From: Ilya Chorny (ichorny_at_gmail.com)
Date: Wed Nov 28 2007 - 21:51:19 CST
Do bulk properties (density and dHv) propigate to single molecule
experiments such as passage through a membrane channel?
Thanks,
Ilya
On Nov 28, 2007 7:34 PM, Jeffrey J. Potoff <jpotoff_at_chem1.eng.wayne.edu>
wrote:
> On Wed, 28 Nov 2007, Ilya Chorny wrote:
>
> > Anyone know where I can find forcefield parameters for the above
> molecules.
> > i.e. charges and atom types. I would steel them from the protein i..e
> LYS
> > but I do not know the charges. Any ideas?
> >
> > Thanks,
>
> I can't help you with NH3 or NH4+, but for CO2, we developed a very
> accurate force field a few years ago [AICHE Journal (2001), 47,
> 1676-1682]. For NH3, I would search J. Chem. Phys., J. Phys. Chem. B and
> Fluid Phase Equilibria. I'm sure someone has already done it.
>
> If you intend to generate your own parameters, charges are relatively easy
> if you have access to Gaussian. Optimize at the HF/6-31g+(d,p) level and
> use the "pop=CHELPG" keyword. The charges that result will be about the
> best you can get without tuning them empirically. For small molecules, we
> generally increase the magnitude of the charges that come out of this
> methodology by 10-20% in our empirical fitting process. As for the LJ
> parameters, "borrowing" them from larger molecules is likely not going to
> work, since you are talking about small polar molecules where the N atom
> is in a very different bonding environment than wherever you took the
> parameters from. If you don't find something satifactory in the
> literature, you will have to fit the epsilons and sigmas to reproduce the
> liquid density and heat of vaporization as a minimum. Again, this will
> get you in the ballpark, but you can do even better with small molecules
> if you fit your parameters to reproduce phase behavior and vapor pressure.
>
> Regards,
> Jeff
>
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>
-- Ilya Chorny Ph.D.
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