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).
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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.
answered May 28, 2015 at 4:30
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$\begingroup$ 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. $\endgroup$ May 28, 2015 at 11:15
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$\begingroup$ 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. $\endgroup$ May 28, 2015 at 12:10