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A novel CdII metal–organic framework, [Cd(C3H2O4)(NH3)]n, was synthesized by liquid diffusion conducted in the presence of ammonia. The CdII atom has seven-coordinate O6N penta­gonal–bipyramidal geometry. Six CdII centers are joined by six malonate ligands to form an S6-symmetric [Cd6(malon­ate)6] metallomacrocycle, which is further extended through a side-on chelating malonate ligand to form a three-dimensional network. Topologically, each CdII center is connected to four others to yield an infinite three-periodic four-coordinated SOD (sodalite) network with point symbol {42·64}. The overall network structure in the crystal is maintained and stabilized by the presence of N—H...O hydrogen bonds.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270112003277/fa3269sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270112003277/fa3269Isup2.hkl
Contains datablock I

mol

MDL mol file https://doi.org/10.1107/S0108270112003277/fa3269Isup3.mol
Supplementary material

CCDC reference: 873874

Comment top

Numerous functional crystalline solids based on coordination bonds, hydrogen bonding and other secondary interactions have been designed and synthesized in the field of crystal engineering (Evans & Lin, 2002; Chen et al., 2010; Leong & Vittal, 2011; Sun et al., 2011). There still remain many challenges to overcome in reaching the goal of tailor-made solid-state materials owing to the fact that structure prediction and synthetic control are often subverted by a host of factors, including weak noncovalent interactions, ligand geometry, the nature of the metal ion, pH value, temperature and solvent (Sun et al., 2010). Malonate has been used widely in the preparation of transition metal and rare earth metal–organic frameworks (MOFs), exhibiting diverse coordination modes such as monodentate bridging or bidentate chelating or bridging (Li et al., 1997; Ruiz-Pérez et al., 2000; Shen et al., 2000; Zhang et al., 2000). Although diverse cadmium malonate MOFs with one and two aqua ligands have been documented (Post & Trotter, 1974; Chung et al., 1995), cadmium malonate MOFs with NH3 have not previously been observed, possibly because of the comparatively weak Cd—N coordination bond and the volatile nature of NH3. Based on our previous work (Sun et al., 2009; Dai et al., 2008) on transition metal polycarboxylate MOFs with or without auxiliary ligands, we undertook a preparation with malonic acid and 1,3,5-tris(1H-imidazol-1-yl)benzene as mixed ligands and surprisingly obtained the title three-dimensional MOF based on an S6-symmetric [Cd6(malonate)6] metallomacrocycle. The description of the three-dimensional network can be simplified to that of a 4-connected uninodal net with a zeolite SOD (sodalite) topology.

The asymmetric unit of poly[ammine-µ3-malonato-cadmium(II)], (I), contains one crystallographically independent CdII center, one malonate ligand and one coordinated NH3 molecule. As shown in Fig. 1, the Cd1 atom is seven-coordinated by six O atoms of three different symmetry-related malonate ligands and one terminal NH3 molecule, with pentagonal–bipyramidal geometry. The Cd1—N1 (ammonia) bond length is 2.2577 (19) Å, and the Cd1—O distances vary from 2.2856 (14) for the axial O1i to 2.5841 (14) Å for Cd1—O1, giving an average Cd—O distance of 2.3977 (14) Å [Table 1; symmetry code: (i) y - 1/3, -x + y + 1/3, -z + 1/3]. These are within the ranges found for similar Cd-based MOFs (Liu et al., 2008). Each malonate ligand is involved in chelating three symmetry-related CdII ions, and each CdII ion is coordinated by three malonate ligands, two of which chelate two symmetry-related CdII ions through O1/O2 and O3/O4, forming four-membered rings with O—Cd1—O bite angles of 52.71 (5) and 53.12 (5)°, respectively. The third malonate unit ligates another CdII to form a distorted boat-like Cd1—O1i—C1i—C2i—C3i—O4i six-membered ring with a larger bite angle of 81.83 (5)°. Interestingly, six CdII ions are linked by 12 chelating carboxylate groups of six malonate ligands to form a [Cd6(malonate)6] metallomacrocycle (Fig. 2a) located at a site of 3 symmetry. The distance between N1 and N1vi [symmetry code: (vi) -x + 2, -y + 2, -z] within one metallomacrocycle is 8.612 (4) Å (Fig. 2b) and the void at the center of the metallomacrocycle is 78 Å3 in volume. Six terminal NH3 molecules point toward the center of the metallomacrocycle. The side-on chelating ligand plays an important role in joining the [Cd6(malonate)6] metallomacrocycles into the resulting three-dimensional network, which is reinforced by hydrogen bonds formed by terminal NH3 molecules and the carboxylate groups of malonate ligands above and below the metallomacrocycle (Table 2).

