organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 65| Part 4| April 2009| Pages o772-o773

Pyrazino[2,3-b]indolizine-10-carbo­nitrile

aUniversity of Gdańsk, Faculty of Chemistry, Sobieskiego 18/19, 80-952 Gdańsk, Poland
*Correspondence e-mail: art@chem.univ.gda.pl

(Received 10 February 2009; accepted 11 March 2009; online 14 March 2009)

In the crystal structure of the title compound, C11H6N4, neighbouring mol­ecules are linked into inversion dimers through pairs of weak C—H⋯N hydrogen bonds, forming an R22(10) ring motif. The dimers forming this motif are further linked by ππ inter­actions. With respective average deviations from planarity of 0.004 (2) and 0.004 (1) Å, the pyrazino[2,3-β]indolizine and cyano fragment are oriented at 0.8 (1)° to each other. The mean planes of the pyrazino[2,3-b]indolizine skeleton either lie parallel or are inclined at an angle of 28.7 (2)° in the crystal.

Related literature

For applications of this class of compounds, see: Akiyama et al. (1978[Akiyama, T., Enomoto, Y. & Shibamoto, T. (1978). J. Agric. Food Chem. 26, 1176-1179.]); Foks et al. (2005[Foks, H., Pancechowska-Ksepko, D., Kédzia, A., Zwolska, Z., Janowiec, M. & Augustynowicz-Kopeć, E. (2005). Farmaco, 60, 513-517.]); Kaliszan et al. (1985[Kaliszan, R., Pilarski, B., Ośmiałowski, K., Strzałkowska-Grad, H. & Hać, E. (1985). Pharm. Weekbl Sci. 7, 141-145.]); Kushner et al. (1952[Kushner, S., Dalalian, H., Sanjurjo, J. L., Bach, F. L. Jr, Safir, S. R., Smith, V. K. Jr & Williams, J. H. (1952). J. Am. Chem. Soc. 74, 3617-3621.]); Mussinan et al. (1973[Mussinan, C. J., Wilson, R. A. & Katz, I. (1973). J. Agric. Food Chem. 21, 871-872.]); Petrusewicz et al. (1993[Petrusewicz, J., Gami-Yilinkou, R., Kaliszan, R., Pilarski, B. & Foks, H. (1993). Gen. Pharmacol. 24, 17-22.], 1995[Petrusewicz, J., Turowski, M., Foks, H., Pilarski, B. & Kaliszan, R. (1995). Life Sci. 56, 667-677.]); Seitz et al. (2002[Seitz, L. E., Suling, W. J. & Reynolds, R. C. (2002). J. Med. Chem. 45, 5604-5606.]). For the synthesis, see: Pilarski & Foks (1981[Pilarski, B. & Foks, H. (1981). Polish Patent No. P-232409.] and 1982[Pilarski, B. & Foks, H. (1982). Polish Patent No. P-234716.]). For the analysis of inter­molecular inter­actions, see: Spek (2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]). For a description of the Cambridge Structural Database, see: Allen (2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]). For hydrogen bonds, see: Steiner (1999[Steiner, T. (1999). Chem. Commun. pp. 313-314.]).

[Scheme 1]

Experimental

Crystal data
  • C11H6N4

  • Mr = 194.20

  • Monoclinic, P 21 /c

  • a = 3.8515 (5) Å

  • b = 14.147 (2) Å

  • c = 16.606 (3) Å

  • β = 91.260 (14)°

  • V = 904.6 (2) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 295 K

  • 0.30 × 0.08 × 0.06 mm

Data collection
  • Oxford Diffraction Ruby CCD diffractometer

  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2008[Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]) Tmin = 0.992, Tmax = 0.999

  • 6832 measured reflections

  • 1606 independent reflections

  • 1186 reflections with I > 2σ(I)

  • Rint = 0.032

Refinement
  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.111

  • S = 1.02

  • 1606 reflections

  • 137 parameters

  • H-atom parameters constrained

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.15 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
C2—H2⋯N12i 0.93 2.61 3.487 (2) 157
Symmetry code: (i) -x+1, -y, -z.

Table 2
ππ interactions (Å, °)

CgI CgJ CgCg Dihedral angle Interplanar distance Offset
A Bii 3.608 (1) 0.6 3.358 (1) 1.320 (1)
Symmetry codes: (ii) -1+x, y, z. Notes: CgA and CgB are the centroids of the N1/C6–C8/C13 and N1/C2–C6 rings, respectively. The dihedral angle is that between the planes of the rings CgI and CgJ. The interplanar distance is the perpendicular distance of CgI from ring J. The offset is the perpendicular distance of ring I from ring J.

