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

Abstract

In the crystal structure of the title compound, C₁₆H₁₄F₃N₃OS·C₃H₈O, the mol­ecules are linked into chains along [010] via N—H⋯O and O—H⋯N hydrogen bonds. The triclinic form was reported by Ren et al. [(2011). Acta Cryst. E67, o270] and the first monoclinic form by Chen et al. [(2012). Acta Cryst. E68, o2015–o2016]. The fused five-and six-membered rings make a dihedral angle of 1.22 (2)°, while the benzene and pyridine rings make a dihedral angle of 10.15 (2)°.

Related literature  

For the use of the title compound as 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 et al. (2010 ▶). For the triclinic polymorph of the title propan-2-ol solvo-polymorph, see: Ren et al. (2011 ▶) and for the monoclinic mono­hydrate, see: Chen et al. (2012 ▶).

Experimental  

Crystal data  

• C₁₆H₁₄F₃N₃OS·C₃H₈O

• M _r = 413.46

• Monoclinic,

• a = 17.4583 (2) Å

• b = 7.4162 (1) Å

• c = 16.9622 (2) Å

• β = 116.255 (2)°

• V = 1969.60 (5) ų

• Z = 4

• Cu Kα radiation

• μ = 1.89 mm⁻¹

• T = 296 K

• 0.31 × 0.23 × 0.15 mm

Data collection  

• Bruker APEXII diffractometer

• Absorption correction: multi-scan (SADABS; Bruker, 2009 ▶) T _min = 0.592, T _max = 0.765

• 13351 measured reflections

• 3410 independent reflections

• 3266 reflections with I > 2σ(I)

• R _int = 0.017

Refinement  

• R[F ² > 2σ(F ²)] = 0.040

• wR(F ²) = 0.116

• S = 1.06

• 3410 reflections

• 254 parameters

• H-atom parameters constrained

• Δρ_max = 0.38 e Å⁻³

• Δρ_min = −0.28 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

Supplementary material file. DOI: 10.1107/S1600536812022143/bg2460Isup3.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
O2—H2B⋯N1i	0.82	2.01	2.8142 (18)	167
N2—H2A⋯O2ii	0.86	1.98	2.8027 (18)	161

Symmetry codes: (i) ; (ii) .

supplementary crystallographic information

Comment

Lansoprazole (Del Rio et al., 2007; Reddy et al., 2008) and many of its analogues are characterized by an anti-ulcer effect (Iwahi et al.,1991) The title compound, (I), is the critical reaction intermediate of lansoprazole Recently, the compound was successfully crystallized from 2-propanol, and the crystal structure is now firstly reported.

The crystral structure (Fig 1) contains one independent molecule and one 2-propanol solvato which are involved in the formation of hydrogen-bonded chains running along [010] via N—H···O and O—H···N hydrogen bonds (Table 1 and Fig. 2). The 2-propanol molecules acts as a hydrogen-bond bridge, providing further stability to the crystal lattice.

Experimental

The raw material was kindly provided by Shanghai Enran Sci-Tech Investment Management Co., Ltd. The compound was dissolved in 2-propanol and suitable crystals of X-ray were obtained by slow evaporation at room temperature over a period of one week.

Refinement

All C-H atoms were constrained to an ideal geometry with C—H distances of 0.98 Å and U_iso(H) = 1.2U_eq(C) for CH; 0.97 Å and U_iso(H) = 1.2U_eq (C) for CH₂; 0.96 Å and U_iso(H) = 1.5U_eq(C) for CH₃; 0.82 Å and U_iso(H) = 1.5U_eq(C)for OH atoms; and 0.86 Å and U_iso(H) = 1.5U_eq(C) for NH atoms.

Figures

Fig. 1.

The content of asymmetric unit (I) showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 30% probability level. Dashed lines denote hydrogen bonds. H atoms have been omitted for clarity.

Fig. 2.

A packing diagram, projected along the [010] chains.

