supplementary materials


HTML versionpdf versioncif file3d viewstructure factorssupplementary materialsCIF check reportsimilar papers Open access

bh2166 scheme

Acta Cryst. (2008). E64, o823    [ doi:10.1107/S1600536808009203 ]

6-(2-Methoxybenzylamino)purine

Z. Trávnícek, M. Matiková-Malarová and J. Mikulík

Abstract top

The title compound, C13H13N5O, consists of discrete molecules connected by N-H...N hydrogen bonds to form infinite chains, with N...N separations of 3.0379 (15) and 2.8853 (15) Å. The benzene and purine ring systems make a dihedral angle of 77.58 (3)°. The crystal structure is further stabilized by intramolecular N...O interactions [2.9541 (12) Å] and intermolecular C-H...C and C...C contacts [3.304 (2), 3.368 (2), 3.667 (2), 3.618 (2) and 3.512 (2) Å] which arrange the molecules into graphite-like layers. The interlayer separations are 3.248 and 3.256 Å.

Comment top

The structure of the title molecule, (I), extends our crystallographic knowledge regarding aromatic cytokinins and cyclin dependent kinase inhibitors derived from 6-benzylaminopurine.

The molecular structure of (I) is shown in Fig. 1. The molecule contains three different aromatic rings: benzene (A), pyrimidine (B) and imidazole (C). Each ring is essentially planar with the maximum deviations from the least-squares planes being 0.0169 (12) Å for C11 (ring A), 0.0147 (12) Å for C6 (ring B), and 0.0054 (13) Å for C8 (ring C). The dihedral angle between benzene ring (A) and purine skeleton (rings B and C) is 77.58 (3)°, whilst the pyrimidine (B) and imidazole (C) rings are almost coplanar, making a dihedral angle of 3.84 (4)° (Brandenburg, 2006). The interatomic parameters of (I) are comparable to those found for compounds bearing an electroneutral N9—H 6-benzylaminopurine moiety, e.g. 6-(2-chlorobenzylamino)purine dihydrate (Maloň et al., 2001), 6-(2-bromobenzylamino)purine (Trávníček & Rosenker, 2006) and 6-(2-chloro-4-fluorobenzylamino)purine (Trávníček et al., 2006). To date, 59 structures of compounds involving the 6-benzylaminopurine skeleton have been deposited in the CSD (Cambridge Structural Database, Version 5.29; Allen, 2002).

The secondary structure of (I) is stabilized by intermolecular hydrogen bonds of the N—H···N type (Table 1, Fig. 2), which connect the molecules into infinite one-dimensional chains. Moreover, intramolecular N···O interactions [N6···O1 = 2.9541 (12) Å, Fig. 2], and non-bonding intermolecular interactions of the type C···C [C2···C5iii = 3.304 (2) Å, C2···C6iii = 3.368 (2) Å] and C—H···C [C16···C14iv = 3.667 (2), C16···C15v = 3.618 (2), and C12···C6iv = 3.512 (2) Å; symmetry codes: (iii) 1 - x, 2 - y, 1-z; (iv) 1 - x, 1 - y, 2-z; (v) -x, 1 - y, 2 - z] also contribute to the stabilization of the crystal structure (Fig. 3). The later non-bonding interactions arrange the molecules into graphite-like layers (Fig. 4). The separations between two layers formed by purine moieties are not equal, with the shortest distances being 3.248 and 3.256 Å. For comparison, the corresponding layer-to-layer separation has been found to be 3.352 Å (Space group P63/mmc, ICSD No. 52230), and 3.395 Å (Space group P63mc, ICSD No. 31170) in the crystal structure of graphite, as deposited in the ICSD (The Inorganic Crystal Structure Database, Version 1.4.2, 2007–2 and calculated using DIAMOND (Brandenburg, 2006).

Related literature top

For related structures of 6-benzylaminopurine derivatives, see: Maloň et al. (2001); Trávníček et al. (2006); Trávníček & Rosenker (2006). For a description of the Cambridge Structural Database, see: Allen (2002).

Experimental top

The title compound, was synthesized by a recently described method (Trávníček & Rosenker, 2006). The obtained microcrystalline product was recrystallized from hot N,N-dimethylformamide. Well shaped colourless single crystals, suitable for X-ray structural analysis, were formed after slow evaporation of the solvent over a period of few days. The crystals were filtered off, washed with EtOH and Et2O and dried in air.

