catena-Poly[[[triaqua­cobalt(II)]-μ-2,6-dioxo-1,2,3,6-tetra­hydro­pyrimidine-4-carboxyl­ato(2–)] 1.72-hydrate]

The Co^II ion in the title complex {[Co(C₅H₂N₂O₄)(H₂O)₃]·1.72H₂O}_n, has a distorted octa­hedral coordination geometry comprised of three water ligands, one deprotonated pyrimidine N atom and an adjacent carboxyl­ate O atom of one orotate ligand. The sixth coordination site is occupied by an exocyclic O atom from a neighbouring orotate moiety, and through this inter­action a helicoidal chain is formed. The mol­ecules are linked by intra­molecular O_water—H...O and inter­molecular N—H...O and O_water—H...O hydrogen bonds, forming a three-dimensional network.

S1. Comment

Orotic acid (vitamin B₁₃, H₃Or) and its metal complexes continue to attract attention because of its multidentate functionality and its great significance in living organisms as a precursor of pyrimidine nucleosides (Genchev, 1970; Rawn, 1989; Lalioti et al., 1998). Metal orotates have potential applications in medicine and some orotate complexes have already been screened as therapeutic agents for cancer treatment (Castan et al., 1990; Kumberger et al., 1993). Orotic acid and its anions, viz. H₂Or⁻, HOr²⁻ and Or³⁻, are also interesting multidentate ligands, especially above the deprotonation pH values. The coordination around the metal ions is formed by the N atom, the two carbonyl O atoms and the carboxylate O atom. H₃Or can act as a dibasic acid, depending on the pH range. In the pH range 3–9, orotic acid exists mainly as the readily coordinating monodeprotonated HOr²⁻ anion (the carboxylic acid group has a pK_a value of 2.07; Lutz, 2001). In basic solutions (pH 9), both the carboxyl group and a heterocylic N atom are deprotonated, so the anion acts as a bidentate ligand. Existing studies of its coordination complexes demonstrate that it occurs as a dianion, often coordinating via the N atom and carboxylic acid group, so forming a five-membered chelate ring (Maistralis et al., 2000; Wysokinski et al., 2002; Icbudak et al., 2003; Ölmez et al., 2004). In polymeric orotic acid complexes, the orotate anion bridges the metal ions through the carboxylate group and N and O atoms, forming one-dimensional polymeric chains (Castan et al., 1990; Sun et al., 2002). We present here the crystal structure of the title Co complex of H₃Or, (I).

A view of the molecule of (I) is presented in Fig. 1. The Co^II ion has a distorted octahedral coordination geometry, comprised of atoms N1 and O4 from a doubly deprotonated bidentate orotate ligand, three aqua molecules (O1W, O2W and O3W) and an exocyclic O atom (O5ⁱ; see Table 1 for symmetry code) from a neighbouring orotate moiety. Atoms N1 and O4 are bonded to Co1 to form a five-membered chelate ring (C4/N1/Co1/O4/C5) and, in conjunction with O3W and O5ⁱ, they define the approximately planar equatorial plane, with an r.m.s. deviation of 0.0179 Å and a largest deviation from the mean plane of 0.026 (3) Å for atom C5. This is apparently due to the strong intermolecular hydrogen-bonding interaction between atom H2 of the pyrimidine ring and carboxylate atom O4ⁱ. Finally, the apical positions of the Co^II coordination octahedron are occupied by O1W and O2W.

All N—Co—O and O—Co—O bond angles of (I) deviate significantly from 90 or 180°, presumably as a result of the steric constraints arising from the shape of the ligand. The angle subtended at the Co atom by the orotate ligand is 77.69 (13)°, which is in agreement with the values reported previously for other Co^II complexes (Zhang & You, 2003).

The orotate group of (I) is essentially planar (r.m.s. deviation = 0.0142 Å), with a slight deviation from planarity arising from the non-zero torsion angle between the carboxylate group and the ring. Of all the N—C bonds in the uracylic ring, N1—C1 and N1—C4 are the shortest. This indicates that there is considerable π-electron delocalization within the C3/C4/N1/C1 skeleton. The dihedral angle between the pyrimidine ring and the five-membered chelate ring is 4.82 (2)°, while that between the pyrimidine ring and the O4/C5/O6 carboxylate group is 6.07 (3)°. The C═O bond lengths for exocyclic atoms O5 and O7 clearly indicate their double-bond character (Table 1).

