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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2459.
Published online 2010 August 28. doi:  10.1107/S1600536810034276
PMCID: PMC3008064

2-Isopropyl-6-methyl­pyrimidin-4(3H)-one

Abstract

The mol­ecular structure of the title compound, C8H12N2O, indicates that 2-isopropyl-6-methyl­pyrimidin-4-ol (the enol–form) undergoes an enol-to-keto tautomerism during the crystallization process. The pyrimidin-4(3H)-one group is essentially planar, with a maximum deviation of 0.081 (1) Å for the O atom. In the crystal structure, symmetry-related mol­ecules are linked into centrosymmetic dimers via pairs of inter­molecular N—H(...)O hydrogen bonds, generating R 2 2(8) rings. These dimers are stacked along the a axis.

Related literature

For applications of pyridinium derivatives, see: Condon et al. (1993 [triangle]); Maeno et al. (1990 [triangle]); Gilchrist (1997 [triangle]); Selby et al. (2002 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

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Object name is e-66-o2459-scheme1.jpg

Experimental

Crystal data

  • C8H12N2O
  • M r = 152.20
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2459-efi1.jpg
  • a = 4.8627 (2) Å
  • b = 22.6320 (8) Å
  • c = 7.4228 (3) Å
  • β = 96.495 (2)°
  • V = 811.66 (5) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 100 K
  • 0.74 × 0.14 × 0.07 mm

Data collection

  • Bruker SMART APEXII CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.940, T max = 0.994
  • 7806 measured reflections
  • 2371 independent reflections
  • 1958 reflections with I > 2σ(I)
  • R int = 0.026

Refinement

  • R[F 2 > 2σ(F 2)] = 0.039
  • wR(F 2) = 0.103
  • S = 1.06
  • 2371 reflections
  • 148 parameters
  • All H-atom parameters refined
  • Δρmax = 0.32 e Å−3
  • Δρmin = −0.20 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/S1600536810034276/lh5121sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810034276/lh5121Isup2.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 also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

supplementary crystallographic information

Comment

Pyrimidine derivatives are very important molecules in biology and have many application in the areas of pesticide and pharmaceutical agents (Condon et al., 1993). For example, imazosulfuron, ethirmol and mepanipyrim have been commercialized as agrochemicals (Maeno et al., 1990). Pyrimidine derivatives have also been developed as antiviral agents, such as AZT, which is the most widely used anti-AIDS drug (Gilchrist, 1997). Recently, a new series of highly active herbicides of substituted azolylpyrimidines were reported (Selby et al., 2002). Keeping in view of the importance of the pyrimidine derivatives, the title compound (I) was presented.

The title molecule, (Fig. 1), exists in the keto-form although 2-isopropyl-4-hydroxy-6-methylpyrimidine (the enol-form) was used for crystallization. This indicates the compound undergoes an enol-to-keto tautomerism during the crystallization process (Fig. 3). The C2═O1 bond length is 1.2497 (11) Å. The pyrimidin-4(3H)-one group is essentially planar with a maximum deviation of 0.081 (1) Å for atom O1. In the crystal structure (Fig. 2), adjacent molecules are linked via pairs of intermolecular N—H···O hydrogen bonds to form dimers, generating R22(8) rings (Bernstein et al., 1995). These dimers are stacked along the a-axis.

Experimental

Hot methanol solution (20 ml) of 2-isopropyl-4-hydroxy-6-methylpyrimidine (46 mg, Aldrich) was warmed over a heating magnetic stirrer for 5 minutes. The resulting solution was allowed to cool slowly at room temperature. Crystals of the title compound appeared from the mother liquor after a few days.

Refinement

All H atoms were located in a difference Fourier map and refined freely.

Figures

Fig. 1.
The molecular structure of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
Fig. 2.
The crystal packing of the title compound, viewed approximately along the a-axis. Hydrogen bonds are shown as dashed lines.
Fig. 3.
The title compound and the tautomeric form.

