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Acta Crystallogr Sect E Struct Rep Online. 2009 February 1; 65(Pt 2): o291–o292.
Published online 2009 January 14. doi:  10.1107/S1600536809000543
PMCID: PMC2968345

(E)-2-[(2-Hydr­oxy-5-nitro­phen­yl)iminiometh­yl]-4-nitro­phenolate

Abstract

The title mol­ecule, C13H9N3O6, consists of a 2-hydr­oxy-5-nitro­phenyl­iminio group and a 4-nitro­phenolate group bonded to a methyl­ene C atom with both of the planar six-membered rings nearly in the plane of the mol­ecule [dihedral angle = 1.3 (4)°]. Each of the nitro O atoms is twisted slightly out of the plane of the mol­ecule. The amine group forms an intra­molecular hydrogen bond with both nearby O atoms, each of which has partial occupancy of attached H atoms [0.36 (3) and 0.64 (3)]. An extended π-delocalization throughout the entire mol­ecule exists producing a zwitterionic effect in this region of the mol­ecule. The shortened phenolate C—O bond [1.2749 (19)°], in concert with the slightly longer phenol C—O bond [1.3316 (19) Å], provides evidence for this effect. The crystal packing is influenced by extensive strong inter­molecular O—H(...)O hydrogen bonding between the depicted phenolate and hydr­oxy O atoms and their respective H atoms within the π-delocalized region of the mol­ecule. As a result, mol­ecules are linked into an infinite polymeric chain diagonally along the [110] plane of the unit cell in an alternate inverted pattern. A MOPAC AM1 calculation provides support for these observations.

Related literature

For related structures, see: Butcher et al. (2007 [triangle]); Ersanlı et al. (2003 [triangle]); Gül et al. (2007 [triangle]); Hijji et al. (2008 [triangle]); Odabaşoğlu et al. (2006 [triangle]); Jasinski et al. (2007 [triangle]). For related literature, see: Schmidt & Polik (2007 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-0o291-scheme1.jpg

Experimental

Crystal data

  • C13H9N3O6
  • M r = 303.23
  • Monoclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-0o291-efi1.jpg
  • a = 7.9649 (1) Å
  • b = 8.6110 (1) Å
  • c = 19.1190 (3) Å
  • β = 98.433 (2)°
  • V = 1297.11 (3) Å3
  • Z = 4
  • Mo Kα radiation
  • μ = 0.13 mm−1
  • T = 296 (2) K
  • 0.37 × 0.27 × 0.18 mm

Data collection

  • Oxford Diffraction Gemini R diffractometer
  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007 [triangle]) T min = 0.954, T max = 0.978
  • 6432 measured reflections
  • 2495 independent reflections
  • 1819 reflections with I > 2σ(I)
  • R int = 0.023

Refinement

  • R[F 2 > 2σ(F 2)] = 0.041
  • wR(F 2) = 0.129
  • S = 1.05
  • 2495 reflections
  • 202 parameters
  • H-atom parameters constrained
  • Δρmax = 0.22 e Å−3
  • Δρmin = −0.17 e Å−3

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

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809000543/hg2463sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809000543/hg2463Isup2.hkl

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

Acknowledgments

Support to YMH and BB was provided by DOE-CETBR grant No. DE—FG02–03ER63580 and NSF-RISE Award No. HRD-0627276. RJB acknowledges the NSF MRI program (grant No. CHE-0619278) for funds to purchase an X-ray diffractometer.

supplementary crystallographic information

Comment

Schiff bases have a wide range of application in chemistry. The title compound, a Schiff base derivative, was synthesized under microwave conditions and recrystallized from ethanol to give brown crystals. The structural data shows that it exists as an iminio-phenolate zwitterion in the solid state. Typically, keto-amine tautomer behavior has been observed in related derivative compounds (Butcher et al. (2007); Jasinski et al. (2007); Gül et al. (2007); Odabaşoğlu et al. (2006)); Ersanlı et al. (2003)). Compounds of this type can be used as anion sensors in acetonitrile (Hijji et al. (2008)) that tend to exist in the keto-amine form, which is generally favored over the phenol-imine form in the solid state. Introduction of electron deficient groups to the aromatic rings tends to increase the acidity of the phenolic proton.