Based on the deconstruction viewpoint (O'Keeffe & Yaghi, 2012), the secondary building units (SBUs) of the three-dimensional network are CdO6N and the malonate ligand (Fig. 3a), from which truncated octahedral subunits are constructed when the malonate ligands are regarded as linkers between the metal centers (Fig. 3b). Each truncated octahedral cage has six square faces and eight hexagonal faces, which are all shared with neighboring cages. The overall network of (I) has the zeolite SOD topology (Baerlocher et al., 2007; Fig. 3c) with point symbol {42.64} as indicated by the program TOPOS (Blatov, 2006), which means that there are two four-membered and four six-membered rings in the 4-connected vertex (Delgado-Friedrichs & O'Keeffe, 2005). Although many zeolite-type MOFs, or so-called zeolitic imidazolate frameworks (ZIFs), have been constructed from simple and angular imidazole-based linkers with divalent and tetrahedral metal ions (Huang et al., 2006; Hayashi et al., 2007; Zhang & Chen 2006; Yamamoto et al., 2003), carboxylate-based zeolite-type MOFs are still rare, which may be due to the diverse coordination modes of carboxylate as compared to the monoanionic imidazolate.

Related literature top

For related literature, see: Baerlocher et al. (2007) Blatov (2006); Chen et al. (2010); Chung et al. (1995); Dai et al. (2008); Delgado-Friedrichs & O'Keeffe (2005); Evans & Lin (2002); Hayashi et al. (2007); Huang et al. (2006); Leong & Vittal (2011); Li et al. (1997); Liu et al. (2008); O'Keeffe & Yaghi (2012); Post & Trotter (1974); Ruiz-Pérez, Sanchiz, Hernandez Molina, Lloret & Julve (2000); Shen et al. (2000); Sun et al. (2009, 2010, 2011); Yamamoto et al. (2003); Zhang & Chen (2006); Zhang et al. (2000).

Experimental top

A mixture of Cd(NO3)2.4H2O (31 mg, 0.1 mmol) and malonic acid (10 mg, 0.1 mmol) was dissolved in dimethylformamide–water (4 ml, 1:1v/v) in the presence of ammonia (1 ml, 14 M) in a test tube. This solution was carefully layered with dimethylformamide (2 ml). Finally, a methanol solution (3 ml) of 1,3,5-tris(1H-imidazol-1-yl)benzene (28 mg, 0.1 mmol) was carefully layered on top of the dimethylformamide solvent. The mixture was capped and allowed to stand at room temperature. Colorless crystals of (I) formed at the solvent interface afetr 1 week at ambient temperature (ca 60% yield). Analysis calculated for C3H5CdNO4: C 15.57, H 2.18, N 6.05%; found: C 15.69, H 2.41, N 5.78%. Although the 1,3,5-tris(1H-imidazol-1-yl)benzene is not present in the crystal, it plays an important role in the formation of (I). When it is not present in the upper solution, no crystalline product was formed.

