7,9-Bis(hy-droxy-meth-yl)-7H-purine-2,6,8(1H,3H,9H)trione.

The structure of the title uric acid derivative, C(7)H(8)N(4)O(5), from human kidney stones, is characterized by the C and O atoms of one of the two hy-droxy-methyl groups being disordered nearly equally over three different sites. In the crystal, mol-ecules are connected by a three-dimensional hydrogen-bonding scheme though they look stacked in planes nearly parallel to ([Formula: see text]04).

Related literature

For related structures, see: Ringertz (1966 ▶) for uric acid and Parkin & Hope (1998 ▶) for the dihydrate. For urolithia­sis, see: Tanagho & McAninch (2000 ▶); Jungers et al. (2005 ▶); Moe (2006 ▶); Knoll (2007 ▶). For recent characterization of new urinary stones, see: Le Bail et al. (2009 ▶); For purine biosynthesis, see: Ashihara et al. (2008 ▶). For hy­droxy­methyl­ation of uric acid, see: Lubczak et al. (2002 ▶).

Experimental

Crystal data

C7H8N4O5

M = 228.17

Monoclinic,

a = 5.3226 (6) Å

b = 11.5541 (13) Å

c = 14.5931 (18) Å

β = 97.340 (7)°

V = 890.09 (18) Å3

Z = 4

Mo Kα radiation

μ = 0.15 mm−1

T = 150 K

0.22 × 0.12 × 0.06 mm

Data collection

Bruker Kappa APEXII CCD diffractometer

Absorption correction: multi-scan (SADABS; Bruker, 2008 ▶) T min = 0.677, T max = 0.746

33302 measured reflections

3075 independent reflections

2127 reflections with I > 2σ(I)

R int = 0.064

Refinement

R[F 2 > 2σ(F 2)] = 0.056

wR(F 2) = 0.166

S = 1.03

3075 reflections

169 parameters

1 restraint

H-atom parameters constrained

Δρmax = 0.78 e Å−3

Δρmin = −0.37 e Å−3

Data collection: APEX2 (Bruker, 2008 ▶); cell refinement: SAINT (Bruker, 2008 ▶) and McMaille (Le Bail, 2004 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶) and ESPOIR (Le Bail, 2001 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2001 ▶) and ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811018186/zl2370sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536811018186/zl2370Isup2.hkl

Supplementary material file. DOI: 10.1107/S1600536811018186/zl2370Isup3.mol

Supplementary material file. DOI: 10.1107/S1600536811018186/zl2370Isup4.cml

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

C7H8N4O5	F(000) = 472.0
Mr = 228.17	Dx = 1.703 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 241 reflections
a = 5.3226 (6) Å	θ = 4–15°
b = 11.5541 (13) Å	µ = 0.15 mm−1
c = 14.5931 (18) Å	T = 150 K
β = 97.340 (7)°	Fragment, pale-green
V = 890.09 (18) Å3	0.22 × 0.12 × 0.06 mm
Z = 4

Bruker Kappa APEXII CCD diffractometer	3075 independent reflections
Radiation source: fine-focus sealed tube	2127 reflections with I > 2σ(I)
graphite	Rint = 0.064
ω scans; 30 settings	θmax = 32.3°, θmin = 3.5°
Absorption correction: multi-scan (SADABS; Bruker, 2008)	h = −7→7
Tmin = 0.677, Tmax = 0.746	k = −17→17
33302 measured reflections	l = −21→21

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)] = 0.056	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.166	H-atom parameters constrained
S = 1.03	w = 1/[σ2(Fo2) + (0.0816P)2 + 0.5575P] where P = (Fo2 + 2Fc2)/3
3075 reflections	(Δ/σ)max < 0.001
169 parameters	Δρmax = 0.78 e Å−3
1 restraint	Δρmin = −0.37 e Å−3

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.

