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Volume 69 
Part 7 
Pages o1013-o1014  
July 2013  

Received 20 May 2013
Accepted 22 May 2013
Online 8 June 2013

Key indicators
Single-crystal X-ray study
T = 100 K
Mean [sigma](C-C) = 0.002 Å
R = 0.042
wR = 0.113
Data-to-parameter ratio = 19.0
Details
Open access

Ethyl 2-[5-(4-fluorophenyl)pyridin-3-yl]-1-[3-(2-oxopyrrolidin-1-yl)propyl]-1H-benzimidazole-5-carboxylate

aInstitute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia, and bX-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
Correspondence e-mail: arazaki@usm.my

In the title compound, C28H27FN4O3·H2O, the benzimidazole ring system is essentially planar with a maximum deviation of 0.028 (1) Å. It makes dihedral angles of 47.59 (5) and 60.31 (5)°, respectively, with the pyridine and benzene rings, which make a dihedral angle of 22.58 (6)° with each other. The pyrrolidine ring shows an envelope conformation with one of the methylene C atoms as the flap. In the crystal, the components are connected into a tape along the b-axis direction through O-H...O and O-H...N hydrogen bonds and a [pi]-[pi] interaction between the pyridine and benzene rings [centroid-centroid distance of 3.685 (8) Å]. The tapes are further linked into layers parallel to the ab plane by C-H...O and C-H...F interactions.

Related literature

For biological applications of benzimidazole derivatives, see: Tanious et al. (2004[Tanious, F. A., Hamelberg, D., Bailly, C., Czarny, A., Boykin, D. W. & Wilson, W. D. (2004). J. Am. Chem. Soc. 126, 143-153.]); Coburn et al. (1987[Coburn, R. A., Clark, M. T., Evans, R. T. & Genco, R. J. (1987). J. Med. Chem. 30, 205-208.]); Rao et al. (2002[Rao, A., Chimirri, A., Clercq, E. D., Monforte, A. M., Monforte, P., Pannecouque, C. & Zappala, M. (2002). Il Farmaco. 57, 819-823.]). For a related structure, see: Yoon et al. (2012[Yoon, Y. K., Ali, M. A., Choon, T. S., Asik, S. I. J. & Razak, I. A. (2012). Acta Cryst. E68, o59.]).

[Scheme 1]

Experimental

Crystal data
  • C28H27FN4O3·H2O

  • Mr = 504.55

  • Monoclinic, P 21 /c

  • a = 16.0640 (15) Å

  • b = 7.6562 (7) Å

  • c = 20.1991 (19) Å

  • [beta] = 98.163 (2)°

  • V = 2459.1 (4) Å3

  • Z = 4

  • Mo K[alpha] radiation

  • [mu] = 0.10 mm-1

  • T = 100 K

  • 0.35 × 0.33 × 0.21 mm

Data collection
  • Bruker APEX Duo CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.967, Tmax = 0.980

  • 24841 measured reflections

  • 6502 independent reflections

  • 5002 reflections with I > 2[sigma](I)

  • Rint = 0.037

Refinement
  • R[F2 > 2[sigma](F2)] = 0.042

  • wR(F2) = 0.113

  • S = 1.03

  • 6502 reflections

  • 343 parameters

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

  • [Delta][rho]max = 0.31 e Å-3

  • [Delta][rho]min = -0.25 e Å-3

Table 1
Hydrogen-bond geometry (Å, °)

D-H...A D-H H...A D...A D-H...A
O1W-H1W1...O3 0.90 (2) 1.89 (2) 2.7881 (16) 174.3 (19)
O1W-H2W1...N2i 0.89 (2) 2.04 (2) 2.9309 (16) 175 (2)
C14-H14A...O1Wii 0.95 2.49 3.4368 (17) 173
C17-H17A...O2iii 0.95 2.45 3.1768 (17) 133
C27-H27A...O2iv 0.99 2.45 3.2749 (18) 141
C28-H28B...F1i 0.98 2.43 3.2851 (18) 145
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) x, y+1, z; (iii) x-1, y, z; (iv) [-x+2, y+{\script{1\over 2}}, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2009[Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).


Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: IS5275 ).


Acknowledgements

The authors would like to express their gratitude to Pharmacogenetic and Novel Therapeutic Research, Institute for Research in Molecular Medicine and Department of Pharmacology, School of Pharmaceutical Sciences, Universiti Sains Malaysia (USM). This work was funded through Research Grant No. RUC 1001/PSK/8620012 and HiCoE Research Grant No. 311.CIPPM.4401005. IAR also thanks USM for the Short Term Grant No. 304/PFIZIK/6312078.

References

Bruker (2009). APEX2, SAINT and SADABS. Bruker AXS Inc., Madison, Wisconsin, USA.
Coburn, R. A., Clark, M. T., Evans, R. T. & Genco, R. J. (1987). J. Med. Chem. 30, 205-208.  [CrossRef] [ChemPort] [PubMed] [Web of Science]
Rao, A., Chimirri, A., Clercq, E. D., Monforte, A. M., Monforte, P., Pannecouque, C. & Zappala, M. (2002). Il Farmaco. 57, 819-823.  [CrossRef] [PubMed] [ChemPort]
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.  [CrossRef] [ChemPort] [IUCr Journals]
Spek, A. L. (2009). Acta Cryst. D65, 148-155.  [Web of Science] [CrossRef] [ChemPort] [IUCr Journals]
Tanious, F. A., Hamelberg, D., Bailly, C., Czarny, A., Boykin, D. W. & Wilson, W. D. (2004). J. Am. Chem. Soc. 126, 143-153.  [Web of Science] [CrossRef] [PubMed] [ChemPort]
Yoon, Y. K., Ali, M. A., Choon, T. S., Asik, S. I. J. & Razak, I. A. (2012). Acta Cryst. E68, o59.  [CrossRef] [IUCr Journals]


Acta Cryst (2013). E69, o1013-o1014   [ doi:10.1107/S1600536813014177 ]

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