(E)-9-(But-2-en-1-yl)-6-chloro-9H-purine

Fredrik Lundvall; Jindrich Kania; Lise-Lotte Gundersen

doi:10.1107/S1600536813010416

. 2013 May 11;69(Pt 6):o849. doi: 10.1107/S1600536813010416

(E)-9-(But-2-en-1-yl)-6-chloro-9H-purine

Fredrik Lundvall ^a,^*, Jindrich Kania ^b,^*, Lise-Lotte Gundersen ^b

PMCID: PMC3684933 PMID: 23795035

Abstract

The asymmetric unit of the title compound, C₉H₉ClN₄, contains two molecules. In the crystal, the molecules are ordered in a chain-like fashion along the a axis, and form layers offset relative to the C plane by approximately 30°. This ordering does not, however, appear to be directed by classical hydrogen bonding.The allylic side chains of both independent molecules are disordered, with occupancies of 0.870 (4) and 0.934 (3) for the major components. The disorder components represent two possible spatial orientations of the atoms around the C=C double bond.

Related literature

For synthetic background and applications, see Kania & Gundersen (2013 ▶).

Experimental

Crystal data

C₉H₉ClN₄
M _r = 208.65
Triclinic,
a = 8.1818 (11) Å
b = 9.7103 (13) Å
c = 13.9435 (19) Å
α = 69.642 (1)°
β = 75.448 (1)°
γ = 67.032 (1)°
V = 947.6 (2) Å³
Z = 4
Mo Kα radiation
μ = 0.37 mm⁻¹
T = 100 K
1.13 × 0.35 × 0.22 mm

Data collection

Bruker APEXII CCD diffractometer
Absorption correction: numerical (SADABS; Bruker, 2005 ▶) T _min = 0.683, T _max = 0.924
10801 measured reflections
4428 independent reflections
4103 reflections with I > 2σ(I)
R _int = 0.017

Refinement

R[F ² > 2σ(F ²)] = 0.027
wR(F ²) = 0.070
S = 1.04
4428 reflections
283 parameters
4 restraints
H-atom parameters constrained
Δρ_max = 0.34 e Å⁻³
Δρ_min = −0.30 e Å⁻³

Data collection: APEX2 (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SIR92 (Altomare et al., 1993 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: DIAMOND (Brandenburg, 2004 ▶) and ChemBioDraw Ultra (CambridgeSoft, 2009) ▶; software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

Click here for additional data file.^{(20.9KB, cif)}

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536813010416/lr2100sup1.cif

e-69-0o849-sup1.cif^{(20.9KB, cif)}

Click here for additional data file.^{(216.9KB, hkl)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536813010416/lr2100Isup2.hkl

e-69-0o849-Isup2.hkl^{(216.9KB, hkl)}

Click here for additional data file.^{(4KB, cml)}

Supplementary material file. DOI: 10.1107/S1600536813010416/lr2100Isup3.cml

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

Acknowledgments

We acknowledge the support from the Norwegian Research Council (KOSK II, project 184929 and RENERGI, project 190980) and from the Department of Chemistry, UiO. We also acknowledge Dr David S. Wragg for invaluable assistance with the refinement.

supplementary crystallographic information

Comment

The title compound is an N-allyl substituted purine intended as a starting material for investigation of the double bond rearragement in N-allylic systems. (E)-9-(but-2-en-1-yl)-6-chloro-9H-purine was recrystallized from a mixture of E/Z-isomers in order to obtain the pure E-isomer for the following rearrangement study. The structure and purity of this compound was originally determined by NMR. Further structure elucidation by SXRD supports the conclusions in our previous report (compound 14a, Kania et al., 2013).

The structure of the title compound, C₉H₉ClN₄, has a triclinic P -1 symmetry. The asymmetric unit consists of two molecules of the title compound, with the full content of the unit cell generated by symmetry operations. The molecule has a planar bicyclic motif with an N-allylic chain oriented out of the plane described by the bicyclic main body. During the initial refinement of the structure it became apparent that the N-allylic chain is slightly disordered, with two possible spacial orientations. By using the PART instruction in SHELXL, the two possible orientations of the chain (A and B) were refined individually for the two molecules that form the asymmetric unit (residue 1 and 2). Orientation A is clearly preferred in the solid state, with the minor orientation B present in about 13% and 6.6% abundance for residue 1 and 2 respectively. The limited occupancy of the minor components prompted the use of restraints to achieve satisfactory refinement of the structure. We employed the SADI instruction in SHELXL and restrained the C10, C11B—C13B and C20, C21B—C23B bond distances in the minor components to be the same as the corresponding distances in the major components (C10, C11A—C13A and C20, C21A—C23A). This ensured realistic bond distances in the chains. Furthermore, C11B—C13B and C21B—C23B were refined isotropically since anisotropic refinement did not give realistic thermal parameters due to the low occupancy of the sites.

Experimental

The title compound was synthesized by the method described in Kania et al. (2013) (compound 14a).