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Acta Crystallogr Sect E Struct Rep Online. 2010 September 1; 66(Pt 9): o2418–o2419.
Published online 2010 August 28. doi:  10.1107/S1600536810033805
PMCID: PMC3007870

2-Hy­droxy-7-meth­oxy-9H-carbazole-3-carbaldehyde

Abstract

The title compound, C14H11NO3, was isolated from the roots of Clausena wallichii. The carbazole ring system is approx­imately planar (r.m.s. deviation = 0.039 Å) and the dihedral angle between the two benzene rings is 4.63 (7)°. An intra­molecular O—H(...)O hydrogen bond generates an S(6) ring motif. In the crystal, mol­ecules are linked into a zigzag network extending parallel to the ac plane by O—H(...)N and N—H(...)O hydrogen bonds.

Related literature

For compounds isolated from plants of genera Rutaceae and their pharmacological activity, see: Ito et al. (1997 [triangle]); Kongkathip & Kongkathip (2009 [triangle]); Laphookhieo et al. (2009 [triangle]); Li et al. (1991 [triangle]); Maneerat & Laphookhieo (2010 [triangle]); Maneerat et al. (2010 [triangle]); Sripisut & Laphookhieo (2010 [triangle]); Tangyuenyongwatthana et al. (1992 [triangle]); Yenjai et al. 2000 [triangle]). For a related structure, see: Fun et al. (2009 [triangle]). For bond-length data, see: Allen et al. (1987 [triangle]). For hydrogen-bond motifs, see: Bernstein et al. (1995 [triangle]). For the stability of the temperature controller used in the data collection, see Cosier & Glazer, (1986 [triangle]).

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Object name is e-66-o2418-scheme1.jpg

Experimental

Crystal data

  • C14H11NO3
  • M r = 241.24
  • Orthorhombic, An external file that holds a picture, illustration, etc.
Object name is e-66-o2418-efi1.jpg
  • a = 12.4352 (4) Å
  • b = 17.6564 (5) Å
  • c = 5.0839 (1) Å
  • V = 1116.23 (5) Å3
  • Z = 4
  • Cu Kα radiation
  • μ = 0.84 mm−1
  • T = 100 K
  • 0.23 × 0.19 × 0.10 mm

Data collection

  • Bruker APEXII DUO CCD area-detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2009 [triangle]) T min = 0.831, T max = 0.918
  • 25207 measured reflections
  • 2026 independent reflections
  • 2018 reflections with I > 2σ(I)
  • R int = 0.027

Refinement

  • R[F 2 > 2σ(F 2)] = 0.030
  • wR(F 2) = 0.097
  • S = 1.31
  • 2026 reflections
  • 170 parameters
  • 1 restraint
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.64 e Å−3
  • Δρmin = −0.63 e Å−3
  • Absolute structure: Flack (1983 [triangle]), 851 Friedel pairs
  • Flack parameter: 0.17 (19)

Data collection: APEX2 (Bruker, 2009 [triangle]); cell refinement: SAINT (Bruker, 2009 [triangle]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 [triangle]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009 [triangle]).

Table 1
Hydrogen-bond geometry (Å, °)

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536810033805/ci5167sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810033805/ci5167Isup2.hkl

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

Acknowledgments

SL and WM are grateful to the Thailand Research Fund through the Royal Golden Jubilee PhD Program (grant No. PHD/0006/2552) and Mae Fah Luang University for financial support. SC thanks Prince of Songkla University for generous support through the Crystal Materials Research Unit. The authors also thank Universiti Sains Malaysia for the Research University Grant (No. 1001/PFIZIK/811160).

supplementary crystallographic information

Comment

Rutaceae plants are known to be rich sources of coumarins and carbazole alkaloids. Many of them have been isolated from several genera of Rutaceae especially from Clausena genus (Laphookhieo et al., 2009; Maneerat et al., 2010; Sripisut & Laphookhieo 2010; Kongkathip & Kongkathip 2009; Ito et al., 1997; Li et al., 1991; Tangyuenyongwatthana et al., 1992) and some of these compounds show interesting pharmacological activities (Maneerat & Laphookhieo 2010; Yenjai et al. 2000). Although Clausena wallichii is one of the Rutaceae plants, however phytochemical reports on the chemical constituents from this plant are rare. As part of our continuing study of chemical constituents and bioactive compounds from Thai medicinal plants, we report herein the crystal structure of the title compound, which was isolated from the roots of C. wallichii collected from Phrae province in the northern region of Thailand.

