research communications
E)-9-(4-nitrobenzylidene)-8,9-dihydropyrido[2,3-d]pyrrolo[1,2-a]pyrimidin-5(7H)-one
of (aS. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str. 77, Tashkent 100170, Uzbekistan, and bA. S. Sadikov Institute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, Mirzo Ulugbek Str. 83, Tashkent 100125, Uzbekistan
*Correspondence e-mail: hamidkhodjaniyazov@yandex.ru
The title compound, C17H12N4O3, a pyridopyrrolopyrimidine derivative, is almost planar. The nitrobenzene ring is inclined to the mean plane of the 8,9-dihydropyrido[2,3-d]pyrrolo[1,2-a]pyrimidin-5(7H)-one moiety (r.m.s. deviation = 0.023 Å) by 6.8 (1)°. In the crystal, molecules are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming layers parallel to (101).
Keywords: crystal structure; pyridopyrimidine; pyridopyrrolopyrimidine; 4-nitrobenzaldehyde; ylidene derivative; hydrogen bonding.
CCDC reference: 1456732
1. Chemical context
Pyrido[2,3-d]pyrimidines, and their derivatives, are an important group of that exhibit biological and pharmacological activities. For example, Le Corre et al. (2010) have produced a library of pyrido[2,3-d]pyrimidines designed as inhibitors of FGFR3 tyrosine kinase. Ramana Reddy et al. (2014) have shown that such compounds are potent inhibitors of cyclin-dependent Kinase 4 (CDK4) and AMPK-related Kinase 5 (ARK5). A series of pyrazolo [4,3-d]pyrimidin-7-ones were synthesizied to study their pyrido kinases (CDKs) inhibitory activities (Geffken et al. 2011). The antitumor activity of some new pyrido[2,3-d][1,2,4]triazolo[4,3-a]pyrimidin-5-one derivatives have also been studied (El-Nassan, 2011), and the antitumor activity of pyrido[2,3-d]pyrimidine and pyrido[2,3-d][1,2,4]triazolo[4,3-a]pyrimidine derivatives that induce apoptosis through G1 cell-cycle arrest have been reported on by Fares et al. (2014). The above observations prompted us to synthesize the title compound, which contains a pyrido[2,3-d]pyrimidin-4-one moiety, and we report herein on its crystal structure.
2. Structural commentary
In the molecular structure of the title compound (Fig. 1), the three fused rings of the 8,9-dihydropyrido[2,3-d]pyrrolo[1,2-a]pyrimidin-5(7H)-one moiety (N1–N3/C1–C10), are essentially planar (r.m.s. deviation = 0.023 Å), with the maximum deviation from the mean plane being 0.036 (2) Å for atom C8. The nitrobenzene ring (C12–C17) is inclined to this mean plane by 6.8 (1)°, while the nitro group (N4/O2/O3) is inclined to the benzene ring by 15.0 (3)°.
3. Supramolecular features
In the crystal, molecules are linked via C—H⋯O and C—H⋯N hydrogen bonds, forming layers lying parallel to (101); see Fig. 2 and Table 1. Within the layers there are R22(7), R33(17), and R33(21) graph-set motifs present (Fig. 2). The layers are separated by an average interplanar distance of ca 3.4 Å, but there are no significant interlayer interactions present (Fig. 3).
4. Database survey
A search of the Cambridge Structural Database (Version 5.37, update November 2015; Groom & Allen, 2014) was carried out for various substructures (S1 and S2; Fig. 4) resembling the title compound. For S1 (8,9-dihydropyrido[2,3-d]pyrrolo[1,2-a]pyrimidin-5(7H)-one), no hits were obtained. For S2 (4H-3λ2-pyrido[2,3-d]pyrimidin-4-one), seven hits were found. Two of these compounds have S3 (pyrido[2′,3′:4,5]pyrimido[1,2-a]indol-5(11H)-one), viz 9-fluoropyrido[2′,3′:4,5]pyrimido[1,2-a]indole-5,11-dione (refcode NIJYIP; CCDC 269950; Hicks et al., 2005), and 9-bromopyrido[2′,3′:4,5]pyrimido[1,2-a]indole-5,11-dione (refcode NIJYOV; CCDC 218226; DiTusa, 2003). They are classed as tryptanthrins, which have been shown to have strong antibacterial activity, for example, against malaria (Hicks et al., 2005).
