Chemistry 362 Spring 2018 Dr. Jean M. Standard March 21, 2018 Project 2. Chemistry of Transient Species in Planetary Atmospheres: Exploring the Potential Energy Surfaces of CH 2 S In this project, you will carry out quantum mechanical calculations to explore the potential energy surfaces of molecules with formula CH 2 S. Some of these molecules were observed in the atmosphere of Jupiter after the comet Shoemaker-Levy 9 crashed into the planet in 1994. Two impact sites on the planet Jupiter from the collision with the cometary fragments are shown in Figure 1. Figure 1. Impact sites on Jupiter from Comet Shoemaker-Levy 9 (http://www.jpl.nasa.gov/sl9/). The computer program that you will use for these simulations is a software package called Gaussian for the quantum mechanical calculations and a software package called Avogadro for visualization. You will be able to access Gaussian and Avogadro in the computer lab located in Julian Hall Room 216. Please note that the computers in the JH 216 are usually available at any time during the day; however, they are occasionally reserved for classes as noted on the schedule posted on the door. This project requires you to complete calculations for a number of molecules using the Avogadro/Gaussian software packages. You may use any of the Macintosh computers in JH 216 to access the Avogadro/Gaussian programs (instructions are provided later in this handout). In fact, you can use one Macintosh for one part of the project, and another Macintosh for another part of the project since none of the data is stored on the Macs. All the calculations actually will be carried out on Linux workstations that you will connect to from the Macintosh through the internet. This project is worth 30 points and is due on Wednesday, April 4, 2018.
2 USING THE COMPUTERS AND THE AVOGADRO SOFTWARE PACKAGE This section contains instructions for logging in to the Macintosh computers in JH 216 and accessing the Linux computers on which the calculations will be performed. In addition, it provides instructions on how to start the Avogadro software package. The use of the Gaussian software package will be described later. Logging In To log in to one of the Macintosh computers in JH 216, enter your ISU ULID and password. Starting X11 In order to access the Linux workstations to run the Avogadro/Gaussian software packages, you must run a software package on the Mac called X11. To find the X11 application, use Launchpad in the Dock at the bottom of the screen and search for X11. Start the X11 package. A single white window should appear on the screen; this is called an "xterm" window, or simply a terminal window. Logging on to the Linux Computers Each person will be assigned one of the six available Linux computers to use for the project. To log on to the Linux computer to which you were assigned, type the following command in the xterm window: ssh Y che362@hostname.che.ilstu.edu Here, "ssh" stands for secure shell; this application provides a secure connection to the remote Linux workstation. Also, hostname is the name of the Linux computer to which you were assigned (options: frodo, samwise, gandalf, aragorn, legolas, gimli). The password is "wavefun". Enter the password as prompted. Once you have done this, you are connected to the Linux computer. Starting the Avogadro Program To start the Avogadro program, type "avogadro" in the xterm window and hit the return key. A window for the Avogadro software package should appear on your screen. At this point, you are ready to begin the project.
PROJECT 2 PROCEDURE: Chemistry of Transient Species in Planetary Atmospheres: Exploring the Potential Energy Surfaces of CH 2 S 3 This project illustrates the role of computational chemistry as a predictive tool for the electronic structure of molecules. In 1994, comet Shoemaker-Levy 9, which had broken into fragments, smashed into the planet Jupiter. After the comet fragments crashed into Jupiter, sulfur-containing compounds were observed in Jupiter's atmosphere, presumably thrown up as a result of the impact of the collision. Most of the sulfur compounds that were observed are not normally found in Jupiter's atmosphere. Some unusual transient sulfur species with chemical formulas HCS and CH 2 S have been proposed in order to account for the formation of the sulfur compounds observed in Jupiter's atmosphere. Such transient species are often difficult to produce and study experimentally. Computational chemistry can be used, either alone or in conjunction with experiments, to determine the structure and properties of these transient compounds. The paper by R. I. Kaiser and coworkers in Science [R. I. Kaiser, C. Ochsenfeld, M. Head-Gordon, and Y. T. Lee, Science 279, 1181-1184 (1998)] illustrates an approach in which both experiments and computer modeling have been used to obtain information about the HCS and CH 2 S transient species. Please read the article, perform the calculations, and respond to the questions that are posed below. Some of the questions are general and do not require the results of the Avogadro/Gaussian calculations. You may find the answers to many of the questions in the Science article; however, some of the questions will require you to find the answers using other resources. The parts that involve direct use of the Avogadro/Gaussian software packages are marked with an asterisk. 1. Sulfur Compounds in Jupiter's Atmosphere 1a. What are the primary atomic and/or molecular components of Jupiter's atmosphere? 1b. From the article in Science, what are some of the sulfur-containing compounds that were observed in Jupiter's atmosphere after the impact of comet Shoemaker-Levy 9? 1c. Where does the atomic carbon come from that is thought to play a role in reactions that form the observed sulfur-containing species? 2. Investigations of Thioformaldehyde There are at least three possible geometries that a transient species with formula CH 2 S might have. These possible geometries depend upon how stable the arrangement of electrons is around a particular grouping of nuclei; that is, on the electronic structure of the species. One possibility is a geometry similar to formaldehyde, or in this case, thioformaldehyde, H 2 C=S. *2a. Start the Avogadro program and build the H 2 C=S molecule. An easy way to do this is to click on the Drawing Tool,. Select Element: Carbon, Bond Order: Single, and make sure to uncheck "Adjust Hydrogens". Click with your mouse in the drawing window to place a single carbon atom. Then switch the element to sulfur and place one sulfur atom on the screen above the carbon atom. Finally, switch the element to hydrogen and place two hydrogen atoms on the screen below and to either side of the carbon atom in order to form the skeleton of the thioformaldehyde molecule as shown in Figure 2.
