Summer 2009 CHEM 1211 – Exp. 11 Molecular Geometry and SPARTAN - Computer lab Room 3019.
Spartan is a modeling program where simple molecules can be drawn and it will give the correct geometry (minimum
energy) and provide information about the charge present on each atom (electron density) and other advanced
calculations.
To start:
1. On the deskstop of the computer, click on the shortcut for Spartan 02. A blue window will come up.
2. Click on FILE, new. A right hand menu (fragment panel) with different atoms will pop.
Some commands (in the top menu the buttons):
V
visualize – to grab and turn around
+
to add fragments (the panel shows on the right)
Red lines
to delete
Blue E with arrow
to Minimize
>?<
to measure bond distance
Etc… Every time you are going to start a new molecule you must close Spartan all the way.
From the assigned compounds, complete the assigned Lewis dot structures for NO2-, H2O, and I3-.
Your lab report should have the following molecules or ions: 3, 4, 5, 6, 7, 8, 9, 10, 13, 18, 27, 28, 42, 43, 46, 48.
NO2Drawing a Molecule in Spartan:
1. From the fragment panel “Exp”, click on nitrogen and then select the type of bond corresponding to your Lewis
dot drawing (the one with two bent lines) and click on the blue area; then select oxygen and select the single
bond, then click at the end of one of the bonds (yellow stick) coming from the nitrogen in the work area at the
left. A red atom should appear, attached to the blue atom. Click on the other bond. Note that on this panel you
have all elements in the periodic table and the different types of bonding to select!
2. Click on the top menu the button with the blue E and an arrow going down (MINIMIZE).
3. Once the minimization is finished, go to the top menu on MODEL, click and look at the different presentations
with the: Ball and wire, Space filling, go back to the Ball and spoke.
4. Go back to Spartan, to the top menu on GEOMETRY, click Measure distance (this function is also the button
with the blue question mark in between two black triangles). Now select the N and one of the O to measure the
bond distance. It will appear in the bottom right corner. Write this number and units on a Word document.
Measure the other bond too. You can turn around the molecule by clicking to it with the left mouse button. Also,
you can click on the bond, and the distance will show in the box on the bottom right.
5. Measure the bond angle by selecting the three atoms and then clicking on the bond angle button on the top
menu. Write it down on the Word document.
6. Go to the top menu on SETUP, click on Surfaces. Click Add.. and select density and in Properties: density
again. Resolution: Intermediate. Click OK. Close the surface windows.
Next set up structure calculations with Spartan. Please, go to FILE and save the file as SpartanNO2
1. Go to the top menu on SETUP, click on Calculations.
2. Select Calculate Equilibrium Geometry:
with Semi-empirical (AM1)
Start from: Initial geometry
Total Charge: Anion
(these you will change if neutral, cation or anion)
Compute: and Print: Select all options
Multiplicity: Singlet
Converge
Global Calculations
Click: OK
3. Go back to SETUP, and click Submit. Dialog boxes will appear to let you know that the calculation has started
and when it is finished. For a small molecule, this calculation will only take a few seconds. For a larger molecule,
it may take several minutes.
4. Go to DISPLAY, Properties. Write down in your report page only the displayed Weight and Dipole (in Debye).
Click on the Dipole square. The dipole arrow will appear. The tip of the arrow pointing to the overall negative
side of the molecule. Copy this structure on your Word document. Go to the top menu on edit, click on copy.
Then paste it on the Word document. A picture like below will show. You can focus on your molecule doing Crop
by selecting the picture and then, go to Format on the Word menu, then select crop and adjust your picture.
5. Go back to DISPLAY, Output. Scroll down and write down in your report the Energy of Formation and the
displayed Charge for each atom. Example: You can see two O atoms have a similar charge. Write these
numbers on your Word document. To be sure your assignments are correct. Go to your structure, click on one
atom – it will get highlighted. Then go to DISPLAY, Properties – the Electrostatic charge will show on the
properties window. (Your atomic charges should match the direction of the dipole and should add to the total
charge of the ion).
6. Go to DISPLAY, surfaces – click on the little square to check it. You’ll see areas with different colors (red is
negative, blue is positive, green is neutral). This should agree with the numerical charge assigned previously
(example: the red areas should be where the oxygens are).
To make the Surface go away, simply de-check the square on the Display surfaces window.
You have finished the exercise for NO2-. Close Spartan. Open Spartan again. A blue window will show. You can start a
new molecule now.
Try drawing now:
H2O
During the set up of calculations remember to change Charge to Neutral.
I3 -
During the set up of calculations remember to change Charge to Anion.
- Water Cluster – Answer all questions below.
Close all Spartan windows.
Open the Spartan document “Water Cluster” from Dr. de la Garza website and save it on the desktop.
1. Move the cluster so you can see how it is disordered.
2. Minimize energy of the cluster. Once is done, move the cluster again. Notice any specific arrangement? Identify
a couple of hydrogen bonds. (Try measuring the distance of a hydrogen bond by clicking on a O atom of one
water and H atom of a different water next to it. Compare to a covalent O-H bond distance). Are hydrogen bonds
stronger or weaker than covalent bonds?
3. Display your water cluster as a space-filling model (Go to MODEL on the top menu and select space filling).
Move the model around so you can see any “empty space” between molecules.
4. Click on add fragment (+) button and then draw ammonia (NH3) in the middle of the cluster.
For this, go the “Exp” tab and select a N atom and a trigonal pyramidal bonding. Then click on an area on the middle
of the cluster while pressing the INSERT on your keyboard. A blue atom should appear with 3 yellow lines. Then
select a H atom and a single bonding. Then click on each of the yellow nitrogen lines.
5. Minimize the energy. Can you see any hydrogen bonds to the ammonia? Are the water arranged differently than
in “pure” water? Would water dissolve ammonia?
6. Delete the ammonia and try methane instead (CH4).
7. Minimize the energy. Has the cluster expanded or contracted in the vicinity of methane? Are there any hydrogen
bonds to methane? (Measure the distances to answer this). Would water dissolve methane?
Save the Word file and send it to yourself in an email. Print it out later and turn it in with your Exp 11 report next
lab.