supplementary materials


jj2169 scheme

Acta Cryst. (2013). E69, o1158    [ doi:10.1107/S1600536813017066 ]

4-Methyl-5-(4-nitrobenzylidene)-2-oxo-2,5-dihydro-1H-pyrrole-3-carbonitrile

G. J. Gainsford, M. D. H. Bhuiyan and A. J. Kay

Abstract top

Molecules of the potential non-linear optical title compound, C13H9N3O3, form dimeric stacks of molecules along the a axis cross-linked around inversion centers by N-H...O hydrogen bonds and weak (phenyl)C-H...O intermolecular interactions, forming a `collaboration' of R22(8) and R22(16) ring motifs. The molecules are then further linked by weak C-H...O and C-H...N interactions into sheets parallel to (121).

Comment top

Oxopyrroles and their analogues are the key intermediate for many biologically active compounds (Shrestha-Dawadi & Lugtenburg, 2007) and pigments (Colin et al., 2002). Many studies have been dedicated to the synthesis and spectroscopic characterization of oxopyrroles (Tarek et al., 2013; Hasan et al. 2012; Bert et al., 2006) to improve their features. Structural modification has been carried out on the oxypyrrole ring through the introduction of a thiophene ring (Stephen et al., 2011) as an efficient donor and as a precursor for use in organic solar cells. Structural modification via the incorporation of an electron-withdrawing group has not been reported.

As a part of our efforts to develop donor-π-acceptor molecules for non-linear optical devices, we have synthesized the title compound in which the oxopyrrole nitrile analogue acts as donor and the nitro group is the acceptor linked by a phenyl-methylene bridge. The molecule crystallizes with one independent molecule in the asymmetric unit (Fig. 1). The 1H-pyrole ring is planar with maximum deviation out of plane of 0.018 (2) Å for C2; it makes an angle of 33.99 (9)° with the planar phenyl ring (C8–C13). The nitro group is further twisted by 5.24 (10)° from the latter ring in response to a hydrogen bond interaction with O2. There are few related structures reported and none with linking 5- and 6-membered rings (Allen, 2002; CSD Version 5.34, with Nov 2012 updates).

The molecules form dimers utilizing N—H···O hydrogen bonds about inversion centers of symmetry, packing into approximate planes parallel to the (1,-2,0) plane (Fig. 2). This interaction is further stabilized by weak phenyl(C9)–H ···O1 intermolecular interactions between the adjacent dimers, producing an overall packing "collaboration" of R22(8) and R22(16) ring motifs (Bernstein et al., 1995). Other three-dimensional cross-links are provided by chain interactions (not shown in Fig. 2) with weak phenylC–H···O and phenylC–H···N intermolecular contacts (Table 1), linling the molecules into sheets parallel to the (121) plane. .

Related literature top

For hydrogen-bonding motifs, see: Bernstein et al. (1995). For chemical synthesis literature, see: Shrestha-Dawadi & Lugtenburg (2007). For background literature, see: Bert et al. (2006); Colin et al. (2002); Hasan et al. (2012); Stephen et al. (2011); Tarek et al. (2013). For a description of the Cambridge Structural Database, see: Allen (2002).

Experimental top

A mixture of 3-cyano-4-methyl-3-pyrrolin-2-one (Shrestha-Dawadi & Lugtenburg, 2007) (1.0 g), 4-nitro benzaldehyde (1.6 g), sodium acetate (1.8 g) and acetic acid (50 ml) was refluxed for 3 h. under an inert atmosphere. The mixture was stirred overnight, and cooled to 0° C. The resultant precipitate was collected by filtration and washed with cold hexanes to yield the pure chromophore 4-methyl-5-(4-nitro-benzylidene)-2-oxo-2,5-dihydro-1H-pyrrole- 3-carbonitrile (1.2 g, 57%) as a yellow solid. Crystals were grown by slow evaporation of an acetone solution. m.p. 277–80° C.

