In the centrosymmetric title compound, [Cd(C
6H
5N
2O
4)
2(H
2O)
4], the Cd
II cation is coordinated by two uracil-1-acetate anions
via carboxylate O atoms, and four water molecules, forming a six-coordinate octahedral environment. O—H
O and N—H
O hydrogen-bonding interactions link adjacent molecules into a three-dimensional network.
Supporting information
CCDC reference: 287449
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (C-C)= 0.003 Å
- R factor = 0.022
- wR factor = 0.054
- Data-to-parameter ratio = 11.0
checkCIF/PLATON results
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Compound (I) was synthesized in a hydrothermal process from a mixture of benzimidazole (2 mmol, 0.24 g), Cd(NO3)2·2H2O (1 mmol, 0.27 g), uracil-1-acetic acid (2 mmol, 0.34 g) and water (20 ml). The reaction was carried out in a 30 ml Teflon-lined stainless-steel reactor. The reactor was heated to 423 K for 3 d and then slowly cooled to 298 K, to yield colourless crystals of (I), which were collected and washed with water.
Water H atoms were located in difference maps and refined, with O—H and H···H distances restrained to be 0.82 (2) and 1.39 (1) Å, respectively, and with Uiso(H) = 1.2Ueq(O). Other H atoms were positioned geometrically and allowed to ride on their parent atoms, with Csp2—H = 0.93 Å and Uiso(H) = 1.2Ueq(C), Csp3—H = 0.97 Å and Uiso(H) = 1.5Ueq(C), and N—H = 0.86 Å and Uiso(H) = 1.2Ueq(N).
Data collection: SMART (Bruker, 2002); cell refinement: SAINT (Bruker, 2002); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2002); software used to prepare material for publication: SHELXL97.
Tetraaquabis(uracil-1-acetato)cadmium(II)
top
Crystal data top
[Cd(C6H5N2O4)2(H2O)4] | F(000) = 524 |
Mr = 522.70 | Dx = 1.930 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ybc | Cell parameters from 3064 reflections |
a = 12.6956 (9) Å | θ = 3.0–25.2° |
b = 5.1295 (4) Å | µ = 1.29 mm−1 |
c = 13.9659 (10) Å | T = 298 K |
β = 98.452 (1)° | Block, colourless |
V = 899.61 (11) Å3 | 0.39 × 0.22 × 0.17 mm |
Z = 2 | |
Data collection top
Bruker APEX area-detector diffractometer | 1611 independent reflections |
Radiation source: fine-focus sealed tube | 1549 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.019 |
ϕ and ω scans | θmax = 25.2°, θmin = 1.6° |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | h = −15→11 |
Tmin = 0.633, Tmax = 0.811 | k = −6→6 |
4458 measured reflections | l = −16→16 |
Refinement top
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)] = 0.022 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.054 | w = 1/[σ2(Fo2) + (0.0226P)2 + 0.8089P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
1611 reflections | Δρmax = 0.22 e Å−3 |
146 parameters | Δρmin = −0.32 e Å−3 |
6 restraints | Extinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0177 (10) |
Crystal data top
[Cd(C6H5N2O4)2(H2O)4] | V = 899.61 (11) Å3 |
Mr = 522.70 | Z = 2 |
Monoclinic, P21/c | Mo Kα radiation |
a = 12.6956 (9) Å | µ = 1.29 mm−1 |
b = 5.1295 (4) Å | T = 298 K |
c = 13.9659 (10) Å | 0.39 × 0.22 × 0.17 mm |
β = 98.452 (1)° | |
Data collection top
