5-Amino-1-methyl-1H-benzimidazole.

The structure of the title compound, C(8)H(9)N(3), a potential anti-tumour drug, was determined in order to give more insight into its structure-function relationships. The benzimidazole core of the mol-ecule was found to be exactly planar, while the substituents are displaced slightly from the mol-ecular plane [C-C-N-C and C-C-C-N torsion angles of 0.8 (3) and 179.0 (1)° for the methyl and amino groups, respectively]. The bond lengths are analysed in detail and compared with those of the parent unsubstituted analogues. The results show that the lone-pair electrons on the amino N atom are involved in conjugation with the adjacent π system and hence affect the charge distribution in the heterocycle. Two inter-molecular N-H⋯N and C-H⋯N hydrogen bonds have been identified.

Related literature

For the synthesis, see: Milata et al. (1989 ▶). For bond-order–bond-length curves, see: Burke-Laing & Laing (1976 ▶). For the biological activity of benzimidazole derivatives, see: Kettmann et al. (2004 ▶); Le et al. (2004 ▶); Nguyen et al. (2004 ▶); Statkova-Abeghe et al. (2005 ▶). For a description of the Cambridge Structural Database, see: Allen (2002 ▶).

Experimental

Crystal data

C8H9N3

M = 147.18

Monoclinic,

a = 5.9128 (2) Å

b = 8.8215 (3) Å

c = 14.8418 (6) Å

β = 100.129 (3)°

V = 762.08 (5) Å3

Z = 4

Mo Kα radiation

μ = 0.08 mm−1

T = 296 K

0.52 × 0.20 × 0.10 mm

Data collection

Oxford Diffraction Gemini R CCD diffractometer

Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009 ▶) based on Clark & Reid (1995 ▶)] T min = 0.944, T max = 0.966

18508 measured reflections

1832 independent reflections

1114 reflections with I > 2σ(I)

R int = 0.039

Refinement

R[F 2 > 2σ(F 2)] = 0.046

wR(F 2) = 0.141

S = 1.02

1832 reflections

101 parameters

H-atom parameters constrained

Δρmax = 0.21 e Å−3

Δρmin = −0.21 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2009 ▶); cell refinement: CrysAlis RED (Oxford Diffraction, 2009 ▶); data reduction: CrysAlis RED; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 (Farrugia, 1997 ▶); software used to prepare material for publication: enCIFer (Allen et al., 2004 ▶).

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809025550/ez2173sup1.cif

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809025550/ez2173Isup2.hkl

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

C8H9N3	F(000) = 312
Mr = 147.18	Dx = 1.283 Mg m−3
Monoclinic, P21/n	Melting point: 431 K
Hall symbol: -P 2yn	Mo Kα radiation, λ = 0.71073 Å
a = 5.9128 (2) Å	Cell parameters from 7029 reflections
b = 8.8215 (3) Å	θ = 3.5–29.5°
c = 14.8418 (6) Å	µ = 0.08 mm−1
β = 100.129 (3)°	T = 296 K
V = 762.08 (5) Å3	Needle, orange
Z = 4	0.52 × 0.20 × 0.10 mm

Oxford Diffraction Gemini R CCD diffractometer	1832 independent reflections
Radiation source: fine-focus sealed tube	1114 reflections with I > 2σ(I)
graphite	Rint = 0.039
Detector resolution: 10.434 pixels mm-1	θmax = 28.0°, θmin = 3.5°
ω scans	h = −7→7
Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009) based on Clark & Reid (1995)]	k = −11→11
Tmin = 0.944, Tmax = 0.966	l = −19→19
18508 measured reflections

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.141	H-atom parameters constrained
S = 1.02	w = 1/[σ2(Fo2) + (0.086P)2] where P = (Fo2 + 2Fc2)/3
1832 reflections	(Δ/σ)max = 0.001
101 parameters	Δρmax = 0.21 e Å−3
0 restraints	Δρmin = −0.21 e Å−3

Experimental. Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by Clark & Reid (1995).

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.Least-squares planes (x,y,z in crystal coordinates) and deviations from them (* indicates atom used to define plane)2.7140 (0.0026) x - 6.5500 (0.0019) y + 5.9298 (0.0054) z = 1.2109 (0.0022)* -0.0006 (0.0010) N1 * -0.0119 (0.0012) C2 * -0.0077 (0.0011) N3 * 0.0063 (0.0010) C4 * -0.0054 (0.0011) C5 * -0.0129 (0.0011) C6 * 0.0007 (0.0011) C7 * 0.0188 (0.0012) C8 * 0.0127 (0.0012) C9 - 0.0337 (0.0017) N5 - 0.0311 (0.0023) C10Rms deviation of fitted atoms = 0.0103

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.

	x	y	z	Uiso*/Ueq
N1	−0.0430 (2)	0.25393 (13)	0.50429 (8)	0.0589 (4)
C2	0.1513 (3)	0.32925 (18)	0.49663 (12)	0.0677 (5)
H2	0.2202	0.3987	0.5401	0.081*
N3	0.2352 (2)	0.29646 (15)	0.42273 (9)	0.0675 (4)
C4	0.0831 (2)	0.11583 (16)	0.29522 (9)	0.0546 (4)
H4	0.1996	0.1333	0.2618	0.066*
C5	−0.0929 (2)	0.01590 (15)	0.26336 (10)	0.0561 (4)
N5	−0.1043 (2)	−0.05967 (15)	0.18037 (9)	0.0746 (4)
H5A	−0.0002	−0.0447	0.1475	0.090*
H5B	−0.2155	−0.1214	0.1619	0.090*
C6	−0.2678 (2)	−0.00852 (17)	0.31522 (11)	0.0646 (5)
H6	−0.3861	−0.0754	0.2930	0.077*
C7	−0.2698 (2)	0.06273 (17)	0.39712 (12)	0.0634 (4)
H7	−0.3862	0.0452	0.4306	0.076*
C8	−0.0905 (2)	0.16230 (15)	0.42807 (9)	0.0509 (4)
C9	0.0833 (2)	0.18977 (15)	0.37784 (10)	0.0512 (4)
C10	−0.1765 (3)	0.2690 (2)	0.57695 (12)	0.0796 (5)
H10A	−0.0975	0.3348	0.6237	0.119*
H10B	−0.1962	0.1711	0.6027	0.119*
H10C	−0.3243	0.3112	0.5525	0.119*

