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In the centrosymmetric title compound, [Cd(C6H5N2O4)2(H2O)4], the CdII 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

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536805029946/bh6032sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536805029946/bh6032Isup2.hkl
Contains datablock I

CCDC reference: 287449

Key indicators

  • Single-crystal X-ray study
  • T = 298 K
  • Mean [sigma](C-C)= 0.003 Å
  • R factor = 0.022
  • wR factor = 0.054
  • Data-to-parameter ratio = 11.0

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Comment top

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).

Experimental top

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.

Refinement top

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).

Computing details top

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.

Figures top
[Figure 1] Fig. 1. The coordination environment of the CdII cation in (I), showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. [Symmetry code: (i) −x, −y, 1 − z.]
[Figure 2] Fig. 2. The three-dimensional network formed by hydrogen-bonding interactions, viewed along [010]. Hydrogen bonds are shown as dashed lines.
Tetraaquabis(uracil-1-acetato)cadmium(II) top
Crystal data top
[Cd(C6H5N2O4)2(H2O)4]F(000) = 524
Mr = 522.70Dx = 1.930 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3064 reflections
a = 12.6956 (9) Åθ = 3.0–25.2°
b = 5.1295 (4) ŵ = 1.29 mm1
c = 13.9659 (10) ÅT = 298 K
β = 98.452 (1)°Block, colourless
V = 899.61 (11) Å30.39 × 0.22 × 0.17 mm
Z = 2
Data collection top
Bruker APEX area-detector
diffractometer
1611 independent reflections
Radiation source: fine-focus sealed tube1549 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.019
ϕ and ω scansθmax = 25.2°, θmin = 1.6°
Absorption correction: multi-scan
(SADABS; Bruker, 2002)
h = 1511
Tmin = 0.633, Tmax = 0.811k = 66
4458 measured reflectionsl = 1616
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)] = 0.022H 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 reflectionsΔρmax = 0.22 e Å3
146 parametersΔρmin = 0.32 e Å3
6 restraintsExtinction correction: SHELXL97 (Sheldrick, 1997), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0177 (10)
Crystal data top
[Cd(C6H5N2O4)2(H2O)4]V = 899.61 (11) Å3
Mr = 522.70Z = 2
Monoclinic, P21/cMo Kα radiation
a = 12.6956 (9) ŵ = 1.29 mm1
b = 5.1295 (4) ÅT = 298 K
c = 13.9659 (10) Å0.39 × 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 = 0.811Rint = 0.019
4458 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0226 restraints
wR(F2) = 0.054H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.22 e Å3
1611 reflectionsΔρmin = 0.32 e Å3
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
xyzUiso*/Ueq
Cd10.00000.00000.50000.02989 (12)
O10.08664 (13)0.2781 (3)0.61021 (12)0.0370 (4)
O20.24887 (13)0.1051 (4)0.64897 (13)0.0415 (4)
O30.22971 (12)0.0856 (3)0.87294 (13)0.0352 (4)
O40.58199 (12)0.2407 (3)0.95463 (12)0.0379 (4)
O50.01909 (13)0.2805 (3)0.62057 (13)0.0368 (4)
H5A0.0153 (17)0.414 (4)0.616 (2)0.044*
H5B0.0823 (13)0.302 (5)0.621 (2)0.044*
O60.16820 (14)0.1565 (4)0.51638 (14)0.0455 (5)
H6A0.190 (2)0.283 (5)0.5438 (18)0.055*
H6B0.202 (2)0.119 (6)0.4643 (15)0.055*
N10.29996 (14)0.4318 (4)0.80170 (13)0.0246 (4)
N20.40475 (14)0.1761 (4)0.91398 (13)0.0269 (4)
H20.40970.04880.95440.032*
C10.17880 (18)0.2643 (4)0.65964 (16)0.0276 (5)
C20.19909 (18)0.4742 (4)0.73754 (17)0.0270 (5)
H2A0.20060.64350.70690.032*
H2B0.14110.47430.77570.032*
C30.30629 (17)0.2237 (4)0.86361 (15)0.0255 (5)
