organic compounds
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
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.
Keywords: crystal structure; molecular salt; benzimidazolium; L-aspartate; hydrogen bonding..
CCDC reference: 1475811
Structure description
Benzimidazole derivatives possess antitumour activities (Lukevics et al., 2001; Ignatovich et al., 2010). Herein, we report on the synthesis and the 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).
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 were obtained within a week.
Refinement
Crystal data, data collection and structure .
details are summarized in Table 2
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Structural data
CCDC reference: 1475811
10.1107/S2414314616006775/su4038sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2414314616006775/su4038Isup2.hkl
Supporting information file. DOI: 10.1107/S2414314616006775/su4038Isup3.cml
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
was filtered and allowed to evaporate slowly at room temperature. Crystals of the title compound suitable for X-ray were obtained within a week.Benzimidazole derivatives possess antitumour activities (Lukevics et al., 2001; Ignatovich et al., 2010). Herein, we report on the synthesis and the
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).
Data collection: APEX2 (Bruker, 2004); cell
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).Fig. 1. The molecular structure of the title molecular salt, showing the atom labelling and 30% probability displacement ellipsoids. | |
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. | |
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. |
C7H7N2+·C4H6NO4− | F(000) = 264 |
Mr = 251.24 | Dx = 1.495 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 9965 reflections |
a = 8.9612 (3) Å | θ = 2.3–28.8° |
b = 5.0796 (2) Å | µ = 0.12 mm−1 |
c = 12.5535 (4) Å | T = 295 K |
β = 102.438 (1)° | Block, colourless |
V = 558.02 (3) Å3 | 0.26 × 0.24 × 0.20 mm |
Z = 2 |
Bruker Kappa APEXII CCD diffractometer | 2797 independent reflections |
Radiation source: fine-focus sealed tube | 2659 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.016 |
ω and φ scan | θmax = 29.3°, θmin = 2.3° |
Absorption correction: multi-scan (SADABS; Bruker, 2004) | h = −12→12 |
Tmin = 0.971, Tmax = 0.977 | k = −6→6 |
15479 measured reflections | l = −17→16 |
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)] = 0.028 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.073 | H-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 parameters | Δρmax = 0.19 e Å−3 |
1 restraint | Δρmin = −0.17 e Å−3 |
C7H7N2+·C4H6NO4− | V = 558.02 (3) Å3 |
Mr = 251.24 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 8.9612 (3) Å | µ = 0.12 mm−1 |
b = 5.0796 (2) Å | T = 295 K |
c = 12.5535 (4) Å | 0.26 × 0.24 × 0.20 mm |
β = 102.438 (1)° |
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 = 0.977 | Rint = 0.016 |
15479 measured reflections |
R[F2 > 2σ(F2)] = 0.028 | 1 restraint |
wR(F2) = 0.073 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.19 e Å−3 |
2797 reflections | Δρmin = −0.17 e Å−3 |
164 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.77000 (15) | 0.8587 (3) | 0.30109 (11) | 0.0413 (3) | |