Refinement top

The H atoms of malonate were placed geometrically and were allowed to ride on their parent atoms, with C—H = 0.97 Å and Uiso(H) = 1.2Ueq(C). The positions of the ammine H atoms were located in difference maps and refned with the N—H distances restrained to 0.89 (2) Å, and the H···H distances restrained to be similar with an s.u. of 0.04 Å and with Uiso(H) = 1.5Ueq(N).

Computing details top

Data collection: APEX2 (Bruker,2005); cell refinement: APEX2 (Bruker,2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2008); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top
[Figure 1] Fig. 1. The structure of (I), showing the atom-numbering scheme and the coordination environment around the CdII centers. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii. [Symmetry codes: (i) y - 1/3, -x + y + 1/3, -z + 1/3; (ii) x - y + 1, x, -z.]
[Figure 2] Fig. 2. (a) Ball-and-stick and (b) space-filling views of the S6-symmetric [Cd6(malonate)6] metallomacrocycle. (Color key in the electronic version of the paper: Cd purple, C gray, O red, N blue and H cyan.)
[Figure 3] Fig. 3. (a) A schematic representation of the truncated octahedron (CdO6N polyhedra are shaded in blue in the electronic version of the paper), (b) a simplified truncated octahedron and (c) the topological SOD net.
poly[ammine-µ3-malonato-cadmium(II)] top
Crystal data top
[Cd(C3H2O4)(NH3)]Dx = 2.315 Mg m3
Mr = 231.48Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3Cell parameters from 4821 reflections
Hall symbol: -R 3θ = 4.5–60.8°
a = 17.3662 (8) ŵ = 3.23 mm1
c = 11.4425 (10) ÅT = 298 K
V = 2988.6 (3) Å3Block, colorless
Z = 180.10 × 0.08 × 0.08 mm
F(000) = 1980
Data collection top
Bruker SMART APEXII CCD
diffractometer
1317 independent reflections
Radiation source: fine-focus sealed tube1281 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.020
/w and /f scansθmax = 26.0°, θmin = 2.4°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 2121
Tmin = 0.738, Tmax = 0.782k = 2119
5110 measured reflectionsl = 1114
Refinement top
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) = 0.035 w = 1/[σ2(Fo2) + (0.0121P)2 + 4.9121P]
where P = (Fo2 + 2Fc2)/3
S = 1.13(Δ/σ)max = 0.002
1317 reflectionsΔρmax = 0.53 e Å3
92 parametersΔρmin = 0.29 e Å3
6 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.00123 (5)
Crystal data top
[Cd(C3H2O4)(NH3)]Z = 18
Mr = 231.48Mo Kα radiation
Trigonal, R3µ = 3.23 mm1
a = 17.3662 (8) ÅT = 298 K
c = 11.4425 (10) Å0.10 × 0.08 × 0.08 mm
V = 2988.6 (3) Å3
Data collection top
Bruker SMART APEXII CCD
diffractometer
1317 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
1281 reflections with I > 2σ(I)
Tmin = 0.738, Tmax = 0.782Rint = 0.020
5110 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0146 restraints
wR(F2) = 0.035H atoms treated by a mixture of independent and constrained refinement
S = 1.13Δρmax = 0.53 e Å3
1317 reflectionsΔρmin = 0.29 e Å3
