2-Thio­ureido-1H-benzimidazol-3-ium chloride monohydrate

Abstract

In the title compound, C₈H₉N₄S⁺·Cl⁻·H₂O, the cation is approximately planar, with a dihedral angle of 7.71 (8)° between the mean planes of the benzo­imidazole ring system and the thio­urea unit. In the crystal, cations, anions and water molecules of crystallization are linked by O—H⋯Cl, N—H⋯O, N—H⋯Cl and N—H⋯S hydrogen bonds into a three-dimensional network. π–π stacking is observed between the benzene and imidazole rings of neighbouring mol­ecules, the centroid–centroid distance being 3.5774 (11) Å.

Related literature  

For the synthesis and biological activity of benzimidazoles, see: Siva & Subhash (2011 ▶); Sharghi et al. (2008 ▶); Refaat (2010 ▶); Puratchikody et al. (2008 ▶); Achar et al. (2010 ▶); Starcevic et al. (2007 ▶). For hydrogen-bond classification, see: Jeffrey et al. (1985 ▶).

Experimental  

Crystal data  

• C₈H₉N₄S⁺·Cl⁺·H₂O

• M _r = 246.72

• Monoclinic,

• a = 9.3027 (6) Å

• b = 8.7038 (5) Å

• c = 14.5503 (8) Å

• β = 109.143 (3)°

• V = 1112.97 (11) ų

• Z = 4

• Mo Kα radiation

• μ = 0.51 mm⁻¹

• T = 293 K

• 0.33 × 0.19 × 0.14 mm

Data collection  

• Bruker SMART APEX CCD area-detector diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2001 ▶) T _min = 0.850, T _max = 0.932

• 10318 measured reflections

• 1958 independent reflections

• 1818 reflections with I > 2σ(I)

• R _int = 0.021

Refinement  

• R[F ² > 2σ(F ²)] = 0.032

• wR(F ²) = 0.083

• S = 1.07

• 1958 reflections

• 136 parameters

• H-atom parameters constrained

• Δρ_max = 0.25 e Å⁻³

• Δρ_min = −0.20 e Å⁻³

Data collection: SMART (Bruker, 2007 ▶); cell refinement: SAINT (Bruker, 2007 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012 ▶) and Mercury (Macrae et al., 2008 ▶); software used to prepare material for publication: publCIF (Westrip, 2010 ▶).

Supplementary Material

CCDC reference: 994075

Additional supporting information: crystallographic information; 3D view; checkCIF report

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1O⋯Cl1i	0.81	2.29	3.0991 (15)	179
O1—H2O⋯Cl1	0.87	2.30	3.1443 (14)	165
N1—H1N⋯O1	0.86	2.32	3.064 (2)	145
N1—H2N⋯O1ii	0.86	2.14	3.000 (2)	174
N2—H2⋯O1	0.86	2.03	2.8667 (19)	165
N3—H3N⋯S1	0.80	2.43	3.0146 (14)	131
N4—H4N⋯Cl1	0.83	2.28	3.1055 (15)	175

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

1. Comment

In recent years, Benzimidazole moiety has gained increased interest in drug industry worldwide, as an important pharmocophore exhibiting a wide spectrum of biological and pharmaceutical activities. They act as anti-HIV agents, anti cancer agents (Refaat, 2010), anti-tumor agents (Starcevic et al., 2007), anti-microbial agents (Puratchikody et al., 2008) analgesic and anti-inflammatory agents (Achar et al., 2010).

The title compound (Fig. 1), C₈H₁₁ClN₄OS, crystallized in monoclinic P2₁/c space group with Z=4 (Fig. 2). Two chloride anions and two water molecules are acting as a bridge to connect four molecules of the title compound which resulted in infinite layered type supramolecular architecture. The title compound is mainly stabilized by N—H···O, N—H···Cl, O—H···Cl intermolecular hydrogen bonding which resulted in generating of ring motifs R²₂ (8) and R¹₂ (6). The intramolecular ring motif S¹₁ (6) is also generated due to intramolecular N—H···S hydrogen bonding.

2. Experimental

A mixture of 5-amino-3H-1, 2, 4-dithiazole-3-thione (1.5 g, 0.01 mol) and o-phenylenediamine (1.08 g, 0.01 mol) in absolute ethanol (25 ml) was refluxed for 24 h. The solvent was removed under reduced pressure and the residue was treated with aqueous sodium hydroxide (1 N, 3 × 20 ml) and then filtered after an hour. The filtrate was adjusted to pH 5 by addition of aqueous hydrochloric acid (1 N) and left in a refrigerator overnight. The precipitate (1.8 g, 74%) was collected, washed with water and dried. The title compound was recrystallized from formic acid-propanol mixture to yield small crystals. The melting point was recorded as 248–251°C.

3. Refinement

The structure refinements were performed by full-matrix least-squares on F2. The H positions bound to C atoms were calculated after each cycle of refinement using a riding model C—H = 0.93 Å and U_iso(H) = 1.2U_eq(C). H atoms bound to N and O atoms were located in a difference Fourier map and refined in riding mode, U_iso(H) = 1.2U_eq(N) and 1.5U_eq(O).

