Re: [AMBER] QM on Adenosine

From: Christina Bergonzo <>
Date: Wed, 2 Jul 2014 08:50:33 -0600

This has been looked at in the context of nucleic acid structure by a few
groups. I can point you to these papers which look at planarity of the
amino group in the context of GA base pairs:

Modified Amber Force Field Correctly Models the Conformational
Preference for Tandem GA pairs in RNA
Asaminew H. Aytenfisu,† Aleksandar Spasic,† Matthew G. Seetin,† John
and David H. Mathews*,†,§ J. Chem. Theory Comput. 2014, 10, 1292−1301

Effects of Restrained Sampling Space and Nonplanar Amino Groups on
Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs
Flanked by GC, CG, iGiC, or iCiG Base Pairs
Yildirim, I., Stern, H.A., Sponer, J., Spackova, N., Turner, D.H.
J Chem Theory Comput. <> 2009
Aug 11;5(8):2088-2100.

And for a comprehensive review which includes a nice discussion about the
non-planarity of amino groups:

Electronic properties, hydrogen bonding, stacking, and cation binding of
DNA and RNA bases
Sponer, J., Leszczynski, J., Hobza, P.
Biopolymers, 2002, 61, 3-31.;2-4/full

Hope this is helpful,

On Wed, Jul 2, 2014 at 8:25 AM, Steven M. Graham <>

> Folks:
> A little off topic, but...
> We've done a series of QM geometry optimizations on adenosine and analogs
> using Hartree-Fock and MP2 at various levels of theory (6-31G* to
> 6-311++G**). We've noticed the exocyclic amino group on the adenine base
> is about 10-15 degrees out of plane in many, if not all cases.
> Has anyone else observed this? I don't recall seeing it in the
> literature. Using FF99 the amino group is, as expected, coplanar with the
> base.
> Steven M. Graham, Ph.D.
> Associate Professor
> Department of Chemistry
> St. John's University
> 8000 Utopia Parkway
> Queens, NY 11439
> Office: 335 St. Albert Hall
> Voice: 718-990-5217
> Fax: 718-990-1876
> _______________________________________________
> AMBER mailing list

Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
(801) 587-9652 / Fax: (801) 585-6208
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Received on Wed Jul 02 2014 - 08:00:03 PDT
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