Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270112003277/fa3269sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270112003277/fa3269Isup2.hkl | |
MDL mol file https://doi.org/10.1107/S0108270112003277/fa3269Isup3.mol |
CCDC reference: 873874
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).
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.
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).
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).
[Cd(C3H2O4)(NH3)] | Dx = 2.315 Mg m−3 |
Mr = 231.48 | Mo Kα radiation, λ = 0.71073 Å |
Trigonal, R3 | Cell parameters from 4821 reflections |
Hall symbol: -R 3 | θ = 4.5–60.8° |
a = 17.3662 (8) Å | µ = 3.23 mm−1 |
c = 11.4425 (10) Å | T = 298 K |
V = 2988.6 (3) Å3 | Block, colorless |
Z = 18 | 0.10 × 0.08 × 0.08 mm |
F(000) = 1980 |
Bruker SMART APEXII CCD diffractometer | 1317 independent reflections |
Radiation source: fine-focus sealed tube | 1281 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.020 |
/w and /f scans | θmax = 26.0°, θmin = 2.4° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −21→21 |
Tmin = 0.738, Tmax = 0.782 | k = −21→19 |
5110 measured reflections | l = −11→14 |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.014 | H 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 reflections | Δρmax = 0.53 e Å−3 |
92 parameters | Δρmin = −0.29 e Å−3 |
6 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.00123 (5) |
[Cd(C3H2O4)(NH3)] | Z = 18 |
Mr = 231.48 | Mo Kα radiation |
Trigonal, R3 | µ = 3.23 mm−1 |
a = 17.3662 (8) Å | T = 298 K |
c = 11.4425 (10) Å | 0.10 × 0.08 × 0.08 mm |
V = 2988.6 (3) Å3 |
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 = 0.782 | Rint = 0.020 |
5110 measured reflections |
R[F2 > 2σ(F2)] = 0.014 | 6 restraints |
wR(F2) = 0.035 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.13 | Δρmax = 0.53 e Å−3 |
1317 reflections | Δρmin = −0.29 e Å−3 |
92 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
Cd1 | 0.600383 (9) | 0.677758 (10) | 0.136161 (12) | 0.02606 (8) | |
C1 | 0.52347 (13) | 0.76754 (13) | 0.02606 (17) | 0.0250 (4) | |
C2 | 0.48023 (14) | 0.80950 (13) | −0.04513 (19) | 0.0298 (4) | |
H2A | 0.4546 | 0.7747 | −0.1154 | 0.036* | |
H2B | 0.4325 | 0.8085 | 0.0000 | 0.036* | |
C3 | 0.54621 (13) | 0.90444 (14) | −0.07877 (17) | 0.0259 (4) | |
N1 | 0.73894 (13) | 0.78882 (13) | 0.09437 (17) | 0.0342 (4) | |
H1C | 0.7576 (18) | 0.7832 (18) | 0.026 (2) | 0.051* | |
H1B | 0.7755 (16) | 0.7936 (18) | 0.1506 (18) | 0.051* | |
H1A | 0.7392 (18) | 0.8395 (14) | 0.094 (2) | 0.051* | |
