Low-temperature redetermination of 3,4,5,6-tetra­hydro­pyrimidin-2(1H)-one

Abstract

The low-temperature structure of the title compound, C₄H₈N₂O, is ordered, whereas the central methyl­ene groups is disordered in the reported room-temperature structure. The molecule lies across a mirror plane; adjacent mol­ecules are linked by an N—H⋯O hydrogen bond into a chain.

Related literature

For the room-temperature, disordered structure of tetra­hydro­pyrimidin-2(1H)-one, see: Calogero et al. (1980 ▶).

Experimental

Crystal data

• C₄H₈N₂O

• M _r = 100.12

• Orthorhombic,

• a = 9.9958 (1) Å

• b = 7.1327 (1) Å

• c = 6.7365 (1) Å

• V = 480.29 (1) ų

• Z = 4

• Mo Kα radiation

• μ = 0.10 mm⁻¹

• T = 100 (2) K

• 0.35 × 0.20 × 0.15 mm

Data collection

• Bruker SMART APEX diffractometer

• Absorption correction: none

• 6595 measured reflections

• 749 independent reflections

• 719 reflections with I > 2σ(I)

• R _int = 0.020

Refinement

• R[F ² > 2σ(F ²)] = 0.036

• wR(F ²) = 0.110

• S = 1.06

• 749 reflections

• 55 parameters

• All H-atom parameters refined

• Δρ_max = 0.49 e Å⁻³

• Δρ_min = −0.21 e Å⁻³

Data collection: APEX2 (Bruker, 2007 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: X-SEED (Barbour, 2001 ▶); software used to prepare material for publication: publCIF (Westrip, 2008 ▶).

Supplementary Material

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O1i	0.89 (1)	1.97 (1)	2.864 (1)	178 (1)

Symmetry code: (i) .

supplementary crystallographic information

Comment

The crystal structure of tetrahydropyrimidin-2(1H)-one (Scheme I) was refined as a disorder model, the second of the three methylene carbon atoms being disordered about a mirror plane by a ratio of 0.7:0.3 (Calogero et al., 1980). However, the structure is ordered at low temperature (Fig. 1); adjacent molecules are linked by a N–H···O hydrogen bond into a chain motif.

Experimental

The commercially available compound was crystalline. A large block was cut into a smaller specimen.

Refinement

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

Figures

Fig. 1.

Thermal ellipsoid plot of tetrahydropyrimidin-2(1H)-one at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.

Crystal data

C4H8N2O	F000 = 216
Mr = 100.12	Dx = 1.385 Mg m−3
Orthorhombic, Pnma	Mo Kα radiation λ = 0.71073 Å
Hall symbol: -P 2ac 2n	Cell parameters from 4972 reflections
a = 9.9958 (1) Å	θ = 3.0–30.4º
b = 7.1327 (1) Å	µ = 0.10 mm−1
c = 6.7365 (1) Å	T = 100 (2) K
V = 480.29 (1) Å3	Block, colorless
Z = 4	0.35 × 0.20 × 0.15 mm

Data collection

Bruker SMART APEXII diffractometer	719 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tube	Rint = 0.020
Monochromator: graphite	θmax = 30.0º
T = 100(2) K	θmin = 3.7º
φ and ω scans	h = −12→13
Absorption correction: none	k = −9→10
6595 measured reflections	l = −9→9
749 independent reflections

Refinement

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.036	All H-atom parameters refined
wR(F2) = 0.110	w = 1/[σ2(Fo2) + (0.0818P)2 + 0.084P] where P = (Fo2 + 2Fc2)/3
S = 1.06	(Δ/σ)max = 0.001
749 reflections	Δρmax = 0.49 e Å−3
55 parameters	Δρmin = −0.21 e Å−3
Primary atom site location: structure-invariant direct methods	Extinction correction: none

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
O1	0.48291 (8)	0.7500	0.51927 (11)	0.0143 (2)
N1	0.58480 (7)	0.58713 (8)	0.27287 (9)	0.0140 (2)
C1	0.54996 (10)	0.7500	0.36064 (14)	0.0113 (2)
C2	0.67121 (7)	0.57605 (10)	0.09858 (11)	0.0145 (2)
C3	0.65258 (11)	0.7500	−0.02874 (14)	0.0146 (3)
H1	0.5642 (13)	0.4836 (18)	0.3405 (19)	0.023 (3)*
H21	0.6483 (11)	0.4643 (17)	0.0232 (17)	0.017 (3)*
H22	0.7668 (11)	0.5621 (17)	0.1397 (17)	0.017 (2)*
H31	0.5609 (18)	0.7500	−0.089 (3)	0.023 (4)*
H32	0.7163 (18)	0.7500	−0.140 (3)	0.023 (4)*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
O1	0.0176 (4)	0.0122 (4)	0.0132 (4)	0.000	0.0045 (3)	0.000
N1	0.0188 (4)	0.0099 (3)	0.0133 (3)	0.0003 (2)	0.0047 (2)	0.00012 (19)
C1	0.0109 (4)	0.0111 (5)	0.0118 (4)	0.000	−0.0008 (3)	0.000
C2	0.0173 (4)	0.0128 (4)	0.0133 (4)	0.0010 (2)	0.0039 (2)	−0.0008 (2)
C3	0.0177 (5)	0.0145 (5)	0.0117 (4)	0.000	0.0013 (3)	0.000

Geometric parameters (Å, °)

O1—C1	1.2614 (12)	C2—H21	0.972 (12)
N1—C1	1.3492 (8)	C2—H22	1.000 (11)
N1—C2	1.4597 (9)	C3—C2i	1.5198 (9)
N1—H1	0.892 (13)	C3—H31	1.001 (18)
C1—N1i	1.3492 (8)	C3—H32	0.982 (19)
C2—C3	1.5198 (9)
C1—N1—C2	123.49 (6)	N1—C2—H22	110.4 (7)
C1—N1—H1	115.4 (8)	C3—C2—H22	110.8 (7)
C2—N1—H1	120.2 (8)	H21—C2—H22	106.8 (10)
O1—C1—N1	120.56 (4)	C2i—C3—C2	109.45 (8)
O1—C1—N1i	120.56 (4)	C2i—C3—H31	109.9 (5)
N1—C1—N1i	118.86 (9)	C2—C3—H31	109.9 (5)
N1—C2—C3	109.71 (6)	C2i—C3—H32	110.5 (5)
N1—C2—H21	109.0 (7)	C2—C3—H32	110.5 (5)
C3—C2—H21	110.2 (7)	H31—C3—H32	106.7 (15)
C2—N1—C1—O1	−174.85 (8)	C1—N1—C2—C3	−30.95 (10)
C2—N1—C1—N1i	7.00 (14)	N1—C2—C3—C2i	52.71 (10)

Symmetry codes: (i) x, −y+3/2, z.

Hydrogen-bond geometry (Å, °)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O1ii	0.89 (1)	1.97 (1)	2.864 (1)	178 (1)

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