organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

Redetermination of 5,5-di­hy­droxy­barbituric acid trihydrate (alloxan tetrahydrate)

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aDepartment of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, England
*Correspondence e-mail: d.a.tocher@ucl.ac.uk

(Received 25 August 2004; accepted 6 September 2004; online 18 September 2004)

The low temperature redetermination of 5,5-di­hydroxy­barbituric acid trihydrate, C4H4N2O5·3H2O, (historically misnamed alloxan tetrahydrate) is reported here. The organic molecule has crystallographic mirror symmetry, as does one of the water molecules.

Comment

The crystal structure of 5,5-di­hydroxy­barbituric acid trihydrate, (I) (originally misnamed alloxan tetrahydrate) was determined by Mootz & Jeffrey (1965[Mootz, D., Jeffrey, G. A. (1965). Acta Cryst. 19, 717-725.]). In that original room-temperature study, only three of the six H atoms in the asymmetric unit could be located by means of difference Fourier syntheses, and the structure refined to a final R value of 0.097. We have redetermined this crystal structure at 150 K, with a final R value of 0.028, to gain more accurate data for our theoretical modelling studies. The low-temperature redetermination located all the H atoms, which were refined isotropically. The precision of the unit-cell dimensions was improved by an order of magnitude. The unit-cell volume decreased by ca. 27 Å3, consistent with the determination at low temperature. In general, the molecular geometric param­eters are not significantly different, the exception being the C6—O6 bond length, which is shorter in the low-temperature structure, while C2—O2 is actually longer in the low-temperature structure, both by ca. 0.1 Å.[link]

[Scheme 1]

Compound (I) crystallizes in the monoclinic space group C2/m, with the organic mol­ecule on a mirror plane plus one water mol­ecule in a general position and a second on a mirror plane (Fig. 1[link]). The crystallographic plane is normal to the pyrimidine ring, passing through atoms O2, C2, C5, O7 and O8. The hydroxyl H atoms attached to the ring are disordered across the mirror plane. The water mol­ecule O2W, in a general position, is disordered with one of the H atoms refined over two positions. The third water of solvation lies on the mirror plane at (0, y, 1), with the mirror bisecting the H—O—H angle.

The C—N bond lengths in the ring range from 1.3666 (11) to 1.3752 (9) Å, and the C5—C6 bond length is 1.5272 (10) Å. The packing (Fig. 2[link]) consists of centrosymmetric dimers hydrogen-bonded to form a chain, with the water mol­ecules lying between these chains, forming a buckled sheet structure. The water mol­ecules in general positions form O—H⋯O bonds to the organic hydroxyl groups, whilst the water mol­ecules on the mirror plane bond to the unique hydrogen-bond carbonyl acceptor on the organic mol­ecules (Fig. 3[link]). The water mol­ecules on the mirror planes and in general positions also hydrogen-bond to each other in the sheet. The DA distance within the bonded chains of mol­ecules is 2.8580 (6) Å, whilst the O—H⋯O hydrogen bonds range from 2.7217 (11) to 2.9343 (9) Å. All potential donors and acceptors are used in the hydrogen bonding.

[Figure 1]
Figure 1
View of the 5,5-di­hydroxy­barbituric acid molecule and three water molecules (twice the asymmetric unit), showing the atom labelling scheme. Displacement ellipsoids are drawn at the 50% probability level. [Symmetry code: (i) x, −y, z.]
[Figure 2]
Figure 2
The crystal packing of 5,5-di­hydroxy­barbituric acid trihydrate, showing the N—H⋯O and O—H⋯O hydrogen-bonding interactions as dashed lines.
[Figure 3]
Figure 3
The hydrogen-bonded sheet structure in 5,5-di­hydroxy­barbituric acid trihydrate, showing the N—H⋯O and O—H⋯O hydrogen-bonding interactions as dashed lines.
[Figure 4]
Figure 4
The crystal morphology of 5,5-di­hydroxy­barbituric acid trihydrate.

Experimental

To complement the results from an experimental polymorph search on alloxan, 5,5-di­hydroxy­barbituric acid trihydrate was obtained from Aldrich as colourless plate-like crystals of alloxan tetrahydrate (Fig. 4[link]). These crystals were very sensitive and decompose rapidly in air.

Crystal data
  • C4H4N2O5·3H2O

  • Mr = 214.14

  • Monoclinic, C2/m

  • a = 9.4614 (8) Å

  • b = 12.2095 (10) Å

  • c = 7.2973 (6) Å

  • β = 91.4650 (10)°

  • V = 842.70 (12) Å3

  • Z = 4

  • Dx = 1.688 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 3125 reflections

  • θ = 2.7–28.2°

  • μ = 0.17 mm−1

  • T = 150 (2) K

  • Plate, colourless

  • 0.72 × 0.62 × 0.11 mm

Data collection
  • Bruker SMART APEX diffractometer

  • ω scans

  • Absorption correction: multi-scan (SADABS; Sheldrick, 1996[Sheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.]) Tmin = 0.889, Tmax = 0.982

