I'm re-posting this as I got only one response (thanks Jiri; see below). Not a criticism - I know if I don't respond right away the post tends to get lost in my inbox.
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?
Jiri: Read your chi(OL) paper - I was already familiar with it. The problem in I want the N/S energy difference at the minima, which you've set to zero to compare the chi torsion profiles and chi dihedral terms. But thanks anyway.
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 Thu Jun 28 2012 - 15:30:02 PDT
