Chemistry - How can I calculate the charge distribution of a water molecule?


Solution 1:

Two suggestions: MolCalc: Calculate Properties > Polarity and Solvation gives you a 3D surface plot with the electrostatic potential superimposed.

Another suggestion is Avogadro/GAMESS/MacMolPlt. See for example here

Solution 2:

You need (some) background knowledge and the tools to

  • generate an input file with the coordinates of your molecule and commands which calculations to perform

  • run the calculation

  • postprocess the results

All tools are out there! Unless you have access to the commercially available suites through your institution, I suggest to use those that are free (as in free beer and free speech). Actually, some of these free tools are a good choice in any case!

  • Input files can be generated using Avogadro, Molden, Gabedit, or wxmacmolplt

  • You can perform your calculations using NWChem, MPQC (both are in the repositories of every recent Linux distribution) or GAMESS-US, which can be downloaded after registration. In addition, there are pyscf and PyQuante, which you mentioned in your question.

  • Most of the tools used to generate the input files can be used for postprocessing too.

To quote the slogan of a shoe company:

Just do it!

Solution 3:

In pyscf, we are routinely running to generate molden file and plot the orbital surface with Jmol. It should not be too hard to write small script to generate density or other charge surface then plot the surface with Jmol. The basic functions you probably needed should be very close to the functions used by dft module, such as eval_ao, eval_rho.

In the recent Pyscf alpha 2 release, a script pyscf/tools/ has been added to generate the Gaussian cube file format. In my linux box, the density looks fine in Jmol. You can use it as an example to generate other Jmol formats.

Solution 4:

If you are not looking to actually learn these calculations and just need the contour plots, you can use Arguslab.

This will give you illustrative plots of orbitals as well as total electron density. They won't be super-accurate but they will be quick.