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

Journal logoCRYSTALLOGRAPHIC
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ISSN: 2056-9890
Volume 66| Part 3| March 2010| Pages o719-o720

1,3,7-Tri­methyl-2,4-dioxo-1,2,3,4-tetra­hydro­pteridine-6-carboxylic acid hemihydrate

aLaboratoire de Chimie Analytique II, Université Claude Bernard, Lyon I, 69622, Villeurbanne Cedex, France, and bDepartamento de Química Inorgánica y Orgánica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus Universitario "Las Lagunillas" (B3), 23071 Jaén, Spain
*Correspondence e-mail: mmoreno@ujaen.es

(Received 17 February 2010; accepted 24 February 2010; online 27 February 2010)

In the title compound, C10H10N4O4·0.5H2O, the two rings of the pteridine system are nearly coplanar [dihedral angle = 4.25 (9)°]. The atoms of the carboxyl group are also coplanar with the pteridine unit [r.m.s. deviation from the mean plane of the pteridine skeleton = 0.092 (2) Å]. In the crystal, the presence of the water molecule of crystallization (O atom site symmetry 2) leads to a hydrogen-bonding pattern different from the one shown by many carboxylic acid compounds (dimers formed through O—H⋯O hydrogen bonds between neighbouring carboxyl groups): in the present structure, the water mol­ecule, which lies on a binary axis, acts as a bridge between two mol­ecules, forming a hydrogen-bonded dimer. In addition to the hydrogen bonds, there are ππ ring stacking inter­actions involving the pyrimidine and pyrazine rings [centroid–centroid distance = 3.689 (1)Å], and two different pyrazine rings [centroid–centroid distance = 3.470 (1)Å]. Finally, there is a C—O⋯π contact involving a carboxyl­ate C—O and the pyrimidine ring with a short O⋯Cg distance of 2.738 (2) Å.

Related literature

The precursor 6-acetyl-1,3,7-trimethyl­lumazine (DLMAceM) was obtained according to literature methods, see: Kim et al. (1999[Kim, Y., Kim, J. & Kang, Y. (1999). J. Korean Chem. Soc. pp. 535-539.]). For the structural features of both free and complexed related pteridine derivatives, see for example: Jiménez-Pulido et al. (2008a[Jiménez-Pulido, S. B., Linares-Ordóñez, F. M., Martínez-Martos, J. M., Moreno-Carretero, M. N., Quirós-Olozábal, M. & Martínez-Expósito, M. J. (2008a). J. Inorg. Biochem. pp. 1677-1683.],b[Jiménez-Pulido, S. B., Linares-Ordóñez, F. M., Moreno-Carretero, M. N. & Quirós-Olozábal, M. (2008b). Inorg. Chem. pp. 1096-1106.], 2009[Jiménez-Pulido, S. B., Linares-Ordóñez, F. M. & Moreno-Carretero, M. N. (2009). Polyhedron, pp. 2641-2648.]).

[Scheme 1]

Experimental

Crystal data
  • C10H10N4O4·0.5H2O

  • Mr = 259.23

  • Monoclinic, C 2/c

  • a = 15.7328 (19) Å

  • b = 11.5784 (16) Å

  • c = 12.4062 (18) Å

  • β = 106.113 (10)°

  • V = 2171.1 (5) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.13 mm−1

  • T = 120 K

  • 0.46 × 0.24 × 0.19 mm

Data collection
  • Nonius KappaCCD diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. University of Göttingen, Germany.]) Tmin = 0.944, Tmax = 0.976

  • 14172 measured reflections

  • 1970 independent reflections

  • 1493 reflections with I > 2σ(I)

  • Rint = 0.038

Refinement
  • R[F2 > 2σ(F2)] = 0.055

  • wR(F2) = 0.140

  • S = 1.21

  • 1970 reflections

  • 180 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.65 e Å−3

  • Δρmin = −0.58 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1w—H1w⋯O4i 0.91 (2) 1.94 (2) 2.841 (2) 172 (3)
O1w—H1w⋯N5i 0.91 (2) 2.52 (3) 2.988 (2) 113 (2)
O61—H61⋯O1w 0.99 (3) 1.87 (3) 2.774 (2) 151 (3)
O61—H61⋯N5 0.99 (3) 2.13 (4) 2.635 (2) 110 (2)
Symmetry code: (i) [-x+1, y, -z+{\script{1\over 2}}].