	U11	U22	U33	U12	U13	U23
N1	0.0648 (8)	0.0597 (7)	0.0537 (8)	0.0113 (6)	0.0147 (6)	0.0011 (6)
C2	0.0660 (10)	0.0668 (9)	0.0681 (11)	0.0043 (8)	0.0053 (8)	−0.0118 (8)
N3	0.0594 (7)	0.0701 (8)	0.0745 (9)	−0.0073 (6)	0.0156 (6)	−0.0147 (7)
C4	0.0524 (7)	0.0571 (8)	0.0564 (9)	0.0039 (6)	0.0155 (6)	0.0016 (7)
C5	0.0588 (8)	0.0517 (8)	0.0554 (9)	0.0108 (6)	0.0037 (6)	−0.0003 (6)
N5	0.0777 (9)	0.0769 (9)	0.0664 (9)	0.0007 (7)	0.0047 (7)	−0.0173 (7)
C6	0.0566 (8)	0.0562 (9)	0.0806 (12)	−0.0067 (7)	0.0115 (8)	−0.0060 (8)
C7	0.0562 (8)	0.0606 (9)	0.0779 (11)	−0.0014 (7)	0.0243 (7)	0.0048 (8)
C8	0.0541 (8)	0.0483 (7)	0.0513 (8)	0.0090 (6)	0.0116 (6)	0.0050 (6)
C9	0.0465 (7)	0.0493 (7)	0.0580 (8)	0.0032 (6)	0.0099 (6)	−0.0005 (6)
C10	0.0964 (12)	0.0869 (12)	0.0616 (10)	0.0198 (9)	0.0307 (9)	0.0024 (9)

N1—C2	1.350 (2)	N5—H5A	0.8600
N1—C8	1.3785 (18)	N5—H5B	0.8600
N1—C10	1.450 (2)	C6—C7	1.370 (2)
C2—N3	1.313 (2)	C6—H6	0.9300
C2—H2	0.9300	C7—C8	1.391 (2)
N3—C9	1.3879 (19)	C7—H7	0.9300
C4—C5	1.382 (2)	C8—C9	1.3926 (19)
C4—C9	1.3888 (19)	C10—H10A	0.9600
C4—H4	0.9300	C10—H10B	0.9600
C5—N5	1.3917 (19)	C10—H10C	0.9600
C5—C6	1.410 (2)
C2—N1—C8	105.84 (12)	C7—C6—H6	118.8
C2—N1—C10	126.90 (14)	C5—C6—H6	118.8
C8—N1—C10	127.25 (14)	C6—C7—C8	117.22 (13)
N3—C2—N1	114.48 (14)	C6—C7—H7	121.4
N3—C2—H2	122.8	C8—C7—H7	121.4
N1—C2—H2	122.8	N1—C8—C7	132.41 (13)
C2—N3—C9	104.04 (12)	N1—C8—C9	105.93 (12)
C5—C4—C9	119.04 (13)	C7—C8—C9	121.62 (13)
C5—C4—H4	120.5	N3—C9—C4	129.96 (12)
C9—C4—H4	120.5	N3—C9—C8	109.71 (12)
C4—C5—N5	121.66 (14)	C4—C9—C8	120.32 (13)
C4—C5—C6	119.40 (14)	N1—C10—H10A	109.5
N5—C5—C6	118.93 (14)	N1—C10—H10B	109.5
C5—N5—H5A	120.0	H10A—C10—H10B	109.5
C5—N5—H5B	120.0	N1—C10—H10C	109.5
H5A—N5—H5B	120.0	H10A—C10—H10C	109.5
C7—C6—C5	122.39 (14)	H10B—C10—H10C	109.5
C8—N1—C2—N3	0.28 (18)	C10—N1—C8—C9	178.60 (13)
C10—N1—C2—N3	−178.55 (14)	C6—C7—C8—N1	177.97 (14)
N1—C2—N3—C9	−0.21 (18)	C6—C7—C8—C9	0.5 (2)
C9—C4—C5—N5	178.96 (12)	C2—N3—C9—C4	178.98 (14)
C9—C4—C5—C6	0.1 (2)	C2—N3—C9—C8	0.05 (17)
C4—C5—C6—C7	−0.5 (2)	C5—C4—C9—N3	−178.28 (14)
N5—C5—C6—C7	−179.37 (13)	C5—C4—C9—C8	0.6 (2)
C5—C6—C7—C8	0.2 (2)	N1—C8—C9—N3	0.11 (16)
C2—N1—C8—C7	−177.99 (16)	C7—C8—C9—N3	178.17 (13)
C10—N1—C8—C7	0.8 (3)	N1—C8—C9—C4	−178.94 (11)
C2—N1—C8—C9	−0.23 (15)	C7—C8—C9—C4	−0.9 (2)

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5A···N3i	0.86	2.47	3.1447 (19)	136
C2—H2···N5ii	0.93	2.58	3.503 (2)	171

Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N5—H5A⋯N3i	0.86	2.47	3.1447 (19)	136
C2—H2⋯N5ii	0.93	2.58	3.503 (2)	171

Symmetry codes: (i) ; (ii) .