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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2446.
Published online 2010 August 28. doi:  10.1107/S1600536810033301
PMCID: PMC3007855

N-(3-Methyl­phen­yl)pyrimidin-2-amine

Abstract

Two independent mol­ecules comprise the asymmetric unit in the title compound, C11H11N3. These differ in terms of the relative orientations of the aromatic rings: the first is somewhat twisted, while the second is approximately planar [dihedral angles between the pyrimidine and phenyl rings = 39.00 (8) and 4.59 (11)°]. The mol­ecules also form distinct patterns in their hydrogen bonding. The first independent mol­ecule forms centrosymmetric dimers featuring an eight-membered {HNCN}2 synthon. The second independent mol­ecule forms an N—H(...)N hydrogen bond with the other pyrimidine N atom of the first mol­ecule. Thereby, tetra­meric aggregates are formed. These associate via C—H(...)N and C—H(...)π inter­actions, consolidating the crystal packing.

Related literature

For background to the fluorescence properties of compounds related to the title compound, see: Kawai et al. (2001 [triangle]); Abdullah (2005 [triangle]). For the structures of related pyrimidine amine derivatives, see: Badaruddin et al. (2009 [triangle]); Fairuz et al. (2010 [triangle]).

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Object name is e-66-o2446-scheme1.jpg

Experimental

Crystal data

  • C11H11N3
  • M r = 185.23
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2446-efi1.jpg
  • a = 9.4461 (10) Å
  • b = 10.0946 (11) Å
  • c = 11.6266 (13) Å
  • α = 80.401 (1)°
  • β = 82.745 (2)°
  • γ = 66.005 (1)°
  • V = 996.55 (19) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 293 K
  • 0.20 × 0.20 × 0.10 mm

Data collection

  • Bruker SMART APEX diffractometer
  • 9569 measured reflections
  • 4539 independent reflections
  • 2881 reflections with I > 2σ(I)
  • R int = 0.035

Refinement

  • R[F 2 > 2σ(F 2)] = 0.051
  • wR(F 2) = 0.167
  • S = 1.02
  • 4539 reflections
  • 264 parameters
  • 2 restraints
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.24 e Å−3
  • Δρmin = −0.22 e Å−3

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 [triangle]); molecular graphics: ORTEP-3 (Farrugia, 1997 [triangle]), DIAMOND (Brandenburg, 2006 [triangle]) and Qmol (Gans & Shalloway, 2001 [triangle]); software used to prepare material for publication: publCIF (Westrip, 2010 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810033301/bt5328sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810033301/bt5328Isup2.hkl

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

Acknowledgments

Z. Abdullah thanks the Ministry of Higher Education, Malaysia, for a research grant (FS143/2008 C). The authors are also grateful to the University of Malaya for support of the crystallographic facility.

supplementary crystallographic information

Comment

The title compound, (I), was investigated as a continuation of structural studies of pyrimidine derivatives related to the title compound (Badaruddin et al., 2009; Fairuz et al., 2010). Interest in these compounds relates to the fluorescence properties of related compounds (Kawai et al. 2001; Abdullah, 2005).

Two independent molecules of comprise the asymmetric unit of (I), Figs 1 and 2. Whereas the pyrimidine and amine residues are super-imposable in the two molecules, there is a large difference in the relative orientations of the tolyl groups, Fig. 3. This is seen in the marked difference in the dihedral angles formed between the pyrimidine and benzene rings of 39.00 (8) ° for the first independent molecule and 4.59 (11) ° for the second. Hence, while the first molecule is significantly twisted about the N3–C5 bond [the C1–N3–C5–C6 torsion angle = 37.2 (3) °], the second molecule is essentially planar [r.m.s. deviation of the 14 non-hydrogen atoms = 0.046 Å; the equivalent C12–N6–C16–C17 torsion angle is 1.1 (3) °]. It is noted that each of the N2 and N4 atoms forms a significant intramolecular C–H···N contact and that the contact formed in the second independent molecule is significantly shorter, Table 1.