Data collection: COLLECT (Nonius, 1998[Nonius (1998). COLLECT. Nonius BV, Delft, the Netherlands.]); cell refinement: DIRAX/LSQ (Duisenberg, 1992[Duisenberg, A. J. M. (1992). J. Appl. Cryst. 25, 92-96.]); data reduction: EVALCCD (Duisenberg et al., 2003[Duisenberg, A. J. M., Kroon-Batenburg, L. M. J. & Schreurs, A. M. M. (2003). J. Appl. Cryst. 36, 220-229.]); 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: Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

The interest in the 6-substituted lumazine derivatives has been increased since new coordination position pathways and new chemical and biological properties are provided while keeping the similarity to natural pterines. In this article we describe a new pteridine derivative, the 6-carboxy-1,3,7-trimetillumazine (6-carboxy-1,3,7-trimethylpteridine-2,4(1H,3H)-dione), which crystallizes as hemihydrate. The two rings of the pteridine system are nearly coplanar (acute dihedral angle 4.25°). The atoms of carboxylic group are also coplanar with the pteridine moiety. The presence of the water molecule makes the hydrogen bond pattern different from the usual one in many carboxylic acid compounds: in the present structure the water molecule, which lies on a binary axis, acts like a bridge between two molecules, using its full ability for H-bond formation (Fig. 1, Table 1). In addition to the H-bonds, there are π-π ring stacking interactions which involves the pirimidine (x,y,z) and pyrazine (1/2-x, 3/2-y,-z) rings (Fig. 2). The perpendicular distances are 3.261 and 3.173 Å, the centroid-centroid separation is 3.689 Å, the dihedral angle between the planes concerned is 4.25 °. Another π-π interaction between the pyrazine ring portions at (x,y,z) and (1/2-x,3/2-y,-z) is observed. The parameters, in the same order as before mentioned, are 3.189 Å, 3.470 Å, 0.02 °, respectively, corresponding to a centroids offset of 1.368 Å. Also, there is an important C—O···π contact involving O62 and the pyrimidine ring in x, 1-y, z-1/2 with a distance between the O62 atom and the centroid of the ring of 2.738 (2) Å, a slipping angle between the O62-centroid vector and the normal to the ring of 11.4° and a C61—O62···centroid angle of 131.2 (1)° .

Related literature top

The precursor 6-acetyl-1,3,7-trimethyllumazine (DLMAceM) was obtained according to literature methods, see: Kim et al. (1999). For the structural features of both free and complexed related pteridine derivatives, see for example: Jiménez-Pulido et al. (2008a,b, 2009).

Experimental top

The new carboxylate ligand was prepared from the oxidation of 6-acetyl-1,3,7-trimethyllumazine with HNO3 (40%). This suspension was stirred at room temperature for 3 hours. The ligand was filtered off and isolated in high yield (75-80%). The pale-yellow solution was kept at room for several days, affording prismatic yellow crystals that were collected and used for X-ray diffraction studies.

(6-acetyl-1,3,7-trimethyllumazine (DLMAceM) was prepared by standard Timmis reaction between 6-amino-5-nitrosopyrimidines and 1,3-dicarbonylic derivatives by the method described by Kim et al.)

Refinement top

The H atoms attached to O61 and O1w were located in subsequents difference Fourier map and refined isotropically. Methyl hydrogens were fixed geometrically and treated as riding with Uiso=1.5Ueq(C).