92 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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*/Ueq
Cd10.600383 (9)0.677758 (10)0.136161 (12)0.02606 (8)
C10.52347 (13)0.76754 (13)0.02606 (17)0.0250 (4)
C20.48023 (14)0.80950 (13)0.04513 (19)0.0298 (4)
H2A0.45460.77470.11540.036*
H2B0.43250.80850.00000.036*
C30.54621 (13)0.90444 (14)0.07877 (17)0.0259 (4)
N10.73894 (13)0.78882 (13)0.09437 (17)0.0342 (4)
H1C0.7576 (18)0.7832 (18)0.026 (2)0.051*
H1B0.7755 (16)0.7936 (18)0.1506 (18)0.051*
H1A0.7392 (18)0.8395 (14)0.094 (2)0.051*
O10.55164 (10)0.79595 (9)0.12742 (12)0.0307 (3)
O20.52947 (11)0.70485 (10)0.01798 (13)0.0338 (3)
O30.56182 (12)0.92514 (10)0.18358 (13)0.0392 (4)
O40.58409 (10)0.96143 (10)0.00090 (12)0.0329 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cd10.02820 (10)0.03050 (11)0.02098 (10)0.01580 (7)0.00183 (5)0.00163 (5)
C10.0233 (9)0.0212 (9)0.0265 (9)0.0081 (8)0.0026 (7)0.0037 (8)
C20.0277 (10)0.0272 (10)0.0329 (11)0.0125 (9)0.0075 (8)0.0010 (8)
C30.0289 (10)0.0297 (10)0.0249 (10)0.0188 (9)0.0019 (8)0.0019 (8)
N10.0339 (10)0.0373 (10)0.0279 (9)0.0151 (9)0.0005 (8)0.0031 (8)
O10.0411 (8)0.0302 (7)0.0249 (7)0.0208 (7)0.0040 (6)0.0005 (6)
O20.0458 (9)0.0310 (8)0.0307 (8)0.0237 (7)0.0038 (6)0.0037 (6)
O30.0538 (10)0.0394 (9)0.0225 (8)0.0219 (8)0.0008 (7)0.0029 (6)
O40.0407 (9)0.0258 (7)0.0244 (7)0.0107 (7)0.0014 (6)0.0012 (6)
Geometric parameters (Å, º) top
Cd1—N12.2577 (19)C1—C21.518 (3)
Cd1—O1i2.2856 (14)C2—C31.513 (3)
Cd1—O4i2.3081 (14)C2—H2A0.9700
Cd1—O22.3299 (15)C2—H2B0.9700
Cd1—O4ii2.4258 (14)C3—O31.242 (2)
Cd1—O3ii2.4525 (16)C3—O41.262 (2)
Cd1—O12.5841 (14)N1—H1C0.87 (3)
C1—O21.250 (2)N1—H1B0.879 (13)
C1—O11.260 (2)N1—H1A0.878 (16)
N1—Cd1—O1i170.71 (6)C3—C2—C1111.87 (16)
N1—Cd1—O4i89.62 (6)C3—C2—H2A109.2
O1i—Cd1—O4i81.83 (5)C1—C2—H2A109.2
N1—Cd1—O296.45 (6)C3—C2—H2B109.2
O1i—Cd1—O287.71 (5)C1—C2—H2B109.2
O4i—Cd1—O2138.80 (5)H2A—C2—H2B107.9
N1—Cd1—O4ii88.67 (6)O3—C3—O4121.18 (19)
O1i—Cd1—O4ii99.96 (5)O3—C3—C2119.84 (18)
O4i—Cd1—O4ii135.38 (5)O4—C3—C2118.98 (17)
O2—Cd1—O4ii85.62 (5)Cd1—N1—H1C113.1 (19)
N1—Cd1—O3ii98.43 (7)Cd1—N1—H1B109.7 (19)
O1i—Cd1—O3ii84.22 (6)H1C—N1—H1B112 (2)
O4i—Cd1—O3ii83.15 (5)Cd1—N1—H1A109.0 (19)
O2—Cd1—O3ii135.40 (5)H1C—N1—H1A107 (2)
O4ii—Cd1—O3ii53.12 (5)H1B—N1—H1A105 (2)
N1—Cd1—O186.89 (6)C1—O1—Cd1iii125.69 (13)
O1i—Cd1—O189.06 (7)C1—O1—Cd186.66 (11)
O4i—Cd1—O187.22 (5)Cd1iii—O1—Cd1141.45 (6)
O2—Cd1—O152.71 (5)C1—O2—Cd198.82 (13)
O4ii—Cd1—O1137.14 (5)C3—O3—Cd1iv92.36 (13)
O3ii—Cd1—O1168.94 (5)C3—O4—Cd1iii126.79 (13)
O2—C1—O1121.81 (19)C3—O4—Cd1iv93.11 (12)
O2—C1—C2118.56 (18)Cd1iii—O4—Cd1iv136.24 (7)
O1—C1—C2119.63 (17)
Symmetry codes: (i) y1/3, x+y+1/3, z+1/3; (ii) xy+1, x, z; (iii) xy+2/3, x+1/3, z+1/3; (iv) y, x+y+1, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1C···O3v0.87 (3)2.19 (3)3.043 (2)166 (3)
N1—H1B···O2vi0.88 (1)2.17 (1)3.033 (2)167 (2)
N1—H1A···O3vii0.88 (2)2.33 (2)3.188 (3)164 (2)
Symmetry codes: (v) x+4/3, y+5/3, z1/3; (vi) x+y+2/3, x+4/3, z+1/3; (vii) y+5/3, xy+4/3, z+1/3.

