supplementary materials
Low-temperature redetermination of 3,4,5,6-tetrahydropyrimidin-2(1H)-one
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.
The commercially available compound was crystalline. A large block was cut into
a smaller specimen.
All hydrogen atoms were located in a difference Fourier map, and were freely
refined.
Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT (Bruker, 2007); data reduction: SAINT (Bruker, 2007); 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).
3,4,5,6-tetrahydropyrimidin-2(1
H)-one
top
Crystal data top
| 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 top
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 top
| 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 |
Crystal data top
| C4H8N2O | V = 480.29 (1) Å3 |
| Mr = 100.12 | Z = 4 |
| Orthorhombic, Pnma | Mo Kα |
| a = 9.9958 (1) Å | µ = 0.10 mm−1 |
| b = 7.1327 (1) Å | T = 100 (2) K |
| c = 6.7365 (1) Å | 0.35 × 0.20 × 0.15 mm |
Data collection top
Bruker SMART APEXII
diffractometer | 749 independent reflections |
| Absorption correction: none | 719 reflections with I > 2σ(I) |
| 6595 measured reflections | Rint = 0.020 |
Refinement top
| R[F2 > 2σ(F2)] = 0.036 | 55 parameters |
| wR(F2) = 0.110 | All H-atom parameters refined |
| S = 1.06 | Δρmax = 0.49 e Å−3 |
| 749 reflections | Δρmin = −0.21 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top| | 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 (Å2) top| | 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, °) top
| 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, °) top
| 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. |
Table 1
Hydrogen-bond geometry (Å, °) top
| 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 codes: (i) −x+1, −y+1, −z+1. |
We thank the University of Malaya for the purchase of the diffractometer.
Barbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.
Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.
Calogero, S., Russo, U. & Del Pra, A. (1980). J. Chem. Soc. Dalton Trans. pp. 646–653.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
Westrip, S. P. (2008). publCIF. In preparation.
![[Figure 1]](./bv2094fig1thm.gif)
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.