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

Lokaj, J.; Kettmann, V.; Milata, V.; Solčan, T.

doi:10.1107/S1600536809025550

organic compounds

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ISSN: 2056-9890

Volume 65| Part 8| August 2009| Page o1788

doi:10.1107/S1600536809025550

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

Jan Lokaj,^a Viktor Kettmann,^b ^* Viktor Milata ^a and Tomáš Solčan ^a

^aFaculty of Food and Chemical Technology, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovak Republic, and ^bFaculty of Pharmacy, Comenius University, Odbojarov 10, SK-83232 Bratislava, Slovak Republic
^*Correspondence e-mail: kettmann@fpharm.uniba.sk

(Received 5 June 2009; accepted 1 July 2009; online 8 July 2009)

The structure of the title compound, C₈H₉N₃, a potential antitumour drug, was determined in order to give more insight into its structure–function relationships. The benzimidazole core of the molecule was found to be exactly planar, while the substituents are displaced slightly from the molecular 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 intermolecular 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 $[Kettmann, V., Košťálová, D. & H\>oltje, H.-D. (2004). J. Comput. Aided Mol. Des. 18, 785-797.]$ ); 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_r = 147.18
Monoclinic, P 2₁ /n
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 $[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ) 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[F² > 2σ(F²)] = 0.046
wR(F²) = 0.141
S = 1.02
1832 reflections
101 parameters
H-atom parameters constrained
Δρ_max = 0.21 e Å⁻³
Δρ_min = −0.21 e Å⁻³

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) $[-x+{\script{1\over 2}}, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ ; (ii) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: CrysAlis CCD (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); cell refinement: CrysAlis RED (Oxford Diffraction, 2009 $[Oxford Diffraction (2009). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Yarnton, England.]$ ); 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 ).

Supporting information

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

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

checkCIF report

Comment top

Benzimidazole derivatives are known to possess a variety of biological properties (Le et al., 2004), the anti-cancer activity being one of the most important (Nguyen et al., 2004). Previously, it was shown that (a) introduction of a small substituent to the benzo-ring of 1H-benzimidazoles has a profound effect on the cytotoxic activity (Statkova-Abeghe et al., 2005) and (2) the activity is related to intercalative interaction of the drug molecule with the nuclear DNA or the DNA-topoisomerase binary complex (Kettmann et al., 2004). It is, however, unclear whether the influence of the substituents reflects their effect on the charge distribution of the heterocycle (and hence the intercalative energy) or results from interaction of the substituents with additional DNA or enzyme functionalities. Consequently, we prepared a series of substituted 1-methylbenzimidazoles and determined and compared their molecular and electronic structures by using theoretical and experimental techniques. In this communication we report the crystal structure of the 5-amino derivative, (I).

As expected, the ring system of the molecule is planar (Fig.1) to within experimental error and the substituents are slightly displaced to the same side of the plane, as indicated by torsion angles of 0.8 (3)° (C7-C8-N1-C10) and 179.0 (1)° (C9-C4-C5-N5) for the methyl and amino groups, respectively.

As mentioned above, the main purpose of this work was to compare precise molecular dimensions in the present derivative, (I), with those of the unsubstituted 1-methylbenzimidazole. As the latter compound has no entry in the Cambridge Structural Database (CSD, version 5.30 of November 2008; Allen, 2002), the CSD was searched for compounds possessing the benzimidazole core and just one substituent with the methylene group in the α-position; 42 such compounds [hereafter (II)] were found. The comparison has shown that the corresponding bond lengths in the benzimidazole heterocycle in (I) and in the molecules of (II) are significantly different. More specifically, the corresponding bond lengths are [the first number concerns compound (I), second number represents an average through 42 compounds (II)]: C4—C5: 1.382 (2), 1.355 (3); C5—C6: 1.410 (2), 1.387 (3); C6—C7: 1.370 (2), 1.387 (3); C7—C8: 1.391 (2), 1.370 (3); C8—C9: 1.393 (2), 1.397 (2); C9—C4: 1.389 (2), 1.403 (3) Å. This, along with the partial double-bond character of C5–N5 (according to the bond-order - bond-length curves proposed by Burke-Laing & Laing, 1976) indicates that the amino group is conjugated with the benzimidazole ring. This further implies that for the present derivative the intercalative energy makes an important contribution to the overall drug-DNA binding energy and hence the enhanced cytotoxic activity of (I) relative to (II) (Kettmann et al., 2004). These results will serve as a basis for subsequent molecular-modelling studies of the DNA-enzyme-ligand interactions.

