboxyl O2 atom [O···O = 2.754 (4) Å]. The uncoordinated water molecule consolidates the crystal structure by forming hydrogen bonds to another coordinated water molecule [O···O = 2.289 (5) Å] and also to an adjacent carboxyl O4 atom [O···O = 2.867 (6) Å]. The hydrogen-bonding scheme renders all four carboxyl O atoms three-coordinate.

Experimental top

The title compound separated as crystals from a cooled filtered aqueous solution of cadmium carbonate and malonic acid (1:2 molar ratio) after one month.

Refinement top

The water H atoms were placed in calculated positions (Nardelli, 1999).

Computing details top

Data collection: CAD-4 EXPRESS (Enraf-Nonius, 1994); cell refinement: CELDIM in CAD-4 Software (Enraf-Nonius, 1989); data reduction: XCAD4 (Harms, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97.

Figures top
[Figure 1] Fig. 1. Part of the structure showing the complete coordination and displacement ellipsoids at the 50% probability level.
[Figure 2] Fig. 2. The polymeric network, omitting the uncoordinated water molecules.
aqua(malonato)cadmium(II) hydrate top
Crystal data top
[Cd(C3H2O4)(H2O)]·H2ODx = 2.404 Mg m3
Mr = 250.48Mo Kα radiation, λ = 0.71073 Å
Tetragonal, R3Cell parameters from 25 reflections
Hall symbol: -R 3θ = 7.5–14.5°
a = 17.0355 (9) ŵ = 3.13 mm1
c = 12.3934 (5) ÅT = 298 K
V = 3114.8 (3) Å3Block, colorless
Z = 180.3 × 0.3 × 0.2 mm
F(000) = 2160
Data collection top
Enraf-Nonius CAD-4
diffractometer
1123 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.053
Graphite monochromatorθmax = 25.0°, θmin = 2.2°
ω–2θ scansh = 620
Absorption correction: ψ scan
(North et al., 1968) in the WinGX suite (Farrugia, 1999)
k = 200
Tmin = 0.458, Tmax = 0.535l = 1314
2010 measured reflections3 standard reflections every 120 min
1223 independent reflections intensity decay: 2%
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)] = 0.030Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.088H-atom parameters constrained
S = 1.15 w = 1/[σ2(Fo2) + (0.0486P)2 + 11.6164P]
where P = (Fo2 + 2Fc2)/3
1223 reflections(Δ/σ)max = 0.001
91 parametersΔρmax = 0.95 e Å3
0 restraintsΔρmin = 0.91 e Å3
Crystal data top
[Cd(C3H2O4)(H2O)]·H2OZ = 18
Mr = 250.48Mo Kα radiation
Tetragonal, R3µ = 3.13 mm1
a = 17.0355 (9) ÅT = 298 K
c = 12.3934 (5) Å0.3 × 0.3 × 0.2 mm
V = 3114.8 (3) Å3
Data collection top
Enraf-Nonius CAD-4
diffractometer
1123 reflections with I > 2σ(I)
Absorption correction: ψ scan
(North et al., 1968) in the WinGX suite (Farrugia, 1999)
Rint = 0.053
Tmin = 0.458, Tmax = 0.5353 standard reflections every 120 min
2010 measured reflections intensity decay: 2%
1223 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0300 restraints
wR(F2) = 0.088H-atom parameters constrained
S = 1.15 w = 1/[σ2(Fo2) + (0.0486P)2 + 11.6164P]
where P = (Fo2 + 2Fc2)/3
1223 reflectionsΔρmax = 0.95 e Å3
91 parametersΔρmin = 0.91 e Å3
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
Cd10.66521 (2)0.06516 (2)0.34972 (2)0.0236 (2)
O10.5620 (2)0.1044 (2)0.2934 (2)0.029 (1)
O20.4925 (2)0.1416 (2)0.1738 (3)0.029 (1)
O30.6968 (2)0.0765 (2)0.1689 (3)0.031 (1)
O40.6834 (2)0.1054 (3)0.0001 (3)0.034 (1)
O1w0.7785 (2)0.0309 (2)0.3608 (2)0.030 (1)
O2w0.7282 (4)0.1284 (3)0.4546 (3)0.063 (1)
C10.5606 (3)0.1388 (3)0.2041 (3)0.022 (1)
C20.6438 (3)0.1806 (3)0.1325 (4)0.028 (1)
