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The structure of β-carboline, also called norharman (systematic name: 9H-pyrido[3,4-b]indole), C11H8N2, has been determined at 110 K. Norharman is prevalent in the environment and the human body and is of wide biological inter­est. The structure exhibits inter­molecular N—H...N hydrogen bonding, which results in a one-dimensional herringbone motif. The three rings of the norharman mol­ecule collectively result in a C-shaped curvature of 3.19 (13)° parallel to the long axis. The diffraction data show shorter pyridyl C—C bonds than those reported at the STO-3G level of theory.

Supporting information


Crystallographic Information File (CIF)
Contains datablocks I, global


Structure factor file (CIF format)
Contains datablock I


Chemical Markup Language (CML) file
Supplementary material

CCDC reference: 838158

Comment top

Norharman, (I), is the prototypical β-carboline alkaloid that is the basic structural unit for a wide range of important naturally occurring compounds. Norharman is found in numerous plants and animals, including humans (Fekkes et al., 1992). It is also prevalent in the environment, for example as a constituent of cigarette smoke, and can be absorbed from numerous foodstuffs and other environmental sources (Herraiz, 2004). The biological function of norharman appears to be varied and its toxicity and therapeutic uses have been investigated. For example, norharman has been implicated as both a neurotoxin relevant to Parkinson's disease (Kuhn et al., 1996) and a mediator in the mutagenesis of DNA in the presence of other small molecules (Mori et al., 1996). Norharman has also been suggested as a potential neuroprotective agent (Haghdoost-Yazdi et al., 2010). The molecular-based interactions between norharman and biological materials such as DNA and proteins are likely to arise primarily from hydrogen-bonding and quadrupolar effects, due to the π-derived electrons. However, no adducts or cocrystals of norharman have been published to date.

Despite considerable investigation into the properties and biological activity of norharman and the calculation of its optimized structure at the STO-3 G level of theory (Konschin et al., 1987), a high-quality crystal structure has not yet been reported. Crystallographic studies undertaken by Ray (1957) and, later, Roychowdhury & Roychowdhury (1981), determined unit-cell parameters and presented gross structural features. Given the ongoing research into the biological function of norharman and the many related β-carboline derivatives, a single-crystal X-ray structure of norharman would be of use in theoretical modelling and related structural work. A fragment search of the Cambridge Structural Database (CSD, Version?; Allen, 2002) using the unsaturated norharman skeleton returned 48 hits for structures where the three-dimensional coordinates have been reported. The bond lengths and distances were subjected to principal-component and cluster analyses (Barr et al., 2005; Fletcher et al., 1996) and correlation coefficients were calculated, but no meaningful trends were observed. Investigation of the bonding in these molecules is restricted in part due to the limited number of structures reported. Therefore, the structure of norharman will be of use as a fundamental reference as more structures of β-carbolines are obtained.

Single crystals of norharman were grown as part of ongoing efforts to explore the metal–ligand bonding and electron distribution in complexes incorporating the norharman motif. The needle-like morphology resulted in poor diffraction, but a data set of sufficient quality to locate H atoms was obtained. The unit-cell parameters and space group are consistent with those previously reported (Ray, 1957). Upon refinement, the H atoms were observed in the difference map, although all but the amino atom H2 (Fig. 1) were refined using a riding model.

The molecular structure of norharman (Fig. 1) exhibits curvature parallel to the longest axis, with angles between the least-squares planes of the phenyl and pyrrole rings, and pyrrole and pyridyl rings, of 0.68 (14) and 2.60 (14)°, respectively, defining a C- rather than S-shaped geometry. X-ray structures of other β-carbolines in the CSD generally exhibit curvature of 0–5°. The bond lengths of the phenyl fragment are identical, within experimental error, to those observed for aniline, where the latter exhibits asymmetry about the Ph—N axis due to hydrogen bonding in the crystal lattice (Fukuyo et al., 1982). Compared with the structure of 3-aminopyridine (Chao et al., 1975), the pyridyl moiety of (I) exhibits lengthening of the N1—C5 and C2—C3 bonds of 0.26 (9) and 0.24 (8) Å, respectively, reflective of conjugation across the π-system of the entire molecule.