H1 | 0.7795 | 0.9053 | 0.3739 | 0.050* | |
C2 | 0.70087 (12) | 0.6516 (2) | 0.14622 (10) | 0.0296 (2) | |
C3 | 0.63857 (16) | 0.4813 (3) | 0.06173 (12) | 0.0427 (3) | |
H3 | 0.5719 | 0.3472 | 0.0710 | 0.051* | |
C4 | 0.6799 (2) | 0.5205 (4) | −0.03576 (13) | 0.0563 (4) | |
H4 | 0.6406 | 0.4100 | −0.0942 | 0.068* | |
C5 | 0.7792 (2) | 0.7209 (4) | −0.04961 (13) | 0.0594 (5) | |
H5 | 0.8049 | 0.7400 | −0.1171 | 0.071* | |
C6 | 0.84112 (17) | 0.8932 (3) | 0.03336 (14) | 0.0504 (4) | |
H6 | 0.9071 | 1.0277 | 0.0233 | 0.061* | |
C7 | 0.79934 (13) | 0.8547 (2) | 0.13322 (10) | 0.0325 (2) | |
C8 | 1.41921 (12) | 0.4035 (2) | 0.38084 (9) | 0.0252 (2) | |
C9 | 1.33481 (12) | 0.6359 (2) | 0.31878 (9) | 0.0257 (2) | |
H9A | 1.4023 | 0.7874 | 0.3290 | 0.031* | |
H9B | 1.3109 | 0.5942 | 0.2416 | 0.031* | |
C10 | 1.18811 (12) | 0.7093 (2) | 0.35329 (9) | 0.0249 (2) | |
H10 | 1.1365 | 0.8433 | 0.3022 | 0.030* | |
C11 | 1.07617 (12) | 0.4790 (2) | 0.35027 (10) | 0.0294 (2) | |
N1 | 0.68539 (12) | 0.6614 (2) | 0.25308 (9) | 0.0352 (2) | |
H1A | 0.6306 | 0.5578 | 0.2831 | 0.042* | |
N2 | 0.83924 (13) | 0.9809 (2) | 0.23273 (10) | 0.0405 (3) | |
H2 | 0.8986 | 1.1151 | 0.2474 | 0.049* | |
N3 | 1.22318 (11) | 0.8297 (2) | 0.46337 (8) | 0.0293 (2) | |
H3A | 1.2919 | 0.7315 | 0.5079 | 0.044* | |
H3B | 1.1382 | 0.8390 | 0.4890 | 0.044* | |
H3C | 1.2605 | 0.9909 | 0.4593 | 0.044* | |
O1 | 1.53603 (9) | 0.32202 (19) | 0.34933 (7) | 0.0364 (2) | |
O2 | 1.37046 (9) | 0.30887 (17) | 0.45807 (7) | 0.03213 (18) | |
O3 | 1.05177 (11) | 0.3459 (2) | 0.26439 (8) | 0.0457 (2) | |
O4 | 1.01562 (12) | 0.4487 (2) | 0.42891 (9) | 0.0497 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0402 (7) | 0.0411 (7) | 0.0413 (6) | 0.0072 (6) | 0.0056 (5) | −0.0072 (6) |
C2 | 0.0237 (5) | 0.0283 (5) | 0.0377 (6) | 0.0031 (4) | 0.0084 (4) | 0.0024 (5) |
C3 | 0.0390 (7) | 0.0341 (7) | 0.0516 (8) | 0.0022 (6) | 0.0022 (6) | −0.0049 (6) |
C4 | 0.0658 (11) | 0.0570 (10) | 0.0425 (8) | 0.0206 (9) | 0.0038 (7) | −0.0090 (7) |
C5 | 0.0665 (10) | 0.0744 (12) | 0.0426 (8) | 0.0330 (10) | 0.0234 (7) | 0.0149 (8) |
C6 | 0.0406 (7) | 0.0497 (8) | 0.0675 (9) | 0.0119 (6) | 0.0259 (7) | 0.0256 (7) |
C7 | 0.0244 (5) | 0.0273 (6) | 0.0462 (6) | 0.0024 (4) | 0.0082 (4) | 0.0057 (5) |
C8 | 0.0234 (5) | 0.0214 (5) | 0.0310 (5) | −0.0023 (4) | 0.0064 (4) | −0.0010 (4) |
C9 | 0.0241 (5) | 0.0260 (5) | 0.0290 (5) | −0.0012 (4) | 0.0098 (4) | 0.0040 (4) |
C10 | 0.0229 (5) | 0.0218 (5) | 0.0306 (5) | −0.0023 (4) | 0.0075 (4) | 0.0023 (4) |
C11 | 0.0210 (5) | 0.0253 (5) | 0.0423 (6) | −0.0026 (4) | 0.0078 (4) | 0.0013 (5) |
N1 | 0.0318 (5) | 0.0357 (5) | 0.0413 (5) | 0.0011 (4) | 0.0150 (4) | 0.0029 (5) |
N2 | 0.0315 (5) | 0.0291 (5) | 0.0572 (7) | −0.0031 (4) | 0.0017 (5) | −0.0041 (5) |
N3 | 0.0300 (5) | 0.0243 (4) | 0.0369 (5) | −0.0049 (4) | 0.0142 (4) | −0.0034 (4) |
O1 | 0.0321 (4) | 0.0341 (4) | 0.0468 (5) | 0.0067 (4) | 0.0168 (4) | 0.0021 (4) |
O2 | 0.0338 (4) | 0.0277 (4) | 0.0366 (4) | −0.0025 (4) | 0.0115 (3) | 0.0067 (4) |
O3 | 0.0422 (5) | 0.0446 (6) | 0.0506 (5) | −0.0180 (5) | 0.0103 (4) | −0.0142 (5) |
O4 | 0.0459 (5) | 0.0505 (6) | 0.0616 (6) | −0.0187 (5) | 0.0317 (5) | −0.0050 (5) |