Refinement top

Eight high angle outlier reflection identified by large (Fc2-Fo2)/σ(Fo2) ratios (>4) were OMITted from the dataset.

The methyl H atoms were constrained to an ideal geometry (C—H = 0.98 Å) with Uiso(H) = 1.5Ueq(C), but were allowed to rotate freely about the adjacent C—C bond. All other H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms with C—H distances of 0.95 Å and N1—H 0 0.88 Å and with Uiso(H) = 1.2Ueq(C,N).

Computing details top

Data collection: CrysAlis PRO (Agilent, 2011); cell refinement: CrysAlis PRO (Agilent, 2011); data reduction: CrysAlis PRO (Agilent, 2011); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2012 (Sheldrick, 2008); molecular graphics: ORTEP-3 in WinGX (Farrugia, 2012) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. Asymmetric unit atoms for (I) with ellipsoid probability of 50% for non-hydrogen atoms.
[Figure 2] Fig. 2. Packing diagram of (I) viewed along the a axis. Intermolecular contacts are shown as blue dotted lines. Symmetry: (i) -1 + x, y, z (ii) 1 - x, 1 - y, 1 - z (iii) 1 - x, -1/2 + y, 1/2 - z.
4-Methyl-5-(4-nitrobenzylidene)-2-oxo-2,5-dihydro-1H-pyrrole-3-carbonitrile top
Crystal data top
C13H9N3O3Z = 4
Mr = 255.23F(000) = 528
Monoclinic, P21/cDx = 1.405 Mg m3
Hall symbol: -P 2ybcCu Kα radiation, λ = 1.54184 Å
a = 3.7456 (2) ŵ = 0.86 mm1
b = 14.9193 (9) ÅT = 120 K
c = 21.6077 (17) ÅNeedle, yellow
β = 92.273 (7)°0.44 × 0.05 × 0.03 mm
V = 1206.52 (14) Å3
Data collection top
Agilent SuperNova (Dual, Cu at zero, Atlas)
diffractometer
2283 independent reflections
Radiation source: fine-focus sealed tube1941 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.042
Detector resolution: 10.6501 pixels mm-1θmax = 70.0°, θmin = 3.6°
ω scansh = 44
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
k = 1718
Tmin = 0.633, Tmax = 1.000l = 2618
7096 measured reflections
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)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.139H-atom parameters constrained
S = 1.05 w = 1/[σ2(Fo2) + (0.0824P)2 + 0.3085P]
where P = (Fo2 + 2Fc2)/3
2283 reflections(Δ/σ)max < 0.001
173 parametersΔρmax = 0.25 e Å3
0 restraintsΔρmin = 0.25 e Å3
Crystal data top
C13H9N3O3V = 1206.52 (14) Å3
Mr = 255.23Z = 4
Monoclinic, P21/cCu Kα radiation
a = 3.7456 (2) ŵ = 0.86 mm1
b = 14.9193 (9) ÅT = 120 K
c = 21.6077 (17) Å0.44 × 0.05 × 0.03 mm
β = 92.273 (7)°
Data collection top
Agilent SuperNova (Dual, Cu at zero, Atlas)
diffractometer
2283 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2011)
1941 reflections with I > 2σ(I)
Tmin = 0.633, Tmax = 1.000Rint = 0.042
7096 measured reflectionsθmax = 70.0°
Refinement top
R[F2 > 2σ(F2)] = 0.048H-atom parameters constrained
wR(F2) = 0.139Δρmax = 0.25 e Å3
S = 1.05Δρmin = 0.25 e Å3
2283 reflectionsAbsolute structure: ?
173 parametersAbsolute structure parameter: ?
0 restraintsRogers parameter: ?
Special details top

Experimental. Absorption correction: CrysAlisPro, Agilent Technologies, Version 1.171.35.19 (release 27-10-2011 CrysAlis171 .NET) (compiled Oct 27 2011,15:02:11) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

(MNa)+ m/z 278.0540; C13H9N3O3 requires (MNa)+ m/z 278.0542). 1H NMR (500 MHz, d6-DMSO) 2.46 (s, 3H, CH3), 6.84 (s, 1H, CH), 7.88 (d, 2H, J = 4.9 Hz, ArH), 8.25 (d, 2H, J = 4.9 Hz, ArH), 10.91 (s, 1H, NH). 13C NMR (75 MHz, d6 –DMSO) 12.3, 105.9, 112.7, 113.4, 123.9, 130.9, 138.2, 139.9, 146.7, 161.7, 166.9.

