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Acta Cryst. (2008). E64, m418    [ doi:10.1107/S1600536808001487 ]

(6-Oxido-2-oxo-1,2-dihydropyrimidine-5-carboxylato-[kappa]2O5,O6)(4-oxido-2-oxo-1,2-dihydropyrimidin-3-ium-5-carboxylato-[kappa]2O4,O5)bis(1,10-phenanthroline-[kappa]2N,N')erbium(III) dihydrate

H.-H. Xing, Z.-L. Chen and S. W. Ng

Abstract top

The erbium(III) atom in the title compound, [Er(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2O, is located on a twofold rotation axis and chelated by two 1,10-phenanthroline heterocycles as well as by a 2,4-dihydroxypyrimidine-5-carboxylate monoanion and a 2,4-dihydroxypyrimidine-5-carboxylate dianion in a square-antiprismatic coordination geometry.

Comment top

2,4-Dihydroxypyrimidine-5-carboxylic acid (uracil-5-carboxylic acid, isoorotic acid) in the form of the singly-, doubly- and triply-deprotonated ion furnishes a number of compounds with both main group and transition metals in which the anion functions in a variety of binding modes. The acid itself exists as hydrated molecules held together by extensive hydrogen bonds (Law et al., 2004). The anion typically uses the 5-carboxylate and the 4-oxo/hydroxy oxygen atoms to chelate as this furnishes a six-membered chelate ring that confers stability.

The 1,10-phenanthroline-chelated rare-earth compounds, Ln(C12H8N2)2(C5H3N2O4)(C5H2N2O4).2H2O (Ln = Eu, Tb and Yb) represent the first examples of mononuclear lanthanum derivatives of the acid (Sun & Jin, 2004). The present erbium analog is isostructural with these, whose structures have been described in detail.

Related literature top

For the structure of 2,4-dihydroxypyridimine-5-carboxylic acid, see: Law et al. (2004). This erbium compound is isostructural with the europium, terbium and ytterbium analogs; see Sun & Jin (2004) for their detailed description.

Experimental top

2,4-Dihydroxypyrimidine-5-carboxylic acid (0.044 g, 0.25 mmol), erbium trichloride hexahydrate (0.096 g, 0.25 mmol), 1,10-phenanthroline (0.050 g, 0.25 mmol), sodium hydroxide (0.010 g, 0.25 mmol) and water (15 ml) was sealed in a 25-ml, Teflon-lined, stainless-steel Parr bomb. The bomb was heated to 383 K for 120 h. It was then cooled over 48 h to give red crystals in 90% yield. CH&N elemental analysis. Found/Calc. for C34H25ErN8O10: C 46.01; H 2.81, N 13.49% (46.78, 2.89, 12.84%).

Refinement top

Carbon-bound hydrogen atoms were generated geometrically, and were included in the refinements in the riding model approximation, as well the nitrogen-bound ones. The oxygen-bound ones were placed in chemically sensible positions on the basis of hydrogen bonding interactions. The final difference Fourier map had a large peak near Er1.