Computing details top

Data collection: COLLECT (Nonius, 1998); cell refinement: DIRAX/LSQ (Duisenberg, 1992); data reduction: EVALCCD (Duisenberg et al., 2003); program(s) used to solve structure: SHELXL97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. View of the H-bonds (light green broken lines) scheme for 6-carboxy-1,3,7-trimethyllumazine showing the atom labels. Thermal ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. View along [100] of the molecular arrangement in the crystal.
1,3,7-Trimethyl-2,4-dioxo-1,2,3,4-tetrahydropteridine-6-carboxylic acid hemihydrate top
Crystal data top
C10H10N4O4·0.5H2OF(000) = 1080
Mr = 259.23Dx = 1.586 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 1970 reflections
a = 15.7328 (19) Åθ = 2.2–25.3°
b = 11.5784 (16) ŵ = 0.13 mm1
c = 12.4062 (18) ÅT = 120 K
β = 106.113 (10)°Prism, light yellow
V = 2171.1 (5) Å30.46 × 0.24 × 0.19 mm
Z = 8
Data collection top
Nonius KappaCCD
diffractometer
1970 independent reflections
Radiation source: fine-focus sealed tube1493 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.038
CCD rotation images, thick slices scansθmax = 25.3°, θmin = 2.2°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 1818
Tmin = 0.944, Tmax = 0.976k = 1313
14172 measured reflectionsl = 1414
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.055H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.140 w = 1/[σ2(Fo2) + (0.0794P)2 + 0.6244P]
where P = (Fo2 + 2Fc2)/3
S = 1.21(Δ/σ)max < 0.001
1970 reflectionsΔρmax = 0.65 e Å3
180 parametersΔρmin = 0.58 e Å3
0 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0125 (14)
Crystal data top
C10H10N4O4·0.5H2OV = 2171.1 (5) Å3
Mr = 259.23Z = 8
Monoclinic, C2/cMo Kα radiation
a = 15.7328 (19) ŵ = 0.13 mm1
b = 11.5784 (16) ÅT = 120 K
c = 12.4062 (18) Å0.46 × 0.24 × 0.19 mm
β = 106.113 (10)°
Data collection top
Nonius KappaCCD
diffractometer
1970 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
1493 reflections with I > 2σ(I)
Tmin = 0.944, Tmax = 0.976Rint = 0.038
14172 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0550 restraints
wR(F2) = 0.140H atoms treated by a mixture of independent and constrained refinement
S = 1.21Δρmax = 0.65 e Å3
1970 reflectionsΔρmin = 0.58 e Å3
180 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F^2^ against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F^2^, conventional R-factors R are based on F, with F set to zero for negative F^2^. The threshold expression of F^2^ > σ(F^2^) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F^2^ 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*/Ueq
O1w0.50000.75980 (19)0.25000.0271 (5)
N10.16439 (11)0.99057 (14)0.04043 (14)0.0213 (4)
C20.22500 (13)1.06607 (18)0.06308 (17)0.0217 (5)
N30.31401 (11)1.03800 (14)0.02157 (14)0.0215 (4)
C40.34674 (13)0.94797 (17)0.04960 (16)0.0201 (5)
C4A0.27938 (13)0.87743 (17)0.07728 (15)0.0181 (5)
N50.30569 (11)0.79181 (13)0.14868 (13)0.0190 (4)
C60.24465 (13)0.73144 (16)0.17889 (16)0.0201 (5)
C70.15435 (14)0.75701 (17)0.13777 (16)0.0211 (5)
N80.12794 (11)0.84253 (14)0.06406 (13)0.0209 (4)
C8A0.18987 (13)0.90176 (17)0.03424 (15)0.0189 (5)
C10.07098 (14)1.0169 (2)0.09039 (18)0.0294 (6)
O20.20238 (10)1.15152 (13)0.11888 (12)0.0303 (4)
C30.37550 (14)1.11665 (19)0.05308 (19)0.0289 (5)
O40.42558 (9)0.92948 (12)0.08549 (12)0.0257 (4)
C610.28018 (14)0.63747 (18)0.26029 (17)0.0246 (5)
