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
CCDC reference: 155836
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (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
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
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.
The water H atoms were placed in calculated positions (Nardelli, 1999).
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.
aqua(malonato)cadmium(II) hydrate
top
Crystal data top
[Cd(C3H2O4)(H2O)]·H2O | Dx = 2.404 Mg m−3 |
Mr = 250.48 | Mo Kα radiation, λ = 0.71073 Å |
Tetragonal, R3 | Cell parameters from 25 reflections |
Hall symbol: -R 3 | θ = 7.5–14.5° |
a = 17.0355 (9) Å | µ = 3.13 mm−1 |
c = 12.3934 (5) Å | T = 298 K |
V = 3114.8 (3) Å3 | Block, colorless |
Z = 18 | 0.3 × 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 tube | Rint = 0.053 |
Graphite monochromator | θmax = 25.0°, θmin = 2.2° |
ω–2θ scans | h = −6→20 |
Absorption correction: ψ scan (North et al., 1968) in the WinGX suite (Farrugia, 1999) | k = −20→0 |
Tmin = 0.458, Tmax = 0.535 | l = −13→14 |
2010 measured reflections | 3 standard reflections every 120 min |
1223 independent reflections | intensity decay: 2% |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.030 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.088 | H-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 parameters | Δρmax = 0.95 e Å−3 |
0 restraints | Δρmin = −0.91 e Å−3 |
Crystal data top
[Cd(C3H2O4)(H2O)]·H2O | Z = 18 |
Mr = 250.48 | Mo Kα radiation |
Tetragonal, R3 | µ = 3.13 mm−1 |
a = 17.0355 (9) Å | T = 298 K |
c = 12.3934 (5) Å | 0.3 × 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 = 0.535 | 3 standard reflections every 120 min |
2010 measured reflections | intensity decay: 2% |
1223 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.030 | 0 restraints |
wR(F2) = 0.088 | H-atom parameters constrained |
S = 1.15 | w = 1/[σ2(Fo2) + (0.0486P)2 + 11.6164P] where P = (Fo2 + 2Fc2)/3 |
1223 reflections | Δρmax = 0.95 e Å−3 |
91 parameters | Δρmin = −0.91 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
Cd1 | 0.66521 (2) | 0.06516 (2) | 0.34972 (2) | 0.0236 (2) | |
O1 | 0.5620 (2) | 0.1044 (2) | 0.2934 (2) | 0.029 (1) | |
O2 | 0.4925 (2) | 0.1416 (2) | 0.1738 (3) | 0.029 (1) | |
