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Acta Crystallogr Sect E Struct Rep Online. 2009 October 1; 65(Pt 10): o2497–o2498.
Published online 2009 September 19. doi:  10.1107/S1600536809036915
PMCID: PMC2970378

Indizoline1

Abstract

The title compound [systematic name: 1-meth­oxy-2-(3-methyl­but-2-en­yl)-9H-carbazole-3-carbaldehyde], C19H19NO2, is a natural carbazole which was isolated from the twigs of Clausena lansium. The carbazole ring system is essentially planar with a mean deviation of 0.0068 (10) Å. The aldehyde substituent is approximately co-planar with the attached benzene ring with a torsion angle of −8.58 (14)°, whereas the meth­oxy group is rotated out of the benzene plane with a torsion angle of −82.17 (11)°. The dihedral angle between the mean planes of the 3-methyl-2-butenyl group and the carbazole ring is 88.06 (5)°. An inter­molecular N—H(...)O inter­action connects the mol­ecules into a chain along the a axis. The crystal is further consolidated by a C—H(...)O hydrogen bond and two π–π inter­actions with centroid–centroid distances of 3.6592 (6) and 3.7440 (6) Å.

Related literature

For bond-length data, see Allen et al. (1987 [triangle]). For background to carbazoles and their biological activity, see: Adebajo et al. (2009 [triangle]); Ito et al. (1998 [triangle]); Kumar et al. (1995 [triangle]); Lin (1989 [triangle]); Ng et al. (2003 [triangle]); Yang et al. (1988 [triangle]). For a related structure, see: Fun et al. (2007 [triangle]). For the stability of the temperature controller used in the data collection, see: Cosier & Glazer (1986 [triangle]).

An external file that holds a picture, illustration, etc.
Object name is e-65-o2497-scheme1.jpg

Experimental

Crystal data

  • C19H19NO2
  • M r = 293.35
  • Triclinic, An external file that holds a picture, illustration, etc.
Object name is e-65-o2497-efi1.jpg
  • a = 9.0467 (1) Å
  • b = 9.3257 (1) Å
  • c = 10.6927 (1) Å
  • α = 65.717 (1)°
  • β = 86.994 (1)°
  • γ = 68.323 (1)°
  • V = 758.86 (2) Å3
  • Z = 2
  • Mo Kα radiation
  • μ = 0.08 mm−1
  • T = 100 K
  • 0.53 × 0.27 × 0.22 mm

Data collection

  • Bruker APEXII CCD area detector diffractometer
  • Absorption correction: multi-scan (SADABS; Bruker, 2005 [triangle]) T min = 0.957, T max = 0.982
  • 20515 measured reflections
  • 4410 independent reflections
  • 3887 reflections with I > 2σ(I)
  • R int = 0.023

Refinement

  • R[F 2 > 2σ(F 2)] = 0.042
  • wR(F 2) = 0.124
  • S = 1.05
  • 4410 reflections
  • 206 parameters
  • H atoms treated by a mixture of independent and constrained refinement
  • Δρmax = 0.47 e Å−3
  • Δρmin = −0.27 e Å−3

Data collection: APEX2 (Bruker, 2005 [triangle]); cell refinement: SAINT (Bruker, 2005 [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/S1600536809036915/is2459sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809036915/is2459Isup2.hkl

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

Acknowledgments

The authors thank Universiti Sains Malaysia for the Research University Golden Goose grant No. 1001/PFIZIK/811012. SL thanks the Thailand Research Fund (grant No. RSA5280011) and Mae Fah Luang University for financial support. WM thanks Mae Fah Luang University for a PhD graduate student research grant.

supplementary crystallographic information

Comment

Clausena lansium (Wampee) belongs to the Rutaceae family. Several parts of this plant have been used as folk medicine in China and Taiwan, for example, the leaves have been used for the treatment of coughs, asthma and gastro-intestinal diseases and the seeds for gastro-intestinal diseases such as acute and chronic gastro-intestinal inflammation and ulcers (Adebajo et al., 2009). In addition, the fruits are used for influenza, colds and abdominal colic pains in Philippines (Lin, 1989). In previous studies, a number of coumarins (Ito et al., 1998; Kumar et al., 1995) and alkaloids (Lin, 1989; Yang et al., 1988) have been isolated from different parts of this plant. As part of our continuing study on the chemical constituents and bioactive compounds from Thai medicinal plants, we report herein the crystal structure of the title compound (I), which was isolated from the twigs of Clausena lansium were collected from Nan province in the northern part of Thailand.

