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Acta Crystallogr Sect E Struct Rep Online. 2008 February 1; 64(Pt 2): m418.
Published online 2008 January 25. doi:  10.1107/S1600536808001487
PMCID: PMC2960368

(6-Oxido-2-oxo-1,2-dihydropyrimidine-5-carboxylato-κ2 O 5,O 6)(4-oxido-2-oxo-1,2-dihydropyrimidin-3-ium-5-carboxyl­ato-κ2 O 4,O 5)bis(1,10-phenanthroline-κ2 N,N′)erbium(III) dihydrate

Abstract

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.

Related literature

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

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Object name is e-64-0m418-scheme1.jpg

Experimental

Crystal data

  • [Er(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2O
  • M r = 872.88
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m418-efi1.jpg
  • a = 17.1602 (7) Å
  • b = 14.4170 (6) Å
  • c = 13.2433 (5) Å
  • β = 101.159 (1)°
  • V = 3214.4 (2) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 2.69 mm−1
  • T = 295 (2) K
  • 0.18 × 0.10 × 0.08 mm

Data collection

  • Bruker APEXII diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.645, T max = 0.814
  • 13567 measured reflections
  • 3680 independent reflections
  • 3495 reflections with I > 2σ(I)
  • R int = 0.024

Refinement

  • R[F 2 > 2σ(F 2)] = 0.024
  • wR(F 2) = 0.061
  • S = 1.05
  • 3680 reflections
  • 240 parameters
  • H-atom parameters constrained
  • Δρmax = 1.13 e Å−3
  • Δρmin = −0.38 e Å−3

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

Table 1
Selected geometric parameters (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808001487/xu2400sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808001487/xu2400Isup2.hkl

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Acknowledgments

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.

supplementary crystallographic information

Comment

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.

Experimental

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

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.

Figures

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.
Fig. 2.
Square antiprismatic coordination geometry of Er.

Crystal data

[Er(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2OF(000) = 1732
Mr = 872.88Dx = 1.804 Mg m3
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 mm1
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

Bruker APEXII diffractometer3680 independent reflections
Radiation source: fine-focus sealed tube3495 reflections with I > 2σ(I)
graphiteRint = 0.024
[var phi] 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

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 = 1.05w = 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 Å3
0 restraintsΔρmin = −0.38 e Å3

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

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)

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, °)

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, °)

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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: XU2400).

References

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