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Volume 69 
Part 5 
Pages o805-o806  
May 2013  

Received 22 January 2013
Accepted 23 April 2013
Online 30 April 2013

Key indicators
Single-crystal X-ray study
T = 105 K
Mean [sigma](C-C) = 0.019 Å
R = 0.051
wR = 0.135
Data-to-parameter ratio = 13.4
Details
Open access

Pyramidalization of a carbonyl C atom in (2S)-N-(selenoacetyl)proline methyl ester

aDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave, Madison, WI 53706-1322, USA,bGraduate Program in Biophysics, University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53706-1534, USA, and cDepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706-1544, USA
Correspondence e-mail: iguzei@chem.wisc.edu, rtraines@wisc.edu

The title compound, C8H13NO2Se, crystallizes as a non-merohedral twin with an approximate 9:1 component ratio with two symmetry-independent molecules in the asymmetric unit. Our density-functional theory (DFT) computations indicate that the carboxy C atom is expected to be slightly pyramidal due to an n[rightwards arrow] [pi]* interaction, wherein the lone pair (n) of the Se atom overlap with the antibonding orbital ([pi]*) of the carbonyl group. Such pyramidalization is observed in one molecule of the title compound but not the other.

Related literature

For background to hybrid density functional theory (DFT) and natural bond orbital (NBO) analysis, see: Glendening et al. (2001[Glendening, E. D., Badenhoop, J. K., Reed, A. E., Carpenter, J. E., Bohmann, J. A., Morales, C. M. & Weinhold, F. (2001). NBO. Theoretical Chemistry Institute, University of Wisconsin, Madison, USA.]); Weinhold (1998[Weinhold, F. (1998). Encyclopedia of Computational Chemistry, edited by P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Shaefer III & P. R. Schreiner, pp. 1792-1811. Chichester, UK: John Wiley & Sons.]); Weinhold & Landis (2005[Weinhold, F. & Landis, C. R. (2005). In Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective. Cambridge University Press.]). For literature related to the synthesis, see: Bhattacharyya & Woollins (2001[Bhattacharyya, P. & Woollins, J. D. (2001). Tetrahedron Lett. 42, 5949-5951.]) and for NBO studies of the title compound, see: Choudhary & Raines (2011a[Choudhary, A. & Raines, R. T. (2011a). ChemBioChem, 12, 1801-1807.]); DeRider et al. (2002[DeRider, M. L., Wilkens, S. J., Waddell, M. J., Bretscher, L. E., Weinhold, F., Raines, R. T. & Markley, J. L. (2002). J. Am. Chem. Soc. 124, 2497-2505.]); Choudhary et al. (2009[Choudhary, A., Gandla, D., Krow, G. R. & Raines, R. T. (2009). J. Am. Chem. Soc. 131, 7244-7246.], 2010a[Choudhary, A., Fry, C. G. & Raines, R. T. (2010a). ARKIVOC, pp. 251-262.],b[Choudhary, A., Pua, K. H. & Raines, R. T. (2010b). Amino Acids, 39, 181-186.]); Jakobsche et al. (2010[Jakobsche, C. E., Choudhary, A., Raines, R. T. & Miller, S. J. (2010). J. Am. Chem. Soc. 132, 6651-6653.]); Bartlett et al. (2010[Bartlett, G. J., Choudhary, A., Raines, R. T. & Woolfson, D. N. (2010). Nat. Chem. Biol. 6, 615-620.]); Choudhary & Raines (2011b[Choudhary, A. & Raines, R. T. (2011b). Protein Sci. 20, 1077-1087.]). For geometrical checks with ConQuest and Mercury, see: Bruno et al. (2002[Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389-397.]). For Gaussian 03 software, see: Frisch (2004[Frisch, M. J., et al. (2004). GAUSSIAN03. Gaussian Inc., Wallingford, CT, USA.]). For puckering parameters, see: Cremer & Pople (1975[Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1358-1367.]).

[Scheme 1]

Experimental

Crystal data
  • C8H13NO2Se

  • Mr = 234.15

  • Triclinic, P 1

  • a = 7.050 (3) Å

  • b = 7.442 (3) Å

  • c = 10.334 (4) Å

  • [alpha] = 85.166 (6)°

  • [beta] = 86.220 (6)°

  • [gamma] = 64.682 (4)°

  • V = 488.1 (3) Å3

  • Z = 2

  • Mo K[alpha] radiation

  • [mu] = 3.81 mm-1

  • T = 105 K

  • 0.47 × 0.37 × 0.35 mm

Data collection
  • Bruker SMART APEX2 area detector diffractometer

  • Absorption correction: multi-scan (TWINABS; Bruker, 2007[Bruker (2007). TWINABS and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.268, Tmax = 0.349

  • 3012 measured reflections

  • 3012 independent reflections

  • 2938 reflections with I > 2[sigma](I)

Refinement
  • R[F2 > 2[sigma](F2)] = 0.051

  • wR(F2) = 0.135

  • S = 1.12

  • 3012 reflections

  • 224 parameters

  • 3 restraints

  • H-atom parameters constrained

  • [Delta][rho]max = 1.46 e Å-3

  • [Delta][rho]min = -0.63 e Å-3

  • Absolute structure: Classical Flack method preferred over Parsons because s.u. lower.

