Re: Re: Parameters for NH3, NH4+, and CO2

From: Jeffrey J. Potoff (
Date: Wed Nov 28 2007 - 23:08:34 CST

On Wed, 28 Nov 2007, Ilya Chorny wrote:

> Do bulk properties (density and dHv) propigate to single molecule
> experiments such as passage through a membrane channel?
Dear Ilya,

The answer to this question depends on how deep you want to get into this.
One has to develop parameters somehow, right? So the question is what
properties do you fit your parameters to? Ab initio calculations can get
you into the ballpark with binding energies, and relative sizes of the atoms,
but even at high levels of theory and large basis sets, there will still
be some fine tuning that needs to be done.

Liquid density is primarily an excluded volume interaction. One needs to
make sure they get the correct liquid density to ensure that their
molecule takes up the right amount of space.

Heat of vaporization is used primarily to set the strength of interactions
between molecules. It is not as good as fitting to reproduce the critical
temperature, but if you don't have critical temperatures (or a way to
predict them with simulation), dHv is the next best thing.

In addition, you want the force field to be consistent (I assume) with
Charmm. In which case you should also perform some calculations to
determine the free energy of solvation in TIP3P water and compare to
experiment. That will give you another data point that you can use to
tune up the parameters.

For molecules moving through a channel, their size and strength of
attraction are certainly key properties, so it is important to get them
right. Furthermore, the molecule-wall interaction will be critical,
so that may involve additional calculations and tuning of parameters.
Will a model parameterized in this way be quantitatively accurate?
Probably not, but it will most likely give you reasonable
relative values of whatever property you are looking at. To get
quantitative accuracy, which to me means within 1% of experiment, you're
talking about a very intensive parameter fitting process.


Jeffrey J. Potoff
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

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