PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2010 February 1; 66(Pt 2): o294.
Published online 2010 January 9. doi:  10.1107/S1600536809055779
PMCID: PMC2979986

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

Abstract

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].

Related literature

For general background to substituted pyrimidines, see: Salas et al. (1995 [triangle]); Holy et al. (1974 [triangle]); Hunt et al. (1980 [triangle]); Baker & Santi (1965 [triangle]); Balasubramani & Fun (2009 [triangle]); For bond-length data, see: Allen et al. (1987 [triangle]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-66-0o294-scheme1.jpg

Experimental

Crystal data

  • C7H11N2O2S+·Cl
  • M r = 222.69
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-0o294-efi1.jpg
  • a = 6.6934 (2) Å
  • b = 8.4713 (2) Å
  • c = 8.8123 (2) Å
  • α = 79.774 (1)°
  • β = 87.294 (1)°
  • γ = 84.494 (1)°
  • V = 489.24 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.57 mm−1
  • T = 100 K
  • 0.32 × 0.22 × 0.14 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.836, T max = 0.922
  • 9438 measured reflections
  • 2126 independent reflections
  • 1889 reflections with I > 2σ(I)
  • R int = 0.022

Refinement

  • R[F 2 > 2σ(F 2)] = 0.027
  • wR(F 2) = 0.078
  • S = 1.03
  • 2126 reflections
  • 125 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.41 e Å−3
  • Δρmin = −0.31 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809055779/ci5011sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809055779/ci5011Isup2.hkl

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

Acknowledgments

MH and HKF thank the Malaysian Government and Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. MH thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

supplementary crystallographic information

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).

In the crystal packing (Fig. 2), atoms N2, C7 and C6 act as donors for intermolecular N—H···Cl and C—H···Cl hydrogen bonds with symmetry related chloride anions (Table 1), forming a two-dimensional network parallel to the (011). Adjacent networks are cross-linked viaπ–π interactions involving the pyrimidinium ring with centroid···centroid distance = 3.5501 (8) Å (symmetry code -x, 1-y, 1-z).

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 Uiso(H) = 1.2 or 1.5 Ueq(C). A rotating group model was applied to the methyl groups.

Figures

Fig. 1.
The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The crystal packing of the title compound, viewed along the a axis.

Crystal data

C7H11N2O2S+·ClZ = 2
Mr = 222.69F(000) = 232
Triclinic, P1Dx = 1.512 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 6.6934 (2) ÅCell parameters from 6382 reflections
b = 8.4713 (2) Åθ = 2.4–30.1°
c = 8.8123 (2) ŵ = 0.57 mm1
α = 79.774 (1)°T = 100 K
β = 87.294 (1)°Block, colourless
γ = 84.494 (1)°0.32 × 0.22 × 0.14 mm
V = 489.24 (2) Å3

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2126 independent reflections
Radiation source: fine-focus sealed tube1889 reflections with I > 2σ(I)
graphiteRint = 0.022
[var phi] and ω scansθmax = 27.0°, θmin = 2.4°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −7→8
Tmin = 0.836, Tmax = 0.922k = −9→10
9438 measured reflectionsl = −11→11

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)] = 0.027Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.078H atoms treated by a mixture of independent and constrained refinement
S = 1.02w = 1/[σ2(Fo2) + (0.0453P)2 + 0.2271P] where P = (Fo2 + 2Fc2)/3
2126 reflections(Δ/σ)max = 0.001
125 parametersΔρmax = 0.41 e Å3
0 restraintsΔρmin = −0.31 e Å3

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.
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
S1−0.25972 (5)0.07775 (4)0.60806 (4)0.01603 (11)
O10.34406 (15)0.34047 (13)0.69667 (11)0.0171 (2)
O20.07854 (16)0.42350 (13)0.19722 (11)0.0174 (2)
N10.06343 (18)0.22322 (15)0.65196 (14)0.0143 (3)
N2−0.05961 (19)0.27213 (15)0.40095 (14)0.0145 (3)
C10.2115 (2)0.31501 (18)0.59794 (17)0.0146 (3)
C20.2360 (2)0.38881 (18)0.44398 (17)0.0154 (3)
H2A0.34260.45010.40990.018*
C30.0918 (2)0.36459 (17)0.34645 (16)0.0144 (3)
C4−0.0672 (2)0.20134 (17)0.55095 (16)0.0140 (3)
C50.3256 (2)0.2515 (2)0.85378 (17)0.0187 (3)
H5A0.43420.27170.91310.028*
H5B0.33050.13840.85130.028*
H5C0.20010.28600.90020.028*
C60.2314 (2)0.52752 (19)0.12795 (18)0.0192 (3)
H6A0.20410.56560.02110.029*
H6B0.36100.46790.13650.029*
H6C0.22990.61760.18060.029*
C7−0.1949 (2)0.0026 (2)0.80670 (17)0.0189 (3)
H7A−0.2778−0.08170.84980.028*
H7B−0.21610.08860.86500.028*
H7C−0.0563−0.03910.81060.028*
Cl10.63752 (5)0.19691 (4)0.19642 (4)0.01942 (12)
H2−0.160 (4)0.258 (3)0.331 (3)0.047 (6)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
S10.0151 (2)0.0185 (2)0.01466 (19)−0.00449 (14)−0.00315 (13)−0.00105 (14)
O10.0169 (5)0.0222 (6)0.0127 (5)−0.0044 (4)−0.0054 (4)−0.0020 (4)
O20.0207 (6)0.0205 (6)0.0106 (5)−0.0057 (4)−0.0044 (4)0.0016 (4)
N10.0147 (6)0.0160 (6)0.0125 (6)−0.0012 (5)−0.0023 (5)−0.0030 (5)
N20.0153 (6)0.0164 (6)0.0123 (6)−0.0027 (5)−0.0045 (5)−0.0018 (5)
C10.0148 (7)0.0156 (7)0.0141 (7)0.0013 (6)−0.0044 (5)−0.0048 (5)
C20.0155 (7)0.0171 (7)0.0136 (7)−0.0037 (6)−0.0020 (5)−0.0016 (6)
C30.0166 (7)0.0140 (7)0.0123 (7)0.0000 (6)−0.0018 (5)−0.0019 (5)
C40.0139 (7)0.0144 (7)0.0136 (7)0.0007 (5)−0.0026 (5)−0.0029 (5)
C50.0201 (8)0.0244 (8)0.0115 (7)−0.0044 (6)−0.0058 (6)−0.0001 (6)
C60.0225 (8)0.0189 (8)0.0157 (7)−0.0048 (6)−0.0003 (6)0.0002 (6)
C70.0208 (8)0.0216 (8)0.0137 (7)−0.0049 (6)−0.0026 (6)0.0007 (6)
Cl10.0191 (2)0.0229 (2)0.01680 (19)−0.00531 (15)−0.00808 (14)−0.00133 (14)