Crystal data

C8H12N2OF(000) = 328
Mr = 152.20Dx = 1.245 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 2995 reflections
a = 4.8627 (2) Åθ = 2.9–30.0°
b = 22.6320 (8) ŵ = 0.08 mm1
c = 7.4228 (3) ÅT = 100 K
β = 96.495 (2)°Needle, colourless
V = 811.66 (5) Å30.74 × 0.14 × 0.07 mm
Z = 4

Data collection

Bruker SMART APEXII CCD area-detector diffractometer2371 independent reflections
Radiation source: fine-focus sealed tube1958 reflections with I > 2σ(I)
graphiteRint = 0.026
[var phi] and ω scansθmax = 30.1°, θmin = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −5→6
Tmin = 0.940, Tmax = 0.994k = −26→31
7806 measured reflectionsl = −10→10

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)] = 0.039Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.103All H-atom parameters refined
S = 1.06w = 1/[σ2(Fo2) + (0.049P)2 + 0.163P] where P = (Fo2 + 2Fc2)/3
2371 reflections(Δ/σ)max < 0.001
148 parametersΔρmax = 0.32 e Å3
0 restraintsΔρmin = −0.20 e Å3

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All s.u.'s (except the s.u. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell s.u.'s are taken into account individually in the estimation of s.u.'s in distances, angles and torsion angles; correlations between s.u.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell s.u.'s is used for estimating s.u.'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 > 2σ(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
O10.77782 (15)0.03007 (3)0.81600 (9)0.02023 (18)
N10.43265 (17)−0.13343 (3)0.84671 (10)0.01613 (18)
N20.75959 (17)−0.06091 (3)0.94759 (10)0.01473 (17)
C10.64511 (19)−0.11546 (4)0.95755 (12)0.01455 (19)
C20.6596 (2)−0.01885 (4)0.82081 (12)0.0158 (2)
C30.4232 (2)−0.03768 (4)0.70385 (12)0.0169 (2)
C40.32239 (19)−0.09370 (4)0.71759 (12)0.0156 (2)
C50.0868 (2)−0.11656 (5)0.58916 (13)0.0190 (2)
C60.7737 (2)−0.15603 (4)1.10544 (13)0.01614 (19)
C70.8468 (3)−0.21559 (5)1.02578 (15)0.0249 (2)
C80.5752 (2)−0.16347 (5)1.25028 (14)0.0222 (2)
H1N20.915 (3)−0.0510 (7)1.0283 (19)0.034 (4)*
H3A0.338 (3)−0.0101 (6)0.6146 (18)0.025 (3)*
H5A−0.064 (3)−0.1299 (6)0.655 (2)0.036 (4)*
H5B0.011 (3)−0.0864 (7)0.503 (2)0.044 (4)*
H5C0.151 (3)−0.1505 (6)0.5237 (19)0.034 (4)*
H6A0.946 (3)−0.1369 (5)1.1613 (16)0.018 (3)*
H7A0.922 (3)−0.2424 (6)1.124 (2)0.031 (3)*
H7B0.984 (3)−0.2117 (6)0.9349 (19)0.031 (4)*
H7C0.681 (3)−0.2348 (6)0.9648 (19)0.036 (4)*
H8A0.661 (3)−0.1874 (6)1.3518 (19)0.029 (3)*
H8B0.408 (3)−0.1849 (6)1.1978 (18)0.031 (4)*
H8C0.519 (3)−0.1249 (6)1.2967 (19)0.032 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0210 (4)0.0159 (3)0.0229 (4)−0.0031 (3)−0.0012 (3)0.0032 (3)
N10.0159 (4)0.0163 (4)0.0157 (4)−0.0010 (3)0.0002 (3)−0.0005 (3)
N20.0146 (4)0.0143 (4)0.0150 (4)−0.0008 (3)0.0005 (3)0.0004 (3)
C10.0146 (4)0.0146 (4)0.0146 (4)0.0003 (3)0.0026 (3)−0.0007 (3)
C20.0159 (4)0.0161 (4)0.0156 (4)0.0005 (3)0.0028 (3)0.0007 (3)
C30.0165 (5)0.0185 (4)0.0153 (4)0.0014 (3)0.0006 (3)0.0019 (3)
C40.0143 (4)0.0185 (5)0.0142 (4)0.0005 (3)0.0019 (3)−0.0018 (3)
C50.0164 (5)0.0227 (5)0.0172 (4)−0.0011 (4)−0.0013 (3)−0.0022 (4)
C60.0157 (4)0.0151 (4)0.0168 (4)−0.0011 (3)−0.0015 (3)0.0009 (3)
C70.0301 (6)0.0172 (5)0.0260 (5)0.0036 (4)−0.0026 (4)−0.0004 (4)
C80.0202 (5)0.0268 (5)0.0193 (5)−0.0016 (4)0.0012 (4)0.0061 (4)

