Pyrimidine-2,4-diamine acetone monosolvate

Sergiu Draguta; Bhupinder Sandhu; Victor N Khrustalev; Marina S Fonari; Tatiana V Timofeeva

doi:10.1107/S1600536813001025

. 2013 Jan 19;69(Pt 2):o251. doi: 10.1107/S1600536813001025

Pyrimidine-2,4-diamine acetone monosolvate

Sergiu Draguta ^a,^*, Bhupinder Sandhu ^b, Victor N Khrustalev ^c, Marina S Fonari ^d, Tatiana V Timofeeva ^b

PMCID: PMC3569783 PMID: 23424529

Abstract

In the title compound, C₄H₆N₄·C₃H₆O, the pyrimidine-2,4-diamine molecule is nearly planar (r.m.s. deviation = 0.005 Å), with the endocyclic angles covering the range 114.36 (10)–126.31 (10)°. In the crystal, N—H⋯N and N—H⋯O hydrogen bonds link the molecules into ribbons along [101], and weak C—H⋯π interactions consolidate further the crystal packing.

Related literature

For the biological activity of pyrimidine derivatives, see: Hall et al. (1993 ▶); Gengeliczki et al. (2011 ▶). For the crystal structures of related compounds, see: Bertolasi et al. (2002 ▶); Draguta et al. (2012 ▶). For bond lengths in organic compounds, see: Allen et al. (1987 ▶). For hydrogen-bonding graph-set notation, see: Bernstein et al. (1995 ▶).

Experimental

Crystal data

C₄H₆N₄·C₃H₆O
M _r = 168.21
Monoclinic,
a = 8.1594 (15) Å
b = 12.728 (2) Å
c = 8.7663 (16) Å
β = 99.395 (3)°
V = 898.2 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.09 mm⁻¹
T = 296 K
0.30 × 0.25 × 0.20 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: multi-scan (SADABS; Sheldrick, 2003 ▶) T _min = 0.974, T _max = 0.982
9693 measured reflections
2170 independent reflections
1752 reflections with I > 2σ(I)
R _int = 0.051

Refinement

R[F ² > 2σ(F ²)] = 0.048
wR(F ²) = 0.139
S = 1.07
2170 reflections
127 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.28 e Å⁻³
Δρ_min = −0.28 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2001 ▶); 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.

Supplementary Material

Click here for additional data file.^{(19.1KB, cif)}

Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S1600536813001025/cv5381sup1.cif

e-69-0o251-sup1.cif^{(19.1KB, cif)}

Click here for additional data file.^{(106.7KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813001025/cv5381Isup2.hkl

e-69-0o251-Isup2.hkl^{(106.7KB, hkl)}

Click here for additional data file.^{(3.5KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536813001025/cv5381Isup3.cml

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

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

Cg is the centroid of the pyrimidine ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2—H2A⋯N1ⁱ	0.875 (18)	2.191 (18)	3.0608 (18)	177.3 (15)
N2—H2B⋯O1	0.871 (16)	2.247 (19)	3.0990 (17)	164.7 (16)
N4—H4A⋯O1ⁱⁱ	0.879 (17)	2.170 (18)	2.9141 (16)	142.2 (15)
N4—H4B⋯N3ⁱⁱ	0.900 (18)	2.120 (19)	3.0171 (17)	174.9 (15)
C9—H9C⋯Cg ⁱⁱⁱ	0.96	2.63	3.5484 (17)	159

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

Acknowledgments

The authors are grateful for NSF support via DMR grant 0934212 (PREM) and CHE 0832622.

supplementary crystallographic information

Comment

Pyrimidine derivatives are biologically important compounds, because they occur in nature as components of nucleic acids. Pyrimidine-2,4-diamine reacts with 3,4,5-trimethoxybenzyl to form trimethoprim which acts as the nucleic acid inhibitor (Hall et al., 1993) as well as with 3,7-dimethylxanthine to form clusters which represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine (Gengeliczki et al. 2011). In the area of drug design and pharmacore mapping, there are several compounds comprising the 2,4-diaminopyrimidinium cations and β- or ζ-diketoenolate anions bound into supramolecular synthons by intermolecular hydrogen bonds (Bertolasi et al., 2002). The presented here crystal structure of the title compound, C₄H₆N₄.C₃H₆O, (I) (Figure 1) was determined to study its hydrogen bonding system and to use it in the future for the design of co-crystals with particular properties.

The asymmetric unit of I consists of a pyrimidine-2,4-diamine molecule and an acetone solvate molecule. The pyrimidine-2,4-diamine molecule is planar (r.m.s. = 0.005 Å), with the endocyclic angles covering range of 114.36 (10)–126.31 (10)°. The endocyclic angles at the C2, C4 and C6 carbon atoms adjacent to the N1 and N3 heteroatoms are larger than 120°, and those at the other atoms of the ring are smaller than 120°. The analogous distribution of the endocyclic angles was recently observed by us within the related pyridine-2,5-diamine (Draguta et al., 2012). The bond lengths have the usual values (Allen et al., 1987).

In the crystal, each pyrimidine molecule is connected to two others ones by the intermolecular N2—H2A···N1ⁱ and N4—H4B···N3ⁱⁱ hydrogen bonds (centrosymmetric R₂² (8) ring motifs (Bernstein et al., 1995); Table 1), forming the infinite ribbons toward [101] (Figure 2). The acetone molecules are bonded to the ribbons as pendant molecules via two intermolecular N2—H2B···O1 and N4—H4A···O1ⁱⁱ hydrogen bonds (Table 1, Figure 2), and are almost coplanar to the ribbon planes (the dihedral angle between the 2,4-pyrimidine and acetone molecules is 7.33 (2)°). The ribbons are packed into layers parallel to (1 0 1), with the interlayer distance of 3.8827 (16) Å). The layers are linked to each other by the intermolecular C9—H9C···π (pyrimidine ring) interactions (Table 1).

Experimental

The compound I was obtained commercially (Aldrich) as a fine-crystalline powder. Crystals suitable for the X-ray diffraction study were grown by slow evaporation from acetone solution. The crystals of I are very sensitive to air and moisture. Therefore, to keep the quality of the crystal during the experiment, the crystal of I was mounted in vaseline oil.