2-{[3-Methyl-4-(2,2,2-trifluoro-eth-oxy)pyridin-2-yl]methyl-sulfan-yl}-1H-benzimidazole monohydrate: a monoclinic polymorph.

The title compound, C(16)H(14)F(3)N(3)OS·H(2)O, 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 P2(1)/c. While the triclinic form is a Z' = 2 crystal, the new monoclinic polymorph includes one main mol-ecule and one water lattice mol-ecule in the asymmetric unit. In the crystal, the water mol-ecule is sandwiched between neighboring main mol-ecules 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 inter-acts 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 = 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

Δρmax = 0.33 e Å−3

Δρmin = −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.

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

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

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

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

C16H14F3N3OS·H2O	F(000) = 768
Mr = 371.39	Dx = 1.481 Mg m−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ybc	Cell parameters from 2713 reflections
a = 7.3886 (15) Å	θ = 3.5–67.0°
b = 25.497 (5) Å	µ = 2.17 mm−1
c = 8.8579 (18) Å	T = 296 K
β = 93.64 (3)°	Column, colorless
V = 1665.4 (6) Å3	0.27 × 0.16 × 0.15 mm
Z = 4

Bruker SMART APEXII diffractometer	2827 independent reflections
Radiation source: fine-focus sealed tube	2713 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
Detector resolution: 0 pixels mm-1	θmax = 67.0°, θmin = 3.5°
φ and ω scans	h = −8→8
Absorption correction: multi-scan (SADABS; Bruker, 2009)	k = −30→29
Tmin = 0.592, Tmax = 0.737	l = −9→10
7679 measured reflections

Refinement on F2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.049	H-atom parameters constrained
wR(F2) = 0.152	w = 1/[σ2(Fo2) + (0.0686P)2 + 1.4537P] where P = (Fo2 + 2Fc2)/3
S = 1.15	(Δ/σ)max = 0.001
2827 reflections	Δρmax = 0.33 e Å−3
227 parameters	Δρmin = −0.54 e Å−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 constraints	Extinction coefficient: 0.0160 (11)
Primary atom site location: structure-invariant direct methods

	x	y	z	Uiso*/Ueq
S1	0.30666 (8)	0.45480 (3)	0.64708 (8)	0.0437 (3)
O1	0.8564 (3)	0.60957 (8)	0.9928 (2)	0.0480 (5)
O1'	0.1360 (3)	0.58511 (9)	0.5422 (3)	0.0625 (6)
H1'B	0.2211	0.5963	0.4904	0.094*
H1'A	0.1850	0.5606	0.5956	0.094*
N1	0.2125 (3)	0.37523 (8)	0.4607 (3)	0.0403 (5)
H1A	0.0998	0.3838	0.4597	0.048*
N2	0.5109 (3)	0.37741 (9)	0.5223 (3)	0.0450 (6)
N3	0.3764 (3)	0.54450 (10)	0.8138 (3)	0.0485 (6)
F1	1.1369 (3)	0.62171 (9)	1.1942 (3)	0.0881 (8)
F2	1.0471 (3)	0.69647 (9)	1.2672 (3)	0.0814 (7)
F3	1.1303 (3)	0.68563 (10)	1.0413 (3)	0.0862 (7)
C1	0.2856 (3)	0.33433 (10)	0.3837 (3)	0.0394 (6)
C2	0.2097 (4)	0.29744 (11)	0.2827 (4)	0.0494 (7)
H2B	0.0858	0.2967	0.2566	0.059*
C3	0.3268 (5)	0.26218 (12)	0.2231 (4)	0.0567 (8)
H3B	0.2811	0.2374	0.1539	0.068*
C4	0.5115 (5)	0.26269 (13)	0.2636 (4)	0.0628 (9)
H4A	0.5861	0.2379	0.2221	0.075*
C5	0.5867 (4)	0.29905 (13)	0.3639 (4)	0.0593 (8)
H5A	0.7104	0.2991	0.3910	0.071*
C6	0.4717 (4)	0.33567 (11)	0.4233 (3)	0.0442 (6)
C7	0.3531 (3)	0.39957 (10)	0.5389 (3)	0.0389 (6)
C8	0.5380 (3)	0.47338 (11)	0.7022 (3)	0.0437 (6)
H8A	0.5965	0.4457	0.7622	0.052*
H8B	0.6051	0.4784	0.6127	0.052*
C9	0.5390 (3)	0.52327 (10)	0.7926 (3)	0.0394 (6)
C10	0.3747 (4)	0.58788 (13)	0.8963 (4)	0.0550 (8)
H10A	0.2631	0.6034	0.9101	0.066*
C11	0.5275 (4)	0.61143 (12)	0.9630 (4)	0.0504 (7)
H11A	0.5192	0.6411	1.0233	0.060*
C12	0.6938 (4)	0.58936 (10)	0.9371 (3)	0.0411 (6)
C13	0.7032 (3)	0.54422 (10)	0.8491 (3)	0.0391 (6)
C14	0.8503 (4)	0.65056 (11)	1.1002 (4)	0.0471 (7)
H14A	0.7841	0.6394	1.1857	0.056*
H14B	0.7905	0.6811	1.0549	0.056*
C15	1.0414 (4)	0.66317 (12)	1.1500 (4)	0.0550 (8)
C16	0.8805 (4)	0.51935 (12)	0.8153 (4)	0.0503 (7)
H16A	0.9786	0.5392	0.8632	0.075*
H16B	0.8918	0.5189	0.7079	0.075*
H16C	0.8845	0.4841	0.8532	0.075*

	U11	U22	U33	U12	U13	U23
S1	0.0305 (4)	0.0399 (4)	0.0604 (5)	−0.0018 (2)	0.0018 (3)	−0.0058 (3)
O1	0.0399 (10)	0.0434 (11)	0.0605 (13)	−0.0046 (8)	0.0004 (9)	−0.0123 (9)
O1'	0.0317 (10)	0.0713 (15)	0.0844 (16)	0.0044 (10)	0.0033 (10)	0.0137 (12)
N1	0.0268 (10)	0.0389 (12)	0.0549 (14)	−0.0020 (9)	−0.0001 (9)	0.0003 (10)
N2	0.0311 (11)	0.0432 (13)	0.0604 (15)	0.0009 (9)	0.0002 (10)	−0.0017 (11)
N3	0.0340 (12)	0.0533 (15)	0.0583 (15)	0.0010 (10)	0.0034 (11)	−0.0086 (11)
F1	0.0793 (15)	0.0701 (14)	0.1096 (18)	0.0313 (11)	−0.0360 (13)	−0.0204 (12)
F2	0.0623 (12)	0.0790 (14)	0.1000 (17)	0.0072 (10)	−0.0181 (11)	−0.0482 (13)
F3	0.0635 (13)	0.0855 (16)	0.1106 (18)	−0.0273 (12)	0.0131 (12)	−0.0078 (14)
C1	0.0371 (14)	0.0354 (13)	0.0455 (14)	−0.0030 (10)	0.0013 (11)	0.0058 (11)
C2	0.0482 (16)	0.0424 (15)	0.0570 (18)	−0.0087 (12)	−0.0022 (13)	0.0007 (13)
C3	0.069 (2)	0.0429 (16)	0.0582 (19)	−0.0049 (15)	0.0002 (15)	−0.0058 (14)
C4	0.067 (2)	0.0494 (18)	0.073 (2)	0.0103 (16)	0.0083 (17)	−0.0107 (16)
C5	0.0447 (17)	0.0555 (19)	0.078 (2)	0.0098 (14)	0.0025 (15)	−0.0061 (16)
C6	0.0374 (14)	0.0377 (14)	0.0577 (17)	0.0010 (11)	0.0036 (12)	0.0029 (12)
C7	0.0302 (12)	0.0360 (13)	0.0504 (15)	−0.0030 (10)	0.0008 (11)	0.0059 (11)
C8	0.0298 (13)	0.0415 (14)	0.0595 (17)	−0.0010 (11)	−0.0004 (11)	−0.0026 (12)
C9	0.0342 (13)	0.0369 (13)	0.0471 (15)	−0.0007 (10)	0.0034 (11)	0.0036 (11)
C10	0.0366 (15)	0.0595 (19)	0.069 (2)	0.0064 (13)	0.0065 (14)	−0.0149 (15)
C11	0.0450 (16)	0.0470 (16)	0.0594 (18)	0.0022 (13)	0.0052 (13)	−0.0100 (13)
C12	0.0380 (14)	0.0381 (14)	0.0468 (15)	−0.0045 (11)	0.0007 (11)	0.0026 (11)
C13	0.0347 (14)	0.0347 (14)	0.0481 (16)	−0.0005 (10)	0.0029 (11)	0.0046 (10)
C14	0.0461 (16)	0.0379 (14)	0.0569 (17)	−0.0021 (12)	0.0008 (13)	−0.0065 (12)
C15	0.0499 (17)	0.0446 (16)	0.069 (2)	0.0029 (13)	−0.0052 (15)	−0.0146 (14)
C16	0.0331 (14)	0.0481 (16)	0.069 (2)	−0.0004 (12)	−0.0021 (13)	−0.0076 (14)

