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Acta Cryst. (2007). E63, m2887-m2888    [ doi:10.1107/S1600536807054050 ]

Tetraaqua(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylato-[kappa]2N3,O)cobalt(II) 2.5-hydrate

B. Sridhar and K. Ravikumar

Abstract top

The CoII ion in the title compound, [Co(C5H2N2O4)(H2O)4]·2.5H2O, is chelated by the orotate dianion through carboxylate O and pyrimidine N atoms, and its octahedral geometry is completed by four water molecules. An intermolecular N-H...O hydrogen bond forms an orotate-orotate dimer. An extensive three-dimensional hydrogen-bonded network of O-H...O and N-H...O bonds and weak [pi]-[pi] interaction [3.754 (2) Å] stabilize the crystal structure. One of the solvent water molecules is located on a twofold rotation axis.

Comment top

Orotic acid (vitamin B13, H3Or) plays a significant role in biosynthesis of pyrimidine nucleosides (Panzeter & Ringer, 1993) and also found in cell and body fluids of many living organisms (Lalioti et al., 1998). Orotic acid is a good organic building block in coordination chemistry and has a multidentate nature. The most potential coordination sites (pH range of 5–9) are the carboxylate oxygen and the adjacent nitrogen atom for the formation of a stable five-membered chelate ring. The crystal structures of nickel(II) orotate pentahydrate (Wysokinski et al., 2002) and the analogous pentahydrate salt of cobalt (Icbudak et al., 2003) were recently reported. In the present study, we are reporting the crystal structure of tetraaqua(orotato)cobalt(II) 2.5 hydrate (I).

The molecular structure of (I) is shown in Fig. 1 and selected geometrical parameters are given in Table 1. Compound (I) comprises of one CoII ion, one orotate ligand, four coordinated water molecule and 2.5 uncoordinated solvent water molecules. The central CoII ion has a distorted octahedral coordination geometry, comprised of atoms N1 and O4 from a doubly deprotonated bidentate orotate ligand and four water (O1W, O2W, O3W and O4W) molecules.

The orotate ligand is essentially planar. The dihedral angle between the pyrimidine ring and the carboxylate group is 0.8 (4)°. The atom N and carboxylate O atom of the orotate ring form a five-membered chelate ring with the CoII ion. The dihedral angle between the five-membered ring and the six-membered pyrimidine ring is 4.3 (1)°. The Co—N distance is 2.104 (4) Å and Co—O distances lie in the range 2.075 (3)–2.123 (4) Å (Table 1).

The structure is stabilized by N—H···O and O—H···O hydrogen bonding. The intramolecular O—H···O hydrogen bond forms an S(6) motif (Bernstein et al., 1995). The intermolecular N—H···O hydrogen bonding leads to the formation of centrosymmetric dimer of R22(8)-type motif. The four water molecules link the carboxylate (O5 & O6) groups and carbonyl (O7 & O8) atoms through intra and intermolecular hydrogen bond interactions (Table. 2). Hydrogen-bonding interactions between the coordinated and uncoordinated water molecules and between the water molecules and the ligand result in a three-dimensional network structure (Fig. 2).

A π-π interaction is observed between the symmetry-related pyrimidine rings (N1/C1/C2/C3/C4/N2/C5). The six-membered ring at (x,y,z) and (x, 1 − y, z + 1/2) are parallel with an interplanar spacing of 3.267 Å; the ring centroid separation is 3.755 (3) Å.

Related literature top

For related literature, see: Bernstein et al. (1995); Icbudak et al. (2003); Lalioti et al. (1998); Panzeter & Ringer (1993); Wysokinski et al. (2002).

Experimental top

A solution of CoCl2·6H2O (1.2 g, 1 mmol) in water (25 ml) was added to a solution of orotic acid (0.9 g, 1 mmol) in water (25 ml). The solution refluxed and stirred in a temperature-controlled bath. The mixture was then left for crystallization.

Refinement top

The H atom attached to the N atom was located in a difference Fourier map and refined isotropically. H atoms of coordinated water molecules were located in a difference Fourier map and refined isotropically with Uiso(H) = 1.5 Ueq(O). The N2—H2N and coordinated water H atoms were restrained to values of 0.85 (1) and 0.89 (1) Å, respectively. The H atom attached to the C atom was positioned geometrically and treated as riding on its parent C atom with C—H distance = 0.93 Å, and with Uiso(H) = 1.2Ueq(C). The O atoms of the uncoordinated water (O5W, O6W & O7W) molecules show high displacement parameters, but attempts to refine them as disordered were unsucessful. Hence, the O atoms were refined isotropically. The H atoms of O5W, O6W and O7W could not be located from electron density maps. These H atoms were not included in the calculations (although they are included in the emprical formula). A maximum (positive) residual density was observed 0.88 Å from atom O5W.