5. Synthesis and crystallization
To a mixture of 2,3-trimethylenepyrido[2,3-d]pyrimidin-4-one (0.094 g, 0.5 mmol) and p-nitrobenzaldehyde (0.094 g, 0.6 mmol) was added acetic acid (3 ml, 98%). This mixture was refluxed in an oil bath (ca. 423-433 K) for 5 h after which it was left to stand for 24 h. During this time a yellow precipitate formed. It was filtered and washed with distilled water, giving yellow crystals of the title compound (yield: 0.144 g, 0.45 mmol, 90%; m.p. 567–568 K). Yellow block-like crystals suitable for X-ray analysis were grown from a solution of ethanol:water (2:1) by slow evaporation at room temperature. The title product is insoluble in benzene, chloroform, acetic acid, acetone, DMF, and DMSO, but soluble in trifluoroacetic acid. 1H NMR (400MHz, CDCl3, δ, p.p.m., J/Hz): 3.15 (2H, td, J = 6.5; 2.9, β-CH2), 4.16 (2H, t, J = 6.5, γ-CH2), 7.44 (2H, d, J = 8.8, H-2′,6′), 7.60 (1H, dd, J = 7.9; 5.9, H-6), 7.83 (1H, t, J = 2.9, =CH), 7.98 (2H, d, J = 8.8, H-3′,5′), 8.63 (1H, dd, J = 5.9; 1.7, H-5), 9.00 (1H, dd, J = 7.9; 1.7, H-7). Rf = 0.47 (chloroform:methanol, 10:1).
6. Refinement
Crystal data, data collection and structure . H atoms were placed in calculated positions and included in the final cycles of using a riding-model approximation: C—H = 0.93–0.97 Å with Uiso(H) = 1.2Ueq(C).
details are summarized in Table 2Supporting information
CCDC reference: 1456732
https://doi.org/10.1107/S2056989016003583/su5283sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016003583/su5283Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989016003583/su5283Isup3.cml
Data collection: CrysAlis PRO (Oxford Diffraction, 2009); cell
CrysAlis PRO (Oxford Diffraction, 2009); data reduction: CrysAlis PRO (Oxford Diffraction, 2009); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: XP in SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).C17H12N4O3 | F(000) = 664 |
Mr = 320.31 | Dx = 1.483 Mg m−3 |
Monoclinic, P21/c | Cu Kα radiation, λ = 1.54184 Å |
a = 7.1755 (3) Å | Cell parameters from 2842 reflections |
b = 11.5855 (3) Å | θ = 4.6–75.6° |
c = 17.2515 (5) Å | µ = 0.88 mm−1 |
β = 90.360 (3)° | T = 293 K |
V = 1434.12 (8) Å3 | Block, yellow |
Z = 4 | 0.20 × 0.18 × 0.15 mm |
Oxford Diffraction Xcalibur Ruby diffractometer | 2194 reflections with I > 2σ(I) |
