From the nonplanarity of the amino group to the structural nonrigidity of the molecule: A post-Hartree-Fock ab initio study of 2-aminoimidazole

Abstract

The results of an ab initio post-Hartree᎐Fock study of the details of the molecular structure and the pathways of the interconversion of the 2-aminoimidazole molecule enantiomers are reported. The geometry of the local minimum and the transition states were optimized by the gradient procedure at the MP2 and DFTrB3LYP levels of theory and were verified by energy second derivative calculations. The medium and wŽ Ž . Ž . Ž . large size basis sets 6-31 q G d, p , 6-311qqG df, pd , D95qq df, pd , and correlation .x consistent aug-cc-pVDZ have been used. Based on an analysis of the equilibrium geometry and the pathways of interconversion, we reveal that the phenomenon of a nonplanar geometry of the amino group in the amines has a more complex nature than previously expected. Our calculations show that this molecule is structurally nonrigid at least with respect to the torsion and umbrella vibration of the amino group. It results in a very complex picture of the amino group motion which includes tunneling of the barrier and an above barrier large amplitude motion. We have found that in contrast to Correspondence to: J. Leszczynski.

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“…Thus, the structure of this group is of fundamental importance in the molecular recognition phenomena. The DNA bases were believed to be planar for many years, until the nonplanarity of their amino groups has been predicted in the 1990s (Aamouche et al, 1997;Hobza & Šponer, 1999;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Komarov & Polozov, 1990;Komarov et al, 1992;Šponer & Hobza, 1994;Šponer et al, 2001). Direct experimental results for the nucleic acid bases amino moieties are not available, but indirect experimental evidence does exist.…”

“…The internal nonplanarity of the amino group originates from the partial sp 3 hybridization of the amino group nitrogen atom (Govorun et al, 1992;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Gorb & Leszczynski, 1998a, 1998bHobza & Šponer, 1999;Šponer & Hobza, 1994).…”

“…The nitrogenous bases with exocyclic amine fragment ≥C-NH 2 are known to have nonrigid structures (for details see (Bludský et al, 1996;Florian et al, 1995;Hovorun & Kondratyuk, 1996;Hovorun et al, 1999)). Their interconversion, i.e.…”

“…So, we demonstrated that Ade (N1C6N6H=0.013°; C5C6N6H=-0.014°) is an effectively planar molecule (effective symmetry C s ) (Hovorun et al, 1995a(Hovorun et al, , 1995b(Hovorun et al, , 1999Hovorun & Kondratyuk, 1996). Its interconversion is accomplished via two plane-symmetric transition states with Gibbs free energy of 14.34 and 14.57 kcal/mol and also through the planar transition state with the activation energy of 0.12 kcal/mol 1 (Table 1).…”

“…The thorough analysis of our results and also interpretation of the data reported in literature (Bludský et al, 1996;Hobza & Šponer, 1999;Hovorun et al, 1995aHovorun et al, , 1995bHovorun et al, , 1999Hovorun & Kondratyuk, 1996;Larsen et al, 1976;Lister et al, 1974;Šponer & Hobza, 1994;S. Wang & Schaefer III, 2006;Zierkiewicz et al, 2008) allow us to offer the following conclusions.…”