6-Amino-2,5-bis­(pivaloylamino)pyrimidin-4(3H)-one dihydrate

Hoong-Kun Fun; Kasthuri Balasubramani; Anita Hazra; Manas Kumar Das; Shyamaprosad Goswami

doi:10.1107/S1600536809019461

. 2009 Jun 6;65(Pt 7):o1484–o1485. doi: 10.1107/S1600536809019461

6-Amino-2,5-bis(pivaloylamino)pyrimidin-4(3H)-one dihydrate

Hoong-Kun Fun ^a,^*,^‡, Kasthuri Balasubramani ^a, Anita Hazra ^b, Manas Kumar Das ^b, Shyamaprosad Goswami ^b

PMCID: PMC2969306 PMID: 21582786

Abstract

The asymmetric unit of the title compound, C₁₄H₂₃N₅O₃·2H₂O, contains two crystallographically independent 6-amino-2,5-bis(pivaloylamino)pyrimidin-4(3H)-one molecules (A and B) with similar geometry and four water molecules. In both independent molecules, one of the amide groups is almost coplanar with the pyrimidine ring [dihedral angle of 12.85 (9) in A and 12.30 (10)° in B], whereas the other amide group is significantly twisted away from it [dihedral angle is 72.18 (7) in A and 71.29 (7)° in B]. In each independent molecule, an intramolecular N—H⋯O hydrogen bond generates an S(6) ring motif. Molecules A and B are linked into chains along the a axis by N—H⋯O and C—H⋯O hydrogen bonds. Adjacent chains are linked into a two-dimensional network parallel to the ac plane by water molecules via N—H⋯O and O—H⋯O hydrogen bonds.

Related literature

For general background on substituted pyrimidines, see: Lednicer & Mitscher (1977 ▶); Blackburn & Gait (1996 ▶); VanAllan (1976 ▶); Goswami et al. (2007 ▶); Brown (1988 ▶). For bond-length data, see: Allen et al. (1987 ▶). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 ▶). For hydrogen-bond motifs, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C₁₄H₂₃N₅O₃·2H₂O
M _r = 345.41
Triclinic,
a = 7.5560 (3) Å
b = 14.1008 (6) Å
c = 18.0713 (6) Å
α = 71.079 (2)°
β = 89.988 (2)°
γ = 86.682 (3)°
V = 1817.98 (12) Å³
Z = 4
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 100 K
0.57 × 0.19 × 0.09 mm

Data collection

Bruker SMART APEXII CCD area-detector diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2005 ▶) T _min = 0.947, T _max = 0.991
10525 measured reflections
10525 independent reflections
8199 reflections with I > 2σ(I)
R _int = 0.0000

Refinement

R[F ² > 2σ(F ²)] = 0.063
wR(F ²) = 0.162
S = 1.11
10525 reflections
447 parameters
H-atom parameters constrained
Δρ_max = 0.42 e Å⁻³
Δρ_min = −0.35 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809019461/ci2809sup1.cif

e-65-o1484-sup1.cif^{(31.4KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809019461/ci2809Isup2.hkl

e-65-o1484-Isup2.hkl^{(504.3KB, hkl)}

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
N4A—H4AA⋯O1Wⁱ	0.86	2.07	2.918 (2)	167
N4B—H4BA⋯O4Wⁱⁱ	0.86	2.08	2.920 (2)	166
N5B—H5BA⋯O4Wⁱⁱⁱ	0.86	2.32	3.160 (2)	166
N5B—H5BB⋯O1A^iv	0.86	2.09	2.861 (2)	149
O1W—H1W1⋯O2W^v	0.87	2.00	2.857 (2)	167
O1W—H2W1⋯O2W^vi	0.90	1.92	2.819 (2)	178
O2W—H2W2⋯O2B^v	0.89	1.96	2.824 (2)	162
O3W—H1W3⋯O2Aⁱⁱⁱ	0.86	1.91	2.722 (2)	158
O3W—H2W3⋯O2A^vii	0.89	1.97	2.833 (2)	162
O4W—H1W4⋯O3W^viii	0.88	1.99	2.865 (2)	174
N3A—H3AA⋯O3A	0.86	1.98	2.633 (2)	132
N5A—H5AA⋯O1W	0.86	2.32	3.163 (2)	167
N5A—H5AB⋯O1B	0.86	2.08	2.854 (2)	149
N3B—H3BA⋯O3B	0.86	1.97	2.632 (2)	132
O2W—H1W2⋯O2B	0.87	1.91	2.717 (2)	154
O4W—H2W4⋯O3W	0.88	1.93	2.811 (2)	173
C14A—H14A⋯O1B	0.96	2.53	3.355 (3)	144

