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Acta Crystallogr Sect E Struct Rep Online. 2008 March 1; 64(Pt 3): m500–m501.
Published online 2008 February 29. doi:  10.1107/S1600536808005230
PMCID: PMC2960886

Diaqua­(2,6-dioxo-1,2,3,6-tetra­hydro­pyrimidin-3-ide-4-carboxyl­ato-κ2 N 3,O 4)(1,10-phenanthroline-κ2 N,N′)manganese(II)

Abstract

The title compound, [Mn(C5H2N2O4)(C12H8N2)(H2O)2], was synthesized by the reaction of manganese(II) acetate and orotic acid in the presence of 1,10-phenanthroline. The crystal structure exhibits inter­molecular N—H(...)O and O—H(...)O hydrogen bonds . The Mn coordination environment consists of an N3O3 donor set in an octa­hedral geometry.

Related literature

For biochemical processes, see: Mukhopadhyay et al., (2004 [triangle]); Ren et al., (2005 [triangle]). For bioinorganic and pharmaceutical studies, see: Lieberman et al., (1955 [triangle]). For coordination chemistry and other aspects, see: Darensbourg et al., (1998 [triangle]). For complexes of the orotate ligand, see: Hambley et al., (1995 [triangle]); Nepveu et al., (1995 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-64-0m500-scheme1.jpg

Experimental

Crystal data

  • [Mn(C5H2N2O4)(C12H8N2)(H2O)2]
  • M r = 425.26
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0m500-efi1.jpg
  • a = 8.3173 (2) Å
  • b = 8.9875 (2) Å
  • c = 11.9509 (3) Å
  • α = 78.2780 (10)°
  • β = 82.9100 (10)°
  • γ = 74.7440 (10)°
  • V = 841.58 (3) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.83 mm−1
  • T = 293 (2) K
  • 0.15 × 0.12 × 0.10 mm

Data collection

  • Bruker SMART diffractometer
  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996 [triangle]) T min = 0.885, T max = 0.921
  • 9718 measured reflections
  • 2950 independent reflections
  • 2539 reflections with I > 2σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 0.072
  • S = 1.05
  • 2950 reflections
  • 257 parameters
  • H-atom parameters constrained
  • Δρmax = 0.21 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: SMART (Bruker, 2007 [triangle]); cell refinement: SAINT (Bruker, 2007 [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: SHELXL97.

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

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808005230/om2206sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808005230/om2206Isup2.hkl

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

Acknowledgments

The authors thank the Postgraduate Foundation of Taishan University for financial support.

supplementary crystallographic information

Comment

Manganese is an important element in organisms and involved in many biochemical processes (Mukhopadhyay et al., 2004 and Ren et al., 2005). It may be observed in the active parts of many enzymes. Orotic acid (2, 6-dioxo-1, 2, 3, 6-tetrahydropyrimidine-4- carboxylic acid), an important pyrimidine derivative as the effective precursor in the biosynthesis of pyrimidine base of nucleic acids in living organisms, plays an important role in bioinorganic chemistry and pharmaceutical studies (Lieberman et al., 1955), material science, coordination chemistry and other aspects (Darensbourg et al., 1998). Many complexes of the orotate ligand have been reported (Hambley et al., 1995).

In the title compound (Fig, 1), Mn(C12H8N2)(C5H2N2O4)(H2O)2, the Mn(II) ion is coordinated by N and O atoms from the orotate (2, 6-dioxo-1, 2, 3, 6-tetrahydropyrimidine- 4-carboxylate) ligand. The bond lengths and angles are in good agreement with reported values (Nepveu et al., 1995). In the crystal structure, the molecule with its two coordinated water molecules is linked into infinite chains by O—H···O and N—H···O hydrogen bonds.

Experimental

Orotic acid (0.0012 mol), 1, 10-phenanthroline (0.0012 mol) and Mn(CH3COO)2.2H2O (0.0012 mol, 0.294 g) in 120 ml of water were stirred at 373 K for 24 h; the pH of the solution was adjusted to 6 using a dilute aqueous solution of ammonia. After evaporation of the solution for two weeks, colorless block-like crystals were isolated by filtration. Analysis, calculated for C17H14N4O6Mn: C 48.01, H 3.32, N 13.17; found: C 48.00, H 3.30, N 13.16. Crystals suitable for single-crystal X-ray analysis were selected directly from the sample.

Refinement

All H atoms were initially located in a difference Fourier map, but placed in idealized positions (C—H 0.93 Å, N—H 0.86 Å), with Uiso(H) = 1.2Ueq(C). The O—H bond lengths were constrained to 0.85Å and the isotropic thermal parameters of the H atoms bonded to water were refined.