S1—C7	1.750 (3)	C3—H3B	0.9300
S1—C8	1.811 (3)	C4—C5	1.376 (5)
O1—C12	1.370 (3)	C4—H4A	0.9300
O1—C14	1.416 (3)	C5—C6	1.388 (4)
O1'—H1'B	0.8499	C5—H5A	0.9300
O1'—H1'A	0.8497	C8—C9	1.503 (4)
N1—C7	1.361 (3)	C8—H8A	0.9700
N1—C1	1.375 (4)	C8—H8B	0.9700
N1—H1A	0.8600	C9—C13	1.390 (4)
N2—C7	1.312 (3)	C10—C11	1.378 (4)
N2—C6	1.397 (4)	C10—H10A	0.9300
N3—C10	1.326 (4)	C11—C12	1.383 (4)
N3—C9	1.342 (4)	C11—H11A	0.9300
F1—C15	1.317 (4)	C12—C13	1.394 (4)
F2—C15	1.340 (4)	C13—C16	1.502 (4)
F3—C15	1.329 (4)	C14—C15	1.488 (4)
C1—C2	1.392 (4)	C14—H14A	0.9700
C1—C6	1.398 (4)	C14—H14B	0.9700
C2—C3	1.376 (5)	C16—H16A	0.9600
C2—H2B	0.9300	C16—H16B	0.9600
C3—C4	1.389 (5)	C16—H16C	0.9600
C7—S1—C8	98.25 (13)	H8A—C8—H8B	108.2
C12—O1—C14	117.0 (2)	N3—C9—C13	124.3 (3)
H1'B—O1'—H1'A	104.1	N3—C9—C8	116.2 (2)
C7—N1—C1	106.6 (2)	C13—C9—C8	119.5 (2)
C7—N1—H1A	126.7	N3—C10—C11	124.3 (3)
C1—N1—H1A	126.7	N3—C10—H10A	117.9
C7—N2—C6	104.4 (2)	C11—C10—H10A	117.9
C10—N3—C9	117.0 (3)	C10—C11—C12	117.6 (3)
N1—C1—C2	132.6 (3)	C10—C11—H11A	121.2
N1—C1—C6	105.6 (2)	C12—C11—H11A	121.2
C2—C1—C6	121.9 (3)	O1—C12—C11	123.7 (3)
C3—C2—C1	116.8 (3)	O1—C12—C13	116.0 (2)
C3—C2—H2B	121.6	C11—C12—C13	120.3 (3)
C1—C2—H2B	121.6	C9—C13—C12	116.4 (2)
C2—C3—C4	121.8 (3)	C9—C13—C16	121.2 (2)
C2—C3—H3B	119.1	C12—C13—C16	122.3 (2)
C4—C3—H3B	119.1	O1—C14—C15	106.8 (2)
C5—C4—C3	121.5 (3)	O1—C14—H14A	110.4
C5—C4—H4A	119.2	C15—C14—H14A	110.4
C3—C4—H4A	119.2	O1—C14—H14B	110.4
C4—C5—C6	117.8 (3)	C15—C14—H14B	110.4
C4—C5—H5A	121.1	H14A—C14—H14B	108.6
C6—C5—H5A	121.1	F1—C15—F3	106.3 (3)
C5—C6—N2	130.0 (3)	F1—C15—F2	106.8 (3)
C5—C6—C1	120.3 (3)	F3—C15—F2	107.2 (3)
N2—C6—C1	109.7 (2)	F1—C15—C14	113.3 (3)
N2—C7—N1	113.7 (2)	F3—C15—C14	112.4 (3)
N2—C7—S1	127.9 (2)	F2—C15—C14	110.5 (3)
N1—C7—S1	118.38 (19)	C13—C16—H16A	109.5
C9—C8—S1	109.75 (18)	C13—C16—H16B	109.5
C9—C8—H8A	109.7	H16A—C16—H16B	109.5
S1—C8—H8A	109.7	C13—C16—H16C	109.5
C9—C8—H8B	109.7	H16A—C16—H16C	109.5
S1—C8—H8B	109.7	H16B—C16—H16C	109.5
C7—N1—C1—C2	−177.4 (3)	C10—N3—C9—C13	−1.1 (4)
C7—N1—C1—C6	1.2 (3)	C10—N3—C9—C8	178.5 (3)
N1—C1—C2—C3	178.3 (3)	S1—C8—C9—N3	−0.8 (3)
C6—C1—C2—C3	0.0 (4)	S1—C8—C9—C13	178.8 (2)
C1—C2—C3—C4	1.1 (5)	C9—N3—C10—C11	−1.3 (5)
C2—C3—C4—C5	−0.9 (6)	N3—C10—C11—C12	2.6 (5)
C3—C4—C5—C6	−0.3 (5)	C14—O1—C12—C11	9.6 (4)
C4—C5—C6—N2	−177.8 (3)	C14—O1—C12—C13	−170.9 (2)
C4—C5—C6—C1	1.3 (5)	C10—C11—C12—O1	178.1 (3)
C7—N2—C6—C5	179.0 (3)	C10—C11—C12—C13	−1.4 (4)
C7—N2—C6—C1	−0.3 (3)	N3—C9—C13—C12	2.1 (4)
N1—C1—C6—C5	−179.9 (3)	C8—C9—C13—C12	−177.5 (2)
C2—C1—C6—C5	−1.2 (4)	N3—C9—C13—C16	−177.5 (3)
N1—C1—C6—N2	−0.6 (3)	C8—C9—C13—C16	3.0 (4)
C2—C1—C6—N2	178.1 (3)	O1—C12—C13—C9	179.7 (2)
C6—N2—C7—N1	1.1 (3)	C11—C12—C13—C9	−0.7 (4)
C6—N2—C7—S1	−179.2 (2)	O1—C12—C13—C16	−0.7 (4)
C1—N1—C7—N2	−1.5 (3)	C11—C12—C13—C16	178.8 (3)
C1—N1—C7—S1	178.72 (18)	C12—O1—C14—C15	176.4 (2)
C8—S1—C7—N2	6.6 (3)	O1—C14—C15—F1	−51.6 (4)
C8—S1—C7—N1	−173.7 (2)	O1—C14—C15—F3	69.0 (3)
C7—S1—C8—C9	176.9 (2)	O1—C14—C15—F2	−171.3 (3)

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
O1′—H1′A···S1	0.85	2.87	3.653 (2)	154

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

Symmetry codes: (i) ; (ii) .