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

Faure, R.; Illán-Cabeza, N.A.; Jiménez-Pulido, S.B.; Linares-Ordóñez, F.M.; Moreno-Carretero, M.N.

doi:10.1107/S1600536810007166

organic compounds

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ISSN: 2056-9890

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

doi:10.1107/S1600536810007166

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

René Faure,^a Nuria A. Illán-Cabeza,^b Sonia B. Jiménez-Pulido,^b Fátima M. Linares-Ordóñez ^b and Miguel N. Moreno-Carretero ^b ^*

^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 π–π 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 ). For the structural features of both free and complexed related pteridine derivatives, see for example: Jiménez-Pulido et al. (2008a ,b , 2009 ).

Experimental

Crystal data

C₁₀H₁₀N₄O₄·0.5H₂O
M_r = 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 ) T_min = 0.944, T_max = 0.976
14172 measured reflections
1970 independent reflections
1493 reflections with I > 2σ(I)
R_int = 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
Δρ_max = 0.65 e Å⁻³
Δρ_min = −0.58 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: DIRAX/LSQ (Duisenberg, 1992 ); data reduction: EVALCCD (Duisenberg et al., 2003 ); program(s) used to solve structure: SHELXS97 (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 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810007166/bg2332sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536810007166/bg2332Isup2.hkl

checkCIF report

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.)

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

	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.
	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

C₁₀H₁₀N₄O₄·0.5H₂O	F(000) = 1080
M_r = 259.23	D_x = 1.586 Mg m⁻³
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2yc	Cell parameters from 1970 reflections
a = 15.7328 (19) Å	θ = 2.2–25.3°
b = 11.5784 (16) Å	µ = 0.13 mm⁻¹
c = 12.4062 (18) Å	T = 120 K
β = 106.113 (10)°	Prism, light yellow
V = 2171.1 (5) Å³	0.46 × 0.24 × 0.19 mm
Z = 8

Data collection top

Nonius KappaCCD diffractometer	1970 independent reflections
Radiation source: fine-focus sealed tube	1493 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.038
CCD rotation images, thick slices scans	θ_max = 25.3°, θ_min = 2.2°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −18→18
T_min = 0.944, T_max = 0.976	k = −13→13
14172 measured reflections	l = −14→14

Refinement top

Refinement on F²	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.055	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.140	w = 1/[σ²(F_o²) + (0.0794P)² + 0.6244P] where P = (F_o² + 2F_c²)/3
S = 1.21	(Δ/σ)_max < 0.001
1970 reflections	Δρ_max = 0.65 e Å⁻³
180 parameters	Δρ_min = −0.58 e Å⁻³
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0125 (14)

Crystal data top

C₁₀H₁₀N₄O₄·0.5H₂O	V = 2171.1 (5) Å³
M_r = 259.23	Z = 8
Monoclinic, C2/c	Mo Kα radiation
a = 15.7328 (19) Å	µ = 0.13 mm⁻¹
b = 11.5784 (16) Å	T = 120 K
c = 12.4062 (18) Å	0.46 × 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)
T_min = 0.944, T_max = 0.976	R_int = 0.038
14172 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.055	0 restraints
wR(F²) = 0.140	H atoms treated by a mixture of independent and constrained refinement
S = 1.21	Δρ_max = 0.65 e Å⁻³
1970 reflections	Δρ_min = −0.58 e Å⁻³
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

