organic compounds
6-(2-Methoxybenzylamino)purine
aDepartment of Inorganic Chemistry, Faculty of Science, Palacký University, Křížkovského 10, CZ-771 47 Olomouc, Czech Republic
*Correspondence e-mail: zdenek.travnicek@upol.cz
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 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); Trávníček et al. (2006); Trávníček & Rosenker (2006). For a description of the Cambridge Structural Database, see: Allen (2002).
Experimental
Crystal data
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Refinement
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Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell CrysAlis RED (Oxford Diffraction, 2007); data reduction: CrysAlis RED; 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 and DIAMOND.
Supporting information
10.1107/S1600536808009203/bh2166sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808009203/bh2166Isup2.hkl
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.
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.
Data collection: CrysAlis CCD (Oxford Diffraction, 2007); cell
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).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) 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. | |
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. | |
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. |
C13H13N5O | Z = 2 |
Mr = 255.28 | F(000) = 268 |
Triclinic, P1 | Dx = 1.470 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 7.3518 (2) Å | Cell parameters from 4019 reflections |
b = 8.0877 (2) Å | θ = 2.8–31.9° |
c = 9.9771 (3) Å | µ = 0.10 mm−1 |
α = 78.439 (3)° | T = 120 K |
β = 85.099 (2)° | Prism, colourless |
γ = 83.803 (2)° | 0.20 × 0.20 × 0.15 mm |
V = 576.56 (3) Å3 |
Oxford Diffraction Xcalibur2 diffractometer | 2026 independent reflections |
Radiation source: Enhance (Mo) X-ray Source | 1709 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.018 |
Detector resolution: 8.3611 pixels mm-1 | θmax = 25.0°, θmin = 2.8° |
rotation method, ω scans | h = −8→6 |
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007) | k = −9→9 |
Tmin = 0.947, Tmax = 0.990 | l = −11→11 |
4904 measured reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.030 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.082 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0452P)2 + 0.0986P] where P = (Fo2 + 2Fc2)/3 |
2026 reflections | (Δ/σ)max < 0.001 |
173 parameters | Δρmax = 0.20 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C13H13N5O | γ = 83.803 (2)° |
Mr = 255.28 | V = 576.56 (3) Å3 |
Triclinic, P1 | Z = 2 |
a = 7.3518 (2) Å | Mo Kα radiation |
b = 8.0877 (2) Å | µ = 0.10 mm−1 |
c = 9.9771 (3) Å | T = 120 K |
α = 78.439 (3)° | 0.20 × 0.20 × 0.15 mm |