Computing details top

Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: Atomic coordinates taken from published analogs (Sun & Jin, 2004); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2008).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot of Er(C12H8N2)2(C5H3N2O4)(C5H2N2O4).2H2O drawn at the 50% probability level. Hydrogen atoms are drawn as spheres of arbitrary radii.
[Figure 2] Fig. 2. Square antiprismatic coordination geometry of Er.
(6-Oxido-2-oxo-1,2-dihydropyrimidine-5-carboxylato- κ2O5,O6)(4-oxido-2-oxo-1,2-dihydropyrimidin-3-ium-5- carboxylato-κ2O4,O5)bis(1,10-phenanthroline- κ2N,N')erbium(III) dihydrate top
Crystal data top
[Er(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2OF(000) = 1732
Mr = 872.88Dx = 1.804 Mg m−3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 8216 reflections
a = 17.1602 (7) Åθ = 2.3–28.5°
b = 14.4170 (6) ŵ = 2.69 mm−1
c = 13.2433 (5) ÅT = 295 K
β = 101.159 (1)°Prism, red
V = 3214.4 (2) Å30.18 × 0.10 × 0.08 mm
Z = 4
Data collection top
Bruker APEXII
diffractometer		3680 independent reflections
Radiation source: fine-focus sealed tube3495 reflections with I > 2σ(I)
graphiteRint = 0.024
φ and ω scansθmax = 27.5°, θmin = 1.9°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		h = −22→22
Tmin = 0.645, Tmax = 0.814k = −18→18
13567 measured reflectionsl = −17→17
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.024Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.061H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0387P)2 + 2.1981P]
where P = (Fo2 + 2Fc2)/3
3680 reflections(Δ/σ)max = 0.001
240 parametersΔρmax = 1.13 e Å−3
0 restraintsΔρmin = −0.38 e Å−3
Crystal data top
[Er(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2OV = 3214.4 (2) Å3
Mr = 872.88Z = 4
Monoclinic, C2/cMo Kα radiation
a = 17.1602 (7) ŵ = 2.69 mm−1
b = 14.4170 (6) ÅT = 295 K
c = 13.2433 (5) Å0.18 × 0.10 × 0.08 mm
β = 101.159 (1)°
Data collection top
Bruker APEXII
diffractometer		3495 reflections with I > 2σ(I)
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)		Rint = 0.024
Tmin = 0.645, Tmax = 0.814θmax = 27.5°
13567 measured reflectionsStandard reflections: 0
3680 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.024H-atom parameters constrained
wR(F2) = 0.061Δρmax = 1.13 e Å−3
S = 1.05Δρmin = −0.38 e Å−3
3680 reflectionsAbsolute structure: ?
240 parametersFlack parameter: ?
0 restraintsRogers parameter: ?
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/UeqOcc. (<1)
Er10.50000.612675 (9)0.75000.02099 (6)
O10.26939 (16)0.37986 (14)0.36337 (19)0.0436 (6)
O20.40471 (11)0.56690 (12)0.61245 (13)0.0293 (4)
O30.43054 (11)0.50209 (13)0.81183 (13)0.0312 (4)
O40.34769 (14)0.39182 (12)0.84072 (15)0.0341 (5)
O1W0.1905 (2)0.3113 (2)0.1608 (2)0.0912 (11)
H1W10.22540.32530.21460.137*
H1W20.20240.26030.13540.137*
N10.28276 (16)0.33178 (16)0.53134 (18)0.0367 (5)