  • 3701 measured reflections

  • 1036 independent reflections

  • 1019 reflections with I > 2σ(I)

  • Rint = 0.015

  • θmax = 28.2°

  • h = −12 → 12

  • k = −15 → 15

  • l = −9 → 9

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.028

  • wR(F2) = 0.078

  • S = 1.12

  • 1036 reflections

  • 100 parameters

  • All H-atom parameters refined

  • w = 1/[σ2(Fo2) + (0.0445P)2 + 0.3397P] where P = (Fo2 + 2Fc2)/3

  • (Δ/σ)max < 0.001

  • Δρmax = 0.41 e Å−3

  • Δρmin = −0.24 e Å−3

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O6i 0.901 (14) 1.970 (14) 2.8580 (10) 168.1 (13)
O7—H7⋯O2Wii 0.83 (3) 1.92 (3) 2.7217 (11) 163 (3)
O8—H8⋯O2Wiii 0.78 (3) 1.98 (3) 2.7250 (10) 160 (3)
O1W—H9⋯O2 0.868 (18) 2.075 (19) 2.9343 (9) 170.6 (16)
O2W—H10⋯O1Wiv 0.85 (2) 1.96 (2) 2.8009 (11) 171.3 (15)
O2W—H11A⋯O7ii 0.77 (4) 1.99 (4) 2.7217 (11) 160 (3)
O2W—H11B⋯O8v 0.82 (3) 1.96 (3) 2.7250 (10) 154 (3)
Symmetry codes: (i) [{\script{1\over 2}}-x,{\script{1\over 2}}-y,1-z]; (ii) [{\script{1\over 2}}-x,{\script{1\over 2}}-y,-z]; (iii) [{\script{1\over 2}}+x,y-{\script{1\over 2}},z]; (iv) x,y,z-1; (v) [x-{\script{1\over 2}},{\script{1\over 2}}+y,z].

The non-H atoms were refined freely with anisotropic displacement parameters, with the H atoms refined independently with an isotropic model.

Data collection: SMART (Bruker, 2000[Bruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990[Sheldrick, G. M. (1990). Acta Cryst. A46, 467-473.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997[Sheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.]); molecular graphics: MERCURY (Bruno et al., 2002[Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M. K., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389-397.]) and SHELXTL (Bruker, 2000[Bruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.]); software used to prepare material for publication: SHELXL97.

Supporting information


Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Mercury (Bruno et al., 2002) and SHELXTL (Bruker, 2000); software used to prepare material for publication: SHELXL97.

5,5-dihydroxybarbituric acid trihydrate top
Crystal data top
C4H4N2O5·3H2OF(000) = 448
Mr = 214.14Dx = 1.688 Mg m3
Monoclinic, C2/mMo Kα radiation, λ = 0.71073 Å
a = 9.4614 (8) ÅCell parameters from 3125 reflections
b = 12.2095 (10) Åθ = 2.7–28.2°
c = 7.2973 (6) ŵ = 0.17 mm1
β = 91.465 (1)°T = 150 K
V = 842.70 (12) Å3Plate, colourless
Z = 40.72 × 0.62 × 0.11 mm
Data collection top
Bruker SMART APEX
diffractometer
1036 independent reflections
Radiation source: fine-focus sealed tube1019 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.015
ω rotation with narrow frames scansθmax = 28.2°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
h = 1212
Tmin = 0.889, Tmax = 0.982k = 1515
3701 measured 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)] = 0.028Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.078All H-atom parameters refined
S = 1.12 w = 1/[σ2(Fo2) + (0.0445P)2 + 0.3397P]
where P = (Fo2 + 2Fc2)/3
1036 reflections(Δ/σ)max < 0.001
100 parametersΔρmax = 0.41 e Å3
0 restraintsΔρmin = 0.24 e Å3
Special details top