Crystal packing in (I) is achieved via intermolecular hydrogen bonding (Fig. 2 and Table 2). Graph-set notation (Bernstein et al., 1995) is used to describe these hydrogen-bonding patterns. Thus, the intramolecular O—H···O hydrogen bond can be described as an S(6) motif. Fig. 2 shows the way in which the three aqua ligands and carboxylate O6 and carbonyl O7 atoms enter into inter- and intramolecular hydrogen-bonding interactions. As a result, zigzag tapes are formed through O2Wⁱ—H2Aⁱ···O7ⁱⁱ, N2ⁱⁱ—H2ⁱⁱ···O4 and O2Wⁱ—H2Bⁱ···O6 interactions [symmetry codes: (i) −x + y, 1 − x, z − 1/3; (ii) y, 1 − x + y, z − 1/6], which define R₂³(10) and R₁¹(6) ring patterns. Furthermore, an R₄⁴(35) motif appears via the O1W^v—H1B^v···O7^iv, O2W^iv—H2A^iv···O7ⁱⁱⁱ and O2Wⁱⁱⁱ—H2Aⁱⁱⁱ···O7 interactions [symmetry codes: (iii) y, −x + y, z − 1/6; (iv) −x + y, −x, z − 1/3; (v) −1 + x, −1 + y, −z]. These helicoidal chains zigzagging along the a axis are interlinked through O1W—H1B···O7^vi and O2Wⁱⁱⁱ—H2Aⁱⁱⁱ···O7 interactions [symmetry code: (vi) 1 − x + y, 1 − x, z − 1/3], which in turn define an R₂²(16) ring pattern (Fig. 3).

S2. Experimental

A solution of Co(CH₃COO)₂·H₂O (1 mmol) in water (Volume?) was added to a solution of orotic acid (2 mmol) [In what? Volume?]. The solution was heated at 338 K and stirred for 1 d to remove CH₃COOH. The mixture was then left for crystallization. After two weeks, the product obtained was filtered off and dried in air. Analysis calculated for C₅H₁₀CoN₂O₉: C 21.0, H 3.50, N 9.8%; found: C 20.32, H 4.09, N 9.12%. IR (KBr, ν, cm⁻¹): 3390–3100 (b), 1652 (vs), 1605 (sh), 1376 (m), 1480 (w), 1021 (m).

S3. Refinement

H atoms bonded to C and N atoms were included in their expected positions and allowed to ride, with C—H and N—H distances restrained to 0.93 and 0.86 Å, respectively. Aqua H atoms were located in difference maps and refined subject to a DFIX restraint of O—H = 0.83 (3) Å. In all cases, H atoms were assigned a U_iso(H) value of 1.2U_eq of the parent atom. Attempts to refine O9 resulted in a partial occupancy of 0.716, which was later fixed at 0.72. The H atoms attached to non-coordinated water molecules O8 and O9 could not be located, though they appeared to be involved in strong hydrogen bonding to a neighbouring O atom.

Computing details

Data collection: X-AREA (Stoe & Cie, 2002); cell refinement: X-AREA; data reduction: X-RED (Stoe & Cie, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures

	Fig. 1. A view of the molecule of (I), with the atom-numbering scheme. The hydrogen bond is indicated by a dashed line. Displacement ellipsoids are drawn at the 30% probability level. [Symmetry code: (i) y, 1 − x + y, z − 1/6.]
	Fig. 2. A perspective view of the molecular packing of compound (I). Dashed lines indicate hydrogen bonds. Other H atoms have been omitted for clarity. [Symmetry codes: (i) −x + y, 1 − x, z − 1/3; (ii) y, 1 − x + y, z − 1/6; (iii) y, −x + y, z − 1/6; (iv) −x + y, −x, z − 1/3; (v) −1 + x, −1 + y, −z.]
	Fig. 3. The molecular structure of (I), viewed along the a axis. Dashed lines indicate hydrogen bonds. Other H atoms have been omitted for clarity. [Symmetry codes: (ii) 1 − x + y, 1 − x, z − 1/3; (iii) y, −x + y, z − 1/6.]