O610.36742 (10)0.63064 (13)0.30013 (12)0.0283 (4)
O620.23356 (10)0.56896 (13)0.28942 (13)0.0362 (5)
C710.08347 (14)0.69621 (18)0.17313 (18)0.0267 (5)
H1W0.5284 (19)0.809 (2)0.305 (2)0.065 (10)*
H1A0.03660.94510.10140.044*
H1B0.06361.05500.16300.044*
H1C0.05011.06830.04040.044*
H3A0.43631.09010.01970.043*
H3B0.36841.19450.02570.043*
H3C0.36311.11820.13500.043*
H610.398 (2)0.694 (3)0.273 (3)0.068 (9)*
H71A0.02640.73300.13790.040*
H71B0.09580.70040.25490.040*
H71C0.08140.61510.14990.040*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O1w0.0226 (11)0.0273 (12)0.0279 (12)0.0000.0013 (9)0.000
N10.0182 (9)0.0239 (9)0.0210 (9)0.0019 (7)0.0040 (7)0.0038 (7)
C20.0226 (11)0.0241 (11)0.0182 (10)0.0020 (9)0.0055 (8)0.0001 (9)
N30.0204 (9)0.0235 (9)0.0206 (9)0.0005 (7)0.0059 (7)0.0031 (7)
C40.0211 (11)0.0217 (11)0.0167 (10)0.0000 (9)0.0036 (8)0.0015 (8)
C4A0.0205 (11)0.0188 (10)0.0153 (10)0.0026 (8)0.0056 (8)0.0013 (8)
N50.0212 (9)0.0189 (9)0.0168 (8)0.0006 (7)0.0053 (7)0.0021 (7)
C60.0230 (11)0.0201 (11)0.0181 (10)0.0025 (9)0.0073 (8)0.0029 (8)
C70.0251 (11)0.0213 (11)0.0178 (10)0.0019 (9)0.0073 (9)0.0048 (8)
N80.0198 (9)0.0228 (9)0.0208 (9)0.0002 (7)0.0067 (7)0.0017 (7)
C8A0.0216 (11)0.0199 (11)0.0152 (10)0.0009 (8)0.0053 (8)0.0040 (8)
C10.0193 (11)0.0373 (13)0.0296 (12)0.0047 (10)0.0037 (9)0.0078 (10)
O20.0283 (9)0.0298 (9)0.0318 (9)0.0052 (7)0.0065 (7)0.0114 (7)
C30.0242 (12)0.0299 (12)0.0332 (12)0.0037 (10)0.0091 (10)0.0082 (10)
O40.0168 (8)0.0304 (8)0.0288 (8)0.0000 (6)0.0047 (6)0.0050 (6)
C610.0276 (12)0.0251 (12)0.0209 (11)0.0005 (9)0.0064 (9)0.0003 (9)
O610.0265 (8)0.0282 (9)0.0277 (8)0.0026 (7)0.0036 (7)0.0056 (7)
O620.0352 (9)0.0340 (9)0.0391 (10)0.0040 (8)0.0100 (8)0.0148 (8)
C710.0234 (11)0.0314 (12)0.0265 (12)0.0048 (10)0.0093 (9)0.0009 (9)
Geometric parameters (Å, º) top
O1w—H1W0.90 (3)N1—C21.379 (3)
O4—C41.215 (2)N1—C11.460 (3)
C4A—N51.317 (3)O61—C611.326 (3)
C4A—C8A1.389 (3)O61—H610.98 (3)
C4A—C41.453 (3)O62—C611.202 (3)
N8—C8A1.325 (3)C7—C711.484 (3)
N8—C71.334 (3)C71—H71A0.9800
N5—C61.323 (3)C71—H71B0.9800
N3—C41.371 (3)C71—H71C0.9800
N3—C21.390 (3)C3—H3A0.9800
N3—C31.459 (3)C3—H3B0.9800
O2—C21.203 (2)C3—H3C0.9800
C8A—N11.367 (3)C1—H1A0.9800
C6—C71.401 (3)C1—H1B0.9800
C6—C611.484 (3)C1—H1C0.9800
N5—C4A—C8A120.46 (18)O2—C2—N1121.85 (19)
N5—C4A—C4117.93 (18)O2—C2—N3120.80 (18)
C8A—C4A—C4121.56 (18)N1—C2—N3117.32 (17)
C8A—N8—C7117.54 (18)C7—C71—H71A109.5
C4A—N5—C6118.07 (18)C7—C71—H71B109.5
C4—N3—C2125.18 (17)H71A—C71—H71B109.5
C4—N3—C3119.27 (17)C7—C71—H71C109.5
C2—N3—C3115.45 (16)H71A—C71—H71C109.5
N8—C8A—N1118.56 (18)H71B—C71—H71C109.5
N8—C8A—C4A122.21 (18)N3—C3—H3A109.5
N1—C8A—C4A119.22 (18)N3—C3—H3B109.5
N5—C6—C7121.83 (18)H3A—C3—H3B109.5
N5—C6—C61114.46 (18)N3—C3—H3C109.5
C7—C6—C61123.70 (18)H3A—C3—H3C109.5
C8A—N1—C2121.70 (17)H3B—C3—H3C109.5
C8A—N1—C1121.06 (17)O62—C61—O61120.23 (19)
C2—N1—C1116.92 (17)O62—C61—C6122.8 (2)
C61—O61—H61112.3 (17)O61—C61—C6116.92 (18)
O4—C4—N3122.20 (18)N1—C1—H1A109.5
O4—C4—C4A123.50 (18)N1—C1—H1B109.5
N3—C4—C4A114.30 (17)H1A—C1—H1B109.5
N8—C7—C6119.86 (18)N1—C1—H1C109.5
N8—C7—C71115.99 (19)H1A—C1—H1C109.5
C6—C7—C71124.13 (18)H1B—C1—H1C109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1w—H1w···O4i0.91 (2)1.94 (2)2.841 (2)172 (3)
O1w—H1w···N5i0.91 (2)2.52 (3)2.988 (2)113 (2)
O61—H61···O1w0.99 (3)1.87 (3)2.774 (2)151 (3)
O61—H61···N50.99 (3)2.13 (4)2.635 (2)110 (2)
Symmetry code: (i) x+1, y, z+1/2.

