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ISSN: 2056-9890

N-(2-Meth­­oxy­benz­yl)-9-(oxolan-2-yl)-9H-purin-6-amine

aDepartment of Inorganic Chemistry, Faculty of Science, Palacký University, 17. listopadu 12, CZ-771 46 Olomouc, Czech Republic, and bDepartment of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
*Correspondence e-mail: zdenek.travnicek@upol.cz

(Received 19 March 2013; accepted 20 March 2013; online 23 March 2013)

The title compound, C17H19N5O2, features an almost planar purine skeleton (r.m.s. deviation = 0.009 Å) substituted by a tetra­hydro­furan ring, which adopts an envelope conformation. The purine and benzene rings subtend a dihedral angle of 66.70 (3)°. In the crystal, pairs of N—H⋯N hydrogen bonds connect adjacent mol­ecules into inversion dimers. C—H⋯N, C—H⋯O, C—H⋯π and ππ inter­actions [pyrimidine ring centroid–centroid distance = 3.3909 (1) Å] connect the dimers into a three-dimensional architecture.

Related literature

For an alternative synthetic procedure and the biological activity of benzyl-substituted 6-benzyl­amino-9-tetra­hydro­pyran-2-yl-9H-purine derivatives, see: Szüčová et al. (2009[Szüčová, L., Spíchal, L., Doležal, K., Zatloukal, M., Greplová, J., Galuszka, P., Kryštof, V., Voller, J., Popa, I., Massino, F. J., Jørgensen, J. E. & Strnad, M. (2009). Bioorg. Med. Chem. 17, 1938-1947.]). For a related structure, see: Štarha et al. (2013[Štarha, P., Popa, I., Dvořák, Z. & Trávníček, Z. (2013). Acta Cryst. E69, o533.]).

[Scheme 1]

Experimental

Crystal data
  • C17H19N5O2

  • Mr = 325.37

  • Monoclinic, P 21 /n

  • a = 8.87210 (19) Å

  • b = 8.37534 (17) Å

  • c = 20.7445 (4) Å

  • β = 90.4360 (19)°

  • V = 1541.42 (6) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 110 K

  • 0.35 × 0.30 × 0.30 mm

Data collection
  • Agilent Xcalibur Sapphire2 diffractometer

  • Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2012[Agilent (2012). CrysAlis PRO. Agilent Technologies Ltd, Yarnton, England.]) Tmin = 0.967, Tmax = 0.972

  • 12687 measured reflections

  • 2719 independent reflections

  • 2415 reflections with I > 2σ(I)

  • Rint = 0.014

Refinement
  • R[F2 > 2σ(F2)] = 0.035

  • wR(F2) = 0.087

  • S = 1.04

  • 2719 reflections

  • 218 parameters

  • H-atom parameters constrained

  • Δρmax = 0.37 e Å−3

  • Δρmin = −0.23 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

Cg is the centroid of the C10–C15 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N6—H6⋯N7i 0.88 2.32 3.145 (2) 157
C8—H8⋯Cgi 0.95 2.86 3.6214 (14) 138
C12—H12⋯O2ii 0.95 2.60 3.459 (2) 150
C13—H13⋯N3ii 0.95 2.55 3.489 (2) 170
Symmetry codes: (i) -x+1, -y+1, -z+1; (ii) [x+{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].

Data collection: CrysAlis PRO (Agilent, 2012[Agilent (2012). CrysAlis PRO. Agilent Technologies Ltd, Yarnton, England.]); cell refinement: CrysAlis PRO; data reduction: CrysAlis PRO; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2011[Brandenburg, K. (2011). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).

Supporting information


Comment top

The molecule of N-(2-methoxybenzyl)-9-(oxolan-2-yl)-9H-purin-6-amine consists of six-membered pyrimidine and five-membered imidazole rings merged to the essentially planar purine skeleton, which is substituted by 2-methoxybenzylamine and oxolan-2-yl at the C6, and N9 position, respectively (Figure 1). Two N6—H6···N7 hydrogen bonds (Table 1) connect the molecules into the centrosymmetric dimers (Figure 2) with coplanar purine moieties (dihedral angle of 0.00 (3)°). Except for the hydrogen bonds, the C—H···N, C—H···O, C—H···π and ππ interactions (Figure 2) also link the individual molecules within the crystal structure into a three-dimensional architecture. The planar pyrimidine (the most deviated atoms from the LSQ-plane fitted through its atoms: C5, 0.0122 (13) Å) and imidazole (the most deviated atom from the LSQ-plane fitted through its atoms: C8, -0.002 (2) Å) rings of the purine moiety form the dihedral angle of 0.72 (4)°. The planes fitted through the atoms of the purine and benzene rings form the dihedral angle of 66.70 (3)°.

