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organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 69| Part 1| January 2013| Page o75
https://doi.org/10.1107/S1600536812048866

2-{[(Di­methyl­amino)­methyl­­idene]amino}-5-nitro­benzo­nitrile

Syed Muhammad Saad,a Syed Moazzam Haider,a Shahnaz Perveen,b Khalid M. Khana and Sammer Yousufa*

aH.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan, and bPCSIR Labortories Complex, Karachi, Shahrah-e-Dr. Salmuzzaman Siddiqui, Karachi 75280, Pakistan
*Correspondence e-mail: dr.sammer.yousuf@gmail.com

(Received 22 November 2012; accepted 28 November 2012; online 12 December 2012)

The title mol­ecule, C10H10N4O2, is almost planar and adopts an E configuration of the azomethine [C=N = 1.298 (2) Å] double bond. The benzene ring is attached to an essentially planar (r.m.s. deviation = 0.0226 Å) amidine moiety (N=CN/Me2), the dihedral angle between the two mean planes being 18.42 (11)°. The cyano group lies in the plane of the benzene ring [the C and N atoms deviating by 0.030 (3) and 0.040 (3) Å, respectively], while the nitro group makes a dihedral angle 5.8 (3)° with the benzene ring. There are two distinct inter­molecular hydrogen bonds, C—H⋯O and C—H⋯N, that stabilize the crystal structure; the former inter­actions result in centrosymmetric dimers about inversion centers resulting in ten-membered rings, while the later give rise to chains of mol­ecules running parallel to the b axis.

Related literature

For the biological activity of amidine derivatives, see: Sienkiewich et al. (2005[Sienkiewich, P., Bielawaski, K., Bielawaska, A. & Palka, J. (2005). Environ. Toxicol. Pharm. 20, 118-124.]); Sasaki et al. (1997[Sasaki, S., Fukushima, J., Arai, H., Kusakabe, K., Hamajima, K., Ishii, N., Hirahara, F., Okuda, K., Kawamoto, S., Ruysschaert, J. M., Vandenbranden, M. & Wahren, B. (1997). Eur. J. Immunol. 27 , 3121-9.]). For a related structure, see: Cizak et al. (1989[Ciszak, E., Gdaniec, M., Jaskólski, M., Kosturkiewicz, Z., Owsiański, J. & Tykarska, E. (1989). Acta Cryst. C45, 433-438.]).

[Scheme 1]

Experimental

Crystal data

  • C10H10N4O2

  • Mr = 218.22

  • Monoclinic, P 21 /n

  • a = 7.6496 (11) Å

  • b = 13.0693 (19) Å

  • c = 11.1617 (17) Å

  • β = 106.475 (3)°

  • V = 1070.1 (3) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.10 mm−1

  • T = 273 K

  • 0.25 × 0.24 × 0.09 mm
Data collection

  • Bruker SMART APEX CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.976, Tmax = 0.991

  • 6194 measured reflections

  • 1976 independent reflections

  • 1427 reflections with I > 2σ(I)

  • Rint = 0.025
Refinement

  • R[F2 > 2σ(F2)] = 0.046

  • wR(F2) = 0.134

  • S = 1.04

  • 1976 reflections

  • 147 parameters

  • H-atom parameters constrained

  • Δρmax = 0.18 e Å−3

  • Δρmin = −0.16 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C1—H1A⋯O1i 0.93 2.48 3.354 (3) 156
C8—H8A⋯N1ii 0.93 2.61 3.525 (2) 166
Symmetry codes: (i) -x+2, -y, -z+2; (ii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{3\over 2}}].

Data collection: SMART (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2000[Bruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL, PARST (Nardelli, 1995[Nardelli, M. (1995). J. Appl. Cryst. 28, 659.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536812048866/pv2610sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536812048866/pv2610Isup2.hkl

Supporting information file. DOI: https://doi.org/10.1107/S1600536812048866/pv2610Isup3.cml

checkCIF report


Comment top

The compounds having amidine group (–N═CHNR2) in their structures are known to have a wide range of pharmacological properties such as anti-HIV (Sasaki et al., 1997) and anticancer (Sienkiewich et al., 2005). The title compound is also an amidine derivatived we have synthesized in order to evaluate its biological potential and determined its crystal structure that is reported here.

In the title compound (Fig. 1) the benzene ring (C1–C6) is attached with an essentially planar amidine moiety (N3/N4/C8–C10) with r.m.s.d 0.0226 Å; the dihedral angle between the two mean planes being 18.42 (11)°. The atoms C7 and N1 of the cyano group lie in the plane of the benzene ring with deviations 0.030 (3) and 0.040 (3) Å, respectively. The nitro group (N2/O1/O2) makes a dihedral angle 5.8 (3) ° with the benzene ring. The bond distances and angles in the title compound agree very well with the corresponding bond distances and angles reported in a closely related compound (Cizak et al., 1989).