H1N0.25880.28020.51370.055*0.50
N20.33356 (13)0.47408 (15)0.49382 (16)0.0276 (5)
H2N0.33850.51570.44890.041*
N30.53478 (13)0.69505 (15)0.59349 (17)0.0278 (5)
N40.59394 (13)0.74961 (15)0.78945 (17)0.0289 (5)
C10.29379 (18)0.39350 (17)0.4575 (2)0.0295 (6)
C20.36564 (14)0.49369 (17)0.59430 (18)0.0229 (5)
C30.35025 (15)0.42826 (17)0.66835 (18)0.0248 (5)
C40.30868 (18)0.3506 (2)0.6303 (2)0.0342 (6)
H40.29770.30740.67770.041*
C50.37729 (15)0.44133 (17)0.78069 (18)0.0247 (5)
C60.50987 (17)0.6671 (2)0.4970 (2)0.0346 (6)
H60.49060.60700.48560.042*
C70.5112 (2)0.7236 (3)0.4122 (2)0.0486 (8)
H70.49460.70080.34590.058*
C80.5368 (2)0.8118 (3)0.4271 (3)0.0556 (9)
H80.53520.85110.37100.067*
C90.5659 (2)0.8442 (2)0.5267 (3)0.0438 (7)
C100.56432 (16)0.78248 (18)0.6084 (2)0.0307 (6)
C110.5963 (2)0.9365 (3)0.5497 (3)0.0598 (10)
H110.59500.97870.49630.072*
C120.6260 (2)0.9627 (2)0.6459 (3)0.0586 (10)
H120.64571.02260.65820.070*
C130.6285 (2)0.9006 (2)0.7304 (3)0.0414 (7)
C140.6628 (2)0.9230 (2)0.8322 (3)0.0501 (9)
H140.68460.98160.84750.060*
C150.6646 (2)0.8603 (2)0.9083 (3)0.0464 (8)
H150.68910.87430.97550.056*
C160.62887 (17)0.7737 (2)0.8840 (2)0.0365 (6)
H160.62970.73100.93690.044*
C170.59569 (16)0.81116 (18)0.7125 (2)0.0289 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Er10.02696 (10)0.01677 (9)0.01709 (9)0.000−0.00108 (6)0.000
O10.0548 (14)0.0334 (12)0.0366 (12)−0.0041 (9)−0.0064 (11)0.0014 (8)
O20.0391 (10)0.0236 (9)0.0213 (9)−0.0088 (8)−0.0037 (7)0.0029 (7)
O30.0431 (11)0.0295 (10)0.0185 (8)−0.0109 (8)0.0001 (8)−0.0010 (7)
O40.0482 (13)0.0337 (11)0.0205 (10)−0.0117 (8)0.0067 (9)0.0007 (7)
O1W0.138 (3)0.0561 (18)0.0636 (19)0.0005 (19)−0.020 (2)0.0078 (15)
N10.0543 (15)0.0264 (11)0.0258 (11)−0.0119 (11)−0.0012 (10)−0.0033 (9)
N20.0369 (12)0.0260 (11)0.0170 (10)−0.0052 (9)−0.0019 (8)0.0019 (8)
N30.0300 (11)0.0262 (11)0.0268 (11)0.0003 (9)0.0044 (9)0.0020 (9)
N40.0279 (11)0.0259 (11)0.0318 (12)−0.0052 (9)0.0032 (9)−0.0043 (9)
C10.0366 (15)0.0267 (13)0.0216 (13)0.0007 (10)−0.0037 (11)−0.0030 (9)
C20.0263 (12)0.0213 (11)0.0193 (11)0.0005 (9)−0.0001 (9)0.0004 (9)
C30.0339 (13)0.0218 (12)0.0179 (11)−0.0048 (10)0.0030 (10)−0.0021 (9)
C40.0488 (17)0.0265 (14)0.0258 (13)−0.0117 (12)0.0038 (12)0.0025 (11)
C50.0325 (13)0.0224 (12)0.0185 (11)−0.0001 (10)0.0033 (9)0.0000 (9)
C60.0353 (14)0.0391 (15)0.0288 (14)−0.0033 (12)0.0046 (11)−0.0005 (12)
C70.0508 (19)0.069 (2)0.0261 (15)−0.0105 (17)0.0074 (13)0.0035 (15)
C80.064 (2)0.065 (2)0.0360 (18)−0.0098 (19)0.0076 (16)0.0225 (16)
C90.0465 (18)0.0383 (17)0.0466 (18)−0.0032 (14)0.0093 (14)0.0143 (14)
C100.0317 (13)0.0262 (13)0.0349 (14)−0.0009 (11)0.0085 (11)0.0053 (11)
C110.073 (3)0.040 (2)0.066 (3)−0.0157 (18)0.014 (2)0.0201 (18)
C120.066 (2)0.0325 (18)0.079 (3)−0.0160 (16)0.017 (2)0.0063 (17)
C130.0412 (17)0.0255 (14)0.060 (2)−0.0080 (12)0.0156 (15)−0.0060 (13)
