DRAWING AND FIXING MOLECULES IN DSVISUALIZER

Sometimes you have to fix aspects of a molecule that you have drawn or copied into DSVisualizer.

Sketching Molecules

From the menu choose View | Toolbars | Sketching. There are sketch "pencils" for creating carbon chains and rings, as well as a free style pencil. Practice making a carbon chain. When you click and drag the ring pencil, what happens? If you want to change an atom's identity, select it with the Selection or Sketch Tool and then type the atomic symbol for the new element. To make multiple bonds, click on an atom and then drag to an adjacent atom. Click the second atom. The sequence starting with a single bond (as with most drawing programs) is double, triple, single.

 

Fixing Molecules

See the fix-geom.pdf document for instructions on changing charge and creating aromatic and partial bonds in a molecule.

 

Practice Molecules

If the molecules do not open in DSV when you click them, then download the files to your PC and open with DSV.

1. Azulene (C10H8) is aromatic. Fix this model of azulene so that it has aromatic bonds.

2. Urea has a C=O. Fix the bond.

3. The isopropyl cation needs to have its central carbon with a +1 charge. (Before and after fixing its charge, choose Structure | Clean geometry to see the effect of changing the charge. Notice also, before and after, the effect on the Data Table (View | Data Table).)

4. The methoxide ion should have a -1 charge on the oxygen. (Before and after fixing its charge, choose Chemistry | Hydrogens | Add to see the effect of changing the charge.)