Figures

Fig. 1.
The structure of the title compound, showing 30% probability displacement ellipsoids and the atom-numbering scheme. The H atoms are omitted.

Crystal data

[Mn(C5H2N2O4)(C12H8N2)(H2O)2]Z = 2
Mr = 425.26F000 = 434
Triclinic, P1Dx = 1.678 Mg m3
a = 8.3173 (2) ÅMo Kα radiation λ = 0.71073 Å
b = 8.9875 (2) ÅCell parameters from 3161 reflections
c = 11.9509 (3) Åθ = 2.4–24.5º
α = 78.2780 (10)ºµ = 0.83 mm1
β = 82.9100 (10)ºT = 293 (2) K
γ = 74.7440 (10)ºBlock, colorless
V = 841.58 (3) Å30.15 × 0.12 × 0.10 mm

Data collection

Bruker SMART diffractometer2950 independent reflections
Radiation source: fine-focus sealed tube2539 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.027
T = 293(2) Kθmax = 25.0º
[var phi] and ω scansθmin = 1.8º
Absorption correction: multi-scan(SADABS; Sheldrick, 1996)h = −9→9
Tmin = 0.886, Tmax = 0.922k = −10→10
9718 measured reflectionsl = −14→13

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.072  w = 1/[σ2(Fo2) + (0.0269P)2 + 0.4894P] where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max = 0.001
2950 reflectionsΔρmax = 0.22 e Å3
257 parametersΔρmin = −0.22 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

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 (Å2)

xyzUiso*/Ueq
Mn10.11775 (4)0.19441 (4)0.78756 (3)0.03047 (11)
N10.2989 (2)−0.03517 (19)0.85359 (15)0.0276 (4)
N20.3993 (2)−0.29802 (19)0.93896 (15)0.0305 (4)
H20.3786−0.38840.96360.037*
N3−0.0891 (2)0.3718 (2)0.68697 (16)0.0336 (4)
N40.1453 (2)0.1395 (2)0.60556 (16)0.0358 (4)
O10.35761 (18)0.24240 (17)0.75978 (15)0.0416 (4)
O20.62451 (19)0.16456 (19)0.79231 (17)0.0532 (5)
O30.13026 (17)−0.20586 (16)0.89654 (13)0.0335 (4)
O40.66615 (18)−0.40215 (16)0.98859 (14)0.0385 (4)
O50.0660 (2)0.33271 (19)0.92439 (14)0.0414 (4)
H5A0.14540.36720.93920.085 (11)*
H5B0.01680.30240.98830.084 (11)*
O6−0.07494 (19)0.08117 (19)0.86706 (15)0.0437 (4)
H6A−0.16730.10300.83650.071 (10)*
H6B−0.0474−0.01820.88530.081 (11)*
C10.4836 (3)0.1428 (2)0.79908 (19)0.0312 (5)
C20.4575 (2)−0.0191 (2)0.85488 (17)0.0258 (4)
C30.5858 (3)−0.1354 (2)0.89906 (19)0.0304 (5)
H30.6906−0.11670.89870.036*
C40.5589 (3)−0.2856 (2)0.94576 (18)0.0294 (5)
C50.2696 (2)−0.1773 (2)0.89586 (17)0.0266 (4)
C6−0.2058 (3)0.4826 (3)0.7282 (2)0.0450 (6)
H6−0.20160.49590.80280.054*
C7−0.3352 (3)0.5805 (3)0.6641 (3)0.0534 (7)
H7−0.41570.65650.69620.064*
C8−0.3428 (3)0.5639 (3)0.5547 (3)0.0506 (7)
H8−0.42730.62990.51100.061*
C9−0.2226 (3)0.4470 (3)0.5079 (2)0.0409 (6)
C10−0.2204 (3)0.4214 (3)0.3930 (2)0.0508 (7)
H10−0.30200.48490.34580.061*
C11−0.1026 (4)0.3072 (3)0.3523 (2)0.0518 (7)
H11−0.10450.29260.27760.062*
C120.0259 (3)0.2076 (3)0.4220 (2)0.0427 (6)
C130.1512 (4)0.0871 (3)0.3838 (2)0.0521 (7)
H130.15340.06810.30990.062*
C140.2700 (3)−0.0023 (3)0.4549 (2)0.0525 (7)
H140.3547−0.08170.43000.063*
C150.2621 (3)0.0277 (3)0.5655 (2)0.0439 (6)
H150.3431−0.03420.61380.053*
C160.0279 (3)0.2301 (3)0.53475 (19)0.0343 (5)
C17−0.0985 (3)0.3524 (2)0.57867 (19)0.0329 (5)