Detector resolution: 10.2576 pixels mm-1 | Rint = 0.045 |
ω scans | θmax = 76.0°, θmin = 4.6° |
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2009) | h = −8→9 |
Tmin = 0.928, Tmax = 1.000 | k = −7→14 |
10375 measured reflections | l = −21→20 |
2965 independent reflections |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.057 | H-atom parameters constrained |
wR(F2) = 0.175 | w = 1/[σ2(Fo2) + (0.0826P)2 + 0.3825P] where P = (Fo2 + 2Fc2)/3 |
S = 1.08 | (Δ/σ)max < 0.001 |
2965 reflections | Δρmax = 0.31 e Å−3 |
217 parameters | Δρmin = −0.20 e Å−3 |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.7005 (3) | −0.09081 (15) | 0.54727 (12) | 0.0677 (6) | |
O2 | 0.9284 (3) | 0.88109 (16) | 0.33072 (13) | 0.0718 (6) | |
O3 | 0.9755 (5) | 0.7632 (2) | 0.23673 (14) | 0.0913 (9) | |
N1 | 0.6413 (3) | 0.24377 (15) | 0.62105 (12) | 0.0462 (5) | |
N2 | 0.7312 (3) | 0.10238 (16) | 0.52922 (11) | 0.0446 (5) | |
N3 | 0.5181 (4) | 0.18637 (18) | 0.73866 (13) | 0.0584 (6) | |
N4 | 0.9345 (3) | 0.78291 (19) | 0.30362 (13) | 0.0560 (6) | |
C1 | 0.7062 (3) | 0.21345 (18) | 0.55449 (13) | 0.0428 (5) | |
C2 | 0.6831 (4) | 0.00730 (19) | 0.57260 (15) | 0.0471 (5) | |
C3 | 0.5521 (4) | −0.0476 (2) | 0.70117 (16) | 0.0527 (6) | |
H3 | 0.5655 | −0.1253 | 0.6891 | 0.063* | |
C4 | 0.4772 (4) | −0.0150 (2) | 0.76967 (16) | 0.0572 (7) | |
H4 | 0.4362 | −0.0698 | 0.8051 | 0.069* | |
C5 | 0.4631 (5) | 0.1021 (2) | 0.78581 (16) | 0.0611 (7) | |
H5 | 0.4114 | 0.1232 | 0.8330 | 0.073* | |
C6 | 0.5898 (3) | 0.15420 (19) | 0.66978 (14) | 0.0454 (5) | |
C7 | 0.6088 (3) | 0.03714 (19) | 0.64897 (13) | 0.0441 (5) | |
C8 | 0.7641 (3) | 0.29244 (19) | 0.49255 (13) | 0.0428 (5) | |
C9 | 0.8364 (4) | 0.2207 (2) | 0.42615 (14) | 0.0506 (6) | |
H9A | 0.9678 | 0.2356 | 0.4178 | 0.061* | |
H9B | 0.7685 | 0.2379 | 0.3787 | 0.061* | |
C10 | 0.8050 (4) | 0.0949 (2) | 0.45079 (15) | 0.0526 (6) | |
H10A | 0.7167 | 0.0572 | 0.4164 | 0.063* | |
H10B | 0.9213 | 0.0522 | 0.4503 | 0.063* | |
C11 | 0.7470 (3) | 0.4070 (2) | 0.50057 (14) | 0.0452 (5) | |
H11 | 0.6939 | 0.4308 | 0.5469 | 0.054* | |
C12 | 0.7990 (3) | 0.50060 (19) | 0.44770 (13) | 0.0422 (5) | |
C13 | 0.8910 (4) | 0.4833 (2) | 0.37725 (15) | 0.0502 (6) | |
H13 | 0.9231 | 0.4089 | 0.3621 | 0.060* | |
