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Acta Crystallographica Section E: Structure Reports Online logoLink to Acta Crystallographica Section E: Structure Reports Online
. 2010 May 8;66(Pt 6):o1268. doi: 10.1107/S1600536810015953

5-(4-Methyl­piperazin-1-yl)-2-nitro­aniline

Chang-jun Luan a, Cheng Guo a,*, Wei Wang a, Jian-qiang Wang a, Ren-jun Du a
PMCID: PMC2979376  PMID: 21579369

Abstract

In the title compound, C11H16N4O2, the dihedral angle between the benzene ring and the plane of the four carbon atoms in the piperazine ring is 12.17 (3)°; the latter ring adopts a chair conformation. An intramolecular N—H⋯O hydrogen bond generates an S(6) ring. In the crystal, the molecules are linked by N—H⋯N hydrogen bonds, forming chains.

Related literature

For bond-length data, see: Allen et al. (1987). For the synthetic procedure and use of the title compound as an inter­mediate in the synthesis of tyrosine kinase inhibitors, see: Renhowe et al. (2009).graphic file with name e-66-o1268-scheme1.jpg

Experimental

Crystal data

  • C11H16N4O2

  • M r = 236.28

  • Monoclinic, Inline graphic

  • a = 11.027 (2) Å

  • b = 6.121 (1) Å

  • c = 17.524 (4) Å

  • β = 103.79 (3)°

  • V = 1148.7 (4) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 293 K

  • 0.30 × 0.20 × 0.05 mm

Data collection

  • Enraf–Nonius CAD-4 diffractometer

  • Absorption correction: ψ scan (North et al., 1968) T min = 0.971, T max = 0.995

  • 2205 measured reflections

  • 2090 independent reflections

  • 1358 reflections with I > 2σ(I)

  • R int = 0.042

  • 3 standard reflections every 200 reflections intensity decay: 1%

Refinement

  • R[F 2 > 2σ(F 2)] = 0.064

  • wR(F 2) = 0.192

  • S = 1.01

  • 2090 reflections

  • 155 parameters

  • H-atom parameters constrained

  • Δρmax = 0.25 e Å−3

  • Δρmin = −0.18 e Å−3

Data collection: CAD-4 Software (Enraf–Nonius, 1985); cell refinement: CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810015953/im2192sup1.cif

e-66-o1268-sup1.cif (17.6KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810015953/im2192Isup2.hkl

e-66-o1268-Isup2.hkl (102.8KB, hkl)

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3C⋯N1i 0.86 2.39 3.156 (4) 148
N3—H3D⋯O1 0.86 2.06 2.669 (4) 127

Symmetry code: (i) Inline graphic.

Acknowledgments

The authors thank the Center of Test and Analysis, Nanjing University, for support.

supplementary crystallographic information

Comment

The title compound, (I), has been reported as an intermediate for the synthesis of novel tyrosine kinase inhibitors (Renhowe, P. A. et al., 2009). We herein report its crystal structure.

In the molecular structure of (I), (Fig.1), bond lengths (Allen et al., 1987) and angles are within normal ranges. N2, N3 and N4 atoms are almost coplanar with the benzene ring to which they are bonded [deviations of 0.078 (1), 0.052 (1) and 0.078 (1) Å]. The plane of C2—C3—C4—C5 is nearly parallel with the benzene ring plane (the torsion angle is 12.17 (3) °). By contrast, due to the piperazine moiety adopting a chair conformation N1—C2—C5 and N2—C3—C4 form two separate planes with torsion angle of 45.87 (2) ° and 25.92 (3) °, respectively, with respect to the benzene ring. The crystal structure of the title compound exhibits N—H···O, C—H···O, and N—H···N intra- and intermolecular hydrogen bonds to form a three dimensional network.

As can be seen from the packing diagram, (Fig. 2), the molecules are stacked along the b axis.

Experimental

The title compound, (I) was prepared by a literature method (Renhowe, P. A. et al., 2009). Crystals suitable for X-ray analysis were obtained by dissolving (I) (0.5 g) in methanol (20 ml) and evaporating the solvent slowly at room temperature for about 7 d.

Refinement

H atoms were positioned geometrically, with N—H = 0.86 Å, C—H = 0.93 Å for aromatic H, 0.97 Å for methylene and 0.96 Å for methyl groups. Refinement was performed using a riding model with Uiso(H) = xUeq(C), where x = 1.5 for methyl and x = 1.2 for all other H atoms.

