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ISSN: 2056-9890

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

aDepartment of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
*Correspondence e-mail: seikweng@um.edu.my

(Received 27 February 2008; accepted 20 April 2008; online 26 April 2008)

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[Calogero, S., Russo, U. & Del Pra, A. (1980). J. Chem. Soc. Dalton Trans. pp. 646-653.]).

[Scheme 1]

Experimental

Crystal data
  • C4H8N2O

  • Mr = 100.12

  • Orthorhombic, P n m a

  • a = 9.9958 (1) Å

  • b = 7.1327 (1) Å

  • c = 6.7365 (1) Å

  • V = 480.29 (1) Å3

  • 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)

  • Rint = 0.020

Refinement
  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.110

  • S = 1.06

  • 749 reflections

  • 55 parameters

  • All H-atom parameters refined

  • Δρmax = 0.49 e Å−3

  • Δρmin = −0.21 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O1i 0.89 (1) 1.97 (1) 2.864 (1) 178 (1)
Symmetry code: (i) -x+1, -y+1, -z+1.

Data collection: APEX2 (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2007[Bruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: X-SEED (Barbour, 2001[Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.]); software used to prepare material for publication: publCIF (Westrip, 2008[Westrip, S. P. (2008). publCIF. In preparation.]).

Supporting information


Comment top

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.

Related literature top

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

Experimental top

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

Refinement top

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

Computing details top

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).

Figures top
[Figure 1] Fig. 1. Thermal ellipsoid plot of tetrahydropyrimidin-2(1H)-one at the 70% probability level; hydrogen atoms are drawn as spheres of arbitrary radius.
3,4,5,6-tetrahydropyrimidin-2(1H)-one top
Crystal data top
C4H8N2OF(000) = 216
Mr = 100.12Dx = 1.385 Mg m3
Orthorhombic, PnmaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2nCell parameters from 4972 reflections
a = 9.9958 (1) Åθ = 3.0–30.4°
b = 7.1327 (1) ŵ = 0.10 mm1
c = 6.7365 (1) ÅT = 100 K
V = 480.29 (1) Å3Block, colorless
Z = 40.35 × 0.20 × 0.15 mm
Data collection top
Bruker SMART APEXII
diffractometer
719 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.020
Graphite monochromatorθmax = 30.0°, θmin = 3.7°
ϕ and ω scansh = 1213
6595 measured reflectionsk = 910
749 independent reflectionsl = 99
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.110All H-atom parameters refined
S = 1.06 w = 1/[σ2(Fo2) + (0.0818P)2 + 0.084P]
where P = (Fo2 + 2Fc2)/3
749 reflections(Δ/σ)max = 0.001
55 parametersΔρmax = 0.49 e Å3
0 restraintsΔρmin = 0.22 e Å3
Crystal data top
C4H8N2OV = 480.29 (1) Å3
Mr = 100.12Z = 4
Orthorhombic, PnmaMo Kα radiation
a = 9.9958 (1) ŵ = 0.10 mm1
b = 7.1327 (1) ÅT = 100 K
c = 6.7365 (1) Å0.35 × 0.20 × 0.15 mm
Data collection top
Bruker SMART APEXII
diffractometer
719 reflections with I > 2σ(I)
6595 measured reflectionsRint = 0.020
749 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.110All H-atom parameters refined
S = 1.06Δρmax = 0.49 e Å3
749 reflectionsΔρmin = 0.22 e Å3
55 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.48291 (8)0.75000.51927 (11)0.0143 (2)
N10.58480 (7)0.58713 (8)0.27287 (9)0.0140 (2)
C10.54996 (10)0.75000.36064 (14)0.0113 (2)
C20.67121 (7)0.57605 (10)0.09858 (11)0.0145 (2)
C30.65258 (11)0.75000.02874 (14)0.0146 (3)
H10.5642 (13)0.4836 (18)0.3405 (19)0.023 (3)*
H210.6483 (11)0.4643 (17)0.0232 (17)0.017 (3)*
H220.7668 (11)0.5621 (17)0.1397 (17)0.017 (2)*
H310.5609 (18)0.75000.089 (3)0.023 (4)*
H320.7163 (18)0.75000.140 (3)0.023 (4)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0176 (4)0.0122 (4)0.0132 (4)0.0000.0045 (3)0.000
N10.0188 (4)0.0099 (3)0.0133 (3)0.0003 (2)0.0047 (2)0.00012 (19)
C10.0109 (4)0.0111 (5)0.0118 (4)0.0000.0008 (3)0.000
C20.0173 (4)0.0128 (4)0.0133 (4)0.0010 (2)0.0039 (2)0.0008 (2)
C30.0177 (5)0.0145 (5)0.0117 (4)0.0000.0013 (3)0.000
Geometric parameters (Å, º) top
O1—C11.2614 (12)C2—H210.972 (12)
N1—C11.3492 (8)C2—H221.000 (11)
N1—C21.4597 (9)C3—C2i1.5198 (9)
N1—H10.892 (13)C3—H311.001 (18)
C1—N1i1.3492 (8)C3—H320.982 (19)
C2—C31.5198 (9)
C1—N1—C2123.49 (6)N1—C2—H22110.4 (7)
C1—N1—H1115.4 (8)C3—C2—H22110.8 (7)
C2—N1—H1120.2 (8)H21—C2—H22106.8 (10)
O1—C1—N1120.56 (4)C2i—C3—C2109.45 (8)
O1—C1—N1i120.56 (4)C2i—C3—H31109.9 (5)
N1—C1—N1i118.86 (9)C2—C3—H31109.9 (5)
N1—C2—C3109.71 (6)C2i—C3—H32110.5 (5)
N1—C2—H21109.0 (7)C2—C3—H32110.5 (5)
C3—C2—H21110.2 (7)H31—C3—H32106.7 (15)
C2—N1—C1—O1174.85 (8)C1—N1—C2—C330.95 (10)
C2—N1—C1—N1i7.00 (14)N1—C2—C3—C2i52.71 (10)
Symmetry code: (i) x, y+3/2, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1ii0.89 (1)1.97 (1)2.864 (1)178 (1)
Symmetry code: (ii) x+1, y+1, z+1.

Experimental details

Crystal data
Chemical formulaC4H8N2O
Mr100.12
Crystal system, space groupOrthorhombic, Pnma
Temperature (K)100
a, b, c (Å)9.9958 (1), 7.1327 (1), 6.7365 (1)
V3)480.29 (1)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.35 × 0.20 × 0.15
Data collection
DiffractometerBruker SMART APEXII
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
6595, 749, 719
Rint0.020
(sin θ/λ)max1)0.703
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.036, 0.110, 1.06
No. of reflections749
No. of parameters55
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.49, 0.22

Computer programs: APEX2 (Bruker, 2007), SAINT (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), X-SEED (Barbour, 2001), publCIF (Westrip, 2008).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O1i0.89 (1)1.97 (1)2.864 (1)178 (1)
Symmetry code: (i) x+1, y+1, z+1.
 

Acknowledgements

We thank the University of Malaya for the purchase of the diffractometer.

References

First citationBarbour, L. J. (2001). J. Supramol. Chem. 1, 189–191.  CrossRef CAS Google Scholar
First citationBruker (2007). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationCalogero, S., Russo, U. & Del Pra, A. (1980). J. Chem. Soc. Dalton Trans. pp. 646–653.  CSD CrossRef Web of Science Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWestrip, S. P. (2008). publCIF. In preparation.  Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

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ISSN: 2056-9890
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