6. Simple computing and visualization of molecular electron potential map

The most used kind of electrostatic potential map (EPM) is a mapping of the electrostatic potential generated by the charge distribution of the molecule, over an electron isodensity surface, but there is a simple and reasonable approximation to EPM using as mapping isosurface the Van der Waals surface of the atoms, and jmol is able to generate such isosurface.

The second requirement for building an EPM is to provide a volumetric grid of electrostatic potential (ESP) around the molecule. jmol does not generate it, but nwchem does it (see section 4). Using the generated data in section 4, we modify our input file l-proline.nw:

property
  esp
  grid
end
task scf property

save it and run nwchem:

linux$ nwchem l-proline

After process finished, some new files have been generated. One of them, a file named l-proline.elp.cube, contains the ESP volume grid and the optimized molecular geometry in cube format. Worth to mention that, although nwchem was always able to generate ESP grid data, dumping it in cube format is only available since version 6.2, so be sure this, or a recent one, is the version installed in your system¹

So next step is to generate the mol file from the optimized geometry contained in the cube file, and load with jmol:

linux$ babel l-proline.elp.cube l-proline.mol
linux$ jmol l-proline.mol

The final step is to generate the molecular surface coloured with the ESP projected on it. So, from jmol console:

jmol$ isosurface ID myepmsurface molecular map "l-proline.elp.cube"

The molecular keyword is just a minor fix that jmol makes over the pure Van der Waals (vdw) surface, in order to slightly fill the spaces between the Van der Waals spheres, thus generating a surface more similar to the one defined in terms of electronic isodensity.

Because cube files are very large even for small molecules and contains much more data than needed in order to display an isosurface, they are not the best suited for loading into a jmol applet from the web. Instead, you can dump the generated isosurfaces into a file, in jvxl file format (a jmol specific file for storing jmol generated data in more convenient way):

jmol$ write isosurface "l-proline.jvxl"

and load them from the applet, using its name as reference. Below we can see the result in a jmol applet initialized with the script

load http://dl.dropbox.com/u/xxxxxxxx/jmol/l-proline2.mol; isosurface color translucent 0.3 "http://dl.dropbox.com/u/xxxxxxxx/jmol/l-proline.jvxl"; spin on; 

The load command is not needed if you only want to see the isosurface. But you may want to make it slightly translucent in order to view the molecule inside it, as actually this script does:

Notes

[1] Check this document if you need to compile nwchem by yourself.