O1 | 0.55164 (10) | 0.79595 (9) | 0.12742 (12) | 0.0307 (3) | |
O2 | 0.52947 (11) | 0.70485 (10) | −0.01798 (13) | 0.0338 (3) | |
O3 | 0.56182 (12) | 0.92514 (10) | −0.18358 (13) | 0.0392 (4) | |
O4 | 0.58409 (10) | 0.96143 (10) | 0.00090 (12) | 0.0329 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
Cd1 | 0.02820 (10) | 0.03050 (11) | 0.02098 (10) | 0.01580 (7) | 0.00183 (5) | 0.00163 (5) |
C1 | 0.0233 (9) | 0.0212 (9) | 0.0265 (9) | 0.0081 (8) | 0.0026 (7) | 0.0037 (8) |
C2 | 0.0277 (10) | 0.0272 (10) | 0.0329 (11) | 0.0125 (9) | −0.0075 (8) | −0.0010 (8) |
C3 | 0.0289 (10) | 0.0297 (10) | 0.0249 (10) | 0.0188 (9) | −0.0019 (8) | 0.0019 (8) |
N1 | 0.0339 (10) | 0.0373 (10) | 0.0279 (9) | 0.0151 (9) | 0.0005 (8) | −0.0031 (8) |
O1 | 0.0411 (8) | 0.0302 (7) | 0.0249 (7) | 0.0208 (7) | −0.0040 (6) | −0.0005 (6) |
O2 | 0.0458 (9) | 0.0310 (8) | 0.0307 (8) | 0.0237 (7) | −0.0038 (6) | −0.0037 (6) |
O3 | 0.0538 (10) | 0.0394 (9) | 0.0225 (8) | 0.0219 (8) | 0.0008 (7) | 0.0029 (6) |
O4 | 0.0407 (9) | 0.0258 (7) | 0.0244 (7) | 0.0107 (7) | −0.0014 (6) | 0.0012 (6) |
Cd1—N1 | 2.2577 (19) | C1—C2 | 1.518 (3) |
Cd1—O1i | 2.2856 (14) | C2—C3 | 1.513 (3) |
Cd1—O4i | 2.3081 (14) | C2—H2A | 0.9700 |
Cd1—O2 | 2.3299 (15) | C2—H2B | 0.9700 |
Cd1—O4ii | 2.4258 (14) | C3—O3 | 1.242 (2) |
Cd1—O3ii | 2.4525 (16) | C3—O4 | 1.262 (2) |
Cd1—O1 | 2.5841 (14) | N1—H1C | 0.87 (3) |
C1—O2 | 1.250 (2) | N1—H1B | 0.879 (13) |
C1—O1 | 1.260 (2) | N1—H1A | 0.878 (16) |
N1—Cd1—O1i | 170.71 (6) | C3—C2—C1 | 111.87 (16) |
N1—Cd1—O4i | 89.62 (6) | C3—C2—H2A | 109.2 |
O1i—Cd1—O4i | 81.83 (5) | C1—C2—H2A | 109.2 |
N1—Cd1—O2 | 96.45 (6) | C3—C2—H2B | 109.2 |
O1i—Cd1—O2 | 87.71 (5) | C1—C2—H2B | 109.2 |
O4i—Cd1—O2 | 138.80 (5) | H2A—C2—H2B | 107.9 |
N1—Cd1—O4ii | 88.67 (6) | O3—C3—O4 | 121.18 (19) |
O1i—Cd1—O4ii | 99.96 (5) | O3—C3—C2 | 119.84 (18) |
O4i—Cd1—O4ii | 135.38 (5) | O4—C3—C2 | 118.98 (17) |
O2—Cd1—O4ii | 85.62 (5) | Cd1—N1—H1C | 113.1 (19) |
N1—Cd1—O3ii | 98.43 (7) | Cd1—N1—H1B | 109.7 (19) |
O1i—Cd1—O3ii | 84.22 (6) | H1C—N1—H1B | 112 (2) |
O4i—Cd1—O3ii | 83.15 (5) | Cd1—N1—H1A | 109.0 (19) |
O2—Cd1—O3ii | 135.40 (5) | H1C—N1—H1A | 107 (2) |
O4ii—Cd1—O3ii | 53.12 (5) | H1B—N1—H1A | 105 (2) |
N1—Cd1—O1 | 86.89 (6) | C1—O1—Cd1iii | 125.69 (13) |
O1i—Cd1—O1 | 89.06 (7) | C1—O1—Cd1 | 86.66 (11) |
O4i—Cd1—O1 | 87.22 (5) | Cd1iii—O1—Cd1 | 141.45 (6) |
O2—Cd1—O1 | 52.71 (5) | C1—O2—Cd1 | 98.82 (13) |
O4ii—Cd1—O1 | 137.14 (5) | C3—O3—Cd1iv | 92.36 (13) |
O3ii—Cd1—O1 | 168.94 (5) | C3—O4—Cd1iii | 126.79 (13) |
O2—C1—O1 | 121.81 (19) | C3—O4—Cd1iv | 93.11 (12) |
O2—C1—C2 | 118.56 (18) | Cd1iii—O4—Cd1iv | 136.24 (7) |
