organic compounds
7,9-Bis(hydroxymethyl)-7H-purine-2,6,8(1H,3H,9H)trione
aLaboratoire de Biochimie A, AP-HP, Hopital Necker, 149 rue de Sèvres, 75743 Paris Cedex 15, France, bLaboratoire de Physique des Solides, Bat. 510, Université Paris XI, 91045 Orsay, France, and cLaboratoire des Oxydes et Fluorures, UMR 6010 CNRS, Université du Maine, Avenue Olivier Messiaen, 72085 Le Mans Cedex 9, France
*Correspondence e-mail: armel.le_bail@univ-lemans.fr
The structure of the title uric acid derivative, C7H8N4O5, from human kidney stones, is characterized by the C and O atoms of one of the two hydroxymethyl groups being disordered nearly equally over three different sites. In the crystal, molecules are connected by a three-dimensional hydrogen-bonding scheme though they look stacked in planes nearly parallel to (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
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Refinement
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Data collection: APEX2 (Bruker, 2008); cell 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).
Supporting information
10.1107/S1600536811018186/zl2370sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536811018186/zl2370Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536811018186/zl2370Isup3.mol
Supporting information file. DOI: 10.1107/S1600536811018186/zl2370Isup4.cml
Samples are coming from human kidney stones, always identified as a green part at the surface of uric acid calculi. Either they could originate from a natural cause or from the consequence of a chemical treatment of the patients (about ten cases). Since the patients took various medications for different unsimilar pathologies or had no treatment at all, the cause looks more probably natural.
H atoms of the N—H and 9-hydroxymethyl groups were positioned from the difference Fourier map. Owing to the disorder, the H atoms bonded to C7, O71, O72 and O73 were positioned geometrically (C—H = 0.99 and O—H = 0.84 Å). All H atoms were constrained to ride on their parent atoms with Uiso(H) values set at 1.2 x Ueq(C or N) and 1.5 x Ueq(O). When refined independently, the occupancies of the three sites O71, O72 and O73 were very similar and their sum was very close to one. In the final model, the sum was constrained to one.
Data collection: APEX2 (Bruker, 2008); cell
SAINT (Bruker, 2008) and McMaille (Le Bail, 2004); data reduction: SAINT (Bruker, 2008); 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).Fig. 1. ORTEP view (Farrugia, 1997) of the title molecule; displacement ellipsoids are drawn at the 50% probability level. The nine hydrogen atoms bonded to C7, O71, O72 and O73, with ~1/3 occupancies are omitted for the sake of clarity. | |
Fig. 2. DIAMOND (Brandenburg, 2001) projection of the structure along the a axis. The N1—H1···O6, N3—H3···O8 and O9—H9···O2 hydrogen bonds ensuring the formation of layers are represented by dashed lines. H atoms with ~1/3 occupancy are not represented. | |
Fig. 3. DIAMOND (Brandenburg, 2001) projection of the structure along the b axis showing the layers stacked parallel to (104). H atoms with ~1/3 occupancy are not represented. The disordered OH group (O71, O72, O73) is mainly involved in inter-layers hydrogen bonding. |
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 monochromator | 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 |
C7H8N4O5 | V = 890.09 (18) Å3 |
Mr = 228.17 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 5.3226 (6) Å | µ = 0.15 mm−1 |
b = 11.5541 (13) Å | T = 150 K |
c = 14.5931 (18) Å | 0.22 × 0.12 × 0.06 mm |
β = 97.340 (7)° |
Bruker Kappa APEXII CCD diffractometer | 3075 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | 2127 reflections with I > 2σ(I) |
Tmin = 0.677, Tmax = 0.746 | Rint = 0.064 |
33302 measured reflections |
R[F2 > 2σ(F2)] = 0.056 | 1 restraint |
wR(F2) = 0.166 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.78 e Å−3 |
3075 reflections | Δρmin = −0.37 e Å−3 |
169 parameters |
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 |
Symmetry codes: (i) −x+1, y+1/2, −z+1/2; (ii) −x+3, −y, −z+1; (iii) −x+1, y−1/2, −z+1/2; (iv) −x+2, −y, −z+1; (v) x+1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C7H8N4O5 |
Mr | 228.17 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 150 |
a, b, c (Å) | 5.3226 (6), 11.5541 (13), 14.5931 (18) |
β (°) | 97.340 (7) |
V (Å3) | 890.09 (18) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.15 |
Crystal size (mm) | 0.22 × 0.12 × 0.06 |
Data collection | |
Diffractometer | Bruker Kappa APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2008) |
Tmin, Tmax | 0.677, 0.746 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 33302, 3075, 2127 |
Rint | 0.064 |
(sin θ/λ)max (Å−1) | 0.752 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.056, 0.166, 1.03 |
No. of reflections | 3075 |
No. of parameters | 169 |
No. of restraints | 1 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.78, −0.37 |
Computer programs: APEX2 (Bruker, 2008), SAINT (Bruker, 2008) and McMaille (Le Bail, 2004), SAINT (Bruker, 2008), SHELXS97 (Sheldrick, 2008) and ESPOIR (Le Bail, 2001), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2001) and ORTEP-3 (Farrugia, 1997), publCIF (Westrip, 2010).