The title molecule, C13H9N3O6, consists of a 2-hydroxy-5-nitrophenyliminio group and a 4-nitrophenolate group bonded to a methylene carbon atom with both of the planar six-membered rings nearly in the plane of the molecule. The dihedral angle between the mean planes of the phenyl and phenolate rings measures 1.3 (4)°. Each of the nitro oxygen atoms are twisted slightly out of the plane of the molecule [torsion angles = 172.16 (17)° (O3—N2—C4—C5); -7.1 (2)° (O4—N2—C4—C5); -7.6 (3)° (O3—N2—C4—C3); 173.17 (15)° (O4—N2—C4—C3); and 178.63 (16)° (O6—N3—C12—C13); -3.4 (3)° (O5—N3—C12—C13); 174.28 (18)° (O5—N3—C12—C11); -3.7 (3)° (O6—N3—C12—C11)]. The phenolate (O1) and hydroxy (O2) oxygen atoms are essentially in the plane of the molecule [torsion angles = 179.03 (16)° (O1—C1—C6—C5); 0.5 (3)° (O1—C1—C6—C7); 179.31 (18)° (O2—C9—C10—C11); -177.90 (15)° (C13—C8—C9—O2)]. The imino group forms an intramolecular hydrogen bond with each of the nearby oxygen atoms (O1 and O2) which have partial occupancy of hydrogen atoms (H1O [0.36 (3)] and H2O [0.64 (3)], respectively) (see Fig. 1 which shows only the predominant component, H2O, and Table 2). There appears to be an extended π delocalization effect throughout the entire molecule producing a zwitterionic effect in this region of the molecule. The shortened C1—O1 bond (1.2749 (19) Å in concert with the slightly longer C9—O2 bond (1.3316 (19) Å) provide structural evidence for this effect.

Crystal packing is influenced by extensive strong intermolecular O—H···O hydrogen bonding between the depicted phenolate and hydroxy oxygen atoms (O1 & O2) and their respective hydrogen atoms within the π delocalized region (O1—H1O(0.36)···O2; 2.5570 (16) Å) and O2—H2O(0.64)···O1; 2.5570 (16) Å) of the molecule. Additional weak intermolecular C—H···O hydrogen bond interactions occur involving the methylene carbon (C7) and the phenyl (C10 & C13) and phenolate (C3) groups (Fig. 2), respectively. All of the hydrogen bond interactions are summarized in Table 1. As a result the molecules are linked into an infinite polymeric chain diagonally along the [110] plane of the unit cell in an alternate inverted pattern (Fig. 2). In addition, weak Cg1–Cg1 (3.517 (2) Å; slippage = 1.09 (8)°; -x, 1 - y, -z) and Cg1–Cg2 (3.830 (6) Å; x, y - 1, z) π-π stacking ring interactions also occur where Cg1 = center of gravity of the C1–C6 ring and Cg2 = center of gravity of the C8–C13 ring.

After a MOPAC AMI calculation [Austin Model 1 approximation together with the Hartree-Fock closed-shell (restricted) wavefunction was used and minimizations were terminated at an r.m.s. gradient of less than 0.01 kJ mol-1 Å-1] of the zwitterionic form with WebMO Pro (Schmidt, 2007). As a result of this energy minimization, the dihedral angle between the phenyl and phenolate rings changes from 1.3 (4)° in the crystal structure to 7.6 (6)°, producing a slightly more twisted molecule than the nearly planar molecule in the crystalline environment. Thus, it is apparent that the extensive hydrogen bonding and π-π stacking intermolecular interactions significantly influence crystal packing with this molecule.

Experimental

The title compound was synthesized as follows: 2-amino-4-nitrophenol (0.15 g, 1 mmol) and 2-hydroxy-5-nitrobenzaldehyde (0.17 g, 1 mmol) were mixed in a loosely capped vial. The reaction mixture was allowed to heat at full power in a conventional microwave for 8 minutes. The compound was recrystallized from ethanol affording a brown solid (0.20 g, 68%). (mp 591–593 K) 1H-NMR (400 MHz, DMSO-d6), δ (p.p.m.): 14.64 (s, br, 1H), 11.74 (s, br, 1H) 9.37 (s, 1H), 8.72 (d, J = 2.87 Hz, 1 H), 8.41 (d, J = 3.3 Hz, 1H), 8..27 (dd, J = 9.2, 3.1 Hz, 1H), 8.13 (1H, dd, J = 9.06, 2.7 Hz, 1 H), 7.16 (d, J = 9.1 Hz, 1H), 7.09 (d, J = 9.2 Hz, 1H), 13C-NMR (100 MHz, DMSO-d6) δ (p.p.m.): 167.90, 162.13, 157.48, 139.89, 138.76, 133.40, 128.95, 128.69, 124.51, 118.78, 118.25, 116.54, 115.24.

