A new polymorph of 5-nitro­uracil monohydrate

Pereira Silva, P.S.; Domingos, S.R.; Ramos Silva, M.; Paixão, J.A.; Matos Beja, A.

doi:10.1107/S1600536808014426

organic compounds

CRYSTALLOGRAPHIC
COMMUNICATIONS

ISSN: 2056-9890

Volume 64| Part 6| June 2008| Page o1091

doi:10.1107/S1600536808014426

Open

access

A new polymorph of 5-nitrouracil monohydrate

P. S. Pereira Silva,^a S. R. Domingos,^a M. Ramos Silva,^a J. A. Paixão ^a and A. Matos Beja ^a ^*

^aCEMDRX, Physics Department, University of Coimbra, P-3004-516 Coimbra, Portugal
^*Correspondence e-mail: psidonio@pollux.fis.uc.pt

(Received 13 May 2008; accepted 13 May 2008; online 17 May 2008)

In the title compound, C₄H₃N₃O₄·H₂O, molecules of 5-nitrouracil are hydrogen bonded in pairs across crystallographic centers of symmetry. The resulting dimers are also hydrogen bonded to the water molecules, forming a three-dimensional network. The pyrimidine ring is almost planar (with a maximum deviation of 0.0156 (9) Å for the one of the N atoms) and the nitro group is rotated by 12.4 (1)° out of the uracil plane, while in the other polymorph the value for the same angle is 5°.

Related literature

For the non-linear optical properties of 5-nitrouracil, see: Bergman et al. (1972 ); Puccetti et al. (1993 ); Youping et al. (1992 ). For the crystal structure of another polymorph, see: Craven (1967 ). For related literature, see: Pettier & Byrn (1982 ); Rao et al. (1995 ).

Experimental

Crystal data

C₄H₃N₃O₄·H₂O
M_r = 175.11
Monoclinic, P 2₁ /c
a = 6.2799 (1) Å
b = 7.8481 (2) Å
c = 13.8068 (3) Å
β = 93.842 (1)°
V = 678.94 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.16 mm⁻¹
T = 293 (2) K
0.44 × 0.22 × 0.20 mm

Data collection

Bruker APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ) T_min = 0.890, T_max = 0.969
15135 measured reflections
2232 independent reflections
1918 reflections with I > 2σ(I)
R_int = 0.018

Refinement

R[F² > 2σ(F²)] = 0.042
wR(F²) = 0.131
S = 1.00
2232 reflections
115 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.35 e Å⁻³
Δρ_min = −0.37 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N3—H3⋯O2ⁱ	0.86	1.99	2.8503 (13)	173
N1—H1⋯O9ⁱⁱ	0.86	1.88	2.6736 (12)	153
O9—H9A⋯O4ⁱⁱⁱ	0.87 (2)	1.92 (2)	2.7640 (13)	165 (2)
O9—H9A⋯O7ⁱⁱⁱ	0.87 (2)	2.41 (3)	2.9101 (13)	117 (2)
O9—H9B⋯O7^iv	0.84 (3)	2.29 (3)	3.0940 (15)	162 (2)
Symmetry codes: (i) -x, -y, -z+1; (ii) x-1, y, z; (iii) $[x, -y+{\script{1\over 2}}, z-{\script{1\over 2}}]$ ; (iv) $[-x+2, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Data collection: APEX2 (Bruker, 2005 ); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003 ); software used to prepare material for publication: SHELXL97.

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536808014426/bt2713sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536808014426/bt2713Isup2.hkl

checkCIF report

Comment top

5-Nitrouracil (5NU) is an interesting molecule due to its nonlinear optical properties (Bergman et al., 1972; Puccetti et al., 1993; Youping et al., 1992) and is also of relevance to biological and pharmaceutical sciences (Rao et al., 1995; Pettier & Byrn, 1982).

In the framework of our study of new compounds with potential NLO properties, we have crystallized a new polymorph of 5-nitrouracil monohydrate (Fig.1). Molecules of 5NU are hydrogen bonded in pairs across crystallographic centers of symmetry. The resulting dimers are also hydrogen bonded by the water molecules forming a three dimensional network (Table 1; Fig. 2). The difference in intermolecular interactions between the two polymorphs seems to have a small effect on the molecular structure of the 5NU moiety, with all bond lengths and angles being in good agreement with the previously reported structure (Craven, 1967). The pyrimidine ring is almost planar and the main conformational difference is the large twist of the nitro group away from the plane of the ring [12.4 (1)°], whereas it approaches coplanarity in the other polymorph (5.0° for the same angle).