	x	y	z	U_iso*/U_eq
O1w	0.5000	0.75980 (19)	0.2500	0.0271 (5)
N1	0.16439 (11)	0.99057 (14)	−0.04043 (14)	0.0213 (4)
C2	0.22500 (13)	1.06607 (18)	−0.06308 (17)	0.0217 (5)
N3	0.31401 (11)	1.03800 (14)	−0.02157 (14)	0.0215 (4)
C4	0.34674 (13)	0.94797 (17)	0.04960 (16)	0.0201 (5)
C4A	0.27938 (13)	0.87743 (17)	0.07728 (15)	0.0181 (5)
N5	0.30569 (11)	0.79181 (13)	0.14868 (13)	0.0190 (4)
C6	0.24465 (13)	0.73144 (16)	0.17889 (16)	0.0201 (5)
C7	0.15435 (14)	0.75701 (17)	0.13777 (16)	0.0211 (5)
N8	0.12794 (11)	0.84253 (14)	0.06406 (13)	0.0209 (4)
C8A	0.18987 (13)	0.90176 (17)	0.03424 (15)	0.0189 (5)
C1	0.07098 (14)	1.0169 (2)	−0.09039 (18)	0.0294 (6)
O2	0.20238 (10)	1.15152 (13)	−0.11888 (12)	0.0303 (4)
C3	0.37550 (14)	1.11665 (19)	−0.05308 (19)	0.0289 (5)
O4	0.42558 (9)	0.92948 (12)	0.08549 (12)	0.0257 (4)
C61	0.28018 (14)	0.63747 (18)	0.26029 (17)	0.0246 (5)
O61	0.36742 (10)	0.63064 (13)	0.30013 (12)	0.0283 (4)
O62	0.23356 (10)	0.56896 (13)	0.28942 (13)	0.0362 (5)
C71	0.08347 (14)	0.69621 (18)	0.17313 (18)	0.0267 (5)
H1W	0.5284 (19)	0.809 (2)	0.305 (2)	0.065 (10)*
H1A	0.0366	0.9451	−0.1014	0.044*
H1B	0.0636	1.0550	−0.1630	0.044*
H1C	0.0501	1.0683	−0.0404	0.044*
H3A	0.4363	1.0901	−0.0197	0.043*
H3B	0.3684	1.1945	−0.0257	0.043*
H3C	0.3631	1.1182	−0.1350	0.043*
H61	0.398 (2)	0.694 (3)	0.273 (3)	0.068 (9)*
H71A	0.0264	0.7330	0.1379	0.040*
H71B	0.0958	0.7004	0.2549	0.040*
H71C	0.0814	0.6151	0.1499	0.040*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1w	0.0226 (11)	0.0273 (12)	0.0279 (12)	0.000	0.0013 (9)	0.000
N1	0.0182 (9)	0.0239 (9)	0.0210 (9)	0.0019 (7)	0.0040 (7)	0.0038 (7)
C2	0.0226 (11)	0.0241 (11)	0.0182 (10)	0.0020 (9)	0.0055 (8)	−0.0001 (9)
N3	0.0204 (9)	0.0235 (9)	0.0206 (9)	−0.0005 (7)	0.0059 (7)	0.0031 (7)
C4	0.0211 (11)	0.0217 (11)	0.0167 (10)	0.0000 (9)	0.0036 (8)	−0.0015 (8)
C4A	0.0205 (11)	0.0188 (10)	0.0153 (10)	0.0026 (8)	0.0056 (8)	−0.0013 (8)
N5	0.0212 (9)	0.0189 (9)	0.0168 (8)	0.0006 (7)	0.0053 (7)	−0.0021 (7)
C6	0.0230 (11)	0.0201 (11)	0.0181 (10)	−0.0025 (9)	0.0073 (8)	−0.0029 (8)
C7	0.0251 (11)	0.0213 (11)	0.0178 (10)	−0.0019 (9)	0.0073 (9)	−0.0048 (8)
N8	0.0198 (9)	0.0228 (9)	0.0208 (9)	−0.0002 (7)	0.0067 (7)	−0.0017 (7)
C8A	0.0216 (11)	0.0199 (11)	0.0152 (10)	0.0009 (8)	0.0053 (8)	−0.0040 (8)
C1	0.0193 (11)	0.0373 (13)	0.0296 (12)	0.0047 (10)	0.0037 (9)	0.0078 (10)
O2	0.0283 (9)	0.0298 (9)	0.0318 (9)	0.0052 (7)	0.0065 (7)	0.0114 (7)
C3	0.0242 (12)	0.0299 (12)	0.0332 (12)	−0.0037 (10)	0.0091 (10)	0.0082 (10)
O4	0.0168 (8)	0.0304 (8)	0.0288 (8)	0.0000 (6)	0.0047 (6)	0.0050 (6)
C61	0.0276 (12)	0.0251 (12)	0.0209 (11)	−0.0005 (9)	0.0064 (9)	0.0003 (9)
O61	0.0265 (8)	0.0282 (9)	0.0277 (8)	0.0026 (7)	0.0036 (7)	0.0056 (7)
O62	0.0352 (9)	0.0340 (9)	0.0391 (10)	−0.0040 (8)	0.0100 (8)	0.0148 (8)
C71	0.0234 (11)	0.0314 (12)	0.0265 (12)	−0.0048 (10)	0.0093 (9)	−0.0009 (9)

