2-Amino-4-meth­oxy-6-methyl­pyrimidin-1-ium picrate

Jerry P Jasinski; Ray J Butcher; H S Yathirajan; B Narayana; K Prakash Kamath

doi:10.1107/S1600536810014583

. 2010 Apr 28;66(Pt 5):o1189–o1190. doi: 10.1107/S1600536810014583

2-Amino-4-methoxy-6-methylpyrimidin-1-ium picrate

Jerry P Jasinski ^a,^*, Ray J Butcher ^b, H S Yathirajan ^c, B Narayana ^d, K Prakash Kamath ^e

PMCID: PMC2979045 PMID: 21579227

Abstract

In the title salt, C₆H₁₀N₃O⁺·C₆H₂N₃O₇ ⁻, the dihedral angle between the mean planes of the benzene and pyridine rings is 3.1 (1)°. In the cation, the methoxy group is almost coplanar with the pyridine ring [C—O—C—N = −0.6 (2)°]. The p-nitro [C—C—N—O = −1.17 (19)°] and one o-nitro [C—C—N—O = 1.83 (19)°] group in the anion are essentially coplanar with the benzene ring. The other disordered o-nitro group containing the major occupancy [0.868 (6)] O atom is twisted −29.0 (2)° from the mean plane of the benzene ring. A bifurcated N—H⋯(O.O) hydrogen bond and weak C—H⋯O intermolecular interaction between the cation and anion produce a network of infinite O—H⋯O—H⋯O—H chains along the c axis in the [101] plane which helps to establish crystal packing. Comparison to a DFT computational calculation indicates that significant conformational changes occur in the free state.

Related literature

For the synthesis of imidazo[1,2-a]pyrimidines, see: Katritzky et al. (2003 ▶). For related structures, see: Ferguson et al. (1984 ▶); Glidewell et al. (2003 ▶); Narayana et al. (2008 ▶); Scheinbeim & Schempp, (1976 ▶); Schlueter et al. (2006 ▶); Subashini et al. (2006 ▶). For density functional theory, see: Hehre et al. (1986 ▶); Schmidt & Polik (2007 ▶).

Experimental

Crystal data

C₆H₁₀N₃O⁺·C₆H₂N₃O₇ ⁻
M _r = 368.28
Monoclinic,
a = 8.9442 (3) Å
b = 6.2793 (3) Å
c = 27.0354 (8) Å
β = 94.471 (3)°
V = 1513.78 (10) Å³
Z = 4
Mo Kα radiation
μ = 0.14 mm⁻¹
T = 200 K
0.52 × 0.46 × 0.35 mm

Data collection

Oxford Diffraction Gemini diffractometer
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 ▶) T _min = 0.986, T _max = 1.000
15870 measured reflections
6133 independent reflections
3107 reflections with I > 2σ(I)
R _int = 0.031

Refinement

R[F ² > 2σ(F ²)] = 0.054
wR(F ²) = 0.160
S = 0.94
6133 reflections
256 parameters
24 restraints
H-atom parameters constrained
Δρ_max = 0.43 e Å⁻³
Δρ_min = −0.29 e Å⁻³

Data collection: CrysAlis PRO (Oxford Diffraction, 2007 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2007 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97) (Sheldrick, 2008 ▶); molecular graphics: SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 ▶).

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810014583/bt5240sup1.cif

e-66-o1189-sup1.cif^{(20.4KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810014583/bt5240Isup2.hkl

e-66-o1189-Isup2.hkl^{(300.3KB, 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
N1B—H1BA⋯O61Bⁱ	0.88	2.09	2.883 (10)	150
N1B—H1BA⋯O61Aⁱ	0.88	2.13	2.9309 (17)	151
N1B—H1BB⋯O1A	0.88	1.95	2.7223 (13)	146
N1B—H1BB⋯O21A	0.88	2.20	2.8855 (14)	134
N2B—H2BA⋯O1A	0.88	1.97	2.7380 (12)	145
N2B—H2BA⋯O62B	0.88	2.55	3.303 (10)	144
N2B—H2BA⋯O62A	0.88	2.62	3.381 (2)	145

Open in a new tab

Symmetry code: (i) Inline graphic .