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT (Bruker, 2001); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL/PC (Sheldrick, 1990) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 1997).

Figures top
[Figure 1] Fig. 1. A view of the (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. A packing diagram for (I), viewed down the c axis. H atom attached to the C atom and three uncoordinated water molecules have been omitted for clarity.
Tetraaqua(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylato- κ2N3,O)cobalt(II) 2.5-hydrate top
Crystal data top
[Co(C5H2N2O4)(H2O)4]·2.5H2OF000 = 1360
Mr = 330.12Dx = 1.673 Mg m−3
Orthorhombic, PbcnMo Kα radiation
λ = 0.71073 Å
Hall symbol: -P 2n 2abCell parameters from 7524 reflections
a = 20.8700 (19) Åθ = 2.4–24.3º
b = 17.1153 (16) ŵ = 1.36 mm−1
c = 7.3375 (7) ÅT = 293 (2) K
V = 2620.9 (4) Å3Block, brown
Z = 80.16 × 0.11 × 0.05 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		2321 independent reflections
Radiation source: fine-focus sealed tube1971 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.038
T = 294(2) Kθmax = 25.0º
ω scansθmin = 1.5º
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		h = −24→24
Tmin = 0.82, Tmax = 0.94k = −20→19
17563 measured reflectionsl = −8→8
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)] = 0.063H atoms treated by a mixture of
independent and constrained refinement
wR(F2) = 0.199  w = 1/[σ2(Fo2) + (0.1193P)2 + 6.0462P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max = 0.001
2321 reflectionsΔρmax = 1.39 e Å−3
183 parametersΔρmin = −0.70 e Å−3
10 restraintsExtinction correction: none
Primary atom site location: structure-invariant direct methods
Crystal data top
[Co(C5H2N2O4)(H2O)4]·2.5H2OV = 2620.9 (4) Å3
Mr = 330.12Z = 8
Orthorhombic, PbcnMo Kα
a = 20.8700 (19) ŵ = 1.36 mm−1
b = 17.1153 (16) ÅT = 293 (2) K
c = 7.3375 (7) Å0.16 × 0.11 × 0.05 mm
Data collection top
Bruker SMART CCD area-detector
diffractometer		2321 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)		1971 reflections with I > 2σ(I)
Tmin = 0.82, Tmax = 0.94Rint = 0.038
17563 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.06310 restraints
wR(F2) = 0.199H atoms treated by a mixture of
independent and constrained refinement
S = 1.12Δρmax = 1.39 e Å−3
2321 reflectionsΔρmin = −0.70 e Å−3
183 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.7263 (2)0.3856 (3)0.3371 (7)0.0385 (12)
C20.6732 (2)0.4366 (3)0.2594 (7)0.0309 (10)
C30.6769 (2)0.5154 (3)0.2676 (7)0.0338 (11)
H30.71180.53990.32160.041*
C40.6257 (2)0.5599 (3)0.1911 (6)0.0312 (11)
C50.5743 (2)0.4364 (3)0.1159 (6)0.0286 (10)
Co10.63880 (3)0.27419 (4)0.18230 (9)0.0331 (3)
N10.62351 (19)0.3957 (2)0.1868 (5)0.0299 (9)
N20.57606 (18)0.5165 (2)0.1237 (5)0.0292 (9)
H2N0.5431 (16)0.542 (3)0.090 (7)0.039 (15)*