O3 | 0.6968 (2) | 0.0765 (2) | 0.1689 (3) | 0.031 (1) | |
O4 | 0.6834 (2) | 0.1054 (3) | −0.0001 (3) | 0.034 (1) | |
O1w | 0.7785 (2) | 0.0309 (2) | 0.3608 (2) | 0.030 (1) | |
O2w | 0.7282 (4) | −0.1284 (3) | 0.4546 (3) | 0.063 (1) | |
C1 | 0.5606 (3) | 0.1388 (3) | 0.2041 (3) | 0.022 (1) | |
C2 | 0.6438 (3) | 0.1806 (3) | 0.1325 (4) | 0.028 (1) | |
C3 | 0.6763 (3) | 0.1167 (3) | 0.0984 (3) | 0.025 (1) | |
H1w1 | 0.7691 | −0.0144 | 0.3999 | 0.080* | |
H1w2 | 0.7939 | 0.0226 | 0.2981 | 0.080* | |
H2w1 | 0.7434 | −0.1582 | 0.4121 | 0.080* | |
H2w2 | 0.7528 | −0.1244 | 0.5161 | 0.080* | |
H2a | 0.6305 | 0.2043 | 0.0683 | 0.034* | |
H2b | 0.6926 | 0.2313 | 0.1705 | 0.034* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Cd1 | 0.0294 (2) | 0.0246 (2) | 0.0190 (2) | 0.0151 (2) | −0.0024 (1) | −0.0002 (1) |
O1 | 0.029 (2) | 0.038 (2) | 0.024 (2) | 0.021 (2) | 0.003 (1) | 0.005 (1) |
O2 | 0.026 (2) | 0.041 (2) | 0.024 (2) | 0.021 (2) | 0.001 (1) | 0.000 (1) |
O3 | 0.039 (2) | 0.040 (2) | 0.023 (2) | 0.027 (2) | 0.000 (1) | 0.001 (1) |
O4 | 0.042 (2) | 0.047 (2) | 0.022 (2) | 0.029 (2) | 0.007 (1) | 0.005 (2) |
O1w | 0.038 (2) | 0.032 (2) | 0.024 (2) | 0.022 (2) | −0.001 (1) | −0.003 (1) |
O2w | 0.117 (4) | 0.062 (3) | 0.032 (2) | 0.061 (3) | 0.011 (2) | 0.009 (2) |
C1 | 0.025 (2) | 0.020 (2) | 0.021 (2) | 0.012 (2) | −0.002 (2) | −0.006 (2) |
C2 | 0.027 (2) | 0.025 (2) | 0.032 (2) | 0.013 (2) | 0.010 (2) | 0.008 (2) |
C3 | 0.018 (2) | 0.027 (2) | 0.025 (2) | 0.009 (2) | 0.003 (2) | 0.002 (2) |
Geometric parameters (Å, º) top
Cd1—O1 | 2.280 (3) | O4—C3 | 1.252 (5) |
Cd1—O1i | 2.543 (3) | C1—C2 | 1.514 (6) |
Cd1—O2i | 2.302 (3) | C2—C3 | 1.508 (6) |
Cd1—O3 | 2.290 (3) | O1w—H1w1 | 0.855 |
Cd1—O3ii | 2.527 (3) | O1w—H1w2 | 0.855 |
Cd1—O4ii | 2.323 (4) | O2w—H2w1 | 0.857 |
Cd1—O1w | 2.283 (3) | O2w—H2w2 | 0.856 |
O1—C1 | 1.258 (5) | C2—H2a | 0.970 |
O2—C1 | 1.244 (5) | C2—H2b | 0.970 |
O3—C3 | 1.263 (5) | | |
| | | |
O1—Cd1—O1i | 93.7 (2) | Cd1—O1—Cd1iii | 143.0 (1) |
O1—Cd1—O2i | 83.8 (1) | C1—O2—Cd1iii | 98.6 (3) |
O1—Cd1—O3 | 81.9 (1) | C3—O3—Cd1 | 127.2 (3) |
O1—Cd1—O3ii | 105.9 (1) | C3—O3—Cd1iv | 87.8 (3) |
O1—Cd1—O4ii | 92.2 (1) | Cd1—O3—Cd1iv | 142.8 (2) |
O1—Cd1—O1w | 165.4 (1) | C3—O4—Cd1iv | 97.6 (3) |
