Introduction to Molecular Modeling.

Gaussian is a molecular modeling program, designed to provide structural (bond lengths, bond angles, etc), thermodynamic (activation energies, reaction energies, etc) and electronic (orbital energies, vibrational energies, etc) information. It is not a drawing package (such as chemsketch). There are basically three classifications of calculation methods: molecular mechanics, semi-empirical methods and ab initio methods. Molecular mechanics (MM) treats molecules as a collection of balls connected with springs. It has defined ideal bond lengths for each bond type (C-C, C-O, C=O, etc), ideal bond angles and typical atomic radii. Any overlap of non-bonded atoms leads to steric strain, deviation from ideal bond lengths or bond angles lead to bond strain or angle strain, the greater the deviation, the greater the strain. The MM engine iteratively adjusts the atoms in the molecule to minimize these strains. MM calculations are fast, even for very large molecules. The results provide information on the bond lengths and bond angles as well as conformational energies. For example, one could calculate the energy difference between staggered ethane and eclipsed ethane, or the energy differences between cis and trans dimethlycyclohexane. MM calculations give good results for most organic molecules that are not unusually strained and have little conjugation affects that must be accounted for. MM calculations do not give any orbital information. Ab initio methods (Hartree-Fock and Density functional) are quantum mechanical calculations that involve the wavefunctions of the electrons of all the atoms of the molecule. Bear in mind that adding a single carbon atom to a molecule adds six electrons. Consequently, ab initio methods do not scale well; doubling the number of atoms could increase the calculation time four to eight fold. These methods look explicitly at electrons; in addition to the structural information MM provides, ab initio methods also provide electron information: orbital energies and excited vs ground state energies (UV-Vis spectroscopy), transition state energies, activation energies, vibrational energies (infrared spectroscopy), electron densities and electron-nuclear shielding (nmr spectroscopy) and more. Semi-empirical calculations are also quantum mechanical, but are simplified. Calculations are only performed in the valence shell electrons. Empirical (experimental) data are used to account for the energies and effects of the inner shell electrons. Empirical data are also used to simplify the quantum mechanical calculations. Consequently, semiempirical methods are much faster than ab initio methods, but also less accurate. However, the results are generally good for molecules that are well represented by the empirical data.

Computational Assignment for the Diels-Alder Reaction

You will perform a Diels-Alder reaction in lab to convert the intensely purple tetraphenylcyclopentadienone (TPC) to the off white 1,2,3,4-tetraphenylnaphthalene (TPN). You will analyze the UV-Visible spectra of the TPC and TPN and discuss the reasons for the differences in the spectra and colors of these two molecules. The calculations below will aid you with those discussions.

-CO2

Tetraphenylcyclopentyldienone

1,2,3,4-Tetraphenylnaphthalene

A. Using Gaussian, build the structures of tetraphenylcyclopentadienone and 1,2,3,4tetraphenylnaphthalene. B. Calculate the AM1 minimized energy structure for those molecules. C. Calculate the AM1 structure of the highest occupied molecular orbital (HOMO) for TPC and for TPN. D. When the calculations complete, view and save the renderings of the orbitals. The molecular orbitals will be rendered in red and blue/green, and will represent lobes of porbitals comprising the -system. Rotate the molecule to give a good perspective on the orbitals, then save the images to a USB drive (or email them to yourself) for inclusion in your Diels-Alder report. Note the location of the orbitals comprising the -system. Is it confined to the central ring(s)? Or does it include the phenyl rings? If the phenyl rings are involved in the conjugation, are all of them involved, or just some of the phenyl rings? Which ones? Consider why this is the case. These will be important factors that you will need to address when you discuss the UV-Vis spectra of these compounds in your Diels-Alder report.

Instructions for Gaussian

Building Tetraphenylcyclopentadienone.
Launch GaussView 4.1. There will be two windows, the gray Control Panel (CP) and the blue Active View Window (AVW). In the CP, click the ring fragment button ( ) in the upper

row of icons. Then select cyclopentadiene from the pull down menu. That molecule will be displayed in the CP. Click in the AVW to add a copy to the build window. This will be a three dimensional structure, which you can rotate by left-clicking in the AVW (not on the molecule) and dragging the mouse. You can resize the molecule by right-clicking and dragging the mouse up and down. Holding down the shift-key while left-clicking will allow you to move (translate) the molecule. Now you need to convert the cyclopentadiene to cyclopentadienone. Click the element fragment button ( ) twice. The first time you will see a tetrahedral carbon displayed in the

CP, the second time will bring up a periodic table. Select oxygen from the periodic table, then select oxygen atom from the fragment menu below the periodic table. Click one of the two Hs of the sp3-C in the AVW to convert that H to an O. To convert the C-O to C=O, click the modify bond button ( ). Then click the C and O atoms, select double bond and click OK. ) and delete the extra H atom on the carbonyl ). You should now have a flat cyclopentadienone ) and select benzene

Finally, click the delete atom button ( carbon. Finally, click the clean button (

molecule. To add the phenyl rings, click the ring fragment button (

from the pull down menu. Then click each of the four remaining Hs in the AVW to replace them with phenyl rings. Do NOT click the clean button after adding the phenyl rings.

Performing Calculations for Tetraphenylcyclopentadienone.

From the CP menu, select Calculate Gaussian Calculation Setup. For Job Type select optimization. For Method select Ground State, Semi-empirical, default spin, AM1. Leave the rest at the default settings. Click submit. You will be prompted to save the file; do so, saving the file to an appropriate location. Submitting the file will launch Gaussian 03, which will perform the calculations. If you receive the error message: Severe Error Message #2070 you will need to resubmit the job. First, close the Active View Window (AVW). Then close the Gaussian-03 window. You will then be prompted to open a result file. Highlight the file with the .chk extention and click ok. A new AVW will open. From the CP menu, select

Calculate Gaussian Calculation Setup. Ensure that the parameters listed above are still selected, then click submit. When prompted to save your file, enter a new name and click save. When the calculations are complete, click Yes to close the Gaussian window and OK to open the results file. This will result in a window displaying the tetraphenylcyclopentadienone in the lowest energy conformation. If you did everything correctly, two of the phenyl rings should be nearly perpendicular to the central cyclopentadienone ring, while the other two phenyl rings should be nearly co-planer. To visualize the molecular orbital, select from the menu Edit MOs. Check that the HOMO is highlighted yellow. Clicking on an orbital will select or deselect that orbital. If the LUMO is also highlighted, feel free to click on it to deselect it. Click on the Visualize tab, then click Update. When the rendering is complete, the molecular orbital will be displayed in the surface pane and a check box will appear next the HOMO in orbitals list. Click OK. Display the molecular orbital in the results pane by selecting from the menu Results Surfaces and Contours, highlighting the HOMO in the Surfaces Available list and then selecting Surface Actions Show Surface. Click Close. Rotate the molecule so that the orbitals and 3D structure are clearly visible since you will need to be able to refer to this when you write your Diels-Alder report. Save the rendering as a JPEG image. Select File Save Image File. Type a file name and select JPEG as the file type. Repeat the exercise described above for 1,2,3,4-tetraphenylnaphthalene. Copy the image files to a usb drive or email copies to yourself.