C14 | 0.9345 (4) | 0.5759 (2) | 0.33012 (14) | 0.0495 (6) | |
H14 | 0.9938 | 0.5643 | 0.2830 | 0.059* | |
C15 | 0.8886 (3) | 0.6858 (2) | 0.35404 (13) | 0.0459 (5) | |
C16 | 0.8010 (4) | 0.7066 (2) | 0.42325 (14) | 0.0474 (5) | |
H16 | 0.7732 | 0.7816 | 0.4385 | 0.057* | |
C17 | 0.7552 (3) | 0.6140 (2) | 0.46970 (14) | 0.0465 (5) | |
H17 | 0.6944 | 0.6270 | 0.5163 | 0.056* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.1034 (16) | 0.0362 (9) | 0.0640 (12) | −0.0012 (9) | 0.0249 (11) | −0.0063 (8) |
O2 | 0.1033 (17) | 0.0415 (10) | 0.0708 (13) | −0.0056 (10) | 0.0169 (12) | 0.0069 (9) |
O3 | 0.151 (2) | 0.0669 (14) | 0.0568 (13) | 0.0001 (14) | 0.0446 (15) | 0.0151 (10) |
N1 | 0.0638 (12) | 0.0332 (9) | 0.0419 (10) | −0.0014 (8) | 0.0163 (9) | −0.0002 (7) |
N2 | 0.0558 (11) | 0.0365 (9) | 0.0416 (10) | 0.0003 (8) | 0.0106 (8) | −0.0027 (7) |
N3 | 0.0854 (16) | 0.0414 (11) | 0.0485 (12) | 0.0009 (10) | 0.0222 (11) | 0.0014 (9) |
N4 | 0.0722 (14) | 0.0476 (11) | 0.0485 (12) | −0.0036 (10) | 0.0120 (10) | 0.0120 (9) |
C1 | 0.0499 (12) | 0.0336 (10) | 0.0448 (12) | 0.0002 (8) | 0.0075 (9) | −0.0014 (8) |
C2 | 0.0582 (13) | 0.0356 (11) | 0.0476 (13) | −0.0007 (9) | 0.0096 (10) | −0.0010 (9) |
C3 | 0.0683 (15) | 0.0383 (11) | 0.0516 (14) | −0.0024 (11) | 0.0052 (12) | 0.0048 (10) |
C4 | 0.0755 (17) | 0.0467 (13) | 0.0496 (14) | −0.0040 (12) | 0.0113 (12) | 0.0123 (11) |
C5 | 0.087 (2) | 0.0504 (14) | 0.0460 (14) | 0.0001 (13) | 0.0224 (13) | 0.0072 (11) |
C6 | 0.0562 (13) | 0.0387 (11) | 0.0414 (11) | 0.0005 (9) | 0.0095 (10) | 0.0026 (9) |
C7 | 0.0517 (12) | 0.0374 (11) | 0.0433 (12) | −0.0003 (9) | 0.0073 (10) | 0.0014 (9) |
C8 | 0.0496 (12) | 0.0422 (12) | 0.0368 (11) | −0.0013 (9) | 0.0102 (9) | −0.0022 (9) |
C9 | 0.0649 (14) | 0.0481 (12) | 0.0389 (12) | −0.0027 (11) | 0.0120 (10) | −0.0025 (10) |
C10 | 0.0688 (16) | 0.0437 (12) | 0.0455 (13) | −0.0001 (11) | 0.0116 (12) | −0.0053 (10) |
C11 | 0.0559 (13) | 0.0409 (11) | 0.0390 (11) | 0.0001 (9) | 0.0124 (9) | 0.0010 (9) |
C12 | 0.0498 (12) | 0.0401 (11) | 0.0369 (11) | −0.0017 (9) | 0.0083 (9) | 0.0012 (8) |
C13 | 0.0695 (15) | 0.0378 (11) | 0.0435 (13) | 0.0005 (10) | 0.0154 (11) | −0.0026 (9) |
C14 | 0.0687 (15) | 0.0463 (12) | 0.0335 (11) | −0.0020 (11) | 0.0165 (10) | −0.0013 (9) |