C40.49735 (17)0.3110 (4)0.90686 (15)0.0266 (5)
C50.48459 (19)0.5278 (4)0.84137 (17)0.0279 (5)
H50.54250.63240.83330.034*
C60.38804 (18)0.5776 (4)0.79194 (16)0.0262 (5)
H60.38050.71740.74910.031*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cd10.02480 (16)0.02813 (17)0.03517 (17)0.00194 (9)0.00075 (10)0.00477 (10)
O10.0292 (9)0.0315 (9)0.0461 (10)0.0047 (7)0.0085 (7)0.0106 (8)
O20.0315 (9)0.0444 (10)0.0459 (10)0.0127 (8)0.0035 (8)0.0146 (9)
O30.0213 (8)0.0355 (9)0.0480 (10)0.0053 (7)0.0020 (7)0.0119 (8)
O40.0233 (8)0.0454 (10)0.0424 (9)0.0041 (7)0.0034 (7)0.0162 (8)
O50.0266 (9)0.0348 (10)0.0490 (10)0.0062 (8)0.0058 (8)0.0013 (8)
O60.0308 (10)0.0504 (12)0.0527 (12)0.0117 (8)0.0032 (8)0.0229 (9)
N10.0230 (10)0.0235 (9)0.0262 (9)0.0006 (8)0.0003 (7)0.0019 (8)
N20.0243 (9)0.0261 (10)0.0295 (9)0.0016 (8)0.0010 (7)0.0084 (8)
C10.0263 (11)0.0255 (11)0.0299 (11)0.0001 (9)0.0001 (9)0.0021 (9)
C20.0247 (12)0.0257 (12)0.0290 (12)0.0033 (9)0.0017 (9)0.0013 (9)
C30.0244 (11)0.0251 (11)0.0268 (11)0.0006 (9)0.0029 (9)0.0001 (9)
C40.0247 (11)0.0291 (12)0.0261 (11)0.0028 (9)0.0038 (9)0.0010 (9)
C50.0274 (12)0.0278 (12)0.0288 (12)0.0060 (9)0.0051 (9)0.0026 (9)
C60.0306 (12)0.0230 (11)0.0254 (11)0.0005 (9)0.0055 (9)0.0015 (9)
Geometric parameters (Å, º) top
Cd1—O5i2.2549 (18)N1—C31.368 (3)
Cd1—O52.2549 (18)N1—C61.369 (3)
Cd1—O12.2619 (15)N1—C21.467 (3)
Cd1—O1i2.2619 (15)N2—C31.363 (3)
Cd1—O6i2.3240 (17)N2—C41.380 (3)
Cd1—O62.3240 (17)N2—H20.8600
O1—C11.270 (3)C1—C21.525 (3)
O2—C11.233 (3)C2—H2A0.9700
O3—C31.225 (3)C2—H2B0.9700
O4—C41.233 (3)C4—C51.434 (3)
O5—H5A0.822 (16)C5—C61.340 (3)
O5—H5B0.811 (16)C5—H50.9300
O6—H6A0.823 (16)C6—H60.9300
O6—H6B0.813 (16)
O5i—Cd1—O5180.0C3—N2—C4126.81 (19)
O5i—Cd1—O190.62 (6)C3—N2—H2116.6
O5—Cd1—O189.38 (6)C4—N2—H2116.6
O5i—Cd1—O1i89.38 (6)O2—C1—O1126.5 (2)
O5—Cd1—O1i90.62 (6)O2—C1—C2120.3 (2)
O1—Cd1—O1i180.0O1—C1—C2113.19 (19)
O5i—Cd1—O6i86.89 (7)N1—C2—C1111.82 (18)
O5—Cd1—O6i93.11 (7)N1—C2—H2A109.3
O1—Cd1—O6i85.58 (6)C1—C2—H2A109.3
O1i—Cd1—O6i94.42 (6)N1—C2—H2B109.3
O5i—Cd1—O693.11 (7)C1—C2—H2B109.3
O5—Cd1—O686.89 (7)H2A—C2—H2B107.9
O1—Cd1—O694.42 (6)O3—C3—N2121.6 (2)
O1i—Cd1—O685.58 (6)O3—C3—N1122.98 (19)
O6i—Cd1—O6180.0N2—C3—N1115.46 (19)
C1—O1—Cd1130.67 (15)O4—C4—N2119.9 (2)
Cd1—O5—H5A111 (2)O4—C4—C5125.5 (2)
Cd1—O5—H5B108 (2)N2—C4—C5114.65 (19)
H5A—O5—H5B115 (2)C6—C5—C4119.0 (2)
Cd1—O6—H6A134 (2)C6—C5—H5120.5
Cd1—O6—H6B102 (2)C4—C5—H5120.5
H6A—O6—H6B115 (2)C5—C6—N1122.9 (2)
C3—N1—C6121.07 (18)C5—C6—H6118.5
C3—N1—C2117.79 (18)N1—C6—H6118.5
C6—N1—C2120.72 (18)
Symmetry code: (i) x, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O5—H5A···O1ii0.82 (2)1.83 (2)2.647 (2)177 (3)
O5—H5B···O3iii0.81 (2)1.97 (2)2.775 (2)171 (3)
O6—H6A···O3iv0.82 (2)2.05 (2)2.863 (2)172 (3)
O6—H6B···O2i0.81 (2)1.98 (2)2.736 (2)156 (3)
N2—H2···O4v0.861.952.806 (2)179
Symmetry codes: (i) x, y, z+1; (ii) x, y1, z; (iii) x, y1/2, 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]
Mr522.70
Crystal system, space groupMonoclinic, P21/c
Temperature (K)298
a, b, c (Å)12.6956 (9), 5.1295 (4), 13.9659 (10)
β (°) 98.452 (1)
V3)899.61 (11)
Z2
Radiation typeMo Kα
µ (mm1)1.29
Crystal size (mm)0.39 × 0.22 × 0.17
Data collection
DiffractometerBruker APEX area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2002)
Tmin, Tmax0.633, 0.811
No. of measured, independent and
observed [I > 2σ(I)] reflections
4458, 1611, 1549
Rint0.019
(sin θ/λ)max1)0.599
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.022, 0.054, 1.06
No. of reflections1611
No. of parameters146
No. of restraints6
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.22, 0.32

