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Acta Crystallogr Sect E Struct Rep Online. 2008 September 1; 64(Pt 9): m1166–m1167.
Published online 2008 August 16. doi:  10.1107/S1600536808025701
PMCID: PMC2960551

(2,4-Dioxo-1,2,3,4-tetra­hydro­pyrimi­dine-5-carboxyl­ato-κ2 O 4,O 5)(4-oxido-2-oxo-1,2-dihydro­pyrimidine-5-carboxyl­ato-κ2 O 4,O 5)bis­(1,10-phenanthroline-κ2 N,N′)yttrium(III) dihydrate

Abstract

In the title compound, [Y(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2O, the YIII ion lies on a twofold rotation axis and exhibits a distorted square-anti­prismatic coordination geometry. It is chelated by two 1,10-phenanthroline ligands, a 2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate mono­anion and a 4-oxido-2-oxo-1,2-dihydro­pyrimidine-5-carboxyl­ate dianion. The H atom involved in an N—H(...)N hydrogen bond between the 1,2-dihydro­pyrimidine units has half occupancy and is disordered around a twofold rotation axis.

Related literature

For the crystal structures of the isostructural Er, Eu, Tb and Yb complexes, see: Sun & Jin (2004 [triangle]); Xing et al. (2008 [triangle]). For other related literature, see: Tobiki et al. (1980 [triangle]); Castan et al. (1990 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-m1166-scheme1.jpg

Experimental

Crystal data

  • [Y(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2O
  • M r = 794.53
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-m1166-efi1.jpg
  • a = 17.1740 (13) Å
  • b = 14.4385 (11) Å
  • c = 13.2365 (10) Å
  • β = 100.881 (1)°
  • V = 3223.2 (4) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 1.89 mm−1
  • T = 295 (2) K
  • 0.24 × 0.08 × 0.06 mm

Data collection

  • Bruker APEXII diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 1998 [triangle]) T min = 0.660, T max = 0.895
  • 12035 measured reflections
  • 3152 independent reflections
  • 2986 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.045
  • wR(F 2) = 0.096
  • S = 1.21
  • 3152 reflections
  • 240 parameters
  • H-atom parameters constrained
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.51 e Å−3

Data collection: APEX2 (Bruker, 2004 [triangle]); cell refinement: SAINT (Bruker, 2004 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Selected geometric parameters (Å, °)
Table 2
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808025701/gk2161sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808025701/gk2161Isup2.hkl

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

Acknowledgments

The authors thank the Science Foundation of Guangxi Province, China (Guikeqing 0542021) and the Scientific Research Foundation for Returned Overseas Chinese Scholars, State Education Ministry, for financial support.

supplementary crystallographic information

Comment

2,4-Dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid has attracted much attention because of its potential biological activity and pharmaceutical properties, such as anticancer, antibacterial and antihypertensive properties (Tobiki et al., 1980; Castan et al., 1990). Here we report the crystal structure of YIII complex with 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid and 1,10-phenenthroline as ligands. The title complex turned out to be isostructural with the analogues Eu, Tb, Yb (Sun & Jin, 2004) and Er (Xing et al., 2008) complexes; see Sun & Jin (2004) for their detailed description.

Experimental

A mixture of 2,4-dihydroxypyrimidine-5-carboxylic acid (0.0312 g, 0.2 mmol), YCl3.6H2O (0.0607 g, 0.2 mmol), phenanthroline dihydrate (0.0396 g, 0.2 mmol), NaOH (0.0160 g, 0.4 mmol) and water (15 ml) was sealed in a 25 ml, Teflon-lined stainless-steel reactor and heated to 383 K for 120 h. It was then cooled over 48 h to give colourless crystals in 70% yield. Elemental analysis calculated for C34H25N8O10Y: C 51.40, H 3.17, N 14.10%; found: C 51.77, H 3.29, N 14.49%.

Refinement

H atoms of the water molecule were located in a difference Fourier map and allowed to ride on their parent atom [Uiso(H) = 1.5Ueq(O)]. Other H atoms were placed at calculated positions (C—H = 0.93 Å and N—H = 0.86 Å) and were included in the refinement in the riding model approximation, with Uiso(H) = 1.2Ueq(C, N). The pyrimidine hydrogen atom H4 is shared by two N—H groups and thus has an occupancy factor of 0.5.

Figures

Fig. 1.
The molecular structure of the title compound with the atom-numbering scheme and 30% displacement ellipsoids.

