MOLECULAR MODELING with SPARTAN Rev 5/11

EXPERIMENT 12

MOLECULAR MODELING WITH SPARTAN rev 5/11

GOALS This experiment should help you develop a better understanding of the three-dimensional shapes of molecules. You will be introduced to molecular modeling and computational chemistry.

INTRODUCTION Molecules are three-dimensional, not flat as they often appear in textbooks and on chalkboards. We build physical models to help us see a molecule’s shape more accurately. Molecular modeling software is even more useful because it not only helps us visualize shapes, but also performs calculations that predict physical and chemical properties. Large drug and chemical companies use very sophisticated and very powerful molecular modeling programs to aid in the development of new products. In this experiment we will be using a modeling program called Spartan to examine structures and some simple molecular properties.

We will use Spartan to predict bond lengths and bond angles. These can be compared to the predictions made from simple Lewis dot structures. Spartan will also calculate charge distributions in molecules. From the charges, we can determine the polarity of the molecule and also likely spots for reactions. Molecular spectra can be predicted by modeling programs. In this experiment, we will ask Spartan to predict IR spectra. Recall that when a molecule absorbs IR radiation, bonds will stretch or bend. Only those wavelengths that correspond to the required amounts of energy will be absorbed.

While models may predict likely properties, the actual shape of a molecule (the bond lengths, bond angles, and arrangement in space) is determined by experimentation, using techniques such as x-ray crystallography or nuclear magnetic resonance spectroscopy. Molecular modeling programs use theory, complex calculations, approximations and intermediate numbers (called parameters) to predict the shapes and other properties of molecules. The more sophisticated models usually predict shapes that are closer to the actual shape. Even a single software program such as Spartan has several different ways of doing these calculations, which give somewhat different answers. Remember that no model perfectly represents reality and thus while a good model gives acceptable predictions most of the time, even the best models fail at times.

LAB NOTEBOOK You do NOT need to record any entries in your notebook this week. This is a computer experiment that you will do independently. Most of this lab can be done on a computer. Part VIII, however, must be done in the Gen Chem lab room during your regular lab period. We STRONGLY encourage you to do most of the computer work BEFORE you come to lab. That way, your instructor can help you with any aspect of the software that gives you trouble. A few computers will be available for use during your regular lab time but we do not have enough computers for everyone to work during the lab period. You must plan time on your own. The entire modeling experiment should take a beginning user about two hours but this time can be divided into multiple sessions.

LABORATORY REPORT Your data and answers to questions are written directly on the pages of this handout. Simply staple the entire thing together and turn it in as your report. Be sure that you know when this final lab report is due.

THE SPARTAN STUDENT SOFTWARE The Spartan Student software is available on computers in the Trexler first floor computer lab and on the four computers in the reading room outside the General Chemistry Lab. It is also available through RCRC (Remote Computing at Roanoke College) on the science computers. You can find instructions on using RCRC at the IT website.

Part I: Familiarize yourself with the software 1. Start the software and then open a new file by clicking on the top left button that looks like a sheet of paper. Slowly move your cursor over each of the buttons at the top of the screen and next to the icons below record what each button does.

2. On the right hand side of the screen are a collection of molecular fragments that are used to build molecules. These fragments are divided among several model building kits that are accessed from tabs: organic, inorganic, peptide, and nucleotide. Look around through the tabs to see what is available. If you don’t see these tabs, it is because you didn’t click on Open New File in step 1. Please follow the directions carefully to be sure that you see what you should. If you want to “go your own way,” that’s okay. You won’t hurt anything but you may need to do some extra clicking around to get where you need to be. The very end of this document has some general troubleshooting advice you can consult if you have trouble.)

3. Below the tabs are buttons that let you select pre-drawn groups and rings. Look around at these to see what is available.

Part II: Methane, CH4 1. If you have placed anything on the large blue window while exploring the features, close the file without saving and open a new file using the buttons across the top of the screen. (If your background window is not blue-green, see the note at the end of this document.)