Over and above the conformational differences between the independent molecules, they form quite distinct patterns in their intermolecular contacts. Thus, centrosymmetrically related molecules of the first independent species associate via an eight-membered {···HNCN}2 synthon, Table 1. The pyrimdine atom not participating in this synthon accepts an N–H hydrogen bond from the second independent molecule. In this way, tetrameric supramolecular aggregates are formed, Fig. 4. Therefore, while each of the nitrogen atoms of the first independent molecule participates in intermolecular interactions, only the amine-nitrogen of the second molecule forms a significant intermolecular interaction. The tetrameric aggregates are consolidated into the three-dimensional structure by C–H···π interactions, Fig. 5 and Table 1.

Experimental

2-Chloropyrimidine (3.1701 g, 30 mmol) was mixed with 3-methylaniline (3 ml, 30 mmol) along with several drops of ethanol. The mixture was heated at 423–433 K for 5 h. The organic phase was dried over sodium sulfate; the evaporation of the solvent gave the colourless crystals.

Refinement

Carbon-bound H-atoms were placed in calculated positions (C—H 0.93 to 0.96 Å) and were included in the refinement in the riding model approximation, with Uiso(H) set to 1.2 to 1.5Uequiv(C). The N-bound H-atoms were located in a difference Fourier map and were were refined with a distance restraint of N–H = 0.86±0.01 Å, and with Uiso(H) = 1.2Ueq(N).

Figures

Fig. 1.
The molecular structure of the first independent molecule in (I) showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
Fig. 2.
The molecular structure of the second independent molecule in (I) showing the atom-labelling scheme and displacement ellipsoids at the 50% probability level.
Fig. 3.
Overlay diagram of the first independent molecule (shown in red) and the second independent molecule (shown in blue).
Fig. 4.
Supramolecular tetrameric aggregate in (I) mediated by N–H···N hydrogen bonding, shown as orange dashed lines.
Fig. 5.
Unit-cell contents for (I) shown in projection down the a axis. The N–H···N hydrogen bonding and C–H···π contacts are shown as orange and purple dashed lines, respectively.

Crystal data

C11H11N3Z = 4
Mr = 185.23F(000) = 392
Triclinic, P1Dx = 1.235 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 9.4461 (10) ÅCell parameters from 2493 reflections
b = 10.0946 (11) Åθ = 4.4–24.7°
c = 11.6266 (13) ŵ = 0.08 mm1
α = 80.401 (1)°T = 293 K
β = 82.745 (2)°Block, colourless
γ = 66.005 (1)°0.20 × 0.20 × 0.10 mm
V = 996.55 (19) Å3

Data collection

Bruker SMART APEX diffractometer2881 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.035
graphiteθmax = 27.5°, θmin = 1.8°
ω scansh = −11→12
9569 measured reflectionsk = −12→13
4539 independent reflectionsl = −15→15

Refinement

Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.051H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.167w = 1/[σ2(Fo2) + (0.0942P)2 + 0.0196P] where P = (Fo2 + 2Fc2)/3
S = 1.02(Δ/σ)max = 0.001
4539 reflectionsΔρmax = 0.24 e Å3
264 parametersΔρmin = −0.22 e Å3
2 restraintsExtinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.016 (4)

Special details

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)

