1-Methyl-1,3-diazinan-2-one

In the crystal structure of the title compound, C₅H₁₀N₂O, mol­ecules are connected via pairs of strong N—H⋯O hydrogen bonds into centrosymmetric dimers, which are stacked along the a axis. The molecule is not planar, the dihedral angle between the N/C/N and C/C/C planes being 42.1(1)°.

Related literature

For substitution of hexa­methyl­phospho­ramide (HMPT) by the cyclic urea 1,3-dimethyl-3,4,5,6-tetra­hydro­pyrimidin-2-one (DMPU), see: Mukhopadhyay & Seebach (1982). For the crystal structure of 3,4,5,6-tetra­hydro­pyrimidin-2-one, see: Rizal et al. (2008) and of 1-methyl-imidazolidin-2-one, see: Caudle et al. (2005).

Experimental

Crystal data

• C₅H₁₀N₂O

• M_r = 114.15

• Orthorhombic, P b c a

• a = 5.8479 (2) Å

• b = 13.3438 (6) Å

• c = 15.0883 (8) Å

• V = 1177.39 (9) ų

• Z = 8

• Mo Kα radiation

• μ = 0.09 mm⁻¹

• T = 100 K

• 0.19 × 0.15 × 0.11 mm

Data collection

• Bruker–Nonius KappaCCD diffractometer

• 2628 measured reflections

• 1434 independent reflections

• 1190 reflections with I > 2σ(I)

• R_int = 0.024

Refinement

• R[F² > 2σ(F²)] = 0.037

• wR(F²) = 0.092

• S = 1.03

• 1434 reflections

• 79 parameters

• H atoms treated by a mixture of independent and constrained refinement

• Δρ_max = 0.27 e Å⁻³

• Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1^i	0.88 (2)	2.00 (2)	2.875 (1)	177 (2)
Symmetry code: (i) -x, -y+1, -z.

Data collection: COLLECT (Hooft, 2004); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: SCALEPACK; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97.

Supporting information

S1. Comment

1,3-Dimethyl-3,4,5,6-tetrahydropyrimidin-2-one (DMPU), a liquid at room temperature, is often used in organic synthesis as a polar aprotic solvent, replacing the carcinogenic hexamethylphosphoramide (HMPT) (Mukhopadhyay & Seebach, 1982). In contast, 3,4,5,6-tetrahydropyrimidin-2-one is a solid with a melting point of 263–267 °C and its ordered crystal structure was quite recently determined (Rizal et al., 2008). The crystal structure of the missing link 1-methyl-3,4,5,6-tetrahydropyrimidin-2-one (I) was previously unknown. Prominent bond parameters for the title molecule are: C1–O1 = 1.248 (1) Å, N1–C1 = 1.357 (1) Å and N2–C1 = 1.362 (1) Å. The bond length between N2 and the terminal C-methyl group (C5) measures 1.453 (1) Å. The C–N2–C angles are: 123.54 (9)° (C4–N2–C1), 120.32 (8)° (C1–N2–C5) and 115.18 (9)° (C5–N2–C4), which indicates a trigonal-planar surrounding of the nitrogen centre by the C atoms. These data are in good agreement with those of the five membered heterocycle 1-methyl-imidazolidin-2-one (Caudle et al., 2005). In contrast to the aforementioned compound, the six membered heterocycle in (I) is non–planar (Fig. 1). The carbon atom C3 is not in the ring plane, the angle between the planes N1/C1/N2 and C2/C3/C4 is 42.1 (1)°. In the packing, each two molecules are linked by strong N–H···O hydrogen bonds, forming centrosymmetric dimers, which are stacked along the a axis (Fig.2). The H···O distance is 2.00 (2) Å, with a nearly linear N–H···O angle of 177 (2)° (Tab.1).

Related literature

For substitution of hexamethylphosphoramide (HMPT) by the cyclic urea 1,3-dimethyl-3,4,5,6-tetrahydropyrimidin-2-one (DMPU), see: Mukhopadhyay & Seebach (1982). For the crystal structure of 3,4,5,6-tetrahydropyrimidin-2-one, see: Rizal et al. (2008) and of 1-methyl-imidazolidin-2-one, see: Caudle et al. (2005).

