Date: Mon, 21 Jan 2013 11:20:49 +0100 (CET)
Hi Steven,
I quickly computed the 1-fluoro-2-methoxyethane rotational curve for the os-c3-c3-f and OS-CT-CT-F parameters, with the methoxy group in the trans conformation. (The partial atomic charges were computed using R.E.D and three input conformations.) Attached you will find the relative energy plot, as computed by gaff and parm99SB force field, and HF/6-31G(d)//HF/6-31G(d) (QM10) and MP2-aug-cc-pVDZ//HF/6-31G(d) (QM50) gas-phase reference curves.
With regards to their performance in an MD simulation, I can only predict that the population sampling between trans and gauche may result in incorrect proportion if one believes the QM data to be an accurate representation of the potential energy surface in a biological context.
Hope this is helpful.
Cheers,
Karl
----- Original Message -----
From: "Steven M. Graham" stjohns.edu>
To: amber.ambermd.org
Sent: Sunday, January 20, 2013 12:00:44 AM
Subject: Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F
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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- application/pdf attachment: Figure_E.gaff.pdf
- application/pdf attachment: Figure_E.parm99SB.pdf
(image/png attachment: torsion_rotation.png)
