PMCCPMCCPMCC

Search tips
Search criteria 

Advanced

 
Logo of actaeInternational Union of Crystallographysearchopen accessarticle submissionjournal home pagethis article
 
Acta Crystallogr Sect E Struct Rep Online. 2008 May 1; 64(Pt 5): o823.
Published online 2008 April 10. doi:  10.1107/S1600536808009203
PMCID: PMC2961176

6-(2-Methoxy­benzyl­amino)purine

Abstract

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.

Related literature

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

An external file that holds a picture, illustration, etc.
Object name is e-64-0o823-scheme1.jpg

Experimental

Crystal data

  • C13H13N5O
  • M r = 255.28
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-64-0o823-efi1.jpg
  • a = 7.3518 (2) Å
  • b = 8.0877 (2) Å
  • c = 9.9771 (3) Å
  • α = 78.439 (3)°
  • β = 85.099 (2)°
  • γ = 83.803 (2)°
  • V = 576.56 (3) Å3
  • Z = 2
  • Mo Kα radiation radiation
  • μ = 0.10 mm−1
  • T = 120 (2) K
  • 0.20 × 0.20 × 0.15 mm

Data collection

  • Oxford Diffraction Xcalibur2 diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 [triangle]) T min = 0.947, T max = 0.990
  • 4904 measured reflections
  • 2026 independent reflections
  • 1709 reflections with I > 2σ(I)
  • R int = 0.018

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 0.082
  • S = 1.09
  • 2026 reflections
  • 173 parameters
  • H-atom parameters constrained
  • Δρmax = 0.20 e Å−3
  • Δρmin = −0.20 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536808009203/bh2166sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536808009203/bh2166Isup2.hkl

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

Acknowledgments

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.

supplementary crystallographic information

Comment

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).

Experimental

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

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.

Figures

Fig. 1.
The molecular structure of (I). Non-H atoms are drawn with 50% probability displacement ellipsoids.
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) ...
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 ...
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 ...

Crystal data

C13H13N5OZ = 2
Mr = 255.28F000 = 268
Triclinic, P1Dx = 1.470 Mg m3
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 mm1
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

Oxford Diffraction Xcalibur2 diffractometer2026 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

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 Å3
173 parametersΔρmin = −0.20 e Å3
Primary atom site location: structure-invariant direct methodsExtinction correction: none

Special details

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

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

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)

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, °)

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, °)

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.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BH2166).

References

  • Allen, F. H. (2002). Acta Cryst. B58, 380–388. [PubMed]
  • 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. [PubMed]
  • Trávníček, Z., Marek, J. & Popa, I. (2006). Acta Cryst. E62, o1536–o1538.
  • Trávníček, Z. & Rosenker, C. J. (2006). Acta Cryst. E62, o3393–o3395.

Articles from Acta Crystallographica Section E: Structure Reports Online are provided here courtesy of International Union of Crystallography