Literature DB >> 26594483

Crystal structure of benzimidazolium salicylate.

M Amudha1, P Praveen Kumar2, G Chakkaravarthi3.   

Abstract

In the anion of the title mol-ecular salt, C7H7N2 (+)·C7H5O3 (-) (systematic name: 1H-benzimidazol-3-ium 2-hy-droxy-ben-zo-ate), there is an intra-molecular O-H⋯O hydrogen bond that generates an S(6) ring motif. The CO2 group makes a dihedral angle of 5.33 (15)° with its attached ring. In the crystal, the dihedral angle between the benzimidazolium ring and the anion benzene ring is 75.88 (5)°. Two cations bridge two anions via two pairs of N-H⋯O hydrogen bonds, enclosing an R (4) 4(16) ring motif, forming a four-membered centrosymmetric arrangement. These units are linked via C-H⋯O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C-H⋯π and π-π inter-actions [inter-centroid distances = 3.4156 (7) and 3.8196 (8) Å], forming a three-dimensional structure.

Entities:  

Keywords:  benzimidazolium; crystal structure; hydrogen bonding; salicylate

Year:  2015        PMID: 26594483      PMCID: PMC4647433          DOI: 10.1107/S2056989015017764

Source DB:  PubMed          Journal:  Acta Crystallogr E Crystallogr Commun


Related literature

For biological applications of benzimidazole derivatives, see: Narasimhan et al. (2012 ▸). For related structures, see: Ennajih et al. (2010 ▸); Haque et al. (2012 ▸); Mani et al. (2015 ▸).

Experimental

Crystal data

C7H7N2 +·C7H5O3 M = 256.26 Monoclinic, a = 7.4776 (3) Å b = 6.7002 (2) Å c = 24.9017 (9) Å β = 94.445 (2)° V = 1243.86 (8) Å3 Z = 4 Mo Kα radiation μ = 0.10 mm−1 T = 295 K 0.34 × 0.30 × 0.25 mm

Data collection

Bruker Kappa APEXII CCD diffractometer Absorption correction: multi-scan (SADABS; Sheldrick, 1996 ▸) T min = 0.967, T max = 0.976 23125 measured reflections 4606 independent reflections 3020 reflections with I > 2σ(I) R int = 0.024

Refinement

R[F 2 > 2σ(F 2)] = 0.048 wR(F 2) = 0.142 S = 1.03 4606 reflections 176 parameters 1 restraint H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.35 e Å−3 Δρmin = −0.26 e Å−3

