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

Hemamalini, M.; Fun, H.-K.

doi:10.1107/S1600536810034276

organic compounds

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ISSN: 2056-9890

Volume 66| Part 9| September 2010| Page o2459

https://doi.org/10.1107/S1600536810034276

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

Madhukar Hemamalini ^a and Hoong-Kun Fun ^a ^*‡

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

(Received 16 August 2010; accepted 25 August 2010; online 28 August 2010)

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 R₂²(8) rings. These dimers are stacked along the a axis.

Related literature

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

Experimental

Crystal data

C₈H₁₂N₂O
M_r = 152.20
Monoclinic, P 2₁ /n
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 ) 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[F² > 2σ(F²)] = 0.039
wR(F²) = 0.103
S = 1.06
2371 reflections
148 parameters
All H-atom parameters refined
Δρ_max = 0.32 e Å⁻³
Δρ_min = −0.20 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H1N2⋯O1ⁱ	0.937 (15)	1.844 (14)	2.7809 (11)	178.7 (10)
Symmetry code: (i) -x+2, -y, -z+2.

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

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536810034276/lh5121sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536810034276/lh5121Isup2.hkl

checkCIF report

Comment top

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.

Related literature top

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

Experimental top

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.

Structure description top

For applications of pyridinium derivatives, see: Condon et al. (1993); Maeno et al. (1990); Gilchrist (1997); Selby et al. (2002). For hydrogen-bond motifs, see: Bernstein et al. (1995). For the stability of the temperature controller used in 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

	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.

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

Crystal data top

C₈H₁₂N₂O	F(000) = 328
M_r = 152.20	D_x = 1.245 Mg m⁻³
Monoclinic, P2₁/n	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2yn	Cell parameters from 2995 reflections
a = 4.8627 (2) Å	θ = 2.9–30.0°
b = 22.6320 (8) Å	µ = 0.08 mm⁻¹
c = 7.4228 (3) Å	T = 100 K
β = 96.495 (2)°	Needle, colourless
V = 811.66 (5) Å³	0.74 × 0.14 × 0.07 mm
Z = 4

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2371 independent reflections
Radiation source: fine-focus sealed tube	1958 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.026
φ and ω scans	θ_max = 30.1°, θ_min = 1.8°
Absorption correction: multi-scan (SADABS; Bruker, 2009)	h = −5→6
T_min = 0.940, T_max = 0.994	k = −26→31
7806 measured reflections	l = −10→10

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.039	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.103	All H-atom parameters refined
S = 1.06	w = 1/[σ²(F_o²) + (0.049P)² + 0.163P] where P = (F_o² + 2F_c²)/3
2371 reflections	(Δ/σ)_max < 0.001
148 parameters	Δρ_max = 0.32 e Å⁻³
0 restraints	Δρ_min = −0.20 e Å⁻³

Crystal data top

C₈H₁₂N₂O	V = 811.66 (5) Å³
M_r = 152.20	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 4.8627 (2) Å	µ = 0.08 mm⁻¹
b = 22.6320 (8) Å	T = 100 K
c = 7.4228 (3) Å	0.74 × 0.14 × 0.07 mm
β = 96.495 (2)°

Data collection top

Bruker SMART APEXII CCD area-detector diffractometer	2371 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2009)	1958 reflections with I > 2σ(I)
T_min = 0.940, T_max = 0.994	R_int = 0.026
7806 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.039	0 restraints
wR(F²) = 0.103	All H-atom parameters refined
S = 1.06	Δρ_max = 0.32 e Å⁻³
2371 reflections	Δρ_min = −0.20 e Å⁻³
148 parameters

