Welcome to the CAChe Molecular Modeling Tutorials

Department of Chemistry

University of Pittsburgh at Johnstown

Home
Getting Started
The Basics of CAChe
The User Interface
Simple Molecules
Inorganic Molecules & Ions
Organic Molecules
The Fragment Library
Viewing & Manipulating
Computing Properties
Optimizing Geometry
Molecular Orbitals
Spectral Properties
Predicting Reactivity
Energy Maps
General Chemistry
Ferrocene

Building an Inorganic Ion

Task: Build a nitrate ion, NO3-

Time: 5 minutes

Like ozone, the nitrate ion also has an unusual bonding structure. As with the ozone and SO2 structures, it will help to draw the Lewis structure and determine the formal charge on every atom.

  1. To open a new Workspace select File|New from the menu bar.
  2. Select the atom icon . Your cursor turns into the atom tool .
  3. Select the arrow button in the element type box and select nitrogen. Make sure the hybridization is sp2  .
  4. Now we want to add the oxygen atoms.  Select the arrow button in the element type box and select oxygen. Since the hybridization is not the same on every oxygen atom, we'll change that after we draw the skeleton. Click on the nitrogen and drag.  When you release the mouse button you will see that an oxygen atom is attached to the nitrogen .
  5. Repeat this step to add two more oxygen atoms.
  6. Compare your structure to the Lewis structure you drew.  Adjust the bond order if necessary.  Follow the same steps as you did for ozone.
  7. Check the hybridization on the oxygen atoms.
    1. Click on the select tool then click on one of the oxygen atoms. The current hybridization will appear in the hybridization type box.
    2. The hybridization on the oxygen atom with the double bond to nitrogen should be sp2 and sp3 on the other two oxygen atoms.
    3. To change the hybridization, select the arrow button in the hybridization type box and select the correct hybridization .
  8. We also need to check the Formal Charges.  Compare the Lewis structure you drew at the beginning of this exercise with your CAChe structure.  If you need to change the charges, click on the select tool , select the atom, then click the up or down arrow button in the charge box to select appropriate charge for that atom. Repeat this step for each of the each atom as needed.
  9. Click on the select tool and click in the workspace (not on any atoms or bonds) to select the entire molecule.
  10. To fix the geometry of the nitrate molecule, select Beautify|Geometry from the menu bar. 
  11. To save your finished molecule select File|Save and save it as "nitrate".

This ends the tutorial on building inorganic molecules.  Next, we will try building some organic molecules.  In the next module of the tutorial you will
bulletBuild the carbon ring of cyclohexane and add the hydrogens
bulletModify cyclohexane to build cyclohexanone
bulletModify cyclohexane to build cyclohexanol
bulletInvert the chirality of the OH group of cyclohexanol