O50.71873 (17)0.3129 (2)0.3242 (5)0.0435 (9)
O60.77339 (19)0.4172 (2)0.4090 (7)0.0578 (12)
O70.62424 (19)0.6324 (2)0.1820 (5)0.0397 (9)
O80.52739 (15)0.40450 (19)0.0404 (5)0.0360 (8)
O1W0.6869 (2)0.2836 (3)−0.0659 (6)0.0688 (15)
H1W0.674 (5)0.306 (5)−0.169 (7)0.108*
H2W0.715 (4)0.252 (5)−0.120 (13)0.108*
O2W0.5526 (2)0.2518 (2)0.0408 (6)0.0525 (10)
H3W0.534 (3)0.298 (2)0.030 (10)0.073*
H4W0.548 (4)0.221 (4)0.137 (6)0.073*
O3W0.6630 (3)0.1565 (3)0.1854 (6)0.0619 (13)
H5W0.686 (5)0.142 (7)0.089 (10)0.144*
H6W0.680 (5)0.144 (7)0.293 (8)0.144*
O4W0.5907 (2)0.2568 (2)0.4340 (5)0.0452 (9)
H7W0.589 (4)0.3028 (18)0.491 (8)0.082*
H8W0.608 (4)0.216 (2)0.491 (8)0.082*
O5W0.6640 (5)0.0575 (6)0.4756 (14)0.148 (3)*
O6W0.5927 (4)0.1499 (6)0.7340 (14)0.141 (3)*
O7W0.50000.1145 (14)0.25000.251 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.029 (2)0.045 (3)0.042 (3)0.004 (2)−0.005 (2)0.010 (2)
C20.024 (2)0.039 (3)0.030 (2)0.0022 (19)−0.0005 (19)0.005 (2)
C30.027 (2)0.040 (3)0.035 (2)−0.003 (2)−0.007 (2)0.005 (2)
C40.032 (2)0.035 (3)0.027 (2)0.003 (2)−0.0020 (19)0.0046 (19)
C50.025 (2)0.031 (2)0.029 (2)0.0065 (18)0.0007 (19)−0.0014 (19)
Co10.0328 (5)0.0306 (5)0.0359 (5)0.0094 (2)0.0009 (3)−0.0006 (3)
N10.0249 (19)0.029 (2)0.035 (2)0.0053 (16)−0.0030 (16)0.0001 (16)
N20.027 (2)0.027 (2)0.034 (2)0.0063 (15)−0.0047 (17)0.0012 (17)
O50.0367 (19)0.038 (2)0.056 (2)0.0099 (16)−0.0112 (16)0.0036 (16)
O60.039 (2)0.050 (2)0.085 (3)−0.0030 (18)−0.027 (2)0.015 (2)
O70.050 (2)0.0253 (19)0.044 (2)−0.0024 (15)−0.0124 (16)0.0031 (15)
O80.0307 (17)0.0303 (17)0.047 (2)0.0050 (13)−0.0119 (15)−0.0028 (15)
O1W0.072 (3)0.087 (3)0.047 (3)0.053 (3)0.023 (2)0.021 (2)
O2W0.049 (2)0.044 (2)0.065 (3)0.0031 (19)−0.011 (2)−0.008 (2)
O3W0.096 (4)0.039 (2)0.051 (3)0.028 (2)0.020 (2)0.0046 (19)
O4W0.054 (2)0.0392 (19)0.042 (2)−0.0014 (18)0.0065 (18)−0.0056 (17)
Geometric parameters (Å, °) top
C1—O61.240 (6)Co1—O1W2.086 (4)
C1—O51.258 (7)Co1—N12.104 (4)
C1—C21.521 (7)Co1—O2W2.112 (4)
C2—C31.352 (7)Co1—O4W2.123 (4)
C2—N11.360 (6)N2—H2N0.85 (4)
C3—C41.427 (7)O1W—H1W0.89 (6)
C3—H30.9300O1W—H2W0.89 (8)
C4—O71.243 (6)O2W—H3W0.88 (4)
C4—N21.367 (6)O2W—H4W0.89 (5)
C5—O81.249 (6)O3W—H5W0.89 (9)
C5—N11.347 (6)O3W—H6W0.89 (7)
C5—N21.374 (6)O4W—H7W0.89 (4)
Co1—O52.075 (4)O4W—H8W0.89 (5)
Co1—O3W2.078 (4)
O6—C1—O5124.2 (5)O5—Co1—O4W89.33 (15)
O6—C1—C2119.1 (5)O3W—Co1—O4W88.23 (16)
O5—C1—C2116.6 (4)O1W—Co1—O4W176.33 (17)
C3—C2—N1125.0 (4)N1—Co1—O4W93.08 (15)
C3—C2—C1121.0 (4)O2W—Co1—O4W89.99 (17)
N1—C2—C1114.0 (4)C5—N1—C2117.8 (4)
C2—C3—C4118.3 (4)C5—N1—Co1128.4 (3)
C2—C3—H3120.9C2—N1—Co1113.6 (3)
C4—C3—H3120.9C4—N2—C5125.3 (4)
O7—C4—N2120.2 (4)C4—N2—H2N116 (4)
O7—C4—C3125.0 (5)C5—N2—H2N118 (4)
N2—C4—C3114.8 (4)C1—O5—Co1117.0 (3)
O8—C5—N1122.9 (4)Co1—O1W—H1W130 (7)
O8—C5—N2118.4 (4)Co1—O1W—H2W131 (7)