Data collection: APEX2 (Bruker, 2004 ▸); cell refinement: SAINT (Bruker, 2004 ▸); data reduction: SAINT; 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 and PLATON. Crystal structure: contains datablock(s) global, I. DOI: 10.1107/S2056989015017764/su5212sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S2056989015017764/su5212Isup2.hkl Click here for additional data file. Supporting information file. DOI: 10.1107/S2056989015017764/su5212Isup3.cml Click here for additional data file. . DOI: 10.1107/S2056989015017764/su5212fig1.tif The mol­ecular structure of the title salt, with atom labelling. The displacement ellipsoids are drawn at the 30% probability level. Click here for additional data file. b . DOI: 10.1107/S2056989015017764/su5212fig2.tif The crystal packing of the title mol­ecular salt, viewed along the b axis. The N—H⋯O and C—H⋯O hydrogen bonds are shown as dashed lines (see Table 1). H atoms not involved in these inter­actions have been omitted for clarity. CCDC reference: 1426331 Additional supporting information: crystallographic information; 3D view; checkCIF report
C7H7N2+·C7H5O3F(000) = 536
Mr = 256.26Dx = 1.368 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 8207 reflections
a = 7.4776 (3) Åθ = 2.7–31.0°
b = 6.7002 (2) ŵ = 0.10 mm1
c = 24.9017 (9) ÅT = 295 K
β = 94.445 (2)°Block, colourless
V = 1243.86 (8) Å30.34 × 0.30 × 0.25 mm
Z = 4
Bruker Kappa APEXII CCD diffractometer4606 independent reflections
Radiation source: fine-focus sealed tube3020 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.024
ω and φ scanθmax = 39.4°, θmin = 2.7°
Absorption correction: multi-scan (SADABS; Sheldrick, 1996)h = −10→10
Tmin = 0.967, Tmax = 0.976k = −11→9
23125 measured reflectionsl = −35→35
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.048H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.142w = 1/[σ2(Fo2) + (0.0618P)2 + 0.2364P] where P = (Fo2 + 2Fc2)/3
S = 1.03(Δ/σ)max < 0.001
4606 reflectionsΔρmax = 0.35 e Å3
176 parametersΔρmin = −0.26 e Å3
1 restraintExtinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.025 (3)
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.
xyzUiso*/Ueq
C10.85922 (14)0.54826 (15)0.16407 (4)0.0321 (2)
C20.94451 (17)0.73153 (18)0.17277 (5)0.0414 (3)
H21.03470.76920.15110.050*
C30.8971 (2)0.8581 (2)0.21304 (5)0.0499 (3)
H30.95540.97980.21870.060*
C40.76260 (19)0.8026 (2)0.24480 (5)0.0503 (3)
H40.72960.88820.27170.060*
C50.67701 (18)0.6234 (2)0.23729 (5)0.0475 (3)
H50.58660.58780.25910.057*
C60.72508 (16)0.49396 (18)0.19710 (4)0.0391 (3)
C70.91104 (17)0.41505 (16)0.12000 (4)0.0375 (2)
C81.27512 (15)1.05724 (17)0.05515 (5)0.0381 (2)
C91.3448 (2)1.0252 (2)0.10764 (6)0.0562 (4)
H91.33551.12030.13450.067*
C101.4287 (2)0.8448 (3)0.11783 (7)0.0697 (5)
H101.47810.81800.15250.084*
C111.4420 (2)0.7016 (3)0.07804 (8)0.0659 (4)
H111.49810.58100.08700.079*
C121.37525 (18)0.7325 (2)0.02618 (6)0.0516 (3)
H121.38540.6367−0.00040.062*
C131.29132 (15)0.91474 (16)0.01517 (5)0.0371 (2)
C141.14314 (16)1.17020 (18)−0.02020 (5)0.0409 (3)
H141.07971.2524−0.04500.049*
N11.18155 (14)1.21523 (14)0.03109 (4)0.0398 (2)
H1A1.15321.32390.04670.048*
N21.20728 (13)0.99240 (14)−0.03137 (4)0.0400 (2)
H2A1.19810.9351−0.06240.048*
O11.02203 (14)0.47695 (13)0.08885 (4)0.0521 (3)
O20.83774 (17)0.24546 (14)0.11610 (4)0.0613 (3)
O30.63621 (17)0.31901 (17)0.19135 (4)0.0653 (3)
H3A0.680 (3)0.261 (3)0.1658 (7)0.098*
U11U22U33U12U13U23
C10.0371 (5)0.0327 (5)0.0266 (4)0.0025 (4)0.0035 (4)−0.0024 (4)
C20.0442 (6)0.0390 (6)0.0411 (6)−0.0041 (5)0.0050 (5)−0.0034 (4)
C30.0594 (8)0.0395 (6)0.0497 (7)−0.0019 (6)−0.0034 (6)−0.0137 (5)
C40.0556 (7)0.0559 (8)0.0389 (6)0.0139 (6)0.0004 (5)−0.0169 (5)