There are two distinct intermolecular hydrogen bonds, C1—H1A···O1 and C8—H8A···N1 that stabilize the crystal structure (Table 2 and Fig. 2). The former interactions result in centrosymmetric dimers about inversion centers resulting in 10-membered rings, while the later give rise to chains of molecules running parallel to the b-axis.

Related literature top

For the biological activity of amidine derivatives, see: Sienkiewich et al. (2005); Sasaki et al. (1997). For a related structure, see: Cizak et al. (1989).

Experimental top

5-Nitroanthranilonitrile (45.8 mmol, 7.47 g) was suspended in N,N-dimethylformamide dimethylacetal (137.4 mmol, 16.5 ml) and the mixture was allow to refluxed for 1.5 h. The progress of the reaction was monitored by thin layer chromatography. After the completion of the reaction, the resulting mixture was cooled to room temperature and refrigerated overnight to obtain yellow crystals. The crystals were filtered, washed with diethyl ether to afford the pure compound (9.4 g, 94% yield). Single-crystal suitable for X-ray diffraction studies were grown from ethanol. All chemicals were purchased by Sigma Aldrich Germany.

Refinement top

The H atoms were positioned geometrically and refined using a riding model, with C—H = 0.93 0.96 Å, for aryl and methyl H-atoms, respectively. The Uiso(H) were allowed at 1.5Ueq(C methyl) or 1.2Ueq(C aryl). A rotating group model was applied to the methyl groups.

Structure description top

The compounds having amidine group (–N═CHNR2) in their structures are known to have a wide range of pharmacological properties such as anti-HIV (Sasaki et al., 1997) and anticancer (Sienkiewich et al., 2005). The title compound is also an amidine derivatived we have synthesized in order to evaluate its biological potential and determined its crystal structure that is reported here.

In the title compound (Fig. 1) the benzene ring (C1–C6) is attached with an essentially planar amidine moiety (N3/N4/C8–C10) with r.m.s.d 0.0226 Å; the dihedral angle between the two mean planes being 18.42 (11)°. The atoms C7 and N1 of the cyano group lie in the plane of the benzene ring with deviations 0.030 (3) and 0.040 (3) Å, respectively. The nitro group (N2/O1/O2) makes a dihedral angle 5.8 (3) ° with the benzene ring. The bond distances and angles in the title compound agree very well with the corresponding bond distances and angles reported in a closely related compound (Cizak et al., 1989).

There are two distinct intermolecular hydrogen bonds, C1—H1A···O1 and C8—H8A···N1 that stabilize the crystal structure (Table 2 and Fig. 2). The former interactions result in centrosymmetric dimers about inversion centers resulting in 10-membered rings, while the later give rise to chains of molecules running parallel to the b-axis.

For the biological activity of amidine derivatives, see: Sienkiewich et al. (2005); Sasaki et al. (1997). For a related structure, see: Cizak et al. (1989).

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with the atom numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. H atoms are presented as small spheres of arbitrary radius.
[Figure 2] Fig. 2. A view of the C—-H···O and C—H···N hydrogen bonds (dotted lines) in the crystal structure of the title compound. H atoms non-participating in hydrogen-bonding were omitted for clarity.
2-{[(Dimethylamino)methylidene]amino}-5-nitrobenzonitrile top
Crystal data top
C10H10N4O2F(000) = 456
Mr = 218.22Dx = 1.355 Mg m−3
Monoclinic, P21/nMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ynCell parameters from 1456 reflections
a = 7.6496 (11) Åθ = 2.5–26.3°
b = 13.0693 (19) ŵ = 0.10 mm−1
c = 11.1617 (17) ÅT = 273 K
β = 106.475 (3)°Block, yellow
V = 1070.1 (3) Å30.25 × 0.24 × 0.09 mm
Z = 4
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer		1976 independent reflections
Radiation source: fine-focus sealed tube1427 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.025
ω scanθmax = 25.5°, θmin = 2.5°
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		h = −9→6
Tmin = 0.976, Tmax = 0.991k = −15→15
6194 measured reflectionsl = −13→13
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)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.134H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.0727P)2 + 0.0566P]
where P = (Fo2 + 2Fc2)/3
1976 reflections(Δ/σ)max < 0.001
147 parametersΔρmax = 0.18 e Å−3
0 restraintsΔρmin = −0.16 e Å−3
Crystal data top
C10H10N4O2V = 1070.1 (3) Å3
Mr = 218.22Z = 4
Monoclinic, P21/nMo Kα radiation
a = 7.6496 (11) ŵ = 0.10 mm−1
b = 13.0693 (19) ÅT = 273 K
c = 11.1617 (17) Å0.25 × 0.24 × 0.09 mm
β = 106.475 (3)°
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer		1976 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2000)		1427 reflections with I > 2σ(I)
Tmin = 0.976, Tmax = 0.991Rint = 0.025
6194 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0460 restraints
wR(F2) = 0.134H-atom parameters constrained
S = 1.04Δρmax = 0.18 e Å−3
1976 reflectionsΔρmin = −0.16 e Å−3
147 parameters
Special details top