	x	y	z	Uiso*/Ueq	Occ. (<1)
O2	1.0659 (2)	−0.20036 (10)	0.35524 (10)	0.0250 (3)
O6	1.3617 (2)	0.14185 (10)	0.48924 (9)	0.0241 (3)
O8	0.5565 (3)	0.35248 (12)	0.28547 (13)	0.0430 (4)
O9	0.2229 (2)	0.11073 (11)	0.19866 (10)	0.0278 (3)
H9	0.1080	0.1830	0.1860	0.042*
N1	1.2092 (3)	−0.02650 (11)	0.41726 (10)	0.0174 (3)
H1	1.3389	−0.0620	0.4458	0.021*
N3	0.8444 (3)	−0.03560 (11)	0.30815 (10)	0.0175 (3)
H3	0.7360	−0.0740	0.2739	0.021*
N7	0.8876 (3)	0.26000 (12)	0.37849 (11)	0.0247 (3)
N9	0.6403 (3)	0.15297 (12)	0.27429 (11)	0.0224 (3)
C2	1.0404 (3)	−0.09345 (13)	0.35937 (11)	0.0167 (3)
C4	0.8172 (3)	0.08053 (13)	0.32201 (11)	0.0162 (3)
C5	0.9722 (3)	0.14401 (13)	0.38595 (11)	0.0165 (3)
C6	1.1933 (3)	0.09272 (13)	0.43511 (11)	0.0161 (3)
C8	0.6827 (4)	0.26569 (15)	0.31068 (14)	0.0273 (4)
C9	0.4761 (3)	0.12956 (15)	0.18565 (13)	0.0236 (4)
H9A	0.4850	0.1962	0.1435	0.028*
H9B	0.5407	0.0606	0.1559	0.028*
C7A	0.9677 (4)	0.35741 (15)	0.44018 (14)	0.0268 (4)	0.339 (3)
H7A1	1.1376	0.3428	0.4744	0.032*	0.339 (3)
H7A2	0.9734	0.4301	0.4045	0.032*	0.339 (3)
O71	0.7889 (9)	0.3644 (4)	0.4997 (3)	0.0325 (11)	0.339 (3)
H71	0.8173	0.3134	0.5407	0.049*	0.339 (3)
C7B	0.9677 (4)	0.35741 (15)	0.44018 (14)	0.0268 (4)	0.340 (6)
H7B1	0.8166	0.3902	0.4638	0.032*	0.340 (6)
H7B2	1.0823	0.3278	0.4938	0.032*	0.340 (6)
O72	1.0842 (9)	0.4407 (3)	0.4008 (3)	0.0244 (13)	0.340 (6)
H72	0.9764	0.4847	0.3717	0.037*	0.340 (6)
C7C	0.9677 (4)	0.35741 (15)	0.44018 (14)	0.0268 (4)	0.321 (6)
H7C1	0.9760	0.3322	0.5053	0.032*	0.321 (6)
H7C2	0.8424	0.4209	0.4298	0.032*	0.321 (6)
O73	1.2214 (10)	0.3999 (4)	0.4221 (4)	0.0344 (15)	0.321 (6)
H73	1.2569	0.3717	0.3723	0.052*	0.321 (6)

	U11	U22	U33	U12	U13	U23
O2	0.0232 (6)	0.0108 (5)	0.0381 (7)	0.0017 (4)	−0.0069 (5)	−0.0015 (5)
O6	0.0215 (6)	0.0168 (5)	0.0301 (7)	0.0027 (4)	−0.0114 (5)	−0.0047 (5)
O8	0.0344 (8)	0.0159 (6)	0.0700 (11)	0.0077 (5)	−0.0270 (8)	−0.0004 (6)
O9	0.0188 (6)	0.0212 (6)	0.0422 (8)	−0.0021 (5)	−0.0010 (5)	0.0016 (5)
N1	0.0157 (6)	0.0121 (6)	0.0224 (7)	0.0027 (5)	−0.0051 (5)	0.0001 (5)
N3	0.0161 (6)	0.0106 (6)	0.0237 (7)	−0.0005 (5)	−0.0057 (5)	−0.0006 (5)
N7	0.0221 (7)	0.0125 (6)	0.0355 (8)	0.0039 (5)	−0.0117 (6)	−0.0033 (5)
N9	0.0200 (7)	0.0122 (6)	0.0313 (8)	0.0000 (5)	−0.0113 (6)	0.0023 (5)
C2	0.0152 (7)	0.0126 (6)	0.0211 (7)	0.0003 (5)	−0.0019 (6)	0.0008 (5)
C4	0.0135 (7)	0.0127 (6)	0.0209 (7)	−0.0001 (5)	−0.0030 (5)	0.0020 (5)
C5	0.0158 (7)	0.0113 (6)	0.0211 (7)	0.0019 (5)	−0.0027 (6)	0.0001 (5)
C6	0.0159 (7)	0.0134 (6)	0.0179 (7)	0.0010 (5)	−0.0016 (5)	−0.0001 (5)
C8	0.0231 (9)	0.0147 (7)	0.0397 (10)	0.0022 (6)	−0.0129 (8)	−0.0005 (7)
C9	0.0204 (8)	0.0193 (8)	0.0282 (9)	−0.0016 (6)	−0.0078 (7)	0.0027 (6)
C7A	0.0307 (10)	0.0149 (7)	0.0329 (9)	0.0015 (6)	−0.0031 (7)	−0.0041 (6)
O71	0.049 (3)	0.024 (2)	0.025 (2)	0.0127 (18)	0.0052 (18)	0.0001 (15)
C7B	0.0307 (10)	0.0149 (7)	0.0329 (9)	0.0015 (6)	−0.0031 (7)	−0.0041 (6)
O72	0.022 (2)	0.0179 (19)	0.032 (2)	−0.0022 (16)	0.0001 (16)	0.0008 (15)
C7C	0.0307 (10)	0.0149 (7)	0.0329 (9)	0.0015 (6)	−0.0031 (7)	−0.0041 (6)
O73	0.028 (3)	0.027 (2)	0.048 (3)	−0.003 (2)	0.002 (2)	0.005 (2)

