7. Computing and visualization of Electrostatic Potential Map over molecular isodensity surface

In the previous post i explained how to compute and visualize an EPM over a Van der Waals surface using nwchem and jmol. However, actually it was found more realistic, theoretically and experimentally, to define the surface of a molecule as an isodensity surface, that is, a surface of equal electronic density, derived from the molecular orbitals influence.

A typically useful isodensity surface for estimating molecular shape and surface, is the one defined by a cutoff of 0.001 electron/Bohr³, that is, the one that encloses the space where the electron density is above such threshold. Such a cutoff encloses more than the 95% of the molecular electronic density.

Taking the case of l-proline again, the nwchem file for generating an electron density grid from the vector files generated in the previous steps would be something like:

dplot
  limitxyz
    -5.0 5.0 100
    -5.0 5.0 100
    -5.0 5.0 100
  gaussian
  output l-proline.den.cube
end
task dplot 

The limitxyz block here is used to define the limits and number of points for each axis. In order to estimate good limits for the grid, you can open the model in jmol and type on the console

jmol$ show boundbox

and substract two unities to the resuling first corner coordinates, and add two unities to the resulting second corner coordinate, and round it.

Once got the density grid output, file, in jmol console you can do:

jmol$ isosurface cutoff 0.001 "l-proline.den.cube" map "l-proline.elp.cube" jmol$ write isosurface "l-proline.den.jvxl"

Compare the result (first figure) with the one obtained previously with VDW surface (second figure):