What are the differences between:
van der waals surface area
solvent accessible surface area
topographical polar surface area
What is the significance of these differences, and what are the differences in how each of the three is used?
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$\begingroup$ Well, you should elaborate. IMO question isn't bad, but it gathered downvotes. $\endgroup$– MithoronCommented Mar 22, 2017 at 23:00
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$\begingroup$ @Mithoron Attempted an edit. idk, if you don't like what I changed, please feel free to edit further, or roll my edits back. $\endgroup$– hBy2PyCommented Mar 23, 2017 at 13:42
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1 Answer
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A Van-der-Waals surface Area (VdW) is a surface constructed by spheres around atoms with the radius of each sphere being the van-der-Waals radius of the respective atom.
The Solvent accessible surface area (SAS) is an surface normally being constructed by "rolling" a sphere the size of the vdw-radius of the solvent molecule around the solute and taking the middle of the solvent sphere as the surface of the solute.
Picture is taken from the original GEPOL publication of Pascual-Ahuir and Silla J. Comp. Chem., 1990, Vol. 11, No. 9, 1047-1060
So the difference is just the size. Both have the same questionable physical meaning. They are used for example in continuum solvation models like COSMO/PCM.
I used the SAS for Frozen-Density-Embedding-models to close unphysical holes (in PCM the surface constitutes an infinite continuum of solvent, so there would be an infinite volume of solvent between two subsystem molecules) between molecules of different subsystems in a QM/QM/Cont. multilayer method. Nonetheless, they are both only viable for qualitative results.
For the PSA, just read the wikipedia article.
The PSA is only the surface of the polar atoms of a molecule and it is used in medicine to calculate permeability of cell membranes of molecules in the body.