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

Lewis, T.C.; Tocher, D.A.

doi:10.1107/S1600536804022019

organic compounds

CRYSTALLOGRAPHIC
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ISSN: 2056-9890

Volume 60| Part 10| October 2004| Pages o1748-o1750

https://doi.org/10.1107/S1600536804022019

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

Thomas C. Lewis ^a and Derek A. Tocher ^a ^*

^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 ). 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.

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). 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) 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). The water molecules on the mirror planes and in general positions also hydrogen-bond to each other in the sheet. The D⋯A 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
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
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
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
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). These crystals were very sensitive and decompose rapidly in air.

Crystal data

C₄H₄N₂O₅·3H₂O
M_r = 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
D_x = 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 ) T_min = 0.889, T_max = 0.982
3701 measured reflections
1036 independent reflections
1019 reflections with I > 2σ(I)
R_int = 0.015
θ_max = 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(F_o²) + (0.0445P)² + 0.3397P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.41 e Å⁻³
Δρ_min = −0.24 e Å⁻³

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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⋯O1W^iv	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⋯O8^v	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 ); 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.

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536804022019/bt6507sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536804022019/bt6507Isup2.hkl

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

C₄H₄N₂O₅·3H₂O	F(000) = 448
M_r = 214.14	D_x = 1.688 Mg m⁻³
Monoclinic, C2/m	Mo Kα radiation, λ = 0.71073 Å
a = 9.4614 (8) Å	Cell parameters from 3125 reflections
b = 12.2095 (10) Å	θ = 2.7–28.2°
c = 7.2973 (6) Å	µ = 0.17 mm⁻¹
β = 91.465 (1)°	T = 150 K
V = 842.70 (12) Å³	Plate, colourless
Z = 4	0.72 × 0.62 × 0.11 mm

Data collection top

Bruker SMART APEX diffractometer	1036 independent reflections
Radiation source: fine-focus sealed tube	1019 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.015
ω rotation with narrow frames scans	θ_max = 28.2°, θ_min = 2.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)	h = −12→12
T_min = 0.889, T_max = 0.982	k = −15→15
3701 measured reflections	l = −9→9

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.078	All H-atom parameters refined
S = 1.12	w = 1/[σ²(F_o²) + (0.0445P)² + 0.3397P] where P = (F_o² + 2F_c²)/3
1036 reflections	(Δ/σ)_max < 0.001
100 parameters	Δρ_max = 0.41 e Å⁻³
0 restraints	Δρ_min = −0.24 e Å⁻³

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

	x	y	z	U_iso*/U_eq	Occ. (<1)
O2	0.07576 (10)	0.0000	0.71087 (12)	0.0213 (2)
O6	0.37126 (7)	0.19208 (5)	0.35604 (9)	0.02282 (19)
O7	0.28600 (10)	0.0000	0.13202 (12)	0.0194 (2)
O8	0.50741 (9)	0.0000	0.28277 (13)	0.0178 (2)
O1W	0.0000	0.15469 (8)	1.0000	0.0266 (2)
O2W	0.15495 (8)	0.33927 (6)	0.11287 (12)	0.0282 (2)
N1	0.21286 (7)	0.09635 (6)	0.51944 (9)	0.01624 (19)
C2	0.16226 (12)	0.0000	0.59004 (16)	0.0154 (2)
C5	0.36230 (12)	0.0000	0.29895 (16)	0.0151 (2)
C6	0.31848 (9)	0.10501 (7)	0.39599 (11)	0.0157 (2)
H1	0.1840 (14)	0.1584 (11)	0.574 (2)	0.032 (3)*
H7	0.303 (3)	0.058 (2)	0.076 (5)	0.040 (8)*	0.50
H8	0.535 (3)	−0.056 (2)	0.244 (4)	0.034 (7)*	0.50
H9	0.0322 (19)	0.1122 (16)	0.915 (2)	0.055 (5)*
H10	0.1164 (17)	0.2799 (16)	0.078 (2)	0.051 (4)*
H11A	0.181 (3)	0.373 (3)	0.031 (5)	0.036 (8)*	0.50
H11B	0.090 (3)	0.373 (3)	0.160 (4)	0.027 (6)*	0.50

