Can Avogadro be used to calculate the energy needed to separate two ions? For example, the energy needed to separate a trityl cation from a tetrafluoborate anion, or a tetrabutyl ammonium cation from a chloride anion (from the distance with minimum energy of the ion pair at certain temperature to infinite distance at the same temperature). Guidance for doing this is appreciated.
You can use Avogadro to set up the geometries / systems, but you would want to use a careful quantum calculation to do the calculation.
For example, if you have the system (trityl + tetrafluoroborate) at the optimized geometry, you can select all the atoms in the \ce{BF4} then switch to the manipulate tool and enter a displacement (e.g., 0.5Å along the X axis), etc.
Thanks for the help! I am having trouble to input the ions. So, I imported from cml file, but either the anion or the cation is lost after importing to Avogadro. I went over the manual, but still could not find a way to input ionic compounds such as tetramethyl ammonium chloride (Me4N cation + Cl anion).
Can you post the CML file?
It’s not hard to create multiple fragments. Here’s a quick tutorial:
- Change to nitrogen and click to create an ammonia molecule:
- Type “c” for carbon and click on the three hydrogens, then drag down from the nitrogen to create a new N-C bond (thus \ce{Me4N})
- Go to “Extensions => Optimize Geometry” to clean up. (It’s a bad geometry)
- Change the element to Chlorine and turn off “adjust hydrogens” (which would make Cl-H … not what we want). Click somewhere to add the chloride.
- Now if you want to set the formal charges on the N and Cl, go to View => Properties => Atom Properties
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Click on the “Formal Charge” cell for N and type 1. Click on the formal charge for Cl and type “-1”.
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There is no step 7.
Wonderful!
I followed the steps, and it worked. Thanks,
The CML file I was trying to use to input tetrabutylammonium acetate into Avogadro was created in ChemDraw and saved as CML file. I was able to open it in Avogadro, but only the tetramethylammonium part showed up. The acetate part did not. Since the above suggested steps worked, not addressing this problem is OK. Thanks again,