Crystal data

[Y(C5H2N2O4)(C5H3N2O4)(C12H8N2)2]·2H2OF000 = 1616
Mr = 794.53Dx = 1.637 Mg m3
Monoclinic, C2/cMo Kα radiation λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 7855 reflections
a = 17.1740 (13) Åθ = 2.3–27.9º
b = 14.4385 (11) ŵ = 1.89 mm1
c = 13.2365 (10) ÅT = 295 (2) K
β = 100.8810 (10)ºPrism, colourless
V = 3223.2 (4) Å30.24 × 0.08 × 0.06 mm
Z = 4

Data collection

Bruker APEXII diffractometer3152 independent reflections
Radiation source: fine-focus sealed tube2986 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.035
T = 295(2) Kθmax = 26.0º
[var phi] and ω scansθmin = 1.9º
Absorption correction: multi-scan(SADABS; Bruker, 1998)h = −21→21
Tmin = 0.660, Tmax = 0.895k = −17→17
12035 measured reflectionsl = −16→16

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.046H-atom parameters constrained
wR(F2) = 0.096  w = 1/[σ2(Fo2) + (0.0141P)2 + 9.88P] where P = (Fo2 + 2Fc2)/3
S = 1.21(Δ/σ)max < 0.001
3152 reflectionsΔρmax = 0.41 e Å3
240 parametersΔρmin = −0.51 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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)

xyzUiso*/UeqOcc. (<1)
Y11.00000.88802 (3)0.25000.02339 (12)
N10.90591 (16)0.75076 (19)0.2117 (2)0.0324 (6)
N20.96510 (16)0.80446 (19)0.4073 (2)0.0304 (6)
N30.83326 (16)1.02589 (19)−0.0065 (2)0.0297 (6)
H30.83790.9842−0.05140.036*
N40.78240 (19)1.1684 (2)0.0310 (2)0.0387 (7)
H40.75851.21990.01310.046*0.50
O10.90470 (14)0.93356 (15)0.11247 (17)0.0329 (6)
O20.93006 (14)0.99886 (16)0.31195 (17)0.0337 (6)
O30.84729 (15)1.10907 (17)0.34049 (17)0.0371 (6)
O40.76917 (16)1.11986 (18)−0.13684 (19)0.0451 (7)
C10.8770 (2)1.0594 (2)0.2805 (2)0.0272 (7)
C20.84980 (19)1.0723 (2)0.1678 (2)0.0269 (7)
C30.86584 (18)1.0066 (2)0.0941 (2)0.0248 (7)
C40.7937 (2)1.1063 (2)−0.0423 (3)0.0324 (7)
C50.8085 (2)1.1498 (2)0.1311 (3)0.0358 (8)
H50.79761.19280.17880.043*
C60.9900 (2)0.8317 (3)0.5036 (3)0.0386 (8)
H61.00890.89200.51480.046*
C70.9896 (3)0.7758 (3)0.5890 (3)0.0512 (11)
H71.00740.79820.65520.061*
C80.9624 (3)0.6872 (3)0.5735 (3)0.0599 (12)
H80.96260.64830.62960.072*
C90.9342 (2)0.6545 (3)0.4735 (3)0.0463 (10)
C100.9355 (2)0.7169 (2)0.3922 (3)0.0327 (8)
C110.9042 (2)0.6886 (2)0.2883 (3)0.0325 (8)
C120.8716 (2)0.5993 (2)0.2699 (3)0.0419 (9)
C130.8735 (3)0.5372 (3)0.3546 (4)0.0607 (13)
