Subject: Re: CCL:DMSO, counter ions and ionization state

From: Andreas Klamt <klamt<<at>>cosmologic.de>
Date: Mon, 06 Dec 2004 08:42:38 +0100

Edgar,

is it dry (water free) DMSO? Then the only way of deprotonation is 
producing DMSO-H+ ions and for protonation building DMSO anions.

We have proposed a pKa model in DMSO in our paper J. Phys. Chem. A 2003, 
107, 9380-9386:
"First Principles Calculations of Aqueous pKa Values for Organic and 
Inorganic Acids Using
COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale
Andreas Klamt,* Frank Eckert, and Michael Diedenhofen, Michael E. Beck

This may outline the way how to do it based on our COSMO-RS method.

Andreas

 Luttmann wrote:

> Dear all,
>
> does anyone have experiences with the treatment of charges during 
> peptide MD simulations (with gromacs) in DMSO?
>
> The pka of the sidechains as well as the termini might be 
> significantly different in DMSO compared to water and thus I wonder if 
> there is a convenient way to estimate the ionization state of the 
> residues. Furthermore would you just put counter ions into the DMSO - 
> or would you keep the peptide neutral?
>
> Any suggestions are welcome and thanks in advance..
>
> Edgar
>

-- 
--------------------------------------------------------------------------------
Dr. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  
Fax:  +49-2171-73168-9
e-mail: klamt=at=cosmologic.de
web:    www.cosmologic.de
--------------------------------------------------------------------------------
COSMOlogic
        Your Competent Partner for
        Computational Chemistry and Fluid Thermodynamics
--------------------------------------------------------------------------------