AMBER Archive (2004)

Subject: Re: AMBER: Nonplanar ring systems in nucleic acid

From: Jiri Sponer (
Date: Thu May 20 2004 - 07:42:16 CDT

Yes, DFT does not work for pyramidalization,
we published it back in 1995, Int. J. Quantum. Chem.
57, 959, 1996.

Correct valuaes are obtained with f-functions,
such as MP2/6-311G(2df,p), MP2 or RI-MP2/cc-pVTZ.
These seems to be converged.
MP2 with medium basis set overestimates pyramidalization,
HF underestimates, DFT is "random" and quite poor.
CCSD(T) does not seem to bring any change compared with
J. Chem. Phys. 105, 1996, 11042.

The pyramidalization is exteremely dependent on the
environment and planar primary H-bonds lead the electronic
structure into sp2.
It may be expressed or even facilitated by molecular
interactions in certain environments, such as
cisWC G/A base pair in DNA and RNA.

all the bestv Jiri

> There is a paper giving spectroscopic evidence for nonplanar adenine by
> roger miller of UNC Chapel Hill:
> Dong F, Miller RE "Vibrational transition moment angles in isolated
> biomolecules: A structural tool"
> SCIENCE 298 (5596): 1227-1230 NOV 8 2002
> He notes that DFT fails to give the nonplanarity captured by MP2
> Tom D
> On Wed, 19 May 2004, Ilyas Yildirim wrote:
> > Hi amberlist members,
> >
> > I am trying to find some papers on nonplanar ring systems of nucleic
> > acids. Particularly, I am interested on the amino group of cytosine ring.
> > Do anyone of you know any reference on this subject? Any papers published
> > by Jiri Sponer or Pavel Hobza on this nonplanar geometry, or by anyone
> > else? Thanks in advance.
> >
> > Best,
> >
> >
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