Data collection: CrysAlis CCD (Oxford Diffraction, 2008[Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2008[Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEPII (Johnson, 1976[Johnson, C. K. (1976). ORTEPII. Report ORNL-5138. Oak Ridge National Laboratory, Tennessee, USA.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Pyrazines play an important role as building block of many pharmaceutical products. They occur in many compounds with pharmaceutical and flavoring applications. Many of them have been found in nature. Pyrazines are responsible for flavour in foodstuffs, e.g. cheese, tea, coffee or cooked meat. (Akiyama et al., 1978; Mussinan et al., 1973). Biological activities of pyrazine derivatives are widely discussed in plentiful scientific publications: antibacterial (Foks et al., 2005), anti-inflammatory (Petrusewicz et al., 1995), chemotherapeutic agent (Kushner et al., 1952), antimycobacterial (Seitz et al., 2002) and antithrombotic (Petrusewicz et al., 1993). Such pharmacological activities in group of pyrazine are possibly the result of their structures. It is known that the pyrazine-acetonitrile shows antiplatelet and analgestic activity (Kaliszan et al., 1985). X-Ray structure of pyrazino[2,3-β]indolizine-10-carbonitrile is subject of the present paper.

In the Cambridge Structural Database (CSD; Version 5.27; Allen, 2002), there are no crystal structures containing the pyrazino[2,3-β]indolizine skeleton.

With average deviations from planarity of 0.004 (2) and 0.004 (1)Å respectively, the pyrazino[2,3-β]indolizine and cyano fragments are oriented at 0.8 (1)° to each other. The mean planes of the pyrazino[2,3-β]indolizine skeleton lie either parallel to or are inclined at an angle of 28.7 (2)° in the lattice.

In the crystal structure, neighbouring molecules are linked through weak C–H···N hydrogen bond forming R22(10) ring motif (Table 1 and Fig. 2). Molecules which forming this motif are linked by ππ interactions between the central ring A and the lateral rings B (Table 2 and Fig. 2). All the interactions demonstrated were found by PLATON (Spek, 2009).

Related literature top

For applications of this class of compounds, see: Akiyama et al. (1978); Foks et al. (2005); Kaliszan et al. (1985); Kushner et al. (1952); Mussinan et al. (1973); Petrusewicz et al. (1993, 1995); Seitz et al. (2002). For the synthesis, see: Pilarski & Foks (1981 and 1982). For the analysis of intermolecular interactions, see: Spek (2009). For a description of the Cambridge Structural Database, see: Allen (2002). For hydrogen bonds, see: Steiner (1999).

Experimental top

Pyrazino[2,3-β]indolizine-10-carbonitrile was obtained by mixing 2,3-dichloropyrazine, 2-pyridylacetonitrile and potassium carbonate in DMSO. The mixture was stirred for 5 h at 333 K. After cooling the reaction mixture to room temperature, water was added. Then mixture was acidified with hydrochloric acid (Pilarski & Foks, 1981 and 1982). The orange-green precipitate was obtained. Single crystals suitable for X-ray analysis were grown in methanol solution (m. p. = 486 K).

Refinement top

All H atoms were positioned geometrically and refined using a riding model, with C–H = 0.93Å and Uiso(H) = 1.2Ueq(C).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffraction, 2008); data reduction: CrysAlis RED (Oxford Diffraction, 2008); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEPII (Johnson, 1976); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound showing the atom-labeling scheme. Displacement ellipsoids are drawn at the 25% probability level and H atoms are shown as small spheres of arbitrary radius. CgA and CgB denote the ring centroids.
[Figure 2] Fig. 2. The arrangement of the molecules in the crystal structure viewed approximately along a axis. The C—H···N interactions are represented by dashed lines and the ππ interactions are represented by dotted lines. H atoms not involved in the interactions have been omitted. [Symmetry codes: (i) 1 - x, - y, - z; (ii) -1 + x, y, z.]
Pyrazino[2,3-b]indolizine-10-carbonitrile top
Crystal data top
C11H6N4F(000) = 400
Mr = 194.20Dx = 1.426 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 6832 reflections
a = 3.8515 (5) Åθ = 3.0–25.0°
b = 14.147 (2) ŵ = 0.09 mm1
c = 16.606 (3) ÅT = 295 K
β = 91.260 (14)°Needle, orange-green
V = 904.6 (2) Å30.30 × 0.08 × 0.06 mm
Z = 4
Data collection top
Oxford Diffraction Ruby CCD
diffractometer
1606 independent reflections
Radiation source: Enhance (Mo) X-ray Source1186 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.032
Detector resolution: 10.4002 pixels mm-1θmax = 25.1°, θmin = 3.1°
ω scansh = 44
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2008)
k = 1615
Tmin = 0.992, Tmax = 0.999l = 1819
6832 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.040H-atom parameters constrained
wR(F2) = 0.111 w = 1/[σ2(Fo2) + (0.0745P)2]
where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max < 0.001
1606 reflectionsΔρmax = 0.18 e Å3
137 parametersΔρmin = 0.15 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.017 (5)
Crystal data top
C11H6N4V = 904.6 (2) Å3
Mr = 194.20Z = 4
Monoclinic, P21/cMo Kα radiation
a = 3.8515 (5) ŵ = 0.09 mm1
b = 14.147 (2) ÅT = 295 K
c = 16.606 (3) Å0.30 × 0.08 × 0.06 mm
β = 91.260 (14)°
Data collection top
Oxford Diffraction Ruby CCD
diffractometer
1606 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2008)
1186 reflections with I > 2σ(I)
Tmin = 0.992, Tmax = 0.999Rint = 0.032
6832 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.111H-atom parameters constrained
S = 1.02Δρmax = 0.18 e Å3
1606 reflectionsΔρmin = 0.15 e Å3
137 parameters
Special details top

