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Acta Crystallogr Sect E Struct Rep Online. 2009 July 1; 65(Pt 7): o1546.
Published online 2009 June 10. doi:  10.1107/S1600536809021643
PMCID: PMC2969452

2-Methyl-4,6-bis­(1-methyl­hydrazino)pyrimidine

Abstract

In the title compound, C7H14N6, the amine groups of the two methyl­hydrazino substituents are orientated in the opposite direction to the methyl substituent at the 2-position of the pyrimidine ring. The mol­ecule is almost planar with only the two amine N atoms lying substanti­ally out of the mean plane of the pyrimidine ring [by 0.1430 (2) and 0.3092 (2) Å]. The H atoms on these amine groups point inwards towards the aromatic ring, such that the lone pair of electrons points outwards from the mol­ecule. Each mol­ecule is linked to two others through N—H(...)N hydrogen bonds between the two amino groups, forming a one-dimensional chain in the [010] direction. Offset face-to-face π–π stacking inter­actions between the pyrimidine rings organize these chains into a two-dimensional array [centroid–centroid distance = 3.789 (2) Å].

Related literature

For the use of related compounds in the synthesis of mol­ecular strands see: Schmitt et al. (2003 [triangle]), Schmitt & Lehn (2003 [triangle]), Gardinier et al. (2000 [triangle]).

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Object name is e-65-o1546-scheme1.jpg

Experimental

Crystal data

  • C7H14N6
  • M r = 182.24
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o1546-efi1.jpg
  • a = 9.2255 (6) Å
  • b = 8.5075 (6) Å
  • c = 12.2323 (7) Å
  • β = 109.233 (3)°
  • V = 906.48 (10) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.09 mm−1
  • T = 90 K
  • 0.40 × 0.32 × 0.18 mm

Data collection

  • Bruker APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2006 [triangle]) T min = 0.905, T max = 0.980
  • 16072 measured reflections
  • 1691 independent reflections
  • 1652 reflections with I > 2σ(I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.035
  • wR(F 2) = 0.096
  • S = 1.04
  • 1691 reflections
  • 133 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.20 e Å−3
  • Δρmin = −0.21 e Å−3

Data collection: APEX2 (Bruker, 2006 [triangle]); cell refinement: APEX2 and SAINT (Bruker 2006 [triangle]); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: SHELXTL (Sheldrick, 2008 [triangle]) and Mercury (Bruno et al., 2002 [triangle]); software used to prepare material for publication: SHELXTL and enCIFer (Allen et al., 2004 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809021643/bv2120sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809021643/bv2120Isup2.hkl

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

Acknowledgments

We wish to thank the New Economic Research Fund (grant No UOO-X0808) of the New Zealand Foundation of Research Science and Technology for financial support.

supplementary crystallographic information

Comment

Although 1 is unstable in air, we were able to isolate X-ray quality crystals. Compound 1 was prepared in quantitative yield through the reaction of methylhydrazine and 4,6-dichloro-2-methylpyrimidine under an inert N2 atmosphere. In 1 the amine groups (N4 and N6) were orientated in the opposite direction to the methyl group (C5). The molecule was planar with only N4 and N6 being out of the mean plane of the pyrimidine ring by 0.1430 (2) and 0.3092 (2) Å, respectively. The hydrogen atoms on these amine groups were located from difference Fourier maps and freely refined. They pointed inwards towards C3 such that the lone pair of electrons on N4 and N6 pointed outwards from the molecule.

Each molecule of 1 was linked to two others through H-bonding between N4 and N6 (Figure 2). The N6—H···N4 distance was measured as 2.177 (16) Å, which corresponded to a N6···N4 distance of 3.093 (2) Å. This H-bond linked molecules of 1 together to form a one dimensional chain in the [0 1 -1] direction. The angle between the planes of adjacent H-bonded molecules was 72.97 (1)°. Offset, face-to-face π-π stacking interactions between the pyrimidine rings organized these chains into a two dimensional array. The centroid to centroid distance for this π-π interaction was 3.789 (2) Å.

Experimental

Under magnetic stirring, 4,6-dichloro-2-methylpyrimidine, (0.4792 g, 2.94 mmol) dissolved in EtOH (30 ml), was added by portions over 20 min to ice cooled methylhydrazine (2.00 ml, 38.0 mmol) flushed with Ar. The mixture was refluxed for 6 h under an inert atmosphere of N2. After cooling, residual methylhydrazine and EtOH were evaporated, K2CO3 (1.025 g) and CHCl3 (50 ml) were added to the solid residue, and the mixture was stirred for 20 min. The liquid phase was filtered and the solid was washed with more CHCl3 (50 ml then 30 ml). The combined liquid fractions were evaporated and the resulting solid was dried in vacuo to gave 1 as a white solid (0.5566 g, quant.), unstable in air: 1H NMR (CDCl3, 500 MHz) δ/p.p.m.: 5.95 (1H, s, H5), 3.99 (4H, bs, NH2), 3.22 (6H, s, H8), 2.37 (3H, s, H7). 13C NMR (CDCl3, 500 MHz) δ/p.p.m.: 166.0 (C2), 165.2 (C4, C6), 78.1 (C5), 39.9 (C8), 26.2 (C7). ESMS m/z Found: 365.1063 [2M+H]+, 183.1353 [M+H]+, 151.0966 [M-(NH2)2]+. Calc. for C7H14N6: [M+H]+ 183.1353. Selected IR (KBr disc) ν/cm-1: 3296 (s, NH str), 3177 (m, CH str), 2933 (m, CH str), 1588 (s, br, NH bend), 1499 (m, pym str), 1399 (m, CH bend), 1136 (w, CN str). Crystals suitable for X-ray determination were grown by slow evaporation of a CDCl3 solution of 1.