The non-hydrogen atoms of the title molecule (Fig. 1) are almost coplanar. The carbazole ring system (C1-C12/N1) is planar with an r.m.s. deviation of 0.039 Å [maximum deviation 0.072 (1) Å for atom C7]. The pyrrole ring makes dihedral angle of 1.66 (7) and 3.12 (8)°, respectively, with the C1–C4/C10–C11 and C5–C9/C12 benzene rings. The dihedral angle between the two benzene rings being 4.63 (7)°. The cabaldehyde and methoxy substituents at atoms C3 and C7, respectively, are coplanar with the benzene ring, as indicated by torsion angles C2–C3–C13–O2 = 0.0 (2)° and C14–O3–C7–C8 = 4.0 (2)°. An intramolecular O1—H1O1···O2 hydrogen bond (Table 1) generates an S(6) ring motif (Fig. 1 and Table 1) (Bernstein et al., 1995). The bond distances are within normal ranges (Allen et al., 1987) and comparable to a related structure (Fun et al., 2009).

The crystal packing of the title compound is stabilized by intermolecular O—H···N and N—H···O hydrogen bonds (Table 1) which link the molecules into a zigzag network extending parallel to the ac plane.

Experimental

The roots of C. wallichii (1.02 Kg) were successively extracted with CH2Cl2 over the period of 3 days each at room temperature to provide the crude CH2Cl2 extract which subjected to quick column chromatography (QCC) over silica gel eluted with a gradient of hexane-EtOAc (100% hexane to 100% EtOAc) to provide nine fractions (A-I). Fraction G (3.12 g) was further separated by QCC with a gradient of 10% EtOAc-hexane to 100% EtOAc to give seven subfractions (G1-G7). Subfraction G4 (118.9 mg) was subjected to repeated column chromatography using 30% EtOAc-hexane to yield the yellow solid of the title compound (12.8 mg). Yellow plate-shaped single crystals of the title compound suitable for X-ray structure determination were recrystallized from CH2Cl2/acetone (1:1 v/v) by the slow evaporation of the solvent at room temperature after several days; m.p. 496.7-498.8 K (decomposition).

Refinement

Atom H1N1 was located in a difference map and refined isotropically. The remaining H atoms were placed in calculated positions with O–H = 0.81, C–H = 0.93 for aromatic and CH, and 0.96 Å for CH3 atoms. The Uiso values were constrained to be 1.5Ueq of the carrier atom for methyl H atoms and 1.2Ueq for the remaining H atoms. A rotating group model was used for the methyl groups. The highest residual electron density peak is located at 1.81 Å from C9 and the deepest hole is located at 1.29 Å from C3. 851 Friedel pairs were used to determine the absolute structure.

Figures

Fig. 1.
The molecular structure of the title compound, showing 50% probability displacement ellipsoids and the atom-numbering scheme. The O—H···O hydrogen bond is shown as a dashed line.
Fig. 2.
Part of the crystal packing of the title compound, viewed along the c axis. Hydrogen bonds are shown as dashed lines.

Crystal data

C14H11NO3Dx = 1.435 Mg m3
Mr = 241.24Melting point = 496.7–498.8 K
Orthorhombic, Pna21Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2c -2nCell parameters from 2026 reflections
a = 12.4352 (4) Åθ = 4.4–69.9°
b = 17.6564 (5) ŵ = 0.84 mm1
c = 5.0839 (1) ÅT = 100 K
V = 1116.23 (5) Å3Plate, yellow
Z = 40.23 × 0.19 × 0.10 mm
F(000) = 504

Data collection

Bruker APEXII DUO CCD area-detector diffractometer2026 independent reflections
Radiation source: sealed tube2018 reflections with I > 2σ(I)
graphiteRint = 0.027
[var phi] and ω scansθmax = 69.9°, θmin = 4.4°
Absorption correction: multi-scan (SADABS; Bruker, 2009)h = −14→14
Tmin = 0.831, Tmax = 0.918k = −21→21
25207 measured reflectionsl = −5→6

Refinement

Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.030w = 1/[σ2(Fo2) + (0.0656P)2 + 0.054P] where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.097(Δ/σ)max = 0.001
S = 1.31Δρmax = 0.64 e Å3
2026 reflectionsΔρmin = −0.63 e Å3
170 parametersExtinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
1 restraintExtinction coefficient: 0.053 (3)
Primary atom site location: structure-invariant direct methodsAbsolute structure: Flack (1983), 851 Friedel pairs
Secondary atom site location: difference Fourier mapFlack parameter: 0.17 (19)

