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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 66| Part 2| February 2010| Page o294
https://doi.org/10.1107/S1600536809055779

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

Madhukar Hemamalinia and Hoong-Kun Funa*‡

aX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
*Correspondence e-mail: hkfun@usm.my

(Received 30 December 2009; accepted 30 December 2009; online 9 January 2010)

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[Salas, J. M., Romero, M. A. & Faure, R. (1995). Acta Cryst. C51, 2532-2534.]); Holy et al. (1974[Holy, A., Votruba, I. & Jost, K. (1974). Collect. Czech. Chem. Commun. 39, 634-646.]); Hunt et al. (1980[Hunt, W. E., Schwalbe, C. H., Bird, K. & Mallinson, P. D. (1980). Biochem. J. 187, 533-536.]); Baker & Santi (1965[Baker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252-1257.]); Balasubramani & Fun (2009[Balasubramani, K. & Fun, H.-K. (2009). Acta Cryst. E65, o1895.]); For bond-length 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.]). For the stability of the temperature controller used for the data collection, see: Cosier & Glazer (1986[Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105-107.]).

[Scheme 1]

Experimental

Crystal data

  • C7H11N2O2S+·Cl−

  • Mr = 222.69

  • Triclinic, [P \overline 1]

  • 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[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.836, Tmax = 0.922

  • 9438 measured reflections

  • 2126 independent reflections

  • 1889 reflections with I > 2σ(I)

  • Rint = 0.022
Refinement

  • R[F2 > 2σ(F2)] = 0.027

  • wR(F2) = 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

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
N2—H2⋯Cl1i 0.96 (3) 2.00 (3) 2.9606 (13) 172 (2)
C6—H6A⋯Cl1ii 0.96 2.77 3.4896 (16) 132
C6—H6B⋯Cl1 0.96 2.80 3.7002 (15) 157
C7—H7A⋯Cl1iii 0.96 2.76 3.5524 (15) 141
Symmetry codes: (i) x-1, y, z; (ii) -x+1, -y+1, -z; (iii) -x, -y, -z+1.

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

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

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536809055779/ci5011Isup2.hkl

checkCIF report


Comment top

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 via π–π interactions involving the pyrimidinium ring with centroid···centroid distance = 3.5501 (8) Å (symmetry code -x, 1-y, 1-z).

Related literature top

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

Experimental top

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 top

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.

Structure description top

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 via π–π interactions involving the pyrimidinium ring with centroid···centroid distance = 3.5501 (8) Å (symmetry code -x, 1-y, 1-z).

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

Computing details top

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

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme.
[Figure 2] Fig. 2. The crystal packing of the title compound, viewed along the a axis.
4,6-Dimethoxy-2-(methylsulfanyl)pyrimidinium chloride top
Crystal data top
C7H11N2O2S+·Cl−Z = 2
Mr = 222.69F(000) = 232
Triclinic, P1Dx = 1.512 Mg m−3
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 mm−1
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 top
Bruker SMART APEXII CCD area-detector
diffractometer		2126 independent reflections
Radiation source: fine-focus sealed tube1889 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.022
φ 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 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)] = 0.027Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.078H atoms treated by a mixture of independent and constrained refinement
S = 1.03 w = 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 Å−3
0 restraintsΔρmin = −0.31 e Å−3
Crystal data top
C7H11N2O2S+·Cl−γ = 84.494 (1)°
Mr = 222.69V = 489.24 (2) Å3
Triclinic, P1Z = 2
a = 6.6934 (2) ÅMo Kα radiation
b = 8.4713 (2) ŵ = 0.57 mm−1
c = 8.8123 (2) ÅT = 100 K
α = 79.774 (1)°0.32 × 0.22 × 0.14 mm
β = 87.294 (1)°
Data collection top
Bruker SMART APEXII CCD area-detector
diffractometer		2126 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2009)		1889 reflections with I > 2σ(I)
Tmin = 0.836, Tmax = 0.922Rint = 0.022
9438 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0270 restraints
wR(F2) = 0.078H atoms treated by a mixture of independent and constrained refinement
S = 1.03Δρmax = 0.41 e Å−3
2126 reflectionsΔρmin = −0.31 e Å−3
125 parameters
Special details top

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) top
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) top
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, º) top
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, º) top
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.

Experimental details

Crystal data
Chemical formulaC7H11N2O2S+·Cl−
Mr222.69
Crystal system, space groupTriclinic, P1
Temperature (K)100
a, b, c (Å)6.6934 (2), 8.4713 (2), 8.8123 (2)
α, β, γ (°)79.774 (1), 87.294 (1), 84.494 (1)
V (Å3)489.24 (2)
Z2
Radiation typeMo Kα
µ (mm−1)0.57
Crystal size (mm)0.32 × 0.22 × 0.14
Data collection
DiffractometerBruker SMART APEXII CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Bruker, 2009)
Tmin, Tmax0.836, 0.922
No. of measured, independent and
observed [I > 2σ(I)] reflections		9438, 2126, 1889
Rint0.022
(sin θ/λ)max (Å−1)0.639
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.027, 0.078, 1.03
No. of reflections2126
No. of parameters125
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)0.41, −0.31

Computer programs: APEX2 (Bruker, 2009), SAINT (Bruker, 2009), SHELXTL (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
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

‡Thomson Reuters ResearcherID: A-3561-2009.

Acknowledgements

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.

References

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 First citationBaker, B. R. & Santi, D. V. (1965). J. Pharm. Sci. 54, 1252–1257.  CrossRef CAS PubMed Web of Science Google Scholar
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 First citationSalas, J. M., Romero, M. A. & Faure, R. (1995). Acta Cryst. C51, 2532–2534.  CSD CrossRef CAS Web of Science IUCr Journals Google Scholar
 First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
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Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 66| Part 2| February 2010| Page o294
https://doi.org/10.1107/S1600536809055779
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