In this section, you will learn how to get started with WebMO. Click to see a video demo of how to build a moleculer and view it in 3D Viewer . In order to play these videos, you should have flashplayer plugin installed. You can download the plugin from

Structure of CH4

1. Use the guest account (username: guest, password: guest) to log in the WebMO demo site.
Click New Job -> Open Editor. A small window opens where you build molecules.

2. Add C atom in the workspace.
Click on the Periodic Table icon (5th down the left side). Choose "C" by clicking on it and click once in the center of the workspace. A gray carbon atom appears.

3. Choose Clean-Up -> Comprehensive Mechanics. You should now have methane, CH4 now. Experiment with the Rotate, Translate, and Zoom tools (Top 3 icons on left side).
Click Close Editor in the main WebMO window. Methane now appears in the Build Molecule window. This structure contains idealized bond lengths and angles. A more accurate structure can be found by carrying out an energy minimization using molecular mechanics, semiempirical methods, or ab initio calculations. To reduce the time required for the calculations and to obtain reasonable results, the semiempirical method PM3 will be used. (This method is available in most molecular modeling programs).

4. Click the blue "continue" arrow in the lower right side of the Build Molecule window.
Choose Mopac as the computational engine.
Choose the following settings: Job Name: CH4PM3Geom Opt, Calculation: Geometry Optimization, Theory: PM3, Charge: 0, Multiplicity: Singlet.
Click on the blue continue arrow. You should now see your job listed. To kill or stop a job, you would click on the red "X" under Actions on the right side. Click Refresh (every ~5 seconds) until you see that your job is Complete (under Status).

5. Click on the hyperlinked name (CH4 PM3 Geom Opt) to open the "View Job" window. Choose the Select arrow (4th icon down on left). Click on one of the H atoms in the structure (the other atoms and bonds will "fade"). Shift and Click the C atom (both atoms are now highlighted). The bond length is displayed just below the molecule.? Record the value of the C-H bond ___________A (1.091 A literature). Check the other C-H bond lengths.

Click on one of the H atoms, then Shift and click the C atom, followed by another H atom. The bond angle is displayed just below the molecule. Record the value of the HCH bond angle ___________degree (109.4712 literature). Check the other HCH bond angles. Scroll down and review the information under Calculated Quantities.

6. When finished, click the Job Manager link under Actions (to the left of the molecule display). To continue on to the next exercise, choose New Job -> Create New Job.

Structure of NH3

1. Build NH3 using the above procedure.

2. Use Job Name H3N PM3 Geom Opt, and perform the geometry optimization as before (PM3). Record the value of the N-H bond length __________A (~0.999 A, 1.012 A literature) Record the value of the H-N-H bond angle __________degree (~107.8 degree, 106.67 degree literature)

3. Scroll down and review the information under Calculated Quantities.? Click on the magnifying glass next to Dipole Moment and rotate the molecule to see the vector.? Does it make sense?

4. Return to Job manager, and choose New Job > Create New Job.


Structure of H2O

1. Build H2O using the above procedure.

2. Use Job Name H2OPM3, and perform the geometry optimization as before (PM3). Perform the PM3 geometry optimization as above. Record the value of the O-H bond length __________A (~0.951 A, 0.959 A literature). Record the value of the H-O-H bond angle __________degree(~107.7 degree, 103.9 degree literature).

3. Return to Job Manager.


Structure of NH4+ (Ammonium cation)

1. Build the NH3 molecule and do the "Clean-Up" step, as before.

2. With NH3 displayed, open the Periodic Table and choose H. Click on the N atom and drag away to add another H bound to the nitrogen atom. Choose Clean-Up > Geometry to get the tetrahedral structure. Use the Select arrow and click on the N atom to highlight it. Choose Adjust > Charge, and type in +1 in the Pop-up window. Click Apply followed by OK.

3. It may be hard to see, but the N atom should now have a "+1" on it. Proceed with the geometry optimization as before (Mopac >PM3). Record the value of the H-N-H bond angle __________degree Does this value make sense?

What conclusion(s) can you make concerning the H-X-H bond angle and the number of unshared (lone) pairs of electrons around the central atom X?

What conclusions can you make concerning the size of the central atom X and the X-H bond length?