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 ▶).
Experimental
Crystal data
C11H16N4O2
M r = 236.28
Monoclinic,
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
Structure factors: contains datablocks I. DOI: 10.1107/S1600536810015953/im2192Isup2.hkl
Additional supplementary materials: crystallographic information; 3D view; checkCIF report
Table 1. 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 |
Symmetry code: (i)
.
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.
The molecular structure of (I), with the atom-numbering scheme. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
A packing diagram of (I). Hydrogen bonds are shown as dashed lines.
Crystal data
| C11H16N4O2 | Dx = 1.366 Mg m−3 |
| 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 mm−1 |
| 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 Å−3 |
| 155 parameters | Δρmin = −0.18 e Å−3 |
| 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
- 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.
- Enraf–Nonius (1985). CAD-4 Software Enraf–Nonius, Delft, The Netherlands.
- Harms, K. & Wocadlo, S. (1995). XCAD4 University of Marburg, Germany.
- North, A. C. T., Phillips, D. C. & Mathews, F. S. (1968). Acta Cryst. A24, 351–359.
- 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]
- 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
Structure factors: contains datablocks I. DOI: 10.1107/S1600536810015953/im2192Isup2.hkl
Additional supplementary materials: crystallographic information; 3D view; checkCIF report