In the structure of (I), C19H19NO2 (Fig. 1), the carbazole ring system (C1–C12/N1) is essentially planar with a mean deviation of 0.0068 (10) Å. The aldehyde substituent is planarly attached to the benzene ring. The methoxy group is in an (+)-anti-clinal [torsion angle C19–O1–C11–C10 = 101.43 (10)°] whereas the 3-methyl-2-butenyl is in an (-)-syn-clinal [C9–C10–C14–C15 = -71.91 (11)°] conformation with respect to the attached benzene ring. The dihedral angle between the 3-methyl-2-butenyl moiety and the mean plane of carbazole ring is 88.06 (5)°. The bond lengths and angles in (I) are within normal ranges (Allen et al., 1987) and are comparable to the related structure (Fun et al., 2007).

In the crystal packing (Fig. 2), an N—H···O intermolecular interaction connects the molecules into one dimensional chains along the [1 0 0] direction. The crystal is further consolidated by C—H···O (Table 1) and π···π interactions with the Cg1···Cg2 distance = 3.7440 (6) Å and Cg2···Cg3 = 3.6592 (6) Å [symmetry code: (1 - x, 1 - y, -z) for both Cg···Cg]. Cg1, Cg2 and Cg3 are the centroids of C1–C6–C7–C12–N1, C1–C6 and C7–C12 rings, respectively.

Experimental

Twigs of Clausena lansium (6.73 kg) were successively extracted with CH2Cl2 and acetone, over the period of 3 days each at room temperature to provide the crude CH2Cl2 and acetone extracts, respectively. The CH2Cl2 and acetone extracts were combined (34.02 g) and then subjected to quick column chromatography over silica gel eluted by gradient of hexane-acetone (100% hexane to 100% acetone) giving seventeen fractions (A—Q). Fraction G (207.1 mg) was subjected to purification by column chromatography using 20% EtOAc-hexane to yield the title compound (27.1 mg). Yellow block-shaped single crystals of the title compound suitable for x-ray structure determination were recrystallized from CH2Cl2/acetone (1:1, v/v) after several days (m.p. 344–345 K).

Refinement

The H atom attached to N1 was located in a difference map and was isotropically refined. The remaining H atoms were placed in calculated positions with C—H = 0.93 Å for aromatic and CH, 0.97 for CH2 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 0.70 Å from C8 and the deepest hole is located at 0.91 Å from C11.

Figures

Fig. 1.
The structure of (I), showing 50% probability displacement ellipsoids and the atom-numbering scheme.
Fig. 2.
The crystal packing of (I) viewed along the b axis, showing one dimensional chains along the [1 0 0] direction. Hydrogen bonds are shown as dashed lines.

Crystal data

C19H19NO2Z = 2
Mr = 293.35F(000) = 312
Triclinic, P1Dx = 1.284 Mg m3
Hall symbol: -P 1Melting point = 344–345 K
a = 9.0467 (1) ÅMo Kα radiation, λ = 0.71073 Å
b = 9.3257 (1) ÅCell parameters from 4410 reflections
c = 10.6927 (1) Åθ = 2.1–30.0°
α = 65.717 (1)°µ = 0.08 mm1
β = 86.994 (1)°T = 100 K
γ = 68.323 (1)°Block, yellow
V = 758.86 (2) Å30.53 × 0.27 × 0.22 mm

Data collection

Bruker APEXII CCD area detector diffractometer4410 independent reflections
Radiation source: sealed tube3887 reflections with I > 2σ(I)
graphiteRint = 0.023
[var phi] and ω scansθmax = 30.0°, θmin = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2005)h = −12→12
Tmin = 0.957, Tmax = 0.982k = −13→13
20515 measured reflectionsl = −15→15