catena-Poly[[[triaquacobalt(II)]-µ-2,6-dioxo-1,2,3,6-tetrahydropyrimidine- 4-carboxylato(2-)] 1.72-hydrate]

Crystal data

[Co(C5H2N2O4)(H2O)3]·1.72H2O	Dx = 1.893 Mg m^−3
Mr = 294.6	Mo Kα radiation, λ = 0.71073 Å
Hexagonal, P61	Cell parameters from 5840 reflections
Hall symbol: P 61	θ = 2.1–28.0°
a = 13.4646 (12) Å	µ = 1.70 mm^−1
c = 9.8777 (7) Å	T = 100 K
V = 1550.9 (2) Å^3	Rod, brown
Z = 6	0.50 × 0.30 × 0.10 mm
F(000) = 892.6

Data collection

Stoe IPDS II diffractometer	1993 independent reflections
Radiation source: fine-focus sealed tube	1810 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.036
Detector resolution: 6.67 pixels mm^-1	θmax = 26.0°, θmin = 2.7°
ω scans	h = −16→11
Absorption correction: integration (X-RED32; Stoe & Cie, 2002)	k = −10→16
Tmin = 0.672, Tmax = 0.875	l = −12→11
5840 measured reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.038	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.087	w = 1/[σ^2(Fo^2) + (0.0318P)^2 + 3.8738P] where P = (Fo^2 + 2Fc^2)/3
S = 1.06	(Δ/σ)max = 0.003
1993 reflections	Δρmax = 0.92 e Å^−3
173 parameters	Δρmin = −0.94 e Å^−3
10 restraints	Absolute structure: Flack (1983), with how many Friedel pairs?
Primary atom site location: structure-invariant direct methods	Absolute structure parameter: −0.03 (3)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
Co1	0.59523 (5)	0.67470 (5)	0.72113 (7)	0.01434 (15)
O1W	0.6577 (3)	0.6615 (3)	0.5343 (4)	0.0222 (8)
H1A	0.704 (4)	0.712 (3)	0.483 (5)	0.027*
H1B	0.663 (5)	0.604 (3)	0.514 (5)	0.027*
O2W	0.5519 (3)	0.6990 (3)	0.9127 (4)	0.0212 (8)
H2A	0.484 (2)	0.665 (4)	0.931 (6)	0.025*
H2B	0.571 (4)	0.763 (3)	0.951 (6)	0.025*
O3W	0.7725 (3)	0.7854 (3)	0.7721 (4)	0.0206 (8)
H3A	0.793 (5)	0.831 (4)	0.836 (4)	0.025*
H3B	0.782 (5)	0.733 (3)	0.797 (5)	0.025*
C1	0.6696 (4)	0.5010 (4)	0.8005 (5)	0.0146 (9)
C2	0.5448 (4)	0.2936 (4)	0.8008 (5)	0.0131 (9)
C3	0.4556 (4)	0.3141 (4)	0.7586 (5)	0.0155 (10)
H3	0.3826	0.2533	0.7402	0.019*
C4	0.4793 (4)	0.4242 (4)	0.7456 (5)	0.0159 (9)
C5	0.3882 (4)	0.4531 (4)	0.6992 (5)	0.0151 (9)
N1	0.5834 (3)	0.5176 (3)	0.7676 (4)	0.0133 (8)
N2	0.6494 (3)	0.3913 (3)	0.8172 (4)	0.0146 (8)
H2	0.7065	0.3830	0.8396	0.017*
O4	0.4236 (3)	0.5578 (3)	0.6776 (4)	0.0201 (8)
O5	0.7706 (3)	0.5851 (3)	0.8176 (4)	0.0213 (8)
O6	0.2871 (3)	0.3742 (3)	0.6879 (3)	0.0192 (8)
O7	0.5352 (3)	0.1976 (3)	0.8214 (3)	0.0170 (7)
O8	0.8309 (5)	0.8593 (8)	0.4053 (11)	0.156 (5)
O9	0.8214 (7)	0.9712 (8)	0.9193 (16)	0.162 (8)	0.72