Related literature top

For the non-linear optical properties of 5-nitrouracil, see: Bergman et al. (1972); Puccetti et al. (1993); Youping et al. (1992). For the crystal structure of another polymorph, see: Craven (1967). For related literature, see: Pettier & Byrn (1982); Rao et al. (1995).

Experimental top

The title compound was prepared by adding 5-nitrouracil (Aldrich, 98%, 1 mmol) to L-serine (Aldrich 99%, 1 mmol) in a solution of water (10 ml) and piridine (Aldrich 99%, 30 ml). The solution was slowly warmed and then left to evaporate under ambient conditions. After a few days, small colourless single crystals were deposited.

Computing details top

Data collection: SMART (Bruker, 2005); cell refinement: SAINT (Bruker, 2005); data reduction: SAINT (Bruker, 2005); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008).

Figures top

	Fig. 1. ORTEPII (Spek,2003) plot of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. Packing diagram, viewed down the a axis, with the hydrogen bonds depicted as dashed lines.

5-nitrouracil monohydrate top

Crystal data top

C₄H₃N₃O₄·H₂O	F(000) = 360
M_r = 175.11	D_x = 1.713 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 8093 reflections
a = 6.2799 (1) Å	θ = 3.0–33.5°
b = 7.8481 (2) Å	µ = 0.16 mm⁻¹
c = 13.8068 (3) Å	T = 293 K
β = 93.842 (1)°	Block, colourless
V = 678.94 (3) Å³	0.44 × 0.22 × 0.20 mm
Z = 4

Data collection top

Bruker APEXII CCD area-detector diffractometer	2232 independent reflections
Radiation source: fine-focus sealed tube	1918 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.018
ϕ and ω scans	θ_max = 33.6°, θ_min = 3.0°
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	h = −9→9
T_min = 0.890, T_max = 0.969	k = −10→11
15135 measured reflections	l = −20→20

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)] = 0.042	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.131	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	w = 1/[σ²(F_o²) + (0.0782P)² + 0.1592P] where P = (F_o² + 2F_c²)/3
2232 reflections	(Δ/σ)_max = 0.002
115 parameters	Δρ_max = 0.35 e Å⁻³
0 restraints	Δρ_min = −0.37 e Å⁻³

Crystal data top

C₄H₃N₃O₄·H₂O	V = 678.94 (3) Å³
M_r = 175.11	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 6.2799 (1) Å	µ = 0.16 mm⁻¹
b = 7.8481 (2) Å	T = 293 K
c = 13.8068 (3) Å	0.44 × 0.22 × 0.20 mm
β = 93.842 (1)°

Data collection top

Bruker APEXII CCD area-detector diffractometer	2232 independent reflections
Absorption correction: multi-scan (SADABS; Sheldrick, 2003)	1918 reflections with I > 2σ(I)
T_min = 0.890, T_max = 0.969	R_int = 0.018
15135 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.042	0 restraints
wR(F²) = 0.131	H atoms treated by a mixture of independent and constrained refinement
S = 1.00	Δρ_max = 0.35 e Å⁻³
2232 reflections	Δρ_min = −0.37 e Å⁻³
115 parameters