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
Mn10.02175 (18)0.03294 (19)0.0356 (2)−0.00587 (13)−0.00776 (14)−0.00124 (14)
N10.0201 (9)0.0290 (9)0.0327 (10)−0.0066 (7)−0.0040 (7)−0.0010 (7)
N20.0263 (9)0.0241 (9)0.0415 (11)−0.0077 (7)−0.0084 (8)−0.0008 (8)
N30.0267 (10)0.0351 (10)0.0387 (11)−0.0079 (8)−0.0068 (8)−0.0029 (8)
N40.0300 (10)0.0404 (10)0.0362 (11)−0.0080 (8)−0.0044 (8)−0.0048 (9)
O10.0251 (8)0.0330 (8)0.0610 (11)−0.0081 (7)−0.0124 (7)0.0117 (7)
O20.0238 (9)0.0409 (9)0.0900 (14)−0.0128 (7)−0.0162 (9)0.0134 (9)
O30.0240 (8)0.0351 (8)0.0431 (9)−0.0116 (6)−0.0060 (7)−0.0026 (7)
O40.0276 (8)0.0280 (8)0.0585 (11)−0.0045 (6)−0.0166 (7)0.0006 (7)
O50.0368 (9)0.0515 (10)0.0428 (10)−0.0209 (8)−0.0032 (8)−0.0105 (8)
O60.0266 (9)0.0398 (10)0.0637 (12)−0.0115 (7)−0.0110 (8)0.0022 (8)
C10.0237 (11)0.0313 (11)0.0374 (13)−0.0075 (9)−0.0050 (9)−0.0011 (9)
C20.0211 (10)0.0297 (10)0.0268 (11)−0.0063 (8)−0.0028 (8)−0.0046 (8)
C30.0213 (11)0.0303 (11)0.0401 (13)−0.0079 (9)−0.0066 (9)−0.0031 (9)
C40.0254 (11)0.0298 (11)0.0338 (12)−0.0055 (9)−0.0067 (9)−0.0069 (9)
C50.0242 (11)0.0298 (11)0.0265 (11)−0.0070 (8)−0.0030 (9)−0.0052 (9)
C60.0357 (14)0.0430 (14)0.0547 (16)−0.0043 (11)−0.0076 (12)−0.0096 (12)
C70.0371 (14)0.0415 (14)0.077 (2)−0.0003 (11)−0.0107 (14)−0.0080 (14)
C80.0368 (14)0.0400 (14)0.073 (2)−0.0092 (11)−0.0255 (13)0.0083 (13)
C90.0365 (13)0.0380 (13)0.0495 (15)−0.0170 (10)−0.0175 (11)0.0083 (11)
C100.0535 (16)0.0579 (16)0.0433 (16)−0.0286 (14)−0.0259 (13)0.0189 (13)
C110.0628 (18)0.0657 (18)0.0334 (14)−0.0306 (15)−0.0145 (13)0.0025 (13)
C120.0473 (15)0.0529 (15)0.0341 (14)−0.0268 (12)−0.0046 (11)−0.0022 (11)
C130.0637 (18)0.0646 (17)0.0367 (15)−0.0308 (15)0.0069 (13)−0.0155 (13)
C140.0529 (17)0.0530 (16)0.0520 (17)−0.0133 (13)0.0118 (14)−0.0193 (13)
C150.0381 (14)0.0452 (14)0.0460 (15)−0.0065 (11)−0.0009 (11)−0.0088 (12)
C160.0335 (12)0.0402 (12)0.0323 (13)−0.0184 (10)−0.0046 (10)0.0006 (10)
C170.0290 (12)0.0359 (12)0.0355 (13)−0.0160 (9)−0.0076 (10)0.0034 (10)

Geometric parameters (Å, °)