C15 | 0.0558 (13) | 0.0405 (11) | 0.0415 (12) | −0.0039 (9) | 0.0040 (10) | 0.0074 (9) |
C16 | 0.0604 (14) | 0.0377 (11) | 0.0440 (12) | 0.0016 (9) | 0.0095 (10) | −0.0019 (9) |
C17 | 0.0552 (13) | 0.0438 (12) | 0.0406 (12) | 0.0019 (10) | 0.0115 (10) | −0.0006 (9) |
O1—C2 | 1.225 (3) | C8—C11 | 1.340 (3) |
O2—N4 | 1.231 (3) | C8—C9 | 1.510 (3) |
O3—N4 | 1.214 (3) | C9—C10 | 1.535 (3) |
N1—C1 | 1.291 (3) | C9—H9A | 0.9700 |
N1—C6 | 1.387 (3) | C9—H9B | 0.9700 |
N2—C1 | 1.371 (3) | C10—H10A | 0.9700 |
N2—C2 | 1.377 (3) | C10—H10B | 0.9700 |
N2—C10 | 1.459 (3) | C11—C12 | 1.467 (3) |
N3—C5 | 1.332 (3) | C11—H11 | 0.9300 |
N3—C6 | 1.350 (3) | C12—C13 | 1.401 (3) |
N4—C15 | 1.461 (3) | C12—C17 | 1.404 (3) |
C1—C8 | 1.469 (3) | C13—C14 | 1.383 (3) |
C2—C7 | 1.466 (3) | C13—H13 | 0.9300 |
C3—C4 | 1.355 (4) | C14—C15 | 1.379 (3) |
C3—C7 | 1.394 (3) | C14—H14 | 0.9300 |
C3—H3 | 0.9300 | C15—C16 | 1.374 (3) |
C4—C5 | 1.389 (4) | C16—C17 | 1.380 (3) |
C4—H4 | 0.9300 | C16—H16 | 0.9300 |
C5—H5 | 0.9300 | C17—H17 | 0.9300 |
C6—C7 | 1.410 (3) | ||
C1—N1—C6 | 115.76 (19) | C8—C9—H9A | 110.7 |
C1—N2—C2 | 123.0 (2) | C10—C9—H9A | 110.7 |
C1—N2—C10 | 113.55 (19) | C8—C9—H9B | 110.7 |
C2—N2—C10 | 123.40 (19) | C10—C9—H9B | 110.7 |
C5—N3—C6 | 116.8 (2) | H9A—C9—H9B | 108.8 |
O3—N4—O2 | 123.0 (2) | N2—C10—C9 | 104.79 (18) |
O3—N4—C15 | 118.5 (2) | N2—C10—H10A | 110.8 |
O2—N4—C15 | 118.5 (2) | C9—C10—H10A | 110.8 |
N1—C1—N2 | 125.9 (2) | N2—C10—H10B | 110.8 |
N1—C1—C8 | 125.7 (2) | C9—C10—H10B | 110.8 |
N2—C1—C8 | 108.39 (19) | H10A—C10—H10B | 108.9 |
O1—C2—N2 | 121.5 (2) | C8—C11—C12 | 130.1 (2) |
O1—C2—C7 | 125.3 (2) | C8—C11—H11 | 114.9 |
N2—C2—C7 | 113.18 (19) | C12—C11—H11 | 114.9 |
C4—C3—C7 | 119.1 (2) | C13—C12—C17 | 118.4 (2) |
C4—C3—H3 | 120.4 | C13—C12—C11 | 123.8 (2) |
C7—C3—H3 | 120.4 | C17—C12—C11 | 117.8 (2) |
C3—C4—C5 | 118.5 (2) | C14—C13—C12 | 120.5 (2) |
C3—C4—H4 | 120.8 | C14—C13—H13 | 119.7 |
C5—C4—H4 | 120.8 | C12—C13—H13 | 119.7 |
N3—C5—C4 | 124.8 (3) | C15—C14—C13 | 119.0 (2) |
N3—C5—H5 | 117.6 | C15—C14—H14 | 120.5 |
C4—C5—H5 | 117.6 | C13—C14—H14 | 120.5 |
N3—C6—N1 | 115.5 (2) | C16—C15—C14 | 122.3 (2) |
N3—C6—C7 | 121.8 (2) | C16—C15—N4 | 119.2 (2) |
N1—C6—C7 | 122.6 (2) | C14—C15—N4 | 118.5 (2) |
C3—C7—C6 | 118.9 (2) | C15—C16—C17 | 118.7 (2) |
C3—C7—C2 | 121.6 (2) | C15—C16—H16 | 120.7 |