Figures

Fig. 1.

Fig. 1.

The molecular structure of (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.

Fig. 2.

Fig. 2.

A packing diagram of (I). Hydrogen bonds are shown as dashed lines.

Crystal data

C11H16N4O2 Dx = 1.366 Mg m3
Mr = 236.28 Melting point: 428 K
Monoclinic, P21/c Mo Kα radiation, λ = 0.71073 Å
a = 11.027 (2) Å Cell parameters from 25 reflections
b = 6.121 (1) Å θ = 9–13°
c = 17.524 (4) Å µ = 0.10 mm1
β = 103.79 (3)° T = 293 K
V = 1148.7 (4) Å3 Block, yellow
Z = 4 0.30 × 0.20 × 0.05 mm
F(000) = 504

Data collection

Enraf–Nonius CAD-4 diffractometer 1358 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube Rint = 0.042
graphite θmax = 25.3°, θmin = 1.9°
ω/2θ scans h = 0→13
Absorption correction: ψ scan (North et al., 1968) k = 0→7
Tmin = 0.971, Tmax = 0.995 l = −21→20
2205 measured reflections 3 standard reflections every 200 reflections
2090 independent reflections intensity decay: 1%

Refinement

Refinement on F2 Secondary atom site location: difference Fourier map
Least-squares matrix: full Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.064 H-atom parameters constrained
wR(F2) = 0.192 w = 1/[σ2(Fo2) + (0.1P)2 + 0.3P] where P = (Fo2 + 2Fc2)/3
S = 1.01 (Δ/σ)max < 0.001
2090 reflections Δρmax = 0.25 e Å3
155 parameters Δρmin = −0.18 e Å3
0 restraints Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods Extinction coefficient: 0.038 (6)

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 > 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)

x y z Uiso*/Ueq
N1 0.6711 (2) 0.0465 (4) 0.16875 (13) 0.0438 (6)
O1 1.3775 (2) −0.0656 (4) 0.56703 (14) 0.0774 (8)
C1 0.5525 (3) 0.1090 (6) 0.11543 (19) 0.0603 (9)
H1A 0.5683 0.2064 0.0760 0.090*
H1B 0.5007 0.1809 0.1447 0.090*
H1C 0.5107 −0.0193 0.0907 0.090*
N2 0.8586 (2) 0.0019 (4) 0.31264 (13) 0.0397 (6)
O2 1.2787 (2) −0.3532 (4) 0.58981 (13) 0.0662 (7)
C2 0.7330 (3) 0.2397 (5) 0.20898 (17) 0.0484 (8)
H2A 0.6826 0.3007 0.2422 0.058*
H2B 0.7409 0.3493 0.1705 0.058*
C3 0.8606 (3) 0.1827 (5) 0.25841 (16) 0.0466 (8)
H3A 0.9143 0.1440 0.2240 0.056*
H3B 0.8960 0.3103 0.2883 0.056*
N3 1.2683 (2) 0.2156 (4) 0.45524 (16) 0.0613 (8)
H3C 1.2595 0.3315 0.4267 0.074*
H3D 1.3359 0.1954 0.4909 0.074*
C4 0.7741 (3) −0.1801 (5) 0.28094 (18) 0.0478 (8)
H4A 0.7577 −0.2645 0.3242 0.057*
H4B 0.8149 −0.2755 0.2506 0.057*
N4 1.2841 (2) −0.1869 (5) 0.55073 (15) 0.0527 (7)
C5 0.6513 (3) −0.1026 (5) 0.22932 (17) 0.0506 (8)
H5A 0.6035 −0.2276 0.2048 0.061*
H5B 0.6033 −0.0292 0.2615 0.061*
C6 0.9667 (2) −0.0433 (4) 0.36840 (15) 0.0367 (7)
C7 1.0669 (2) 0.1023 (5) 0.38534 (15) 0.0398 (7)
H7A 1.0610 0.2307 0.3563 0.048*
C8 1.1758 (2) 0.0647 (5) 0.44396 (16) 0.0415 (7)
C9 1.1820 (2) −0.1317 (5) 0.48727 (15) 0.0422 (7)
C10 1.0839 (3) −0.2817 (5) 0.46870 (17) 0.0475 (8)
H10A 1.0901 −0.4120 0.4966 0.057*
C11 0.9799 (3) −0.2428 (5) 0.41112 (17) 0.0444 (7)
H11A 0.9169 −0.3471 0.3995 0.053*