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) top
xyzUiso*/Ueq
O10.8538 (3)0.44087 (8)0.56486 (6)0.0277 (3)
O20.9729 (4)0.64031 (9)0.18759 (7)0.0452 (4)
O31.1572 (4)0.52825 (10)0.13455 (7)0.0453 (4)
N10.7576 (4)0.40243 (9)0.46186 (7)0.0243 (3)
H10.84910.45020.44460.029*
N20.3889 (4)0.24706 (12)0.63898 (9)0.0403 (4)
N31.0168 (4)0.55927 (10)0.17993 (8)0.0323 (4)
C10.7387 (4)0.39026 (11)0.52376 (8)0.0236 (4)
C20.5581 (4)0.30283 (11)0.53143 (9)0.0253 (4)
C30.4940 (4)0.26523 (11)0.47533 (8)0.0252 (4)
C40.6126 (4)0.32905 (11)0.42854 (8)0.0246 (4)
C50.4693 (5)0.27012 (11)0.59072 (9)0.0283 (4)
C60.3332 (5)0.17567 (11)0.46080 (9)0.0296 (4)
H6A0.14070.18250.42910.044*
H6B0.23620.15010.49840.044*
H6C0.51710.13560.44540.044*
C70.5892 (4)0.31806 (11)0.36711 (8)0.0264 (4)
H70.49450.26240.35270.032*
C80.6925 (4)0.38178 (11)0.31925 (8)0.0256 (4)
C90.6636 (4)0.47494 (11)0.32720 (9)0.0268 (4)
H90.57240.49810.36440.032*
C100.7663 (5)0.53323 (11)0.28161 (9)0.0283 (4)
H100.74630.59620.28690.034*
C110.8990 (4)0.49794 (12)0.22809 (8)0.0276 (4)
C120.9235 (5)0.40627 (12)0.21750 (9)0.0287 (4)
H121.01160.38380.17990.034*
C130.8157 (5)0.34892 (12)0.26339 (8)0.0285 (4)
H130.82550.28600.25690.034*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0363 (6)0.0202 (6)0.0267 (7)0.0029 (5)0.0031 (5)0.0007 (5)
O20.0724 (10)0.0219 (7)0.0415 (9)0.0063 (6)0.0049 (7)0.0049 (6)
O30.0579 (9)0.0402 (8)0.0392 (9)0.0065 (7)0.0202 (7)0.0088 (7)
N10.0314 (7)0.0158 (7)0.0258 (8)0.0023 (5)0.0032 (6)0.0007 (6)
N20.0449 (9)0.0378 (9)0.0387 (11)0.0049 (7)0.0067 (8)0.0095 (8)
N30.0379 (8)0.0273 (8)0.0315 (9)0.0017 (6)0.0015 (7)0.0049 (7)
C10.0264 (7)0.0178 (8)0.0268 (9)0.0020 (6)0.0036 (6)0.0007 (7)
C20.0278 (8)0.0184 (8)0.0300 (10)0.0014 (6)0.0054 (7)0.0025 (7)
C30.0268 (8)0.0179 (8)0.0313 (10)0.0005 (6)0.0048 (7)0.0010 (7)
C40.0283 (8)0.0168 (8)0.0289 (9)0.0012 (6)0.0045 (7)0.0001 (7)
C50.0311 (8)0.0196 (8)0.0342 (11)0.0010 (6)0.0023 (7)0.0024 (7)
C60.0348 (8)0.0188 (8)0.0356 (10)0.0040 (7)0.0060 (7)0.0009 (7)
C70.0296 (8)0.0179 (8)0.0320 (10)0.0005 (6)0.0041 (7)0.0014 (7)
C80.0256 (7)0.0230 (8)0.0280 (10)0.0008 (6)0.0003 (7)0.0004 (7)
C90.0285 (8)0.0231 (9)0.0290 (10)0.0015 (6)0.0038 (7)0.0033 (7)
C100.0332 (8)0.0197 (8)0.0318 (10)0.0006 (7)0.0000 (7)0.0001 (7)
C110.0289 (8)0.0253 (9)0.0285 (10)0.0012 (7)0.0014 (7)0.0035 (8)
C120.0336 (8)0.0256 (9)0.0272 (10)0.0031 (7)0.0043 (7)0.0007 (7)