Crystal data

C16H14F3N3OS·C3H8O	F(000) = 864
Mr = 413.46	Dx = 1.394 Mg m−3
Monoclinic, P21/c	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: -P 2ybc	Cell parameters from 3266 reflections
a = 17.4583 (2) Å	θ = 6.1–67.0°
b = 7.4162 (1) Å	µ = 1.89 mm−1
c = 16.9622 (2) Å	T = 296 K
β = 116.255 (2)°	Column, colorless
V = 1969.60 (5) Å3	0.31 × 0.23 × 0.15 mm
Z = 4

Data collection

Bruker APEXII diffractometer	3410 independent reflections
Radiation source: fine-focus sealed tube	3266 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.017
Detector resolution: 0 pixels mm-1	θmax = 67.0°, θmin = 6.1°
phi and ω scans	h = −19→20
Absorption correction: multi-scan (SADABS; Bruker, 2009)	k = −8→8
Tmin = 0.592, Tmax = 0.765	l = −20→19
13351 measured reflections

Refinement

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)] = 0.040	H-atom parameters constrained
wR(F2) = 0.116	w = 1/[σ2(Fo2) + (0.0697P)2 + 0.5861P] where P = (Fo2 + 2Fc2)/3
S = 1.06	(Δ/σ)max = 0.002
3410 reflections	Δρmax = 0.38 e Å−3
254 parameters	Δρmin = −0.28 e Å−3
0 restraints	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0024 (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	0.22271 (3)	0.11157 (5)	1.05242 (3)	0.04524 (17)
O1	0.09818 (8)	0.61043 (16)	0.71885 (7)	0.0497 (3)
O2	0.32047 (8)	0.67645 (16)	0.17242 (10)	0.0573 (4)
H2B	0.3016	0.5801	0.1800	0.086*
N1	0.28104 (9)	0.32274 (18)	1.20227 (9)	0.0417 (3)
N2	0.29844 (8)	0.02492 (18)	1.22301 (8)	0.0419 (3)
H2A	0.2958	−0.0880	1.2105	0.050*
N3	0.14436 (10)	0.1600 (2)	0.87641 (9)	0.0476 (4)
F1	0.13495 (9)	0.8359 (2)	0.61276 (11)	0.0938 (5)
F2	0.01560 (8)	0.89596 (15)	0.61011 (8)	0.0681 (3)
F3	0.02040 (11)	0.76215 (19)	0.50116 (8)	0.0893 (5)
C1	0.26983 (10)	0.1637 (2)	1.16472 (10)	0.0375 (3)
C1'	0.47122 (13)	0.6930 (4)	0.26857 (17)	0.0747 (6)
H1'A	0.4639	0.6167	0.3104	0.112*
H1'B	0.4658	0.8169	0.2816	0.112*
H1'C	0.5269	0.6734	0.2717	0.112*
C2	0.32070 (10)	0.2857 (2)	1.29233 (11)	0.0415 (4)
C2'	0.40380 (12)	0.6487 (3)	0.17709 (15)	0.0594 (5)
H2'A	0.4095	0.5217	0.1646	0.071*
C3	0.34706 (13)	0.4014 (3)	1.36387 (13)	0.0556 (5)
H3B	0.3384	0.5251	1.3561	0.067*
C3'	0.41146 (15)	0.7633 (4)	0.10808 (17)	0.0729 (6)
H3'A	0.3673	0.7311	0.0513	0.109*
H3'B	0.4663	0.7440	0.1092	0.109*
H3'C	0.4057	0.8880	0.1196	0.109*
C4	0.38645 (14)	0.3274 (3)	1.44666 (13)	0.0631 (5)
H4A	0.4048	0.4029	1.4954	0.076*
C5	0.39947 (13)	0.1429 (3)	1.45925 (13)	0.0595 (5)
H5A	0.4272	0.0979	1.5162	0.071*
C6	0.37235 (11)	0.0253 (3)	1.38953 (11)	0.0519 (4)
H6A	0.3803	−0.0985	1.3980	0.062*
C7	0.33245 (10)	0.0997 (2)	1.30578 (11)	0.0408 (4)
C8	0.20875 (11)	0.3377 (2)	1.00826 (11)	0.0443 (4)
H8A	0.1736	0.4076	1.0281	0.053*
H8B	0.2638	0.3969	1.0285	0.053*
