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3-Amino-1-methyl­pyrazin-1-ium chloride

aDepartment of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada, M5B 2K3, and bDepartment of Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3H6
*Correspondence e-mail: alough@chem.utoronto.ca

(Received 24 November 2009; accepted 27 November 2009; online 4 December 2009)

In the cation of the title compound, C5H8N3+·Cl, the C—N(H2) bond distance [1.348 (3) Å] is at the lower end of the range for aryl amines. In the crystal structure, cations and anions are linked via N—H⋯Cl hydrogen bonds, forming one-dimensional chains along [100].

Related literature

For the synthesis and characterization of the title compound, see: Foucher et al. (1993[Foucher, D. A., Macartney, D. H., Warrack, L. J. & Wilson, J. P. (1993). Inorg. Chem. 32, 3425-3432.]). Additional preparative details of similar compounds are given by Goto et al. (1968[Goto, T., Isobe, M., Ohtsuru, M. & Tori, K. (1968). Tetrahedron Lett. 12, 1511-1514.]). For related structures, see Chao et al. (1976[Chao, M., Schempp, E. & Rosenstein, R. D. (1976). Acta Cryst. B32, 288-290.]); Kazheva et al. (2006[Kazheva, O. N., Ziolkovskiy, D. V., Alexandrov, G. G., Chekhlov, A. N., Dyachenko, O. A., Starodub, V. A. & Khotkevich, A. V. (2006). Synth. Met. 156, 1010-1016.]); Foucher et al. (1989[Foucher, D. A., Fortier, S. & Macartney, D. H. (1989). Acta Cryst. C45, 112-114.]); Lu & Xi (2008[Lu, W. & Xi, C. (2008). Tetrahedron Lett. 49, 4011-4015.]). For the crystal structure of 3-amino-1- methylpyrazin-1-ium iodide, see: Foucher et al. (2009[Foucher, D., Wylie, S., Macartney, D. H. & Lough, A. J. (2010). Acta Cryst. E66, o60.]). For comparative bond-distance data, see: Allen et al. (1987[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.]).

[Scheme 1]

Experimental

Crystal data
  • C5H8N3+·Cl

  • Mr = 145.59

  • Orthorhombic, P b c a

  • a = 11.3164 (3) Å

  • b = 9.5029 (5) Å

  • c = 12.3877 (5) Å

  • V = 1332.16 (10) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.48 mm−1

  • T = 150 K

  • 0.24 × 0.16 × 0.12 mm

Data collection
  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan (SORTAV; Blessing 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.]) Tmin = 0.819, Tmax = 0.946

  • 9107 measured reflections

  • 1526 independent reflections

  • 1144 reflections with I > 2σ(I)

  • Rint = 0.047

Refinement
  • R[F2 > 2σ(F2)] = 0.040

  • wR(F2) = 0.111

  • S = 1.10

  • 1526 reflections

  • 91 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.46 e Å−3

  • Δρmin = −0.28 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N7—H1N⋯Cl1 0.91 (3) 2.40 (3) 3.297 (2) 168 (2)
N7—H2N⋯Cl1i 0.94 (3) 2.37 (3) 3.289 (2) 168 (3)
Symmetry code: (i) [x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1].

Data collection: COLLECT (Nonius BV, 2002[Nonius BV (2002). COLLECT. Delft, The Netherlands.]); cell refinement: DENZO-SMN (Otwinowski & Minor, 1997[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.]); data reduction: DENZO-SMN; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]); software used to prepare material for publication: SHELXTL.

Supporting information


Comment top

The title chloride compound, (I), was recovered from the ion exchange (Dowex 1-X8 ion exchange resin saturated with Cl- anions) of the iodide precursor of N-methyl-3-aminopyrazinium iodide (Foucher et al., 1993). The proximity of the amine group to one of the diazine N atoms makes it an ideal chelating ligand to metals and geometrically suggests the possibility for amine-imine tautomerism. We have investigated the possibility that a smaller counter ion might induce a preference for the imine tautomer in these salts.

The molecular structure of (I) is shown in Fig. 1. The cation is the amine tautomer and resembles closely in terms of bond angles and bond lengths, other N-methylated amino pyrazinium salts (Kazheva et al., 2006; Foucher et al., 1989). The C5—N4—C3 bond angle in (I) [121.02 (18) °] is significantly wider than in 2-aminopyrazine [116.6 (1)°] (Chao et al., 1976) but similar to the angle found in N-methyl-3-aminopyrazinium iodide (121.3 (5)°; Foucher et al., 2010). 2-Aminopyrazine and both N-methyl-3-aminopyrazium salts are characterized by short amine-ring bond distances [N7—C6 in (I) = 1.348 (3) Å, 1.341 (1)Å (Chao et al., 1976) and 1.338 (8)Å (Foucher et al., 2009)] compared to typical values for C(sp2)-NH2 bond lengths, i.e. 1.36 Å (Allen et al., 1987)] although these distances are significantly longer than the C=N(H) bond [1.285 (4) Å] in N-(4-imino-3,5-dimethylcyclohexa-2,5-dienylidene)-2,6-dimethylaniline (Lu & Xi, 2008). 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···Cl hydrogen bonds to form one-dimensional chains along [100], Table 1 and Fig. 2.