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
N1 0.0385 (13) 0.0422 (14) 0.0464 (13) −0.0004 (11) 0.0017 (10) 0.0030 (11)
O1 0.0545 (14) 0.0794 (18) 0.0820 (17) −0.0125 (13) −0.0158 (12) 0.0122 (14)
C1 0.0411 (17) 0.067 (2) 0.065 (2) 0.0050 (16) −0.0025 (15) 0.0064 (18)
N2 0.0357 (12) 0.0346 (12) 0.0458 (13) −0.0029 (10) 0.0040 (10) 0.0048 (11)
O2 0.0610 (15) 0.0616 (15) 0.0674 (15) 0.0125 (12) −0.0015 (12) 0.0190 (12)
C2 0.0527 (18) 0.0375 (16) 0.0502 (17) 0.0004 (14) 0.0030 (14) 0.0085 (14)
C3 0.0449 (17) 0.0396 (16) 0.0503 (17) −0.0067 (14) 0.0016 (14) 0.0084 (14)
N3 0.0486 (15) 0.0509 (16) 0.0724 (17) −0.0149 (13) −0.0094 (13) 0.0073 (14)
C4 0.0440 (16) 0.0354 (15) 0.0605 (18) −0.0053 (13) 0.0057 (14) 0.0075 (14)
N4 0.0484 (15) 0.0537 (17) 0.0516 (15) 0.0041 (14) 0.0033 (12) 0.0020 (13)
C5 0.0383 (16) 0.0456 (17) 0.0636 (19) −0.0060 (14) 0.0036 (14) 0.0058 (16)
C6 0.0354 (14) 0.0369 (15) 0.0393 (14) 0.0018 (12) 0.0118 (12) −0.0007 (12)
C7 0.0414 (15) 0.0320 (15) 0.0443 (15) 0.0013 (12) 0.0071 (12) 0.0025 (12)
C8 0.0391 (15) 0.0386 (16) 0.0455 (16) −0.0015 (13) 0.0075 (13) −0.0057 (13)
C9 0.0398 (15) 0.0469 (17) 0.0377 (15) 0.0063 (13) 0.0051 (12) 0.0029 (13)
C10 0.0470 (17) 0.0444 (18) 0.0510 (17) 0.0014 (14) 0.0116 (14) 0.0123 (14)
C11 0.0391 (15) 0.0395 (16) 0.0527 (17) −0.0031 (13) 0.0071 (13) 0.0101 (14)

Geometric parameters (Å, °)

