Step 8 - Analysis Sites

Time to calculate some properties, but first we need to create some analysis sites on our ions.

Cation

To be consistent with the original study our focal site on the cation will be at the midpoint of the two nitrogens of the imidazolium:

Go to the   EMIM   species tab, and click on the Sites section

Select both nitrogen atoms by holding down the Shift key and clicking on them in the viewer (you can also draw individual boxes around them)

Right click the selection and click Create site from ⇨ Atoms to create a new site with the origin at the midpoint of the these two atoms

Now select one of the nitrogens on its own and right click it

Click Modify current site ⇨ Set X-Axis Atoms to define the direction of the x axis

Finally, select the carbon atom in between the nitrogens and right click it, selecting Modify current site ⇨ Set Y-Axis Atoms in the toolbar to define the direction of the y axis

Double-click the site in the list and rename it to RingNN

Anion

For the anion we’ll use a simple centre-of-mass site:

Go to the   Acetate   species tab, and click on the Sites section

Select all atoms in the acetate (draw a box around everything with the mouse)

Right click the selection and click Create site from ⇨ Atoms to create a new site

In the site Definition the Weight by mass option

This locates the site more-or-less on the carbon atom of the carboxylate group

Double-click the site in the list and rename it to COM

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