Related literature top

For the synthesis and characterization of the title compound, see: Foucher et al. (1993). Additional preparative details of similar compounds are given by Goto et al. (1968). For related structures, see Chao et al. (1976); Kazheva et al. (2006); Foucher et al. (1989); Lu & Xi (2008). For the crystal structure of N-methyl-3-aminopyrazinium iodide, see: Foucher et al. (2010). For comparative bond-distance data, see: Allen et al. (1987).

Experimental top

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 recovered from the ion exchange (Dowex 1-X8 ion exchange resin saturated with Cl- anion) of a concentrated aqueous solution containing 0.30 g (1.266 mmol) of N-methyl-3-pyrazinium iodide (Foucher et al., 1993). The aqueous fractions containing the crude title compound were collected and brought to dryness. Crystals suitable for X-ray diffraction were isolated from the recrystallization of the crude product from boiling ethanol. Yield 0.11 g, 78%. Characterization by NMR agreed with previous literature (Foucher et al., 1993).

Refinement top

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-model approximation with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(Cmethyl). H atoms bonded to the amine group N atom were refined independently with isotropic displacement parameters.

Computing details top

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

Figures top
[Figure 1] Fig. 1. The asymmetric unit of (I) with displacement ellipsoids drawn at the 30% probability level. The dashed line indicates a hydrogen bond.
[Figure 2] Fig. 2. Part of the crystal structure of (I) with hydrogen bonds shown as dashed lines.
3-Amino-1-methylpyrazin-1-ium chloride top
Crystal data top
C5H8N3+·ClF(000) = 608
Mr = 145.59Dx = 1.452 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 9107 reflections
a = 11.3164 (3) Åθ = 3.3–27.5°
b = 9.5029 (5) ŵ = 0.48 mm1
c = 12.3877 (5) ÅT = 150 K
V = 1332.16 (10) Å3Needle, pale yellow
Z = 80.24 × 0.16 × 0.12 mm
Data collection top
Nonius KappaCCD
diffractometer
1526 independent reflections
Radiation source: fine-focus sealed tube1144 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.047
Detector resolution: 9 pixels mm-1θmax = 27.5°, θmin = 3.3°
ϕ scans and ω scans with κ offsetsh = 1414
Absorption correction: multi-scan
(SORTAV; Blessing 1995)
k = 1112
Tmin = 0.819, Tmax = 0.946l = 1615
9107 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)] = 0.040Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.111H atoms treated by a mixture of independent and constrained refinement
S = 1.10 w = 1/[σ2(Fo2) + (0.0514P)2 + 0.7939P]
where P = (Fo2 + 2Fc2)/3
1526 reflections(Δ/σ)max < 0.001
91 parametersΔρmax = 0.46 e Å3
0 restraintsΔρmin = 0.28 e Å3
Crystal data top
C5H8N3+·ClV = 1332.16 (10) Å3
Mr = 145.59Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 11.3164 (3) ŵ = 0.48 mm1
b = 9.5029 (5) ÅT = 150 K
c = 12.3877 (5) Å0.24 × 0.16 × 0.12 mm
Data collection top
Nonius KappaCCD
diffractometer
1526 independent reflections
Absorption correction: multi-scan
(SORTAV; Blessing 1995)
1144 reflections with I > 2σ(I)
Tmin = 0.819, Tmax = 0.946Rint = 0.047
9107 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0400 restraints
wR(F2) = 0.111H atoms treated by a mixture of independent and constrained refinement
S = 1.10Δρmax = 0.46 e Å3
1526 reflectionsΔρmin = 0.28 e Å3
91 parameters
Special details top

