The best option currently is probably high-quality
wave function theory such as MP2 optimization with
subsequent Complete Basis Set extrapolation for energies,
all done in implicit solvent such as COSMO.
See for example discussion in Zgarbova et al
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 7, 2886-2902.
Of course it is not any perfect method.
Force fields may not be fully balanced for north/south
to achieve accurate description.
Jiri
On Sun, 24 Jun 2012, Steven M. Graham wrote:
> Date: Sun, 24 Jun 2012 13:53:23 -0400
> From: Steven M. Graham <grahams.stjohns.edu>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Re [amber] north/sout energy difference
>
> I'm going on the assumption that there are no 'silly questions'...
>
> How would one calculate the energy difference between a north conformation and a south conformation of a nucleoside in solution? Clearly, one could build a periodic box of H2O for each structure and optimize, but wouldn't the water energy dominate? One could delete the water molecules, but now that's a vacuum calculation. Let's assume using a distance-dependent dielectric is not going to give realistic values. Perhaps a solvent model, like GB or PB?
>
> Steve
>
> Steven M. Graham. Ph.D.
> Associate Professor
> Department of Chemistry
> St. John's University
> 8000 Utopia Parkway
> Queens, NY 11439
> 718-990-5217
> grahams.stjohns.edu
>
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Received on Sun Jun 24 2012 - 13:00:02 PDT