C50.0454 (6)0.0626 (8)0.0357 (6)0.0047 (6)0.0106 (5)−0.0078 (5)
C60.0413 (6)0.0431 (6)0.0334 (5)−0.0024 (5)0.0065 (4)−0.0031 (4)
C70.0508 (6)0.0334 (5)0.0290 (5)0.0041 (4)0.0074 (4)−0.0012 (4)
C80.0342 (5)0.0409 (6)0.0400 (6)−0.0039 (4)0.0077 (4)−0.0050 (4)
C90.0551 (8)0.0698 (9)0.0426 (7)−0.0019 (7)−0.0021 (6)−0.0076 (6)
C100.0627 (9)0.0871 (12)0.0566 (9)0.0073 (9)−0.0127 (7)0.0111 (8)
C110.0541 (8)0.0583 (9)0.0838 (11)0.0114 (7)−0.0049 (8)0.0125 (8)
C120.0431 (7)0.0421 (6)0.0701 (9)0.0045 (5)0.0083 (6)−0.0051 (6)
C130.0321 (5)0.0367 (5)0.0433 (6)−0.0031 (4)0.0089 (4)−0.0040 (4)
C140.0436 (6)0.0393 (6)0.0409 (6)−0.0013 (5)0.0113 (5)0.0021 (4)
N10.0439 (5)0.0342 (5)0.0426 (5)−0.0009 (4)0.0119 (4)−0.0064 (4)
N20.0454 (5)0.0404 (5)0.0354 (5)−0.0036 (4)0.0100 (4)−0.0066 (4)
O10.0708 (6)0.0415 (5)0.0480 (5)0.0047 (4)0.0301 (4)−0.0018 (4)
O20.0956 (8)0.0428 (5)0.0487 (5)−0.0176 (5)0.0264 (5)−0.0168 (4)
O30.0751 (7)0.0598 (6)0.0656 (7)−0.0275 (5)0.0340 (5)−0.0142 (5)
C1—C21.3929 (16)C8—C131.3913 (16)
C1—C61.3939 (15)C9—C101.376 (2)
C1—C71.4889 (14)C9—H90.9300
C2—C31.3803 (17)C10—C111.388 (3)
C2—H20.9300C10—H100.9300
C3—C41.378 (2)C11—C121.364 (2)
C3—H30.9300C11—H110.9300
C4—C51.367 (2)C12—C131.3902 (17)
C4—H40.9300C12—H120.9300
C5—C61.3922 (16)C13—N21.3769 (15)
C5—H50.9300C14—N21.3219 (15)
C6—O31.3496 (15)C14—N11.3220 (15)
C7—O11.2499 (14)C14—H140.9300
C7—O21.2620 (14)N1—H1A0.8600
C8—N11.3798 (15)N2—H2A0.8600
C8—C91.3861 (18)O3—H3A0.834 (9)
C2—C1—C6118.68 (10)C10—C9—H9121.9
C2—C1—C7120.07 (10)C8—C9—H9121.9
C6—C1—C7121.25 (10)C9—C10—C11122.17 (14)
C3—C2—C1120.96 (12)C9—C10—H10118.9
C3—C2—H2119.5C11—C10—H10118.9
C1—C2—H2119.5C12—C11—C10121.97 (14)
C4—C3—C2119.41 (12)C12—C11—H11119.0
C4—C3—H3120.3C10—C11—H11119.0
C2—C3—H3120.3C11—C12—C13116.52 (13)
C5—C4—C3120.90 (11)C11—C12—H12121.7
C5—C4—H4119.5C13—C12—H12121.7
C3—C4—H4119.5N2—C13—C12131.86 (11)
C4—C5—C6120.08 (12)N2—C13—C8106.47 (10)
C4—C5—H5120.0C12—C13—C8121.64 (12)
C6—C5—H5120.0N2—C14—N1110.72 (11)
O3—C6—C5117.70 (11)N2—C14—H14124.6
O3—C6—C1122.34 (10)N1—C14—H14124.6
C5—C6—C1119.96 (11)C14—N1—C8108.01 (10)
O1—C7—O2123.80 (10)C14—N1—H1A126.0
O1—C7—C1118.80 (10)C8—N1—H1A126.0
O2—C7—C1117.40 (10)C14—N2—C13108.22 (10)
N1—C8—C9132.02 (11)C14—N2—H2A125.9
N1—C8—C13106.57 (10)C13—N2—H2A125.9
C9—C8—C13121.41 (12)C6—O3—H3A105.2 (16)
C10—C9—C8116.28 (14)
C6—C1—C2—C3−0.37 (17)C13—C8—C9—C10−0.6 (2)
C7—C1—C2—C3179.30 (11)C8—C9—C10—C11−0.5 (2)
C1—C2—C3—C4−0.42 (19)C9—C10—C11—C121.1 (3)
C2—C3—C4—C50.6 (2)C10—C11—C12—C13−0.6 (2)
C3—C4—C5—C6−0.1 (2)C11—C12—C13—N2−178.38 (13)
C4—C5—C6—O3−179.93 (12)C11—C12—C13—C8−0.51 (19)
C4—C5—C6—C1−0.75 (19)N1—C8—C13—N20.10 (12)
C2—C1—C6—O3−179.91 (12)C9—C8—C13—N2179.49 (11)
C7—C1—C6—O30.42 (18)N1—C8—C13—C12−178.25 (11)
C2—C1—C6—C50.96 (17)C9—C8—C13—C121.14 (18)
C7—C1—C6—C5−178.71 (11)N2—C14—N1—C8−0.50 (13)
C2—C1—C7—O1−5.18 (17)C9—C8—N1—C14−179.06 (14)
C6—C1—C7—O1174.49 (11)C13—C8—N1—C140.23 (13)
C2—C1—C7—O2175.54 (12)N1—C14—N2—C130.56 (13)
C6—C1—C7—O2−4.79 (17)C12—C13—N2—C14177.72 (13)
N1—C8—C9—C10178.60 (14)C8—C13—N2—C14−0.40 (12)
D—H···AD—HH···AD···AD—H···A
O3—H3A···O20.83 (1)1.78 (1)2.5425 (14)152 (2)
N1—H1A···O1i0.861.812.6139 (13)155
N2—H2A···O2ii0.861.812.6448 (13)164
C14—H14···O1iii0.932.223.1161 (16)161
C3—H3···Cg3iv0.932.813.5779 (15)141
C10—H10···Cg3v0.932.883.6302 (17)139
Table 1

Hydrogen-bond geometry (, )

Cg3 is the centroid of the C1C6 ring.

DHA DHHA D A DHA
O3H3AO20.83(1)1.78(1)2.5425(14)152(2)
N1H1AO1i 0.861.812.6139(13)155
N2H2AO2ii 0.861.812.6448(13)164
C14H14O1iii 0.932.223.1161(16)161
C3H3Cg3iv 0.932.813.5779(15)141
C10H10Cg3v 0.932.883.6302(17)139

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

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