As a new feature, COSMOtherm now is able to generate VRML files for the visualization of the screening charge density s on the molecular surface. This gives a very vivid picture of the molecules, showing the local positions of strongly interacting sites. Even details like lone-pairs are well resolved. Note, that s is a much more local and detailed property compared to electrostatic potential (ESP). This can specially be seen for ions, for which the ESP is dominated by the ionic charge, while s still resolves a lot of details (see e.g. chf2coo_sig.wrz). We are convinced, that, as a supplement to the s-profiles, these pictures are useful for a better understanding of the physics underlying solvation phenomena. In the same way as s, any property derived from s, i.e. logarithmic partition coefficients, activity coefficients and solubility could be visualized as a surface property. As an example, find surfaces colored by logPOW in this directory. Finally, the molecular structures are given as ball&stick models in the *_mol.wrl files.
The visualization makes use of the VRML file format. Thus you need a (free) VRML viewer as a plug-in for your Browser. One of them can be found at:
www.parallelgraphics.com/products/cortona/download
After installing that you just click on the WRL file and you get a very nice, rotatable model of the molecules. Find a few examples attached. In the *_sig.wrl files blue codes strong positive polarity (negative s) and red codes strongly negative polar surface pieces, green/yellow is in the weekly polar range.
In the *_logP.wrl files you see lipophilic regions red, while hydrophilic regions are blue to deep violet.
Download of complete wrz-archive (compressed):
σ-surface (9.7MB), logP-surface (9.5 MB), ball & stick (80K)