Experimental details

Crystal data
Chemical formula[Cd(C3H2O4)(NH3)]
Mr231.48
Crystal system, space groupTrigonal, R3
Temperature (K)298
a, c (Å)17.3662 (8), 11.4425 (10)
V3)2988.6 (3)
Z18
Radiation typeMo Kα
µ (mm1)3.23
Crystal size (mm)0.10 × 0.08 × 0.08
Data collection
DiffractometerBruker SMART APEXII CCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 1996)
Tmin, Tmax0.738, 0.782
No. of measured, independent and
observed [I > 2σ(I)] reflections
5110, 1317, 1281
Rint0.020
(sin θ/λ)max1)0.617
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.014, 0.035, 1.13
No. of reflections1317
No. of parameters92
No. of restraints6
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.53, 0.29

Computer programs: APEX2 (Bruker,2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2008), publCIF (Westrip, 2010).

Selected geometric parameters (Å, º) top
Cd1—N12.2577 (19)Cd1—O4ii2.4258 (14)
Cd1—O1i2.2856 (14)Cd1—O3ii2.4525 (16)
Cd1—O4i2.3081 (14)Cd1—O12.5841 (14)
Cd1—O22.3299 (15)
N1—Cd1—O1i170.71 (6)O1i—Cd1—O3ii84.22 (6)
N1—Cd1—O4i89.62 (6)O4i—Cd1—O3ii83.15 (5)
O1i—Cd1—O4i81.83 (5)O2—Cd1—O3ii135.40 (5)
N1—Cd1—O296.45 (6)O4ii—Cd1—O3ii53.12 (5)
O1i—Cd1—O287.71 (5)N1—Cd1—O186.89 (6)
O4i—Cd1—O2138.80 (5)O1i—Cd1—O189.06 (7)
N1—Cd1—O4ii88.67 (6)O4i—Cd1—O187.22 (5)
O1i—Cd1—O4ii99.96 (5)O2—Cd1—O152.71 (5)
O4i—Cd1—O4ii135.38 (5)O4ii—Cd1—O1137.14 (5)
O2—Cd1—O4ii85.62 (5)O3ii—Cd1—O1168.94 (5)
N1—Cd1—O3ii98.43 (7)
Symmetry codes: (i) y1/3, x+y+1/3, z+1/3; (ii) xy+1, x, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1C···O3iii0.87 (3)2.19 (3)3.043 (2)166 (3)
N1—H1B···O2iv0.879 (13)2.171 (14)3.033 (2)167 (2)
N1—H1A···O3v0.878 (16)2.334 (18)3.188 (3)164 (2)
Symmetry codes: (iii) x+4/3, y+5/3, z1/3; (iv) x+y+2/3, x+4/3, z+1/3; (v) y+5/3, xy+4/3, z+1/3.
 

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