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Co1	0.0105 (3)	0.0121 (3)	0.0227 (3)	0.0073 (2)	0.0003 (3)	0.0018 (3)
O1W	0.0279 (18)	0.0142 (16)	0.029 (2)	0.0138 (15)	0.0069 (16)	0.0059 (15)
O2W	0.0193 (17)	0.0141 (16)	0.028 (2)	0.0068 (14)	0.0056 (15)	−0.0023 (15)
O3W	0.0141 (17)	0.0168 (17)	0.032 (2)	0.0085 (14)	−0.0001 (14)	0.0003 (15)
C1	0.011 (2)	0.012 (2)	0.019 (2)	0.0046 (18)	−0.0011 (17)	−0.0004 (17)
C2	0.0079 (19)	0.013 (2)	0.015 (2)	0.0029 (17)	0.0043 (18)	0.0015 (18)
C3	0.009 (2)	0.014 (2)	0.022 (3)	0.0041 (18)	0.0029 (17)	0.0031 (17)
C4	0.011 (2)	0.018 (2)	0.019 (3)	0.0070 (18)	−0.0014 (18)	0.0013 (18)
C5	0.013 (2)	0.014 (2)	0.018 (3)	0.0061 (18)	0.0009 (18)	−0.0009 (18)
N1	0.0087 (18)	0.0132 (18)	0.018 (2)	0.0056 (15)	−0.0009 (14)	0.0013 (15)
N2	0.0084 (17)	0.0130 (19)	0.023 (2)	0.0059 (15)	−0.0045 (15)	0.0027 (15)
O4	0.0111 (15)	0.0146 (16)	0.037 (2)	0.0084 (14)	−0.0025 (14)	0.0023 (14)
O5	0.0104 (15)	0.0110 (16)	0.042 (2)	0.0051 (13)	−0.0087 (15)	−0.0028 (15)
O6	0.0072 (15)	0.0146 (15)	0.032 (2)	0.0024 (13)	−0.0024 (13)	0.0010 (14)
O7	0.0140 (15)	0.0093 (15)	0.0252 (18)	0.0040 (13)	0.0003 (13)	0.0060 (13)
O8	0.026 (3)	0.142 (7)	0.249 (11)	0.004 (4)	−0.006 (5)	0.147 (8)
O9	0.040 (4)	0.051 (5)	0.35 (2)	−0.015 (4)	0.083 (8)	−0.092 (8)

Geometric parameters (Å, º)