Experimental details

Crystal data
Chemical formulaC10H10N4O4·0.5H2O
Mr259.23
Crystal system, space groupMonoclinic, C2/c
Temperature (K)120
a, b, c (Å)15.7328 (19), 11.5784 (16), 12.4062 (18)
β (°) 106.113 (10)
V3)2171.1 (5)
Z8
Radiation typeMo Kα
µ (mm1)0.13
Crystal size (mm)0.46 × 0.24 × 0.19
Data collection
DiffractometerNonius KappaCCD
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.944, 0.976
No. of measured, independent and
observed [I > 2σ(I)] reflections
14172, 1970, 1493
Rint0.038
(sin θ/λ)max1)0.600
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.055, 0.140, 1.21
No. of reflections1970
No. of parameters180
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.65, 0.58

Computer programs: COLLECT (Nonius, 1998), DIRAX/LSQ (Duisenberg, 1992), EVALCCD (Duisenberg et al., 2003), SHELXL97 (Sheldrick, 2008), Mercury (Macrae et al., 2006), WinGX (Farrugia, 1999) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1w—H1w···O4i0.91 (2)1.94 (2)2.841 (2)172 (3)
O1w—H1w···N5i0.91 (2)2.52 (3)2.988 (2)113 (2)
O61—H61···O1w0.99 (3)1.87 (3)2.774 (2)151 (3)
O61—H61···N50.99 (3)2.13 (4)2.635 (2)110 (2)
Symmetry code: (i) x+1, y, z+1/2.
 

Acknowledgements

Thanks are due to the Plan de Apoyo a la Investigación, al Desarrollo Tecnológico y a la Innovación de la Universidad de Jaén (RFC PP2008 UJA 08 16 08) and the Junta de Andalucía (FQM-273) for financial support.

References

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Volume 66| Part 3| March 2010| Pages o719-o720
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