Refinement

H1A, H1O and H2O were obtained from a difference Fourier map. The occupancies of H1O and H2O refined to values of 0.36 (3) and 0.64 (3), respectively. The rest of the H atoms were placed in their calculated positions and then refined using the riding model with C(N,O)—H = 0.82 to 0.93 Å, and with Uiso(H) = 1.15–1.20Ueq(C,N).

Figures

Fig. 1.
The molecular structure of C13H9N3O6, showing the atom numbering scheme and 50% probability displacement ellipsoids. H1O (0.36 (3) occupancy) has been omitted from O1 in the diagram and only the predominant component, H2O (0.64 (3) occupancy), ...
Fig. 2.
The molecular packing for C13H9N3O6 viewed down the c axis. Dashed lines indicate intermolecular O–H···O, C–H···O and intramolecular N–H···O hydrogen bonds. ...

Crystal data

C13H9N3O6F(000) = 624
Mr = 303.23Dx = 1.553 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 3209 reflections
a = 7.9649 (1) Åθ = 3.9–73.2°
b = 8.6110 (1) ŵ = 0.13 mm1
c = 19.1190 (3) ÅT = 296 K
β = 98.433 (2)°Prism, orange-brown
V = 1297.11 (3) Å30.37 × 0.27 × 0.18 mm
Z = 4

Data collection

Oxford Diffraction Gemini R diffractometer2495 independent reflections
Radiation source: fine-focus sealed tube1819 reflections with I > 2σ(I)
graphiteRint = 0.023
Detector resolution: 10.5081 pixels mm-1θmax = 26.2°, θmin = 2.6°
[var phi] and ω scansh = −9→9
Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2007)k = −8→10
Tmin = 0.954, Tmax = 0.978l = −23→23
6432 measured reflections

Refinement

Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.041Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.129H-atom parameters constrained
S = 1.05w = 1/[σ2(Fo2) + (0.0833P)2] where P = (Fo2 + 2Fc2)/3
2495 reflections(Δ/σ)max < 0.001
202 parametersΔρmax = 0.22 e Å3
0 restraintsΔρmin = −0.17 e Å3