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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.124H atoms treated by a mixture of independent and constrained refinement
S = 1.05w = 1/[σ2(Fo2) + (0.0684P)2 + 0.2509P] where P = (Fo2 + 2Fc2)/3
4410 reflections(Δ/σ)max = 0.001
206 parametersΔρmax = 0.47 e Å3
0 restraintsΔρmin = −0.27 e Å3

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 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
O10.26909 (8)0.78512 (9)0.28630 (7)0.01884 (16)
O20.90034 (9)0.78623 (10)0.07678 (8)0.02297 (17)
N10.23115 (10)0.73264 (11)0.03746 (9)0.01646 (17)
C10.26191 (11)0.70558 (11)−0.08151 (10)0.01576 (18)
C20.16804 (12)0.67357 (12)−0.15826 (11)0.0196 (2)
H2A0.06920.6690−0.13360.024*
C30.22843 (13)0.64886 (13)−0.27314 (11)0.0212 (2)
H3A0.16850.6274−0.32640.025*
C40.37714 (13)0.65536 (13)−0.31088 (10)0.0204 (2)
H4A0.41400.6386−0.38860.024*
C50.47039 (12)0.68656 (12)−0.23362 (10)0.01765 (19)
H5A0.56940.6902−0.25850.021*
C60.41224 (11)0.71237 (11)−0.11773 (9)0.01449 (17)
C70.47446 (11)0.74608 (11)−0.01497 (9)0.01365 (17)
C80.61476 (11)0.76411 (11)0.00817 (9)0.01443 (17)
H8A0.69380.7538−0.05050.017*
C90.63649 (11)0.79781 (11)0.11998 (9)0.01434 (17)
C100.51798 (11)0.81249 (11)0.21241 (9)0.01415 (17)
C110.38006 (11)0.78850 (11)0.19182 (9)0.01450 (18)
C120.35762 (11)0.75789 (11)0.07777 (9)0.01417 (17)
C130.78581 (11)0.81675 (12)0.14115 (10)0.01751 (19)
H13A0.79400.85430.20770.021*
C140.54154 (12)0.84670 (12)0.33525 (10)0.01731 (18)
H14A0.57510.94210.30460.021*
H14B0.44000.87840.37180.021*
C150.66415 (12)0.69530 (12)0.44873 (10)0.01723 (19)
H15A0.66190.58950.46790.021*
C160.77577 (12)0.69655 (12)0.52484 (10)0.01787 (19)
C170.79953 (15)0.85421 (14)0.50890 (13)0.0288 (2)
H17A0.73490.94900.42730.043*
H17B0.91030.83740.50100.043*
H17C0.76860.87690.58820.043*
C180.88710 (13)0.53395 (13)0.63786 (11)0.0229 (2)
H18A0.85570.44220.64850.034*
H18B0.88190.54630.72300.034*
H18C0.99470.50970.61410.034*
C190.13064 (13)0.94117 (15)0.24419 (12)0.0251 (2)
H19A0.06250.93330.31660.038*
H19B0.07300.96070.16210.038*
H19C0.16391.03390.22560.038*
H1N10.145 (2)0.7418 (19)0.0698 (16)0.029 (4)*

Atomic displacement parameters (Å2)