O2—C2	1.2450 (19)	N9—C4	1.380 (2)
O6—C6	1.2524 (19)	N9—C8	1.414 (2)
O8—C8	1.236 (2)	N9—C9	1.491 (2)
O9—C9	1.401 (2)	C4—C5	1.376 (2)
O9—H9	1.0371	C5—C6	1.426 (2)
N1—C2	1.387 (2)	C9—H9A	0.9900
N1—C6	1.406 (2)	C9—H9B	0.9900
N1—H1	0.8627	C7A—O71	1.371 (5)
N3—C4	1.3673 (19)	C7A—H7A1	0.9900
N3—C2	1.377 (2)	C7A—H7A2	0.9900
N3—H3	0.8402	O71—H71	0.8400
N7—C8	1.377 (2)	O72—H72	0.8400
N7—C5	1.414 (2)	O73—H73	0.8400
N7—C7A	1.470 (2)
C9—O9—H9	114.0	C4—C5—C6	120.28 (14)
C2—N1—C6	127.52 (13)	N7—C5—C6	131.83 (14)
C2—N1—H1	116.4	O6—C6—N1	120.36 (14)
C6—N1—H1	116.1	O6—C6—C5	127.36 (14)
C4—N3—C2	118.90 (13)	N1—C6—C5	112.28 (13)
C4—N3—H3	121.9	O8—C8—N7	127.05 (17)
C2—N3—H3	118.8	O8—C8—N9	125.52 (16)
C8—N7—C5	108.41 (13)	N7—C8—N9	107.43 (14)
C8—N7—C7A	123.00 (14)	O9—C9—N9	112.21 (16)
C5—N7—C7A	127.88 (14)	O9—C9—H9A	109.2
C4—N9—C8	107.66 (13)	N9—C9—H9A	109.2
C4—N9—C9	127.92 (14)	O9—C9—H9B	109.2
C8—N9—C9	122.74 (14)	N9—C9—H9B	109.2
O2—C2—N3	122.35 (14)	H9A—C9—H9B	107.9
O2—C2—N1	121.10 (14)	O71—C7A—N7	105.2 (2)
N3—C2—N1	116.54 (13)	O71—C7A—H7A1	110.7
N3—C4—C5	123.92 (14)	N7—C7A—H7A1	110.7
N3—C4—N9	126.78 (14)	O71—C7A—H7A2	110.7
C5—C4—N9	109.29 (13)	N7—C7A—H7A2	110.7
C4—C5—N7	107.20 (13)	H7A1—C7A—H7A2	108.8

D—H···A	D—H	H···A	D···A	D—H···A
O9—H9···O2i	1.04	1.70	2.7270 (18)	169
N1—H1···O6ii	0.86	1.98	2.8388 (18)	179
N3—H3···O8iii	0.84	1.88	2.7104 (19)	167
O71—H71···O2iv	0.84	2.04	2.873 (4)	172
O72—H72···O9i	0.84	2.01	2.834 (5)	169
O73—H73···O8v	0.84	2.17	2.892 (6)	144

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O9—H9⋯O2i	1.04	1.70	2.7270 (18)	169
N1—H1⋯O6ii	0.86	1.98	2.8388 (18)	179
N3—H3⋯O8iii	0.84	1.88	2.7104 (19)	167
O71—H71⋯O2iv	0.84	2.04	2.873 (4)	172
O72—H72⋯O9i	0.84	2.01	2.834 (5)	169
O73—H73⋯O8v	0.84	2.17	2.892 (6)	144

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .