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

Yu-Feng Chen; Jin-Yao Chen; Ming-Huang Hong; Jie Lu; Guo-Bin Ren

doi:10.1107/S1600536812022131

. 2012 Jun 13;68(Pt 7):o2015–o2016. doi: 10.1107/S1600536812022131

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

Yu-Feng Chen ^a,^b, Jin-Yao Chen ^b, Ming-Huang Hong ^b, Jie Lu ^c, Guo-Bin Ren ^a,^b,^*

PMCID: PMC3393285 PMID: 22807842

Abstract

The title compound, C₁₆H₁₄F₃N₃OS·H₂O, which had been previously characterized in the space group P-1 [Ren et al. (2011 ▶). Acta Cryst. E67, o270], has now been crystallized from 1-propanol in the monoclinic form in the space group P2₁/c. While the triclinic form is a Z′ = 2 crystal, the new monoclinic polymorph includes one main molecule and one water lattice molecule in the asymmetric unit. In the crystal, the water molecule is sandwiched between neighboring main molecules and behaves as both donor and acceptor in O—H⋯N and N—H⋯O hydrogen bonds with the imidazole N atoms. This pattern of chains parallel to [100] further interacts via O—H⋯N(pyridine) contacts.

Related literature

For the role of the title compound 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 ▶). For the triclinic polymorph of the title hydrate, see: Ren et al. (2011 ▶) and for the structure of the propan-2-ol solvo-polymorph, see: Ma et al. (2012 ▶)

Experimental

Crystal data

C₁₆H₁₄F₃N₃OS·H₂O
M _r = 371.39
Monoclinic,
a = 7.3886 (15) Å
b = 25.497 (5) Å
c = 8.8579 (18) Å
β = 93.64 (3)°
V = 1665.4 (6) Å³
Z = 4
Cu Kα radiation
μ = 2.17 mm⁻¹
T = 296 K
0.27 × 0.16 × 0.15 mm

Data collection

Bruker SMART APEXII diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.592, T _max = 0.737
7679 measured reflections
2827 independent reflections
2713 reflections with I > 2σ(I)
R _int = 0.021

Refinement

R[F ² > 2σ(F ²)] = 0.049
wR(F ²) = 0.152
S = 1.15
2827 reflections
227 parameters
H-atom parameters constrained
Δρ_max = 0.33 e Å⁻³
Δρ_min = −0.54 e Å⁻³

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

Supplementary Material

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812022131/bh2435sup1.cif

e-68-o2015-sup1.cif^{(19.5KB, cif)}

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812022131/bh2435Isup2.hkl

e-68-o2015-Isup2.hkl^{(138.8KB, hkl)}

Supplementary material file. DOI: 10.1107/S1600536812022131/bh2435Isup3.cml

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
O1′—H1′B⋯N2ⁱ	0.85	2.10	2.869 (3)	150
N1—H1A⋯O1′ⁱⁱ	0.86	1.91	2.765 (3)	170
O1′—H1′A⋯N3	0.85	2.36	3.077 (4)	143

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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 and the National Natural Science Foundation of China (Nos. 81102391 and 21176102).

supplementary crystallographic information

Comment

The title compound is the critical reaction intermediate for the synthesis of lansoprazole (Del Rio et al., 2007; Reddy et al., 2008), and its analogs, used as drugs for their anti-ulcer effects (Iwahi et al., 1991). Recently, the compound was successfully crystallized from 1-propanol, and the crystal structure is reported here. A first polymorph was X-ray characterized in space group P1 (Ren et al., 2011).

The asymmetric unit (Fig. 1) contains one independent molecule and one water molecule which are involved in the formation of hydrogen-bonded chains via, N—H···O and O—H···N hydrogen bonds. These chains further interact through O—H···N(pyridine) contacts (Fig. 2). The water molecule could thus be considered to be a hydrogen-bond bridge, which provides stability to the crystal lattice. The hydrogen bond characteristics and geometric parameters are given in Table 1. The geometry of the main molecule is close to that reported for analog systems (Hakim Al-arique et al., 2010; Swamy & Ravikumar, 2007).

Experimental

The raw material was kindly provided by Shanghai Enran Sci-Tech Investment Management Co., Ltd. The compound was dissolved in 1-propanol and suitable crystals were obtained by slow evaporation at room temperature over a period of one week.