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Acta Crystallogr Sect E Struct Rep Online. 2010 January 1; 66(Pt 1): o60.
Published online 2009 December 4. doi:  10.1107/S1600536809051253
PMCID: PMC2980151

3-Amino-1-methyl­pyrazin-1-ium iodide

Abstract

In the cation of the title compound, C5H8N3 +·I, the C—N(H2) bond distance [1.338 (8) Å] is at the lower end of the range for aryl amines. In the crystal structure, cations and anions are linked via N—H(...)I hydrogen bonds, forming centrosymmetric four-component clusters.

Related literature

For the synthesis and characterization of the title compound, see: Foucher et al. (1993 [triangle]). Additional preparative details of similar compounds are given by Goto et al. (1968 [triangle]). For related structures, see Chao et al. (1976 [triangle]); Foucher et al. (1989 [triangle]); Kazheva et al. (2006 [triangle]). For the crystal structure of 3-amino-1-methylpyrazin-1-ium chloride, see the following paper. For comparative bond-distance data, see: Allen et al. (1987 [triangle]).

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Object name is e-66-00o60-scheme1.jpg

Experimental

Crystal data

  • C5H8N3 +·I
  • M r = 237.04
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-00o60-efi1.jpg
  • a = 6.9759 (5) Å
  • b = 13.2966 (15) Å
  • c = 8.3668 (9) Å
  • β = 90.951 (7)°
  • V = 775.96 (13) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 4.05 mm−1
  • T = 100 K
  • 0.20 × 0.08 × 0.06 mm

Data collection

  • Nonius KappaCCD diffractometer
  • Absorption correction: multi-scan (DENZO-SMN; Otwinowski & Minor, 1997 [triangle]) T min = 0.498, T max = 0.793
  • 3835 measured reflections
  • 1382 independent reflections
  • 1020 reflections with I > 2σ(I)
  • R int = 0.067

Refinement

  • R[F 2 > 2σ(F 2)] = 0.037
  • wR(F 2) = 0.088
  • S = 0.92
  • 1382 reflections
  • 92 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 1.16 e Å−3
  • Δρmin = −1.33 e Å−3

Data collection: COLLECT (Nonius, 2002 [triangle]); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997 [triangle]); data reduction: DENZO-SMN; program(s) used to solve structure: SIR92 (Altomare et al., 1994 [triangle]); program(s) used to refine structure: SHELXTL (Sheldrick, 2008 [triangle]); molecular graphics: PLATON (Spek, 2009 [triangle]); software used to prepare material for publication: SHELXTL.

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809051253/tk2585sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809051253/tk2585Isup2.hkl

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

Acknowledgments

The authors acknowledge NSERC Canada, the University of Toronto and the Dean’s Seed Fund Initiative (Ryerson University) for funding.

supplementary crystallographic information

Comment

The title compound, (I), is prepared in moderate yield from the reaction of 2-aminopyrazine with methyl iodide in carbon tetrachloride (Foucher et al., 1993). The proximity of the amine group to one of the diazine nitrogen atoms makes it an ideal chelating ligand to metals and geometrically suggests the possibility for amine-imine tautomerism.

The molecular structure of (I) is shown in Fig. 1. The cation in (I) is the amine tautomer and resembles closely in terms of bond angles and bond lengths, other aromatic 1,4-diazines (Foucher et al., 1989). In a comparison, the major structural difference between 2-aminopyrazine (Chao et al., 1976) and (I) is observed in the C5—N4—C3 angle which is 121.3 (5)° in (I) and is 116.6 (1) in 2-aminopyrazine. These two structures are characterized by short amine-ring bond distances [1.338 (8) Å for C6—N7 in (I) and 1.341 (1) Å in 2-aminopyrazine] compared to typical bond lengths of sp2(C)—NH2 bond lengths, i.e. 1.36 Å (Allen et al., 1987). These short bond lengths are suggestive of a considerable degree of double bond character, where the lone pair of the amine participates in the resonance of the ring π system. In the crystal structure, cations and anions are linked via intermolecular N—H···I hydrogen bonds to form centrosymmetric four component clusters (Fig. 2).

Experimental

General procedures for the synthesis of this type of compound are given by Goto et al. (1968) and Kazheva et al. (2006). The title compound was prepared by the slow addition of an excess of methyl iodide (16 mmol) to a refluxing solution of the 2-aminopyrazine (7.9 mmol) in CCl4 for 12 h. The crude products were filtered off and recrystallized from a 4:1 ethanol/water mixture giving crystals suitable for X-ray analysis. Yield 1.12 g, 60%. Characterization by NMR agreed with previous literature (Foucher et al., 1993).

Refinement

H atoms bonded to C atoms were placed in calculated positions with C—H = 0.95 and 0.98 Å, and included in a riding-motion approximation with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(Cmethyl). H atoms bonded to the amine-N atom were refined independently but with the N—H distance refined as a free variable [SHELXL (Sheldrick, 2008) command: DFIX 21.00 0.01 N7 H1N N7 H2N] and with isotropic displacement parameters. The maximum and minimum residual electron density peaks of 1.15 and -1.33 eÅ-3, respectively are located 1.63 Å and 0.98 Å from the atoms N4 and I1, respectively.

Figures

Fig. 1.
The asymmetric unit of (I) with displacement ellipsoids drawn at the 30% probability level. The dashed line indicates a hydrogen bond.
Fig. 2.
Part of the crystal structure of (I) with hydrogen bonds shown as dashed lines.