Special details top

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) top

	x	y	z	U_iso*/U_eq
O1	0.77782 (15)	0.03007 (3)	0.81600 (9)	0.02023 (18)
N1	0.43265 (17)	−0.13343 (3)	0.84671 (10)	0.01613 (18)
N2	0.75959 (17)	−0.06091 (3)	0.94759 (10)	0.01473 (17)
C1	0.64511 (19)	−0.11546 (4)	0.95755 (12)	0.01455 (19)
C2	0.6596 (2)	−0.01885 (4)	0.82081 (12)	0.0158 (2)
C3	0.4232 (2)	−0.03768 (4)	0.70385 (12)	0.0169 (2)
C4	0.32239 (19)	−0.09370 (4)	0.71759 (12)	0.0156 (2)
C5	0.0868 (2)	−0.11656 (5)	0.58916 (13)	0.0190 (2)
C6	0.7737 (2)	−0.15603 (4)	1.10544 (13)	0.01614 (19)
C7	0.8468 (3)	−0.21559 (5)	1.02578 (15)	0.0249 (2)
C8	0.5752 (2)	−0.16347 (5)	1.25028 (14)	0.0222 (2)
H1N2	0.915 (3)	−0.0510 (7)	1.0283 (19)	0.034 (4)*
H3A	0.338 (3)	−0.0101 (6)	0.6146 (18)	0.025 (3)*
H5A	−0.064 (3)	−0.1299 (6)	0.655 (2)	0.036 (4)*
H5B	0.011 (3)	−0.0864 (7)	0.503 (2)	0.044 (4)*
H5C	0.151 (3)	−0.1505 (6)	0.5237 (19)	0.034 (4)*
H6A	0.946 (3)	−0.1369 (5)	1.1613 (16)	0.018 (3)*
H7A	0.922 (3)	−0.2424 (6)	1.124 (2)	0.031 (3)*
H7B	0.984 (3)	−0.2117 (6)	0.9349 (19)	0.031 (4)*
H7C	0.681 (3)	−0.2348 (6)	0.9648 (19)	0.036 (4)*
H8A	0.661 (3)	−0.1874 (6)	1.3518 (19)	0.029 (3)*
H8B	0.408 (3)	−0.1849 (6)	1.1978 (18)	0.031 (4)*
H8C	0.519 (3)	−0.1249 (6)	1.2967 (19)	0.032 (4)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0210 (4)	0.0159 (3)	0.0229 (4)	−0.0031 (3)	−0.0012 (3)	0.0032 (3)
N1	0.0159 (4)	0.0163 (4)	0.0157 (4)	−0.0010 (3)	0.0002 (3)	−0.0005 (3)
N2	0.0146 (4)	0.0143 (4)	0.0150 (4)	−0.0008 (3)	0.0005 (3)	0.0004 (3)
C1	0.0146 (4)	0.0146 (4)	0.0146 (4)	0.0003 (3)	0.0026 (3)	−0.0007 (3)
C2	0.0159 (4)	0.0161 (4)	0.0156 (4)	0.0005 (3)	0.0028 (3)	0.0007 (3)
C3	0.0165 (5)	0.0185 (4)	0.0153 (4)	0.0014 (3)	0.0006 (3)	0.0019 (3)
C4	0.0143 (4)	0.0185 (5)	0.0142 (4)	0.0005 (3)	0.0019 (3)	−0.0018 (3)
C5	0.0164 (5)	0.0227 (5)	0.0172 (4)	−0.0011 (4)	−0.0013 (3)	−0.0022 (4)
C6	0.0157 (4)	0.0151 (4)	0.0168 (4)	−0.0011 (3)	−0.0015 (3)	0.0009 (3)
C7	0.0301 (6)	0.0172 (5)	0.0260 (5)	0.0036 (4)	−0.0026 (4)	−0.0004 (4)
C8	0.0202 (5)	0.0268 (5)	0.0193 (5)	−0.0016 (4)	0.0012 (4)	0.0061 (4)

Geometric parameters (Å, º) top

O1—C2	1.2497 (11)	C5—H5B	0.978 (16)
N1—C1	1.3105 (12)	C5—H5C	0.978 (15)
N1—C4	1.3777 (12)	C6—C7	1.5297 (14)
N2—C1	1.3595 (12)	C6—C8	1.5332 (14)
N2—C2	1.3874 (12)	C6—H6A	0.990 (12)
N2—H1N2	0.937 (15)	C7—H7A	0.985 (14)
C1—C6	1.5114 (13)	C7—H7B	1.004 (14)
C2—C3	1.4254 (13)	C7—H7C	0.980 (15)
C3—C4	1.3672 (13)	C8—H8A	0.982 (14)
C3—H3A	0.968 (13)	C8—H8B	0.987 (14)
C4—C5	1.4972 (13)	C8—H8C	0.988 (15)
C5—H5A	0.973 (16)