C130.0365 (9)0.0206 (8)0.0287 (10)0.0018 (7)0.0027 (7)0.0019 (7)
Geometric parameters (Å, º) top
O1—C11.231 (2)C6—H6B0.9800
O2—N31.232 (2)C6—H6C0.9800
O3—N31.222 (2)C7—C81.468 (2)
N1—C11.354 (2)C7—H70.9500
N1—C41.407 (2)C8—C131.398 (2)
N1—H10.8800C8—C91.405 (2)
N2—C51.149 (3)C9—C101.380 (2)
N3—C111.467 (2)C9—H90.9500
C1—C21.482 (2)C10—C111.381 (3)
C2—C31.349 (3)C10—H100.9500
C2—C51.423 (3)C11—C121.390 (2)
C3—C41.470 (2)C12—C131.382 (3)
C3—C61.494 (2)C12—H120.9500
C4—C71.337 (3)C13—H130.9500
C6—H6A0.9800
C1—N1—C4111.50 (14)H6A—C6—H6C109.5
C1—N1—H1124.3H6B—C6—H6C109.5
C4—N1—H1124.3C4—C7—C8127.68 (16)
O3—N3—O2122.93 (16)C4—C7—H7116.2
O3—N3—C11118.96 (15)C8—C7—H7116.2
O2—N3—C11118.11 (16)C13—C8—C9118.82 (16)
O1—C1—N1126.85 (15)C13—C8—C7119.10 (15)
O1—C1—C2127.44 (16)C9—C8—C7122.06 (16)
N1—C1—C2105.70 (15)C10—C9—C8120.73 (16)
C3—C2—C5128.83 (16)C10—C9—H9119.6
C3—C2—C1109.36 (15)C8—C9—H9119.6
C5—C2—C1121.80 (16)C9—C10—C11118.51 (16)
C2—C3—C4107.50 (15)C9—C10—H10120.7
C2—C3—C6128.09 (16)C11—C10—H10120.7
C4—C3—C6124.41 (16)C10—C11—C12122.76 (16)
C7—C4—N1127.73 (15)C10—C11—N3118.99 (16)
C7—C4—C3126.41 (16)C12—C11—N3118.24 (16)
N1—C4—C3105.85 (15)C13—C12—C11117.89 (16)
N2—C5—C2176.98 (19)C13—C12—H12121.1
C3—C6—H6A109.5C11—C12—H12121.1
C3—C6—H6B109.5C12—C13—C8121.21 (16)
H6A—C6—H6B109.5C12—C13—H13119.4
C3—C6—H6C109.5C8—C13—H13119.4
C4—N1—C1—O1177.31 (15)C3—C4—C7—C8177.49 (16)
C4—N1—C1—C21.53 (17)C4—C7—C8—C13148.90 (18)
O1—C1—C2—C3175.91 (16)C4—C7—C8—C932.6 (3)
N1—C1—C2—C32.92 (18)C13—C8—C9—C102.2 (3)
O1—C1—C2—C55.4 (3)C7—C8—C9—C10179.34 (16)
N1—C1—C2—C5175.75 (15)C8—C9—C10—C110.2 (3)
C5—C2—C3—C4175.48 (16)C9—C10—C11—C121.9 (3)
C1—C2—C3—C43.06 (18)C9—C10—C11—N3178.58 (16)
C5—C2—C3—C64.5 (3)O3—N3—C11—C10174.92 (17)
C1—C2—C3—C6176.91 (15)O2—N3—C11—C104.3 (3)
C1—N1—C4—C7179.52 (16)O3—N3—C11—C125.6 (3)
C1—N1—C4—C30.25 (18)O2—N3—C11—C12175.26 (17)
C2—C3—C4—C7178.61 (16)C10—C11—C12—C131.2 (3)
C6—C3—C4—C71.4 (3)N3—C11—C12—C13179.27 (16)
C2—C3—C4—N12.11 (18)C11—C12—C13—C81.3 (3)
C6—C3—C4—N1177.87 (15)C9—C8—C13—C122.9 (3)
N1—C4—C7—C83.4 (3)C7—C8—C13—C12178.56 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.881.982.8256 (18)159
C9—H9···O1ii0.952.433.336 (2)159
C12—H12···N2iii0.952.593.374 (3)141
C13—H13···O2iv0.952.583.372 (2)141
Symmetry codes: (i) x+2, y+1, z+1; (ii) x+1, y+1, z+1; (iii) x+1, y+1/2, z1/2; (iv) x+2, y1/2, z+1/2.