Crystal data

C5H8N3+·IF(000) = 448
Mr = 237.04Dx = 2.029 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 3835 reflections
a = 6.9759 (5) Åθ = 4.1–25.4°
b = 13.2966 (15) ŵ = 4.05 mm1
c = 8.3668 (9) ÅT = 100 K
β = 90.951 (7)°Needle, colourless
V = 775.96 (13) Å30.20 × 0.08 × 0.06 mm
Z = 4

Data collection

Nonius KappaCCD diffractometer1382 independent reflections
Radiation source: fine-focus sealed tube1020 reflections with I > 2σ(I)
graphiteRint = 0.067
Detector resolution: 9 pixels mm-1θmax = 25.4°, θmin = 4.1°
[var phi] scans and ω scans with κ offsetsh = −7→7
Absorption correction: multi-scan DENZO-SMN (Otwinowski & Minor, 1997)k = −16→16
Tmin = 0.498, Tmax = 0.793l = −10→10
3835 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.037Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.088H atoms treated by a mixture of independent and constrained refinement
S = 0.92w = 1/[σ2(Fo2) + (0.0489P)2] where P = (Fo2 + 2Fc2)/3
1382 reflections(Δ/σ)max < 0.001
92 parametersΔρmax = 1.16 e Å3
2 restraintsΔρmin = −1.33 e Å3

Special details

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)

xyzUiso*/Ueq
I10.17537 (5)0.57745 (3)0.29944 (5)0.02643 (18)
N10.3523 (7)0.1982 (4)0.6511 (7)0.0263 (13)
C20.2488 (10)0.1169 (5)0.6907 (8)0.0283 (15)
H2A0.30600.06920.76130.034*
C30.0667 (9)0.0987 (4)0.6357 (8)0.0234 (15)
H3A−0.00150.04050.66800.028*
N4−0.0138 (6)0.1666 (4)0.5332 (6)0.0235 (12)
C50.0814 (8)0.2476 (5)0.4871 (7)0.0255 (15)
H5A0.02580.29340.41260.031*
C60.2673 (8)0.2643 (5)0.5513 (8)0.0266 (15)
N70.3625 (8)0.3480 (4)0.5128 (8)0.0309 (14)
H1N0.470 (8)0.362 (6)0.565 (8)0.04 (2)*
H2N0.309 (11)0.401 (5)0.467 (10)0.06 (3)*
C8−0.2119 (8)0.1506 (5)0.4716 (9)0.0317 (17)
H8A−0.28400.21370.47860.048*
H8B−0.27470.09890.53550.048*
H8C−0.20780.12880.35980.048*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
I10.0231 (3)0.0253 (3)0.0309 (3)0.00012 (19)0.00021 (16)−0.0010 (2)
N10.024 (3)0.030 (3)0.025 (3)−0.001 (2)0.000 (2)−0.002 (2)
C20.035 (4)0.023 (4)0.026 (4)−0.001 (3)−0.002 (3)−0.002 (3)
C30.023 (3)0.018 (4)0.030 (4)−0.002 (2)−0.001 (3)−0.001 (3)
N40.015 (3)0.027 (3)0.029 (3)0.000 (2)0.000 (2)−0.004 (2)
C50.026 (3)0.021 (4)0.029 (4)0.003 (3)−0.004 (3)−0.001 (3)
C60.025 (3)0.033 (4)0.022 (4)0.003 (3)0.000 (3)−0.003 (3)
N70.028 (3)0.027 (3)0.037 (4)0.001 (3)−0.003 (3)0.011 (3)
C80.019 (3)0.031 (4)0.045 (5)0.000 (3)0.001 (3)−0.001 (3)

Geometric parameters (Å, °)

N1—C61.344 (8)C5—C61.413 (8)
N1—C21.344 (8)C5—H5A0.9500
C2—C31.366 (9)C6—N71.338 (8)
C2—H2A0.9500N7—H1N0.88 (5)
C3—N41.360 (8)N7—H2N0.88 (5)
C3—H3A0.9500C8—H8A0.9800
N4—C51.326 (8)C8—H8B0.9800
N4—C81.482 (7)C8—H8C0.9800
C6—N1—C2116.5 (6)N7—C6—N1118.5 (6)
N1—C2—C3124.1 (6)N7—C6—C5119.7 (6)
N1—C2—H2A118.0N1—C6—C5121.8 (6)
C3—C2—H2A118.0C6—N7—H1N119 (5)
N4—C3—C2117.8 (6)C6—N7—H2N124 (6)
N4—C3—H3A121.1H1N—N7—H2N113 (7)
C2—C3—H3A121.1N4—C8—H8A109.5
C5—N4—C3121.3 (5)N4—C8—H8B109.5
C5—N4—C8118.9 (5)H8A—C8—H8B109.5
C3—N4—C8119.8 (5)N4—C8—H8C109.5
N4—C5—C6118.6 (6)H8A—C8—H8C109.5
N4—C5—H5A120.7H8B—C8—H8C109.5
C6—C5—H5A120.7

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N7—H2N···I10.88 (5)2.88 (5)3.758 (6)173 (7)
N7—H1N···I1i0.88 (5)2.82 (5)3.698 (6)173 (7)

Symmetry codes: (i) −x+1, −y+1, −z+1.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: TK2585).

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.
  • Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst.27, 435.
  • Chao, M., Schempp, E. & Rosenstein, R. D. (1976). Acta Cryst. B32, 288–290.
  • Foucher, D. A., Fortier, S. & Macartney, D. H. (1989). Acta Cryst. C45, 112–114.
  • Foucher, D. A., Macartney, D. H., Warrack, L. J. & Wilson, J. P. (1993). Inorg. Chem.32, 3425–3432.
  • Goto, T., Isobe, M., Ohtsuru, M. & Tori, K. (1968). Tetrahedron Lett.12, 1511–1514.
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  • Nonius (2002). COLLECT Delft, The Netherlands.
  • Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A edited by C. W. Carter & R. M. Sweet pp. 307–326. London: Academic Press.
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  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

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