4 Figure 2. Placement of atoms on the screen to form the beginnings of the H 2 C=S molecule. Now, use the mouse to draw single bonds between the carbon and hydrogen atoms. Change the Bond Order to "Double" and draw a bond between the carbon and sulfur atoms in order to complete the construction of the H 2 CS molecule. When finished, your structure should look similar to the one shown in Figure 3. [Note that sometimes there is a bug in Avogadro in which double bonds are displayed between carbon and hydrogen. You can ignore this bug; the carbon-hydrogen bonds will be calculated correctly as single bonds.] Figure 3. Completed drawing of the H 2 C=S molecule.
Before starting the quantum mechanical calculation, it is helpful to clean up the initial structure in case the bond lengths as initially drawn were much too long. A rapid energy minimization algorithm based upon a classical 5 force field will be used. To begin, click on the Auto Optimization Tool,. Click on the "Start" button to the left, and continue until the energy (listed as "Auto Opt E") shown on the screen is constant to two decimal places. When this condition is met, click "Stop". Next, perform a quantum mechanical calculation of the H 2 CS molecule using the Gaussian software package. The equilibrium geometry and vibrational frequencies of the molecule will be determined. From the Avogadro menus at the top of the window, select "Extensions Gaussian". Use the settings below: Calculation: Frequencies Processors: 2 Theory: B3LYP Basis: 6-31G(d) Charge: 0 Multiplicity: 1 Once the settings are correct, click "Compute". You will be prompted to enter a filename. Use the filename 'h2cs-xyz.com', where 'XYZ' corresponds to your initials. After the filename is entered, click "Save". The calculation will begin and you should see a popup window appear that says "Running Gaussian calculation ". When the popup window disappears, your calculation of the H 2 CS molecule should be complete. Close the initial structure file by selecting "File Close" and discarding any changes. *2b. The results that you need for the H 2 CS molecule include the equilibrium geometry, dipole moment, and total energy. To obtain the equilibrium geometrical parameters, you may use the molecular structure that popped up when the Gaussian job completed. If the structure did not appear, the from the Avogadro menu select "File Open". The file type should be set to "Computational Chemistry Output", and the filename you select should be 'h2cs- XYZ.log' (where 'XYZ' corresponds to your initials). Click "Open" and the optimized H 2 CS molecule should appear in the Avogadro window. Use the Measure Tool, bond angles of thioformaldehyde and report them., to measure the equilibrium bond lengths and To obtain the dipole moment and total energy of H 2 CS, you will have to search the results file directly. To do this, first close Avogadro by selecting "File Quit". You may be asked to save changes, but you can safely discard any changes because the file you need is already saved. Next, in the terminal window, type "gedit h2cs-xyz.log" (where 'XYZ' corresponds to your initials). You will see a window open on the screen similar to that shown in Figure 4. The file you are viewing contains the results from the Gaussian calculation that you ran for H 2 CS.