xyzUiso*/Ueq
N10.78783 (16)0.67552 (15)0.14005 (12)0.0480 (4)
N20.71434 (16)0.88285 (15)−0.00792 (12)0.0511 (4)
N30.53298 (16)0.84550 (16)0.12674 (12)0.0499 (4)
H30.4675 (17)0.9178 (15)0.0846 (14)0.055 (5)*
N41.05919 (19)0.15235 (17)0.35892 (15)0.0635 (4)
N51.0388 (2)0.39503 (18)0.35802 (17)0.0721 (5)
N60.84789 (17)0.35680 (16)0.28605 (12)0.0482 (4)
H60.810 (2)0.4518 (10)0.2708 (16)0.060 (6)*
C10.68337 (19)0.79917 (17)0.08648 (13)0.0425 (4)
C20.9333 (2)0.6381 (2)0.09545 (16)0.0556 (5)
H21.00930.55420.13080.067*
C30.9782 (2)0.7156 (2)0.00069 (17)0.0624 (5)
H3A1.08110.6871−0.02850.075*
C40.8615 (2)0.8385 (2)−0.04876 (16)0.0574 (5)
H40.88720.8931−0.11420.069*
C50.46706 (18)0.78759 (16)0.22835 (14)0.0425 (4)
C60.5414 (2)0.73374 (18)0.33221 (14)0.0485 (4)
H6A0.64000.73130.33700.058*
C70.4663 (2)0.6841 (2)0.42779 (15)0.0574 (5)
H70.51580.64640.49730.069*
C80.3197 (2)0.6892 (2)0.42267 (16)0.0580 (5)
H80.27180.65440.48850.070*
C90.2421 (2)0.74531 (17)0.32074 (15)0.0494 (4)
C100.31905 (19)0.79320 (17)0.22345 (15)0.0458 (4)
H100.27000.82970.15370.055*
C110.0801 (2)0.7550 (2)0.3143 (2)0.0685 (6)
H11A0.01430.80420.37710.103*
H11B0.08180.65830.32070.103*
H11C0.04080.80860.24090.103*
C120.9877 (2)0.29674 (18)0.33629 (14)0.0464 (4)
C131.1733 (3)0.3396 (3)0.4079 (2)0.0846 (7)
H131.21230.40410.42600.102*
C141.2576 (2)0.1932 (3)0.4342 (2)0.0733 (6)
H141.35220.15720.46820.088*
C151.1951 (2)0.1040 (2)0.4078 (2)0.0715 (6)
H151.24940.00360.42450.086*
C160.75431 (19)0.29091 (18)0.25653 (14)0.0444 (4)
C170.7885 (3)0.1426 (2)0.2762 (2)0.0712 (6)
H170.87900.07830.31100.085*
C180.6869 (3)0.0911 (2)0.2434 (3)0.0877 (8)
H180.7101−0.00870.25720.105*
C190.5535 (3)0.1820 (2)0.1916 (2)0.0752 (6)
H190.48790.14380.16960.090*
C200.5161 (2)0.3304 (2)0.17184 (17)0.0576 (5)
C210.6174 (2)0.38285 (19)0.20499 (15)0.0511 (4)
H210.59300.48290.19230.061*
C220.3675 (3)0.4331 (3)0.1169 (2)0.0877 (8)
H22A0.28410.40520.15080.132*
H22B0.37930.42840.03430.132*
H22C0.34460.53120.13070.132*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
N10.0448 (8)0.0418 (8)0.0489 (8)−0.0109 (6)−0.0080 (6)0.0043 (6)
N20.0493 (9)0.0483 (8)0.0462 (8)−0.0143 (7)−0.0032 (6)0.0064 (6)
N30.0418 (8)0.0474 (8)0.0475 (8)−0.0107 (7)−0.0077 (6)0.0143 (6)
N40.0607 (10)0.0478 (9)0.0775 (11)−0.0105 (8)−0.0246 (8)−0.0092 (8)
N50.0761 (12)0.0559 (10)0.0930 (13)−0.0330 (9)−0.0399 (10)0.0119 (9)
N60.0512 (8)0.0402 (8)0.0525 (8)−0.0177 (7)−0.0127 (7)0.0020 (6)
C10.0456 (9)0.0385 (8)0.0404 (8)−0.0144 (7)−0.0086 (7)0.0015 (6)
C20.0466 (10)0.0502 (10)0.0570 (11)−0.0077 (8)−0.0090 (8)0.0016 (8)
C30.0473 (10)0.0673 (12)0.0577 (11)−0.0125 (9)0.0037 (8)−0.0002 (9)
C40.0563 (11)0.0601 (11)0.0470 (10)−0.0200 (9)0.0022 (8)0.0042 (8)
C50.0454 (9)0.0329 (8)0.0435 (8)−0.0112 (7)−0.0037 (7)0.0006 (6)
C60.0511 (10)0.0465 (9)0.0459 (9)−0.0178 (8)−0.0091 (7)0.0002 (7)
C70.0656 (12)0.0569 (11)0.0439 (9)−0.0205 (9)−0.0103 (8)0.0045 (8)
C80.0694 (13)0.0531 (11)0.0475 (10)−0.0263 (10)0.0060 (9)0.0025 (8)
C90.0498 (10)0.0371 (9)0.0579 (10)−0.0154 (8)0.0013 (8)−0.0055 (7)
C100.0477 (10)0.0379 (9)0.0472 (9)−0.0132 (7)−0.0069 (7)−0.0002 (7)
C110.0579 (12)0.0648 (13)0.0832 (14)−0.0285 (10)0.0022 (10)−0.0046 (11)
C120.0487 (10)0.0473 (10)0.0418 (8)−0.0184 (8)−0.0072 (7)0.0003 (7)
C130.0835 (16)0.0721 (15)0.1102 (19)−0.0391 (13)−0.0499 (14)0.0114 (13)
C140.0601 (13)0.0768 (15)0.0808 (14)−0.0206 (11)−0.0286 (11)−0.0028 (11)
C150.0639 (13)0.0549 (12)0.0852 (15)−0.0046 (10)−0.0276 (11)−0.0132 (10)
C160.0460 (9)0.0450 (9)0.0418 (8)−0.0181 (8)−0.0038 (7)−0.0031 (7)
C170.0688 (13)0.0477 (11)0.1000 (16)−0.0234 (10)−0.0330 (12)0.0043 (11)
C180.0877 (16)0.0487 (12)0.137 (2)−0.0316 (12)−0.0446 (15)0.0017 (13)
C190.0666 (13)0.0669 (14)0.1044 (18)−0.0318 (11)−0.0199 (12)−0.0187 (12)
C200.0494 (10)0.0616 (12)0.0615 (11)−0.0174 (9)−0.0082 (8)−0.0150 (9)
C210.0509 (10)0.0442 (9)0.0555 (10)−0.0140 (8)−0.0091 (8)−0.0072 (8)
C220.0640 (14)0.0809 (16)0.117 (2)−0.0156 (12)−0.0360 (13)−0.0204 (14)