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 (Å2) top
xyzUiso*/UeqOcc. (<1)
O20.07576 (10)0.00000.71087 (12)0.0213 (2)
O60.37126 (7)0.19208 (5)0.35604 (9)0.02282 (19)
O70.28600 (10)0.00000.13202 (12)0.0194 (2)
O80.50741 (9)0.00000.28277 (13)0.0178 (2)
O1W0.00000.15469 (8)1.00000.0266 (2)
O2W0.15495 (8)0.33927 (6)0.11287 (12)0.0282 (2)
N10.21286 (7)0.09635 (6)0.51944 (9)0.01624 (19)
C20.16226 (12)0.00000.59004 (16)0.0154 (2)
C50.36230 (12)0.00000.29895 (16)0.0151 (2)
C60.31848 (9)0.10501 (7)0.39599 (11)0.0157 (2)
H10.1840 (14)0.1584 (11)0.574 (2)0.032 (3)*
H70.303 (3)0.058 (2)0.076 (5)0.040 (8)*0.50
H80.535 (3)0.056 (2)0.244 (4)0.034 (7)*0.50
H90.0322 (19)0.1122 (16)0.915 (2)0.055 (5)*
H100.1164 (17)0.2799 (16)0.078 (2)0.051 (4)*
H11A0.181 (3)0.373 (3)0.031 (5)0.036 (8)*0.50
H11B0.090 (3)0.373 (3)0.160 (4)0.027 (6)*0.50
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O20.0226 (4)0.0201 (5)0.0216 (5)0.0000.0089 (3)0.000
O60.0270 (4)0.0156 (3)0.0263 (4)0.0019 (2)0.0091 (3)0.0007 (2)
O70.0256 (5)0.0181 (5)0.0145 (4)0.0000.0013 (3)0.000
O80.0157 (4)0.0151 (4)0.0229 (4)0.0000.0058 (3)0.000
O1W0.0331 (5)0.0177 (5)0.0296 (5)0.0000.0112 (4)0.000
O2W0.0274 (4)0.0198 (4)0.0369 (4)0.0010 (3)0.0067 (3)0.0012 (3)
N10.0183 (3)0.0130 (4)0.0177 (4)0.0003 (2)0.0041 (3)0.0011 (3)
C20.0152 (5)0.0158 (5)0.0153 (5)0.0000.0008 (4)0.000
C50.0162 (5)0.0153 (5)0.0141 (5)0.0000.0026 (4)0.000
C60.0171 (4)0.0153 (4)0.0146 (4)0.0001 (3)0.0005 (3)0.0006 (3)
Geometric parameters (Å, º) top
O2—C21.2183 (15)O2W—H11A0.77 (4)
O6—C61.2132 (11)O2W—H11B0.82 (3)
O7—C51.4000 (14)N1—C61.3666 (11)
O7—H70.83 (3)N1—C21.3752 (9)
O8—C51.3810 (14)N1—H10.901 (14)
O8—H80.78 (3)C2—N1i1.3752 (9)
O1W—H90.868 (18)C5—C61.5272 (10)
O2W—H100.85 (2)C5—C6i1.5272 (10)
C5—O7—H7109 (2)N1—C2—N1i117.62 (10)
C5—O8—H8112 (2)O8—C5—O7114.66 (10)
H10—O2W—H11A111 (3)O8—C5—C6108.78 (6)
H10—O2W—H11B104 (2)O7—C5—C6105.27 (6)
H11A—O2W—H11B108 (3)O8—C5—C6i108.78 (6)
C6—N1—C2125.49 (8)O7—C5—C6i105.27 (6)
C6—N1—H1117.5 (8)C6—C5—C6i114.19 (9)
C2—N1—H1116.2 (9)O6—C6—N1122.59 (8)
O2—C2—N1121.19 (5)O6—C6—C5120.40 (7)
O2—C2—N1i121.19 (5)N1—C6—C5116.90 (7)
C6—N1—C2—O2173.91 (10)O7—C5—C6—O680.59 (10)
C6—N1—C2—N1i6.06 (16)C6i—C5—C6—O6164.45 (6)
C2—N1—C6—O6170.32 (9)O8—C5—C6—N1140.99 (8)
C2—N1—C6—C513.52 (13)O7—C5—C6—N195.66 (9)
O8—C5—C6—O642.76 (12)C6i—C5—C6—N119.30 (13)
Symmetry code: (i) x, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O6ii0.901 (14)1.970 (14)2.8580 (10)168.1 (13)
O7—H7···O2Wiii0.83 (3)1.92 (3)2.7217 (11)163 (3)
O8—H8···O2Wiv0.78 (3)1.98 (3)2.7250 (10)160 (3)
O1W—H9···O20.868 (18)2.075 (19)2.9343 (9)170.6 (16)
O2W—H10···O1Wv0.85 (2)1.96 (2)2.8009 (11)171.3 (15)
O2W—H11A···O7iii0.77 (4)1.99 (4)2.7217 (11)160 (3)
O2W—H11B···O8vi0.82 (3)1.96 (3)2.7250 (10)154 (3)
Symmetry codes: (ii) x+1/2, y+1/2, z+1; (iii) x+1/2, y+1/2, z; (iv) x+1/2, y1/2, z; (v) x, y, z1; (vi) x1/2, y+1/2, z.
 

Acknowledgements

This research was supported by the EPSRC in funding a studentship for TCL. The authors acknowledge the Research Councils UK Basic Technology Programme for supporting `Control and Prediction of the Organic Solid State'. For more information on this work, please visit https://www.chem.ucl.ac.uk/basictechorg/.

References

First citationBruker (2000). SMART, SAINT and SHELXTL. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationBruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M. K., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389–397.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMootz, D., Jeffrey, G. A. (1965). Acta Cryst. 19, 717–725.  CSD CrossRef CAS IUCr Journals Web of Science Google Scholar
First citationSheldrick, G. M. (1990). Acta Cryst. A46, 467–473.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationSheldrick, G. M. (1996). SADABS. University of Göttingen, Germany.  Google Scholar
First citationSheldrick, G. M. (1997). SHELXL97. University of Göttingen, Germany.  Google Scholar

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