6 Figure 4. Results file from a Gaussian calculation of the H 2 CS molecule. To obtain the computed value of the dipole moment, first search the file for the string 'Stationary point' by selecting "Search Find" from the menu. If this string is found, it verifies that the calculation completed successfully. Next, search for the string 'Dipole moment'. Click through until you find the last instance of the string 'Dipole moment' in the file (this will be the final equilibrium value). Record the dipole moment of the molecule in units of Debye; this is the value listed as 'Tot' (i.e., total) in the results file; for H 2 C=S, it should be between 1 and 2 Debye. To obtain the total energy, which is the sum of the electronic and vibrational zero-point energies of the molecule, search the results file for the string 'zero-point'. The third instance of the string (the occurrences are all bunched closely together) should be a line that says: Sum of electronic and zero-point Energies= 437.437429 The energy listed on the line as shown above is the total energy. Record this value; it is given in hartrees. When you are finished, select "File Quit" to close the results file. 2c. Compare the dipole moment of thioformaldehyde to the dipole moment of formaldehyde. You will need to look up the dipole moment of formaldehyde in the literature and compare that to your calculated value for thioformaldehyde. Use a reputable source! Discuss what the dipole moments suggest about the polarities of the two molecules.
3. Exploring the Geometries of the HCSH intermediates 7 Other than thioformaldehyde, the arrangement of the atoms in compounds with formula CH 2 S may also be such as to give a structure related to a carbene molecule. Methylene, CH 2, is the simplest carbene and is a highly reactive species. Each of the hydrogens in methylene can be replaced by other substituents. In this case, one of the hydrogens is replaced by a thiol group, or S-H. This would form thiohydroxycarbene, HCSH. This molecule can exist in either a cis or trans configuration. In addition, since carbenes can exist with either all electron spins paired (a singlet state) or with two electron spins unpaired (a triplet state), you will also explore the energy differences between the singlet and triplet states. *3a. Repeat the procedure that you carried out in step 2a to build the cis-thiohydroxycarbene molecule, cis-hcsh using Avogadro. Arrange the atoms such that the connectivity is H-C-S-H with all single bonds and with the hydrogen atoms cis to one another, as illustrated in Figure 5. [This time, do not carry out the AutoOptimization step; make sure that you bonds are not too long, though.] Figure 5. Completed drawing of the cis-hcsh molecule. Set up a calculation of cis-hcsh using Gaussian in the same way that you did in step 2a. Note that you are leaving the Multiplicity set to its default value of a singlet state, so your calculation is for singlet cis-hcsh, or cis- 1 HCSH. Submit the calculation. When the calculation is complete, follow the same procedure given in step 2b to measure the equilibrium bond lengths and bond angles of singlet cis-thiohydroxycarbene and report them. Make sure that you also measure the H-C-S-H dihedral angle. Finally, follow the same procedure given in step 2b to open the results file and record the total energy of the cis- 1 HCSH molecule in hartrees. Note that in this case, it is not necessary to record the dipole moment.
*3b. Repeat the procedures that you carried in step 3a to build the trans-singlet thiohydroxycarbene molecule, trans- 1 HCSH, and perform a Gaussian calculation. This time when drawing the molecule, arrange the atoms so that the hydrogens are in a trans configuration. 8 When the calculation is complete, follow the same procedure as for the other molecules to measure the equilibrium bond lengths and bond angles of trans-singlet thiohydroxycarbene and report them. Make sure that you also measure the H-C-S-H dihedral angle. Finally, follow the same procedure as for the other molecules to open the results file and record the total energy of the trans- 1 HCSH molecule in hartrees. *3c. The next calculation that must be performed is for the triplet state thiohydroxycarbene, 3 HCSH. Note that in this case, cis and trans forms do not exist; rather, the H-C-S-H dihedral angle is skewed to about 90 degrees. In order to build this structure, begin by using the Drawing Tool to again create the H-C-S-H arrangement in the cis configuration. Next, click on the Bond Manipulation tool,. Then, click on the C-S bond. To adjust the dihedral angle, click on one of the hydrogen atoms and drag it to adjust the H-C-S-H dihedral angle to around 90 degrees. Set up the Gaussian calculation in the same way that you did in step 2a, except this time change the "Multiplicity" to 3 in the window to select the triplet state. Then, run the calculation. When the calculation is complete, follow the same procedure as for the other molecules to measure the equilibrium bond lengths and bond angles of triplet thiohydroxycarbene and report them. Make sure that you also measure the H-C-S-H dihedral angle. Finally, follow the same procedure as for the other molecules to open the results file and record the total energy of the 3 HCSH molecule in hartrees. 3d. As mentioned previously, methylene (CH 2 ) is the simplest carbene. What would you expect for the hybridization of the carbon atom in singlet methylene (and also therefore in singlet thiohydroxycarbene)? Explain. What bond angle would be predicted by this hybridization? Find in the literature the experimental bond angle of singlet methylene. Again, please use a reputable source. Compare this bond angle with that predicted by the expected hybridization and also with the H-C-S bond angle in singlet thiohydroxycarbene. Discuss the possible reasons for any observed differences.