Bruker APEX area-detector diffractometer | 1611 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2002) | 1549 reflections with I > 2σ(I) |
Tmin = 0.633, Tmax = 0.811 | Rint = 0.019 |
4458 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.022 | 6 restraints |
wR(F2) = 0.054 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.06 | Δρmax = 0.22 e Å−3 |
1611 reflections | Δρmin = −0.32 e Å−3 |
146 parameters | |
Special details top
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 (Å2) top | x | y | z | Uiso*/Ueq | |
Cd1 | 0.0000 | 0.0000 | 0.5000 | 0.02989 (12) | |
O1 | 0.08664 (13) | 0.2781 (3) | 0.61021 (12) | 0.0370 (4) | |
O2 | 0.24887 (13) | 0.1051 (4) | 0.64897 (13) | 0.0415 (4) | |
O3 | 0.22971 (12) | 0.0856 (3) | 0.87294 (13) | 0.0352 (4) | |
O4 | 0.58199 (12) | 0.2407 (3) | 0.95463 (12) | 0.0379 (4) | |
O5 | −0.01909 (13) | −0.2805 (3) | 0.62057 (13) | 0.0368 (4) | |
H5A | 0.0153 (17) | −0.414 (4) | 0.616 (2) | 0.044* | |
H5B | −0.0823 (13) | −0.302 (5) | 0.621 (2) | 0.044* | |
O6 | −0.16820 (14) | 0.1565 (4) | 0.51638 (14) | 0.0455 (5) | |
H6A | −0.190 (2) | 0.283 (5) | 0.5438 (18) | 0.055* | |
H6B | −0.202 (2) | 0.119 (6) | 0.4643 (15) | 0.055* | |
N1 | 0.29996 (14) | 0.4318 (4) | 0.80170 (13) | 0.0246 (4) | |
N2 | 0.40475 (14) | 0.1761 (4) | 0.91398 (13) | 0.0269 (4) | |
H2 | 0.4097 | 0.0488 | 0.9544 | 0.032* | |
C1 | 0.17880 (18) | 0.2643 (4) | 0.65964 (16) | 0.0276 (5) | |
C2 | 0.19909 (18) | 0.4742 (4) | 0.73754 (17) | 0.0270 (5) | |
H2A | 0.2006 | 0.6435 | 0.7069 | 0.032* | |
H2B | 0.1411 | 0.4743 | 0.7757 | 0.032* | |
C3 | 0.30629 (17) | 0.2237 (4) | 0.86361 (15) | 0.0255 (5) | |
C4 | 0.49735 (17) | 0.3110 (4) | 0.90686 (15) | 0.0266 (5) | |
C5 | 0.48459 (19) | 0.5278 (4) | 0.84137 (17) | 0.0279 (5) | |
H5 | 0.5425 | 0.6324 | 0.8333 | 0.034* | |
C6 | 0.38804 (18) | 0.5776 (4) | 0.79194 (16) | 0.0262 (5) | |
H6 | 0.3805 | 0.7174 | 0.7491 | 0.031* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Cd1 | 0.02480 (16) | 0.02813 (17) | 0.03517 (17) | 0.00194 (9) | −0.00075 (10) | −0.00477 (10) |
O1 | 0.0292 (9) | 0.0315 (9) | 0.0461 (10) | 0.0047 (7) | −0.0085 (7) | −0.0106 (8) |
O2 | 0.0315 (9) | 0.0444 (10) | 0.0459 (10) | 0.0127 (8) | −0.0035 (8) | −0.0146 (9) |
O3 | 0.0213 (8) | 0.0355 (9) | 0.0480 (10) | −0.0053 (7) | 0.0020 (7) | 0.0119 (8) |
O4 | 0.0233 (8) | 0.0454 (10) | 0.0424 (9) | −0.0041 (7) | −0.0034 (7) | 0.0162 (8) |
O5 | 0.0266 (9) | 0.0348 (10) | 0.0490 (10) | 0.0062 (8) | 0.0058 (8) | 0.0013 (8) |
O6 | 0.0308 (10) | 0.0504 (12) | 0.0527 (12) | 0.0117 (8) | −0.0032 (8) | −0.0229 (9) |
N1 | 0.0230 (10) | 0.0235 (9) | 0.0262 (9) | 0.0006 (8) | 0.0003 (7) | 0.0019 (8) |
N2 | 0.0243 (9) | 0.0261 (10) | 0.0295 (9) | −0.0016 (8) | 0.0010 (7) | 0.0084 (8) |
C1 | 0.0263 (11) | 0.0255 (11) | 0.0299 (11) | 0.0001 (9) | 0.0001 (9) | 0.0021 (9) |
C2 | 0.0247 (12) | 0.0257 (12) | 0.0290 (12) | 0.0033 (9) | −0.0017 (9) | 0.0013 (9) |
C3 | 0.0244 (11) | 0.0251 (11) | 0.0268 (11) | 0.0006 (9) | 0.0029 (9) | −0.0001 (9) |
C4 | 0.0247 (11) | 0.0291 (12) | 0.0261 (11) | −0.0028 (9) | 0.0038 (9) | −0.0010 (9) |
