Dear AMBER users:
I have a question about how amber handles the 'gauche effect' - the tendency for two electronegative groups in a X-CT-CT-X fragment to prefer a gauche rather than an anti conformation. The gauche effect impacts the gamma bond (O5'-C5'-C4'-O4') and the endocyclic O4'-C4'-C3'-O3' in deoxyribonucleos(t)ides (and the endocyclic O4'-C1'-C2'-O2' in ribonucleosides). It is one of the factors that determines the N/S (C3'-endo/C2'-endo) equilibrium.
FF99 uses a two-fold Fourier term to model the OS-CT-CT-OS (OS-CT-CT-OH and OH-CT-CT-OH ) superimposed on a typical 3-fold term. Interestingly, the F-CT-CT-CT gauche effect is modeled with a one fold term with a phase shift of 180 degrees (effectively penalizing the anti conformation.
Short version: amber can handle the O-CT-CT-O and F-CT-CT-F gauche effects. BUT: has anyone investigated the torsion parameters for the O-CT-CT-F gauche effect, as one would find in a 2'- or 3'- fluoro substituted nucleos(t)ide?
Steven M. Graham, Ph.D.
Associate Professor
Department of Chemistry
St. John's University
8000 Utopia Parkway
Queens, NY 11439
grahams.stjohns.edu
Office: 335 St. Albert Hall
Voice: 718-990-5217
Fax: 718-990-1876
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Received on Sat Jan 19 2013 - 15:30:02 PST