H130.85340.47760.34230.073*
C140.9036 (3)0.5634 (3)0.4513 (4)0.0618 (13)
H140.90450.52150.50480.074*
C150.8370 (2)0.5768 (3)0.1686 (4)0.0510 (11)
H150.81480.51850.15330.061*
C160.8357 (2)0.6401 (3)0.0926 (3)0.0490 (10)
H160.81190.62620.02520.059*
C170.8707 (2)0.7264 (3)0.1173 (3)0.0397 (9)
H170.86930.76930.06470.048*
O50.6925 (3)0.1887 (2)0.6600 (3)0.0956 (14)
H510.67930.24540.66440.143*
H520.70820.16810.72080.143*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Y10.0287 (2)0.0187 (2)0.0207 (2)0.000−0.00062 (16)0.000
N10.0322 (16)0.0288 (15)0.0352 (16)−0.0037 (12)0.0040 (12)−0.0035 (12)
N20.0318 (15)0.0294 (15)0.0297 (15)−0.0002 (12)0.0051 (12)0.0008 (12)
N30.0389 (16)0.0276 (15)0.0204 (13)0.0051 (12)0.0001 (12)−0.0021 (11)
N40.057 (2)0.0273 (15)0.0278 (15)0.0107 (14)−0.0016 (14)0.0018 (12)
O10.0421 (14)0.0265 (12)0.0255 (12)0.0100 (10)−0.0052 (10)−0.0034 (9)
O20.0441 (14)0.0324 (13)0.0226 (12)0.0133 (11)0.0011 (10)0.0006 (10)
O30.0510 (15)0.0374 (14)0.0227 (12)0.0125 (12)0.0064 (11)−0.0021 (10)
O40.0562 (17)0.0369 (15)0.0358 (14)0.0044 (13)−0.0074 (12)0.0002 (12)
C10.0345 (18)0.0240 (16)0.0224 (16)−0.0025 (14)0.0032 (13)0.0017 (13)
C20.0328 (17)0.0263 (16)0.0207 (16)0.0053 (14)0.0031 (13)0.0002 (13)
C30.0284 (16)0.0237 (16)0.0209 (15)−0.0008 (13)0.0014 (13)0.0007 (12)
C40.0373 (19)0.0291 (18)0.0280 (17)−0.0006 (15)−0.0012 (14)0.0021 (14)
C50.050 (2)0.0292 (18)0.0263 (18)0.0094 (16)0.0031 (16)−0.0026 (14)
C60.039 (2)0.042 (2)0.0339 (19)−0.0026 (17)0.0042 (16)−0.0029 (16)
C70.056 (3)0.070 (3)0.028 (2)−0.010 (2)0.0082 (18)0.0061 (19)
C80.066 (3)0.069 (3)0.044 (2)−0.008 (2)0.009 (2)0.024 (2)
C90.048 (2)0.043 (2)0.048 (2)−0.0034 (19)0.0101 (19)0.0158 (19)
C100.0306 (18)0.0296 (18)0.0384 (19)−0.0007 (14)0.0078 (15)0.0034 (15)
C110.0311 (18)0.0269 (17)0.0399 (19)−0.0005 (14)0.0072 (15)−0.0017 (15)
C120.042 (2)0.0279 (19)0.058 (2)−0.0074 (16)0.0137 (19)−0.0027 (17)
C130.074 (3)0.030 (2)0.080 (3)−0.018 (2)0.017 (3)0.004 (2)
C140.076 (3)0.042 (3)0.068 (3)−0.017 (2)0.016 (3)0.021 (2)
C150.051 (2)0.035 (2)0.069 (3)−0.0161 (19)0.016 (2)−0.018 (2)
C160.047 (2)0.050 (2)0.049 (2)−0.0137 (19)0.0063 (19)−0.022 (2)
C170.039 (2)0.039 (2)0.040 (2)−0.0064 (17)0.0052 (16)−0.0062 (16)
O50.145 (4)0.059 (2)0.067 (2)0.004 (2)−0.017 (2)−0.0089 (19)

