Often crystal structures found online from past published crystallography experiments are of the salt of a molecule of biologic interest, as opposed to the freebase form of the molecule itself. For example, I have a CIF file for mescaline hydrobromide (CCDC 1211316) at the moment that I would like to create a 3D model of mescaline from. Would removing the extra hydrogen atom on the amine group (i.e., changing the $\ce{NH_{3}^+}$ to $\ce{NH_2}$) and the free bromide ion suffice or will I also have to optimize the structure's geometry? If I do need to optimize it, or otherwise modify it beyond the procedure I just pointed out, please tell me how to do it with free software (Avogadro, for instance).


1 Answer 1


In general, the crystal structure of a molecule is a highly accurate geometry. So yes, you can take a salt and modify as needed. (The caveat in the comment is useful - keep in mind that different groups may be protonated or deprotonated depending on solvent and pH.)

There are two other caveats:

1) The conformation in the crystal structure is not necessarily the lowest energy conformer in solution or the gas phase. You may wish to perform a conformer search to find a low-energy minima.

2) If you are performing further calculations (e.g., DFT for electronic structure, force fields for MD, etc.) the geometry of the crystal structure will not likely be a minima of the computational method, so geometry optimization or equilibration (for MD) is needed before further simulation.

That said, the crystal geometry is a good place to start for many uses. Certainly if a crystal structure is available, I'd suggest you use it rather than build a geometry by hand.

  • $\begingroup$ How would I do a conformer search for a low-energy minima & those further calculations in Avogadro? I'm a newbie when it comes to Avogadro, so step-by-step instructions in Avogadro would be much appreciated. $\endgroup$
    – Josh Pinto
    May 28, 2015 at 11:15
  • $\begingroup$ avogadro.cc/wiki/Extensions_Menu - There's Extensions > Molecular Mechanics > Conformer Search $\endgroup$ May 28, 2015 at 11:47
  • $\begingroup$ So which type of conformer search should I use? Systematic rotor, random rotor, weighted rotor or genetic algorithm? What parameters should I use? Like I realize some of these parameters will be up to myself to decide but which ones would likely give the best results? How do I do DFT for electronic structure and MD? It might help if you could give their full names too so I might look them up for myself. Thanks for your time, though, I do appreciate it. $\endgroup$
    – Josh Pinto
    May 28, 2015 at 12:10

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.