C30.6763 (3)0.1167 (3)0.0984 (3)0.025 (1)
H1w10.76910.01440.39990.080*
H1w20.79390.02260.29810.080*
H2w10.74340.15820.41210.080*
H2w20.75280.12440.51610.080*
H2a0.63050.20430.06830.034*
H2b0.69260.23130.17050.034*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cd10.0294 (2)0.0246 (2)0.0190 (2)0.0151 (2)0.0024 (1)0.0002 (1)
O10.029 (2)0.038 (2)0.024 (2)0.021 (2)0.003 (1)0.005 (1)
O20.026 (2)0.041 (2)0.024 (2)0.021 (2)0.001 (1)0.000 (1)
O30.039 (2)0.040 (2)0.023 (2)0.027 (2)0.000 (1)0.001 (1)
O40.042 (2)0.047 (2)0.022 (2)0.029 (2)0.007 (1)0.005 (2)
O1w0.038 (2)0.032 (2)0.024 (2)0.022 (2)0.001 (1)0.003 (1)
O2w0.117 (4)0.062 (3)0.032 (2)0.061 (3)0.011 (2)0.009 (2)
C10.025 (2)0.020 (2)0.021 (2)0.012 (2)0.002 (2)0.006 (2)
C20.027 (2)0.025 (2)0.032 (2)0.013 (2)0.010 (2)0.008 (2)
C30.018 (2)0.027 (2)0.025 (2)0.009 (2)0.003 (2)0.002 (2)
Geometric parameters (Å, º) top
Cd1—O12.280 (3)O4—C31.252 (5)
Cd1—O1i2.543 (3)C1—C21.514 (6)
Cd1—O2i2.302 (3)C2—C31.508 (6)
Cd1—O32.290 (3)O1w—H1w10.855
Cd1—O3ii2.527 (3)O1w—H1w20.855
Cd1—O4ii2.323 (4)O2w—H2w10.857
Cd1—O1w2.283 (3)O2w—H2w20.856
O1—C11.258 (5)C2—H2a0.970
O2—C11.244 (5)C2—H2b0.970
O3—C31.263 (5)
O1—Cd1—O1i93.7 (2)Cd1—O1—Cd1iii143.0 (1)
O1—Cd1—O2i83.8 (1)C1—O2—Cd1iii98.6 (3)
O1—Cd1—O381.9 (1)C3—O3—Cd1127.2 (3)
O1—Cd1—O3ii105.9 (1)C3—O3—Cd1iv87.8 (3)
O1—Cd1—O4ii92.2 (1)Cd1—O3—Cd1iv142.8 (2)
O1—Cd1—O1w165.4 (1)C3—O4—Cd1iv97.6 (3)
O1i—Cd1—O2i53.2 (1)O2—C1—O1121.3 (4)
O1i—Cd1—O389.2 (1)O2—C1—C2118.5 (4)
O1i—Cd1—O3ii124.7 (1)O1—C1—C2120.2 (4)
O1i—Cd1—O4ii174.1 (1)C3—C2—C1114.8 (4)
O1i—Cd1—O1w85.2 (1)O4—C3—O3121.1 (4)
O2i—Cd1—O3138.6 (1)O4—C3—C2118.9 (4)
O2i—Cd1—O3ii77.8 (1)O3—C3—C2120.0 (4)
O2i—Cd1—O4ii127.9 (1)Cd1—O1w—H1w1117.6
O2i—Cd1—O1w106.8 (1)Cd1—O1w—H1w2110.9
O3—Cd1—O3ii143.6 (1)H1w1—O1w—H1w2107.5
O3—Cd1—O4ii91.3 (1)H2w1—O2w—H2w2108.3
O3—Cd1—O1w83.5 (1)C3—C2—H2a108.6
O3ii—Cd1—O4ii53.5 (1)C1—C2—H2a108.6
O3ii—Cd1—O1w86.4 (1)C3—C2—H2b108.6
O4ii—Cd1—O1w89.0 (1)C1—C2—H2b108.6
C1—O1—Cd1127.0 (3)H2a—C2—H2b107.5
C1—O1—Cd1iii86.9 (2)
O1w—Cd1—O1—C113.2 (7)O2i—Cd1—O3—Cd1iv150.0 (2)
O3—Cd1—O1—C116.7 (4)O4ii—Cd1—O3—Cd1iv46.9 (3)
O2i—Cd1—O1—C1124.4 (4)O3ii—Cd1—O3—Cd1iv33.0 (3)
O4ii—Cd1—O1—C1107.7 (4)O1i—Cd1—O3—Cd1iv127.2 (3)
O3ii—Cd1—O1—C1160.3 (3)Cd1iii—O2—C1—O12.6 (5)
O1i—Cd1—O1—C172.0 (4)Cd1iii—O2—C1—C2179.3 (3)
O1w—Cd1—O1—Cd1iii139.3 (4)Cd1—O1—C1—O2166.1 (3)
O3—Cd1—O1—Cd1iii135.8 (3)Cd1iii—O1—C1—O22.3 (4)
O2i—Cd1—O1—Cd1iii83.1 (2)Cd1—O1—C1—C215.8 (6)
O4ii—Cd1—O1—Cd1iii44.8 (2)Cd1iii—O1—C1—C2179.7 (4)
O3ii—Cd1—O1—Cd1iii7.8 (3)O2—C1—C2—C3122.6 (4)
O1i—Cd1—O1—Cd1iii135.5 (3)O1—C1—C2—C359.3 (6)
O1—Cd1—O3—C318.1 (4)Cd1iv—O4—C3—O31.4 (5)
O1w—Cd1—O3—C3161.0 (4)Cd1iv—O4—C3—C2179.5 (3)
O2i—Cd1—O3—C352.9 (4)Cd1—O3—C3—O4167.7 (3)
O4ii—Cd1—O3—C3110.2 (4)Cd1iv—O3—C3—O41.3 (4)
O3ii—Cd1—O3—C3124.1 (4)Cd1—O3—C3—C213.2 (6)
O1i—Cd1—O3—C375.7 (4)Cd1iv—O3—C3—C2179.6 (4)
O1—Cd1—O3—Cd1iv139.0 (3)C1—C2—C3—O4123.3 (5)
O1w—Cd1—O3—Cd1iv41.9 (3)C1—C2—C3—O357.5 (6)
Symmetry codes: (i) xy+1/3, x1/3, z+2/3; (ii) y+2/3, xy2/3, z+1/3; (iii) y+1/3, x+y+2/3, z+2/3; (iv) x+y+4/3, x+2/3, z1/3.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1w—H1w2···O2v0.861.912.753 (4)169
O1w—H1w1···O2w0.861.842.669 (5)165
O2w—H2w1···O4v0.862.022.867 (6)170
O2w—H2w2···O1wvi0.862.222.895 (5)136
Symmetry codes: (v) y+2/3, x+y+1/3, z+1/3; (vi) xy, x1, z+1.