Related literature top

For an alternative synthetic procedure and the biological activity of ring-substituted 6-benzylamino-9-tetrahydropyran-2-yl and 9-tetrahydrofuran-2-ylpurine derivatives, see: Szüčová et al. (2009). For a related structure, see: Štarha et al. (2013).

Experimental top

N-(2-methoxybenzyl)-9-(oxolan-2-yl)-9H-purin-6-amine, a perspective ligand of the transition metal complexes, was synthesized by a modification of the recently reported method (Szüčová et al., 2009). 6-Chloropurine reacted with 2,3-dihydrofurane in a molar ratio of 1:2 for 15 min at laboratory temperature in a minimum volume of ethanol, followed by the addition of CF3COOH (1.30 molar equivalent of 6-chloropurine). The mixture was stirred at laboratory temperature for 24 h and after that it was neutralized by 10% NH4OH, evaporated to dryness, washed by distilled water, methanol and diethyl ether and dried in desiccator over P4O10. The obtained intermediate, i.e. 6-chloro-9-(oxolan-2-yl)-9H-purine interacted with 2-methoxybenzylamine and triethylamine (molar ratio of 1: 1.33: 1.67, respectively) in N,N`-dimethylformamide (90 °C, 150 min). Again, the solvents were partly evaporated and the obtained product was separated by filtration after it was suspended in distilled water. The title compound was washed with distilled water, methanol and diethyl ether and dried (in a desiccator over P4O10). Single-crystals were prepared by recrystallization of the product from ethanol. Analysis calculated for C17H19N5O2: C 62.8, H 5.9, N 21.5%; found: C 62.6, H 6.1, N 21.2%. Elemental analysis (C, H, N) was performed on a Thermo Scientific Flash 2000 CHNO-S Analyzer.

Refinement top

Non-hydrogen atoms were refined anisotropically and hydrogen atoms were located in difference maps and refined using the riding model with C—H = 0.95 (CH), C—H = 0.99 (CH2), C—H = 0.98 (CH3) Å, and N—H = 0.88 Å, with Uiso(H) = 1.2Ueq(CH, CH2, NH) and 1.5Ueq(CH3). The maximum and minimum residual electron density peaks of 0.37 and -0.23 e Å-3 were located 0.81 Å, and 0.72 Å from the H18A, and C17 atoms, respectively.