C9	0.16630 (10)	0.3261 (2)	0.90919 (10)	0.0385 (3)
C10	0.15158 (10)	0.4812 (2)	0.85880 (10)	0.0393 (4)
C11	0.11201 (10)	0.4568 (2)	0.76766 (10)	0.0405 (4)
C12	0.08915 (12)	0.2862 (2)	0.73202 (11)	0.0493 (4)
H12A	0.0628	0.2686	0.6715	0.059*
C13	0.10670 (13)	0.1429 (2)	0.78931 (12)	0.0536 (5)
H13A	0.0913	0.0278	0.7657	0.064*
C14	0.05724 (12)	0.5917 (2)	0.62635 (11)	0.0454 (4)
H14A	−0.0010	0.5500	0.6070	0.054*
H14B	0.0875	0.5051	0.6076	0.054*
C15	0.05779 (11)	0.7721 (3)	0.58855 (11)	0.0495 (4)
C16	0.17477 (13)	0.6669 (3)	0.89758 (12)	0.0548 (5)
H16A	0.1592	0.7539	0.8511	0.082*
H16B	0.2352	0.6730	0.9344	0.082*
H16C	0.1448	0.6924	0.9320	0.082*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
S1	0.0616 (3)	0.0325 (3)	0.0362 (2)	−0.00018 (16)	0.0168 (2)	0.00201 (14)
O1	0.0649 (8)	0.0411 (7)	0.0345 (6)	−0.0002 (5)	0.0143 (5)	0.0050 (5)
O2	0.0481 (7)	0.0306 (6)	0.0920 (10)	−0.0005 (5)	0.0299 (7)	0.0013 (6)
N1	0.0517 (8)	0.0324 (7)	0.0404 (7)	0.0030 (6)	0.0199 (6)	0.0036 (5)
N2	0.0523 (8)	0.0304 (7)	0.0395 (7)	0.0015 (6)	0.0172 (6)	0.0040 (5)
N3	0.0613 (9)	0.0367 (7)	0.0395 (8)	−0.0012 (6)	0.0174 (7)	0.0000 (6)
F1	0.0650 (8)	0.1046 (11)	0.1088 (12)	−0.0198 (7)	0.0357 (8)	0.0334 (9)
F2	0.0844 (8)	0.0471 (7)	0.0706 (8)	0.0098 (5)	0.0322 (7)	0.0056 (5)
F3	0.1476 (14)	0.0680 (8)	0.0367 (6)	−0.0046 (8)	0.0267 (7)	0.0095 (6)
C1	0.0419 (8)	0.0318 (8)	0.0383 (8)	0.0007 (6)	0.0172 (7)	0.0037 (6)
C1'	0.0519 (11)	0.0715 (15)	0.0859 (16)	0.0019 (10)	0.0171 (11)	0.0122 (12)
C2	0.0444 (8)	0.0411 (9)	0.0408 (9)	0.0024 (7)	0.0203 (7)	0.0022 (7)
C2'	0.0493 (10)	0.0350 (9)	0.0896 (15)	0.0018 (8)	0.0268 (10)	−0.0054 (9)
C3	0.0682 (12)	0.0485 (11)	0.0517 (11)	−0.0001 (9)	0.0280 (9)	−0.0078 (8)
C3'	0.0667 (13)	0.0789 (16)	0.0785 (15)	−0.0071 (11)	0.0369 (12)	−0.0080 (12)
C4	0.0703 (12)	0.0766 (14)	0.0434 (10)	−0.0044 (11)	0.0260 (9)	−0.0130 (9)
C5	0.0584 (11)	0.0791 (14)	0.0382 (9)	0.0024 (10)	0.0188 (8)	0.0082 (9)
C6	0.0554 (10)	0.0533 (11)	0.0442 (10)	0.0035 (8)	0.0195 (8)	0.0122 (8)
C7	0.0419 (8)	0.0412 (9)	0.0401 (8)	0.0006 (6)	0.0190 (7)	0.0044 (6)
C8	0.0566 (10)	0.0334 (8)	0.0365 (9)	0.0009 (7)	0.0147 (7)	0.0028 (7)
C9	0.0404 (8)	0.0363 (8)	0.0365 (8)	0.0010 (6)	0.0149 (6)	0.0004 (6)
C10	0.0406 (8)	0.0374 (8)	0.0367 (8)	0.0014 (6)	0.0143 (6)	0.0014 (6)
C11	0.0425 (8)	0.0388 (8)	0.0375 (8)	0.0016 (7)	0.0152 (6)	0.0044 (7)
C12	0.0595 (10)	0.0467 (10)	0.0337 (8)	−0.0012 (8)	0.0134 (7)	−0.0017 (7)
C13	0.0726 (12)	0.0376 (9)	0.0421 (9)	−0.0051 (8)	0.0176 (9)	−0.0053 (7)
C14	0.0536 (9)	0.0453 (10)	0.0341 (8)	0.0029 (7)	0.0165 (7)	0.0017 (7)
C15	0.0548 (10)	0.0539 (11)	0.0365 (8)	−0.0026 (8)	0.0170 (7)	0.0045 (7)
C16	0.0733 (12)	0.0383 (9)	0.0422 (9)	−0.0022 (8)	0.0159 (9)	0.0010 (7)