Geometric parameters (Å, °)

S1—C41.7380 (16)C2—C31.375 (2)
S1—C71.8113 (15)C2—H2A0.93
O1—C11.3292 (17)C5—H5A0.96
O1—C51.4598 (18)C5—H5B0.96
O2—C31.3251 (17)C5—H5C0.96
O2—C61.4556 (19)C6—H6A0.96
N1—C41.3244 (18)C6—H6B0.96
N1—C11.336 (2)C6—H6C0.96
N2—C41.3519 (19)C7—H7A0.96
N2—C31.358 (2)C7—H7B0.96
N2—H20.97 (3)C7—H7C0.96
C1—C21.399 (2)
C4—S1—C799.97 (7)O1—C5—H5A109.5
C1—O1—C5116.16 (12)O1—C5—H5B109.5
C3—O2—C6116.90 (12)H5A—C5—H5B109.5
C4—N1—C1116.84 (13)O1—C5—H5C109.5
C4—N2—C3120.03 (13)H5A—C5—H5C109.5
C4—N2—H2121.1 (14)H5B—C5—H5C109.5
C3—N2—H2118.8 (14)O2—C6—H6A109.5
O1—C1—N1118.30 (13)O2—C6—H6B109.5
O1—C1—C2117.18 (13)H6A—C6—H6B109.5
N1—C1—C2124.51 (13)O2—C6—H6C109.5
C3—C2—C1115.49 (14)H6A—C6—H6C109.5
C3—C2—H2A122.3H6B—C6—H6C109.5
C1—C2—H2A122.3S1—C7—H7A109.5
O2—C3—N2112.49 (12)S1—C7—H7B109.5
O2—C3—C2127.29 (14)H7A—C7—H7B109.5
N2—C3—C2120.22 (13)S1—C7—H7C109.5
N1—C4—N2122.85 (14)H7A—C7—H7C109.5
N1—C4—S1120.43 (11)H7B—C7—H7C109.5
N2—C4—S1116.73 (11)
C5—O1—C1—N15.85 (19)C4—N2—C3—C2−1.1 (2)
C5—O1—C1—C2−175.01 (13)C1—C2—C3—O2178.56 (14)
C4—N1—C1—O1179.41 (12)C1—C2—C3—N2−1.0 (2)
C4—N1—C1—C20.3 (2)C1—N1—C4—N2−2.6 (2)
O1—C1—C2—C3−177.67 (13)C1—N1—C4—S1177.53 (10)
N1—C1—C2—C31.4 (2)C3—N2—C4—N13.0 (2)
C6—O2—C3—N2178.64 (12)C3—N2—C4—S1−177.09 (10)
C6—O2—C3—C2−0.9 (2)C7—S1—C4—N1−4.31 (13)
C4—N2—C3—O2179.30 (12)C7—S1—C4—N2175.82 (11)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H2···Cl1i0.96 (3)2.00 (3)2.9606 (13)172 (2)
C6—H6A···Cl1ii0.962.773.4896 (16)132
C6—H6B···Cl10.962.803.7002 (15)157
C7—H7A···Cl1iii0.962.763.5524 (15)141

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI5011).

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.
  • Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci.54, 1252–1257. [PubMed]
  • Balasubramani, K. & Fun, H.-K. (2009). Acta Cryst. E65, o1895. [PMC free article] [PubMed]
  • Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
  • Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst.19, 105–107.
  • Holy, A., Votruba, I. & Jost, K. (1974). Collect. Czech. Chem. Commun.39, 634–646.
  • Hunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). Biochem. J.187, 533–536. [PubMed]
  • Salas, J. M., Romero, M. A. & Faure, R. (1995). Acta Cryst. C51, 2532–2534.
  • Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. [PubMed]
  • Spek, A. L. (2009). Acta Cryst. D65, 148–155. [PMC free article] [PubMed]

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography