Computational Chemistry Gauss View and Gaussian Chemistry 105 Experimental Directives & Results IV.

. Exploring the Potential Energy Curve of the H2 Molecule In this portion of the experiment you are going to explore the potential energy of the H2 molecule as a function of the distance between the two hydrogen atoms. In general, the potential energy of a molecule can be represented as a multi-dimensional surface that corresponds to the total energy of the molecular system as a function of all of the degrees of freedom of the molecule. In a diatomic molecule, however, there is only one degree of freedom, and that is the distance between the two nuclei, so a plot of the energy as a function of the internuclear separation is the potential energy surface. On a blank Gaussian drawing screen (Ctrl-N), add two hydrogen atoms for this calculation, it doesnt matter if you draw a bond between them or not. To generate the potential surface plot in Gaussian you choose scan as your job type, and in the second box choose rigid, as shown below.

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For our purposes we will do a Hartree-Fock (ab initio) calculation set up as shown here:

Go the Link 0 tab and give the calculation 48 MB of memory. Also, please type in the words shown in the Additional Keywords section. Before doing anything else, click on Edit in the Link 0 file.

This will open up several windows. Please save your file as H2.gjf and when saved, it should open up the instruction file for calculation, which should look similar to this:

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You need to edit this file. You want to scan from B1 = 0.30 Angstroms (Note: 1 Angstrom = 10-10 m) upwards in increments of 0.10 Angstroms and you will do 60 of these increments. To do that, change the file to look as it does below. If you type, tab from one entry to the next. Alternatively, you can copy the text below the image:

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Here is a copy of the text if you want to copy whats inside the box... 01 H H1 B1 1 2 1.0 2 and paste it by selecting Paste Special, then Unformatted text. Now save the file, close the editing program, and run the calculation. When the calculation is finished, choose {your filename}.LOG from the popup window that appears. (If you miss the popup, open the file using File/Open.) What you will see is a molecule image with a green button at the upper left. Click on the results tab in Gauss View and then the scan button. This will open a plot of your scan results (energy versus the scan number). Rotate the two hydrogens in the window until you can see both of them and move windows around so that you can also see the plot. Click on the green button and see what happens. Data Analysis of the Hydrogen Potential Curve: Go to the results tab and click on view file. Go to the bottom of the file and scroll up until you see a three column table of the scan number, value of B1 (the bond length, in angstroms) and the energy, SCF (in atomic units for energy--Hartrees). This contains the raw data that is plotted in the plot. If you want to answer some of the results questions later, you might want to copy/paste this information into a file and email it to yourself. 1) What is the equilibrium bond length, in Angstroms, of H2 that is predicted by these calculations? Explain how you determined it. Compare with the value listed in your textbook or with an online source (cite it). 2) Something is different with this curve when compared with what you learned in lecture. What value should the interaction energy approach when the atoms get very, very far apart? Does it look like it approaches this value? It turns out that there are two reasons why this curve doesnt approach this value first, there is an inherent inaccuracy with the way the method approximately solves the Schrodinger Equation, and second, the CHEM105 Computational Lab Results p.4

B1 0.30 S 59 0.10

calculation sets the zero of energy to be something other than two isolated H atoms, which is what is done in class. 3) Despite this inaccuracy and difference, you can still use this curve/data to estimate the bond strength of H2, i.e. the amount of energy required to break the bond and pull the two atoms apart. To get a rough estimate, subtract the energy at the equilibrium bond length from the energy when the atoms are very far apart. Using the fact that one Hartree equals 2625 kJ/mol, how accurate is this estimate? (The bond enthalpy of H2 is experimentally measured to be about 430 kJ/mol.)

4) In one sentence, hypothesize about why your estimate is so far off (Dont worry about your answer being right..just come up with a hypothesis that sounds reasonable to you)