Refinement top

All H atoms were located in difference maps and refined using a riding model, with C—H distances fixed to 0.95 (CH) or 0.98 (CH3) Å, N—H distances to 0.88 Å, and with Uiso(H) values of 1.2Ueq(CH, N) or 1.5Ueq(CH3). The highest unassigned difference Fourier peak, 0.198 e.Å-3, is located at 0.24 Å from atom H16A.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell refinement: CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED (Oxford Diffraction, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2006); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and DIAMOND (Brandenburg, 2006).

Figures top
[Figure 1] Fig. 1. The molecular structure of (I). Non-H atoms are drawn with 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. Part of the crystal structure of (I), showing the formation of infinite chains, N—H···N hydrogen bonds [N6···N7i = 3.0379 (15) Å, N9···N3ii = 2.8853 (15) Å] and O···N non-bonding contacts [N6···O1 = 2.9541 (12) Å] (dashed lines). Symmetry codes: (i) 1 - x, 1 - y, -z + 1; (ii) 2 - x, 2 - y, -z + 1.
[Figure 3] Fig. 3. Part of the crystal structure of (I), showing the C···C and C—H···C interactions (dashed lines) connecting molecules among layers. H-atoms not involved into hydrogen bonding have been omitted for clarity. Symmetry codes: (iii) 1 - x, 2 - y, 1 - z; (iv) 1 - x, 1 - y, 2 - z; (v) -x, 1 - y, 2 - z.
[Figure 4] Fig. 4. Part of the crystal structure of (I), showing the formation of graphite-like layers. Dashed lines represent the shortest distances between two neighbouring layers formed by purine moieties (d1 = 3.256, d2 = 3.248 Å). H-atoms have been omitted for clarity.
6-(2-Methoxybenzylamino)purine top
Crystal data top
C13H13N5OZ = 2
Mr = 255.28F000 = 268
Triclinic, P1Dx = 1.470 Mg m−3
Hall symbol: -P 1Mo Kα radiation
λ = 0.71073 Å
a = 7.3518 (2) ÅCell parameters from 4019 reflections
b = 8.0877 (2) Åθ = 2.8–31.9º
c = 9.9771 (3) ŵ = 0.10 mm−1
α = 78.439 (3)ºT = 120 (2) K
β = 85.099 (2)ºPrism, colourless
γ = 83.803 (2)º0.20 × 0.20 × 0.15 mm
V = 576.56 (3) Å3
Data collection top
Oxford Diffraction Xcalibur2
diffractometer		2026 independent reflections
Radiation source: Enhance (Mo) X-ray Source1709 reflections with I > 2σ(I)
Monochromator: graphiteRint = 0.018
Detector resolution: 8.3611 pixels mm-1θmax = 25.0º
T = 120(2) Kθmin = 2.8º
rotation method, ω scansh = −8→6
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2007)		k = −9→9
Tmin = 0.947, Tmax = 0.990l = −11→11
4904 measured reflections
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H-atom parameters constrained
wR(F2) = 0.082  w = 1/[σ2(Fo2) + (0.0452P)2 + 0.0986P]
where P = (Fo2 + 2Fc2)/3
S = 1.09(Δ/σ)max < 0.001
2026 reflectionsΔρmax = 0.20 e Å−3
173 parametersΔρmin = −0.20 e Å−3
Primary atom site location: structure-invariant direct methodsExtinction correction: none
Crystal data top
C13H13N5Oγ = 83.803 (2)º
Mr = 255.28V = 576.56 (3) Å3
Triclinic, P1Z = 2
a = 7.3518 (2) ÅMo Kα
b = 8.0877 (2) ŵ = 0.10 mm−1
c = 9.9771 (3) ÅT = 120 (2) K
α = 78.439 (3)º0.20 × 0.20 × 0.15 mm
β = 85.099 (2)º
Data collection top
Oxford Diffraction Xcalibur2
diffractometer		2026 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2007)		1709 reflections with I > 2σ(I)
Tmin = 0.947, Tmax = 0.990Rint = 0.018
4904 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.030173 parameters
wR(F2) = 0.082H-atom parameters constrained
S = 1.09Δρmax = 0.20 e Å−3
2026 reflectionsΔρmin = −0.20 e Å−3
Special details top

