Despite wide variety of existing experimental methods producing electron/charge density maps, I failed to find a good dataset of experimental data for small (1-3 atoms) molecules.

There are datasets for integral properties such as https://cccbdb.nist.gov/ . It is fairly trivial to find atomic spectra data on NIST site and with some effort it is possible to obtain electronic spectra data for some molecules (though apparently there is no good unified database).

Regrettably, I failed to find any collection of experimental charge density data for small molecules. Furthermore, on second though I cannot remember where charge density maps in QC textbooks come from. Calculated charge densities are fairly easy to obtains, but experimental charge densities are a different matter. In fact, "experimental charge density hydrogen molecule" search gave me zero relevant references.

Any suggestions?


1 Answer 1


My background is macromolecular crystallography; while experimental data was kept locked in the research laboratories in the 1980s, they are now widely available through the international protein database. For example, you can view the electron density of crambin at http://www.rcsb.org/3d-view/1EJG.

The database for smaller structures is the Cambridge Structural Database. They have implemented depositing experimental data (structure factors) in the 2000s, but I did not find an efficient way to search for those structures that come with structure factors.

Charge density maps are often visualized as 2D-sections of the experimental density minus the density expected from isolated atoms (deformation density). One software program to calculate these is MoPro. Another program is CrystalExplorer, which shows deformation densities in 3D. In all cases, you would have to have access to the structure factors to make your own figures.

Is there any collection of charge density maps for small molecules? Any good data at all?

I don't think so.

  • $\begingroup$ Say I want a small (7-15 molecule) set of die hard, hi quality experimental electron density data for well-defined small molecules (3-6, definitely no more than 8 atoms including hydrogen), what would you suggest to go for? $\endgroup$
    – permeakra
    Mar 2, 2020 at 7:31
  • 1
    $\begingroup$ I would contact the authors of MoPro (Christian Jelsch, Benoît Guillot, Cristian Iordache) - they must have a set of structures with experimental data. Also, maybe contact the CCSD - they have a freely-available teaching set of coordinates, and maybe they want to include a new set where structure factors are available. The classic structures are oxalic acid dihydrate and formamide. If the molecule is much smaller, it is not in the solid phase (or contains heavy metals that are difficult computationally). Of course, ionic structures like sodium carbonate would work. @permeakra $\endgroup$
    – Karsten
    Mar 2, 2020 at 13:47

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.