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) ; (vi) ; (vii) ; (viii) .

Acknowledgments

HKF and KB thank the Malaysian Government and Universiti Sains Malaysia for the Science Fund grant No. 305/PFIZIK/613312. KB thanks Universiti Sains Malaysia for a post-doctoral research fellowship. HKF also thanks Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. SG thanks DST (SR/S1/OC-13/2005), Government of India, for financial support. AH and MD thank the CSIR, Government of India, for research fellowships.

supplementary crystallographic information

Comment

Various drugs and biologically active molecules contain substituted pyrimidines (Lednicer & Mitscher, 1977). Adenine, uracil, thyamine are pyrimidine-based bases in nucleic acids (Blackburn & Gait, 1996). 2 5,6-Triamino-3H- pyrimidin-4-one dihydrochloride (VanAllan, 1976; Goswami et al. 2007) is an important component for the synthesis of pterin molecules (Brown, 1988). The title compound was selectively synthesized by the reaction of 2,5,6-triamino-3H-pyrimidin-4-one dihydrochloride with pivalic anhydride and its crystal structure is reported here.

There are two crystallographically independent 6-amino-2,5-dipivaloyl-3H-pyrimidin-4-one molecules, A and B, and four water molecules in the asymmetric unit of the title compound (Fig 1). Molecules A and B have similar geometry. The bond lengths (Allen et al., 1987) and angles are normal. In both A and B, one of the amide groups is almost coplanar with the pyrimidine ring (dihedral angle is 12.85 (9)° in A and 12.30 (10)° in B) whereas the other is significantly twisted away from the pyrimidine ring (dihedral angle is 72.18 (7)° in A and 71.29 (07)° in B) In each independent molecule, an intramolecular N—H···O hydrogen bond generates an S(6) ring motif (Bernstein et al., 1995).

The independent molecules are linked into chains along the a axis by N—H···O and C—H···O hydrogen bonds. The adjacent chains are linked into a two-dimensional network parallel to the ac plane (Fig.2) by water molecules via N—H···O and O—H···O hydrogen bonds (Table 1).

Experimental

2,5,6-Triaminopyrimidine-4-(3H)-one dihydrochloride (200mg, 0.93mmol) was heated with pivalic anhydride (1 ml) at 393 K for 6 h in the presence of a catalytic amount of 4-dimethylaminopyridine (DMAP) (10 mol%). After the formation of a major amount of dipivaloyl product as monitored by TLC, the solid residue was washed with petroleum ether to remove the excess pivalic anhydride. The solid residue was purified through silica gel (100–200 mesh) column chromatography eluting 3% methanol in chloroform to get the pure crystalline solid. Single crystals were grown by slow evaporation of a chloroform solution (m.p. 523-525 K). IR: 3416, 3217, 2965, 2873,1645, 1568, 1488, 1438, 1240, 1176, 763 cm^-1. ¹H NMR (CDCl₃, 400 MHz): δ(p.p.m.): 11.61 (bs, 1H), 8.27 (bs, 1H), 7.64 (bs, 1H), 5.35 (bs, 2H), 1.28 (s, 9H), 1.24 (s, 9H). LC—MS: m/z (%): 310.4[(M+H)⁺,40], 292.3 (100), 186.3.