Hydrogen bonding has been implicated as key to the biological activity of β-carbolines (Guan et al., 2006). Norharman exhibits intermolecular hydrogen bonding (Fig. 2), resulting in a one-dimensional herringbone chain motif parallel to the b axis. The distance between atoms N2 and N1(-x, 1/2 + y, 3/2 - z) is 2.888 (3) Å and the angle between the least-squares planes of adjacent norharman molecules is 71.55 (4)°. The hydrogen-bonding interaction is nonlinear, exhibiting an N2—H2—N'1 angle of 153 (3)°, and the location of atom H2 identifies N2—H2 and N'1 as the hydrogen-bond donor and acceptor, respectively. The alternative neutral tautomer of norharman could be derived via formal proton migration from N2 to N1, although loss of aromaticity in the pyridyl moiety would suggest this isomer would not be the molecular ground state. However, there are several structures of N-alkylated analogues where this alternative tautomer is observed (Bonazzi et al., 2010; Mahboobi et al., 2000). Moreover, in addition to locating atom H2 in the difference map, the C1—N1—C5 angle of 118.0 (2)° is diagnostic of unprotonated substituted pyridines, where on protonation an angle of 120–122° would be expected (Krygowski et al., 2005). Furthermore, comparison between the experimental and reported theoretical geometric parameters determined at the STO-3 G level of theory (Konschin et al., 1987) shows that the latter overestimates the bond lengths of the pyridyl moiety, as judged by the C—C and C—N bond lengths, and the calculated structure is flat. For the calculated structure it was suggested that overestimation of the C—N bond lengths may occur due to an insufficiently large basis set (Konschin et al., 1987).

With respect to the hydrogen bonding, related β-carbolines exhibit a range of hydrogen-bonding motifs that are dependent on the stereochemistry about atoms N1 and N2 and any ring substituents that are also capable of hydrogen-bonding interactions. For example, in the structural analogue harman, where atom C1 is substituted with a methyl group, the additional steric interaction induces a helical chain motif (El-Sayed et al. 1986), whereas the addition of an ester (Kubicki & Codding, 2001; Bertolasi et al., 1984) or amide (Muir & Codding, 1984) functionality at C5 results in a flat chain motif derived from hydrogen bonding between the ester or amide and atom H2.

Related literature top

For related literature, see: Allen (2002); Barr et al. (2005); Bertolasi et al. (1984); Bonazzi et al. (2010); Chao et al. (1975); El-Sayed, Barnhart, Ammon & Wassel (1986); Fekkes et al. (1992); Fletcher et al. (1996); Fukuyo et al. (1982); Guan et al. (2006); Hagen et al. (1987); Haghdoost-Yazdi, Hosseini, Faraji, Nahid & Jahanihashemi (2010); Herraiz (2004); Konschin et al. (1987); Krygowski et al. (2005); Kubicki & Codding (2001); Kuhn et al. (1996); Lippke et al. (1983); Mahboobi et al. (2000); Mori et al. (1996); Muir & Codding (1984); Ray (1957); Roychowdhury & Roychowdhury (1981).

Experimental top

Norharman was prepared using a literature method (Lippke et al. 1983; Hagen et al. 1987). Crystals of (I) suitable for X-ray diffraction were grown from a supersaturated solution of norharman in ethyl acetate at 277 K over a period of 24 h.

Refinement top

H atoms were found in difference Fourier maps and were subsequently treated as riding, with C—H = 0.95 Å, with the exception of atom H2, which was refined. There was insufficient Friedel-pair coverage to determine the absolute structure, so Friedel pairs were merged and an arbitrary enantiomer is presented.