V. Visualizing Molecular Orbitals The goal of this section is to review orbitals, wave functions, nodes, molecular orbital (MO) theory, and to see a practical application of MO theory to understanding the reactivity of molecules. Earlier this semester you studied orbitals and wave functions. Orbitals are described by wave functions (), the mathematical solution to the Schrdinger Equation for an atom. Although they give us a sense of where electrons are in an atom, they can't be directly related to physical meaning. For example, wave functions switch from positive to negative whenever they go through a node. This doesn't mean that electrons change sign or that they have a negative probability in some regions. If we want to get direct physical meaning, we must look at wave function squared, which physically correlates to electron density. Read Brown et al. 12th ed., Section 9.7 if you need a refresher. We will perform calculations on two diatomic molecules: nitrogen (homonuclear diatomic) and carbon monoxide (heteronuclear diatomic). Build an N2 molecule (think about its Lewis structure first to get the correct type of bond between the atoms!) and perform an optimization calculation (tight convergence) using Hartree-Fock STO-3G (i.e. choose STO-3G for basis set) with default spin and singlet settings. When the calculation is finished, open the appropriate checkfile (.chk) from within Gaussian. Measure and record the bond length here. Now click on the orbital icon and you will see an energy-level diagram showing the filled and virtual (empty) molecular orbitals. Note that unlike the discussion in the text, the 1s orbitals of the atoms are included in this calculation, hence the total of 10 molecular orbitals. This diagram lists orbitals by increasing energy but shows no degeneracy. CHEM105 Computational Lab Results p.5

In order to make the diagram appear more familiar, click on the Diagram tab and enter 0.001 for the degeneracy threshold (two levels will be degenerate if their energies agree to less than 0.001). Now reexamine the energy diagram. Make the window large enough that you can see all the relevant orbitals. Take a snapshot of the energy diagram and paste it here (To take a snapshot, click to select the window you want to capture, press altPrintScrn to copy and ctrl-V to paste). Click on the Visualize tab, and set the parameters to look like this:

Now press the Update button (not the OK one). Gaussian will construct 3-D surfaces for all 10 orbitals, and this may take a few minutes. When this is complete, examine each of the orbitals. To do this, check the box next to an orbital and use your mouses scroll button to fit the MO on in its window. Practice taking a snapshot of the orbitals (you will have to copy the entire window; altPrintScrn). Paste your favorite orbital here. Now answer the following questions based on the orbital plots: Do these images look like what you expected (i.e. compared to images you have seen in lecture or in your textbook)? What does such a picture of an orbital represent? Explain this as clearly and concisely as you can. What is the bond order in the nitrogen molecule, as predicted by MO theory? Paste copies of each of the valence MOs here, (i.e.-highest energy level orbitalsno orbitals from 1s electrons, for example) labeling each MO as sigma or pi and bonding or antibonding. Label the HOMO and the LUMO.

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VI. CO Binding to Metal Surfaces In this exercise you will examine how MO theory can be used to understand the binding of CO to metal surfaces -- an important step in the conversion of harmful CO to less harmful CO2 in a catalytic converter found in the exhaust system of an automobile. Many experimental studies have demonstrated that the binding of CO to metal surfaces is invariably accompanied by the net donation of electrons from CO to the metal. Assume that electron donation occurs from the atom that has the most electron density. In terms of electronegativity, which atom of the CO do you expect to bind to the metal surface: C or O? Why? Perform an optimization calculation on CO using tight convergence (Note: the oxygen is represented with a red atom and the carbon is represented with a white atom.) Think about the Lewis structure for CO to help build the molecule correctly. Set up the calculation as shown here:

When the calculation is complete, open the .chk file and examine the HOMO and LUMO molecular orbitals. Answer the following questions based on this calculation: Does this MO diagram look at all like the simple MO diagrams you have drawn in class or the MO diagram you just saw for N2? How is it different? The reason for this difference is that we are using a much larger basis set (recall how you set a basis set in the Method tab of calculation setup) this allows us more flexibility in how we approximately solve for the true wavefunction of the molecule. All CHEM105 Computational Lab Results p.7

other things equal, a larger basis set generally will give you more accurate, quantitative resultsbut it takes longer! In contrast, the MO diagrams we draw in class are HIGHLY simplified from reality and can make only very simple, basic predictions because they are using a basis set built from atomic orbitals, which is practically the smallest basis set possible.