Experimental details

Crystal data
Chemical formulaC13H9N3O3
Mr255.23
Crystal system, space groupMonoclinic, P21/c
Temperature (K)120
a, b, c (Å)3.7456 (2), 14.9193 (9), 21.6077 (17)
β (°) 92.273 (7)
V3)1206.52 (14)
Z4
Radiation typeCu Kα
µ (mm1)0.86
Crystal size (mm)0.44 × 0.05 × 0.03
Data collection
DiffractometerAgilent SuperNova (Dual, Cu at zero, Atlas)
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2011)
Tmin, Tmax0.633, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
7096, 2283, 1941
Rint0.042
(sin θ/λ)max1)0.609
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.139, 1.05
No. of reflections2283
No. of parameters173
No. of restraints0
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.25, 0.25

Computer programs: CrysAlis PRO (Agilent, 2011), SHELXS97 (Sheldrick, 2008), SHELXL2012 (Sheldrick, 2008), ORTEP-3 in WinGX (Farrugia, 2012) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.881.982.8256 (18)159
C9—H9···O1ii0.952.433.336 (2)159
C12—H12···N2iii0.952.593.374 (3)141
C13—H13···O2iv0.952.583.372 (2)141
Symmetry codes: (i) x+2, y+1, z+1; (ii) x+1, y+1, z+1; (iii) x+1, y+1/2, z1/2; (iv) x+2, y1/2, z+1/2.
Acknowledgements top

The authors thank Dr J. Wikaira of the University of Canterbury for the data collection.

references
References top

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Farrugia, L. J. (2012). J. Appl. Cryst. 45, 849–854.

Hasan, Z.-B., Mehdi, M., Khadijeh, H. & Maryam, G. (2012). J. Org. Chem. 77, 5808–5812.

Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466–470.

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Shrestha-Dawadi, P. B. & Lugtenburg, J. (2007). Eur. J. Org. Chem. pp. 1294–1300.

Spek, A. L. (2009). Acta Cryst. D65, 148–155.

Stephen, L., Carson, J. B., Hiroyuki, M., Rocio, P. O., Antonio, F., Samuel, I. S. & Tobin, J. M. (2011). J. Am. Chem. Soc. 133, 8142–8145.

Tarek, A., Stanislav, L. Jr, Antonín, L., Jan, V., Zdenek, E., Ales, R., Zdenka, P. & Radim, H. (2013). Dyes Pigments, 98, 530–539.