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) −x+1, y+1/2, −z+1/2; (ii) −x+3, −y, −z+1; (iii) −x+1, y−1/2, −z+1/2; (iv) −x+2, −y, −z+1; (v) x+1, y, z. |
Acknowledgements
The authors thank the reviewer for strong improvements of the description of the disordered part of the structure.
References
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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.
Urolithiasis, which is as old as mankind is now the third most common urinary disease (Jungers et al., 2005; Moe, 2006; Knoll, 2007). This disease constitutes a major health problem and there is evidence to show that its incidence has increased continually in past decades (Tanagho & McAninch, 2000). Among the different chemical phases found in kidney stones, let's quote calcium oxalate, calcium phosphate, uric acid, ammonium hydrogen urate and magnesium ammonium phosphate which are the main components of stones, with differences in their distribution being found in different population groups.
Recently, at the surface of uric acid kidney stones, a green deposit has been observed for different patients. Since classical FTIR measurements were not able to characterize such deposit, X-ray diffraction experiments have been performed.
Powder diffraction revealed a mixture of uric acid (Ringertz, 1966) together with traces of its dihydrate (Parkin & Hope, 1998) and an unknown phase which could be indexed by using the McMaille software (Le Bail, 2004). An hypothesis for an uric acid derivative was suggested by the direct space software ESPOIR (Le Bail, 2001), however the structure could not be completed till a tiny single-crystal was selected in the powder. From the structure solution, a hydroxymethyl group was found attached to N9. High thermal parameters at room temperature obscured the nature of some disorder occurring around of the C7 atom: three peaks on the Fourier difference map, all looking lighter than a C atom, but heavier than a H one, two of them at 0.9 Å from each other were observed. At 150 K, the thermal motions were considerably smaller, allowing to propose an interpretation: a second hydroxymethyl group, CH2OH attached to N7, nearly equally disordered over three different O atom sites. The largest difference densities (0.78, 0.54) in the final structural model are close to C9 of the not disordered hydroxymethyl group (exactly between H9A and H9B) and O8. If O8 may be slightly splitted, given its large U33, the most intense residue close to C9 is unclear, possibly due to some disorder also for this hydroxymethyl group. Positional disorder was observed in uric acid dihydrate with superimposition of the six- and five-membered rings (Parkin and Hope, 1998). Such a disorder is unlikely to occur in the title compound. Different parts of the samples examined by powder diffraction may show variations in cell parameters as well as strong peak asymetries suggesting inhomogeneities, possibly corresponding to more or less disorder.
The ORTEP diagram of the title compound is shown in Fig. 1. Atoms numbering adopts the purine system. Molecules are connected by a three-dimensional hydrogen bonding scheme (Fig. 2 and Table 2), though they are stacked in planes nearly parallel to (104) (Fig. 3), corresponding by far to the most intense reflection.
In humans, uric acid is the main urinary metabolite of purines, therefore, its alteration is a mark of disorders associated with purine metabolism. A review on the biosynthesis of caffeine and related purine alkaloids was published recently (Ashihara et al., 2008). But how the title compound is biosynthesized in humans is not yet fully understood. Hydroxymethylation of uric acid is known to occur with formaldehyde (Lubczak et al., 2002).