Geometric parameters (Å, º) top

O1w—H1W	0.90 (3)	N1—C2	1.379 (3)
O4—C4	1.215 (2)	N1—C1	1.460 (3)
C4A—N5	1.317 (3)	O61—C61	1.326 (3)
C4A—C8A	1.389 (3)	O61—H61	0.98 (3)
C4A—C4	1.453 (3)	O62—C61	1.202 (3)
N8—C8A	1.325 (3)	C7—C71	1.484 (3)
N8—C7	1.334 (3)	C71—H71A	0.9800
N5—C6	1.323 (3)	C71—H71B	0.9800
N3—C4	1.371 (3)	C71—H71C	0.9800
N3—C2	1.390 (3)	C3—H3A	0.9800
N3—C3	1.459 (3)	C3—H3B	0.9800
O2—C2	1.203 (2)	C3—H3C	0.9800
C8A—N1	1.367 (3)	C1—H1A	0.9800
C6—C7	1.401 (3)	C1—H1B	0.9800
C6—C61	1.484 (3)	C1—H1C	0.9800

N5—C4A—C8A	120.46 (18)	O2—C2—N1	121.85 (19)
N5—C4A—C4	117.93 (18)	O2—C2—N3	120.80 (18)
C8A—C4A—C4	121.56 (18)	N1—C2—N3	117.32 (17)
C8A—N8—C7	117.54 (18)	C7—C71—H71A	109.5
C4A—N5—C6	118.07 (18)	C7—C71—H71B	109.5
C4—N3—C2	125.18 (17)	H71A—C71—H71B	109.5
C4—N3—C3	119.27 (17)	C7—C71—H71C	109.5
C2—N3—C3	115.45 (16)	H71A—C71—H71C	109.5
N8—C8A—N1	118.56 (18)	H71B—C71—H71C	109.5
N8—C8A—C4A	122.21 (18)	N3—C3—H3A	109.5
N1—C8A—C4A	119.22 (18)	N3—C3—H3B	109.5
N5—C6—C7	121.83 (18)	H3A—C3—H3B	109.5
N5—C6—C61	114.46 (18)	N3—C3—H3C	109.5
C7—C6—C61	123.70 (18)	H3A—C3—H3C	109.5
C8A—N1—C2	121.70 (17)	H3B—C3—H3C	109.5
C8A—N1—C1	121.06 (17)	O62—C61—O61	120.23 (19)
C2—N1—C1	116.92 (17)	O62—C61—C6	122.8 (2)
C61—O61—H61	112.3 (17)	O61—C61—C6	116.92 (18)
O4—C4—N3	122.20 (18)	N1—C1—H1A	109.5
O4—C4—C4A	123.50 (18)	N1—C1—H1B	109.5
N3—C4—C4A	114.30 (17)	H1A—C1—H1B	109.5
N8—C7—C6	119.86 (18)	N1—C1—H1C	109.5
N8—C7—C71	115.99 (19)	H1A—C1—H1C	109.5
C6—C7—C71	124.13 (18)	H1B—C1—H1C	109.5

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2.

Experimental details

Crystal data
Chemical formula	C₁₀H₁₀N₄O₄·0.5H₂O
M_r	259.23
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	120
a, b, c (Å)	15.7328 (19), 11.5784 (16), 12.4062 (18)
β (°)	106.113 (10)
V (Å³)	2171.1 (5)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.13
Crystal size (mm)	0.46 × 0.24 × 0.19

Data collection
Diffractometer	Nonius KappaCCD diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2003)
T_min, T_max	0.944, 0.976
No. of measured, independent and observed [I > 2σ(I)] reflections	14172, 1970, 1493
R_int	0.038
(sin θ/λ)_max (Å⁻¹)	0.600

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.055, 0.140, 1.21
No. of reflections	1970
No. of parameters	180
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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+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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ISSN: 2056-9890

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

doi:10.1107/S1600536810007166

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

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

Related literature

Experimental

Crystal data

Data collection

Refinement

Supporting information

Acknowledgements

References

organic compounds

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