N1—C5 1.455 (3) N3—H3C 0.8600
N1—C2 1.460 (4) N3—H3D 0.8600
N1—C1 1.466 (3) C4—C5 1.514 (4)
O1—N4 1.246 (3) C4—H4A 0.9700
C1—H1A 0.9600 C4—H4B 0.9700
C1—H1B 0.9600 N4—C9 1.422 (4)
C1—H1C 0.9600 C5—H5A 0.9700
N2—C6 1.377 (3) C5—H5B 0.9700
N2—C3 1.462 (3) C6—C7 1.395 (4)
N2—C4 1.473 (3) C6—C11 1.421 (4)
O2—N4 1.236 (3) C7—C8 1.401 (4)
C2—C3 1.507 (4) C7—H7A 0.9300
C2—H2A 0.9700 C8—C9 1.415 (4)
C2—H2B 0.9700 C9—C10 1.396 (4)
C3—H3A 0.9700 C10—C11 1.356 (4)
C3—H3B 0.9700 C10—H10A 0.9300
N3—C8 1.355 (3) C11—H11A 0.9300
C5—N1—C2 106.8 (2) N2—C4—H4B 109.1
C5—N1—C1 111.2 (2) C5—C4—H4B 109.1
C2—N1—C1 109.8 (2) H4A—C4—H4B 107.8
N1—C1—H1A 109.5 O2—N4—O1 120.6 (3)
N1—C1—H1B 109.5 O2—N4—C9 119.7 (3)
H1A—C1—H1B 109.5 O1—N4—C9 119.7 (3)
N1—C1—H1C 109.5 N1—C5—C4 111.3 (2)
H1A—C1—H1C 109.5 N1—C5—H5A 109.4
H1B—C1—H1C 109.5 C4—C5—H5A 109.4
C6—N2—C3 118.0 (2) N1—C5—H5B 109.4
C6—N2—C4 118.6 (2) C4—C5—H5B 109.4
C3—N2—C4 115.7 (2) H5A—C5—H5B 108.0
N1—C2—C3 110.8 (2) N2—C6—C7 122.0 (2)
N1—C2—H2A 109.5 N2—C6—C11 120.6 (2)
C3—C2—H2A 109.5 C7—C6—C11 117.4 (2)
N1—C2—H2B 109.5 C6—C7—C8 123.2 (3)
C3—C2—H2B 109.5 C6—C7—H7A 118.4
H2A—C2—H2B 108.1 C8—C7—H7A 118.4
N2—C3—C2 113.1 (2) N3—C8—C7 118.6 (3)
N2—C3—H3A 109.0 N3—C8—C9 124.2 (2)
C2—C3—H3A 109.0 C7—C8—C9 117.2 (2)
N2—C3—H3B 109.0 C10—C9—C8 119.9 (2)
C2—C3—H3B 109.0 C10—C9—N4 116.8 (3)
H3A—C3—H3B 107.8 C8—C9—N4 123.3 (3)
C8—N3—H3C 120.0 C11—C10—C9 121.9 (3)
C8—N3—H3D 120.0 C11—C10—H10A 119.0
H3C—N3—H3D 120.0 C9—C10—H10A 119.0
N2—C4—C5 112.5 (2) C10—C11—C6 120.3 (3)
N2—C4—H4A 109.1 C10—C11—H11A 119.8
C5—C4—H4A 109.1 C6—C11—H11A 119.8
C5—N1—C2—C3 64.5 (3) C6—C7—C8—N3 179.3 (3)
C1—N1—C2—C3 −174.7 (2) C6—C7—C8—C9 −0.1 (4)
C6—N2—C3—C2 −170.8 (2) N3—C8—C9—C10 −177.0 (3)
C4—N2—C3—C2 40.4 (3) C7—C8—C9—C10 2.4 (4)
N1—C2—C3—N2 −53.1 (3) N3—C8—C9—N4 3.6 (4)
C6—N2—C4—C5 171.8 (2) C7—C8—C9—N4 −177.1 (2)
C3—N2—C4—C5 −39.5 (3) O2—N4—C9—C10 −5.1 (4)
C2—N1—C5—C4 −64.2 (3) O1—N4—C9—C10 175.8 (3)
C1—N1—C5—C4 175.9 (3) O2—N4—C9—C8 174.4 (3)
N2—C4—C5—N1 52.0 (3) O1—N4—C9—C8 −4.8 (4)
C3—N2—C6—C7 13.8 (4) C8—C9—C10—C11 −1.8 (4)
C4—N2—C6—C7 161.8 (2) N4—C9—C10—C11 177.7 (3)
C3—N2—C6—C11 −166.2 (2) C9—C10—C11—C6 −1.2 (5)
C4—N2—C6—C11 −18.2 (4) N2—C6—C11—C10 −176.7 (3)
N2—C6—C7—C8 177.3 (2) C7—C6—C11—C10 3.3 (4)
C11—C6—C7—C8 −2.7 (4)

Hydrogen-bond geometry (Å, °)

D—H···A D—H H···A D···A D—H···A
N3—H3C···N1i 0.86 2.39 3.156 (4) 148
N3—H3D···O1 0.86 2.06 2.669 (4) 127
C10—H10A···O2 0.93 2.35 2.671 (4) 100

Symmetry codes: (i) −x+2, y+1/2, −z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IM2192).

References

  1. Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1–19.
  2. Enraf–Nonius (1985). CAD-4 Software Enraf–Nonius, Delft, The Netherlands.
  3. Harms, K. & Wocadlo, S. (1995). XCAD4 University of Marburg, Germany.
  4. North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.
  5. Renhowe, P. A., Pecchi, S., Shafer, C. M., Machajewski, T. D., Jazan, E. M., Taylor, C., Antonius-McCrea, W., McBride, C. M., Frazier, K., Wiesmann, M., Lapointe, G. R., Feucht, P. H., Warne, R. L., Heise, C. C., Menezes, D., Aardalen, K., Ye, H., He, M., Le, V., Vora, J., Jansen, J. M., Wernette-Hammond, M. E. & Harris, A. L. (2009). J. Med. Chem.52, 278–292. [DOI] [PubMed]
  6. Sheldrick, G. M. (2008). Acta Cryst A64, 112–122. [DOI] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810015953/im2192sup1.cif

e-66-o1268-sup1.cif (17.6KB, cif)

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810015953/im2192Isup2.hkl

e-66-o1268-Isup2.hkl (102.8KB, hkl)

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


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