Figures

Fig. 1.

ORTEP diagram of 1-(1H-benzo[d]imidazol-2-yl)thiourea salt hydrate (Thermal ellipsoids are drawn at 30% probability level).

Fig. 2.

Crystal packing diagram of the title compound (I).

Fig. 3.

Synthetic scheme of the title compound (I).

Crystal data

C8H9N4S+·Cl+·H2O	F(000) = 512
Mr = 246.72	Dx = 1.472 Mg m−3
Monoclinic, P21/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -p 2ybc	Cell parameters from 5220 reflections
a = 9.3027 (6) Å	θ = 2.3–27.9°
b = 8.7038 (5) Å	µ = 0.51 mm−1
c = 14.5503 (8) Å	T = 293 K
β = 109.143 (3)°	Block, yellow
V = 1112.97 (11) Å3	0.33 × 0.19 × 0.14 mm
Z = 4

Data collection

Bruker SMART APEX CCD area-detector diffractometer	1958 independent reflections
Radiation source: fine-focus sealed tube	1818 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
ω scans	θmax = 25.0°, θmin = 2.3°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −11→11
Tmin = 0.850, Tmax = 0.932	k = −10→10
10318 measured reflections	l = −17→17

Refinement

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)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.083	H-atom parameters constrained
S = 1.07	w = 1/[σ2(Fo2) + (0.041P)2 + 0.391P] where P = (Fo2 + 2Fc2)/3
1958 reflections	(Δ/σ)max < 0.001
136 parameters	Δρmax = 0.25 e Å−3
0 restraints	Δρmin = −0.20 e Å−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.37873 (6)	−0.13735 (5)	0.83964 (4)	0.05278 (17)
N1	0.45104 (18)	0.12730 (17)	0.77931 (11)	0.0483 (4)
H1N	0.4545	0.2261	0.7785	0.058*
H2N	0.4887	0.0771	0.7417	0.058*
N2	0.33167 (17)	0.15159 (16)	0.89088 (10)	0.0415 (3)
H2	0.3490	0.2470	0.8830	0.050*
N3	0.25238 (15)	−0.02567 (16)	0.99381 (10)	0.0372 (3)
H3N	0.2705	−0.1020	0.9695	0.045*
N4	0.22253 (15)	0.22080 (16)	1.00973 (10)	0.0394 (3)
H4N	0.2267	0.3140	0.9987	0.047*
C1	0.38850 (19)	0.0537 (2)	0.83586 (12)	0.0383 (4)
C2	0.27105 (19)	0.11420 (19)	0.96112 (12)	0.0366 (4)
C3	0.19110 (17)	−0.00866 (19)	1.06892 (11)	0.0348 (4)
C4	0.1550 (2)	−0.1157 (2)	1.12841 (13)	0.0421 (4)
H4	0.1668	−0.2207	1.1213	0.051*
C5	0.1006 (2)	−0.0573 (2)	1.19897 (14)	0.0475 (4)
H5	0.0780	−0.1248	1.2418	0.057*
C6	0.0785 (2)	0.1001 (2)	1.20790 (14)	0.0487 (4)
H6	0.0397	0.1343	1.2556	0.058*
C7	0.11296 (19)	0.2059 (2)	1.14772 (13)	0.0445 (4)
H7	0.0972	0.3106	1.1531	0.053*
C8	0.17212 (18)	0.14874 (18)	1.07901 (12)	0.0360 (4)
O1	0.44295 (16)	0.44905 (15)	0.86287 (10)	0.0522 (3)
H1O	0.5262	0.4440	0.9042	0.078*
H2O	0.3841	0.4980	0.8881	0.078*
Cl1	0.23786 (6)	0.57314 (5)	0.98063 (4)	0.05321 (17)

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
S1	0.0756 (4)	0.0303 (3)	0.0653 (3)	−0.0048 (2)	0.0406 (3)	−0.0053 (2)
N1	0.0621 (10)	0.0372 (8)	0.0539 (9)	−0.0004 (7)	0.0303 (8)	0.0037 (7)
N2	0.0569 (9)	0.0264 (7)	0.0446 (8)	−0.0004 (6)	0.0210 (7)	0.0028 (6)
N3	0.0462 (8)	0.0258 (7)	0.0404 (7)	0.0011 (6)	0.0152 (6)	−0.0025 (6)
N4	0.0479 (8)	0.0243 (7)	0.0456 (8)	0.0015 (6)	0.0150 (6)	0.0010 (6)
C1	0.0400 (9)	0.0361 (9)	0.0372 (8)	−0.0004 (7)	0.0104 (7)	0.0009 (7)
C2	0.0411 (9)	0.0288 (8)	0.0372 (8)	0.0000 (7)	0.0092 (7)	0.0006 (7)
C3	0.0347 (8)	0.0307 (8)	0.0371 (8)	0.0004 (6)	0.0094 (7)	−0.0016 (7)
C4	0.0455 (9)	0.0320 (9)	0.0489 (10)	0.0001 (7)	0.0156 (8)	0.0012 (7)
C5	0.0490 (10)	0.0459 (10)	0.0513 (11)	−0.0029 (8)	0.0214 (9)	0.0050 (8)
C6	0.0484 (10)	0.0511 (11)	0.0529 (11)	0.0017 (8)	0.0248 (9)	−0.0047 (9)
C7	0.0445 (10)	0.0356 (9)	0.0531 (10)	0.0049 (7)	0.0156 (8)	−0.0057 (8)
C8	0.0358 (8)	0.0313 (9)	0.0389 (9)	0.0001 (6)	0.0096 (7)	0.0001 (7)
O1	0.0616 (8)	0.0418 (7)	0.0558 (8)	0.0010 (6)	0.0227 (6)	−0.0045 (6)
Cl1	0.0654 (3)	0.0333 (3)	0.0646 (3)	0.0053 (2)	0.0264 (2)	0.0047 (2)

