4,6-Dimethoxy-2-(methylsulfanyl)pyrimidinium chloride

In the title compound, C7H11N2O2S+·Cl−, the 4,6-dimethoxy-2-(methylsulfanyl)pyrimidinium cation is essentially planar (r.m.s. deviation = 0.043 Å). In the crystal, the anions and cations are connected by intermolecular N—H⋯Cl and C—H⋯Cl hydrogen bonds, forming a two-dimensional network parallel to (011). Adjacent networks are cross-linked via π–π interactions involving the pyrimidinium ring [centroid–centroid distance = 3.5501 (8) Å].


Comment
Pyrimidine and aminopyrimidine derivatives are biologically important compounds as they occur in nature as components of nucleic acids. Some aminopyrimidine derivatives are used as antifolate drugs (Hunt et al. 1980;Baker & Santi, 1965). We have recently reported the crystal structure of 4,6-dimethoxy-2(methylsulfanyl)pyrimidine (Balasubramani & Fun, 2009).
In continuation of our studies of pyrimidinium derivatives, the crystal structure determination of the title compound has been undertaken.
The asymmetric unit of the title compound ( Fig. 1) consists of a chloride anion and a 4,6-dimethoxy-2(methylsulfanyl)pyridinium cation. Protonation of the pyrimidine base on the N2 site is reflected in a change in the bond angle. The C4-N1-C1 angle at unprotonated atom N1 is 116.84(13 Å, whereas for protonated atom N2 the C4-N2-C3 angle is 120.03 (13) Å. The bond lengths and angles are normal (Allen et al. 1987).

Experimental
To a hot methanol solution (20 ml) of 4,6-dimethoxy-2-(methylsulfanyl)pyrimidine (46 mg, Aldrich) was added a few drops of hydrochloric acid. The solution was warmed over a water bath for a few minutes. The resulting solution was allowed to cool slowly to room temperature. Crystals of the title compound appeared from the mother liquor after a few days.

Refinement
Atom H2 was located in a difference Fourier map and refined freely. The remaining H atoms were positioned geometrically [C-H = 0.93 or 0.96 Å] and were refined using a riding model, with U iso (H) = 1.2 or 1.5 U eq (C). A rotating group model was applied to the methyl groups.

Special details
Experimental. The crystal was placed in the cold stream of an Oxford Cyrosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K. Refinement. Refinement of F 2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F 2 , conventional R-factors R are based on F, with F set to zero for negative F 2 . The threshold expression of F 2 > σ(F 2 ) is used only for calculating Rfactors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F 2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.