Computing details top

Data collection: CrysAlis PRO (Agilent, 2012); cell refinement: CrysAlis PRO (Agilent, 2012); data reduction: CrysAlis PRO (Agilent, 2012); 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).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the non-hydrogen atoms depicted as thermal ellipsoids at the 50% probability level and given with the atom numbering scheme.
[Figure 2] Fig. 2. Part of the crystal structure, showing the N6—H6···N7 hydrogen bonds (dashed green lines; see Table 1 for parameters), C8—H8···π interactions (dashed orange lines; see Table 1 for C8—H8···Cg parameters) and ππ interactions (dashed orange lines; the CgCgi distance = 3.39090 (10) Å).
N-(2-Methoxybenzyl)-9-(oxolan-2-yl)-9H-purin-6-amine top
Crystal data top
C17H19N5O2F(000) = 688
Mr = 325.37Dx = 1.402 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 11022 reflections
a = 8.87210 (19) Åθ = 2.9–31.9°
b = 8.37534 (17) ŵ = 0.10 mm1
c = 20.7445 (4) ÅT = 110 K
β = 90.4360 (19)°Prism, colourless
V = 1541.42 (6) Å30.35 × 0.30 × 0.30 mm
Z = 4
Data collection top
Agilent Xcalibur Sapphire2
diffractometer
2719 independent reflections
Radiation source: Enhance (Mo) X-ray Source2415 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.014
Detector resolution: 8.3611 pixels mm-1θmax = 25.0°, θmin = 3.1°
ω scansh = 910
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)
k = 99
Tmin = 0.967, Tmax = 0.972l = 2324
12687 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.035Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.087H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0396P)2 + 0.7716P]
where P = (Fo2 + 2Fc2)/3
2719 reflections(Δ/σ)max = 0.001
218 parametersΔρmax = 0.37 e Å3
0 restraintsΔρmin = 0.23 e Å3
Crystal data top
C17H19N5O2V = 1541.42 (6) Å3
Mr = 325.37Z = 4
Monoclinic, P21/nMo Kα radiation
a = 8.87210 (19) ŵ = 0.10 mm1
b = 8.37534 (17) ÅT = 110 K
c = 20.7445 (4) Å0.35 × 0.30 × 0.30 mm
β = 90.4360 (19)°
Data collection top
Agilent Xcalibur Sapphire2
diffractometer
2719 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Agilent, 2012)
2415 reflections with I > 2σ(I)
Tmin = 0.967, Tmax = 0.972Rint = 0.014
12687 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0350 restraints
wR(F2) = 0.087H-atom parameters constrained
S = 1.04Δρmax = 0.37 e Å3
2719 reflectionsΔρmin = 0.23 e Å3
218 parameters
Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.08392 (13)0.72477 (14)0.53161 (5)0.0216 (3)
O10.39104 (11)1.15624 (12)0.40650 (5)0.0265 (2)
O20.14507 (12)0.19144 (12)0.72047 (5)0.0295 (3)
C20.02259 (15)0.65607 (17)0.56768 (6)0.0214 (3)
H20.11420.71420.57090.026*
N30.01895 (12)0.51849 (14)0.59968 (5)0.0208 (3)
C40.11411 (15)0.44422 (16)0.59082 (6)0.0184 (3)
C50.23360 (15)0.49756 (16)0.55428 (6)0.0188 (3)
N60.32579 (13)0.71553 (14)0.48978 (6)0.0241 (3)
H60.40780.65970.48220.029*
C60.21608 (15)0.64750 (16)0.52444 (6)0.0190 (3)
N70.35162 (13)0.38842 (14)0.55594 (6)0.0241 (3)
C80.30091 (16)0.27427 (18)0.59319 (7)0.0257 (3)
H80.35820.18180.60360.031*
N90.15811 (12)0.29976 (14)0.61589 (6)0.0216 (3)
C90.31619 (17)0.87629 (17)0.46427 (7)0.0247 (3)
H9A0.39130.94440.48670.030*
H9B0.21490.92010.47330.030*
C100.34376 (14)0.88340 (16)0.39253 (7)0.0197 (3)
C110.38461 (14)1.02956 (17)0.36481 (7)0.0203 (3)
C120.41548 (16)1.03960 (19)0.29956 (7)0.0257 (3)
H120.44601.13830.28120.031*
C130.40157 (16)0.90491 (19)0.26119 (7)0.0291 (4)
H130.42190.91190.21640.035*
C140.35861 (16)0.76098 (19)0.28742 (7)0.0270 (3)
H140.34840.66920.26080.032*
C150.33028 (15)0.75093 (17)0.35321 (7)0.0228 (3)
H150.30130.65150.37130.027*
C160.42614 (18)1.30910 (18)0.38005 (8)0.0307 (4)
H16A0.42161.39010.41410.046*
H16B0.35311.33540.34600.046*
H16C0.52781.30670.36190.046*
C170.06967 (16)0.20020 (17)0.66006 (7)0.0242 (3)
H170.03130.25060.66630.029*
C180.04761 (17)0.02969 (18)0.63684 (7)0.0278 (3)
H18A0.06220.02180.58970.033*
H18B0.05440.00980.64750.033*
C190.16852 (17)0.06373 (18)0.67324 (7)0.0275 (3)
H19A0.13730.17570.68050.033*
H19B0.26560.06250.65000.033*
C200.17883 (17)0.02796 (18)0.73579 (7)0.0292 (4)
H20A0.10550.01420.76720.035*