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
O2	−0.10857 (13)	0.07025 (12)	0.38353 (6)	0.0403 (2)
O4	0.51917 (15)	0.21379 (14)	0.54232 (6)	0.0478 (3)
O7	0.75926 (14)	0.44337 (13)	0.44352 (7)	0.0459 (2)
O8	0.67663 (18)	0.46987 (19)	0.29111 (8)	0.0674 (4)
N1	0.11205 (14)	0.24517 (12)	0.30605 (6)	0.0306 (2)
H1	0.0210	0.2540	0.2569	0.037*
N3	0.20903 (15)	0.14746 (12)	0.46071 (6)	0.0330 (2)
H3	0.1773	0.0894	0.5106	0.040*
N5	0.63828 (16)	0.41810 (13)	0.37147 (7)	0.0371 (2)
C2	0.06017 (16)	0.14825 (13)	0.38398 (7)	0.0290 (2)
C4	0.40561 (16)	0.22918 (14)	0.46790 (7)	0.0309 (2)
C5	0.44553 (16)	0.32373 (13)	0.38070 (7)	0.0292 (2)
C6	0.29851 (16)	0.32614 (14)	0.30377 (7)	0.0307 (2)
H6	0.3287	0.3858	0.2481	0.037*
O9	0.90537 (17)	0.18878 (17)	0.13340 (7)	0.0555 (3)
H9A	0.790 (4)	0.206 (3)	0.0966 (18)	0.083*
H9B	0.975 (4)	0.119 (3)	0.1021 (18)	0.083*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O2	0.0332 (4)	0.0481 (5)	0.0381 (4)	−0.0115 (3)	−0.0090 (3)	0.0058 (3)
O4	0.0397 (5)	0.0639 (6)	0.0370 (4)	−0.0138 (4)	−0.0176 (3)	0.0143 (4)
O7	0.0378 (5)	0.0521 (5)	0.0457 (5)	−0.0136 (4)	−0.0137 (4)	0.0035 (4)
O8	0.0525 (6)	0.1010 (10)	0.0474 (6)	−0.0336 (6)	−0.0066 (4)	0.0276 (6)
N1	0.0274 (4)	0.0381 (4)	0.0251 (4)	−0.0006 (3)	−0.0067 (3)	0.0008 (3)
N3	0.0301 (4)	0.0406 (5)	0.0271 (4)	−0.0066 (3)	−0.0066 (3)	0.0064 (3)
N5	0.0308 (4)	0.0408 (5)	0.0387 (5)	−0.0065 (4)	−0.0055 (3)	0.0064 (4)
C2	0.0272 (4)	0.0313 (4)	0.0278 (4)	−0.0005 (3)	−0.0046 (3)	−0.0010 (3)
C4	0.0278 (5)	0.0353 (5)	0.0286 (4)	−0.0025 (4)	−0.0067 (3)	0.0020 (3)
C5	0.0259 (4)	0.0324 (5)	0.0285 (4)	−0.0023 (3)	−0.0040 (3)	0.0017 (3)
C6	0.0292 (5)	0.0358 (5)	0.0264 (4)	0.0003 (4)	−0.0030 (3)	0.0022 (3)
O9	0.0458 (5)	0.0762 (7)	0.0413 (5)	0.0151 (5)	−0.0218 (4)	−0.0152 (5)

Geometric parameters (Å, º) top

O2—C2	1.2234 (12)	N3—C4	1.3888 (13)
O4—C4	1.2169 (11)	N3—H3	0.8600
O7—N5	1.2268 (13)	N5—C5	1.4320 (13)
O8—N5	1.2206 (14)	C4—C5	1.4502 (14)
N1—C6	1.3345 (13)	C5—C6	1.3601 (13)
N1—C2	1.3745 (13)	C6—H6	0.9300
N1—H1	0.8600	O9—H9A	0.87 (2)
N3—C2	1.3651 (12)	O9—H9B	0.84 (3)

C6—N1—C2	122.44 (8)	N3—C2—N1	115.09 (9)
C6—N1—H1	118.8	O4—C4—N3	118.84 (9)
C2—N1—H1	118.8	O4—C4—C5	128.88 (10)
C2—N3—C4	127.78 (9)	N3—C4—C5	112.29 (8)
C2—N3—H3	116.1	C6—C5—N5	117.19 (9)
C4—N3—H3	116.1	C6—C5—C4	120.62 (9)
O8—N5—O7	122.28 (10)	N5—C5—C4	122.19 (9)
O8—N5—C5	118.20 (10)	N1—C6—C5	121.72 (9)
O7—N5—C5	119.52 (9)	N1—C6—H6	119.1
O2—C2—N3	123.33 (9)	C5—C6—H6	119.1
O2—C2—N1	121.57 (9)	H9A—O9—H9B	104 (2)