Experimental. empirical absorption correction using spherical harmonics implemented in SCALE3 ABSPACK scaling algorithm.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.27430 (12)0.38665 (11)0.87665 (9)0.0239 (2)
N10.47080 (14)0.91080 (13)0.69756 (10)0.0198 (3)
C20.61005 (17)1.00797 (16)0.68033 (13)0.0212 (3)
H2A0.59241.10140.72600.025*
N30.77035 (14)0.99274 (13)0.60829 (10)0.0203 (3)
C40.77955 (16)0.86036 (15)0.54352 (12)0.0179 (3)
C50.64716 (17)0.74864 (15)0.55142 (12)0.0184 (3)
C60.48638 (16)0.77580 (15)0.63459 (12)0.0178 (3)
N60.34980 (14)0.67530 (13)0.65272 (10)0.0196 (3)
H6A0.36240.58560.61420.023*
N70.69973 (14)0.63329 (14)0.46629 (10)0.0232 (3)
C80.85956 (18)0.67833 (17)0.41063 (13)0.0247 (3)
H8A0.92980.62190.34590.030*
N90.91613 (14)0.81253 (13)0.45352 (10)0.0210 (3)
H9C1.01960.85910.42840.025*
C90.18057 (16)0.70950 (16)0.73431 (12)0.0196 (3)
H9A0.08680.64090.71340.024*
H9B0.13570.83040.70600.024*
C100.19889 (16)0.67198 (15)0.88728 (12)0.0178 (3)
C110.24921 (16)0.50695 (15)0.95637 (12)0.0189 (3)
C120.27108 (17)0.47421 (17)1.09645 (13)0.0233 (3)
H12A0.30900.36281.14240.028*
C130.23723 (17)0.60508 (18)1.16864 (13)0.0252 (3)
H13A0.25400.58311.26420.030*
C140.17943 (17)0.76710 (17)1.10332 (13)0.0244 (3)
H14A0.15150.85541.15390.029*
C150.16273 (16)0.79907 (16)0.96262 (13)0.0208 (3)
H15A0.12560.91090.91710.025*
C160.32229 (18)0.21625 (16)0.94300 (14)0.0277 (3)
H16A0.33150.14190.87580.042*
H16B0.22780.18081.01540.042*
H16C0.44050.20890.98340.042*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0292 (5)0.0175 (5)0.0249 (5)−0.0026 (4)−0.0002 (4)−0.0043 (4)
N10.0205 (6)0.0192 (6)0.0199 (5)−0.0039 (4)−0.0013 (4)−0.0033 (4)
C20.0225 (7)0.0211 (7)0.0209 (7)−0.0036 (5)−0.0015 (5)−0.0050 (5)
N30.0201 (6)0.0212 (6)0.0203 (6)−0.0046 (4)−0.0015 (4)−0.0046 (4)
C40.0187 (6)0.0191 (6)0.0153 (6)−0.0034 (5)−0.0034 (5)−0.0003 (5)
C50.0225 (6)0.0178 (6)0.0149 (6)−0.0040 (5)−0.0034 (5)−0.0009 (5)
C60.0205 (6)0.0186 (6)0.0137 (6)−0.0038 (5)−0.0039 (5)0.0008 (5)
N60.0214 (6)0.0198 (6)0.0188 (5)−0.0079 (4)0.0017 (4)−0.0046 (4)
N70.0262 (6)0.0247 (6)0.0207 (6)−0.0082 (5)0.0033 (5)−0.0081 (5)
C80.0270 (7)0.0255 (7)0.0239 (7)−0.0096 (6)0.0044 (5)−0.0088 (6)
N90.0196 (6)0.0240 (6)0.0204 (6)−0.0084 (4)0.0021 (4)−0.0049 (4)
C90.0181 (6)0.0192 (6)0.0218 (7)−0.0042 (5)−0.0016 (5)−0.0031 (5)
C100.0113 (6)0.0214 (6)0.0208 (7)−0.0052 (5)0.0009 (5)−0.0030 (5)
C110.0137 (6)0.0211 (7)0.0225 (7)−0.0049 (5)0.0027 (5)−0.0058 (5)
C120.0198 (7)0.0254 (7)0.0225 (7)−0.0026 (5)−0.0010 (5)0.0010 (5)
C130.0201 (7)0.0373 (8)0.0185 (7)−0.0057 (6)0.0013 (5)−0.0057 (6)
C140.0204 (7)0.0299 (7)0.0260 (7)−0.0050 (5)0.0016 (5)−0.0130 (6)
C150.0156 (6)0.0201 (7)0.0267 (7)−0.0033 (5)0.0002 (5)−0.0044 (5)
C160.0259 (7)0.0186 (7)0.0366 (8)−0.0018 (5)0.0039 (6)−0.0032 (6)
Geometric parameters (Å, °) top
O1—C111.3636 (15)N9—H9C0.8800
O1—C161.4252 (15)C9—C101.5100 (17)
N1—C21.3359 (16)C9—H9A0.9900
N1—C61.3549 (16)C9—H9B0.9900