C1—N2 | 1.3177 (19) | C8—O1 | 1.2657 (13) |
C1—N1 | 1.3211 (18) | C8—C9 | 1.5227 (15) |
C1—H1 | 0.9300 | C9—C10 | 1.5166 (15) |
C2—N1 | 1.3789 (16) | C9—H9A | 0.9700 |
C2—C3 | 1.3890 (18) | C9—H9B | 0.9700 |
C2—C7 | 1.3901 (17) | C10—N3 | 1.4816 (14) |
C3—C4 | 1.368 (2) | C10—C11 | 1.5365 (15) |
C3—H3 | 0.9300 | C10—H10 | 0.9800 |
C4—C5 | 1.387 (3) | C11—O4 | 1.2342 (15) |
C4—H4 | 0.9300 | C11—O3 | 1.2511 (15) |
C5—C6 | 1.382 (3) | N1—H1A | 0.8600 |
C5—H5 | 0.9300 | N2—H2 | 0.8600 |
C6—C7 | 1.3972 (19) | N3—H3A | 0.8900 |
C6—H6 | 0.9300 | N3—H3B | 0.8900 |
C7—N2 | 1.3809 (17) | N3—H3C | 0.8900 |
C8—O2 | 1.2427 (13) | ||
N2—C1—N1 | 111.40 (12) | C8—C9—H9A | 108.7 |
N2—C1—H1 | 124.3 | C10—C9—H9B | 108.7 |
N1—C1—H1 | 124.3 | C8—C9—H9B | 108.7 |
N1—C2—C3 | 131.10 (12) | H9A—C9—H9B | 107.6 |
N1—C2—C7 | 106.66 (11) | N3—C10—C9 | 110.19 (9) |
C3—C2—C7 | 122.23 (12) | N3—C10—C11 | 110.09 (9) |
C4—C3—C2 | 116.82 (15) | C9—C10—C11 | 114.02 (9) |
C4—C3—H3 | 121.6 | N3—C10—H10 | 107.4 |
C2—C3—H3 | 121.6 | C9—C10—H10 | 107.4 |
C3—C4—C5 | 121.56 (16) | C11—C10—H10 | 107.4 |
C3—C4—H4 | 119.2 | O4—C11—O3 | 126.64 (11) |
C5—C4—H4 | 119.2 | O4—C11—C10 | 118.17 (11) |
C6—C5—C4 | 122.33 (14) | O3—C11—C10 | 115.13 (10) |
C6—C5—H5 | 118.8 | C1—N1—C2 | 107.65 (11) |
C4—C5—H5 | 118.8 | C1—N1—H1A | 126.2 |
C5—C6—C7 | 116.47 (15) | C2—N1—H1A | 126.2 |
C5—C6—H6 | 121.8 | C1—N2—C7 | 107.69 (12) |
C7—C6—H6 | 121.8 | C1—N2—H2 | 126.2 |
N2—C7—C2 | 106.60 (11) | C7—N2—H2 | 126.2 |
N2—C7—C6 | 132.80 (13) | C10—N3—H3A | 109.5 |
C2—C7—C6 | 120.59 (13) | C10—N3—H3B | 109.5 |
O2—C8—O1 | 124.80 (11) | H3A—N3—H3B | 109.5 |
O2—C8—C9 | 118.66 (10) | C10—N3—H3C | 109.5 |
O1—C8—C9 | 116.53 (10) | H3A—N3—H3C | 109.5 |
C10—C9—C8 | 114.21 (9) | H3B—N3—H3C | 109.5 |
C10—C9—H9A | 108.7 | ||
N1—C2—C3—C4 | −178.37 (13) | C8—C9—C10—N3 | 70.83 (12) |
C7—C2—C3—C4 | 0.71 (19) | C8—C9—C10—C11 | −53.54 (13) |
C2—C3—C4—C5 | −0.1 (2) | N3—C10—C11—O4 | 9.95 (15) |
C3—C4—C5—C6 | −0.4 (3) | C9—C10—C11—O4 | 134.37 (12) |
C4—C5—C6—C7 | 0.4 (2) | N3—C10—C11—O3 | −172.69 (10) |
N1—C2—C7—N2 | −0.28 (13) | C9—C10—C11—O3 | −48.26 (14) |
C3—C2—C7—N2 | −179.56 (11) | N2—C1—N1—C2 | 0.53 (15) |
N1—C2—C7—C6 | 178.49 (11) | C3—C2—N1—C1 | 179.06 (13) |
C3—C2—C7—C6 | −0.79 (18) | C7—C2—N1—C1 | −0.13 (13) |
C5—C6—C7—N2 | 178.63 (14) | N1—C1—N2—C7 | −0.71 (15) |
C5—C6—C7—C2 | 0.24 (19) | C2—C7—N2—C1 | 0.59 (14) |
O2—C8—C9—C10 | −5.63 (14) | C6—C7—N2—C1 | −177.96 (14) |
O1—C8—C9—C10 | 174.79 (10) |
Cg2 is the centroid of the C2–C7 ring. |
D—H···A | D—H | H···A | D···A | 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+1/2, −z+1; (iv) −x+2, y+1/2, −z+1; (v) −x+2, y+1/2, −z; (vi) −x+1, y−1/2, −z. |
Cg2 is the centroid of the C2–C7 ring. |
D—H···A | D—H | H···A | D···A | 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+1/2, −z+1; (iv) −x+2, y+1/2, −z+1; (v) −x+2, y+1/2, −z; (vi) −x+1, y−1/2, −z. |
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) |
V (Å3) | 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) |
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 (Å−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 (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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