2-{[3-Methyl-4-(2,2,2-trifluoro­eth­oxy)pyridin-2-yl]methyl­sulfan­yl}-1H-benzimidazole monohydrate

Guo-Bin Ren; Ming-Huang Hong; Jia-Liang Zhong; Dong-Xu Yi; Le-Hui Xu

doi:10.1107/S1600536810053730

. 2011 Jan 8;67(Pt 2):o270. doi: 10.1107/S1600536810053730

2-{[3-Methyl-4-(2,2,2-trifluoroethoxy)pyridin-2-yl]methylsulfanyl}-1H-benzimidazole monohydrate

Guo-Bin Ren ^a,^*, Ming-Huang Hong ^a, Jia-Liang Zhong ^a, Dong-Xu Yi ^a, Le-Hui Xu ^a

PMCID: PMC3051707 PMID: 21522962

Abstract

The asymmetric unit of the title compound, C₁₆H₁₄F₃N₃OS·H₂O, contains two independent molecules (A and B) and two water molecules, one of which is disordered over two positions in a 0.790 (8):0.210 (8) ratio. The molecular conformations are close, the benzimidazole mean plane and pyridine ring forming dihedral angles of 1.8 (3) and 0.1 (2)° in molecules A and B, respectively. The water molecules are involved in formation of two independent hydrogen-bonded chains via N—H⋯O and O—H⋯N hydrogen bonds. Chains propagating along the a axis are formed by molecule A and one independent water molecule, while chains propagating along the b axis are formed by molecule B and the other independent water molecule. The crystal packing exhibits π–π interactions, as indicated by short distances of 3.607 (3) and 3.701 (3) Å between the centroids of the imidazole and pyridine rings of neighbouring molecules.

Related literature

The title compound is an intermediate in the synthesis of the anti-ulcer drug lansoprazole [systematic name (RS)-2-([3-methyl-4-(2,2,2-trifluoroethoxy)pyridin-2-yl]methylsulfinyl)-1H-benzo[d]imidazole], see: Del Rio et al. (2007 ▶); Reddy et al. (2008 ▶); Iwahi et al. (1991 ▶). For related structures, see: Swamy & Ravikumar (2007 ▶); Hakim Al-arique et al. (2010 ▶).

Experimental

Crystal data

C₁₆H₁₄F₃N₃OS·H₂O
M _r = 371.39
Triclinic,
a = 7.3526 (1) Å
b = 7.4702 (1) Å
c = 30.6500 (3) Å
α = 88.27°
β = 87.79°
γ = 89.13°
V = 1681.27 (4) Å³
Z = 4
Cu Kα radiation
μ = 2.15 mm⁻¹
T = 296 K
0.28 × 0.12 × 0.10 mm

Data collection

Bruker SMART APEX diffractometer
12461 measured reflections
5446 independent reflections
5282 reflections with I > 2σ(I)
R _int = 0.017

Refinement

R[F ² > 2σ(F ²)] = 0.041
wR(F ²) = 0.117
S = 1.06
5446 reflections
462 parameters
H-atom parameters constrained
Δρ_max = 0.41 e Å⁻³
Δρ_min = −0.32 e Å⁻³

Data collection: SMART (Bruker, 2005 ▶); cell refinement: SAINT (Bruker, 2005 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: XP in SHELXTL (Sheldrick, 2008 ▶); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810053730/cv5015sup1.cif

e-67-0o270-sup1.cif^{(30.4KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536810053730/cv5015Isup2.hkl

e-67-0o270-Isup2.hkl^{(266.6KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

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

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N2A—H2AA⋯OA	0.86	1.95	2.771 (2)	161
OA—HA1⋯N1Aⁱ	0.83	2.00	2.806 (2)	161
N2B—H2BA⋯OB	0.86	1.98	2.799 (3)	160
OB—HB1⋯N1Bⁱⁱ	0.84	2.03	2.798 (3)	152

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Symmetry codes: (i) Inline graphic ; (ii) .

Acknowledgments

This work was supported by the ‘New Drug Innovation 2009ZX09301–007’ project of the Ministry of Science and Technology of China.

supplementary crystallographic information

Comment

The title compound, (I), is important intermediate in the synthesis of lansoprazole (Del Rio et al., 2007; Reddy et al., 2008), which exhibits anti-ulcer effect (Iwahi et al.,1991). Herewith we present its crystal structure.

The asymmetric unit of (I) contains two independent molecules (Fig. 1), A and B, respectively, and two crystalline water molecules, one of which is disordered over two positions in a ratio 0.790 (8):0.210 (8). The molecular conformations of A and B are close - the benzimidazole mean plane and pyridine ring form the dihedral angles of 1.8 (3)° and 0.1 (2)° in A and B, respectively. The bond lengths and angles in A and B are normal and comparable with those observed in the related compounds (Swamy et al., 2007; Hakim,et al., 2010). The torsion angle of C7—S1—C8—C9 in A is 178.85 (12) ° (179.88 (14) ° in B).

The crystalline water molecules are involved in formation of two independent hydrogen-bonded chains via N—H···O and O—H···N hydrogen bonds (Table 1). The chains propagating along the axis a are formed by the molecule A and one independent water molecule, while the chains propagating along the axis b are formed by the molecule B and another independent water molecule. The crystal packing exhibits π-π interactions proved by short distances of 3.607 (3) and 3.701 (3) Å between the centroids of imidazole and pyridine rings from the neighbouring molecules.

Experimental

The raw material was kindly provided by Shanghai Enran Sci-Tech Investment Management Co., Ltd.The compound was dissolved in acetonitrile and suitable crystals of X-ray were obtained by slow evaporation at room temperature over a period of one week.