Refinement

All H-atoms bound to carbon were refined using a riding model with d(C—H) = 0.93 Å, Uiso=1.2Ueq (C) for the CH H atoms and d(C—H) = 0.96 Å, Uiso=1.5Ueq (C) for the CH3 H atoms. All H-atoms bound to nitrogen were located from difference Fourier maps and freely refined with Uiso=1.5Ueq (N).

Figures

Fig. 1.
The asymmetric unit of (1) showing the atom numbering with displacement ellipsoids drawn at the 50% probability level.
Fig. 2.
View of the arrangement of 1 into one-dimensional chains through H-bonding and organization of the chains into a two-dimensional array through π-π stacking.

Crystal data

C7H14N6F(000) = 392
Mr = 182.24Dx = 1.335 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71069 Å
Hall symbol: -P 2ynCell parameters from 6739 reflections
a = 9.2255 (6) Åθ = 2.4–39.2°
b = 8.5075 (6) ŵ = 0.09 mm1
c = 12.2323 (7) ÅT = 90 K
β = 109.233 (3)°Rhomb, colourless
V = 906.48 (10) Å30.40 × 0.32 × 0.18 mm
Z = 4

Data collection

Bruker APEXII CCD area-detector diffractometer1691 independent reflections
Radiation source: fine-focus sealed tube1652 reflections with I > 2σ(I)
graphiteRint = 0.026
[var phi] and ω scansθmax = 25.5°, θmin = 3.0°
Absorption correction: multi-scan (SADABS; Bruker, 2006)h = −11→11
Tmin = 0.905, Tmax = 0.980k = −10→10
16072 measured reflectionsl = −14→14

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)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H atoms treated by a mixture of independent and constrained refinement
S = 1.04w = 1/[σ2(Fo2) + (0.0521P)2 + 0.3928P] where P = (Fo2 + 2Fc2)/3
1691 reflections(Δ/σ)max < 0.001
133 parametersΔρmax = 0.20 e Å3
0 restraintsΔρmin = −0.21 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
C10.73886 (13)0.17687 (13)0.47904 (9)0.0164 (3)
C20.93621 (12)0.07975 (13)0.63049 (9)0.0154 (3)
C31.04186 (12)0.15748 (13)0.59004 (9)0.0161 (3)
H31.14690.15100.62890.019*
C40.98251 (13)0.24539 (13)0.48866 (10)0.0157 (3)
C50.56857 (13)0.18783 (15)0.41657 (10)0.0222 (3)
H5A0.51980.09270.42840.033*
H5B0.55010.20240.33530.033*
H5C0.52730.27540.44620.033*
C60.87526 (13)−0.07473 (15)0.78187 (10)0.0208 (3)
H6A0.8765−0.00700.84490.031*
H6B0.9064−0.17860.81080.031*
H6C0.7734−0.07850.72680.031*
C71.01177 (14)0.42150 (15)0.33820 (11)0.0233 (3)
H7A0.95430.35590.27490.035*
H7B1.09400.47120.31940.035*
H7C0.94540.50040.35190.035*
N10.78212 (10)0.08954 (11)0.57463 (8)0.0164 (2)
N20.82871 (11)0.25598 (11)0.43155 (8)0.0167 (2)
N30.98058 (10)−0.01433 (12)0.72595 (8)0.0186 (2)
N41.13791 (11)−0.04093 (12)0.78658 (8)0.0186 (2)
H4A1.1891 (17)0.0522 (19)0.8151 (13)0.028*
H4B1.1821 (17)−0.0851 (19)0.7376 (14)0.028*
N51.07451 (11)0.32649 (12)0.44126 (8)0.0196 (2)
N61.23407 (11)0.29663 (13)0.47455 (9)0.0202 (2)
H611.2826 (18)0.3324 (19)0.5497 (14)0.030*
H621.2505 (17)0.187 (2)0.4720 (13)0.030*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
C10.0154 (6)0.0164 (5)0.0172 (6)0.0002 (4)0.0053 (4)−0.0020 (4)
C20.0170 (5)0.0143 (5)0.0147 (5)0.0007 (4)0.0048 (4)−0.0043 (4)
C30.0129 (5)0.0173 (5)0.0171 (5)−0.0002 (4)0.0035 (4)−0.0027 (4)
C40.0156 (5)0.0142 (5)0.0175 (5)−0.0010 (4)0.0059 (4)−0.0041 (4)
C50.0146 (6)0.0280 (7)0.0226 (6)−0.0004 (5)0.0044 (5)0.0059 (5)
C60.0194 (6)0.0255 (6)0.0187 (6)0.0002 (5)0.0078 (5)0.0020 (5)
C70.0199 (6)0.0246 (6)0.0265 (6)0.0002 (5)0.0090 (5)0.0065 (5)
N10.0142 (5)0.0180 (5)0.0171 (5)0.0004 (4)0.0052 (4)−0.0008 (4)
N20.0144 (5)0.0179 (5)0.0174 (5)−0.0002 (4)0.0047 (4)−0.0002 (4)
N30.0135 (5)0.0244 (5)0.0172 (5)0.0009 (4)0.0040 (4)0.0036 (4)
N40.0146 (5)0.0213 (5)0.0179 (5)0.0020 (4)0.0026 (4)0.0000 (4)
N50.0121 (5)0.0238 (5)0.0228 (5)−0.0001 (4)0.0056 (4)0.0035 (4)
N60.0138 (5)0.0238 (6)0.0226 (5)−0.0011 (4)0.0056 (4)−0.0020 (4)