Co1—O2W	2.054 (4)	C1—N1	1.328 (6)
Co1—O5^i	2.074 (3)	C1—N2	1.372 (6)
Co1—O1W	2.072 (4)	C2—O7	1.249 (6)
Co1—O4	2.089 (3)	C2—N2	1.374 (6)
Co1—N1	2.091 (4)	C2—C3	1.422 (6)
Co1—O3W	2.148 (3)	C3—C4	1.358 (6)
O1W—H1A	0.83 (3)	C3—H3	0.9300
O1W—H1B	0.83 (3)	C4—N1	1.353 (6)
O2W—H2A	0.81 (3)	C4—C5	1.531 (6)
O2W—H2B	0.86 (3)	C5—O6	1.244 (5)
O3W—H3A	0.82 (3)	C5—O4	1.260 (6)
O3W—H3B	0.82 (3)	N2—H2	0.8600
C1—O5	1.272 (5)	O5—Co1^ii	2.074 (3)
O2W—Co1—O5^i	90.60 (14)	O5—C1—N1	121.2 (4)
O2W—Co1—O1W	173.65 (14)	O5—C1—N2	119.4 (4)
O5^i—Co1—O1W	89.67 (14)	N1—C1—N2	119.4 (4)
O2W—Co1—O4	90.83 (14)	O7—C2—N2	119.8 (4)
O5^i—Co1—O4	93.73 (13)	O7—C2—C3	126.0 (4)
O1W—Co1—O4	95.48 (15)	N2—C2—C3	114.1 (4)
O2W—Co1—N1	94.28 (14)	C4—C3—C2	118.7 (4)
O5^i—Co1—N1	170.17 (15)	C4—C3—H3	120.7
O1W—Co1—N1	86.43 (14)	C2—C3—H3	120.7
O4—Co1—N1	77.69 (13)	N1—C4—C3	124.6 (4)
O2W—Co1—O3W	88.80 (14)	N1—C4—C5	113.6 (4)
O5^i—Co1—O3W	90.19 (13)	C3—C4—C5	121.7 (4)
O1W—Co1—O3W	84.86 (14)	O6—C5—O4	125.5 (4)
O4—Co1—O3W	176.07 (13)	O6—C5—C4	118.9 (4)
N1—Co1—O3W	98.43 (14)	O4—C5—C4	115.6 (4)
Co1—O1W—H1A	130 (4)	C1—N1—C4	118.0 (4)
Co1—O1W—H1B	121 (4)	C1—N1—Co1	126.4 (3)
H1A—O1W—H1B	103 (4)	C4—N1—Co1	115.1 (3)
Co1—O2W—H2A	116 (4)	C1—N2—C2	125.0 (4)
Co1—O2W—H2B	127 (4)	C1—N2—H2	117.5
H2A—O2W—H2B	100 (4)	C2—N2—H2	117.5
Co1—O3W—H3A	122 (4)	C5—O4—Co1	117.8 (3)
Co1—O3W—H3B	94 (4)	C1—O5—Co1^ii	132.5 (3)
H3A—O3W—H3B	106 (4)
O7—C2—C3—C4	177.6 (5)	O4—Co1—N1—C1	173.0 (4)
N2—C2—C3—C4	−3.3 (7)	O3W—Co1—N1—C1	−7.7 (4)
C2—C3—C4—N1	1.3 (8)	O2W—Co1—N1—C4	91.3 (3)
C2—C3—C4—C5	179.4 (4)	O1W—Co1—N1—C4	−95.0 (3)
N1—C4—C5—O6	−173.6 (4)	O4—Co1—N1—C4	1.4 (3)
C3—C4—C5—O6	8.1 (7)	O3W—Co1—N1—C4	−179.3 (3)
N1—C4—C5—O4	5.4 (6)	O5—C1—N2—C2	−179.5 (4)
C3—C4—C5—O4	−172.9 (5)	N1—C1—N2—C2	0.9 (8)
O5—C1—N1—C4	177.3 (5)	O7—C2—N2—C1	−178.4 (5)
N2—C1—N1—C4	−3.1 (7)	C3—C2—N2—C1	2.3 (7)
O5—C1—N1—Co1	5.9 (7)	O6—C5—O4—Co1	174.6 (4)
N2—C1—N1—Co1	−174.5 (3)	C4—C5—O4—Co1	−4.4 (5)
C3—C4—N1—C1	2.1 (7)	O2W—Co1—O4—C5	−92.4 (4)
C5—C4—N1—C1	−176.2 (4)	O5^i—Co1—O4—C5	177.0 (4)
C3—C4—N1—Co1	174.4 (4)	O1W—Co1—O4—C5	87.0 (4)
C5—C4—N1—Co1	−3.8 (5)	N1—Co1—O4—C5	1.8 (4)
O2W—Co1—N1—C1	−97.1 (4)	N1—C1—O5—Co1^ii	172.4 (3)
O1W—Co1—N1—C1	76.6 (4)	N2—C1—O5—Co1^ii	−7.2 (8)

Symmetry codes: (i) y, −x+y+1, z−1/6; (ii) x−y+1, x, z+1/6.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O4^ii	0.86	1.93	2.736 (5)	155
O1W—H1A···O8	0.83 (3)	2.01 (3)	2.819 (7)	164 (6)
O1W—H1B···O7^iii	0.83 (3)	1.89 (3)	2.719 (4)	173 (5)
O2W—H2A···O7^iv	0.81 (3)	1.95 (3)	2.717 (5)	157 (5)
O2W—H2B···O6^v	0.86 (3)	1.90 (3)	2.750 (5)	174 (5)
O3W—H3A···O9	0.82 (3)	1.92 (3)	2.676 (9)	153 (5)
O3W—H3B···O5	0.82 (3)	1.92 (3)	2.722 (5)	164 (5)

Symmetry codes: (ii) x−y+1, x, z+1/6; (iii) −x+y+1, −x+1, z−1/3; (iv) x−y, x, z+1/6; (v) −y+1, x−y+1, z+1/3.