H20B0.28140.01900.75460.035*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0222 (6)0.0213 (6)0.0211 (6)0.0008 (5)0.0011 (5)0.0005 (5)
O10.0342 (6)0.0177 (5)0.0276 (5)0.0020 (4)0.0020 (4)0.0026 (4)
O20.0407 (6)0.0234 (6)0.0245 (5)0.0000 (5)0.0005 (5)0.0013 (4)
C20.0208 (7)0.0209 (7)0.0224 (7)0.0018 (6)0.0021 (5)0.0016 (6)
N30.0202 (6)0.0216 (6)0.0207 (6)0.0003 (5)0.0022 (5)0.0009 (5)
C40.0198 (7)0.0182 (7)0.0171 (6)0.0017 (5)0.0017 (5)0.0016 (5)
C50.0191 (7)0.0202 (7)0.0170 (7)0.0011 (5)0.0000 (5)0.0010 (5)
N60.0225 (6)0.0234 (6)0.0265 (6)0.0029 (5)0.0064 (5)0.0077 (5)
C60.0220 (7)0.0208 (7)0.0142 (6)0.0023 (6)0.0002 (5)0.0015 (5)
N70.0204 (6)0.0221 (6)0.0298 (7)0.0009 (5)0.0041 (5)0.0043 (5)
C80.0191 (7)0.0223 (8)0.0360 (8)0.0020 (6)0.0042 (6)0.0061 (6)
N90.0181 (6)0.0202 (6)0.0266 (6)0.0002 (5)0.0023 (5)0.0046 (5)
C90.0286 (8)0.0219 (8)0.0237 (7)0.0017 (6)0.0036 (6)0.0044 (6)
C100.0137 (6)0.0223 (7)0.0232 (7)0.0020 (5)0.0012 (5)0.0039 (6)
C110.0153 (6)0.0210 (7)0.0246 (7)0.0004 (5)0.0011 (5)0.0018 (6)
C120.0228 (7)0.0290 (8)0.0254 (7)0.0026 (6)0.0003 (6)0.0092 (6)
C130.0263 (8)0.0407 (9)0.0202 (7)0.0004 (7)0.0012 (6)0.0022 (7)
C140.0234 (7)0.0309 (8)0.0267 (8)0.0001 (6)0.0017 (6)0.0049 (6)
C150.0166 (7)0.0213 (7)0.0303 (8)0.0003 (5)0.0008 (6)0.0033 (6)
C160.0365 (9)0.0194 (8)0.0363 (9)0.0038 (6)0.0038 (7)0.0071 (6)
C170.0186 (7)0.0244 (8)0.0296 (8)0.0002 (6)0.0026 (6)0.0041 (6)
C180.0262 (8)0.0239 (8)0.0334 (8)0.0044 (6)0.0024 (6)0.0023 (7)
C190.0269 (8)0.0207 (8)0.0350 (8)0.0009 (6)0.0006 (6)0.0015 (6)
C200.0298 (8)0.0242 (8)0.0334 (8)0.0004 (6)0.0019 (6)0.0043 (7)
Geometric parameters (Å, º) top
N1—C21.3396 (18)C10—C151.382 (2)
N1—C61.3485 (18)C10—C111.4014 (19)
O1—C111.3698 (17)C11—C121.385 (2)
O1—C161.4282 (17)C12—C131.386 (2)
O2—C171.4179 (18)C12—H120.9500
O2—C201.4366 (18)C13—C141.377 (2)
C2—N31.3302 (18)C13—H130.9500
C2—H20.9500C14—C151.392 (2)
N3—C41.3482 (17)C14—H140.9500
C4—N91.3725 (18)C15—H150.9500
C4—C51.3821 (19)C16—H16A0.9800
C5—N71.3902 (17)C16—H16B0.9800
C5—C61.4082 (19)C16—H16C0.9800
N6—C61.3414 (17)C17—C181.519 (2)
N6—C91.4490 (18)C17—H171.0000
N6—H60.8800C18—C191.523 (2)
N7—C81.3111 (19)C18—H18A0.9900
C8—N91.3716 (18)C18—H18B0.9900
C8—H80.9500C19—C201.510 (2)
N9—C171.4701 (18)C19—H19A0.9900
C9—C101.5111 (19)C19—H19B0.9900
C9—H9A0.9900C20—H20A0.9900
C9—H9B0.9900C20—H20B0.9900
C2—N1—C6118.24 (12)C11—C12—H12120.2
C11—O1—C16117.38 (11)C14—C13—C12120.62 (13)
C17—O2—C20109.94 (11)C14—C13—H13119.7
N3—C2—N1129.52 (13)C12—C13—H13119.7
N3—C2—H2115.2C13—C14—C15119.51 (14)
N1—C2—H2115.2C13—C14—H14120.2
C2—N3—C4110.46 (11)C15—C14—H14120.2
N3—C4—N9127.00 (12)C10—C15—C14120.98 (13)
N3—C4—C5126.99 (13)C10—C15—H15119.5
N9—C4—C5106.00 (12)C14—C15—H15119.5
C4—C5—N7110.77 (12)O1—C16—H16A109.5
C4—C5—C6116.54 (12)O1—C16—H16B109.5
N7—C5—C6132.67 (12)H16A—C16—H16B109.5
C6—N6—C9123.33 (12)O1—C16—H16C109.5
C6—N6—H6118.3H16A—C16—H16C109.5
C9—N6—H6118.3H16B—C16—H16C109.5
N6—C6—N1119.37 (12)O2—C17—N9109.25 (11)
N6—C6—C5122.43 (12)O2—C17—C18106.88 (11)
N1—C6—C5118.20 (12)N9—C17—C18113.81 (12)
C8—N7—C5103.43 (11)O2—C17—H17108.9
N7—C8—N9114.26 (13)N9—C17—H17108.9
N7—C8—H8122.9C18—C17—H17108.9
N9—C8—H8122.9C17—C18—C19103.72 (12)
C8—N9—C4105.54 (11)C17—C18—H18A111.0
C8—N9—C17128.64 (12)C19—C18—H18A111.0
C4—N9—C17125.77 (11)C17—C18—H18B111.0
N6—C9—C10112.76 (12)C19—C18—H18B111.0
N6—C9—H9A109.0H18A—C18—H18B109.0
C10—C9—H9A109.0C20—C19—C18101.68 (12)
N6—C9—H9B109.0C20—C19—H19A111.4
C10—C9—H9B109.0C18—C19—H19A111.4
H9A—C9—H9B107.8C20—C19—H19B111.4
C15—C10—C11118.73 (12)C18—C19—H19B111.4
C15—C10—C9122.39 (12)H19A—C19—H19B109.3
C11—C10—C9118.88 (12)O2—C20—C19106.47 (12)
O1—C11—C12124.21 (13)O2—C20—H20A110.4
O1—C11—C10115.28 (12)C19—C20—H20A110.4
C12—C11—C10120.51 (13)O2—C20—H20B110.4
C13—C12—C11119.63 (13)C19—C20—H20B110.4
C13—C12—H12120.2H20A—C20—H20B108.6
Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C10–C15 ring.
D—H···AD—HH···AD···AD—H···A
N6—H6···N7i0.882.323.145 (2)157
C8—H8···Cgi0.952.863.6214 (14)138
C12—H12···O2ii0.952.603.459 (2)150
C13—H13···N3ii0.952.553.489 (2)170
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1/2, y+3/2, z1/2.