2. Choose the tab for the organic tool kit. Click on the C atom with 4 single bonds.

3. Click once in the middle of the blue display window. A C atom with 4 bonds should appear.

4. Click on the View button at the top of the screen. The drawing tools will disappear and Spartan will add hydrogen atoms to each of the open bonds.

5. Hold down the left mouse button and move the cursor around on the screen. What effect does this have?

6. Hold down the right mouse button and move the cursor around on the screen. What effect does this have?

7. Choose the Model dropdown menu from the top of the screen. Choose each of the types of models in turn. Draw and describe how each shows the molecules

a. Wire

b. Ball and Wire

c. Tube

d. Ball and Spoke

e. Space Filling

8. Set the model type back to Ball and Spoke. Save your file to one of your drives, naming it Methane.

9. Let’s get Spartan to calculate the best structure for methane. Choose the dropdown menu Setup, then choose Calculations. Check to see that the Calculate window here says: Equilibrium Geometry. Click Submit. You will see a dialog box indicating that a calculation has started, and then a second dialog box when it is complete. Clear these from the screen.

10. Spartan has calculated what it thinks is the best structure and displayed it for you. Measure the C-H bond distances by clicking on the bonds. The bond distance will be displayed in a small box at the lower right of the screen. Check all of the C-H distances. Record what you find. Note that Spartan reports bond distances in angstroms, Ǻ. 1 Ǻ = 10-10 m You can get the same information by clicking on the Distances button and then clicking on two atoms.

11. Measure the H-C-H bond angles by clicking on the Angle button and then clicking on three atoms, H, C, H, in a row. The order that you click on atoms matters! Check all of the bond angles and record what you find.

12. Draw a Lewis dot structure for CH4. What bond angles do you expect? How does this compare to the angles predicted by Spartan? Look up a typical C-H bond distance in Table 9.4 in your textbook. Record this here. How does this compare to the bond distance Spartan predicted?

Part III: Ethane, CH3CH3 1. Click the Add Fragment button at the top the screen. The drawing tools should re-appear.

2. From the Organic tool kit, click on the C atom with 4 bonds. Place your cursor on one of the yellow spokes of the first C atom already on your big blue window. Click to bond a second carbon atom to the first. Click the View button. Spartan will add hydrogen atoms to all of the open bonds.

Click Save As and name your file Ethane.

3. Let’s set up a slightly more complicated calculation that will return charge distributions and an IR spectrum in addition to the predicted structure. From the Setup dropdown menu, choose Surfaces. Click on the Add button. Set the Surface: to density, and the Property: to potential. Then click OK. Close the Surfaces dialog box. Now choose Setup, Calculations. Be sure that the Calculate box says Equilibrium Geometry and that the With box says Hartree Fock 3-21G. Click on the IR checkbox. Finally click Submit.

4. After you see the dialog box notifying you that the calculation is complete, check the bond distances and angles as you did for methane and complete the table. Data for Ethane: C – C distance: ______C – H distance: ______

H – C – H bond angle: ______H – C – C bond angle: ______

5. Draw a Lewis dot structure for CH3CH3. What bond angles do you expect based upon this structure? How do these compare to what Spartan has predicted?

6. Compare the carbon-hydrogen distances in ethane to those Spartan predicted for methane.

7. Now display the potential surface by clicking on the dropdown menu Display and then Surfaces. (You may need to click View first, depending on how you left your structure. In general, if Spartan seems to hesitate to do something, try clicking View to clear out previous choices.) Click the yellow box by density. This surface shows areas of positive and negative charge densities on the surface of the molecule. Red is negative; Blue is positive. If the display is solid and doesn’t let you see the atoms, change the display to transparent. To do this, click anywhere on the molecule surface. A new menu box in the lower right of the screen will let you change to a transparent style. Use your mouse to rotate the molecule around. What color and charge corresponds to the positions of the hydrogen atoms? What color and charge corresponds to the areas between hydrogen atoms?

8. Click the yellow box again to turn off the surfaces display. To examine the IR spectrum, click Display, Spectra, and then Draw IR spectrum. Use your mouse to move the Spectra dialog box to one corner of the screen so that you can see the spectrum clearly. The dialog box contains a list of the frequencies at which our molecule absorbs IR light. Click on the yellow box next to several frequencies to see the effect it has on the molecule. Note that some cause specific bonds to stretch, while others cause bending or twisting. You may need to rotate your model to see the effect clearly. Complete the table below.

Frequencies Effect on Molecule 3200-3300 cm-1 1600-1700 cm-1 1004 cm-1 311cm-1

Click off the frequencies so that the molecule stops moving. Close the spectra dialog box. To remove the IR spectrum, click the Delete button at the top of the screen and then click anywhere on the IR spectrum. Close the file.

Part IV: Ethene, CH2 = CH2 1. Open a new file.

From the Organic tool kit tab, choose the C atom with two single bonds and a double bond. Click anywhere on the blue window. Note that the double bond spoke has a small yellow ball at its end. Click on that ball to add a second carbon atom. Now click the View button. Save the file, naming it Ethene.

2. Setup and run the same calculation that you did on ethane.

From the Setup dropdown menu, choose Surfaces. Click on the Add button. Set the Surface: to density, and the Property: to potential. Then click OK. Close the Surfaces dialog box. Now choose Setup, Calculations. Be sure that the Calculate box says Equilibrium Geometry and the With box says Hartree Fock 3-21G. Click on the IR checkbox. Finally click Submit.

3. Examine the bond angles and distances. Complete the following.

Data for Ethene: C = C distance: ______C – H distance: ______

H – C – H bond angle: ______H – C = C bond angle: ______

4. Draw a Lewis dot structure for CH2CH2. What bond angles do you expect based upon this structure? How do these compare to what Spartan has predicted?

5. Compare the carbon-carbon distances in ethene to those Spartan predicted for ethane. Explain the cause of the difference.

6. Examine the potential surface as you did on ethane (See step 7 above) Rotate the molecule around so that you view it from all sides. What color and charge is associated with the hydrogen positions? Where does the surface show the most negative charge?

7. Recall that a C = C double bond is actually one sigma and one pi bond. Below is a sketch of ethene including everything except the pi bond. Add p-orbitals to the sketch so that they will overlap to form a pi bond. Note where the orbitals overlap. Compare this to the charges you noted on the potential surface. What do you notice?

H H C C H H

8. Get rid of the potential surface by clicking it off in the surface dialog box. If you closed this box earlier, you can bet it back by choosing Display, Surfaces. We will modify your current structure into the next molecule you will study, so keep it on the screen.

Part V: cis-1,2-dichlorethene 1. With your ethene molecule still on screen, click the Add Fragment button. From the organic tool kit tab, choose the Cl- atom. Attach one Cl to each Cl Cl carbon atom by clicking on an open yellow spoke. Be sure that you make the cis isomer by C C getting both Cl atoms on the same side of the double bond to form cis-1,2-dichloroethene. H H 2. Click Save As and name the file cisdichloroethene. Setup and run the same calculation that you did above for ethene. See the box on page 6.

3. After the calculation is complete, click on Display, Properties. In the lower left of the dialog box, you’ll find the dipole moment. Record the value below and click the checkbox to display dipole moment on screen. Dipole moment = ______Explain why this molecule is polar and why the vector points in this particular direction.

4. Close the Properties dialog box and choose Display, Surfaces. Rotate the molecule around and describe what you see. When you are done, close this file.

H Part VI: Benzene 1. Start a new file by clicking on the New File button. H C H The molecule we want to examine next is benzene, which is a common ring in organic C C chemistry. Rings are available below the other fragments on the organic tool kit tab. C C Find benzene from among the available rings and then click to place a benzene ring in H C H the blue window. H 2. Click the View button and then save the file, naming it Benzene.

3. Set up and run the same calculation you did above for ethene. See on box on page 6.

4. When the calculation is complete, measure and record the six carbon-carbon bond distances. Did you find the alternating bonds suggested by the Lewis structure above?

5. Let’s compare bond distances in several molecules. Look back at earlier sections to find this information. C-C distance in ethane: ______

C=C distance in ethene: ______

C to C distance in benzene: ______What is the best “bond order” for benzene? (Recall that a single bond is bond order=1, double bond is bond order=2, etc.)