β = 85.099 (2)° |
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 = 0.990 | Rint = 0.018 |
4904 measured reflections |
R[F2 > 2σ(F2)] = 0.030 | 0 restraints |
wR(F2) = 0.082 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.20 e Å−3 |
2026 reflections | Δρmin = −0.20 e Å−3 |
173 parameters |
Experimental. empirical absorption correction using spherical harmonics implemented in SCALE3 ABSPACK scaling algorithm. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.27430 (12) | 0.38665 (11) | 0.87665 (9) | 0.0239 (2) | |
N1 | 0.47080 (14) | 0.91080 (13) | 0.69756 (10) | 0.0198 (3) | |
C2 | 0.61005 (17) | 1.00797 (16) | 0.68033 (13) | 0.0212 (3) | |
H2A | 0.5924 | 1.1014 | 0.7260 | 0.025* | |
N3 | 0.77035 (14) | 0.99274 (13) | 0.60829 (10) | 0.0203 (3) | |
C4 | 0.77955 (16) | 0.86036 (15) | 0.54352 (12) | 0.0179 (3) | |
C5 | 0.64716 (17) | 0.74864 (15) | 0.55142 (12) | 0.0184 (3) | |
C6 | 0.48638 (16) | 0.77580 (15) | 0.63459 (12) | 0.0178 (3) | |
N6 | 0.34980 (14) | 0.67530 (13) | 0.65272 (10) | 0.0196 (3) | |
H6A | 0.3624 | 0.5856 | 0.6142 | 0.023* | |
N7 | 0.69973 (14) | 0.63329 (14) | 0.46629 (10) | 0.0232 (3) | |
C8 | 0.85956 (18) | 0.67833 (17) | 0.41063 (13) | 0.0247 (3) | |
H8A | 0.9298 | 0.6219 | 0.3459 | 0.030* | |
N9 | 0.91613 (14) | 0.81253 (13) | 0.45352 (10) | 0.0210 (3) | |
H9C | 1.0196 | 0.8591 | 0.4284 | 0.025* | |
C9 | 0.18057 (16) | 0.70950 (16) | 0.73431 (12) | 0.0196 (3) | |
H9A | 0.0868 | 0.6409 | 0.7134 | 0.024* | |
H9B | 0.1357 | 0.8304 | 0.7060 | 0.024* | |
C10 | 0.19889 (16) | 0.67198 (15) | 0.88728 (12) | 0.0178 (3) | |
C11 | 0.24921 (16) | 0.50695 (15) | 0.95637 (12) | 0.0189 (3) | |
C12 | 0.27108 (17) | 0.47421 (17) | 1.09645 (13) | 0.0233 (3) | |
H12A | 0.3090 | 0.3628 | 1.1424 | 0.028* | |
C13 | 0.23723 (17) | 0.60508 (18) | 1.16864 (13) | 0.0252 (3) | |
H13A | 0.2540 | 0.5831 | 1.2642 | 0.030* | |
C14 | 0.17943 (17) | 0.76710 (17) | 1.10332 (13) | 0.0244 (3) | |
H14A | 0.1515 | 0.8554 | 1.1539 | 0.029* | |
C15 | 0.16273 (16) | 0.79907 (16) | 0.96262 (13) | 0.0208 (3) | |
H15A | 0.1256 | 0.9109 | 0.9171 | 0.025* | |
C16 | 0.32229 (18) | 0.21625 (16) | 0.94300 (14) | 0.0277 (3) | |
H16A | 0.3315 | 0.1419 | 0.8758 | 0.042* | |
H16B | 0.2278 | 0.1808 | 1.0154 | 0.042* | |
H16C | 0.4405 | 0.2089 | 0.9834 | 0.042* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0292 (5) | 0.0175 (5) | 0.0249 (5) | −0.0026 (4) | −0.0002 (4) | −0.0043 (4) |
N1 | 0.0205 (6) | 0.0192 (6) | 0.0199 (5) | −0.0039 (4) | −0.0013 (4) | −0.0033 (4) |
C2 | 0.0225 (7) | 0.0211 (7) | 0.0209 (7) | −0.0036 (5) | −0.0015 (5) | −0.0050 (5) |
N3 | 0.0201 (6) | 0.0212 (6) | 0.0203 (6) | −0.0046 (4) | −0.0015 (4) | −0.0046 (4) |
C4 | 0.0187 (6) | 0.0191 (6) | 0.0153 (6) | −0.0034 (5) | −0.0034 (5) | −0.0003 (5) |