Acknowledgments

KPK thanks the UGC, New Delhi, for the sanction of a Faculty Improvement Programme. RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.

supplementary crystallographic information

Comment

The synthesis of imidazo[1,2-a]pyrimidines has been widely investigated and is one of the most common strategies in the use of 2-aminopyrimidine as the starting material (Katritzky et al., 2003). Recently, the hydrogen-bonding patterns in 2-amino-4,6-dimethylpyrimidinium picrate has been reported (Subashini et al., 2006). In continuation of our work on picrates of biologically important molecules, we have prepared a new picrate of 2-amino-4-methoxy-6-methylpyrimidine, [C₆H₁₀N₃ O]⁺, [C₆H₂N₃O₇]^- and its crystal structure is reported.

The title compound,(I), C₁₂H₁₂N₆O₈, crystallizes as a salt with one C₆H₁₀N₃ O⁺, C₆H₂N₃O₇^- , cation-anion pair in the asymmetric unit (Fig. 1). The dihedral angle between the mean planes of the benzene and pyridine rings is 3.10°. In the cation the methoxy group is almost coplanar with the pyridine ring [C6B-O1B-C5B-N3B torsion angle = -0.63 (19)°]. Bond distances and angles in both the cation and anion are in normal ranges (Allen, 2002). The p [torsion angle C3A-C4A-N4A-O41A = 1.17 (18)°] and one o [torsion angle C1A-C2A-N2A-O21A = 1.83 (19)°] nitro group in the anion are nearly coplanar with the benzene ring. The other disordered o nitro group containing the predomoinate oxygen atom (occupancy = 0.868 (6)) is twisted -29.0 (2)\5 from the mean plane of the benzene ring. Bifurcated intramolecular donor, N1B, [O1A [N1B—H1BB···O21A. & N1B—H1BB···O1A] and acceptor, O1A, [N1B—H1BB···O1A & N2B—H2BA···O1A] hydrogen bonds and a weak C3B—H3BB···O62A(0.868 (6)) hydrogen bond interaction (Table 2) between the cation and anion produces a network of infinite O—H···O—H···O—H chains along the c axis in the [101] plane which helps to establish crystal packing (Fig. 2).

A density functional theory (DFT) geometry optimization molecular orbital calculation (Schmidt & Polik, 2007) was performed on the independent cation-anion pair (C₆H₁₀N₃ O⁺, C₆H₂N₃O₇^- ) within the asymmetric unit with the B3LYP 6-31-G(d) basis set (Hehre et al., 1986). Starting geometries were taken from X-ray refinement data. The dihedral angle between the mean planes of the benzene and pyridine rings increases to 28.10°. In the anion, the mean planes of the two o-nitro groups become twisted by 23.14° and 24.20°, respectively, from the mean plane of the benzene ring. The mean plane of the p-nitro group remains planar to the benzene ring. The mean plane of the methoxy group in the cation also remains planar to the pyridine ring. These observations suggest that the bifurcated N—H···(O,O) donor and acceptor hydrogen bonds and weak C—H···O intermolecular interactions play a significant role in crystal stability.

Experimental

4-Methoxy-6-methylpyrimidin-2-amine (1.39 g, 0.01 mol) was dissolved in 25 ml of ethanol. Picric acid (2.29 g, 0.01 mol) was dissolved in 15 ml of water. Both the solutions were mixed and to this, 5 ml of 5M HCl was added and stirred for few minutes. The formed complex was filtered and dried. Good quality crystals were grown from ethanol solution by slow evaporation (m. p.: 399 K). Composition: Found (Calculated): C: 39.09 (39.14); H: 3.24 (3.28); N: 22.77% (22.82%).