Experimental. Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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) top
xyzUiso*/Ueq
N10.1906 (3)0.18749 (8)0.01142 (7)0.0395 (3)
C20.3590 (4)0.15549 (12)0.05644 (9)0.0463 (4)
H20.42960.09280.05970.056*
C30.4196 (4)0.21534 (13)0.11734 (10)0.0541 (5)
H30.53030.19430.16320.065*
C40.3135 (4)0.31070 (13)0.11094 (11)0.0554 (5)
H40.35740.35230.15290.066*
C50.1475 (4)0.34299 (12)0.04437 (10)0.0506 (4)
H50.08040.40600.04150.061*
C60.0772 (4)0.28097 (10)0.02016 (9)0.0412 (4)
C70.0876 (4)0.29055 (10)0.09485 (9)0.0431 (4)
C80.0708 (4)0.20124 (11)0.13408 (9)0.0410 (4)
N90.1882 (3)0.17236 (10)0.20656 (8)0.0500 (4)
C100.1199 (4)0.08189 (13)0.22182 (10)0.0538 (5)
H100.19060.05690.27060.065*
C110.0522 (4)0.02209 (12)0.16866 (10)0.0528 (4)
H110.08900.04030.18440.063*
N120.1684 (3)0.04892 (9)0.09592 (8)0.0482 (4)
C130.1002 (3)0.13879 (10)0.08115 (9)0.0387 (4)
C140.2351 (4)0.37523 (12)0.12502 (10)0.0528 (5)
N150.3567 (4)0.44383 (12)0.14836 (11)0.0782 (5)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0429 (6)0.0342 (7)0.0413 (7)0.0010 (5)0.0001 (5)0.0047 (5)
C20.0487 (8)0.0447 (9)0.0455 (9)0.0043 (7)0.0020 (7)0.0093 (7)
C30.0561 (10)0.0600 (12)0.0466 (10)0.0024 (8)0.0074 (8)0.0039 (8)
C40.0558 (9)0.0571 (11)0.0533 (11)0.0042 (8)0.0013 (8)0.0129 (8)
C50.0533 (9)0.0398 (9)0.0586 (11)0.0007 (7)0.0023 (8)0.0044 (8)
C60.0401 (7)0.0331 (8)0.0501 (10)0.0016 (6)0.0033 (7)0.0045 (7)
C70.0463 (8)0.0351 (9)0.0479 (9)0.0010 (6)0.0007 (7)0.0075 (7)
C80.0407 (8)0.0406 (9)0.0415 (9)0.0042 (6)0.0013 (6)0.0059 (7)
N90.0535 (7)0.0499 (10)0.0467 (9)0.0028 (6)0.0035 (6)0.0017 (6)
C100.0568 (9)0.0560 (12)0.0485 (10)0.0065 (8)0.0020 (8)0.0058 (8)
C110.0607 (9)0.0430 (10)0.0543 (10)0.0034 (8)0.0049 (8)0.0086 (8)
N120.0545 (7)0.0373 (8)0.0525 (8)0.0030 (6)0.0043 (6)0.0006 (6)
C130.0407 (7)0.0339 (9)0.0413 (9)0.0012 (6)0.0026 (6)0.0032 (6)
C140.0552 (9)0.0436 (11)0.0597 (11)0.0000 (8)0.0016 (8)0.0123 (8)
N150.0841 (11)0.0517 (11)0.0992 (13)0.0092 (8)0.0080 (10)0.0274 (9)
Geometric parameters (Å, º) top
N1—C21.3883 (19)C7—C141.422 (2)
N1—C131.3980 (18)C7—C81.422 (2)
N1—C61.4014 (18)C8—N91.3580 (19)
C2—C31.343 (2)C8—C131.419 (2)
C2—H20.9300N9—C101.330 (2)
C3—C41.414 (3)C10—C111.400 (2)
C3—H30.9300C10—H100.9300
C4—C51.368 (2)C11—N121.352 (2)
C4—H40.9300C11—H110.9300
C5—C61.416 (2)N12—C131.3201 (19)
C5—H50.9300C14—N151.149 (2)
C6—C71.412 (2)
C2—N1—C13129.87 (13)C6—C7—C14125.53 (14)
C2—N1—C6122.96 (13)C6—C7—C8107.47 (12)
C13—N1—C6107.18 (11)C14—C7—C8126.98 (15)
C3—C2—N1119.85 (15)N9—C8—C13122.01 (14)
C3—C2—H2120.1N9—C8—C7131.34 (14)
N1—C2—H2120.1C13—C8—C7106.65 (13)
C2—C3—C4119.29 (15)C10—N9—C8112.96 (13)
C2—C3—H3120.4N9—C10—C11123.77 (15)
C4—C3—H3120.4N9—C10—H10118.1
C5—C4—C3121.36 (16)C11—C10—H10118.1
C5—C4—H4119.3N12—C11—C10124.36 (15)