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) top
xyzUiso*/Ueq
O11.0056 (2)0.13577 (12)1.04462 (17)0.0870 (6)
O20.8695 (2)0.25597 (13)1.11451 (17)0.0883 (6)
N10.4989 (2)−0.15217 (12)0.71893 (17)0.0660 (5)
N20.8674 (2)0.18015 (13)1.04982 (17)0.0619 (5)
N30.1940 (2)0.02940 (11)0.75738 (14)0.0482 (4)
N4−0.1087 (2)0.05091 (12)0.65346 (15)0.0543 (5)
C10.6835 (3)0.05189 (13)0.91041 (16)0.0463 (5)
H1A0.78890.01510.91400.056*
C20.6912 (3)0.14214 (13)0.97521 (17)0.0459 (5)
C30.5357 (3)0.19632 (13)0.97190 (17)0.0488 (5)
H3B0.54390.25651.01760.059*
C40.3696 (3)0.16215 (13)0.90195 (17)0.0501 (5)
H4A0.26570.19940.90110.060*
C50.3520 (2)0.07166 (12)0.83108 (16)0.0426 (4)
C60.5146 (3)0.01730 (12)0.83973 (16)0.0421 (4)
C70.5035 (3)−0.07743 (14)0.77211 (17)0.0490 (5)
C80.0485 (3)0.08563 (14)0.72313 (16)0.0481 (5)
H8A0.05580.15350.74910.058*
C9−0.2656 (3)0.11779 (17)0.6087 (2)0.0711 (7)
H9A−0.24290.18150.65330.107*
H9B−0.37130.08570.62230.107*
H9C−0.28610.13030.52100.107*
C10−0.1270 (3)−0.05486 (17)0.6095 (2)0.0753 (7)
H10A−0.0086−0.08580.62750.113*
H10B−0.1837−0.05600.52090.113*
H10C−0.2008−0.09230.65100.113*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0470 (10)0.0792 (11)0.1247 (15)0.0011 (8)0.0079 (10)−0.0227 (9)
O20.0709 (12)0.0766 (11)0.1064 (13)−0.0137 (8)0.0075 (10)−0.0416 (9)
N10.0732 (13)0.0482 (10)0.0718 (11)0.0013 (8)0.0125 (10)−0.0114 (8)
N20.0528 (12)0.0526 (10)0.0734 (12)−0.0048 (8)0.0068 (9)−0.0053 (8)
N30.0436 (10)0.0425 (8)0.0543 (9)0.0004 (7)0.0070 (8)−0.0005 (6)
N40.0458 (11)0.0553 (10)0.0566 (10)0.0019 (7)0.0059 (8)0.0004 (7)
C10.0453 (12)0.0409 (9)0.0520 (11)0.0044 (8)0.0127 (9)0.0026 (7)
C20.0456 (12)0.0400 (9)0.0493 (10)−0.0033 (8)0.0087 (9)0.0021 (7)
C30.0559 (13)0.0358 (9)0.0518 (11)0.0005 (8)0.0103 (9)−0.0021 (7)
C40.0491 (12)0.0407 (10)0.0577 (11)0.0074 (8)0.0103 (10)−0.0007 (8)
C50.0457 (11)0.0373 (9)0.0432 (10)0.0000 (8)0.0100 (8)0.0063 (7)
C60.0472 (12)0.0342 (8)0.0438 (9)0.0003 (7)0.0109 (8)0.0035 (7)
C70.0506 (12)0.0420 (10)0.0514 (10)0.0023 (8)0.0098 (9)0.0022 (8)
C80.0520 (13)0.0441 (10)0.0449 (10)0.0007 (8)0.0083 (9)0.0033 (7)
C90.0523 (14)0.0767 (15)0.0736 (14)0.0061 (11)0.0004 (11)0.0162 (11)
C100.0629 (16)0.0674 (14)0.0909 (17)−0.0132 (11)0.0141 (13)−0.0176 (12)
Geometric parameters (Å, º) top
O1—N21.222 (2)C3—C41.364 (3)
O2—N21.224 (2)C3—H3B0.9300
N1—C71.138 (2)C4—C51.408 (2)
N2—C21.456 (2)C4—H4A0.9300
N3—C81.298 (2)C5—C61.412 (2)
N3—C51.371 (2)C6—C71.440 (2)
N4—C81.314 (2)C8—H8A0.9300
N4—C91.454 (2)C9—H9A0.9600
N4—C101.460 (2)C9—H9B0.9600
C1—C21.376 (2)C9—H9C0.9600
C1—C61.385 (2)C10—H10A0.9600
C1—H1A0.9300C10—H10B0.9600
C2—C31.375 (3)C10—H10C0.9600
O1—N2—O2123.09 (18)C4—C5—C6116.26 (16)
O1—N2—C2118.95 (17)C1—C6—C5122.42 (16)
O2—N2—C2117.96 (17)C1—C6—C7119.09 (16)
C8—N3—C5119.04 (15)C5—C6—C7118.50 (16)
C8—N4—C9121.57 (17)N1—C7—C6178.4 (2)
C8—N4—C10120.69 (17)N3—C8—N4122.92 (17)
C9—N4—C10117.54 (17)N3—C8—H8A118.5
C2—C1—C6118.24 (17)N4—C8—H8A118.5
C2—C1—H1A120.9N4—C9—H9A109.5
C6—C1—H1A120.9N4—C9—H9B109.5
C3—C2—C1121.29 (17)H9A—C9—H9B109.5
C3—C2—N2119.53 (16)N4—C9—H9C109.5
C1—C2—N2119.18 (17)H9A—C9—H9C109.5
C4—C3—C2120.32 (17)H9B—C9—H9C109.5
C4—C3—H3B119.8N4—C10—H10A109.5
C2—C3—H3B119.8N4—C10—H10B109.5
C3—C4—C5121.44 (17)H10A—C10—H10B109.5
C3—C4—H4A119.3N4—C10—H10C109.5
C5—C4—H4A119.3H10A—C10—H10C109.5
N3—C5—C4127.10 (17)H10B—C10—H10C109.5
N3—C5—C6116.62 (15)
C6—C1—C2—C30.9 (3)C3—C4—C5—N3−179.98 (17)
C6—C1—C2—N2−179.79 (16)C3—C4—C5—C61.8 (3)
O1—N2—C2—C3−174.48 (18)C2—C1—C6—C50.7 (3)
O2—N2—C2—C35.1 (3)C2—C1—C6—C7−179.46 (16)
O1—N2—C2—C16.2 (3)N3—C5—C6—C1179.62 (15)
O2—N2—C2—C1−174.19 (18)C4—C5—C6—C1−2.0 (3)
C1—C2—C3—C4−1.1 (3)N3—C5—C6—C7−0.2 (2)
N2—C2—C3—C4179.63 (17)C4—C5—C6—C7178.12 (16)
C2—C3—C4—C5−0.4 (3)C5—N3—C8—N4−179.43 (17)
C8—N3—C5—C417.3 (3)C9—N4—C8—N3−175.20 (18)
C8—N3—C5—C6−164.50 (16)C10—N4—C8—N3−0.5 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···O1i0.932.483.354 (3)156
C8—H8A···N1ii0.932.613.525 (2)166
Symmetry codes: (i) −x+2, −y, −z+2; (ii) −x+1/2, y+1/2, −z+3/2.