C1—N1—C4	116.83 (8)	H5A—C5—H5C	107.8 (12)
C1—N2—C2	123.08 (8)	H5B—C5—H5C	109.9 (12)
C1—N2—H1N2	119.2 (9)	C1—C6—C7	110.47 (8)
C2—N2—H1N2	117.7 (9)	C1—C6—C8	109.54 (8)
N1—C1—N2	123.11 (9)	C7—C6—C8	111.50 (8)
N1—C1—C6	119.97 (8)	C1—C6—H6A	107.5 (7)
N2—C1—C6	116.92 (8)	C7—C6—H6A	108.9 (7)
O1—C2—N2	120.02 (9)	C8—C6—H6A	108.9 (7)
O1—C2—C3	126.12 (9)	C6—C7—H7A	109.9 (8)
N2—C2—C3	113.86 (8)	C6—C7—H7B	112.5 (8)
C4—C3—C2	120.21 (9)	H7A—C7—H7B	109.4 (11)
C4—C3—H3A	121.2 (8)	C6—C7—H7C	110.8 (9)
C2—C3—H3A	118.6 (8)	H7A—C7—H7C	106.5 (12)
C3—C4—N1	122.85 (9)	H7B—C7—H7C	107.6 (11)
C3—C4—C5	121.86 (9)	C6—C8—H8A	110.7 (8)
N1—C4—C5	115.27 (8)	C6—C8—H8B	109.4 (8)
C4—C5—H5A	110.6 (9)	H8A—C8—H8B	106.8 (12)
C4—C5—H5B	112.3 (9)	C6—C8—H8C	111.6 (8)
H5A—C5—H5B	107.2 (12)	H8A—C8—H8C	109.3 (11)
C4—C5—H5C	108.9 (8)	H8B—C8—H8C	109.0 (11)

C4—N1—C1—N2	−1.11 (13)	C2—C3—C4—N1	2.79 (14)
C4—N1—C1—C6	178.69 (8)	C2—C3—C4—C5	−175.72 (8)
C2—N2—C1—N1	0.98 (14)	C1—N1—C4—C3	−0.79 (13)
C2—N2—C1—C6	−178.83 (8)	C1—N1—C4—C5	177.82 (8)
C1—N2—C2—O1	−178.41 (8)	N1—C1—C6—C7	52.88 (12)
C1—N2—C2—C3	0.98 (12)	N2—C1—C6—C7	−127.31 (9)
O1—C2—C3—C4	176.61 (9)	N1—C1—C6—C8	−70.32 (11)
N2—C2—C3—C4	−2.73 (13)	N2—C1—C6—C8	109.50 (9)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H1N2···O1ⁱ	0.937 (15)	1.844 (14)	2.7809 (11)	178.7 (10)

Symmetry code: (i) −x+2, −y, −z+2.

Experimental details

Crystal data
Chemical formula	C₈H₁₂N₂O
M_r	152.20
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	100
a, b, c (Å)	4.8627 (2), 22.6320 (8), 7.4228 (3)
β (°)	96.495 (2)
V (Å³)	811.66 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.74 × 0.14 × 0.07

Data collection
Diffractometer	Bruker SMART APEXII CCD area-detector
Absorption correction	Multi-scan (SADABS; Bruker, 2009)
T_min, T_max	0.940, 0.994
No. of measured, independent and observed [I > 2σ(I)] reflections	7806, 2371, 1958
R_int	0.026
(sin θ/λ)_max (Å⁻¹)	0.705

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.039, 0.103, 1.06
No. of reflections	2371
No. of parameters	148
H-atom treatment	All H-atom parameters refined
Δρ_max, Δρ_min (e Å⁻³)	0.32, −0.20

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H1N2···O1ⁱ	0.937 (15)	1.844 (14)	2.7809 (11)	178.7 (10)

Symmetry code: (i) −x+2, −y, −z+2.

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 also thanks Universiti Sains Malaysia for a post-doctoral research fellowship.

References

Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573. CrossRef CAS Web of Science Google Scholar
Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Condon, M. E., Brady, T. E., Feist, D., Malefyt, T., Marc, P., Quakenbush, L. S., Rodaway, S. J., Shaner, D. L. & Tecle, B. (1993). Brighton Crop Protection Conference on Weeds, pp. 41–46. Alton, Hampshire, England: BCPC Publications. Google Scholar
Cosier, J. & Glazer, A. M. (1986). J. Appl. Cryst. 19, 105–107. CrossRef CAS Web of Science IUCr Journals Google Scholar
Gilchrist, T. L. (1997). Heterocyclic Chemistry, 3rd ed., pp. 261–276. Singapore: Addison Wesley Longman. Google Scholar
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. Google Scholar
Selby, T. P., Drumm, J. E., Coats, R. A., Coppo, F. T., Gee, S. K., Hay, J. V., Pasteris, R. J. & Stevenson, T. M. (2002). ACS Symposium Series, Vol. 800, Synthesis and Chemistry of Agrochemicals VI, pp. 74–84. Washington DC: American Chemical Society. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar