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ISSN: 2414-3146

Benzimidazolium L-aspartate

aDepartment of Physics, Presidency College, Chennai 600 005, India, bDepartment of Physics, Aalim Muhammed Salegh College of Engineering, Chennai 600 055, India, and cDepartment of Physics, CPCL Polytechnic College, Chennai 600 068, India
*Correspondence e-mail: ppkpresidency@gmail.com, chakkaravarthi_2005@yahoo.com

Edited by H. Stoeckli-Evans, University of Neuchâtel, Switzerland (Received 15 April 2016; accepted 21 April 2016; online 4 May 2016)

In the cation of the title mol­ecular salt, C7H7N2+·C4H6NO4 (systematic name: 1H-benzo[d]imidazol-3-ium 2-aza­niumylsuccinate), the benzimidazole ring system is almost planar (r.m.s. deviation = 0.012 Å). The cation is protonated at the N atom and the L-aspartate zwitterion is deprotonated at both carboxyl groups. In the anion, an N—H⋯O hydrogen bond and an N—H⋯O short contact generate S(6) graph-set motifs. In the crystal, the anions are linked via three N—H⋯O hydrogen bonds involving the NH3+ group, forming layers parallel to the ab plane. The benzimidazolium cations are linked to these layers by N—H⋯O hydrogen bonds. The layers are linked via C—H⋯O hydrogen bonds involving the benzimidazolium cation, forming a three-dimensional structure. There are also C—H⋯π inter­actions present involving inversion-related benzimidazolium cations.

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Benzimidazole derivatives possess anti­tumour activities (Lukevics et al., 2001[Lukevics, E., Arsenyan, P., Shestakova, I., Domracheva, I., Nesterova, A. & Pudova, O. (2001). Eur. J. Med. Chem. 36, 507-515.]; Ignatovich et al., 2010[Ignatovich, I., Muravenko, V., Shestakova, I., Domrachova, I., Popelis, J. & Lukevics, E. (2010). Appl. Organomet. Chem. 24, 158-161.]). Herein, we report on the synthesis and the crystal structure of the title mol­ecular salt.

The title compound, Fig. 1[link], contains a benzimidazole cation, which is protonated at atom N1, and a deprotonated L-aspartate zwitterion. The geometric parameters are comparable with those reported for similar structures (Ennajih et al., 2010[Ennajih, H., Bouhfid, R., Zouihri, H., Essassi, E. M. & Ng, S. W. (2010). Acta Cryst. E66, o455.]; Haque et al., 2012[Haque, R. A., Iqbal, M. A., Budagumpi, S., Hemamalini, M. & Fun, H.-K. (2012). Acta Cryst. E68, o573.]). The benzimidazole ring system is almost planar [maximum deviation = 0.016 (1) Å]. In the anion, N3—H3A⋯O2 and N3—H3B⋯O4 short contacts (Table 1[link]) generate S(6) graph-set motifs.

Table 1
Hydrogen-bond geometry (Å, °)

Cg2 is the centroid of the C2–C7 ring.

D—H⋯A D—H H⋯A DA D—H⋯A
N3—H3A⋯O2 0.89 2.38 2.9637 (14) 123
N3—H3B⋯O4 0.89 2.31 2.6544 (15) 103
N1—H1A⋯O1i 0.86 1.77 2.6306 (14) 174
N2—H2⋯O3ii 0.86 1.78 2.6261 (14) 166
N3—H3A⋯O1iii 0.89 2.15 2.8286 (13) 133
N3—H3B⋯O4iv 0.89 1.97 2.8320 (13) 163
N3—H3C⋯O2ii 0.89 1.89 2.7764 (13) 171
C5—H5⋯O3v 0.93 2.53 3.424 (2) 163
C3—H3⋯Cg2vi 0.93 2.98 3.6907 (16) 134
Symmetry codes: (i) x-1, y, z; (ii) x, y+1, z; (iii) [-x+3, y+{\script{1\over 2}}, -z+1]; (iv) [-x+2, y+{\script{1\over 2}}, -z+1]; (v) [-x+2, y+{\script{1\over 2}}, -z]; (vi) [-x+1, y-{\script{1\over 2}}, -z].
[Figure 1]
Figure 1
The mol­ecular structure of the title mol­ecular salt, showing the atom labelling and 30% probability displacement ellipsoids.

In the crystal, the anions are linked via three N—H⋯O hydrogen bonds involving the NH3+ group, forming layers parallel to the ab plane (Table 1[link] and Fig. 2[link]). The benz­imid­azolium cations are linked to these layers by N—H⋯O hydrogen bonds (Table 1[link]), and the layers are linked via C—H⋯O hydrogen bonds, forming a three-dimensional structure (Table 1[link] and Fig. 3[link]). There are also C—H⋯π inter­actions present involving inversion-related benzimidazolium cations (Table 1[link]).

[Figure 2]
Figure 2
A partial view of the crystal packing of the title compound, viewed along the c axis. The N—H⋯O hydrogen bonds linking the anions are shown as dashed lines (see Table 1[link]), and the cations have been omitted for clarity.
[Figure 3]
Figure 3
The crystal packing of the title compound, viewed along the b axis. The hydrogen bonds are shown as dashed lines (see Table 1[link]), and the majority of the C-bound H atoms have been omitted for clarity.

Synthesis and crystallization

Benzimidazole (3 g) and L-aspartic acid (3.35 g) were dissolved in deionized water in a 1:1 molar ratio and stirred well for about 4 h. The homogeneous solution was filtered and allowed to evaporate slowly at room temperature. Crystals of the title compound suitable for X-ray diffraction analysis were obtained within a week.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link].

Table 2
Experimental details

Crystal data
Chemical formula C7H7N2+·C4H6NO4
Mr 251.24
Crystal system, space group Monoclinic, P21
Temperature (K) 295
a, b, c (Å) 8.9612 (3), 5.0796 (2), 12.5535 (4)
β (°) 102.438 (1)
V3) 558.02 (3)
Z 2
Radiation type Mo Kα
μ (mm−1) 0.12
Crystal size (mm) 0.26 × 0.24 × 0.20
 
Data collection
Diffractometer Bruker Kappa APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2004[Bruker (2004). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.971, 0.977
No. of measured, independent and observed [I > 2σ(I)] reflections 15479, 2797, 2659
Rint 0.016
(sin θ/λ)max−1) 0.688
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.028, 0.073, 1.04
No. of reflections 2797
No. of parameters 164
No. of restraints 1
H-atom treatment H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.19, −0.17
Computer programs: APEX2 and SAINT (Bruker, 2004[Bruker (2004). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXS97 and SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]) and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Structural data


Experimental top

Benzimidazole (3 g) and L-aspartic acid (3.35 g) were dissolved in deionized water in a 1:1 molar ratio and stirred well for about 4 h. The saturated solution was filtered and allowed to evaporate slowly at room temperature. Crystals of the title compound suitable for X-ray diffraction analysis were obtained within a week.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2.

Structure description top

Benzimidazole derivatives possess antitumour activities (Lukevics et al., 2001; Ignatovich et al., 2010). Herein, we report on the synthesis and the crystal structure of the title molecular salt.

The title compound, Fig. 1, contains a benzimidazole cation, which is protonated at atom N1, and a deprotonated L-aspartate zwitterion. The geometric parameters are comparable with those reported for similar structures (Ennajih et al., 2010; Haque et al., 2012). The benzimidazole ring system is almost planar [maximum deviation = 0.016 (1) Å]. In the anion, N3—H3A···O2 and N3—H3B···O4 short contacts (Table 1) generate S(6) graph-set motifs.

In the crystal, the anions are linked via three N—H···O hydrogen bonds involving the NH3+ group, forming layers parallel to the ab plane (Table 1 and Fig. 2). The benzimidazolium cations are linked to these layers by N—H···O hydrogen bonds (Table 1), and the layers are linked via C—H···O hydrogen bonds, forming a three-dimensional structure (Table 1 and Fig. 3). There are also C—H···π interactions present involving inversion-related benzimidazolium cations (Table 1).

Computing details top

Data collection: APEX2 (Bruker, 2004); cell refinement: SAINT (Bruker, 2004); data reduction: SAINT (Bruker, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title molecular salt, showing the atom labelling and 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. A partial view of the crystal packing of the title compound, viewed along the c axis. The N—H···O hydrogen bonds linking the anions are shown as dashed lines (see Table 1), and the cations have been omitted for clarity.
[Figure 3] Fig. 3. The crystal packing of the title compound, viewed along the b axis. The hydrogen bonds are shown as dashed lines (see Table 1), and C-bound H atoms have been omitted for clarity.
1H-benzo[d]imidazol-3-ium 2-azaniumylsuccinate top
Crystal data top
C7H7N2+·C4H6NO4F(000) = 264
Mr = 251.24Dx = 1.495 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 9965 reflections
a = 8.9612 (3) Åθ = 2.3–28.8°
b = 5.0796 (2) ŵ = 0.12 mm1
c = 12.5535 (4) ÅT = 295 K
β = 102.438 (1)°Block, colourless
V = 558.02 (3) Å30.26 × 0.24 × 0.20 mm
Z = 2
Data collection top
Bruker Kappa APEXII CCD
diffractometer
2797 independent reflections
Radiation source: fine-focus sealed tube2659 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
ω and φ scanθmax = 29.3°, θmin = 2.3°
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
h = 1212
Tmin = 0.971, Tmax = 0.977k = 66
15479 measured reflectionsl = 1716
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)] = 0.028Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.073H-atom parameters constrained
S = 1.04 w = 1/[σ2(Fo2) + (0.037P)2 + 0.0908P]
where P = (Fo2 + 2Fc2)/3
2797 reflections(Δ/σ)max < 0.001
164 parametersΔρmax = 0.19 e Å3
1 restraintΔρmin = 0.17 e Å3
Crystal data top
C7H7N2+·C4H6NO4V = 558.02 (3) Å3
Mr = 251.24Z = 2
Monoclinic, P21Mo Kα radiation
a = 8.9612 (3) ŵ = 0.12 mm1
b = 5.0796 (2) ÅT = 295 K
c = 12.5535 (4) Å0.26 × 0.24 × 0.20 mm
β = 102.438 (1)°
Data collection top
Bruker Kappa APEXII CCD
diffractometer
2797 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2004)
2659 reflections with I > 2σ(I)
Tmin = 0.971, Tmax = 0.977Rint = 0.016
15479 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0281 restraint
wR(F2) = 0.073H-atom parameters constrained
S = 1.04Δρmax = 0.19 e Å3
2797 reflectionsΔρmin = 0.17 e Å3
164 parameters
Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 > 2sigma(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
C10.77000 (15)0.8587 (3)0.30109 (11)0.0413 (3)
H10.77950.90530.37390.050*
C20.70087 (12)0.6516 (2)0.14622 (10)0.0296 (2)
C30.63857 (16)0.4813 (3)0.06173 (12)0.0427 (3)
H30.57190.34720.07100.051*
C40.6799 (2)0.5205 (4)0.03576 (13)0.0563 (4)
H40.64060.41000.09420.068*
C50.7792 (2)0.7209 (4)0.04961 (13)0.0594 (5)
H50.80490.74000.11710.071*
C60.84112 (17)0.8932 (3)0.03336 (14)0.0504 (4)
H60.90711.02770.02330.061*
C70.79934 (13)0.8547 (2)0.13322 (10)0.0325 (2)
C81.41921 (12)0.4035 (2)0.38084 (9)0.0252 (2)
C91.33481 (12)0.6359 (2)0.31878 (9)0.0257 (2)
H9A1.40230.78740.32900.031*
H9B1.31090.59420.24160.031*
C101.18811 (12)0.7093 (2)0.35329 (9)0.0249 (2)
H101.13650.84330.30220.030*
C111.07617 (12)0.4790 (2)0.35027 (10)0.0294 (2)
N10.68539 (12)0.6614 (2)0.25308 (9)0.0352 (2)
H1A0.63060.55780.28310.042*
N20.83924 (13)0.9809 (2)0.23273 (10)0.0405 (3)
H20.89861.11510.24740.049*
N31.22318 (11)0.8297 (2)0.46337 (8)0.0293 (2)
H3A1.29190.73150.50790.044*
H3B1.13820.83900.48900.044*
H3C1.26050.99090.45930.044*
O11.53603 (9)0.32202 (19)0.34933 (7)0.0364 (2)
O21.37046 (9)0.30887 (17)0.45807 (7)0.03213 (18)
O31.05177 (11)0.3459 (2)0.26439 (8)0.0457 (2)
O41.01562 (12)0.4487 (2)0.42891 (9)0.0497 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0402 (7)0.0411 (7)0.0413 (6)0.0072 (6)0.0056 (5)0.0072 (6)
C20.0237 (5)0.0283 (5)0.0377 (6)0.0031 (4)0.0084 (4)0.0024 (5)
C30.0390 (7)0.0341 (7)0.0516 (8)0.0022 (6)0.0022 (6)0.0049 (6)
C40.0658 (11)0.0570 (10)0.0425 (8)0.0206 (9)0.0038 (7)0.0090 (7)
C50.0665 (10)0.0744 (12)0.0426 (8)0.0330 (10)0.0234 (7)0.0149 (8)
C60.0406 (7)0.0497 (8)0.0675 (9)0.0119 (6)0.0259 (7)0.0256 (7)
C70.0244 (5)0.0273 (6)0.0462 (6)0.0024 (4)0.0082 (4)0.0057 (5)
C80.0234 (5)0.0214 (5)0.0310 (5)0.0023 (4)0.0064 (4)0.0010 (4)
C90.0241 (5)0.0260 (5)0.0290 (5)0.0012 (4)0.0098 (4)0.0040 (4)
C100.0229 (5)0.0218 (5)0.0306 (5)0.0023 (4)0.0075 (4)0.0023 (4)
C110.0210 (5)0.0253 (5)0.0423 (6)0.0026 (4)0.0078 (4)0.0013 (5)
N10.0318 (5)0.0357 (5)0.0413 (5)0.0011 (4)0.0150 (4)0.0029 (5)
N20.0315 (5)0.0291 (5)0.0572 (7)0.0031 (4)0.0017 (5)0.0041 (5)
N30.0300 (5)0.0243 (4)0.0369 (5)0.0049 (4)0.0142 (4)0.0034 (4)
O10.0321 (4)0.0341 (4)0.0468 (5)0.0067 (4)0.0168 (4)0.0021 (4)
O20.0338 (4)0.0277 (4)0.0366 (4)0.0025 (4)0.0115 (3)0.0067 (4)
O30.0422 (5)0.0446 (6)0.0506 (5)0.0180 (5)0.0103 (4)0.0142 (5)
O40.0459 (5)0.0505 (6)0.0616 (6)0.0187 (5)0.0317 (5)0.0050 (5)
Geometric parameters (Å, º) top
C1—N21.3177 (19)C8—O11.2657 (13)
C1—N11.3211 (18)C8—C91.5227 (15)
C1—H10.9300C9—C101.5166 (15)
C2—N11.3789 (16)C9—H9A0.9700
C2—C31.3890 (18)C9—H9B0.9700
C2—C71.3901 (17)C10—N31.4816 (14)
C3—C41.368 (2)C10—C111.5365 (15)
C3—H30.9300C10—H100.9800
C4—C51.387 (3)C11—O41.2342 (15)
C4—H40.9300C11—O31.2511 (15)
C5—C61.382 (3)N1—H1A0.8600
C5—H50.9300N2—H20.8600
C6—C71.3972 (19)N3—H3A0.8900
C6—H60.9300N3—H3B0.8900
C7—N21.3809 (17)N3—H3C0.8900
C8—O21.2427 (13)
N2—C1—N1111.40 (12)C8—C9—H9A108.7
N2—C1—H1124.3C10—C9—H9B108.7
N1—C1—H1124.3C8—C9—H9B108.7
N1—C2—C3131.10 (12)H9A—C9—H9B107.6
N1—C2—C7106.66 (11)N3—C10—C9110.19 (9)
C3—C2—C7122.23 (12)N3—C10—C11110.09 (9)
C4—C3—C2116.82 (15)C9—C10—C11114.02 (9)
C4—C3—H3121.6N3—C10—H10107.4
C2—C3—H3121.6C9—C10—H10107.4
C3—C4—C5121.56 (16)C11—C10—H10107.4
C3—C4—H4119.2O4—C11—O3126.64 (11)
C5—C4—H4119.2O4—C11—C10118.17 (11)
C6—C5—C4122.33 (14)O3—C11—C10115.13 (10)
C6—C5—H5118.8C1—N1—C2107.65 (11)
C4—C5—H5118.8C1—N1—H1A126.2
C5—C6—C7116.47 (15)C2—N1—H1A126.2
C5—C6—H6121.8C1—N2—C7107.69 (12)
C7—C6—H6121.8C1—N2—H2126.2
N2—C7—C2106.60 (11)C7—N2—H2126.2
N2—C7—C6132.80 (13)C10—N3—H3A109.5
C2—C7—C6120.59 (13)C10—N3—H3B109.5
O2—C8—O1124.80 (11)H3A—N3—H3B109.5
O2—C8—C9118.66 (10)C10—N3—H3C109.5
O1—C8—C9116.53 (10)H3A—N3—H3C109.5
C10—C9—C8114.21 (9)H3B—N3—H3C109.5
C10—C9—H9A108.7
N1—C2—C3—C4178.37 (13)C8—C9—C10—N370.83 (12)
C7—C2—C3—C40.71 (19)C8—C9—C10—C1153.54 (13)
C2—C3—C4—C50.1 (2)N3—C10—C11—O49.95 (15)
C3—C4—C5—C60.4 (3)C9—C10—C11—O4134.37 (12)
C4—C5—C6—C70.4 (2)N3—C10—C11—O3172.69 (10)
N1—C2—C7—N20.28 (13)C9—C10—C11—O348.26 (14)
C3—C2—C7—N2179.56 (11)N2—C1—N1—C20.53 (15)
N1—C2—C7—C6178.49 (11)C3—C2—N1—C1179.06 (13)
C3—C2—C7—C60.79 (18)C7—C2—N1—C10.13 (13)
C5—C6—C7—N2178.63 (14)N1—C1—N2—C70.71 (15)
C5—C6—C7—C20.24 (19)C2—C7—N2—C10.59 (14)
O2—C8—C9—C105.63 (14)C6—C7—N2—C1177.96 (14)
O1—C8—C9—C10174.79 (10)
Hydrogen-bond geometry (Å, º) top
Cg2 is the centroid of the C2–C7 ring.
D—H···AD—HH···AD···AD—H···A
N3—H3A···O20.892.382.9637 (14)123
N3—H3B···O40.892.312.6544 (15)103
N1—H1A···O1i0.861.772.6306 (14)174
N2—H2···O3ii0.861.782.6261 (14)166
N3—H3A···O1iii0.892.152.8286 (13)133
N3—H3B···O4iv0.891.972.8320 (13)163
N3—H3C···O2ii0.891.892.7764 (13)171
C5—H5···O3v0.932.533.424 (2)163
C3—H3···Cg2vi0.932.983.6907 (16)134
Symmetry codes: (i) x1, y, z; (ii) x, y+1, z; (iii) x+3, y+1/2, z+1; (iv) x+2, y+1/2, z+1; (v) x+2, y+1/2, z; (vi) x+1, y1/2, z.
Hydrogen-bond geometry (Å, º) top
Cg2 is the centroid of the C2–C7 ring.
D—H···AD—HH···AD···AD—H···A
N3—H3A···O20.892.382.9637 (14)123
N3—H3B···O40.892.312.6544 (15)103
N1—H1A···O1i0.861.772.6306 (14)174
N2—H2···O3ii0.861.782.6261 (14)166
N3—H3A···O1iii0.892.152.8286 (13)133
N3—H3B···O4iv0.891.972.8320 (13)163
N3—H3C···O2ii0.891.892.7764 (13)171
C5—H5···O3v0.932.533.424 (2)163
C3—H3···Cg2vi0.932.983.6907 (16)134
Symmetry codes: (i) x1, y, z; (ii) x, y+1, z; (iii) x+3, y+1/2, z+1; (iv) x+2, y+1/2, z+1; (v) x+2, y+1/2, z; (vi) x+1, y1/2, z.

Experimental details

Crystal data
Chemical formulaC7H7N2+·C4H6NO4
Mr251.24
Crystal system, space groupMonoclinic, P21
Temperature (K)295
a, b, c (Å)8.9612 (3), 5.0796 (2), 12.5535 (4)
β (°) 102.438 (1)
V3)558.02 (3)
Z2
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.26 × 0.24 × 0.20
Data collection
DiffractometerBruker Kappa APEXII CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2004)
Tmin, Tmax0.971, 0.977
No. of measured, independent and
observed [I > 2σ(I)] reflections
15479, 2797, 2659
Rint0.016
(sin θ/λ)max1)0.688
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.028, 0.073, 1.04
No. of reflections2797
No. of parameters164
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.19, 0.17

Computer programs: APEX2 (Bruker, 2004), SAINT (Bruker, 2004), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

 

Acknowledgements

The authors acknowledge the SAIF, IIT, Madras, for the data collection.

References

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