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
Cl10.52068 (5)0.20079 (5)0.55295 (4)0.02322 (19)
N10.80709 (16)0.15734 (19)0.21473 (15)0.0255 (4)
C20.7861 (2)0.0803 (2)0.12664 (17)0.0257 (5)
H2A0.84380.07950.07100.031*
C30.68473 (19)0.0018 (2)0.11251 (17)0.0256 (5)
H3A0.67300.05190.04870.031*
N40.60290 (15)0.00317 (17)0.19137 (13)0.0202 (4)
C50.61964 (18)0.0768 (2)0.28134 (16)0.0207 (5)
H5A0.56180.07670.33690.025*
C60.72478 (18)0.1552 (2)0.29291 (17)0.0212 (5)
N70.74454 (18)0.2293 (2)0.38395 (16)0.0301 (5)
C80.49086 (19)0.0728 (2)0.17540 (19)0.0256 (5)
H8A0.46460.11260.24430.038*
H8B0.50260.14880.12310.038*
H8C0.43080.00750.14820.038*
H1N0.691 (2)0.227 (3)0.438 (2)0.035 (7)*
H2N0.821 (3)0.263 (3)0.397 (2)0.058 (9)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Cl10.0224 (3)0.0264 (3)0.0209 (3)0.0013 (2)0.0005 (2)0.00014 (19)
N10.0213 (9)0.0295 (9)0.0257 (10)0.0032 (8)0.0023 (8)0.0047 (8)
C20.0255 (11)0.0306 (11)0.0210 (11)0.0062 (9)0.0037 (9)0.0048 (9)
C30.0299 (12)0.0267 (11)0.0202 (11)0.0069 (9)0.0027 (9)0.0000 (9)
N40.0211 (9)0.0195 (8)0.0199 (9)0.0032 (7)0.0003 (7)0.0014 (7)
C50.0206 (10)0.0225 (10)0.0191 (11)0.0037 (8)0.0011 (8)0.0008 (8)
C60.0206 (11)0.0218 (10)0.0212 (11)0.0029 (8)0.0004 (8)0.0025 (8)
N70.0209 (10)0.0421 (12)0.0272 (11)0.0047 (9)0.0017 (9)0.0085 (9)
C80.0241 (11)0.0273 (11)0.0254 (12)0.0029 (9)0.0020 (9)0.0047 (9)
Geometric parameters (Å, º) top
N1—C21.335 (3)C5—C61.411 (3)
N1—C61.344 (3)C5—H5A0.9500
C2—C31.380 (3)C6—N71.348 (3)
C2—H2A0.9500N7—H1N0.91 (3)
C3—N41.346 (3)N7—H2N0.94 (3)
C3—H3A0.9500C8—H8A0.9800
N4—C51.330 (3)C8—H8B0.9800
N4—C81.472 (3)C8—H8C0.9800
C2—N1—C6117.23 (18)N1—C6—N7118.70 (19)
N1—C2—C3123.2 (2)N1—C6—C5121.26 (19)
N1—C2—H2A118.4N7—C6—C5120.03 (19)
C3—C2—H2A118.4C6—N7—H1N119.8 (16)
N4—C3—C2118.34 (19)C6—N7—H2N118.6 (19)
N4—C3—H3A120.8H1N—N7—H2N120 (2)
C2—C3—H3A120.8N4—C8—H8A109.5
C5—N4—C3121.02 (18)N4—C8—H8B109.5
C5—N4—C8119.57 (17)H8A—C8—H8B109.5
C3—N4—C8119.35 (18)N4—C8—H8C109.5
N4—C5—C6118.90 (19)H8A—C8—H8C109.5
N4—C5—H5A120.6H8B—C8—H8C109.5
C6—C5—H5A120.6
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N7—H1N···Cl10.91 (3)2.40 (3)3.297 (2)168 (2)
N7—H2N···Cl1i0.94 (3)2.37 (3)3.289 (2)168 (3)
Symmetry code: (i) x+1/2, y+1/2, z+1.

Experimental details

Crystal data
Chemical formulaC5H8N3+·Cl
Mr145.59
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)150
a, b, c (Å)11.3164 (3), 9.5029 (5), 12.3877 (5)
V3)1332.16 (10)
Z8
Radiation typeMo Kα
µ (mm1)0.48
Crystal size (mm)0.24 × 0.16 × 0.12
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(SORTAV; Blessing 1995)
Tmin, Tmax0.819, 0.946
No. of measured, independent and
observed [I > 2σ(I)] reflections
9107, 1526, 1144
Rint0.047
(sin θ/λ)max1)0.650
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.040, 0.111, 1.10
No. of reflections1526
No. of parameters91
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.46, 0.28

Computer programs: COLLECT (Nonius BV, 2002), DENZO-SMN (Otwinowski & Minor, 1997), SIR92 (Altomare et al., 1994), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N7—H1N···Cl10.91 (3)2.40 (3)3.297 (2)168 (2)
N7—H2N···Cl1i0.94 (3)2.37 (3)3.289 (2)168 (3)
Symmetry code: (i) x+1/2, y+1/2, z+1.
 

Acknowledgements

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

References

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