C140.0486 (19)0.0355 (17)0.068 (2)−0.0169 (15)0.0155 (17)−0.0174 (17)
C150.0415 (17)0.0477 (18)0.049 (2)−0.0117 (15)0.0063 (15)−0.0215 (16)
C160.0352 (15)0.0401 (16)0.0330 (15)−0.0091 (12)0.0036 (12)−0.0077 (12)
C170.0269 (13)0.0220 (12)0.0383 (15)−0.0022 (10)0.0075 (11)−0.0009 (10)
Geometric parameters (Å, °) top
Er1—O22.297 (2)C2—C31.422 (3)
Er1—O2i2.297 (2)C3—C41.371 (4)
Er1—O32.238 (2)C3—C51.482 (3)
Er1—O3i2.238 (2)C4—H40.9300
Er1—N32.558 (2)C6—C71.391 (4)
Er1—N3i2.558 (2)C6—H60.9300
Er1—N42.538 (2)C7—C81.346 (5)
Er1—N4i2.538 (2)C7—H70.9300
O1—C11.252 (4)C8—C91.398 (5)
O2—C21.248 (3)C8—H80.9300
O3—C51.275 (3)C9—C101.405 (4)
O4—C51.247 (3)C9—C111.440 (5)
O1W—H1W10.85C10—C171.441 (4)
O1W—H1W20.85C11—C121.332 (6)
N1—C41.327 (3)C11—H110.9300
N1—C11.362 (4)C12—C131.428 (5)
N1—H1N0.8600C12—H120.9300
N2—C21.368 (3)C13—C141.400 (5)
N2—C11.385 (3)C13—C171.409 (4)
N2—H2N0.8600C14—C151.349 (6)
N3—C61.329 (3)C14—H140.9300
N3—C101.359 (3)C15—C161.401 (4)
N4—C161.326 (4)C15—H150.9300
N4—C171.356 (3)C16—H160.9300
O2—Er1—O2i146.6 (1)N1—C4—H4117.2
O2—Er1—O374.8 (1)C3—C4—H4117.2
O2—Er1—O3i81.6 (1)O4—C5—O3122.8 (2)
O2—Er1—N374.5 (1)O4—C5—C3118.7 (2)
O2—Er1—N3i122.3 (1)O3—C5—C3118.5 (2)
O2—Er1—N4135.5 (1)N3—C6—C7123.1 (3)
O2—Er1—N4i74.6 (1)N3—C6—H6118.5
O3—Er1—O3i89.2 (1)C7—C6—H6118.5
O3—Er1—N3148.4 (1)C8—C7—C6119.4 (3)
O3—Er1—N3i79.0 (1)C8—C7—H7120.3
O3—Er1—N4147.2 (1)C6—C7—H7120.3
O3—Er1—N4i105.5 (1)C7—C8—C9120.0 (3)
N3—Er1—N3i124.7 (1)C7—C8—H8120.0
N3—Er1—N464.4 (1)C9—C8—H8120.0
N3—Er1—N4i73.2 (1)C8—C9—C10117.3 (3)
N4—Er1—N4i77.9 (1)C8—C9—C11123.9 (3)
C2—O2—Er1131.99 (15)C10—C9—C11118.9 (3)
C5—O3—Er1140.34 (16)N3—C10—C9122.6 (3)
H1W1—O1W—H1W2110.3N3—C10—C17117.7 (2)
C4—N1—C1120.6 (2)C9—C10—C17119.7 (3)
C4—N1—H1N119.7C12—C11—C9121.4 (3)
C1—N1—H1N119.7C12—C11—H11119.3
C2—N2—C1126.1 (2)C9—C11—H11119.3
C2—N2—H2N116.9C11—C12—C13121.3 (3)
C1—N2—H2N116.9C11—C12—H12119.3
C6—N3—C10117.5 (2)C13—C12—H12119.3
C6—N3—Er1123.81 (18)C14—C13—C17116.9 (3)
C10—N3—Er1116.89 (17)C14—C13—C12123.6 (3)
C16—N4—C17117.8 (2)C17—C13—C12119.5 (3)
C16—N4—Er1123.46 (19)C15—C14—C13120.6 (3)
C17—N4—Er1117.38 (16)C15—C14—H14119.7
O1—C1—N1123.1 (2)C13—C14—H14119.7
O1—C1—N2121.6 (2)C14—C15—C16118.7 (3)
N1—C1—N2115.2 (2)C14—C15—H15120.7
O2—C2—N2117.5 (2)C16—C15—H15120.7
O2—C2—C3126.3 (2)N4—C16—C15123.2 (3)
N2—C2—C3116.1 (2)N4—C16—H16118.4
C4—C3—C2116.2 (2)C15—C16—H16118.4
C4—C3—C5120.8 (2)N4—C17—C13122.6 (3)
C2—C3—C5123.0 (2)N4—C17—C10118.2 (2)
N1—C4—C3125.5 (3)C13—C17—C10119.2 (3)
O3—Er1—O2—C2−23.0 (2)O2—C2—C3—C4−177.3 (3)
O3i—Er1—O2—C268.4 (2)N2—C2—C3—C43.4 (4)
O2i—Er1—O2—C223.4 (2)O2—C2—C3—C52.4 (4)
N4—Er1—O2—C2172.0 (2)N2—C2—C3—C5−176.9 (2)
N4i—Er1—O2—C2−134.2 (2)C1—N1—C4—C3−2.7 (5)
N3i—Er1—O2—C2−89.1 (2)C2—C3—C4—N10.6 (5)
N3—Er1—O2—C2149.3 (2)C5—C3—C4—N1−179.1 (3)
O3i—Er1—O3—C5−72.0 (3)Er1—O3—C5—O4−175.83 (19)
O2—Er1—O3—C59.5 (3)Er1—O3—C5—C35.0 (4)
O2i—Er1—O3—C5−146.7 (3)C4—C3—C5—O4−15.3 (4)