C2—N31.3342 (16)C10—C151.3815 (17)
C2—H2A0.9500C10—C111.4007 (17)
N3—C41.3500 (16)C11—C121.3893 (18)
C4—N91.3659 (15)C12—C131.3853 (19)
C4—C51.3850 (17)C12—H12A0.9500
C5—N71.3874 (16)C13—C141.3810 (19)
C5—C61.4083 (17)C13—H13A0.9500
C6—N61.3371 (16)C14—C151.3891 (19)
N6—C91.4594 (16)C14—H14A0.9500
N6—H6A0.8800C15—H15A0.9500
N7—C81.3121 (17)C16—H16A0.9800
C8—N91.3594 (17)C16—H16B0.9800
C8—H8A0.9500C16—H16C0.9800
C11—O1—C16117.32 (10)N6—C9—H9B108.6
C2—N1—C6118.43 (11)C10—C9—H9B108.6
N3—C2—N1129.36 (12)H9A—C9—H9B107.6
N3—C2—H2A115.3C15—C10—C11118.51 (11)
N1—C2—H2A115.3C15—C10—C9120.72 (11)
C2—N3—C4110.81 (10)C11—C10—C9120.75 (11)
N3—C4—N9127.62 (11)O1—C11—C12124.23 (11)
N3—C4—C5126.45 (12)O1—C11—C10115.33 (11)
N9—C4—C5105.89 (11)C12—C11—C10120.43 (12)
C4—C5—N7110.49 (11)C13—C12—C11119.59 (12)
C4—C5—C6117.01 (11)C13—C12—H12A120.2
N7—C5—C6132.41 (11)C11—C12—H12A120.2
N6—C6—N1119.26 (11)C14—C13—C12120.74 (12)
N6—C6—C5122.86 (11)C14—C13—H13A119.6
N1—C6—C5117.88 (11)C12—C13—H13A119.6
C6—N6—C9122.18 (10)C13—C14—C15119.07 (12)
C6—N6—H6A118.9C13—C14—H14A120.5
C9—N6—H6A118.9C15—C14—H14A120.5
C8—N7—C5103.37 (10)C10—C15—C14121.55 (12)
N7—C8—N9114.30 (11)C10—C15—H15A119.2
N7—C8—H8A122.8C14—C15—H15A119.2
N9—C8—H8A122.8O1—C16—H16A109.5
C8—N9—C4105.94 (10)O1—C16—H16B109.5
C8—N9—H9C127.0H16A—C16—H16B109.5
C4—N9—H9C127.0O1—C16—H16C109.5
N6—C9—C10114.61 (10)H16A—C16—H16C109.5
N6—C9—H9A108.6H16B—C16—H16C109.5
C10—C9—H9A108.6
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···N7i0.882.193.0379 (15)162
N9—H9C···N3ii0.882.022.8853 (15)167
C16—H16C···C14iii0.982.873.6666 (18)139
C16—H16B···C15iv0.982.853.6182 (18)136
C12—H12A···C6iii0.952.773.5119 (17)136
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+2, −y+2, −z+1; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+2.
Table 1
Hydrogen-bond geometry (Å, °) top
D—H···AD—HH···AD···AD—H···A
N6—H6A···N7i0.882.193.0379 (15)162
N9—H9C···N3ii0.882.022.8853 (15)167
C16—H16C···C14iii0.982.873.6666 (18)139
C16—H16B···C15iv0.982.853.6182 (18)136
C12—H12A···C6iii0.952.773.5119 (17)136
Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x+2, −y+2, −z+1; (iii) −x+1, −y+1, −z+2; (iv) −x, −y+1, −z+2.
Acknowledgements top

The financial support of this work by the Ministry of Education, Youth and Sports of the Czech Republic (MSM6198959218) and the Grant Agency of the Czech Republic (GAČR 203/08/P436) is gratefully acknowledged.

references
References top

Allen, F. H. (2002). Acta Cryst. B58, 380–388.

Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany.

Maloň, M., Trávníček, Z., Maryško, M., Zbořil, R., Mašláň, M., Marek, J., Doležal, K., Rolčík, J., Kryštof, V. & Strnad, M. (2001). Inorg. Chim. Acta, 323, 119–129.

Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.

Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.

Trávníček, Z., Marek, J. & Popa, I. (2006). Acta Cryst. E62, o1536–o1538.

Trávníček, Z. & Rosenker, C. J. (2006). Acta Cryst. E62, o3393–o3395.