O1—C1—C2 | 119.63 (17) |
Symmetry codes: (i) y−1/3, −x+y+1/3, −z+1/3; (ii) x−y+1, x, −z; (iii) x−y+2/3, x+1/3, −z+1/3; (iv) y, −x+y+1, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1C···O3v | 0.87 (3) | 2.19 (3) | 3.043 (2) | 166 (3) |
N1—H1B···O2vi | 0.88 (1) | 2.17 (1) | 3.033 (2) | 167 (2) |
N1—H1A···O3vii | 0.88 (2) | 2.33 (2) | 3.188 (3) | 164 (2) |
Symmetry codes: (v) −x+4/3, −y+5/3, −z−1/3; (vi) −x+y+2/3, −x+4/3, z+1/3; (vii) −y+5/3, x−y+4/3, z+1/3. |
Experimental details
Crystal data | |
Chemical formula | [Cd(C3H2O4)(NH3)] |
Mr | 231.48 |
Crystal system, space group | Trigonal, R3 |
Temperature (K) | 298 |
a, c (Å) | 17.3662 (8), 11.4425 (10) |
V (Å3) | 2988.6 (3) |
Z | 18 |
Radiation type | Mo Kα |
µ (mm−1) | 3.23 |
Crystal size (mm) | 0.10 × 0.08 × 0.08 |
Data collection | |
Diffractometer | Bruker SMART APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.738, 0.782 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5110, 1317, 1281 |
Rint | 0.020 |
(sin θ/λ)max (Å−1) | 0.617 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.014, 0.035, 1.13 |
No. of reflections | 1317 |
No. of parameters | 92 |
No. of restraints | 6 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.53, −0.29 |
Computer programs: APEX2 (Bruker,2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2008), publCIF (Westrip, 2010).
Cd1—N1 | 2.2577 (19) | Cd1—O4ii | 2.4258 (14) |
Cd1—O1i | 2.2856 (14) | Cd1—O3ii | 2.4525 (16) |
Cd1—O4i | 2.3081 (14) | Cd1—O1 | 2.5841 (14) |
Cd1—O2 | 2.3299 (15) | ||
N1—Cd1—O1i | 170.71 (6) | O1i—Cd1—O3ii | 84.22 (6) |
N1—Cd1—O4i | 89.62 (6) | O4i—Cd1—O3ii | 83.15 (5) |
O1i—Cd1—O4i | 81.83 (5) | O2—Cd1—O3ii | 135.40 (5) |
N1—Cd1—O2 | 96.45 (6) | O4ii—Cd1—O3ii | 53.12 (5) |
O1i—Cd1—O2 | 87.71 (5) | N1—Cd1—O1 | 86.89 (6) |
O4i—Cd1—O2 | 138.80 (5) | O1i—Cd1—O1 | 89.06 (7) |
N1—Cd1—O4ii | 88.67 (6) | O4i—Cd1—O1 | 87.22 (5) |
O1i—Cd1—O4ii | 99.96 (5) | O2—Cd1—O1 | 52.71 (5) |
O4i—Cd1—O4ii | 135.38 (5) | O4ii—Cd1—O1 | 137.14 (5) |
O2—Cd1—O4ii | 85.62 (5) | O3ii—Cd1—O1 | 168.94 (5) |
N1—Cd1—O3ii | 98.43 (7) |
Symmetry codes: (i) y−1/3, −x+y+1/3, −z+1/3; (ii) x−y+1, x, −z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1C···O3iii | 0.87 (3) | 2.19 (3) | 3.043 (2) | 166 (3) |
N1—H1B···O2iv | 0.879 (13) | 2.171 (14) | 3.033 (2) | 167 (2) |
N1—H1A···O3v | 0.878 (16) | 2.334 (18) | 3.188 (3) | 164 (2) |
Symmetry codes: (iii) −x+4/3, −y+5/3, −z−1/3; (iv) −x+y+2/3, −x+4/3, z+1/3; (v) −y+5/3, x−y+4/3, z+1/3. |
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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.