Geometric parameters (Å, º)

S1—C1	1.7517 (16)	C3'—H3'A	0.9600
S1—C8	1.8088 (17)	C3'—H3'B	0.9600
O1—C11	1.366 (2)	C3'—H3'C	0.9600
O1—C14	1.414 (2)	C4—C5	1.388 (3)
O2—C2'	1.436 (2)	C4—H4A	0.9300
O2—H2B	0.8200	C5—C6	1.374 (3)
N1—C1	1.313 (2)	C5—H5A	0.9300
N1—C2	1.397 (2)	C6—C7	1.390 (2)
N2—C1	1.360 (2)	C6—H6A	0.9300
N2—C7	1.376 (2)	C8—C9	1.510 (2)
N2—H2A	0.8600	C8—H8A	0.9700
N3—C13	1.331 (2)	C8—H8B	0.9700
N3—C9	1.337 (2)	C9—C10	1.387 (2)
F1—C15	1.311 (2)	C10—C11	1.398 (2)
F2—C15	1.326 (2)	C10—C16	1.502 (2)
F3—C15	1.331 (2)	C11—C12	1.383 (3)
C1'—C2'	1.512 (3)	C12—C13	1.380 (3)
C1'—H1'A	0.9600	C12—H12A	0.9300
C1'—H1'B	0.9600	C13—H13A	0.9300
C1'—H1'C	0.9600	C14—C15	1.486 (3)
C2—C3	1.388 (3)	C14—H14A	0.9700
C2—C7	1.398 (2)	C14—H14B	0.9700
C2'—C3'	1.499 (3)	C16—H16A	0.9600
C2'—H2'A	0.9800	C16—H16B	0.9600
C3—C4	1.375 (3)	C16—H16C	0.9600
C3—H3B	0.9300
C1—S1—C8	99.09 (8)	C7—C6—H6A	121.5
C11—O1—C14	117.24 (13)	N2—C7—C6	132.68 (16)
C2'—O2—H2B	109.5	N2—C7—C2	105.36 (14)
C1—N1—C2	104.42 (13)	C6—C7—C2	121.96 (17)
C1—N2—C7	106.91 (13)	C9—C8—S1	108.55 (11)
C1—N2—H2A	126.5	C9—C8—H8A	110.0
C7—N2—H2A	126.5	S1—C8—H8A	110.0
C13—N3—C9	117.35 (15)	C9—C8—H8B	110.0
N1—C1—N2	113.52 (14)	S1—C8—H8B	110.0
N1—C1—S1	128.56 (12)	H8A—C8—H8B	108.4
N2—C1—S1	117.92 (12)	N3—C9—C10	124.55 (15)
C2'—C1'—H1'A	109.5	N3—C9—C8	115.14 (14)
C2'—C1'—H1'B	109.5	C10—C9—C8	120.30 (14)
H1'A—C1'—H1'B	109.5	C9—C10—C11	116.09 (15)
C2'—C1'—H1'C	109.5	C9—C10—C16	123.33 (14)
H1'A—C1'—H1'C	109.5	C11—C10—C16	120.58 (14)
H1'B—C1'—H1'C	109.5	O1—C11—C12	123.98 (14)
C3—C2—N1	130.27 (16)	O1—C11—C10	115.48 (14)
C3—C2—C7	119.94 (16)	C12—C11—C10	120.53 (15)
N1—C2—C7	109.79 (15)	C13—C12—C11	117.74 (16)
O2—C2'—C3'	108.28 (17)	C13—C12—H12A	121.1
O2—C2'—C1'	109.59 (18)	C11—C12—H12A	121.1
C3'—C2'—C1'	112.37 (18)	N3—C13—C12	123.72 (17)
O2—C2'—H2'A	108.8	N3—C13—H13A	118.1
C3'—C2'—H2'A	108.8	C12—C13—H13A	118.1
C1'—C2'—H2'A	108.8	O1—C14—C15	107.09 (14)