Geometric parameters (Å, °)

C1—N11.3308 (15)C6—H6A0.9600
C1—N21.3397 (15)C6—H6B0.9600
C1—C51.5067 (17)C6—H6C0.9600
C2—N11.3619 (16)C7—N51.4480 (16)
C2—N31.3625 (15)C7—H7A0.9600
C2—C31.3965 (16)C7—H7B0.9600
C3—C41.3963 (17)C7—H7C0.9600
C3—H30.9300N3—N41.4138 (14)
C4—N21.3626 (16)N4—H4A0.930 (16)
C4—N51.3626 (16)N4—H4B0.909 (16)
C5—H5A0.9600N5—N61.4151 (15)
C5—H5B0.9600N6—H610.932 (16)
C5—H5C0.9600N6—H620.945 (17)
C6—N31.4540 (15)
N1—C1—N2127.74 (10)H6A—C6—H6C109.5
N1—C1—C5116.17 (10)H6B—C6—H6C109.5
N2—C1—C5116.09 (10)N5—C7—H7A109.5
N1—C2—N3115.80 (10)N5—C7—H7B109.5
N1—C2—C3121.89 (10)H7A—C7—H7B109.5
N3—C2—C3122.28 (10)N5—C7—H7C109.5
C4—C3—C2116.94 (10)H7A—C7—H7C109.5
C4—C3—H3121.5H7B—C7—H7C109.5
C2—C3—H3121.5C1—N1—C2115.87 (9)
N2—C4—N5115.97 (10)C1—N2—C4115.66 (10)
N2—C4—C3121.89 (10)C2—N3—N4120.69 (9)
N5—C4—C3122.15 (10)C2—N3—C6123.50 (10)
C1—C5—H5A109.5N4—N3—C6115.24 (9)
C1—C5—H5B109.5N3—N4—H4A111.5 (9)
H5A—C5—H5B109.5N3—N4—H4B109.0 (9)
C1—C5—H5C109.5H4A—N4—H4B108.5 (13)
H5A—C5—H5C109.5C4—N5—N6121.43 (10)
H5B—C5—H5C109.5C4—N5—C7121.78 (10)
N3—C6—H6A109.5N6—N5—C7115.49 (9)
N3—C6—H6B109.5N5—N6—H61110.0 (10)
H6A—C6—H6B109.5N5—N6—H62109.3 (9)
N3—C6—H6C109.5H61—N6—H62108.9 (13)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N6—H61···N4i0.932 (16)2.177 (17)3.0933 (18)167.5 (14)
N4—H4B···N2ii0.909 (16)2.504 (16)3.3319 (18)151.6 (12)
N6—H62···N1ii0.945 (17)2.418 (17)3.334 (2)163.3 (13)
N4—H4A···N2iii0.930 (16)2.268 (16)3.1722 (18)164.2 (13)

Symmetry codes: (i) −x+5/2, y+1/2, −z+3/2; (ii) −x+2, −y, −z+1; (iii) x+1/2, −y+1/2, z+1/2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BV2120).

References

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  • Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst.32, 115–119.
  • Bruker (2006). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389–397. [PubMed]
  • Gardinier, K. M., Khoury, R. G. & Lehn, J.-M. (2000). Chem. Eur. J.6, 4124–4131. [PubMed]
  • Schmitt, J.-L. & Lehn, J.-M. (2003). Helv. Chim. Acta, 86, 3417–3426.
  • Schmitt, J.-L., Stadler, A.-M., Kyritsakas, N. & Lehn, J.-M. (2003). Helv. Chim. Acta, 86, 1598–1624.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]

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