N4—Er1—O3—C5169.9 (2)C2—C3—C5—O4165.0 (3)
N4i—Er1—O3—C578.3 (3)C4—C3—C5—O3163.9 (3)
N3i—Er1—O3—C5137.6 (3)C2—C3—C5—O3−15.7 (4)
N3—Er1—O3—C5−4.7 (3)C10—N3—C6—C7−1.4 (4)
O3—Er1—N3—C6−6.7 (3)Er1—N3—C6—C7162.9 (2)
O3i—Er1—N3—C663.3 (2)N3—C6—C7—C8−1.8 (5)
O2—Er1—N3—C6−20.9 (2)C6—C7—C8—C93.6 (6)
O2i—Er1—N3—C6127.3 (2)C7—C8—C9—C10−2.2 (5)
N4—Er1—N3—C6176.5 (2)C7—C8—C9—C11178.5 (4)
N4i—Er1—N3—C6−99.1 (2)C6—N3—C10—C92.9 (4)
N3i—Er1—N3—C6−139.7 (2)Er1—N3—C10—C9−162.5 (2)
O3—Er1—N3—C10157.69 (17)C6—N3—C10—C17−176.4 (2)
O3i—Er1—N3—C10−132.33 (19)Er1—N3—C10—C1718.2 (3)
O2—Er1—N3—C10143.5 (2)C8—C9—C10—N3−1.1 (5)
O2i—Er1—N3—C10−68.3 (2)C11—C9—C10—N3178.3 (3)
N4—Er1—N3—C10−19.07 (17)C8—C9—C10—C17178.2 (3)
N4i—Er1—N3—C1065.31 (19)C11—C9—C10—C17−2.4 (5)
N3i—Er1—N3—C1024.68 (17)C8—C9—C11—C12−177.4 (4)
O3—Er1—N4—C168.6 (3)C10—C9—C11—C123.2 (6)
O3i—Er1—N4—C16−105.1 (2)C9—C11—C12—C13−0.6 (7)
O2—Er1—N4—C16161.2 (2)C11—C12—C13—C14176.5 (4)
O2i—Er1—N4—C16−36.1 (2)C11—C12—C13—C17−2.7 (6)
N4i—Er1—N4—C16108.5 (2)C17—C13—C14—C150.7 (5)
N3i—Er1—N4—C1641.9 (2)C12—C13—C14—C15−178.6 (4)
N3—Er1—N4—C16−174.5 (2)C13—C14—C15—C16−2.3 (5)
O3—Er1—N4—C17−157.77 (17)C17—N4—C16—C152.3 (4)
O3i—Er1—N4—C1788.48 (19)Er1—N4—C16—C15−164.0 (2)
O2—Er1—N4—C17−5.2 (2)C14—C15—C16—N40.8 (5)
O2i—Er1—N4—C17157.4 (2)C16—N4—C17—C13−4.1 (4)
N4i—Er1—N4—C17−57.88 (17)Er1—N4—C17—C13163.1 (2)
N3i—Er1—N4—C17−124.5 (2)C16—N4—C17—C10174.5 (2)
N3—Er1—N4—C1719.09 (18)Er1—N4—C17—C10−18.3 (3)
C4—N1—C1—O1−178.8 (3)C14—C13—C17—N42.6 (4)
C4—N1—C1—N20.5 (4)C12—C13—C17—N4−178.1 (3)
C2—N2—C1—O1−176.8 (3)C14—C13—C17—C10−175.9 (3)
C2—N2—C1—N13.9 (4)C12—C13—C17—C103.4 (4)
Er1—O2—C2—N2−158.37 (17)N3—C10—C17—N4−0.1 (4)
Er1—O2—C2—C322.3 (4)C9—C10—C17—N4−179.4 (3)
C1—N2—C2—O2174.7 (3)N3—C10—C17—C13178.5 (3)
C1—N2—C2—C3−5.9 (4)C9—C10—C17—C13−0.8 (4)
Symmetry codes: (i) −x+1, y, −z+3/2.
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N1—H1n···N1ii0.861.822.675 (5)174
N2—H2n···O4iii0.861.992.846 (3)178
O1w—H1w1···O10.852.122.933 (4)157
O1w—H1w2···O4ii0.852.403.000 (4)128
Symmetry codes: (ii) −x+1/2, −y+1/2, −z+1; (iii) x, −y+1, z−1/2.
Table 1
Selected geometric parameters (Å, °) top
Er1—O22.297 (2)Er1—N32.558 (2)
Er1—O32.238 (2)Er1—N42.538 (2)
O2—Er1—O2i146.6 (1)O3—Er1—N3148.4 (1)
O2—Er1—O374.8 (1)O3—Er1—N3i79.0 (1)
O2—Er1—O3i81.6 (1)O3—Er1—N4147.2 (1)
O2—Er1—N374.5 (1)O3—Er1—N4i105.5 (1)
O2—Er1—N3i122.3 (1)N3—Er1—N3i124.7 (1)
O2—Er1—N4135.5 (1)N3—Er1—N464.4 (1)
O2—Er1—N4i74.6 (1)N3—Er1—N4i73.2 (1)
O3—Er1—O3i89.2 (1)N4—Er1—N4i77.9 (1)
Symmetry codes: (i) −x+1, y, −z+3/2.
Acknowledgements top

The authors thank the Scientifc Research Foundation of Guangxi Normal University, China, the Science Foundation of Guangxi Province, China (Grant No. 0542021) and the University of Malaya for supporting this study.

references
References top

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