U11U22U33U12U13U23
O10.0144 (3)0.0228 (3)0.0189 (3)−0.0072 (3)0.0064 (3)−0.0089 (3)
O20.0127 (3)0.0318 (4)0.0239 (4)−0.0103 (3)0.0028 (3)−0.0097 (3)
N10.0107 (4)0.0217 (4)0.0199 (4)−0.0077 (3)0.0032 (3)−0.0102 (3)
C10.0129 (4)0.0159 (4)0.0182 (4)−0.0051 (3)0.0004 (3)−0.0070 (3)
C20.0148 (4)0.0203 (4)0.0247 (5)−0.0065 (3)−0.0012 (3)−0.0103 (4)
C30.0208 (5)0.0206 (4)0.0226 (5)−0.0067 (4)−0.0033 (4)−0.0100 (4)
C40.0237 (5)0.0197 (4)0.0182 (4)−0.0073 (4)0.0003 (4)−0.0090 (3)
C50.0175 (4)0.0177 (4)0.0176 (4)−0.0064 (3)0.0026 (3)−0.0077 (3)
C60.0123 (4)0.0139 (4)0.0161 (4)−0.0043 (3)0.0005 (3)−0.0056 (3)
C70.0108 (4)0.0138 (4)0.0153 (4)−0.0045 (3)0.0014 (3)−0.0052 (3)
C80.0105 (4)0.0158 (4)0.0160 (4)−0.0050 (3)0.0027 (3)−0.0060 (3)
C90.0107 (4)0.0147 (4)0.0163 (4)−0.0051 (3)0.0006 (3)−0.0050 (3)
C100.0120 (4)0.0142 (4)0.0153 (4)−0.0047 (3)0.0007 (3)−0.0055 (3)
C110.0112 (4)0.0160 (4)0.0160 (4)−0.0054 (3)0.0034 (3)−0.0064 (3)
C120.0102 (4)0.0150 (4)0.0166 (4)−0.0048 (3)0.0011 (3)−0.0060 (3)
C130.0133 (4)0.0201 (4)0.0178 (4)−0.0077 (3)−0.0002 (3)−0.0052 (3)
C140.0152 (4)0.0192 (4)0.0179 (4)−0.0052 (3)0.0007 (3)−0.0093 (3)
C150.0171 (4)0.0177 (4)0.0166 (4)−0.0071 (3)0.0021 (3)−0.0066 (3)
C160.0156 (4)0.0200 (4)0.0173 (4)−0.0065 (3)0.0017 (3)−0.0075 (3)
C170.0303 (6)0.0248 (5)0.0321 (6)−0.0115 (4)−0.0063 (4)−0.0109 (4)
C180.0216 (5)0.0231 (5)0.0200 (4)−0.0078 (4)−0.0023 (4)−0.0053 (4)
C190.0161 (5)0.0297 (5)0.0280 (5)−0.0041 (4)0.0061 (4)−0.0152 (4)

Geometric parameters (Å, °)