Experimental details

Crystal data
Chemical formulaC10H10N4O2
Mr218.22
Crystal system, space groupMonoclinic, P21/n
Temperature (K)273
a, b, c (Å)7.6496 (11), 13.0693 (19), 11.1617 (17)
β (°) 106.475 (3)
V (Å3)1070.1 (3)
Z4
Radiation typeMo Kα
µ (mm−1)0.10
Crystal size (mm)0.25 × 0.24 × 0.09
Data collection
DiffractometerBruker SMART APEX CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2000)
Tmin, Tmax0.976, 0.991
No. of measured, independent and
observed [I > 2σ(I)] reflections		6194, 1976, 1427
Rint0.025
(sin θ/λ)max (Å−1)0.606
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.046, 0.134, 1.04
No. of reflections1976
No. of parameters147
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å−3)0.18, −0.16

Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PARST (Nardelli, 1995) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C1—H1A···O1i0.93002.48003.354 (3)156.00
C8—H8A···N1ii0.93002.61003.525 (2)166.00
Symmetry codes: (i) −x+2, −y, −z+2; (ii) −x+1/2, y+1/2, −z+3/2.
 

Acknowledgements

The authors are thankful to the Higher Education Commission (HEC) Pakistan (Project No. 20–2073) and the Pakistan Academy of Sciences (PAS) for their financial support.

References

First citationBruker (2000). SADABS, SMART and SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
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Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 69| Part 1| January 2013| Page o75
https://doi.org/10.1107/S1600536812048866
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