JBPC  Vol.2 No.1 , February 2011
Interaction of small aromatic molecules: An ab initio studies on benzene and pyridine molecules
Abstract: The use of appropriate level of theories for studying weak interactions such as stacking of aromatic molecules has been an important aspect, since the high level methods have limitations for application to large molecules. The differences in the stacking energies of various structures are found significant for identifying the most favored stacked benzene rings and the pyridine rings. The most favored structure of benzene rings obtained from various methods are similar, and also comparable with that of reported accurate CCSD(T) method. The effect of basis set in the stacking energies of MP2 calculations is small. Thus the moderately accurate methods may be feasible for studying the stacking interactions as demonstrated for benzene and pyridine molecules.
Cite this paper: nullBezbaruah, B. , Hazarika, P. , Gogoi, A. , Medhi, O. and Medhi, C. (2011) Interaction of small aromatic molecules: An ab initio studies on benzene and pyridine molecules. Journal of Biophysical Chemistry, 2, 32-36. doi: 10.4236/jbpc.2011.21005.

[1]   Castonguay, L.A., Rappe′, A.K. and Casewit, C.J. (1991) Π-stacking and the platinum-catalyzed asymmetric hydroformylation reaction: A molecular modeling study. Journal of the American Chemical Society, 113(19), 7177–7183.

[2]   Kolb, H.C., Andersson, P.G. and Sharpless, K.B. (1994) Toward an understanding of the high enantioselectivity in the osmium-catalyzed asymmetric dihydroxylation (AD). 1. Kinetics. Journal of the American Chemical Society, 116(4), 1278–1291.

[3]   Smith, D.A., Ulmer II, C.W., and Gilbert M.J. (1992) Structural studies of aromatic amines and the dna intercalating compounds m-amsa and o-amsa: Comparison of mndo, am1, and pm3 to experimental and ab initio results. Journal of Computational Chemistry, 13 (5), 640.

[4]   Barone, G., Guerra, C.F., Gambino, N., Silvestri, A., Lauria, A., Almerico, A.M. and Bickelhaupt, F.M. (2008) Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug. Journal of Biomolecular Structure and Dynamics, 26(1), 115-30.

[5]   Gilman, A.G., Rall, T.W., Mies, A.S. and Taylor, P. (1993) The pharmaceutical basis of therapeutics. 8th Ed., McGraw Hill, Inc., New York.

[6]   Ishida, T., Doi, M., Ueda, H., Inoue, M. and Scheldrick, G.M. (1988) Specific ring stacking interaction on the tryptophan-7-methylguanine system: Comparative crystallographic studies of indole derivatives-7-methylguani- ne base, nucleoside, and nucleotide complexes. Journal of the American Chemical Society, 110 (7), 2286–2294

[7]   Hobza, P., Selzle, H.L. and Schlag, E.W. (1994) Potential energy surface of the benzene dimer: Ab initio theoretical study. Journal of the American Chemical society, 116(8), 3500-3506.

[8]   Bernstein, E.R., Sun, S. (1996) Aromatic van der waals clusters: Structure and nonrigidity. Journal of Physical Chemistry, 100(32), 13348-13366.

[9]   Hobza, P., Selzle, H.L., Schlag, E.W. (1996) Potential energy surface for the benzene dimer. Results of ab initio CCSD(T) calculations show two nearly isoenergetic structures: T-Shaped and parallel-displaced. Journal of Physical Chemistry, 100(48), 18790.

[10]   Tsuzuki, S., Honda, K., Uchimaru, T., Mikami, M. and Tanabe, K. (2002) Origin of attraction and directionality of the π-π interaction: Model chemistry calculations of benzene dimer interaction. Journal of the American Chemical Society, 124(1), 104-112.

[11]   Sinnokrot, M.O., Valeev, E. F. and Sherrill, C.D. (2002), Estimates of the ab initio limit for π-π interactions: The benzene dimer. Journal of the American Chemical Society, 124(36), 10887-10893.

[12]   Zhikol, O.A., Shishkin, O.V., Lyssenko, K.A. and Leszczynski, J. (2005) Electron density distribution in stacked benzene dimers: A new approach towards the estimation of stacking interaction energies. Journal of Chemical Physics, 122(14), 144104.

[13]   Parthasarathi, R., Subramanian, V. (2005) Stacking interactions in benzene and cytosine dimers: From molecular electron density perspective. Structural Chemistry, 16(3), 243-255.

[14]   Steven, E.W., Anne, J.M, Peter, M, Timothy, M.S, and Houk, K.N. (2010) Probing substituent effects in aryl-aryl interactions using stereoselective diels-alder cycloadditions. Journal of the American Chemical Society, 132(10), 3304-3311.

[15]   Frisch, M.J. et al. Gaussian 03, Gaussian Inc., Pittsburgh PA.