Geometric parameters (Å, °)

Y1—O2i2.247 (2)C2—C31.423 (4)
Y1—O22.247 (2)C5—H50.9300
Y1—O1i2.302 (2)C6—C71.391 (5)
Y1—O12.302 (2)C6—H60.9300
Y1—N12.547 (3)C7—C81.362 (6)
Y1—N1i2.547 (3)C7—H70.9300
Y1—N2i2.573 (3)C8—C91.403 (6)
Y1—N22.573 (3)C8—H80.9300
N1—C171.329 (4)C9—C101.407 (5)
N1—C111.358 (4)C9—C141.426 (6)
N2—C61.326 (4)C10—C111.439 (5)
N2—C101.363 (4)C11—C121.408 (5)
N3—C31.373 (4)C12—C151.399 (6)
N3—C41.383 (4)C12—C131.431 (6)
N3—H30.8600C13—C141.342 (6)
N4—C51.343 (4)C13—H130.9300
N4—C41.362 (4)C14—H140.9300
N4—H40.8600C15—C161.355 (6)
O1—C31.247 (4)C15—H150.9300
O2—C11.275 (4)C16—C171.395 (5)
O3—C11.248 (4)C16—H160.9300
O4—C41.258 (4)C17—H170.9300
C1—C21.489 (4)O5—H510.8533
C2—C51.364 (4)O5—H520.8518
O2i—Y1—O289.15 (13)C3—C2—C1122.6 (3)
O2i—Y1—O1i74.69 (8)O1—C3—N3117.7 (3)
O2—Y1—O1i81.79 (9)O1—C3—C2126.6 (3)
O2i—Y1—O181.79 (8)N3—C3—C2115.7 (3)
O2—Y1—O174.69 (8)O4—C4—N4122.7 (3)
O1i—Y1—O1146.81 (11)O4—C4—N3121.5 (3)
O2i—Y1—N1147.62 (8)N4—C4—N3115.8 (3)
O2—Y1—N1105.31 (9)N4—C5—C2124.8 (3)
O1i—Y1—N1135.17 (8)N4—C5—H5117.6
O1—Y1—N174.65 (9)C2—C5—H5117.6
O2i—Y1—N1i105.31 (9)N2—C6—C7124.0 (4)
O2—Y1—N1i147.62 (8)N2—C6—H6118.0
O1i—Y1—N1i74.65 (9)C7—C6—H6118.0
O1—Y1—N1i135.17 (8)C8—C7—C6118.5 (4)
N1—Y1—N1i77.82 (13)C8—C7—H7120.7
O2i—Y1—N2i79.43 (8)C6—C7—H7120.7
O2—Y1—N2i148.38 (8)C7—C8—C9120.4 (4)
O1i—Y1—N2i122.30 (9)C7—C8—H8119.8
O1—Y1—N2i74.55 (8)C9—C8—H8119.8
N1—Y1—N2i73.15 (9)C8—C9—C10117.0 (4)
N1i—Y1—N2i63.90 (9)C8—C9—C14123.6 (4)
O2i—Y1—N2148.38 (8)C10—C9—C14119.4 (4)
O2—Y1—N279.43 (9)N2—C10—C9122.8 (3)
O1i—Y1—N274.55 (8)N2—C10—C11117.7 (3)
O1—Y1—N2122.30 (9)C9—C10—C11119.5 (3)
N1—Y1—N263.90 (9)N1—C11—C12122.7 (3)
N1i—Y1—N273.15 (9)N1—C11—C10118.0 (3)
N2i—Y1—N2124.07 (12)C12—C11—C10119.3 (3)
C17—N1—C11117.1 (3)C15—C12—C11117.5 (4)
C17—N1—Y1123.5 (2)C15—C12—C13123.2 (4)
C11—N1—Y1117.9 (2)C11—C12—C13119.3 (4)
C6—N2—C10117.4 (3)C14—C13—C12121.2 (4)
C6—N2—Y1123.8 (2)C14—C13—H13119.4
C10—N2—Y1117.0 (2)C12—C13—H13119.4
C3—N3—C4125.9 (3)C13—C14—C9121.2 (4)
C3—N3—H3117.0C13—C14—H14119.4
C4—N3—H3117.0C9—C14—H14119.4
C5—N4—C4120.3 (3)C16—C15—C12119.9 (4)
C5—N4—H4119.9C16—C15—H15120.0
C4—N4—H4119.9C12—C15—H15120.0
C3—O1—Y1132.1 (2)C15—C16—C17118.8 (4)
C1—O2—Y1140.2 (2)C15—C16—H16120.6
O3—C1—O2122.6 (3)C17—C16—H16120.6
O3—C1—C2118.5 (3)N1—C17—C16123.9 (4)
O2—C1—C2118.8 (3)N1—C17—H17118.1
C5—C2—C3117.2 (3)C16—C17—H17118.1
C5—C2—C1120.2 (3)H51—O5—H52108.2
O2i—Y1—N1—C17−8.9 (4)C4—N3—C3—O1−174.8 (3)
O2—Y1—N1—C17104.9 (3)C4—N3—C3—C26.6 (5)
O1i—Y1—N1—C17−161.4 (3)C5—C2—C3—O1177.5 (3)