The crystal packing is dominated by two intermolecular N–H···N and C–H···N hydrogen bonds (Table 1). It is notable that the amino N5 atom accepts a (weak) hydrogen bond but only one of the two N–H donors is involved in hydrogen bonding.

Related literature top

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 top

As described in detail previously (Milata et al., 1989), the title compound, (I), was synthesized by starting from 2,4-dinitrochlorobenzene via nucleophilic substitution of the chlorine with methylamine, followed by partial Zinnin reduction of the ortho-nitro group and subsequent cyclization to obtain 1-methyl-5-nitrobenzimidazole which after reduction gives the target compound (m.p. 430–432 K).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2009); cell refinement: CrysAlis RED (Oxford Diffraction, 2009); data reduction: CrysAlis RED (Oxford Diffraction, 2009); 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).

Figures top

Fig. 1. Perspective view of (I), with the atom numbering scheme. Thermal ellipsoids are drawn at the 50% probability level.

5-Amino-1-methyl-1H-benzimidazole top

Crystal data top

C₈H₉N₃	F(000) = 312
M_r = 147.18	D_x = 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

Data collection top

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

Refinement top

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(F_o²) + (0.086P)²] where P = (F_o² + 2F_c²)/3
1832 reflections	(Δ/σ)_max = 0.001
101 parameters	Δρ_max = 0.21 e Å⁻³
0 restraints	Δρ_min = −0.21 e Å⁻³

Crystal data top

C₈H₉N₃	V = 762.08 (5) Å³
M_r = 147.18	Z = 4
Monoclinic, P2₁/n	Mo Kα radiation
a = 5.9128 (2) Å	µ = 0.08 mm⁻¹
b = 8.8215 (3) Å	T = 296 K
c = 14.8418 (6) Å	0.52 × 0.20 × 0.10 mm
β = 100.129 (3)°

Data collection top

Oxford Diffraction Gemini R CCD diffractometer	1832 independent reflections
Absorption correction: analytical [CrysAlis RED (Oxford Diffraction, 2009) based on Clark & Reid (1995)]	1114 reflections with I > 2σ(I)
T_min = 0.944, T_max = 0.966	R_int = 0.039
18508 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.046	0 restraints
wR(F²) = 0.141	H-atom parameters constrained
S = 1.02	Δρ_max = 0.21 e Å⁻³
1832 reflections	Δρ_min = −0.21 e Å⁻³
101 parameters

Special details top

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) C10

Rms 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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
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*

Atomic displacement parameters (Å²) top

	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)

Geometric parameters (Å, º) top

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)

Hydrogen-bond geometry (Å, º) top

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) −x+1/2, y−1/2, −z+1/2; (ii) x+1/2, −y+1/2, z+1/2.

Experimental details

Crystal data
Chemical formula	C₈H₉N₃
M_r	147.18
Crystal system, space group	Monoclinic, P2₁/n
Temperature (K)	296
a, b, c (Å)	5.9128 (2), 8.8215 (3), 14.8418 (6)
β (°)	100.129 (3)
V (Å³)	762.08 (5)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.52 × 0.20 × 0.10

Data collection
Diffractometer	Oxford Diffraction Gemini R CCD diffractometer
Absorption correction	Analytical [CrysAlis RED (Oxford Diffraction, 2009) based on Clark & Reid (1995)]
T_min, T_max	0.944, 0.966
No. of measured, independent and observed [I > 2σ(I)] reflections	18508, 1832, 1114
R_int	0.039
(sin θ/λ)_max (Å⁻¹)	0.661

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.046, 0.141, 1.02
No. of reflections	1832
No. of parameters	101
H-atom treatment	H-atom parameters constrained
Δρ_max, Δρ_min (e Å⁻³)	0.21, −0.21

Computer programs: CrysAlis CCD (Oxford Diffraction, 2009), CrysAlis RED (Oxford Diffraction, 2009), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), enCIFer (Allen et al., 2004).

Selected bond lengths (Å) top

C4—C5	1.382 (2)	C6—C7	1.370 (2)
C4—C9	1.3888 (19)	C7—C8	1.391 (2)
C5—N5	1.3917 (19)	C8—C9	1.3926 (19)
C5—C6	1.410 (2)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N5—H5A···N3ⁱ	0.86	2.47	3.1447 (19)	136.4
C2—H2···N5ⁱⁱ	0.93	2.58	3.503 (2)	170.6

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

Acknowledgements

This work was supported by the Grant Agency of the Slovak Republic (project Nos. 1/4298/07 and 1/0225/08) as well as by the Science and Technology Assistance Agency (contract No. APVT-0055–07), AV 4/2006/08. The authors also thank the Structural Funds, Interreg IIIA, for financial support in purchasing the diffractometer.

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