Computing details top

Data collection: CrysAlis PRO (Oxford Diffraction, 2010); cell refinement: CrysAlis PRO (Oxford Diffraction, 2010); data reduction: CrysAlis PRO (Oxford Diffraction, 2010); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of norharman, (I). Displacement ellipsoids are drawn at the 50% probability level.
[Figure 2] Fig. 2. The hydrogen-bonding network of norharman, viewed parallel to the b axis. [Symmetry codes: (a) -x, y - 1/2, -z + 3/2; (b) x, y, z; (c) -x, y + 1/2, -z + 3/2; (d) x, y + 1, z.]
9H-pyrido[3,4-b]indole top
Crystal data top
C11H8N2Dx = 1.356 Mg m3
Mr = 168.19Mo Kα radiation, λ = 0.7107 Å
Orthorhombic, P212121Cell parameters from 1334 reflections
a = 5.8272 (4) Åθ = 3.5–25.0°
b = 9.8245 (4) ŵ = 0.08 mm1
c = 14.3943 (11) ÅT = 110 K
V = 824.06 (9) Å3Needle, colourless
Z = 40.30 × 0.01 × 0.01 mm
F(000) = 352
Data collection top
Oxford SuperNova
866 independent reflections
Radiation source: SuperNova (Mo) X-ray Source676 reflections with I > 2σ(I)
Mirror monochromatorRint = 0.039
Detector resolution: 16.1450 pixels mm-1θmax = 25.0°, θmin = 3.5°
ω scansh = 64
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
k = 1011
Tmin = 0.899, Tmax = 1.000l = 1317
2818 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)] = 0.038Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.073H atoms treated by a mixture of independent and constrained refinement
S = 1.00 w = 1/[σ2(Fo2) + (0.0303P)2]
where P = (Fo2 + 2Fc2)/3
866 reflections(Δ/σ)max < 0.001
122 parametersΔρmax = 0.17 e Å3
0 restraintsΔρmin = 0.16 e Å3
Crystal data top
C11H8N2V = 824.06 (9) Å3
Mr = 168.19Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 5.8272 (4) ŵ = 0.08 mm1
b = 9.8245 (4) ÅT = 110 K
c = 14.3943 (11) Å0.30 × 0.01 × 0.01 mm
Data collection top
Oxford SuperNova
866 independent reflections
Absorption correction: multi-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
676 reflections with I > 2σ(I)
Tmin = 0.899, Tmax = 1.000Rint = 0.039
2818 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0380 restraints
wR(F2) = 0.073H atoms treated by a mixture of independent and constrained refinement
S = 1.00Δρmax = 0.17 e Å3
866 reflectionsΔρmin = 0.16 e Å3
122 parameters
Special details top

Experimental. CrysAlisPro, Oxford Diffraction Ltd., Version Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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. Crystal was weakly diffracting and required a long diffraction time. Insufficient coverage to determine stereochemistry so friedel pairs merged.