S2. Experimental

The title compound was obtained as a byproduct by reaction of 1-Methyl-2-dimethylamino-1,4,5,6-tetrahydropyrimidinium-chloride with excess aqueous sodium hydroxide at room temperature. After distillation of the crude product in vacuo, a colourless liquid was obtained. The compound crystallized spontaneously upon standing at room temperature after several days, forming colourless single crystals.

S3. Refinement

The N-bound H atom was located in a difference Fourier map and was refined freely. The hydrogen atoms of the methyl group were allowed to rotate with a fixed angle around the C–N bond to best fit the experimental electron density, with U(H) set to 1.5 U_eq(C) and d(C—H) = 0.98 Å. The remaining H atoms were placed in calculated positions with d(C—H) = 0.99 Å and were included in the refinement in the riding model approximation, with U(H) set to 1.2 U_eq(C).

Computing details

Data collection: COLLECT (Hooft, 2004); cell refinement: SCALEPACK (Otwinowski & Minor, 1997); data reduction: SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg & Putz, 2005); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures

	Fig. 1. The molecular structure of the title molecule. Anisotropic displacement ellipsoids are shown at the 50% probability level.
	Fig. 2. Packing diagram of the title compound, bc-view. The N–H···O hydrogen bonds are indicated by dashed lines.

1-Methyl-1,3-diazinan-2-one

Crystal data

C5H10N2O	F(000) = 496
Mr = 114.15	Dx = 1.288 Mg m^−3
Orthorhombic, Pbca	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2ab	Cell parameters from 1677 reflections
a = 5.8479 (2) Å	θ = 0.4–28.3°
b = 13.3438 (6) Å	µ = 0.09 mm^−1
c = 15.0883 (8) Å	T = 100 K
V = 1177.39 (9) Å^3	Lath-shaped, colourless
Z = 8	0.19 × 0.15 × 0.11 mm

Data collection

Bruker–Nonius KappaCCD diffractometer	1190 reflections with I > 2σ(I)
Radiation source: sealed tube	Rint = 0.024
Graphite monochromator	θmax = 28.2°, θmin = 2.7°
ϕ scans, and ω scans	h = −7→7
2628 measured reflections	k = −17→17
1434 independent reflections	l = −19→19

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.037	H atoms treated by a mixture of independent and constrained refinement
wR(F^2) = 0.092	w = 1/[σ^2(Fo^2) + (0.0424P)^2 + 0.4078P] where P = (Fo^2 + 2Fc^2)/3
S = 1.03	(Δ/σ)max < 0.001
1434 reflections	Δρmax = 0.27 e Å^−3
79 parameters	Δρmin = −0.18 e Å^−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.023 (3)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
O1	0.13599 (13)	0.58154 (5)	0.07922 (5)	0.0178 (2)
N1	0.21849 (16)	0.41809 (6)	0.05287 (6)	0.0162 (2)
H1	0.108 (3)	0.4198 (11)	0.0134 (10)	0.032 (4)*
N2	0.44922 (16)	0.51361 (6)	0.14565 (6)	0.0147 (2)
C1	0.26381 (18)	0.50789 (7)	0.09125 (6)	0.0127 (2)
C2	0.3761 (2)	0.33384 (7)	0.05379 (7)	0.0170 (2)
H2A	0.4901	0.3415	0.0058	0.020*
H2B	0.2913	0.2706	0.0439	0.020*
C3	0.4956 (2)	0.33051 (8)	0.14262 (7)	0.0203 (3)
H3A	0.6120	0.2766	0.1427	0.024*
H3B	0.3834	0.3162	0.1901	0.024*
C4	0.6091 (2)	0.43089 (8)	0.15938 (8)	0.0209 (3)
H4A	0.6673	0.4330	0.2210	0.025*
H4B	0.7411	0.4387	0.1189	0.025*
C5	0.5230 (2)	0.60977 (8)	0.18066 (7)	0.0182 (3)
H5A	0.4106	0.6613	0.1650	0.027*
H5B	0.6719	0.6274	0.1553	0.027*
H5C	0.5362	0.6055	0.2453	0.027*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0179 (4)	0.0130 (4)	0.0226 (4)	0.0039 (3)	−0.0052 (3)	−0.0015 (3)
N1	0.0153 (5)	0.0118 (4)	0.0213 (5)	0.0022 (4)	−0.0052 (4)	−0.0026 (3)
N2	0.0148 (5)	0.0120 (4)	0.0173 (4)	0.0003 (4)	−0.0034 (3)	0.0002 (3)
C1	0.0131 (5)	0.0122 (4)	0.0128 (4)	−0.0013 (4)	0.0008 (4)	0.0015 (4)
C2	0.0195 (5)	0.0118 (5)	0.0196 (5)	0.0036 (4)	−0.0003 (4)	−0.0011 (4)
C3	0.0260 (6)	0.0142 (5)	0.0206 (5)	0.0071 (5)	−0.0023 (5)	0.0023 (4)
C4	0.0193 (6)	0.0195 (5)	0.0241 (6)	0.0063 (5)	−0.0066 (5)	−0.0012 (4)
C5	0.0196 (5)	0.0160 (5)	0.0190 (5)	−0.0038 (4)	−0.0034 (4)	−0.0010 (4)