Experimental details

Crystal data
Chemical formulaC17H19N5O2
Mr325.37
Crystal system, space groupMonoclinic, P21/n
Temperature (K)110
a, b, c (Å)8.87210 (19), 8.37534 (17), 20.7445 (4)
β (°) 90.4360 (19)
V3)1541.42 (6)
Z4
Radiation typeMo Kα
µ (mm1)0.10
Crystal size (mm)0.35 × 0.30 × 0.30
Data collection
DiffractometerAgilent Xcalibur Sapphire2
diffractometer
Absorption correctionMulti-scan
(CrysAlis PRO; Agilent, 2012)
Tmin, Tmax0.967, 0.972
No. of measured, independent and
observed [I > 2σ(I)] reflections
12687, 2719, 2415
Rint0.014
(sin θ/λ)max1)0.595
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.035, 0.087, 1.04
No. of reflections2719
No. of parameters218
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.37, 0.23

Computer programs: CrysAlis PRO (Agilent, 2012), CrysAlis PRO (Agilent, 2012), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2011), publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top
Cg is the centroid of the C10–C15 ring.
D—H···AD—HH···AD···AD—H···A
N6—H6···N7i0.882.323.145 (2)157
C8—H8···Cgi0.952.863.6214 (14)138
C12—H12···O2ii0.952.603.459 (2)150
C13—H13···N3ii0.952.553.489 (2)170
Symmetry codes: (i) x+1, y+1, z+1; (ii) x+1/2, y+3/2, z1/2.
 

Acknowledgements

This work was supported by Palacký University (grant No. PrF_2013_015). The authors wish to thank Mr Tomáš Šilha for performing the CHN elemental analysis.

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