6-(3,5-Dimeth­oxy­benzyl­amino)-9-(oxan-2-yl)-9H-purine

Pavel Štarha; Igor Popa; Zdeněk Dvořák; Zdeněk Trávníček

doi:10.1107/S1600536813006697

. 2013 Mar 13;69(Pt 4):o533. doi: 10.1107/S1600536813006697

6-(3,5-Dimethoxybenzylamino)-9-(oxan-2-yl)-9H-purine

Pavel Štarha ^a, Igor Popa ^a, Zdeněk Dvořák ^b, Zdeněk Trávníček ^a,^*

PMCID: PMC3629587 PMID: 23634074

Abstract

The molecule of the title compound, C₁₉H₂₃N₅O₃, contains six-membered pyrimidine and five-membered imidazole rings merged into the essentially planar purine skeleton (r.m.s. deviation = 0.01 Å). In the crystal, pairs of N—H⋯N hydrogen bonds link molecules into inversion dimers. The dimers are linked via C—H⋯O hydrogen bonds, forming double-stranded chains propagating along [001]. These chains are linked via C—H⋯π and parallel slipped π–π interactions [centroid–centroid distance = 3.467 (1) Å; slippage 0.519 Å], forming a three-dimensional network.

Related literature

For the alternative synthetic procedure and biological activity of the title compound, see: Szüčová et al. (2009 ▶). For the structures of similar compounds, see: Soriano-Garcia et al. (2003 ▶); Taddei et al. (2004 ▶). For puckering parameters, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C₁₉H₂₃N₅O₃
M _r = 369.42
Triclinic,
a = 8.6978 (3) Å
b = 8.8318 (3) Å
c = 12.1517 (4) Å
α = 84.808 (3)°
β = 78.674 (3)°
γ = 82.039 (3)°
V = 904.53 (5) Å³
Z = 2
Mo Kα radiation
μ = 0.10 mm⁻¹
T = 110 K
0.40 × 0.40 × 0.35 mm

Data collection

Agilent Xcalibur Sapphire2 diffractometer
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012 ▶). T _min = 0.963, T _max = 0.968
6684 measured reflections
3177 independent reflections
2784 reflections with I > 2σ(I)
R _int = 0.010

Refinement

R[F ² > 2σ(F ²)] = 0.044
wR(F ²) = 0.116
S = 1.07
3177 reflections
246 parameters
H-atom parameters constrained
Δρ_max = 0.45 e Å⁻³
Δρ_min = −0.22 e Å⁻³

Data collection: CrysAlis PRO (Agilent, 2012 ▶); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2011 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Click here for additional data file.^{(19.3KB, cif)}

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536813006697/zq2196sup1.cif

e-69-0o533-sup1.cif^{(19.3KB, cif)}

Click here for additional data file.^{(155.8KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813006697/zq2196Isup2.hkl

e-69-0o533-Isup2.hkl^{(155.8KB, hkl)}

Click here for additional data file.^{(7.7KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536813006697/zq2196Isup3.cml

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

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

Cg is the centroid of the C10–C15 ring.

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N6—H6⋯N7ⁱ	0.88	2.38	3.155 (2)	147
C17—H17A⋯O3ⁱⁱ	0.98	2.44	3.216 (3)	136
C8—H8⋯Cg ⁱ	0.95	2.72	3.506 (2)	142
C21—H21B⋯Cg ⁱⁱⁱ	0.99	2.93	3.904 (3)	169

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

Acknowledgments

This work was supported by Palacký University (grant No. PrF_2012_009). The authors thank Mr Tomáš Šilha for performing the CHN elemental analyses.

supplementary crystallographic information

Comment

The title compound, 6-(3,5-dimethoxybenzylamino)-9-(tetrahydropyran-2-yl)-9H-purine (Fig. 1), is formed by the essentially planar purine moiety substituted by 3,5-dimethoxybenzylamine and tetrahydropyran-2-yl at the C6, and N9 position, respectively (for related structures, see: Soriano-Garcia et al., 2003; Taddei et al., 2004). The six-membered pyrimidine and five-membered imidazole rings of the purine moiety form the dihedral angle of 1.50 (6)° (Fig. 2), while the planes fitted through all the non-hydrogen atoms of purine and benzene rings form the dihedral angle of 63.87 (4)° (Fig. 3). The most deviated atoms from the planes created through the pyrimidine, imidazole, purine and benzene rings are C5 (0.006 (2) Å), C8 (-0.005 (2) Å), C5 (0.021 (2) Å), and C12 (0.011 (2) Å), respectively. The crystal structure is stabilized by the N6—H6···N7 hydrogen bonds (see Table 1 for parameters) and C—H···O, C—H···π and parallel slipped π–π interactions [centroid–centroid distance = 3.467 (1) Å; slippage 0.519 Å] (Fig. 4 and Fig. 5). The tetrahydropyranyl ring adopts a chair conformation. The Cremer-Pople puckering parameters (Cremer & Pople, 1975) are Q_T = 0.691 (2) Å, Θ₂ = 89.4 (2)°, q₂ = 0.691 (2)°, q₃ = 0.007 (2)° and φ₂ = 148.8 (2)°.

Experimental

The title compound, synthesized with the aim of its possible utilization as a suitable ligand in coordination chemistry of transition metals, was prepared by a slightly modified method reported by Szüčová et al., 2009. The starting compounds 6-chloropurine and 3,4-dihydro-2H-pyrane (a molar ratio of 1:2) were stirred in a minimum volume of ethanol (15 min, laboratory temperature) and then CF₃COOH (1.30 molar equivalent of 6-chloropurine) was slowly poured. The reaction mixture was neutralized by 10% NH₄OH after 24 h of stirring at laboratory temperature. The solvents were evaporated and yellowish product was washed (distilled water, methanol, diethyl ether) and dried in desiccator over P₄O₁₀. The obtained 6-chloro-9-(tetrahydropyran-2-yl)-9H-purine was dissolved in a minimum volume of N,N`-dimethylformamide and 3,5-dimethoxybenzylamine (1.33 molar equivalent) and triethylamine (1.67 molar equivalent) were poured in. The reaction mixture was stirred at 90 °C for 150 min and then it was evaporated to dryness. The solid was suspended in cold distilled water, filtered off, washed (distilled water, methanol, diethyl ether) and dried in desiccator over P₄O₁₀. The powder product was recrystallized from ethanol and the obtained microcrystals, suitable for single-crystal X-ray analysis, were collected by filtration. Analysis calculated for C₁₉H₂₃N₅O₃: C 61.8, H 6.3, N 19.0%; found: C 61.7, H 6.4, N 18.8%. Elemental analysis (C, H, N) was performed on a Thermo Scientific Flash 2000 CHNO-S Analyzer.