Geometric parameters (Å, º)

S1—C1	1.6673 (18)	C3—C4	1.386 (2)
N1—C1	1.319 (2)	C3—C8	1.395 (2)
N1—H1N	0.8607	C4—C5	1.382 (3)
N1—H2N	0.8592	C4—H4	0.9300
N2—C2	1.359 (2)	C5—C6	1.397 (3)
N2—C1	1.387 (2)	C5—H5	0.9300
N2—H2	0.8606	C6—C7	1.379 (3)
N3—C2	1.339 (2)	C6—H6	0.9300
N3—C3	1.396 (2)	C7—C8	1.382 (2)
N3—H3N	0.7964	C7—H7	0.9300
N4—C2	1.332 (2)	O1—H1O	0.8112
N4—C8	1.393 (2)	O1—H2O	0.8651
N4—H4N	0.8304
C1—N1—H1N	121.3	C4—C3—N3	131.46 (15)
C1—N1—H2N	120.4	C8—C3—N3	106.54 (14)
H1N—N1—H2N	118.4	C5—C4—C3	116.06 (16)
C2—N2—C1	128.15 (14)	C5—C4—H4	122.0
C2—N2—H2	118.3	C3—C4—H4	122.0
C1—N2—H2	113.1	C4—C5—C6	122.05 (18)
C2—N3—C3	108.39 (14)	C4—C5—H5	119.0
C2—N3—H3N	122.0	C6—C5—H5	119.0
C3—N3—H3N	129.5	C7—C6—C5	121.59 (17)
C2—N4—C8	108.90 (13)	C7—C6—H6	119.2
C2—N4—H4N	122.2	C5—C6—H6	119.2
C8—N4—H4N	128.9	C6—C7—C8	116.69 (17)
N1—C1—N2	113.04 (15)	C6—C7—H7	121.7
N1—C1—S1	123.02 (14)	C8—C7—H7	121.7
N2—C1—S1	123.94 (13)	C7—C8—N4	132.05 (15)
N4—C2—N3	109.79 (15)	C7—C8—C3	121.58 (16)
N4—C2—N2	121.94 (15)	N4—C8—C3	106.37 (14)
N3—C2—N2	128.26 (15)	H1O—O1—H2O	107.1
C4—C3—C8	121.98 (16)
C2—N2—C1—N1	−174.63 (16)	C3—C4—C5—C6	2.0 (3)
C2—N2—C1—S1	5.7 (3)	C4—C5—C6—C7	−1.3 (3)
C8—N4—C2—N3	1.18 (19)	C5—C6—C7—C8	−0.8 (3)
C8—N4—C2—N2	−177.76 (15)	C6—C7—C8—N4	−177.98 (17)
C3—N3—C2—N4	−1.16 (18)	C6—C7—C8—C3	2.1 (2)
C3—N3—C2—N2	177.68 (16)	C2—N4—C8—C7	179.38 (17)
C1—N2—C2—N4	178.93 (15)	C2—N4—C8—C3	−0.71 (18)
C1—N2—C2—N3	0.2 (3)	C4—C3—C8—C7	−1.5 (3)
C2—N3—C3—C4	−177.73 (17)	N3—C3—C8—C7	179.93 (15)
C2—N3—C3—C8	0.69 (18)	C4—C3—C8—N4	178.62 (15)
C8—C3—C4—C5	−0.6 (2)	N3—C3—C8—N4	0.01 (17)
N3—C3—C4—C5	177.59 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1O···Cl1i	0.81	2.29	3.0991 (15)	179
O1—H2O···Cl1	0.87	2.30	3.1443 (14)	165
N1—H1N···O1	0.86	2.32	3.064 (2)	145
N1—H2N···O1ii	0.86	2.14	3.000 (2)	174
N2—H2···O1	0.86	2.03	2.8667 (19)	165
N3—H3N···S1	0.80	2.43	3.0146 (14)	131
N4—H4N···Cl1	0.83	2.28	3.1055 (15)	175

Symmetry codes: (i) −x+1, −y+1, −z+2; (ii) −x+1, y−1/2, −z+3/2.