O1—Y1—N1—C1735.9 (3)C1—C2—C3—O1−1.8 (5)
N1i—Y1—N1—C17−108.3 (3)C5—C2—C3—N3−4.0 (5)
N2i—Y1—N1—C17−42.2 (3)C1—C2—C3—N3176.7 (3)
N2—Y1—N1—C17174.6 (3)C5—N4—C4—O4178.8 (4)
O2i—Y1—N1—C11157.1 (2)C5—N4—C4—N3−0.5 (5)
O2—Y1—N1—C11−89.1 (2)C3—N3—C4—O4176.4 (3)
O1i—Y1—N1—C114.6 (3)C3—N3—C4—N4−4.3 (5)
O1—Y1—N1—C11−158.1 (3)C4—N4—C5—C22.7 (6)
N1i—Y1—N1—C1157.7 (2)C3—C2—C5—N4−0.3 (6)
N2i—Y1—N1—C11123.8 (3)C1—C2—C5—N4179.0 (3)
N2—Y1—N1—C11−19.3 (2)C10—N2—C6—C71.8 (5)
O2i—Y1—N2—C67.0 (4)Y1—N2—C6—C7−162.4 (3)
O2—Y1—N2—C6−63.6 (3)N2—C6—C7—C80.4 (6)
O1i—Y1—N2—C620.7 (3)C6—C7—C8—C9−1.3 (7)
O1—Y1—N2—C6−127.8 (3)C7—C8—C9—C100.0 (7)
N1—Y1—N2—C6−176.6 (3)C7—C8—C9—C14−178.8 (5)
N1i—Y1—N2—C699.0 (3)C6—N2—C10—C9−3.2 (5)
N2i—Y1—N2—C6139.5 (3)Y1—N2—C10—C9162.2 (3)
O2i—Y1—N2—C10−157.3 (2)C6—N2—C10—C11176.5 (3)
O2—Y1—N2—C10132.1 (2)Y1—N2—C10—C11−18.1 (4)
O1i—Y1—N2—C10−143.6 (2)C8—C9—C10—N22.3 (6)
O1—Y1—N2—C1067.9 (2)C14—C9—C10—N2−178.8 (4)
N1—Y1—N2—C1019.1 (2)C8—C9—C10—C11−177.4 (4)
N1i—Y1—N2—C10−65.3 (2)C14—C9—C10—C111.5 (6)
N2i—Y1—N2—C10−24.8 (2)C17—N1—C11—C124.1 (5)
O2i—Y1—O1—C3−68.1 (3)Y1—N1—C11—C12−162.8 (3)
O2—Y1—O1—C323.3 (3)C17—N1—C11—C10−174.4 (3)
O1i—Y1—O1—C3−23.2 (3)Y1—N1—C11—C1018.7 (4)
N1—Y1—O1—C3134.3 (3)N2—C10—C11—N1−0.2 (5)
N1i—Y1—O1—C3−171.6 (3)C9—C10—C11—N1179.6 (3)
N2i—Y1—O1—C3−149.3 (3)N2—C10—C11—C12−178.7 (3)
N2—Y1—O1—C389.8 (3)C9—C10—C11—C121.1 (5)
O2i—Y1—O2—C172.0 (3)N1—C11—C12—C15−2.7 (6)
O1i—Y1—O2—C1146.7 (4)C10—C11—C12—C15175.7 (3)
O1—Y1—O2—C1−9.7 (3)N1—C11—C12—C13178.8 (4)
N1—Y1—O2—C1−78.6 (3)C10—C11—C12—C13−2.8 (6)
N1i—Y1—O2—C1−170.0 (3)C15—C12—C13—C14−176.4 (5)
N2i—Y1—O2—C14.0 (4)C11—C12—C13—C142.0 (7)
N2—Y1—O2—C1−137.6 (4)C12—C13—C14—C90.6 (8)
Y1—O2—C1—O3176.0 (2)C8—C9—C14—C13176.5 (5)
Y1—O2—C1—C2−4.6 (5)C10—C9—C14—C13−2.3 (7)
O3—C1—C2—C515.4 (5)C11—C12—C15—C16−0.1 (6)
O2—C1—C2—C5−164.0 (3)C13—C12—C15—C16178.4 (4)
O3—C1—C2—C3−165.3 (3)C12—C15—C16—C171.3 (6)
O2—C1—C2—C315.2 (5)C11—N1—C17—C16−2.8 (5)
Y1—O1—C3—N3158.7 (2)Y1—N1—C17—C16163.3 (3)
Y1—O1—C3—C2−22.8 (5)C15—C16—C17—N10.2 (6)

Symmetry codes: (i) −x+2, y, −z+1/2.

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N3—H3···O3ii0.861.992.853 (4)178
N3—H3···O2ii0.862.633.189 (4)124
N4—H4···N4iii0.861.812.667 (6)174
O5—H51···O3iv0.852.152.998 (4)173
O5—H52···O4v0.852.102.935 (4)169

Symmetry codes: (ii) x, −y+2, z−1/2; (iii) −x+3/2, −y+5/2, −z; (iv) −x+3/2, −y+3/2, −z+1; (v) x, y−1, z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GK2161).

References

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