Mn1—O12.1231 (15)C2—C31.356 (3)
Mn1—O62.1439 (15)C3—C41.416 (3)
Mn1—O52.1852 (16)C3—H30.9300
Mn1—N12.2686 (16)C6—C71.396 (3)
Mn1—N32.2880 (18)C6—H60.9300
Mn1—N42.2979 (19)C7—C81.356 (4)
N1—C51.348 (3)C7—H70.9300
N1—C21.366 (2)C8—C91.401 (4)
N2—C41.375 (3)C8—H80.9300
N2—C51.378 (3)C9—C171.402 (3)
N2—H20.8600C9—C101.435 (4)
N3—C61.323 (3)C10—C111.344 (4)
N3—C171.355 (3)C10—H100.9300
N4—C151.323 (3)C11—C121.432 (4)
N4—C161.356 (3)C11—H110.9300
O1—C11.256 (2)C12—C131.399 (4)
O2—C11.229 (2)C12—C161.405 (3)
O3—C51.250 (2)C13—C141.362 (4)
O4—C41.248 (2)C13—H130.9300
O5—H5A0.8500C14—C151.392 (4)
O5—H5B0.8500C14—H140.9300
O6—H6A0.8499C15—H150.9300
O6—H6B0.8501C16—C171.442 (3)
C1—C21.531 (3)
O1—Mn1—O6157.87 (6)O4—C4—N2119.95 (18)
O1—Mn1—O587.31 (6)O4—C4—C3125.78 (19)
O6—Mn1—O588.81 (6)N2—C4—C3114.26 (18)
O1—Mn1—N174.55 (6)O3—C5—N1123.06 (18)
O6—Mn1—N185.75 (6)O3—C5—N2118.06 (18)
O5—Mn1—N1106.65 (6)N1—C5—N2118.87 (17)
O1—Mn1—N3116.16 (6)N3—C6—C7122.6 (3)
O6—Mn1—N385.65 (6)N3—C6—H6118.7
O5—Mn1—N390.50 (6)C7—C6—H6118.7
N1—Mn1—N3160.61 (6)C8—C7—C6119.6 (3)
O1—Mn1—N489.63 (7)C8—C7—H7120.2
O6—Mn1—N4101.40 (7)C6—C7—H7120.2
O5—Mn1—N4159.04 (7)C7—C8—C9119.7 (2)
N1—Mn1—N492.45 (6)C7—C8—H8120.1
N3—Mn1—N472.31 (7)C9—C8—H8120.1
C5—N1—C2117.78 (17)C8—C9—C17117.0 (2)
C5—N1—Mn1129.53 (13)C8—C9—C10123.6 (2)
C2—N1—Mn1112.58 (12)C17—C9—C10119.4 (2)
C4—N2—C5125.27 (17)C11—C10—C9121.2 (2)
C4—N2—H2117.4C11—C10—H10119.4
C5—N2—H2117.4C9—C10—H10119.4
C6—N3—C17118.0 (2)C10—C11—C12121.0 (2)
C6—N3—Mn1125.65 (16)C10—C11—H11119.5
C17—N3—Mn1116.18 (14)C12—C11—H11119.5
C15—N4—C16118.1 (2)C13—C12—C16117.5 (2)
C15—N4—Mn1126.10 (16)C13—C12—C11123.3 (2)
C16—N4—Mn1115.76 (15)C16—C12—C11119.2 (2)
C1—O1—Mn1120.96 (13)C14—C13—C12120.0 (2)
Mn1—O5—H5A117.0C14—C13—H13120.0
Mn1—O5—H5B121.2C12—C13—H13120.0
H5A—O5—H5B106.8C13—C14—C15118.7 (2)
Mn1—O6—H6A119.7C13—C14—H14120.6
Mn1—O6—H6B117.1C15—C14—H14120.6
H6A—O6—H6B105.6N4—C15—C14123.4 (2)
O2—C1—O1124.9 (2)N4—C15—H15118.3
O2—C1—C2118.71 (18)C14—C15—H15118.3
O1—C1—C2116.29 (17)N4—C16—C12122.2 (2)
C3—C2—N1124.23 (19)N4—C16—C17117.9 (2)
C3—C2—C1120.98 (18)C12—C16—C17119.9 (2)
N1—C2—C1114.78 (17)N3—C17—C9123.0 (2)
C2—C3—C4119.51 (18)N3—C17—C16117.71 (19)
C2—C3—H3120.2C9—C17—C16119.2 (2)
C4—C3—H3120.2
O1—Mn1—N1—C5−176.35 (19)C5—N2—C4—O4178.6 (2)
O6—Mn1—N1—C513.84 (18)C5—N2—C4—C3−2.7 (3)
O5—Mn1—N1—C5101.32 (18)C2—C3—C4—O4179.8 (2)
N3—Mn1—N1—C5−50.0 (3)C2—C3—C4—N21.1 (3)