N1—C5—N2118.7 (4)H1W—O1W—H2W94 (8)
O5—Co1—O3W96.2 (2)Co1—O2W—H3W105 (5)
O5—Co1—O1W91.51 (19)Co1—O2W—H4W79 (5)
O3W—Co1—O1W88.13 (17)H3W—O2W—H4W123 (7)
O5—Co1—N178.39 (15)Co1—O3W—H5W113 (8)
O3W—Co1—N1174.4 (2)Co1—O3W—H6W109 (8)
O1W—Co1—N190.59 (17)H5W—O3W—H6W115 (10)
O5—Co1—O2W171.62 (15)Co1—O4W—H7W108 (5)
O3W—Co1—O2W92.1 (2)Co1—O4W—H8W109 (5)
O1W—Co1—O2W89.7 (2)H7W—O4W—H8W119 (5)
N1—Co1—O2W93.31 (16)
O6—C1—C2—C30.1 (8)O1W—Co1—N1—C588.8 (4)
O5—C1—C2—C3179.7 (5)O2W—Co1—N1—C5−0.9 (4)
O6—C1—C2—N1−179.0 (5)O4W—Co1—N1—C5−91.1 (4)
O5—C1—C2—N10.6 (7)O5—Co1—N1—C25.7 (3)
N1—C2—C3—C4−1.5 (8)O1W—Co1—N1—C2−85.7 (4)
C1—C2—C3—C4179.6 (4)O2W—Co1—N1—C2−175.4 (3)
C2—C3—C4—O7−176.6 (5)O4W—Co1—N1—C294.4 (3)
C2—C3—C4—N22.9 (7)O7—C4—N2—C5175.7 (4)
O8—C5—N1—C2177.5 (4)C3—C4—N2—C5−3.9 (7)
N2—C5—N1—C2−1.3 (6)O8—C5—N2—C4−175.7 (4)
O8—C5—N1—Co13.2 (7)N1—C5—N2—C43.2 (7)
N2—C5—N1—Co1−175.6 (3)O6—C1—O5—Co1−175.9 (4)
C3—C2—N1—C50.6 (7)C2—C1—O5—Co14.5 (6)
C1—C2—N1—C5179.6 (4)O3W—Co1—O5—C1172.9 (4)
C3—C2—N1—Co1175.7 (4)O1W—Co1—O5—C184.7 (4)
C1—C2—N1—Co1−5.2 (5)N1—Co1—O5—C1−5.6 (4)
O5—Co1—N1—C5−179.8 (4)O4W—Co1—O5—C1−98.9 (4)
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O8i0.85 (4)1.98 (4)2.818 (5)168 (5)
O1W—H2W···O5ii0.89 (6)1.82 (9)2.694 (5)166 (10)
O1W—H1W···O7iii0.89 (8)1.84 (4)2.683 (5)157 (9)
O3W—H5W···O6ii0.89 (9)1.87 (10)2.732 (6)164 (11)
O3W—H6W···O5W0.89 (7)2.03 (9)2.721 (11)134 (10)
O4W—H7W···O7iv0.89 (7)1.94 (4)2.720 (5)146 (6)
O4W—H8W···O6W0.89 (5)2.14 (5)2.862 (11)138 (7)
O2W—H3W···O80.88 (4)1.82 (3)2.666 (5)157 (7)
O2W—H4W···O7W0.89 (5)2.24 (5)3.014 (19)146 (7)
O2W—H4W···O4W0.89 (5)2.43 (7)2.994 (6)122 (6)
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+3/2, −y+1/2, z−1/2; (iii) x, −y+1, z−1/2; (iv) x, −y+1, z+1/2.
Table 1
Selected geometric parameters (Å, °) top
Co1—O52.075 (4)Co1—O2W2.112 (4)
Co1—O3W2.078 (4)Co1—O4W2.123 (4)
Co1—O1W2.086 (4)
O5—Co1—O3W96.2 (2)O3W—Co1—O2W92.1 (2)
O5—Co1—O1W91.51 (19)O1W—Co1—O2W89.7 (2)
O3W—Co1—O1W88.13 (17)N1—Co1—O2W93.31 (16)
O5—Co1—N178.39 (15)O5—Co1—O4W89.33 (15)
O1W—Co1—N190.59 (17)O3W—Co1—O4W88.23 (16)
Table 2
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N2—H2N···O8i0.85 (4)1.98 (4)2.818 (5)168 (5)
O1W—H2W···O5ii0.89 (6)1.82 (9)2.694 (5)166 (10)
O1W—H1W···O7iii0.89 (8)1.84 (4)2.683 (5)157 (9)
O3W—H5W···O6ii0.89 (9)1.87 (10)2.732 (6)164 (11)
O3W—H6W···O5W0.89 (7)2.03 (9)2.721 (11)134 (10)
O4W—H7W···O7iv0.89 (7)1.94 (4)2.720 (5)146 (6)
O4W—H8W···O6W0.89 (5)2.14 (5)2.862 (11)138 (7)
O2W—H3W···O80.88 (4)1.82 (3)2.666 (5)157 (7)
O2W—H4W···O7W0.89 (5)2.24 (5)3.014 (19)146 (7)
O2W—H4W···O4W0.89 (5)2.43 (7)2.994 (6)122 (6)
Symmetry codes: (i) −x+1, −y+1, −z; (ii) −x+3/2, −y+1/2, z−1/2; (iii) x, −y+1, z−1/2; (iv) x, −y+1, z+1/2.
references
References top

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