5-(6-Amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetra­hydropyrimidin-5-yl)-1,3-dimethyl-1H-chromeno[2,3-d]pyrim­idine-2,4(3H,5H)-dione 3.5-hydrate

Subhadip Roy; Subrata Das

doi:10.1107/S1600536813013986

. 2013 May 25;69(Pt 6):o974–o975. doi: 10.1107/S1600536813013986

5-(6-Amino-1,3-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-1,3-dimethyl-1H-chromeno[2,3-d]pyrimidine-2,4(3H,5H)-dione 3.5-hydrate

Subhadip Roy ^a, Subrata Das ^a,^*

PMCID: PMC3685110 PMID: 23795129

Abstract

The title compound, C₁₉H₁₉N₅O₅·3.5H₂O, crystallizes with 3.5 molecules of water in the asymmetric unit, one of which lies on a mirror plane. One of the water molecules links the molecules, forming centrosymmetric dimers. These dimers are then linked through further N—H⋯O and O—H⋯O hydrogen bonding, leading to the observed three-dimensional structure.

Related literature

Many chromene derivatives occur in natural products, see: Hatakeyama et al. (1988 ▶). For the biological activity of functionalized chromenes, see: Brooks (1998 ▶); Valenti et al. (1993 ▶); Tang et al. (2007 ▶). For the use of 6-amino-uracil derivatives as precursors in the synthesis of biologically significant fused uracils, see: Shaw (1996 ▶). The fusion of a chromene unit to the uracil ring is found to increase the biological activity, see: Sabry et al. (2011 ▶).

Experimental

Crystal data

C₁₉H₁₉N₅O₅·3.5H₂O
M _r = 460.45
Monoclinic,
a = 29.993 (4) Å
b = 7.9105 (6) Å
c = 21.458 (3) Å
β = 119.860 (16)°
V = 4415.3 (10) Å³
Z = 8
Mo Kα radiation
μ = 0.11 mm⁻¹
T = 298 K
0.32 × 0.12 × 0.06 mm

Data collection

Oxford Diffraction Xcalibur (Eos, Gemini) diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Oxford Diffraction, 2007 ▶) T _min = 0.93, T _max = 1.00
9327 measured reflections
4554 independent reflections
2538 reflections with I > 2σ(I)
R _int = 0.069

Refinement

R[F ² > 2σ(F ²)] = 0.060
wR(F ²) = 0.137
S = 0.98
4554 reflections
308 parameters
H-atom parameters constrained
Δρ_max = 0.24 e Å⁻³
Δρ_min = −0.25 e Å⁻³

Data collection: CrysAlis PRO (Oxford Diffraction, 2007 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: OLEX.SOLVE (Bourhis et al., 2013 ▶); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008 ▶); molecular graphics: OLEX2 (Dolomanov et al., 2009 ▶); software used to prepare material for publication: OLEX2.

Supplementary Material

Click here for additional data file.^{(364.8KB, cif)}

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813013986/go2089sup1.cif

e-69-0o974-sup1.cif^{(364.8KB, cif)}

Click here for additional data file.^{(249.9KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813013986/go2089Isup2.hkl

e-69-0o974-Isup2.hkl^{(249.9KB, hkl)}

Click here for additional data file.^{(5.1KB, cdx)}

Supplementary material file. DOI: 10.1107/S1600536813013986/go2089Isup3.cdx

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

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N6—H6A⋯O6W ⁱ	0.86	2.18	3.009 (3)	161
N6—H6B⋯O8W	0.86	2.09	2.905 (3)	158
O6W—H6WA⋯O1ⁱⁱ	0.85	2.01	2.830 (3)	162
O6W—H6WB⋯O7W	0.85	2.00	2.835 (3)	167
O7W—H7WA⋯O3ⁱⁱⁱ	0.84	1.94	2.781 (3)	177
O7W—H7WB⋯O2	0.85	1.93	2.773 (3)	170
O8W—H8WA⋯O9W	0.85	1.99	2.838 (4)	177
O8W—H8WB⋯O6W ^iv	0.85	2.01	2.840 (3)	164
O9W—H9W⋯O7W	0.85	1.93	2.772 (3)	170

Open in a new tab

Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) .

Acknowledgments

Financial assistance from the Department of Biotechnology (DBT), Government of India (vide sanction NO BCIL/NER-BPMC/2012.1549) is gratefully acknowledged.

supplementary crystallographic information

Comment

Functionlized chromenes are of great interest as they have shown to possess antimicrobial, antitumoral, spasmolytic, anticoagulant and antianaphylactic characteristics (Brooks, 1998; Valenti et al., 1993; Tang et al., 2007). Many chromene derivatives also occur in various natural products (Hatakeyama et al., 1988). 6-Amino-uracil derivatives belong to nitrogen-containing heterocycles of pyrimidine family and are used as key precursors for the synthesis of numerous biologically significant fused uracils (Shaw, 1996). The fusion of chromene unit to uracil ring is found to increase biological activity (Sabry et al., 2011). In this context, the synthesis and crystal structure of the title compound are reported.

The molecules are held together through a tightly woven intermolecular hydrogen bonding network, utilizing the three and a half water molecules to establish the three-dimensional structure. The two short hydrogen bonds (D···A = 2.773 (3) and 2.781 (3) Å) show D—H···A angles of 170° and 177° respectively, which are close to the ideal 180°, yield to the formation of 'dimers' (Fig. 2), which are further strongly connected to another dimer (Fig. 3), eventually leading to layers utilizing the many hydrogen bonding interactions available to the system. Finally, these layers are held together by relatively weak C—H···O and N—H···O interactions (Fig. 4 & Fig. 5) so producing a complex three-dimensional structure.

Experimental

Distilled water (30 ml) was added to 6-amino-1,3-dimethyluracil (1 mmol) in a 100 ml round-bottomed flask and the mixture was stirred at room temperature until all the 6-amino- 1,3-dimethyluracil had dissolved. Salicylaldehyde (0.5 mmol) was added drop wise to the 6- amino-1,3-dimethyluracil solution with constant stirring and then after 4 h the product appeared as brown precipitate and stirring was continued for further 3 h so that all of the reactants were converted into product. The brown precipitate was filtered and recrystallized from distilled ethanol to yield white transparent crystals suitable for single-crystal X-ray diffraction (yield 93%; m.p. 520–522 K).