Geometric parameters (Å, º)

O1—C1	1.2480 (13)	C2—H2B	0.9900
N1—C1	1.3570 (13)	C3—C4	1.5162 (16)
N1—C2	1.4537 (13)	C3—H3A	0.9900
N1—H1	0.881 (18)	C3—H3B	0.9900
N2—C1	1.3620 (14)	C4—H4A	0.9900
N2—C5	1.4532 (13)	C4—H4B	0.9900
N2—C4	1.4614 (14)	C5—H5A	0.9800
C2—C3	1.5123 (15)	C5—H5B	0.9800
C2—H2A	0.9900	C5—H5C	0.9800
C1—N1—C2	123.71 (9)	C4—C3—H3A	109.9
C1—N1—H1	114.2 (9)	C2—C3—H3B	109.9
C2—N1—H1	119.6 (10)	C4—C3—H3B	109.9
C1—N2—C5	120.32 (8)	H3A—C3—H3B	108.3
C1—N2—C4	123.54 (9)	N2—C4—C3	111.31 (9)
C5—N2—C4	115.18 (9)	N2—C4—H4A	109.4
O1—C1—N1	121.08 (10)	C3—C4—H4A	109.4
O1—C1—N2	121.36 (9)	N2—C4—H4B	109.4
N1—C1—N2	117.52 (9)	C3—C4—H4B	109.4
N1—C2—C3	108.92 (8)	H4A—C4—H4B	108.0
N1—C2—H2A	109.9	N2—C5—H5A	109.5
C3—C2—H2A	109.9	N2—C5—H5B	109.5
N1—C2—H2B	109.9	H5A—C5—H5B	109.5
C3—C2—H2B	109.9	N2—C5—H5C	109.5
H2A—C2—H2B	108.3	H5A—C5—H5C	109.5
C2—C3—C4	108.92 (8)	H5B—C5—H5C	109.5
C2—C3—H3A	109.9
C2—N1—C1—O1	170.94 (10)	C1—N1—C2—C3	37.71 (14)
C2—N1—C1—N2	−11.24 (15)	N1—C2—C3—C4	−55.31 (12)
C5—N2—C1—O1	−9.34 (16)	C1—N2—C4—C3	−25.76 (14)
C4—N2—C1—O1	−177.57 (10)	C5—N2—C4—C3	165.46 (9)
C5—N2—C1—N1	172.84 (9)	C2—C3—C4—N2	50.42 (12)
C4—N2—C1—N1	4.62 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1^i	0.88 (2)	2.00 (2)	2.875 (1)	177 (2)

Symmetry code: (i) −x, −y+1, −z.