O1—C111.3857 (11)C9—C131.4658 (13)
O1—C191.4363 (13)C10—C111.3895 (12)
O2—C131.2235 (12)C10—C141.5155 (12)
N1—C121.3727 (11)C11—C121.4018 (12)
N1—C11.3909 (12)C13—H13A0.9300
N1—H1N10.822 (17)C14—C151.5071 (13)
C1—C21.3948 (13)C14—H14A0.9700
C1—C61.4113 (13)C14—H14B0.9700
C2—C31.3892 (14)C15—C161.3360 (13)
C2—H2A0.9300C15—H15A0.9300
C3—C41.3999 (15)C16—C171.5035 (14)
C3—H3A0.9300C16—C181.5054 (14)
C4—C51.3895 (14)C17—H17A0.9600
C4—H4A0.9300C17—H17B0.9600
C5—C61.3978 (13)C17—H17C0.9600
C5—H5A0.9300C18—H18A0.9600
C6—C71.4500 (12)C18—H18B0.9600
C7—C81.3875 (12)C18—H18C0.9600
C7—C121.4167 (12)C19—H19A0.9600
C8—C91.3951 (13)C19—H19B0.9600
C8—H8A0.9300C19—H19C0.9600
C9—C101.4271 (13)
C11—O1—C19113.68 (8)N1—C12—C11128.96 (9)
C12—N1—C1108.62 (8)N1—C12—C7109.54 (8)
C12—N1—H1N1128.2 (11)C11—C12—C7121.50 (8)
C1—N1—H1N1122.8 (11)O2—C13—C9124.13 (9)
N1—C1—C2128.87 (9)O2—C13—H13A117.9
N1—C1—C6109.20 (8)C9—C13—H13A117.9
C2—C1—C6121.92 (9)C15—C14—C10112.82 (8)
C3—C2—C1117.16 (9)C15—C14—H14A109.0
C3—C2—H2A121.4C10—C14—H14A109.0
C1—C2—H2A121.4C15—C14—H14B109.0
C2—C3—C4121.77 (9)C10—C14—H14B109.0
C2—C3—H3A119.1H14A—C14—H14B107.8
C4—C3—H3A119.1C16—C15—C14127.08 (9)
C5—C4—C3120.78 (9)C16—C15—H15A116.5
C5—C4—H4A119.6C14—C15—H15A116.5
C3—C4—H4A119.6C15—C16—C17124.45 (9)
C4—C5—C6118.63 (9)C15—C16—C18120.70 (9)
C4—C5—H5A120.7C17—C16—C18114.84 (9)
C6—C5—H5A120.7C16—C17—H17A109.5
C5—C6—C1119.73 (9)C16—C17—H17B109.5
C5—C6—C7133.90 (9)H17A—C17—H17B109.5
C1—C6—C7106.36 (8)C16—C17—H17C109.5
C8—C7—C12119.22 (8)H17A—C17—H17C109.5
C8—C7—C6134.49 (8)H17B—C17—H17C109.5
C12—C7—C6106.27 (8)C16—C18—H18A109.5
C7—C8—C9119.55 (8)C16—C18—H18B109.5
C7—C8—H8A120.2H18A—C18—H18B109.5
C9—C8—H8A120.2C16—C18—H18C109.5
C8—C9—C10121.40 (8)H18A—C18—H18C109.5
C8—C9—C13118.14 (8)H18B—C18—H18C109.5
C10—C9—C13120.46 (8)O1—C19—H19A109.5
C11—C10—C9118.94 (8)O1—C19—H19B109.5
C11—C10—C14119.26 (8)H19A—C19—H19B109.5
C9—C10—C14121.76 (8)O1—C19—H19C109.5
O1—C11—C10120.95 (8)H19A—C19—H19C109.5
O1—C11—C12119.63 (8)H19B—C19—H19C109.5
C10—C11—C12119.33 (8)
C12—N1—C1—C2179.57 (9)C13—C9—C10—C14−0.39 (13)
C12—N1—C1—C60.45 (10)C19—O1—C11—C10101.43 (10)
N1—C1—C2—C3−179.21 (9)C19—O1—C11—C12−82.17 (11)
C6—C1—C2—C3−0.19 (14)C9—C10—C11—O1173.69 (8)
C1—C2—C3—C40.09 (15)C14—C10—C11—O1−3.97 (13)
C2—C3—C4—C50.20 (15)C9—C10—C11—C12−2.73 (13)
C3—C4—C5—C6−0.37 (14)C14—C10—C11—C12179.61 (8)
C4—C5—C6—C10.27 (14)C1—N1—C12—C11−179.49 (9)
C4—C5—C6—C7179.54 (9)C1—N1—C12—C7−0.48 (10)
N1—C1—C6—C5179.20 (8)O1—C11—C12—N14.24 (15)
C2—C1—C6—C50.01 (14)C10—C11—C12—N1−179.30 (9)
N1—C1—C6—C7−0.25 (10)O1—C11—C12—C7−174.67 (8)
C2—C1—C6—C7−179.44 (8)C10—C11—C12—C71.79 (14)
C5—C6—C7—C8−0.63 (18)C8—C7—C12—N1−178.66 (8)
C1—C6—C7—C8178.71 (10)C6—C7—C12—N10.31 (10)
C5—C6—C7—C12−179.38 (10)C8—C7—C12—C110.44 (13)
C1—C6—C7—C12−0.04 (10)C6—C7—C12—C11179.42 (8)
C12—C7—C8—C9−1.64 (13)C8—C9—C13—O2−8.58 (14)
C6—C7—C8—C9179.73 (9)C10—C9—C13—O2170.98 (9)
C7—C8—C9—C100.67 (13)C11—C10—C14—C15105.69 (10)
C7—C8—C9—C13−179.77 (8)C9—C10—C14—C15−71.91 (11)
C8—C9—C10—C111.55 (13)C10—C14—C15—C16139.14 (10)
C13—C9—C10—C11−177.99 (8)C14—C15—C16—C17−0.51 (17)
C8—C9—C10—C14179.15 (8)C14—C15—C16—C18178.19 (9)

Hydrogen-bond geometry (Å, °)

D—H···AD—HH···AD···AD—H···A
N1—H1N1···O2i0.825 (19)2.099 (19)2.8843 (13)158.8 (15)
C18—H18A···O1ii0.962.593.5369 (15)168

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

Footnotes

1This paper is dedicated to Dato’ Dr Chatar Singh, Foundation Dean, School of Physics, Universiti Sains Malaysia, whose 80th birthday falls on the 9th September 2009.

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS2459).

References

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