C5 | 0.0225 (6) | 0.0178 (6) | 0.0149 (6) | −0.0040 (5) | −0.0034 (5) | −0.0009 (5) |
C6 | 0.0205 (6) | 0.0186 (6) | 0.0137 (6) | −0.0038 (5) | −0.0039 (5) | 0.0008 (5) |
N6 | 0.0214 (6) | 0.0198 (6) | 0.0188 (5) | −0.0079 (4) | 0.0017 (4) | −0.0046 (4) |
N7 | 0.0262 (6) | 0.0247 (6) | 0.0207 (6) | −0.0082 (5) | 0.0033 (5) | −0.0081 (5) |
C8 | 0.0270 (7) | 0.0255 (7) | 0.0239 (7) | −0.0096 (6) | 0.0044 (5) | −0.0088 (6) |
N9 | 0.0196 (6) | 0.0240 (6) | 0.0204 (6) | −0.0084 (4) | 0.0021 (4) | −0.0049 (4) |
C9 | 0.0181 (6) | 0.0192 (6) | 0.0218 (7) | −0.0042 (5) | −0.0016 (5) | −0.0031 (5) |
C10 | 0.0113 (6) | 0.0214 (6) | 0.0208 (7) | −0.0052 (5) | 0.0009 (5) | −0.0030 (5) |
C11 | 0.0137 (6) | 0.0211 (7) | 0.0225 (7) | −0.0049 (5) | 0.0027 (5) | −0.0058 (5) |
C12 | 0.0198 (7) | 0.0254 (7) | 0.0225 (7) | −0.0026 (5) | −0.0010 (5) | 0.0010 (5) |
C13 | 0.0201 (7) | 0.0373 (8) | 0.0185 (7) | −0.0057 (6) | 0.0013 (5) | −0.0057 (6) |
C14 | 0.0204 (7) | 0.0299 (7) | 0.0260 (7) | −0.0050 (5) | 0.0016 (5) | −0.0130 (6) |
C15 | 0.0156 (6) | 0.0201 (7) | 0.0267 (7) | −0.0033 (5) | 0.0002 (5) | −0.0044 (5) |
C16 | 0.0259 (7) | 0.0186 (7) | 0.0366 (8) | −0.0018 (5) | 0.0039 (6) | −0.0032 (6) |
O1—C11 | 1.3636 (15) | N9—H9C | 0.8800 |
O1—C16 | 1.4252 (15) | C9—C10 | 1.5100 (17) |
N1—C2 | 1.3359 (16) | C9—H9A | 0.9900 |
N1—C6 | 1.3549 (16) | C9—H9B | 0.9900 |
C2—N3 | 1.3342 (16) | C10—C15 | 1.3815 (17) |
C2—H2A | 0.9500 | C10—C11 | 1.4007 (17) |
N3—C4 | 1.3500 (16) | C11—C12 | 1.3893 (18) |
C4—N9 | 1.3659 (15) | C12—C13 | 1.3853 (19) |
C4—C5 | 1.3850 (17) | C12—H12A | 0.9500 |
C5—N7 | 1.3874 (16) | C13—C14 | 1.3810 (19) |
C5—C6 | 1.4083 (17) | C13—H13A | 0.9500 |
C6—N6 | 1.3371 (16) | C14—C15 | 1.3891 (19) |
N6—C9 | 1.4594 (16) | C14—H14A | 0.9500 |
N6—H6A | 0.8800 | C15—H15A | 0.9500 |
N7—C8 | 1.3121 (17) | C16—H16A | 0.9800 |
C8—N9 | 1.3594 (17) | C16—H16B | 0.9800 |
C8—H8A | 0.9500 | C16—H16C | 0.9800 |
C11—O1—C16 | 117.32 (10) | N6—C9—H9B | 108.6 |
C2—N1—C6 | 118.43 (11) | C10—C9—H9B | 108.6 |
N3—C2—N1 | 129.36 (12) | H9A—C9—H9B | 107.6 |
N3—C2—H2A | 115.3 | C15—C10—C11 | 118.51 (11) |
N1—C2—H2A | 115.3 | C15—C10—C9 | 120.72 (11) |
C2—N3—C4 | 110.81 (10) | C11—C10—C9 | 120.75 (11) |
N3—C4—N9 | 127.62 (11) | O1—C11—C12 | 124.23 (11) |
N3—C4—C5 | 126.45 (12) | O1—C11—C10 | 115.33 (11) |
N9—C4—C5 | 105.89 (11) | C12—C11—C10 | 120.43 (12) |
C4—C5—N7 | 110.49 (11) | C13—C12—C11 | 119.59 (12) |
C4—C5—C6 | 117.01 (11) | C13—C12—H12A | 120.2 |
N7—C5—C6 | 132.41 (11) | C11—C12—H12A | 120.2 |
N6—C6—N1 | 119.26 (11) | C14—C13—C12 | 120.74 (12) |
N6—C6—C5 | 122.86 (11) | C14—C13—H13A | 119.6 |
N1—C6—C5 | 117.88 (11) | C12—C13—H13A | 119.6 |
C6—N6—C9 | 122.18 (10) | C13—C14—C15 | 119.07 (12) |