Experimental details

Crystal data
Chemical formula[Cd(C3H2O4)(H2O)]·H2O
Mr250.48
Crystal system, space groupTetragonal, R3
Temperature (K)298
a, c (Å)17.0355 (9), 12.3934 (5)
V3)3114.8 (3)
Z18
Radiation typeMo Kα
µ (mm1)3.13
Crystal size (mm)0.3 × 0.3 × 0.2
Data collection
DiffractometerEnraf-Nonius CAD-4
diffractometer
Absorption correctionψ scan
(North et al., 1968) in the WinGX suite (Farrugia, 1999)
Tmin, Tmax0.458, 0.535
No. of measured, independent and
observed [I > 2σ(I)] reflections
2010, 1223, 1123
Rint0.053
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.030, 0.088, 1.15
No. of reflections1223
No. of parameters91
H-atom treatmentH-atom parameters constrained
w = 1/[σ2(Fo2) + (0.0486P)2 + 11.6164P]
where P = (Fo2 + 2Fc2)/3
Δρmax, Δρmin (e Å3)0.95, 0.91

Computer programs: CAD-4 EXPRESS (Enraf-Nonius, 1994), CELDIM in CAD-4 Software (Enraf-Nonius, 1989), XCAD4 (Harms, 1997), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPII (Johnson, 1976), SHELXL97.

Selected geometric parameters (Å, º) top
Cd1—O12.280 (3)Cd1—O3ii2.527 (3)
Cd1—O1i2.543 (3)Cd1—O4ii2.323 (4)
Cd1—O2i2.302 (3)Cd1—O1w2.283 (3)
Cd1—O32.290 (3)
O1—Cd1—O1i93.7 (2)O2i—Cd1—O3138.6 (1)
O1—Cd1—O2i83.8 (1)O2i—Cd1—O3ii77.8 (1)
O1—Cd1—O381.9 (1)O2i—Cd1—O4ii127.9 (1)
O1—Cd1—O3ii105.9 (1)O2i—Cd1—O1w106.8 (1)
O1—Cd1—O4ii92.2 (1)O3—Cd1—O3ii143.6 (1)
O1—Cd1—O1w165.4 (1)O3—Cd1—O4ii91.3 (1)
O1i—Cd1—O2i53.2 (1)O3—Cd1—O1w83.5 (1)
O1i—Cd1—O389.2 (1)O3ii—Cd1—O4ii53.5 (1)
O1i—Cd1—O3ii124.7 (1)O3ii—Cd1—O1w86.4 (1)
O1i—Cd1—O4ii174.1 (1)O4ii—Cd1—O1w89.0 (1)
O1i—Cd1—O1w85.2 (1)
Symmetry codes: (i) xy+1/3, x1/3, z+2/3; (ii) y+2/3, xy2/3, z+1/3.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1w—H1w2···O2iii0.861.912.753 (4)169
O1w—H1w1···O2w0.861.842.669 (5)165
O2w—H2w1···O4iii0.862.022.867 (6)170
O2w—H2w2···O1wiv0.862.222.895 (5)136
Symmetry codes: (iii) y+2/3, x+y+1/3, z+1/3; (iv) xy, x1, z+1.
 

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