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*/UeqOcc. (<1)
O10.03590 (18)0.47993 (15)0.16546 (7)0.0582 (4)
H1O0.00380.54170.19340.070*0.36 (3)
O20.11482 (19)0.12327 (15)0.24445 (7)0.0600 (4)
H2O0.08210.07520.27690.072*0.64 (3)
O30.1437 (2)0.91245 (18)−0.08314 (9)0.0810 (5)
O40.32836 (18)0.73565 (16)−0.09586 (7)0.0624 (4)
O50.57970 (19)−0.17153 (18)0.04796 (7)0.0688 (4)
O60.5900 (2)−0.35343 (18)0.12493 (8)0.0745 (5)
N10.22628 (18)0.25045 (16)0.13638 (7)0.0452 (4)
H1N0.15890.29150.16240.054*
N20.2182 (2)0.79148 (18)−0.06471 (8)0.0518 (4)
N30.54401 (19)−0.22526 (18)0.10334 (8)0.0515 (4)
C10.0787 (2)0.5537 (2)0.11302 (9)0.0448 (4)
C20.0151 (2)0.7055 (2)0.09352 (10)0.0496 (4)
H2A−0.05870.75350.12020.060*
C30.0605 (2)0.7798 (2)0.03718 (9)0.0480 (4)
H3A0.01730.87820.02530.058*
C40.1732 (2)0.70949 (19)−0.00398 (9)0.0440 (4)
C50.2393 (2)0.56601 (19)0.01239 (9)0.0432 (4)
H5A0.31390.5216−0.01500.052*
C60.1948 (2)0.48596 (18)0.07028 (8)0.0413 (4)
C70.2629 (2)0.3352 (2)0.08516 (9)0.0451 (4)
H7A0.33760.29560.05650.054*
C80.2832 (2)0.09769 (19)0.15516 (8)0.0423 (4)
C90.2213 (2)0.0350 (2)0.21425 (8)0.0468 (4)
C100.2737 (3)−0.1128 (2)0.23769 (9)0.0552 (5)
H10A0.2348−0.15510.27710.066*
C110.3830 (2)−0.1967 (2)0.20269 (9)0.0521 (5)
H11A0.4196−0.29470.21870.062*
C120.4378 (2)−0.1335 (2)0.14340 (8)0.0443 (4)
C130.3896 (2)0.01318 (19)0.11899 (8)0.0434 (4)
H13A0.42810.05390.07920.052*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0756 (9)0.0495 (7)0.0590 (8)0.0052 (7)0.0411 (7)0.0022 (6)
O20.0794 (9)0.0546 (8)0.0554 (8)0.0097 (7)0.0411 (7)0.0059 (6)
O30.1039 (12)0.0618 (9)0.0839 (11)0.0172 (9)0.0357 (9)0.0286 (8)
O40.0727 (9)0.0637 (8)0.0571 (8)−0.0062 (7)0.0302 (7)0.0013 (7)
O50.0802 (10)0.0740 (10)0.0606 (8)0.0124 (8)0.0375 (7)−0.0015 (7)
O60.0804 (10)0.0618 (9)0.0859 (11)0.0272 (8)0.0270 (8)0.0051 (8)
N10.0526 (8)0.0419 (7)0.0464 (8)0.0009 (6)0.0247 (6)−0.0008 (6)
N20.0598 (9)0.0486 (9)0.0496 (8)−0.0094 (7)0.0163 (7)−0.0001 (7)
N30.0475 (8)0.0537 (9)0.0547 (9)0.0054 (7)0.0127 (7)−0.0049 (7)
C10.0481 (9)0.0434 (9)0.0467 (9)−0.0053 (8)0.0193 (7)−0.0017 (7)
C20.0519 (10)0.0444 (9)0.0572 (10)0.0024 (8)0.0233 (8)−0.0053 (8)
C30.0513 (10)0.0380 (9)0.0566 (10)0.0011 (7)0.0146 (8)−0.0003 (8)
C40.0470 (9)0.0397 (9)0.0469 (9)−0.0046 (7)0.0121 (7)−0.0017 (7)
C50.0442 (9)0.0413 (9)0.0473 (9)−0.0035 (7)0.0171 (7)−0.0056 (7)
C60.0436 (9)0.0372 (8)0.0459 (9)−0.0030 (7)0.0159 (7)−0.0041 (7)
C70.0480 (9)0.0462 (9)0.0459 (9)−0.0011 (8)0.0228 (7)−0.0025 (7)
C80.0490 (9)0.0393 (8)0.0407 (8)−0.0009 (7)0.0139 (7)0.0008 (7)
C90.0552 (10)0.0489 (10)0.0405 (8)0.0009 (8)0.0207 (8)−0.0001 (7)
C100.0739 (13)0.0542 (10)0.0420 (9)0.0033 (9)0.0237 (9)0.0097 (8)
C110.0639 (12)0.0459 (9)0.0483 (9)0.0081 (8)0.0145 (8)0.0081 (8)
C120.0437 (9)0.0476 (9)0.0437 (8)0.0022 (7)0.0127 (7)−0.0030 (7)
C130.0475 (9)0.0447 (9)0.0411 (8)−0.0049 (7)0.0167 (7)0.0017 (7)

Geometric parameters (Å, °)