4. Structural and Energetic Comparisons of Transient CH 2 S Species 9 4a. Compare the geometries that you obtained for the four compounds (H 2 CS, cis- 1 HCSH, trans- 1 HCSH, and 3 HCSH) to the values listed in the Science article. Are your calculations in good agreement with the literature? Comparisons including percent differences are appropriate whenever possible throughout this project. 4b. Report the total energies for each structure from your calculations in kj/mol. [To convert from hartrees to kj/mol, the conversion factor is 1 hartree = 2625.5 kj/mol. Note that the energies in kj/mol will be big negative numbers; please be sure to report them to 0.1 kj/mol.] Which molecule has the lowest energy? It is the most stable one (i.e., the global minimum). Next, select the most stable molecule and compute relative energies by subtracting the total energy of the most stable one from the total energy of each of the four molecules. This will put the most stable molecule at a relative energy of zero and the other ones at higher energies. Report the relative energies in kj/mol. 4c. Compare the relative energies that you obtained in step 4b to those that are reported in the Science article. Are your calculations in good agreement with literature? Remember that comparisons using percent differences are appropriate whenever possible. 4d. Which conformer is lower in energy, cis- 1 HCSH or trans- 1 HCSH? Explain with a discussion using steric or electronic arguments why you would expect one conformer to be lower in energy. 4e. Which multiplicity is lower in energy, 1 HCSH (cis or trans) or 3 HCSH? Explain with a discussion using steric or electronic arguments why you would expect one multiplicity to be lower in energy. 5. Reaction Pathway for Conversion of cis- 1 HCSH to trans- 1 HCSH One pathway on the potential energy surface for molecules with formula CH 2 S leads to the conversion of cis- 1 HCSH to trans- 1 HCSH. In this part of the project, you will calculate the structure and energy of the transition state for this process. *5a. Using Avogadro, follow the same procedure that you used for the triplet state in step 3c to build a new copy of HCSH with a dihedral angle of about 90 degrees. This time, though, the Multiplicity should be set to a singlet state with a value of 1. As a check, make sure to use the following settings: Calculation: Frequencies Processors: 2 Theory: B3LYP Basis: 6-31G(d) Charge: 0 Multiplicity: 1 In addition, you should see on the second line in the white input box the following line: #n B3LYP/6-31G(d) Opt Freq Edit the line so that it has the following form: #n B3LYP/6-31G(d) Opt=(TS, CalcFC, NoEigentest) Freq When you are finished, the Gaussian input window should appear similar to the one shown in Figure 6. If it does, click "Compute" to submit the calculation as usual.
10 Figure 6. Gaussian input window for the calculation of a transition state. When the calculation is complete, follow the same procedure as for the other molecules to measure the equilibrium bond lengths and bond angles of the transition state and report them. Make sure that you also measure the H-C-S-H dihedral angle. Also, follow the same procedure as for the other molecules to open the results file and record the total energy of the transition state in hartrees. *5b. To view the motion along the reaction path at the transition state, select "File Open" from within Avogadro. The file type should be set to "Computational Chemistry Output", and the filename you select should be the name of the file corresponding to the transition state that you created in part 5a. Click "Open" and the structure of the transition state should appear in the Avogadro window. To obtain a listing of the vibrational frequencies, select "Extensions Vibrations". To display an animation of a particular vibrational mode, click on the row in the Molecular Vibrations window corresponding to the vibrational frequency that you want to view, and then click the "Start Animation" button. You may need to rotate the molecule on the screen to get a better visual idea of the vibrational motion. A molecule may be rotated using the left mouse button if the Navigation Tool is selected. Record the vibrational frequencies in cm 1 and list a short description of each vibration. Pay particular attention to the first vibration. It is listed as a negative value (really it is imaginary), indicating that the curvature in that direction is negative, which is indicative of a saddle point. The vibrational motion of this mode provides a snapshot of the motion along the reaction coordinate. What is it? When you are finished, select "File Close" (you may discard any changes).
11 5c. From the total energy results of the transition state and the stable structures, calculate the activation energy in kj/mol for conversion of cis- to trans- 1 HCSH. How does this compare with the thermal energy available at 300 K? (Thermal energy is roughly equal to RT.) Would the molecule be able to convert from cis- to trans-hcsh at 300 K? 6. More on HCS and HCSH 6a. Are there other possible molecules with empirical formula H 2 CS that have not been studied in parts 1-5 of this project? Draw some possible structures of other compounds that you might find mentioned in the Science article or that you think of yourself. 6b. From the article in Science, what are the reactions of HCS and HCSH that produce the compounds CS, CS 2, and COS? Give complete chemical equations.