Explain the reasons for the observations you have made by citing resonance. See pages 384 and 924 of your textbook for help.

Part VII: Aspirin O H 1. You will convert your benzene structure into an aspirin structure. Click on the Add Fragment button, which will get your drawing tools back. O C

H C O CH 2. Notice that aspirin looks like a benzene ring that has been modified in two 3 C C C places. The C atom at the top has a carboxylic acid group attached to it. You could add each atom separately, but since this is one of the pre-draw groups, C C O let’s add it all at once. From the Groups section of the organic tool kit, H C H choose carboxylic acid. Click on the yellow spoke of the top C atom of benzene to add this to your structure. H

3. We’ll add the ester group one atom at a time to give you practice with that. Look at the structure above. You will need to add an O atom with two bonds, then a C atom with two single and one double bond. Then add an O atom with a double bond to that double bond on the C atom. Finally add a C atom with four single bonds to the C atom.

4. If you have built your structure properly, Spartan will recognize it as aspirin. Look down at the bottom right of the Spartan screen. If you don’t see the word “aspirin,” go back and fix your structure. If you see the word “aspirin,” click on the small up arrow directly next to the word aspirin. Now click Replace.

5. Spartan has a database with optimized structures already calculated for many common compounds. We’ll use this pre-run calculation. Click the View button to get Spartan to add hydrogen atoms to your structure. Find the dipole moment under Display, Properties. Record the value here and click the box to display the arrow on screen. Explain why the dipole moment is in this direction.

6. Rotate the aspirin molecule around on screen. Describe which parts of the structure are planar and which are not.

Part VIII: Aspirin physical model This part must be done during your regular lab period. A lab assistant will be available in the lab to help you if you need it.

1. Use the ball and stick models to build a physical model of aspirin. Use black balls with 4 holes to represent the carbon atoms and red balls with 4 holes to represent the oxygen atoms. For hydrogen atoms, use small white balls. Single bonds are made with the shorter sticks. For double bonds, use two of the longer, flexible sticks. The lab assistant will help you as needed. 2. Now examine the ball and stick model. Figure out which bonds can be rotated and which cannot. 3. The lab assistant has a Spartan model of aspirin on one of the computers. Rotate the computer model and compare to your physical ball and stick model. 4. When you are done with your physical model of aspirin, return it to the lab assistant who will check it for correctness and initial your report sheet.

5. Rotate your physical model of aspirin around in your hands. Which parts of the molecule appear flat and which parts are not flat?

6. In your physical model of aspirin, which parts of the molecule appear flexible or able to rotate and which do not?

7. Now compare the Spartan model to the physical model: a. Which gave you a better sense of the overall shape? Explain.

b. Which gave you a better sense of the bonds that could rotate and where the molecule was more rigid? Explain.

c. Which did you find faster to build?

d. What can Spartan do that physical models can’t? (Look back at earlier parts of the assignment.)

e. Which do you think you would prefer if you wanted to model a very large molecule with hundreds of atoms? Explain.

f. Lab assistant’s initials, physical model was correct: ______

General Troubleshooting Advice:  If you don’t see what the handout suggests you should, o Try clicking View to clear out previous selections. o Close your file and then open a new one. Start that molecule over.  If you see two molecules on the screen at the same time, o You have opened a new file without closing the previous one. Click on the molecule you don’t want, and then click to Close File. o You have may have opened a new file when the directions said to add a fragment. Just close the file to get rid of one of the molecules.  If your main window in Spartan is not blue-green, then the defaults on your computer have been changed. You can still use the program, but you may not see the standard color-code for elements: carbon (grey), hydrogen (white), oxygen (red), nitrogen (blue), chlorine (green), etc. You can adjust the colors if you like. To change the background color, click on the background and then from the far upper right of the screen, choose Options, Colors. Adjust the sliders to the color you want. Similarly, the colors of atoms may be adjusted. View the molecule with the V button. Click on an atom and then choose Options, Colors. You may also want to try re-setting the default colors of your monitor.