O1—C11.2749 (19)C3—C41.414 (2)
O1—H1O0.8200C3—H3A0.9300
O2—C91.3316 (19)C4—C51.361 (2)
O2—H2O0.8200C5—C61.393 (2)
O3—N21.225 (2)C5—H5A0.9300
O4—N21.2283 (19)C6—C71.420 (2)
O5—N31.2264 (19)C7—H7A0.9300
O6—N31.216 (2)C8—C131.378 (2)
N1—C71.288 (2)C8—C91.405 (2)
N1—C81.420 (2)C9—C101.393 (3)
N1—H1N0.8600C10—C111.378 (2)
N2—C41.448 (2)C10—H10A0.9300
N3—C121.455 (2)C11—C121.384 (2)
C1—C21.431 (2)C11—H11A0.9300
C1—C61.444 (2)C12—C131.381 (2)
C2—C31.347 (2)C13—H13A0.9300
C2—H2A0.9300
C1—O1—H1O109.5C6—C5—H5A120.1
C9—O2—H2O109.5C5—C6—C7118.51 (14)
C7—N1—C8128.10 (14)C5—C6—C1120.56 (15)
C7—N1—H1N116.0C7—C6—C1120.92 (14)
C8—N1—H1N116.0N1—C7—C6123.19 (15)
O3—N2—O4122.95 (15)N1—C7—H7A118.4
O3—N2—C4118.60 (15)C6—C7—H7A118.4
O4—N2—C4118.45 (15)C13—C8—C9121.00 (15)
O6—N3—O5122.63 (16)C13—C8—N1124.02 (14)
O6—N3—C12118.91 (15)C9—C8—N1114.98 (14)
O5—N3—C12118.43 (15)O2—C9—C10124.19 (15)
O1—C1—C2122.32 (15)O2—C9—C8116.76 (15)
O1—C1—C6120.74 (15)C10—C9—C8119.05 (15)
C2—C1—C6116.94 (14)C11—C10—C9120.25 (15)
C3—C2—C1121.08 (15)C11—C10—H10A119.9
C3—C2—H2A119.5C9—C10—H10A119.9
C1—C2—H2A119.5C10—C11—C12119.28 (16)
C2—C3—C4120.53 (16)C10—C11—H11A120.4
C2—C3—H3A119.7C12—C11—H11A120.4
C4—C3—H3A119.7C13—C12—C11122.07 (16)
C5—C4—C3121.09 (15)C13—C12—N3118.20 (14)
C5—C4—N2119.60 (14)C11—C12—N3119.68 (16)
C3—C4—N2119.31 (15)C8—C13—C12118.30 (14)
C4—C5—C6119.79 (15)C8—C13—H13A120.8
C4—C5—H5A120.1C12—C13—H13A120.8
O1—C1—C2—C3−178.96 (18)C7—N1—C8—C13−0.8 (3)
C6—C1—C2—C30.9 (3)C7—N1—C8—C9179.85 (17)
C1—C2—C3—C4−0.3 (3)C13—C8—C9—O2−177.90 (15)
C2—C3—C4—C5−0.4 (3)N1—C8—C9—O21.5 (2)
C2—C3—C4—N2179.32 (16)C13—C8—C9—C102.3 (3)
O3—N2—C4—C5172.16 (17)N1—C8—C9—C10−178.38 (16)
O4—N2—C4—C5−7.1 (2)O2—C9—C10—C11179.31 (18)
O3—N2—C4—C3−7.6 (3)C8—C9—C10—C11−0.9 (3)
O4—N2—C4—C3173.17 (15)C9—C10—C11—C12−1.0 (3)
C3—C4—C5—C60.5 (3)C10—C11—C12—C131.6 (3)
N2—C4—C5—C6−179.26 (15)C10—C11—C12—N3−175.91 (16)
C4—C5—C6—C7178.68 (15)O6—N3—C12—C13178.63 (16)
C4—C5—C6—C10.2 (3)O5—N3—C12—C13−3.4 (3)
O1—C1—C6—C5179.03 (16)O6—N3—C12—C11−3.7 (3)
C2—C1—C6—C5−0.8 (2)O5—N3—C12—C11174.28 (18)
O1—C1—C6—C70.5 (3)C9—C8—C13—C12−1.7 (2)
C2—C1—C6—C7−179.29 (16)N1—C8—C13—C12179.01 (16)
C8—N1—C7—C6178.42 (16)C11—C12—C13—C8−0.3 (3)
C5—C6—C7—N1−178.28 (16)N3—C12—C13—C8177.31 (15)
C1—C6—C7—N10.2 (3)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1O···O2i0.821.772.5570 (16)161
O2—H2O···O1ii0.821.752.5570 (16)166
N1—H1N···O10.861.902.6001 (19)138
C3—H3A···O3iii0.932.563.295 (2)137
C7—H7A···O4iv0.932.673.289 (2)125
C7—H7A···O5v0.932.443.312 (2)156
C10—H10A···O4vi0.932.533.321 (2)143
C13—H13A···O4iv0.932.643.195 (2)119
C13—H13A···O5v0.932.633.512 (2)160

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: HG2463).

References

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