Geometric parameters (Å, °)

N1—C21.328 (2)C8—H80.9300
N1—C11.347 (2)C9—C101.392 (2)
N2—C41.325 (2)C9—C111.504 (3)
N2—C11.3470 (19)C10—H100.9300
N3—C11.349 (2)C11—H11A0.9600
N3—C51.416 (2)C11—H11B0.9600
N3—H30.863 (9)C11—H11C0.9600
N4—C121.329 (2)C13—C141.365 (3)
N4—C151.339 (2)C13—H130.9300
N5—C131.328 (3)C14—C151.351 (3)
N5—C121.336 (2)C14—H140.9300
N6—C121.371 (2)C15—H150.9300
N6—C161.404 (2)C16—C171.381 (2)
N6—H60.872 (9)C16—C211.388 (2)
C2—C31.367 (2)C17—C181.378 (3)
C2—H20.9300C17—H170.9300
C3—C41.376 (3)C18—C191.364 (3)
C3—H3A0.9300C18—H180.9300
C4—H40.9300C19—C201.378 (3)
C5—C101.384 (2)C19—H190.9300
C5—C61.390 (2)C20—C211.385 (2)
C6—C71.376 (2)C20—C221.508 (3)
C6—H6A0.9300C21—H210.9300
C7—C81.374 (3)C22—H22A0.9600
C7—H70.9300C22—H22B0.9600
C8—C91.386 (3)C22—H22C0.9600
C2—N1—C1115.41 (14)C9—C11—H11B109.5
C4—N2—C1115.85 (14)H11A—C11—H11B109.5
C1—N3—C5128.18 (13)C9—C11—H11C109.5
C1—N3—H3116.6 (12)H11A—C11—H11C109.5
C5—N3—H3115.1 (12)H11B—C11—H11C109.5
C12—N4—C15115.44 (18)N4—C12—N5126.19 (16)
C13—N5—C12115.19 (17)N4—C12—N6119.78 (16)
C12—N6—C16130.75 (14)N5—C12—N6114.03 (15)
C12—N6—H6114.5 (13)N5—C13—C14123.7 (2)
C16—N6—H6114.7 (13)N5—C13—H13118.1
N1—C1—N2125.62 (15)C14—C13—H13118.1
N1—C1—N3119.24 (14)C15—C14—C13115.9 (2)
N2—C1—N3115.13 (14)C15—C14—H14122.0
N1—C2—C3123.91 (16)C13—C14—H14122.0
N1—C2—H2118.0N4—C15—C14123.5 (2)
C3—C2—H2118.0N4—C15—H15118.3
C2—C3—C4115.81 (17)C14—C15—H15118.3
C2—C3—H3A122.1C17—C16—C21118.40 (16)
C4—C3—H3A122.1C17—C16—N6124.64 (16)
N2—C4—C3123.38 (16)C21—C16—N6116.96 (15)
N2—C4—H4118.3C18—C17—C16119.19 (19)
C3—C4—H4118.3C18—C17—H17120.4
C10—C5—C6119.87 (15)C16—C17—H17120.4
C10—C5—N3117.36 (14)C19—C18—C17122.1 (2)
C6—C5—N3122.68 (15)C19—C18—H18119.0
C7—C6—C5118.69 (16)C17—C18—H18119.0
C7—C6—H6A120.7C18—C19—C20119.86 (19)
C5—C6—H6A120.7C18—C19—H19120.1
C8—C7—C6121.37 (17)C20—C19—H19120.1
C8—C7—H7119.3C19—C20—C21118.31 (18)
C6—C7—H7119.3C19—C20—C22120.71 (18)