Special details

Experimental. The crystal was placed in the cold stream of an Oxford Cryosystems Cobra open-flow nitrogen cryostat (Cosier & Glazer, 1986) operating at 100.0 (1) K.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
O10.59667 (8)0.17861 (6)0.4400 (2)0.0264 (3)
H1O10.65370.17960.51490.056 (7)*
O20.72058 (8)0.20104 (6)0.8557 (3)0.0294 (3)
O30.12071 (9)0.59553 (6)0.5822 (3)0.0325 (3)
N10.32559 (9)0.37021 (7)0.3111 (3)0.0203 (3)
H1N10.2898 (14)0.3514 (10)0.185 (5)0.029 (5)*
C10.46098 (10)0.26763 (8)0.3568 (3)0.0213 (3)
H1A0.43660.23910.21500.026*
C20.54764 (10)0.24453 (8)0.5070 (3)0.0212 (3)
C30.58509 (11)0.28796 (8)0.7249 (3)0.0220 (3)
C40.53291 (10)0.35607 (8)0.7921 (3)0.0208 (3)
H4A0.55690.38470.93390.025*
C50.36091 (11)0.50464 (7)0.8333 (3)0.0226 (3)
H5A0.40920.51170.97080.027*
C60.27613 (11)0.55440 (8)0.7967 (3)0.0241 (3)
H6A0.26800.59550.90940.029*
C70.20217 (11)0.54348 (8)0.5906 (3)0.0238 (3)
C80.21259 (10)0.48413 (7)0.4134 (3)0.0222 (4)
H8A0.16440.47740.27560.027*
C90.29943 (10)0.43496 (7)0.4528 (3)0.0195 (3)
C100.41167 (10)0.33567 (7)0.4277 (3)0.0196 (3)
C110.44591 (10)0.37986 (8)0.6456 (3)0.0194 (3)
C120.37263 (11)0.44372 (8)0.6603 (3)0.0203 (3)
C130.67188 (10)0.26163 (8)0.8877 (3)0.0244 (3)
H13A0.69300.29231.02730.029*
C140.03861 (12)0.58496 (9)0.3899 (4)0.0354 (4)
H14A−0.01790.62110.41840.053*
H14B0.01010.53460.40430.053*
H14C0.06840.59210.21740.053*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0261 (5)0.0281 (5)0.0251 (6)0.0080 (4)−0.0009 (4)−0.0024 (5)
O20.0282 (5)0.0358 (6)0.0241 (7)0.0098 (4)−0.0016 (4)0.0011 (5)
O30.0345 (6)0.0291 (6)0.0340 (7)0.0104 (4)−0.0052 (5)−0.0053 (5)
N10.0207 (6)0.0215 (6)0.0187 (6)0.0000 (4)−0.0025 (5)−0.0007 (5)
C10.0224 (6)0.0225 (7)0.0188 (8)−0.0013 (5)0.0010 (6)−0.0003 (5)
C20.0202 (6)0.0226 (6)0.0209 (8)0.0007 (5)0.0047 (5)0.0017 (6)
C30.0206 (7)0.0242 (7)0.0212 (8)−0.0011 (5)0.0019 (6)0.0032 (6)
C40.0207 (6)0.0234 (7)0.0183 (8)−0.0035 (5)0.0000 (5)0.0005 (6)
C50.0257 (7)0.0221 (7)0.0199 (7)−0.0044 (5)−0.0007 (6)0.0000 (6)
C60.0303 (7)0.0204 (6)0.0217 (8)−0.0017 (5)0.0022 (6)−0.0028 (6)
C70.0258 (7)0.0210 (7)0.0246 (8)0.0016 (5)0.0025 (6)0.0029 (6)
C80.0226 (7)0.0224 (7)0.0216 (9)−0.0004 (5)−0.0014 (5)0.0023 (6)
C90.0201 (6)0.0195 (6)0.0191 (8)−0.0028 (5)0.0020 (5)0.0005 (6)
C100.0179 (6)0.0217 (7)0.0193 (8)−0.0026 (4)0.0014 (5)0.0020 (6)
C110.0211 (6)0.0191 (6)0.0180 (8)−0.0036 (5)0.0023 (5)0.0016 (5)
C120.0214 (7)0.0188 (6)0.0206 (8)−0.0030 (5)0.0015 (5)0.0031 (6)
C130.0238 (6)0.0297 (7)0.0198 (9)−0.0003 (5)−0.0001 (6)0.0025 (6)
C140.0353 (8)0.0360 (9)0.0348 (11)0.0131 (6)−0.0077 (7)−0.0022 (8)

Geometric parameters (Å, °)