C6—C7—C2 | 119.5 (2) | C17—C16—H16 | 120.7 |
C11—C8—C1 | 121.0 (2) | C16—C17—C12 | 121.1 (2) |
C11—C8—C9 | 131.0 (2) | C16—C17—H17 | 119.5 |
C1—C8—C9 | 108.02 (19) | C12—C17—H17 | 119.5 |
C8—C9—C10 | 105.11 (19) | ||
C6—N1—C1—N2 | −1.3 (4) | N1—C1—C8—C11 | −2.2 (4) |
C6—N1—C1—C8 | 178.0 (2) | N2—C1—C8—C11 | 177.2 (2) |
C2—N2—C1—N1 | 2.0 (4) | N1—C1—C8—C9 | 178.3 (2) |
C10—N2—C1—N1 | 179.3 (2) | N2—C1—C8—C9 | −2.4 (3) |
C2—N2—C1—C8 | −177.4 (2) | C11—C8—C9—C10 | −175.8 (3) |
C10—N2—C1—C8 | −0.1 (3) | C1—C8—C9—C10 | 3.7 (3) |
C1—N2—C2—O1 | 177.2 (3) | C1—N2—C10—C9 | 2.5 (3) |
C10—N2—C2—O1 | 0.2 (4) | C2—N2—C10—C9 | 179.7 (2) |
C1—N2—C2—C7 | −1.9 (4) | C8—C9—C10—N2 | −3.7 (3) |
C10—N2—C2—C7 | −178.9 (2) | C1—C8—C11—C12 | 178.5 (2) |
C7—C3—C4—C5 | −1.2 (5) | C9—C8—C11—C12 | −2.1 (5) |
C6—N3—C5—C4 | 1.1 (5) | C8—C11—C12—C13 | −4.0 (4) |
C3—C4—C5—N3 | 0.0 (5) | C8—C11—C12—C17 | 176.6 (3) |
C5—N3—C6—N1 | 178.4 (3) | C17—C12—C13—C14 | −1.1 (4) |
C5—N3—C6—C7 | −1.0 (4) | C11—C12—C13—C14 | 179.6 (3) |
C1—N1—C6—N3 | −178.6 (2) | C12—C13—C14—C15 | 1.0 (4) |
C1—N1—C6—C7 | 0.8 (4) | C13—C14—C15—C16 | 0.0 (4) |
C4—C3—C7—C6 | 1.2 (4) | C13—C14—C15—N4 | −179.7 (2) |
C4—C3—C7—C2 | −177.2 (3) | O3—N4—C15—C16 | −165.0 (3) |
N3—C6—C7—C3 | −0.1 (4) | O2—N4—C15—C16 | 14.5 (4) |
N1—C6—C7—C3 | −179.4 (2) | O3—N4—C15—C14 | 14.8 (4) |
N3—C6—C7—C2 | 178.4 (2) | O2—N4—C15—C14 | −165.7 (3) |
N1—C6—C7—C2 | −1.0 (4) | C14—C15—C16—C17 | −1.0 (4) |
O1—C2—C7—C3 | 0.8 (4) | N4—C15—C16—C17 | 178.8 (2) |
N2—C2—C7—C3 | 179.9 (2) | C15—C16—C17—C12 | 0.9 (4) |
O1—C2—C7—C6 | −177.7 (3) | C13—C12—C17—C16 | 0.1 (4) |
N2—C2—C7—C6 | 1.4 (3) | C11—C12—C17—C16 | 179.5 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
C3—H3···N3i | 0.93 | 2.58 | 3.292 (3) | 133 |
C4—H4···N1i | 0.93 | 2.57 | 3.480 (3) | 166 |
C13—H13···O3ii | 0.93 | 2.51 | 3.363 (3) | 153 |
C16—H16···O1iii | 0.93 | 2.45 | 3.259 (3) | 145 |
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) −x+2, y−1/2, −z+1/2; (iii) x, y+1, z. |
Acknowledgements
This work was supported by a Fundamental grant (FA-F7-T207: Theoretical aspects of formation of asymmetrical centers in biologically active heterocyclic molecules) from the Academy of Sciences of the Republic of Uzbekistan.
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