N4—Mn1—N1—C5−87.41 (18)C2—N1—C5—O3−178.39 (19)
O1—Mn1—N1—C27.66 (13)Mn1—N1—C5—O35.8 (3)
O6—Mn1—N1—C2−162.15 (14)C2—N1—C5—N20.6 (3)
O5—Mn1—N1—C2−74.67 (14)Mn1—N1—C5—N2−175.20 (13)
N3—Mn1—N1—C2133.99 (19)C4—N2—C5—O3−179.11 (19)
N4—Mn1—N1—C296.60 (14)C4—N2—C5—N11.8 (3)
O1—Mn1—N3—C6−101.28 (19)C17—N3—C6—C7−1.0 (3)
O6—Mn1—N3—C674.74 (19)Mn1—N3—C6—C7−175.60 (18)
O5—Mn1—N3—C6−14.03 (19)N3—C6—C7—C8−0.6 (4)
N1—Mn1—N3—C6138.6 (2)C6—C7—C8—C91.2 (4)
N4—Mn1—N3—C6178.2 (2)C7—C8—C9—C17−0.3 (3)
O1—Mn1—N3—C1784.04 (15)C7—C8—C9—C10−179.7 (2)
O6—Mn1—N3—C17−99.94 (15)C8—C9—C10—C11−179.8 (2)
O5—Mn1—N3—C17171.29 (15)C17—C9—C10—C110.7 (4)
N1—Mn1—N3—C17−36.1 (3)C9—C10—C11—C12−0.4 (4)
N4—Mn1—N3—C173.49 (14)C10—C11—C12—C13180.0 (2)
O1—Mn1—N4—C1560.93 (19)C10—C11—C12—C160.1 (4)
O6—Mn1—N4—C15−99.75 (19)C16—C12—C13—C14−0.5 (4)
O5—Mn1—N4—C15142.4 (2)C11—C12—C13—C14179.6 (2)
N1—Mn1—N4—C15−13.59 (19)C12—C13—C14—C150.8 (4)
N3—Mn1—N4—C15178.6 (2)C16—N4—C15—C14−0.4 (3)
O1—Mn1—N4—C16−120.22 (15)Mn1—N4—C15—C14178.45 (18)
O6—Mn1—N4—C1679.11 (15)C13—C14—C15—N4−0.4 (4)
O5—Mn1—N4—C16−38.7 (3)C15—N4—C16—C120.7 (3)
N1—Mn1—N4—C16165.26 (15)Mn1—N4—C16—C12−178.23 (16)
N3—Mn1—N4—C16−2.52 (14)C15—N4—C16—C17−179.66 (19)
O6—Mn1—O1—C119.9 (3)Mn1—N4—C16—C171.4 (2)
O5—Mn1—O1—C1100.05 (18)C13—C12—C16—N4−0.3 (3)
N1—Mn1—O1—C1−8.05 (17)C11—C12—C16—N4179.6 (2)
N3—Mn1—O1—C1−170.71 (16)C13—C12—C16—C17−179.9 (2)
N4—Mn1—O1—C1−100.69 (18)C11—C12—C16—C170.0 (3)
Mn1—O1—C1—O2−175.75 (19)C6—N3—C17—C92.0 (3)
Mn1—O1—C1—C26.9 (3)Mn1—N3—C17—C9177.10 (16)
C5—N1—C2—C3−2.1 (3)C6—N3—C17—C16−179.21 (19)
Mn1—N1—C2—C3174.40 (17)Mn1—N3—C17—C16−4.1 (2)
C5—N1—C2—C1176.54 (18)C8—C9—C17—N3−1.4 (3)
Mn1—N1—C2—C1−7.0 (2)C10—C9—C17—N3178.1 (2)
O2—C1—C2—C31.8 (3)C8—C9—C17—C16179.9 (2)
O1—C1—C2—C3179.4 (2)C10—C9—C17—C16−0.6 (3)
O2—C1—C2—N1−176.8 (2)N4—C16—C17—N31.8 (3)
O1—C1—C2—N10.7 (3)C12—C16—C17—N3−178.55 (19)
N1—C2—C3—C41.2 (3)N4—C16—C17—C9−179.33 (19)
C1—C2—C3—C4−177.38 (19)C12—C16—C17—C90.3 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···O4i0.861.972.831 (2)177
O5—H5A···O4ii0.852.002.829 (2)164
O5—H5B···O3iii0.851.952.769 (2)162
O6—H6A···O2iv0.851.792.627 (2)170
O6—H6B···O30.851.922.675 (2)147

Symmetry codes: (i) −x+1, −y−1, −z+2; (ii) −x+1, −y, −z+2; (iii) −x, −y, −z+2; (iv) x−1, y, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: OM2206).

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