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Volume 67 
Part 8 
Page o2190  
August 2011  

Received 23 May 2011
Accepted 25 July 2011
Online 30 July 2011

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Key indicators
Single-crystal X-ray study
T = 298 K
Mean [sigma](C-C) = 0.002 Å
R = 0.037
wR = 0.038
Data-to-parameter ratio = 12.8
Details
Open access

(R)-(+)-2-{[(3-Methyl-4-nitropyridin-2-yl)methyl]sulfinyl}-1H-benzimidazole1

Manne Naga Raju,a Neelam Uday Kumar,a Naveenkumar Kolla,a Rakeshwar Bandichhora and Peddy Vishweshwarb*

aResearch and Development, API-PDT-03, Integrated Product Development (IPD), Innovation Plaza, Dr Reddy's Laboratories Ltd, Bachupally, Qutubullapur, Hyderabad 500 072, India, and bCentre of Excellence in Polymorphism and Particle Engineering, Integrated Product Development (IPD), Innovation Plaza, Dr Reddy's Laboratories Ltd, Bachupally, Qutubullapur, Hyderabad 500 072, India
Correspondence e-mail: vishweshwarp@drreddys.com

The title compound, C14H12N4O3S, is an intermediate of Dexlansoprazole, a proton pump inhibitor (PPI) mainly developed for anti-ulcer activity. The absolute configuration of the title compound was determined as R. The crystal structure reveals that the molecules form chains along the b axis through N-H...N and C-H...O hydrogen-bonded dimers. These chains are connected via weak C-H...O hydrogen bonds.

Related literature

For the synthesis of the title compound, see: Kumar et al. (2009[Kumar, K. N., Nagaraju, M., Srinivas, G., Kumar, N. U., Anitha, N., Reddy, B. S., Vishwasrao, P. S., Kumar, T. A., Reddy, P. S., Gulabrao, S. S., Ashok, S. & Varma, M. S. (2009). Patent WO 2009/117489 A1.]). For background to this class of anti-ulcer drugs, see: Arimori et al. (1998[Arimori, K., Yasuda, K., Katsuki, H. & Nakana, M. (1998). J. Pharm. Pharmacol. 50, 1241-1245.]); Masa et al. (2001[Masa, K., Hamada, A., Arimori, K., Fujii, J. & Nakano, M. (2001). Biol. Pharm. Bull. 24, 274-277.]). For a related structure, see: Fujishima et al. (2002[Fujishima, A., Aoki, I. & Kamiyama, K. (2002). US Patent No. 6462058B1.]).

[Scheme 1]

Experimental

Crystal data

  • C14H12N4O3S

  • Mr = 316.33

  • Monoclinic, P 21

  • a = 7.7422 (13) Å

  • b = 11.0505 (15) Å

  • c = 8.2318 (13) Å

  • [beta] = 103.697 (7)°

  • V = 684.24 (18) Å3

  • Z = 2

  • Mo K[alpha] radiation

  • [mu] = 0.26 mm-1

  • T = 298 K

  • 0.22 × 0.20 × 0.18 mm
Data collection

  • Rigaku Mercury diffractometer

  • Absorption correction: multi-scan (REQAB; Jacobson, 1998[Jacobson, R. (1998). REQAB. Private communication to Rigaku Corporation, Tokyo, Japan.]) Tmin = 0.942, Tmax = 0.950

  • 7636 measured reflections

  • 2752 independent reflections

  • 2601 reflections with F2 > 2[sigma](F2)

  • Rint = 0.025
Refinement

  • R[F2 > 2[sigma](F2)] = 0.037

  • wR(F2) = 0.038

  • S = 1.25

  • 2752 reflections

  • 215 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • [Delta][rho]max = 0.48 e Å-3

  • [Delta][rho]min = -0.37 e Å-3

  • Absolute structure: Flack (1983[Flack, H. D. (1983). Acta Cryst. A39, 876-881.]), with 1292 Friedel pairs

  • Flack parameter: -0.02 (4)

Table 1
Hydrogen-bond geometry (Å, °)

D-H...A D-H H...A D...A D-H...A
N1-H1...N2i 0.881 (17) 2.553 (18) 3.425 (2) 170.5 (13)
C2-H2...O1ii 0.95 2.33 3.251 (2) 164
C12-H12...O2iii 0.95 2.55 3.164 (2) 122
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+1]; (ii) [-x+1, y-{\script{1\over 2}}, -z+1]; (iii) [-x-1, y+{\script{1\over 2}}, -z].

Data collection: CrystalClear (Rigaku, 2005[Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.]); cell refinement: CrystalClear; data reduction: CrystalStructure (Molecular Structure Corporation & Rigaku, 2006[Molecular Structure Corporation & Rigaku (2006). CrystalStructure. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.]); program(s) used to solve structure: SIR2004 (Burla et al. 2005[Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381-388.]); program(s) used to refine structure: CRYSTALS (Betteridge et al. 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: X-SEED (Barbour, 2001[Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.]); software used to prepare material for publication: CrystalStructure.

Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: GW2104 ).

Acknowledgements

The authors are grateful to the management of IPDO-API and Dr Reddy's Laboratories Ltd for encouragement. Many thanks to our colleagues Srinivas Gangula, Naredla Anitha and Baddam Sudhakar Reddy for their support in the overall process development.

References

Arimori, K., Yasuda, K., Katsuki, H. & Nakana, M. (1998). J. Pharm. Pharmacol. 50, 1241-1245.  [ChemPort]
Barbour, L. J. (2001). J. Supramol. Chem. 1, 189-191.  [CrossRef] [ChemPort]
Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.  [CrossRef] [details]
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381-388.  [ISI] [CrossRef] [ChemPort] [details]
Flack, H. D. (1983). Acta Cryst. A39, 876-881.  [CrossRef] [details]
Fujishima, A., Aoki, I. & Kamiyama, K. (2002). US Patent No. 6462058B1.
Jacobson, R. (1998). REQAB. Private communication to Rigaku Corporation, Tokyo, Japan.
Kumar, K. N., Nagaraju, M., Srinivas, G., Kumar, N. U., Anitha, N., Reddy, B. S., Vishwasrao, P. S., Kumar, T. A., Reddy, P. S., Gulabrao, S. S., Ashok, S. & Varma, M. S. (2009). Patent WO 2009/117489 A1.
Masa, K., Hamada, A., Arimori, K., Fujii, J. & Nakano, M. (2001). Biol. Pharm. Bull. 24, 274-277.  [ChemPort]
Molecular Structure Corporation & Rigaku (2006). CrystalStructure. MSC, The Woodlands, Texas, USA, and Rigaku Corporation, Tokyo, Japan.
Rigaku (2005). CrystalClear. Rigaku Corporation, Tokyo, Japan.

Acta Cryst (2011). E67, o2190  [ doi:10.1107/S1600536811029990 ]

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