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
C10.1184 (5)0.1890 (3)0.74587 (19)0.0219 (7)
C20.1739 (5)0.2875 (2)0.68048 (18)0.0189 (7)
C30.3863 (5)0.2819 (2)0.63298 (19)0.0176 (6)
C40.5357 (5)0.1761 (2)0.65437 (19)0.0209 (7)
C50.4675 (5)0.0827 (3)0.72045 (18)0.0252 (7)
C60.1740 (5)0.4606 (3)0.5787 (2)0.0201 (7)
C70.1149 (5)0.5735 (2)0.52573 (18)0.0242 (7)
C80.2698 (5)0.6180 (3)0.4606 (2)0.0245 (7)
C90.4826 (5)0.5529 (3)0.44769 (19)0.0258 (7)
C100.5415 (5)0.4407 (2)0.50103 (18)0.0215 (7)
C110.3865 (5)0.3936 (2)0.56733 (18)0.0168 (6)
N10.2633 (4)0.0865 (2)0.76570 (16)0.0243 (6)
N20.0468 (4)0.3958 (2)0.64748 (15)0.0209 (6)
H20.093 (6)0.436 (3)0.678 (2)0.057 (11)*
Atomic displacement parameters (Å2) top
C10.0204 (17)0.0227 (16)0.0225 (17)0.0015 (15)0.0017 (15)0.0043 (13)
C20.0230 (19)0.0153 (14)0.0183 (16)0.0006 (14)0.0029 (13)0.0037 (13)
C30.0177 (15)0.0168 (14)0.0185 (15)0.0008 (13)0.0033 (14)0.0049 (13)
C40.0162 (16)0.0228 (14)0.0236 (16)0.0005 (13)0.0010 (14)0.0026 (13)
C50.0244 (18)0.0238 (16)0.0275 (18)0.0031 (15)0.0012 (15)0.0011 (14)
C60.0217 (18)0.0158 (13)0.0229 (16)0.0017 (12)0.0009 (14)0.0056 (13)
C70.0251 (17)0.0148 (13)0.0326 (17)0.0013 (13)0.0032 (15)0.0044 (13)
C80.0318 (18)0.0155 (13)0.0262 (17)0.0018 (15)0.0024 (15)0.0006 (14)
C90.0302 (19)0.0221 (14)0.0251 (17)0.0067 (15)0.0055 (15)0.0002 (14)
C100.0189 (15)0.0192 (13)0.0264 (16)0.0033 (13)0.0013 (14)0.0069 (13)
C110.0164 (15)0.0158 (13)0.0182 (15)0.0016 (13)0.0006 (14)0.0031 (12)
N10.0232 (14)0.0240 (13)0.0257 (15)0.0004 (13)0.0017 (12)0.0004 (12)
N20.0193 (14)0.0189 (12)0.0246 (14)0.0009 (11)0.0059 (12)0.0006 (11)
Geometric parameters (Å, º) top
C1—H10.9500C6—C111.412 (4)
C1—C21.388 (4)C6—N21.391 (3)
C1—N11.345 (3)C7—H70.9500
C2—C31.415 (4)C7—C81.372 (4)
C2—N21.381 (3)C8—H80.9500
C3—C41.390 (3)C8—C91.408 (4)
C3—C111.448 (4)C9—H90.9500
C4—H40.9500C9—C101.386 (3)
C4—C51.381 (4)C10—H100.9500
C5—H50.9500C10—C111.393 (3)
C5—N11.357 (4)N2—H21.00 (3)
C6—C71.389 (3)
C1—C2—C3120.3 (2)C8—C7—C6117.8 (3)
C1—N1—C5118.0 (2)C8—C7—H7121.1
C2—C3—C11106.7 (2)C9—C8—H8119.2
C2—N2—C6108.2 (2)C9—C10—H10120.6
C2—N2—H2126.1 (17)C9—C10—C11118.9 (3)
C3—C4—H4121.0C10—C9—C8120.4 (3)
C4—C3—C2118.0 (2)C10—C9—H9119.8
C4—C3—C11135.3 (3)C10—C11—C3134.4 (2)
C4—C5—H5117.8C10—C11—C6119.5 (2)
C5—C4—C3118.0 (3)C11—C10—H10120.6
C6—C7—H7121.1N1—C1—C2121.3 (3)
C6—C11—C3106.1 (2)N1—C5—C4124.4 (3)
C6—N2—H2124.0 (17)N1—C5—H5117.8
C7—C6—C11121.7 (3)N2—C2—C1130.2 (3)
C7—C6—N2128.6 (3)N2—C2—C3109.4 (2)
C7—C8—H8119.2N2—C6—C11109.6 (2)
C7—C8—C9121.7 (3)
C1—C2—C3—C40.4 (4)C7—C6—N2—C2179.6 (3)
C1—C2—C3—C11177.3 (2)C7—C8—C9—C100.1 (4)
C1—C2—N2—C6176.8 (3)C8—C9—C10—C110.1 (4)
C2—C1—N1—C50.6 (4)C9—C10—C11—C3179.0 (3)
C2—C3—C4—C50.2 (4)C9—C10—C11—C60.1 (4)
C2—C3—C11—C60.0 (3)C11—C3—C4—C5176.6 (3)
C2—C3—C11—C10179.1 (3)C11—C6—C7—C80.7 (4)
C3—C2—N2—C60.2 (3)C11—C6—N2—C20.3 (3)
C3—C4—C5—N10.4 (4)N1—C1—C2—C30.1 (4)
C4—C3—C11—C6177.0 (3)N1—C1—C2—N2176.7 (3)
C4—C3—C11—C102.0 (5)N2—C2—C3—C4177.8 (2)
C4—C5—N1—C10.9 (4)N2—C2—C3—C110.1 (3)
C6—C7—C8—C90.5 (4)N2—C6—C7—C8179.2 (3)
C7—C6—C11—C3179.7 (2)N2—C6—C11—C30.2 (3)
C7—C6—C11—C100.5 (4)N2—C6—C11—C10179.4 (2)
Hydrogen-bond geometry (Å, º) top
N2—H2···N1i1.00 (3)1.96 (3)2.888 (3)153 (3)
Symmetry code: (i) x, y+1/2, z+3/2.

Experimental details

Crystal data
Chemical formulaC11H8N2
Crystal system, space groupOrthorhombic, P212121
Temperature (K)110
a, b, c (Å)5.8272 (4), 9.8245 (4), 14.3943 (11)
V3)824.06 (9)
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.30 × 0.01 × 0.01
Data collection
DiffractometerOxford SuperNova
Absorption correctionMulti-scan
(CrysAlis PRO; Oxford Diffraction, 2010)
Tmin, Tmax0.899, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
2818, 866, 676
(sin θ/λ)max1)0.594
R[F2 > 2σ(F2)], wR(F2), S 0.038, 0.073, 1.00
No. of reflections866
No. of parameters122
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.17, 0.16

Computer programs: CrysAlis PRO (Oxford Diffraction, 2010), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), OLEX2 (Dolomanov et al., 2009).

Hydrogen-bond geometry (Å, º) top
N2—H2···N1i1.00 (3)1.96 (3)2.888 (3)153 (3)
Symmetry code: (i) x, y+1/2, z+3/2.

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