O1i—Cd1—O2i | 53.2 (1) | O2—C1—O1 | 121.3 (4) |
O1i—Cd1—O3 | 89.2 (1) | O2—C1—C2 | 118.5 (4) |
O1i—Cd1—O3ii | 124.7 (1) | O1—C1—C2 | 120.2 (4) |
O1i—Cd1—O4ii | 174.1 (1) | C3—C2—C1 | 114.8 (4) |
O1i—Cd1—O1w | 85.2 (1) | O4—C3—O3 | 121.1 (4) |
O2i—Cd1—O3 | 138.6 (1) | O4—C3—C2 | 118.9 (4) |
O2i—Cd1—O3ii | 77.8 (1) | O3—C3—C2 | 120.0 (4) |
O2i—Cd1—O4ii | 127.9 (1) | Cd1—O1w—H1w1 | 117.6 |
O2i—Cd1—O1w | 106.8 (1) | Cd1—O1w—H1w2 | 110.9 |
O3—Cd1—O3ii | 143.6 (1) | H1w1—O1w—H1w2 | 107.5 |
O3—Cd1—O4ii | 91.3 (1) | H2w1—O2w—H2w2 | 108.3 |
O3—Cd1—O1w | 83.5 (1) | C3—C2—H2a | 108.6 |
O3ii—Cd1—O4ii | 53.5 (1) | C1—C2—H2a | 108.6 |
O3ii—Cd1—O1w | 86.4 (1) | C3—C2—H2b | 108.6 |
O4ii—Cd1—O1w | 89.0 (1) | C1—C2—H2b | 108.6 |
C1—O1—Cd1 | 127.0 (3) | H2a—C2—H2b | 107.5 |
C1—O1—Cd1iii | 86.9 (2) | | |
| | | |
O1w—Cd1—O1—C1 | −13.2 (7) | O2i—Cd1—O3—Cd1iv | 150.0 (2) |
O3—Cd1—O1—C1 | −16.7 (4) | O4ii—Cd1—O3—Cd1iv | −46.9 (3) |
O2i—Cd1—O1—C1 | 124.4 (4) | O3ii—Cd1—O3—Cd1iv | −33.0 (3) |
O4ii—Cd1—O1—C1 | −107.7 (4) | O1i—Cd1—O3—Cd1iv | 127.2 (3) |
O3ii—Cd1—O1—C1 | −160.3 (3) | Cd1iii—O2—C1—O1 | −2.6 (5) |
O1i—Cd1—O1—C1 | 72.0 (4) | Cd1iii—O2—C1—C2 | 179.3 (3) |
O1w—Cd1—O1—Cd1iii | 139.3 (4) | Cd1—O1—C1—O2 | 166.1 (3) |
O3—Cd1—O1—Cd1iii | 135.8 (3) | Cd1iii—O1—C1—O2 | 2.3 (4) |
O2i—Cd1—O1—Cd1iii | −83.1 (2) | Cd1—O1—C1—C2 | −15.8 (6) |
O4ii—Cd1—O1—Cd1iii | 44.8 (2) | Cd1iii—O1—C1—C2 | −179.7 (4) |
O3ii—Cd1—O1—Cd1iii | −7.8 (3) | O2—C1—C2—C3 | −122.6 (4) |
O1i—Cd1—O1—Cd1iii | −135.5 (3) | O1—C1—C2—C3 | 59.3 (6) |
O1—Cd1—O3—C3 | 18.1 (4) | Cd1iv—O4—C3—O3 | 1.4 (5) |
O1w—Cd1—O3—C3 | −161.0 (4) | Cd1iv—O4—C3—C2 | −179.5 (3) |
O2i—Cd1—O3—C3 | −52.9 (4) | Cd1—O3—C3—O4 | −167.7 (3) |
O4ii—Cd1—O3—C3 | 110.2 (4) | Cd1iv—O3—C3—O4 | −1.3 (4) |
O3ii—Cd1—O3—C3 | 124.1 (4) | Cd1—O3—C3—C2 | 13.2 (6) |
O1i—Cd1—O3—C3 | −75.7 (4) | Cd1iv—O3—C3—C2 | 179.6 (4) |
O1—Cd1—O3—Cd1iv | −139.0 (3) | C1—C2—C3—O4 | 123.3 (5) |
O1w—Cd1—O3—Cd1iv | 41.9 (3) | C1—C2—C3—O3 | −57.5 (6) |
Symmetry codes: (i) x−y+1/3, x−1/3, −z+2/3; (ii) −y+2/3, x−y−2/3, z+1/3; (iii) y+1/3, −x+y+2/3, −z+2/3; (iv) −x+y+4/3, −x+2/3, z−1/3. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1w—H1w2···O2v | 0.86 | 1.91 | 2.753 (4) | 169 |
O1w—H1w1···O2w | 0.86 | 1.84 | 2.669 (5) | 165 |