  • Flack parameter: 0.01 (3)

Data collection: APEX2 (Bruker, 2012[Bruker (2012). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT-Plus (Bruker, 2007[Bruker (2007). TWINABS and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT-Plus; 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: OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]) and NBOView (Wendt & Weinhold, 2001[Wendt, M. & Weinhold, F. (2001). NBOView. Theoretical Chemistry Institute, University of Wisconsin-Madison: Madison, Wisconsin, USA.]); software used to prepare material for publication: OLEX2, GX and FCF_filter (Guzei, 2012[Guzei, I. A. (2012). GX and FCF_filter. Department of Chemistry University of Wisconsin-Madison, Madison, Wisconsin, USA.]).


Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: KJ2221 ).


Acknowledgements

This project has been funded in part by NIH grant R01 AR044276.

References

Bartlett, G. J., Choudhary, A., Raines, R. T. & Woolfson, D. N. (2010). Nat. Chem. Biol. 6, 615-620.  [CrossRef] [ChemPort] [PubMed]
Bhattacharyya, P. & Woollins, J. D. (2001). Tetrahedron Lett. 42, 5949-5951.  [CrossRef] [ChemPort]
Bruker (2007). TWINABS and SAINT-Plus. Bruker AXS Inc., Madison, Wisconsin, USA.
Bruker (2012). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.
Bruno, I. J., Cole, J. C., Edgington, P. R., Kessler, M., Macrae, C. F., McCabe, P., Pearson, J. & Taylor, R. (2002). Acta Cryst. B58, 389-397.  [ISI] [CrossRef] [details]
Choudhary, A., Fry, C. G. & Raines, R. T. (2010a). ARKIVOC, pp. 251-262.  [CrossRef]
Choudhary, A., Gandla, D., Krow, G. R. & Raines, R. T. (2009). J. Am. Chem. Soc. 131, 7244-7246.  [CrossRef] [PubMed] [ChemPort]
Choudhary, A., Pua, K. H. & Raines, R. T. (2010b). Amino Acids, 39, 181-186.  [PubMed]
Choudhary, A. & Raines, R. T. (2011a). ChemBioChem, 12, 1801-1807.  [CrossRef] [ChemPort] [PubMed]
Choudhary, A. & Raines, R. T. (2011b). Protein Sci. 20, 1077-1087.  [CrossRef] [ChemPort] [PubMed]
Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1358-1367.  [CrossRef] [ChemPort] [ISI]
DeRider, M. L., Wilkens, S. J., Waddell, M. J., Bretscher, L. E., Weinhold, F., Raines, R. T. & Markley, J. L. (2002). J. Am. Chem. Soc. 124, 2497-2505.  [CrossRef] [PubMed] [ChemPort]
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.  [ISI] [CrossRef] [ChemPort] [details]
Frisch, M. J., et al. (2004). GAUSSIAN03. Gaussian Inc., Wallingford, CT, USA.
Glendening, E. D., Badenhoop, J. K., Reed, A. E., Carpenter, J. E., Bohmann, J. A., Morales, C. M. & Weinhold, F. (2001). NBO. Theoretical Chemistry Institute, University of Wisconsin, Madison, USA.
Guzei, I. A. (2012). GX and FCF_filter. Department of Chemistry University of Wisconsin-Madison, Madison, Wisconsin, USA.
Jakobsche, C. E., Choudhary, A., Raines, R. T. & Miller, S. J. (2010). J. Am. Chem. Soc. 132, 6651-6653.  [CrossRef] [ChemPort] [PubMed]
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.  [CrossRef] [ChemPort] [details]
Weinhold, F. (1998). Encyclopedia of Computational Chemistry, edited by P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Shaefer III & P. R. Schreiner, pp. 1792-1811. Chichester, UK: John Wiley & Sons.
Weinhold, F. & Landis, C. R. (2005). In Valency and Bonding: A Natural Bond Orbital Donor-Acceptor Perspective. Cambridge University Press.
Wendt, M. & Weinhold, F. (2001). NBOView. Theoretical Chemistry Institute, University of Wisconsin-Madison: Madison, Wisconsin, USA.


Acta Cryst (2013). E69, o805-o806   [ doi:10.1107/S1600536813011112 ]

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