First, it was kind of you to do that. Interestingly, NONE of the methods find the gauche conformer is more stable than the trans. At least the QM methods find the two conformers are close in energy.
I must admit to being uncertain as to what the atom type 'c3' is.
But my real question is: what exactly where the torsion angle parameters used by FF99SB? Your message implises that you had values for 'F-CT-CT-OS'. If so, what were they? If 'F-CT-CT-OS' is not in a parameter list, what gets used instead? The generic CT-CT-CT-CT?
Cheers
Steve
-----Original Message-----
From: Karl N. Kirschner [mailto:kkirsch.scai.fraunhofer.de]
Sent: Monday, January 21, 2013 5:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] [AMBER: gauche effect in OS-CT-CT-F
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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Received on Mon Jan 21 2013 - 13:00:02 PST