O1—C21.3574 (17)C5—C61.3850 (19)
O1—H1O10.81C5—C121.397 (2)
O2—C131.2401 (17)C5—H5A0.93
O3—C71.3685 (16)C6—C71.407 (2)
O3—C141.426 (2)C6—H6A0.93
N1—C101.3671 (18)C7—C81.388 (2)
N1—C91.3899 (18)C8—C91.4000 (17)
N1—H1N10.85 (2)C8—H8A0.93
C1—C21.382 (2)C9—C121.402 (2)
C1—C101.3960 (18)C10—C111.420 (2)
C1—H1A0.93C11—C121.4517 (18)
C2—C31.425 (2)C13—H13A0.93
C3—C41.4086 (19)C14—H14A0.96
C3—C131.438 (2)C14—H14B0.96
C4—C111.379 (2)C14—H14C0.96
C4—H4A0.93
C2—O1—H1O1104.9C8—C7—C6121.71 (13)
C7—O3—C14117.62 (13)C7—C8—C9116.58 (13)
C10—N1—C9109.00 (13)C7—C8—H8A121.7
C10—N1—H1N1124.3 (12)C9—C8—H8A121.7
C9—N1—H1N1126.2 (12)N1—C9—C8128.06 (14)
C2—C1—C10116.99 (14)N1—C9—C12109.20 (12)
C2—C1—H1A121.5C8—C9—C12122.69 (13)
C10—C1—H1A121.5N1—C10—C1128.02 (14)
O1—C2—C1117.68 (14)N1—C10—C11109.13 (12)
O1—C2—C3120.64 (13)C1—C10—C11122.84 (13)
C1—C2—C3121.67 (13)C4—C11—C10119.28 (13)
C4—C3—C2119.83 (13)C4—C11—C12134.53 (14)
C4—C3—C13118.83 (14)C10—C11—C12106.18 (12)
C2—C3—C13121.25 (13)C5—C12—C9119.41 (12)
C11—C4—C3119.36 (14)C5—C12—C11134.10 (14)
C11—C4—H4A120.3C9—C12—C11106.45 (12)
C3—C4—H4A120.3O2—C13—C3124.75 (14)
C6—C5—C12118.88 (14)O2—C13—H13A117.6
C6—C5—H5A120.6C3—C13—H13A117.6
C12—C5—H5A120.6O3—C14—H14A109.5
C5—C6—C7120.71 (14)O3—C14—H14B109.5
C5—C6—H6A119.6H14A—C14—H14B109.5
C7—C6—H6A119.6O3—C14—H14C109.5
O3—C7—C8123.77 (14)H14A—C14—H14C109.5
O3—C7—C6114.52 (14)H14B—C14—H14C109.5
C10—C1—C2—O1−179.79 (13)C2—C1—C10—N1179.92 (13)
C10—C1—C2—C30.13 (19)C2—C1—C10—C11−1.0 (2)
O1—C2—C3—C4−179.74 (12)C3—C4—C11—C10−0.9 (2)
C1—C2—C3—C40.3 (2)C3—C4—C11—C12177.97 (14)
O1—C2—C3—C13−3.2 (2)N1—C10—C11—C4−179.38 (12)
C1—C2—C3—C13176.88 (12)C1—C10—C11—C41.4 (2)
C2—C3—C4—C110.0 (2)N1—C10—C11—C121.49 (15)
C13—C3—C4—C11−176.59 (13)C1—C10—C11—C12−177.74 (12)
C12—C5—C6—C70.7 (2)C6—C5—C12—C90.8 (2)
C14—O3—C7—C84.0 (2)C6—C5—C12—C11−176.30 (14)
C14—O3—C7—C6−175.73 (14)N1—C9—C12—C5−178.86 (12)
C5—C6—C7—O3178.13 (13)C8—C9—C12—C5−1.4 (2)
C5—C6—C7—C8−1.7 (2)N1—C9—C12—C11−1.06 (15)
O3—C7—C8—C9−178.74 (13)C8—C9—C12—C11176.40 (12)
C6—C7—C8—C91.0 (2)C4—C11—C12—C5−1.9 (3)
C10—N1—C9—C8−175.26 (13)C10—C11—C12—C5177.08 (15)
C10—N1—C9—C122.04 (15)C4—C11—C12—C9−179.18 (15)
C7—C8—C9—N1177.45 (14)C10—C11—C12—C9−0.25 (15)
C7—C8—C9—C120.49 (19)C4—C3—C13—O2176.58 (13)
C9—N1—C10—C1176.99 (13)C2—C3—C13—O20.0 (2)
C9—N1—C10—C11−2.19 (15)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
O1—H1O1···O20.811.962.6453 (17)143
O1—H1O1···N1i0.812.533.0457 (15)123
N1—H1N1···O2ii0.85 (2)2.10 (2)2.941 (2)172 (2)

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

Footnotes

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: CI5167).

References

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