Re: filling hydrophobic cavity with... methane?

From: Axel Kohlmeyer (
Date: Thu Dec 18 2008 - 17:44:23 CST

On Thu, 18 Dec 2008, Sebastian Stolzenberg wrote:

SS> Dear All,
SS> I need to fill a ~2000A^3 hydrophobic protein cavity with methane or some
SS> other suitable molecule (in reality, people don't know what type of molecule
SS> is in there).
SS> At 310K, methane is a gas with a particle density several orders of
SS> magnitude lower than the one for water - so it is unlikely, that all niches
SS> of this cavity can be entirely filled with methane


please make some simple estimates using the ideal gas equation
and you'll find out that you can fit only a few gas molecules
in this amount of space (about five, if my back-of-the-envelope
estimate is correct). so that space will be practically empty.
this is not really a matter of "filling" the niches...

SS> - unless...
SS> 1.)
SS> In a buried hydrophobic protein cavity environment, how (much) could one
SS> expect the methane density to change? So far, I didn't find any papers on
SS> this highly unusual topic.

please have a look at simulations in the grand canonical ensemble
simulations. the density inside is determined by the chemical
potential of the molecule in question. depending on the properties
of the surface of the cavity, you may also have adsorption, though.


SS> 2.)
SS> Is there any other molecule that I could use instead? We were thinking about
SS> ethanol, which, however, has hydrophilic parts.

SS> Thank you very much,
SS> Sebastian

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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