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O2	0.0226 (4)	0.0201 (5)	0.0216 (5)	0.000	0.0089 (3)	0.000
O6	0.0270 (4)	0.0156 (3)	0.0263 (4)	−0.0019 (2)	0.0091 (3)	0.0007 (2)
O7	0.0256 (5)	0.0181 (5)	0.0145 (4)	0.000	−0.0013 (3)	0.000
O8	0.0157 (4)	0.0151 (4)	0.0229 (4)	0.000	0.0058 (3)	0.000
O1W	0.0331 (5)	0.0177 (5)	0.0296 (5)	0.000	0.0112 (4)	0.000
O2W	0.0274 (4)	0.0198 (4)	0.0369 (4)	0.0010 (3)	−0.0067 (3)	−0.0012 (3)
N1	0.0183 (3)	0.0130 (4)	0.0177 (4)	0.0003 (2)	0.0041 (3)	−0.0011 (3)
C2	0.0152 (5)	0.0158 (5)	0.0153 (5)	0.000	0.0008 (4)	0.000
C5	0.0162 (5)	0.0153 (5)	0.0141 (5)	0.000	0.0026 (4)	0.000
C6	0.0171 (4)	0.0153 (4)	0.0146 (4)	0.0001 (3)	0.0005 (3)	0.0006 (3)

Geometric parameters (Å, º) top

O2—C2	1.2183 (15)	O2W—H11A	0.77 (4)
O6—C6	1.2132 (11)	O2W—H11B	0.82 (3)
O7—C5	1.4000 (14)	N1—C6	1.3666 (11)
O7—H7	0.83 (3)	N1—C2	1.3752 (9)
O8—C5	1.3810 (14)	N1—H1	0.901 (14)
O8—H8	0.78 (3)	C2—N1ⁱ	1.3752 (9)
O1W—H9	0.868 (18)	C5—C6	1.5272 (10)
O2W—H10	0.85 (2)	C5—C6ⁱ	1.5272 (10)

C5—O7—H7	109 (2)	N1—C2—N1ⁱ	117.62 (10)
C5—O8—H8	112 (2)	O8—C5—O7	114.66 (10)
H10—O2W—H11A	111 (3)	O8—C5—C6	108.78 (6)
H10—O2W—H11B	104 (2)	O7—C5—C6	105.27 (6)
H11A—O2W—H11B	108 (3)	O8—C5—C6ⁱ	108.78 (6)
C6—N1—C2	125.49 (8)	O7—C5—C6ⁱ	105.27 (6)
C6—N1—H1	117.5 (8)	C6—C5—C6ⁱ	114.19 (9)
C2—N1—H1	116.2 (9)	O6—C6—N1	122.59 (8)
O2—C2—N1	121.19 (5)	O6—C6—C5	120.40 (7)
O2—C2—N1ⁱ	121.19 (5)	N1—C6—C5	116.90 (7)

C6—N1—C2—O2	173.91 (10)	O7—C5—C6—O6	−80.59 (10)
C6—N1—C2—N1ⁱ	−6.06 (16)	C6ⁱ—C5—C6—O6	164.45 (6)
C2—N1—C6—O6	−170.32 (9)	O8—C5—C6—N1	−140.99 (8)
C2—N1—C6—C5	13.52 (13)	O7—C5—C6—N1	95.66 (9)
O8—C5—C6—O6	42.76 (12)	C6ⁱ—C5—C6—N1	−19.30 (13)

Symmetry code: (i) x, −y, z.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O6ⁱⁱ	0.901 (14)	1.970 (14)	2.8580 (10)	168.1 (13)
O7—H7···O2Wⁱⁱⁱ	0.83 (3)	1.92 (3)	2.7217 (11)	163 (3)
O8—H8···O2W^iv	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···O1W^v	0.85 (2)	1.96 (2)	2.8009 (11)	171.3 (15)
O2W—H11A···O7ⁱⁱⁱ	0.77 (4)	1.99 (4)	2.7217 (11)	160 (3)
O2W—H11B···O8^vi	0.82 (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, y−1/2, z; (v) x, y, z−1; (vi) x−1/2, 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/.

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