C4—C3—C2	117.96 (19)	O1—C14—H14A	110.3
C4—C3—H3B	121.0	C15—C14—H14A	110.3
C2—C3—H3B	121.0	O1—C14—H14B	110.3
C2'—C3'—H3'A	109.5	C15—C14—H14B	110.3
C2'—C3'—H3'B	109.5	H14A—C14—H14B	108.6
H3'A—C3'—H3'B	109.5	F1—C15—F2	106.44 (17)
C2'—C3'—H3'C	109.5	F1—C15—F3	107.37 (16)
H3'A—C3'—H3'C	109.5	F2—C15—F3	106.68 (16)
H3'B—C3'—H3'C	109.5	F1—C15—C14	113.07 (16)
C3—C4—C5	121.61 (19)	F2—C15—C14	113.23 (14)
C3—C4—H4A	119.2	F3—C15—C14	109.68 (15)
C5—C4—H4A	119.2	C10—C16—H16A	109.5
C6—C5—C4	121.53 (18)	C10—C16—H16B	109.5
C6—C5—H5A	119.2	H16A—C16—H16B	109.5
C4—C5—H5A	119.2	C10—C16—H16C	109.5
C5—C6—C7	116.97 (19)	H16A—C16—H16C	109.5
C5—C6—H6A	121.5	H16B—C16—H16C	109.5
C2—N1—C1—N2	0.47 (18)	C13—N3—C9—C10	0.8 (3)
C2—N1—C1—S1	179.51 (12)	C13—N3—C9—C8	179.99 (15)
C7—N2—C1—N1	−0.99 (18)	S1—C8—C9—N3	3.65 (19)
C7—N2—C1—S1	179.85 (11)	S1—C8—C9—C10	−177.14 (12)
C8—S1—C1—N1	6.99 (17)	N3—C9—C10—C11	−0.9 (2)
C8—S1—C1—N2	−174.00 (12)	C8—C9—C10—C11	179.94 (14)
C1—N1—C2—C3	−179.33 (18)	N3—C9—C10—C16	178.21 (17)
C1—N1—C2—C7	0.23 (18)	C8—C9—C10—C16	−0.9 (2)
N1—C2—C3—C4	−178.76 (18)	C14—O1—C11—C12	0.6 (2)
C7—C2—C3—C4	1.7 (3)	C14—O1—C11—C10	−179.17 (14)
C2—C3—C4—C5	−0.3 (3)	C9—C10—C11—O1	−179.78 (13)
C3—C4—C5—C6	−1.1 (3)	C16—C10—C11—O1	1.1 (2)
C4—C5—C6—C7	1.0 (3)	C9—C10—C11—C12	0.5 (2)
C1—N2—C7—C6	−178.20 (18)	C16—C10—C11—C12	−178.69 (17)
C1—N2—C7—C2	1.05 (17)	O1—C11—C12—C13	−179.70 (17)
C5—C6—C7—N2	179.62 (17)	C10—C11—C12—C13	0.0 (3)
C5—C6—C7—C2	0.5 (3)	C9—N3—C13—C12	−0.2 (3)
C3—C2—C7—N2	178.81 (15)	C11—C12—C13—N3	−0.2 (3)
N1—C2—C7—N2	−0.81 (18)	C11—O1—C14—C15	−174.15 (14)
C3—C2—C7—C6	−1.8 (3)	O1—C14—C15—F1	59.7 (2)
N1—C2—C7—C6	178.54 (15)	O1—C14—C15—F2	−61.42 (19)
C1—S1—C8—C9	−178.94 (12)	O1—C14—C15—F3	179.55 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O2—H2B···N1i	0.82	2.01	2.8142 (18)	167
N2—H2A···O2ii	0.86	1.98	2.8027 (18)	161

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