C5 | 0.0274 (12) | 0.0278 (12) | 0.0288 (12) | −0.0060 (9) | 0.0051 (9) | 0.0026 (9) |
C6 | 0.0306 (12) | 0.0230 (11) | 0.0254 (11) | −0.0005 (9) | 0.0055 (9) | 0.0015 (9) |
Geometric parameters (Å, º) top
Cd1—O5i | 2.2549 (18) | N1—C3 | 1.368 (3) |
Cd1—O5 | 2.2549 (18) | N1—C6 | 1.369 (3) |
Cd1—O1 | 2.2619 (15) | N1—C2 | 1.467 (3) |
Cd1—O1i | 2.2619 (15) | N2—C3 | 1.363 (3) |
Cd1—O6i | 2.3240 (17) | N2—C4 | 1.380 (3) |
Cd1—O6 | 2.3240 (17) | N2—H2 | 0.8600 |
O1—C1 | 1.270 (3) | C1—C2 | 1.525 (3) |
O2—C1 | 1.233 (3) | C2—H2A | 0.9700 |
O3—C3 | 1.225 (3) | C2—H2B | 0.9700 |
O4—C4 | 1.233 (3) | C4—C5 | 1.434 (3) |
O5—H5A | 0.822 (16) | C5—C6 | 1.340 (3) |
O5—H5B | 0.811 (16) | C5—H5 | 0.9300 |
O6—H6A | 0.823 (16) | C6—H6 | 0.9300 |
O6—H6B | 0.813 (16) | | |
| | | |
O5i—Cd1—O5 | 180.0 | C3—N2—C4 | 126.81 (19) |
O5i—Cd1—O1 | 90.62 (6) | C3—N2—H2 | 116.6 |
O5—Cd1—O1 | 89.38 (6) | C4—N2—H2 | 116.6 |
O5i—Cd1—O1i | 89.38 (6) | O2—C1—O1 | 126.5 (2) |
O5—Cd1—O1i | 90.62 (6) | O2—C1—C2 | 120.3 (2) |
O1—Cd1—O1i | 180.0 | O1—C1—C2 | 113.19 (19) |
O5i—Cd1—O6i | 86.89 (7) | N1—C2—C1 | 111.82 (18) |
O5—Cd1—O6i | 93.11 (7) | N1—C2—H2A | 109.3 |
O1—Cd1—O6i | 85.58 (6) | C1—C2—H2A | 109.3 |
O1i—Cd1—O6i | 94.42 (6) | N1—C2—H2B | 109.3 |
O5i—Cd1—O6 | 93.11 (7) | C1—C2—H2B | 109.3 |
O5—Cd1—O6 | 86.89 (7) | H2A—C2—H2B | 107.9 |
O1—Cd1—O6 | 94.42 (6) | O3—C3—N2 | 121.6 (2) |
O1i—Cd1—O6 | 85.58 (6) | O3—C3—N1 | 122.98 (19) |
O6i—Cd1—O6 | 180.0 | N2—C3—N1 | 115.46 (19) |
C1—O1—Cd1 | 130.67 (15) | O4—C4—N2 | 119.9 (2) |
Cd1—O5—H5A | 111 (2) | O4—C4—C5 | 125.5 (2) |
Cd1—O5—H5B | 108 (2) | N2—C4—C5 | 114.65 (19) |
H5A—O5—H5B | 115 (2) | C6—C5—C4 | 119.0 (2) |
Cd1—O6—H6A | 134 (2) | C6—C5—H5 | 120.5 |
Cd1—O6—H6B | 102 (2) | C4—C5—H5 | 120.5 |
H6A—O6—H6B | 115 (2) | C5—C6—N1 | 122.9 (2) |
C3—N1—C6 | 121.07 (18) | C5—C6—H6 | 118.5 |
C3—N1—C2 | 117.79 (18) | N1—C6—H6 | 118.5 |
C6—N1—C2 | 120.72 (18) | | |
Symmetry code: (i) −x, −y, −z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H5A···O1ii | 0.82 (2) | 1.83 (2) | 2.647 (2) | 177 (3) |
O5—H5B···O3iii | 0.81 (2) | 1.97 (2) | 2.775 (2) | 171 (3) |
O6—H6A···O3iv | 0.82 (2) | 2.05 (2) | 2.863 (2) | 172 (3) |
O6—H6B···O2i | 0.81 (2) | 1.98 (2) | 2.736 (2) | 156 (3) |
N2—H2···O4v | 0.86 | 1.95 | 2.806 (2) | 179 |
Symmetry codes: (i) −x, −y, −z+1; (ii) x, y−1, z; (iii) −x, y−1/2, −z+3/2; (iv) −x, y+1/2, −z+3/2; (v) −x+1, −y, −z+2. |
Experimental details
Crystal data |
Chemical formula | [Cd(C6H5N2O4)2(H2O)4] |
Mr | 522.70 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 298 |
a, b, c (Å) | 12.6956 (9), 5.1295 (4), 13.9659 (10) |
β (°) | 98.452 (1) |
V (Å3) | 899.61 (11) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 1.29 |
Crystal size (mm) | 0.39 × 0.22 × 0.17 |
|
Data collection |
Diffractometer | Bruker APEX area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2002) |
Tmin, Tmax | 0.633, 0.811 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4458, 1611, 1549 |
Rint | 0.019 |
(sin θ/λ)max (Å−1) | 0.599 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.022, 0.054, 1.06 |
No. of reflections | 1611 |