C3—C4—H4119.3N12—C11—H11117.8
C4—C5—C6120.35 (16)C10—C11—H11117.8
C4—C5—H5119.8C13—N12—C11111.60 (13)
C6—C5—H5119.8N12—C13—N1125.19 (13)
N1—C6—C7109.19 (12)N12—C13—C8125.30 (14)
N1—C6—C5116.18 (13)N1—C13—C8109.50 (13)
C7—C6—C5134.63 (14)N15—C14—C7179.0 (2)
C13—N1—C2—C3179.88 (14)C6—C7—C8—C130.94 (16)
C6—N1—C2—C30.1 (2)C14—C7—C8—C13179.67 (14)
N1—C2—C3—C40.6 (2)C13—C8—N9—C101.07 (19)
C2—C3—C4—C50.6 (2)C7—C8—N9—C10179.86 (16)
C3—C4—C5—C60.1 (2)C8—N9—C10—C110.5 (2)
C2—N1—C6—C7179.16 (12)N9—C10—C11—N120.1 (3)
C13—N1—C6—C70.67 (14)C10—C11—N12—C130.2 (2)
C2—N1—C6—C50.79 (19)C11—N12—C13—N1179.34 (12)
C13—N1—C6—C5179.38 (12)C11—N12—C13—C80.4 (2)
C4—C5—C6—N10.8 (2)C2—N1—C13—N121.2 (2)
C4—C5—C6—C7179.16 (15)C6—N1—C13—N12178.99 (13)
N1—C6—C7—C14179.76 (14)C2—N1—C13—C8179.75 (12)
C5—C6—C7—C140.3 (3)C6—N1—C13—C80.07 (14)
N1—C6—C7—C81.01 (15)N9—C8—C13—N121.1 (2)
C5—C6—C7—C8179.06 (15)C7—C8—C13—N12179.60 (14)
C6—C7—C8—N9179.88 (14)N9—C8—C13—N1179.82 (11)
C14—C7—C8—N91.2 (3)C7—C8—C13—N10.55 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···N12i0.932.613.487 (2)157
Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC11H6N4
Mr194.20
Crystal system, space groupMonoclinic, P21/c
Temperature (K)295
a, b, c (Å)3.8515 (5), 14.147 (2), 16.606 (3)
β (°) 91.260 (14)
V3)904.6 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.09
Crystal size (mm)0.30 × 0.08 × 0.06
Data collection
DiffractometerOxford Diffraction Ruby CCD
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2008)
Tmin, Tmax0.992, 0.999
No. of measured, independent and
observed [I > 2σ(I)] reflections
6832, 1606, 1186
Rint0.032
(sin θ/λ)max1)0.596
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.111, 1.02
No. of reflections1606
No. of parameters137
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.18, 0.15

Computer programs: CrysAlis CCD (Oxford Diffraction, 2008), CrysAlis RED (Oxford Diffraction, 2008), SHELXS97 (Sheldrick, 2008), ORTEPII (Johnson, 1976), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···N12i0.932.613.487 (2)157
Symmetry code: (i) x+1, y, z.
ππ interactions (Å, °) top
CgICgJCg···CgDihedral angleInterplanar distanceOffset
ABii3.608 (1)0.63.358 (1)1.320 (1)
Symmetry codes: (ii) -1 + x, y, z. Notes: CgA and CgB are the centroids of the N1/C6–C8/C13 and N1/C2–C6 rings, respectively. The dihedral angle is that between the planes of the rings CgI and CgJ. The interplanar distance is the perpendicular distance of CgI from ring J. The offset is the perpendicular distance of ring I from ring J.
 

Acknowledgements

This scientific work has been supported by `Funds for Science in Year 2009' as a research project (DS/8410–4–0139–9).

References

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Volume 65| Part 4| April 2009| Pages o772-o773
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