C6—N6—H6A | 118.9 | C13—C14—H14A | 120.5 |
C9—N6—H6A | 118.9 | C15—C14—H14A | 120.5 |
C8—N7—C5 | 103.37 (10) | C10—C15—C14 | 121.55 (12) |
N7—C8—N9 | 114.30 (11) | C10—C15—H15A | 119.2 |
N7—C8—H8A | 122.8 | C14—C15—H15A | 119.2 |
N9—C8—H8A | 122.8 | O1—C16—H16A | 109.5 |
C8—N9—C4 | 105.94 (10) | O1—C16—H16B | 109.5 |
C8—N9—H9C | 127.0 | H16A—C16—H16B | 109.5 |
C4—N9—H9C | 127.0 | O1—C16—H16C | 109.5 |
N6—C9—C10 | 114.61 (10) | H16A—C16—H16C | 109.5 |
N6—C9—H9A | 108.6 | H16B—C16—H16C | 109.5 |
C10—C9—H9A | 108.6 |
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···N7i | 0.88 | 2.19 | 3.0379 (15) | 162 |
N9—H9C···N3ii | 0.88 | 2.02 | 2.8853 (15) | 167 |
C16—H16C···C14iii | 0.98 | 2.87 | 3.6666 (18) | 139 |
C16—H16B···C15iv | 0.98 | 2.85 | 3.6182 (18) | 136 |
C12—H12A···C6iii | 0.95 | 2.77 | 3.5119 (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. |
Experimental details
Crystal data | |
Chemical formula | C13H13N5O |
Mr | 255.28 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 120 |
a, b, c (Å) | 7.3518 (2), 8.0877 (2), 9.9771 (3) |
α, β, γ (°) | 78.439 (3), 85.099 (2), 83.803 (2) |
V (Å3) | 576.56 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.10 |
Crystal size (mm) | 0.20 × 0.20 × 0.15 |
Data collection | |
Diffractometer | Oxford Diffraction Xcalibur2 diffractometer |
Absorption correction | Multi-scan (CrysAlis RED; Oxford Diffraction, 2007) |
Tmin, Tmax | 0.947, 0.990 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 4904, 2026, 1709 |
Rint | 0.018 |
(sin θ/λ)max (Å−1) | 0.596 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.030, 0.082, 1.09 |
No. of reflections | 2026 |
No. of parameters | 173 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.20, −0.20 |
Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), CrysAlis RED (Oxford Diffraction, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008) and DIAMOND (Brandenburg, 2006).
D—H···A | D—H | H···A | D···A | D—H···A |
N6—H6A···N7i | 0.88 | 2.19 | 3.0379 (15) | 161.9 |
N9—H9C···N3ii | 0.88 | 2.02 | 2.8853 (15) | 167.2 |
C16—H16C···C14iii | 0.98 | 2.87 | 3.6666 (18) | 139 |
C16—H16B···C15iv | 0.98 | 2.85 | 3.6182 (18) | 136 |
C12—H12A···C6iii | 0.95 | 2.77 | 3.5119 (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
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
Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
Brandenburg, K. (2006). DIAMOND. Crystal Impact GbR, Bonn, Germany. Google Scholar
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. Web of Science CSD CrossRef CAS Google Scholar
Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England. Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
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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).