O2w—H2w1···O4v | 0.86 | 2.02 | 2.867 (6) | 170 |
O2w—H2w2···O1wvi | 0.86 | 2.22 | 2.895 (5) | 136 |
Symmetry codes: (v) y+2/3, −x+y+1/3, −z+1/3; (vi) x−y, x−1, −z+1. |
Experimental details
Crystal data |
Chemical formula | [Cd(C3H2O4)(H2O)]·H2O |
Mr | 250.48 |
Crystal system, space group | Tetragonal, R3 |
Temperature (K) | 298 |
a, c (Å) | 17.0355 (9), 12.3934 (5) |
V (Å3) | 3114.8 (3) |
Z | 18 |
Radiation type | Mo Kα |
µ (mm−1) | 3.13 |
Crystal size (mm) | 0.3 × 0.3 × 0.2 |
|
Data collection |
Diffractometer | Enraf-Nonius CAD-4 diffractometer |
Absorption correction | ψ scan (North et al., 1968) in the WinGX suite (Farrugia, 1999) |
Tmin, Tmax | 0.458, 0.535 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2010, 1223, 1123 |
Rint | 0.053 |
(sin θ/λ)max (Å−1) | 0.595 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.088, 1.15 |
No. of reflections | 1223 |
No. of parameters | 91 |
H-atom treatment | H-atom parameters constrained |
| w = 1/[σ2(Fo2) + (0.0486P)2 + 11.6164P] where P = (Fo2 + 2Fc2)/3 |
Δρmax, Δρmin (e Å−3) | 0.95, −0.91 |
Selected geometric parameters (Å, º) topCd1—O1 | 2.280 (3) | Cd1—O3ii | 2.527 (3) |
Cd1—O1i | 2.543 (3) | Cd1—O4ii | 2.323 (4) |
Cd1—O2i | 2.302 (3) | Cd1—O1w | 2.283 (3) |
Cd1—O3 | 2.290 (3) | | |
| | | |
O1—Cd1—O1i | 93.7 (2) | O2i—Cd1—O3 | 138.6 (1) |
O1—Cd1—O2i | 83.8 (1) | O2i—Cd1—O3ii | 77.8 (1) |
O1—Cd1—O3 | 81.9 (1) | O2i—Cd1—O4ii | 127.9 (1) |
O1—Cd1—O3ii | 105.9 (1) | O2i—Cd1—O1w | 106.8 (1) |
O1—Cd1—O4ii | 92.2 (1) | O3—Cd1—O3ii | 143.6 (1) |
O1—Cd1—O1w | 165.4 (1) | O3—Cd1—O4ii | 91.3 (1) |
O1i—Cd1—O2i | 53.2 (1) | O3—Cd1—O1w | 83.5 (1) |
O1i—Cd1—O3 | 89.2 (1) | O3ii—Cd1—O4ii | 53.5 (1) |
O1i—Cd1—O3ii | 124.7 (1) | O3ii—Cd1—O1w | 86.4 (1) |
O1i—Cd1—O4ii | 174.1 (1) | O4ii—Cd1—O1w | 89.0 (1) |
O1i—Cd1—O1w | 85.2 (1) | | |
Symmetry codes: (i) x−y+1/3, x−1/3, −z+2/3; (ii) −y+2/3, x−y−2/3, z+1/3. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1w—H1w2···O2iii | 0.86 | 1.91 | 2.753 (4) | 169 |
O1w—H1w1···O2w | 0.86 | 1.84 | 2.669 (5) | 165 |
O2w—H2w1···O4iii | 0.86 | 2.02 | 2.867 (6) | 170 |
O2w—H2w2···O1wiv | 0.86 | 2.22 | 2.895 (5) | 136 |
Symmetry codes: (iii) y+2/3, −x+y+1/3, −z+1/3; (iv) x−y, x−1, −z+1. |
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.