No. of parameters | 146 |
No. of restraints | 6 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.22, −0.32 |
Selected geometric parameters (Å, º) topCd1—O5 | 2.2549 (18) | N1—C6 | 1.369 (3) |
Cd1—O1 | 2.2619 (15) | N1—C2 | 1.467 (3) |
Cd1—O6 | 2.3240 (17) | N2—C3 | 1.363 (3) |
O1—C1 | 1.270 (3) | N2—C4 | 1.380 (3) |
O2—C1 | 1.233 (3) | C1—C2 | 1.525 (3) |
O3—C3 | 1.225 (3) | C4—C5 | 1.434 (3) |
O4—C4 | 1.233 (3) | C5—C6 | 1.340 (3) |
N1—C3 | 1.368 (3) | | |
| | | |
O5i—Cd1—O5 | 180.0 | O5—Cd1—O6i | 93.11 (7) |
O5i—Cd1—O1 | 90.62 (6) | O1—Cd1—O6i | 85.58 (6) |
O5—Cd1—O1 | 89.38 (6) | O1—Cd1—O6 | 94.42 (6) |
O5i—Cd1—O6i | 86.89 (7) | O6i—Cd1—O6 | 180.0 |
Symmetry code: (i) −x, −y, −z+1. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H5A···O1ii | 0.822 (16) | 1.826 (17) | 2.647 (2) | 177 (3) |
O5—H5B···O3iii | 0.811 (16) | 1.972 (17) | 2.775 (2) | 171 (3) |
O6—H6A···O3iv | 0.823 (16) | 2.046 (16) | 2.863 (2) | 172 (3) |
O6—H6B···O2i | 0.813 (16) | 1.975 (17) | 2.736 (2) | 156 (3) |
N2—H2···O4v | 0.86 | 1.95 | 2.806 (2) | 179 |
Symmetry codes: (i) −x, −y, −z+1; (ii) x, y−1, z; (iii) −x, y−1/2, −z+3/2; (iv) −x, y+1/2, −z+3/2; (v) −x+1, −y, −z+2. |
The interaction of metal ions with nucleic acid bases is of great interest because of their relevance to the essential medical or toxic bioactivity of metal centres (Chruscinska et al., 1998). Uracil is a component of RNA. Some of the 5-substituted uracils, e.g. 5-fluorouracil and 5-bromouracil, exhibit significant pharmacological activity and are used as antitumour, antibacterial and antiviral drugs. These molecules may coordinate as exogenous ligands (e.g. inhibitors) in metalloproteins, function as cofactors in enzymatic systems or construct important cell structures, e.g. RNA (Lewandowski et al., 2005). As a result, great efforts have been expended in the investigation of uracil derivatives and their complexes (Hueso-Ureña et al., 1999, 2003; Terrón et al., 2004; Hu & Wang, 2005; Hu et al., 2005). Cadmium is an environmental pollutant, which inhibits RNA polymerase activity in vivo and reacts readily with proteins and other biological molecules (López-Garzón et al., 1995). In addition, cadmium(II) has a d10 electron configuration which adapts to a wide variety of stereochemical environments (Sen et al., 1999). Thus, we have selected CdII and 1-(carboxymethyl)uracil (Xiong et al., 2005), which we synthesized previously, to extend this area of research, and we present here the crystal structure of the title uracil-1-acetate-based complex, (I).
The mononuclear complex, (I), consists of a CdII cation, four coordinated water molecules and two uracil-1-acetate anions, binding through their carboxylate O atoms. The CdII cation lies on an inversion centre and the geometry around the metal centre is octahedral (Fig.1 and Table 1). The equatorial square is formed by atoms O5, O5i, O6 and O6i [symmetry code: (i) −x, −y, 1 − z] and is constrained to be planar by symmetry.
In the crystal structure, N—H···O and O—H···O hydrogen bonds link the mononuclear units to form a three-dimensional network (Fig. 2 and Table 2).