Computer programs: SMART (Bruker, 2002), SAINT (Bruker, 2002), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2002), SHELXL97.

Selected geometric parameters (Å, º) top
Cd1—O52.2549 (18)N1—C61.369 (3)
Cd1—O12.2619 (15)N1—C21.467 (3)
Cd1—O62.3240 (17)N2—C31.363 (3)
O1—C11.270 (3)N2—C41.380 (3)
O2—C11.233 (3)C1—C21.525 (3)
O3—C31.225 (3)C4—C51.434 (3)
O4—C41.233 (3)C5—C61.340 (3)
N1—C31.368 (3)
O5i—Cd1—O5180.0O5—Cd1—O6i93.11 (7)
O5i—Cd1—O190.62 (6)O1—Cd1—O6i85.58 (6)
O5—Cd1—O189.38 (6)O1—Cd1—O694.42 (6)
O5i—Cd1—O6i86.89 (7)O6i—Cd1—O6180.0
Symmetry code: (i) x, y, z+1.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O5—H5A···O1ii0.822 (16)1.826 (17)2.647 (2)177 (3)
O5—H5B···O3iii0.811 (16)1.972 (17)2.775 (2)171 (3)
O6—H6A···O3iv0.823 (16)2.046 (16)2.863 (2)172 (3)
O6—H6B···O2i0.813 (16)1.975 (17)2.736 (2)156 (3)
N2—H2···O4v0.861.952.806 (2)179
Symmetry codes: (i) x, y, z+1; (ii) x, y1, z; (iii) x, y1/2, z+3/2; (iv) x, y+1/2, z+3/2; (v) x+1, y, z+2.
 

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