Geometric parameters (Å, °)

O1—C21.2497 (11)C5—H5B0.978 (16)
N1—C11.3105 (12)C5—H5C0.978 (15)
N1—C41.3777 (12)C6—C71.5297 (14)
N2—C11.3595 (12)C6—C81.5332 (14)
N2—C21.3874 (12)C6—H6A0.990 (12)
N2—H1N20.937 (15)C7—H7A0.985 (14)
C1—C61.5114 (13)C7—H7B1.004 (14)
C2—C31.4254 (13)C7—H7C0.980 (15)
C3—C41.3672 (13)C8—H8A0.982 (14)
C3—H3A0.968 (13)C8—H8B0.987 (14)
C4—C51.4972 (13)C8—H8C0.988 (15)
C5—H5A0.973 (16)
C1—N1—C4116.83 (8)H5A—C5—H5C107.8 (12)
C1—N2—C2123.08 (8)H5B—C5—H5C109.9 (12)
C1—N2—H1N2119.2 (9)C1—C6—C7110.47 (8)
C2—N2—H1N2117.7 (9)C1—C6—C8109.54 (8)
N1—C1—N2123.11 (9)C7—C6—C8111.50 (8)
N1—C1—C6119.97 (8)C1—C6—H6A107.5 (7)
N2—C1—C6116.92 (8)C7—C6—H6A108.9 (7)
O1—C2—N2120.02 (9)C8—C6—H6A108.9 (7)
O1—C2—C3126.12 (9)C6—C7—H7A109.9 (8)
N2—C2—C3113.86 (8)C6—C7—H7B112.5 (8)
C4—C3—C2120.21 (9)H7A—C7—H7B109.4 (11)
C4—C3—H3A121.2 (8)C6—C7—H7C110.8 (9)
C2—C3—H3A118.6 (8)H7A—C7—H7C106.5 (12)
C3—C4—N1122.85 (9)H7B—C7—H7C107.6 (11)
C3—C4—C5121.86 (9)C6—C8—H8A110.7 (8)
N1—C4—C5115.27 (8)C6—C8—H8B109.4 (8)
C4—C5—H5A110.6 (9)H8A—C8—H8B106.8 (12)
C4—C5—H5B112.3 (9)C6—C8—H8C111.6 (8)
H5A—C5—H5B107.2 (12)H8A—C8—H8C109.3 (11)
C4—C5—H5C108.9 (8)H8B—C8—H8C109.0 (11)
C4—N1—C1—N2−1.11 (13)C2—C3—C4—N12.79 (14)
C4—N1—C1—C6178.69 (8)C2—C3—C4—C5−175.72 (8)
C2—N2—C1—N10.98 (14)C1—N1—C4—C3−0.79 (13)
C2—N2—C1—C6−178.83 (8)C1—N1—C4—C5177.82 (8)
C1—N2—C2—O1−178.41 (8)N1—C1—C6—C752.88 (12)
C1—N2—C2—C30.98 (12)N2—C1—C6—C7−127.31 (9)
O1—C2—C3—C4176.61 (9)N1—C1—C6—C8−70.32 (11)
N2—C2—C3—C4−2.73 (13)N2—C1—C6—C8109.50 (9)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N2—H1N2···O1i0.937 (15)1.844 (14)2.7809 (11)178.7 (10)

Symmetry codes: (i) −x+2, −y, −z+2.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: LH5121).

References

  • Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl.34, 1555–1573.
  • Bruker (2009). APEX2, SAINT and SADABS Bruker AXS Inc., Madison, Wisconsin, USA.
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  • Gilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261–276. Singapore: Addison Wesley Longman.
  • Maeno, S., Miura, I., Masuda, K. & Nagata, T. (1990). Brighton Crop Protection Conference on Pests and Diseases, pp. 415–422. Alton, Hampshire, England: BCPC Publications.
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