C4—N3—C2—O2	179.00 (11)	O7—N5—C5—C4	−11.85 (17)
C4—N3—C2—N1	−1.51 (16)	O4—C4—C5—C6	179.88 (12)
C6—N1—C2—O2	−177.51 (10)	N3—C4—C5—C6	0.19 (15)
C6—N1—C2—N3	2.99 (15)	O4—C4—C5—N5	−0.29 (19)
C2—N3—C4—O4	−179.72 (11)	N3—C4—C5—N5	−179.97 (10)
C2—N3—C4—C5	0.00 (16)	C2—N1—C6—C5	−2.99 (16)
O8—N5—C5—C6	−12.45 (17)	N5—C5—C6—N1	−178.58 (10)
O7—N5—C5—C6	168.00 (11)	C4—C5—C6—N1	1.27 (17)
O8—N5—C5—C4	167.71 (13)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O2ⁱ	0.86	1.99	2.8503 (13)	173
N1—H1···O9ⁱⁱ	0.86	1.88	2.6736 (12)	153
O9—H9A···O4ⁱⁱⁱ	0.87 (2)	1.92 (2)	2.7640 (13)	165 (2)
O9—H9A···O7ⁱⁱⁱ	0.87 (2)	2.41 (3)	2.9101 (13)	117 (2)
O9—H9B···O7^iv	0.84 (3)	2.29 (3)	3.0940 (15)	162 (2)

Symmetry codes: (i) −x, −y, −z+1; (ii) x−1, y, z; (iii) x, −y+1/2, z−1/2; (iv) −x+2, y−1/2, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₄H₃N₃O₄·H₂O
M_r	175.11
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	293
a, b, c (Å)	6.2799 (1), 7.8481 (2), 13.8068 (3)
β (°)	93.842 (1)
V (Å³)	678.94 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.16
Crystal size (mm)	0.44 × 0.22 × 0.20

Data collection
Diffractometer	Bruker APEXII CCD area-detector diffractometer
Absorption correction	Multi-scan (SADABS; Sheldrick, 2003)
T_min, T_max	0.890, 0.969
No. of measured, independent and observed [I > 2σ(I)] reflections	15135, 2232, 1918
R_int	0.018
(sin θ/λ)_max (Å⁻¹)	0.779

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.042, 0.131, 1.00
No. of reflections	2232
No. of parameters	115
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.35, −0.37

Computer programs: SMART (Bruker, 2005), SAINT (Bruker, 2005), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), PLATON (Spek, 2003).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N3—H3···O2ⁱ	0.86	1.99	2.8503 (13)	173.1
N1—H1···O9ⁱⁱ	0.86	1.88	2.6736 (12)	152.8
O9—H9A···O4ⁱⁱⁱ	0.87 (2)	1.92 (2)	2.7640 (13)	165 (2)
O9—H9A···O7ⁱⁱⁱ	0.87 (2)	2.41 (3)	2.9101 (13)	117 (2)
O9—H9B···O7^iv	0.84 (3)	2.29 (3)	3.0940 (15)	162 (2)

Symmetry codes: (i) −x, −y, −z+1; (ii) x−1, y, z; (iii) x, −y+1/2, z−1/2; (iv) −x+2, y−1/2, −z+1/2.

Acknowledgements

This work was supported by Fundação para a Ciência e a Tecnologia (FCT) under project POCI/FIS/58309/2004

References

Bergman, J. G., Crane, G. R., Levine, B. F. & Bethea, C. G. (1972). Appl. Phys. Lett. 20, 21–23. CrossRef CAS Web of Science Google Scholar
Bruker (2005). APEX2 and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Craven, B. M. (1967). Acta Cryst. 23, 376–383. CSD CrossRef IUCr Journals Web of Science Google Scholar
Pettier, P. R. & Byrn, S. R. (1982). J. Org. Chem. 47, 4671–4676. Google Scholar
Puccetti, G., Perigaud, A., Badan, J., Ledoux, I. & Zyss, J. (1993). J. Opt. Soc. Am. B, 10, 733–744. CrossRef CAS Google Scholar
Rao, T. S., Rando, R. F., Huffman, J. H. & Revankar, G. R. (1995). Nucleosides Nucleotides, 14, 1997–2008. CrossRef CAS Web of Science Google Scholar
Sheldrick, G. M. (2003). SADABS. University of Göttingen, Germany. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
Spek, A. L. (2003). J. Appl. Cryst. 36, 7–13. Web of Science CrossRef CAS IUCr Journals Google Scholar
Youping, H., Genbo, S., Bochang, W. & Rihong, J. (1992). J. Cryst. Growth, 119, 393–398. CrossRef Google Scholar