C7—C8—C9120.87 (16)C21—C20—C22120.98 (18)
C7—C8—H8119.6C20—C21—C16122.16 (17)
C9—C8—H8119.6C20—C21—H21118.9
C8—C9—C10117.80 (16)C16—C21—H21118.9
C8—C9—C11121.64 (16)C20—C22—H22A109.5
C10—C9—C11120.56 (17)C20—C22—H22B109.5
C5—C10—C9121.37 (16)H22A—C22—H22B109.5
C5—C10—H10119.3C20—C22—H22C109.5
C9—C10—H10119.3H22A—C22—H22C109.5
C9—C11—H11A109.5H22B—C22—H22C109.5
C2—N1—C1—N21.8 (3)C15—N4—C12—N5−0.2 (3)
C2—N1—C1—N3−179.59 (15)C15—N4—C12—N6179.91 (17)
C4—N2—C1—N1−1.1 (3)C13—N5—C12—N4−0.6 (3)
C4—N2—C1—N3−179.76 (15)C13—N5—C12—N6179.29 (19)
C5—N3—C1—N16.3 (3)C16—N6—C12—N43.7 (3)
C5—N3—C1—N2−174.88 (16)C16—N6—C12—N5−176.17 (17)
C1—N1—C2—C3−1.0 (3)C12—N5—C13—C141.2 (4)
N1—C2—C3—C4−0.3 (3)N5—C13—C14—C15−0.9 (4)
C1—N2—C4—C3−0.4 (3)C12—N4—C15—C140.5 (3)
C2—C3—C4—N21.1 (3)C13—C14—C15—N40.0 (4)
C1—N3—C5—C10−146.27 (17)C12—N6—C16—C171.1 (3)
C1—N3—C5—C637.2 (3)C12—N6—C16—C21−179.49 (16)
C10—C5—C6—C71.3 (2)C21—C16—C17—C180.4 (3)
N3—C5—C6—C7177.79 (16)N6—C16—C17—C18179.8 (2)
C5—C6—C7—C8−1.0 (3)C16—C17—C18—C190.3 (4)
C6—C7—C8—C9−0.3 (3)C17—C18—C19—C20−0.8 (4)
C7—C8—C9—C101.4 (3)C18—C19—C20—C210.5 (3)
C7—C8—C9—C11−178.53 (18)C18—C19—C20—C22−178.7 (2)
C6—C5—C10—C9−0.2 (2)C19—C20—C21—C160.3 (3)
N3—C5—C10—C9−176.90 (15)C22—C20—C21—C16179.48 (19)
C8—C9—C10—C5−1.1 (2)C17—C16—C21—C20−0.7 (3)
C11—C9—C10—C5178.82 (16)N6—C16—C21—C20179.82 (16)

Hydrogen-bond geometry (Å, °)

Cg1 and Cg2 are the centroids of the N4,N5,C12–C15 and C5–C10 rings, respectively.
D—H···AD—HH···AD···AD—H···A
N3—H3···N2i0.86 (1)2.19 (1)3.0377 (19)170.(2)
N6—H6···N10.87 (1)2.45 (1)3.2391 (19)151.(2)
C6—H6a···N10.932.552.961 (2)107
C17—H17···N40.932.282.886 (3)123
C11—H11a···Cg1ii0.962.963.766 (2)143
C15—H15···Cg2iii0.932.823.620 (2)144

Symmetry codes: (i) −x+1, −y+2, −z; (ii) −x+1, −y+1, −z+1; (iii) x+1, y−1, z.

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: BT5328).

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