From which MO of CO will electron donation occur? (i.e. which MO participates in bonding?) Paste a 3D image of that MO here, and in one sentence explain how you knew this was the MO from which donation will occur. Experiments have shown that CO binds to metal via the C end. After looking at the MO you chose above, rationalize why CO binds to metal surfaces via the C end. (Hint: recall that electrons get donated from the CO to the metal based on looking at this orbital, where are these electrons more likely to reside on the CO molecule? Remember, the oxygen atom appears orangish-red and the carbon atom appears white.) Next, draw a simple valence MO diagram for CO based on what you learned in lecture (you dont need to turn in your drawing, but use it to answer and explain your answer to this question). Based on your drawing, from which orbital would you expect donation to occur? Note that in an MO diagram, an MO often has more electron density on the atom whose atomic orbitals are closer to energy to its energy. Using this idea, would this MO diagram predict that CO binds to metals via the C end or the O end? Explain your reasoning. Is this the correct prediction? Based on your answer to the last question, explain in one sentence why it is often important to use more sophisticated computer calculations when making predictions, rather than drawing simple, qualitative MO diagrams. VII. Vibrational Spectra of Molecules from the Nylon 6.6 Synthesis As you have seen in the Job Type menu in Gaussian, it is possible to perform vibrational analyses, and to predict IR spectra. To illustrate this, build yourself a methane molecule (CH4) and then perform an optimization and frequency combined calculation (Job type = Opt + Freq with tight convergence) at the Hartree-Fock 6-31G(d) level with default spin and singlet settings. When the calculation is finished, open the .log file from within Gaussian and then under results click on Vibrations. Examine the window that shows up. Molecules are expected to have 3n-6 vibrations, where n is the number of atoms. Is there the correct number of vibrations? CHEM105 Computational Lab Results p.8

Click on a vibration and then click on Start. You may need to adjust the sliders to get a reasonable motion. Why do some of the vibrations have zero calculated intensity (zero in the infrared column, indicating zero intensity on an infrared spectrum)? (Hint: in order for a vibrational motion to have a detectable IR intensity, the dipole moment of the molecule must CHANGE over the course of the vibrational motion) Why do some have the same energy (frequency)? (Hint: think about the symmetry of the molecule) If you wished to compare these frequencies to experimental values you would find they were too high. Experience has shown that for such molecules, and for this method, the calculated frequencies need to be multiplied by a factor of 0.8929 due a neglect of electron correlation in the model that leads to results that are systematically too high.

Performing such calculations on larger molecules such as those used in the synthesis of nylon can be a time consuming process. The choices open to you are to spend that time (maybe several hours per molecule), use a lower level of theory, or use results files created previously. We are going to follow that last track. Vibrational calculations have been performed for you on hexamethylenediamine, adipoyl chloride and one unit of nylon 6.6. To use these results, save them from the Lab 07 website. In Gaussian, choose File/Open, and open each .log file. Do not clean up or optimize the files. For each of the three molecules, look at the three vibrations with the highest intensity (the highest number in the infrared column), and describe them qualitatively, as follows: What is the frequency? What atoms are involved (C, H, O, N and Cl)? Be sure to note whether these are atoms at the end of the molecules or in the middle. Is the principle motion bond stretching or bond angle bending?

Based on the data you looked at, are there any vibrations in the product that are not found in one of the reactants? Explain clearly in one sentence why it would be useful to know the answer to this question. Do the frequencies of the calculated highest intensity peaks for Nylon 6.6, when multiplied by a factor of 0.8929 (see above), come close to matching one of the characteristic experimental peaks that are listed in Lab 6, and that you looked for using FTIR? (Note: this is a think outside the box question; dont worry if your answer is wrong) take a guess as to how you think a computer calculates/predicts the vibrational frequencies and motions of a molecule. CHEM105 Computational Lab Results p.9

VIII. Molecular Orbitals of Polyatomic Molecules (to be done outside of lab) It is possible to read most introductory chemistry texts and leave with the impression that molecular orbital theory is useful only when discussing diatomic molecules. That is not the case, and it is important to develop some sense of the molecular orbitals in polyatomic systems. In this exercise you will look at the results of molecular orbital calculations on water to get a sense of what MOs can look like on polyatomic molecules . Look at http://www.wellesley.edu/Chemistry/Flick/testfile6.html. Use the mouse to rotate the image, and the mouse scroller to zoom in and out. In this calculation, the atomic orbitals that were used were the 1s, 2s and 2p orbitals on oxygen and the 1s orbitals on the two hydrogen atoms. Therefore there are seven total molecular orbitals since the total number of molecular orbitals always equals the total number of atomic orbitals used in the calculation. How many total electrons are in the water molecule? How many molecular orbitals will those electrons occupy? Is your answer consistent with orbital number 5 being labeled as the Highest Occupied Molecular Orbital? Does the molecular orbital picture of water look like what you are accustomed to seeing in a Lewis or VSEPR structure? If not, how do the various representations differ? As mentioned in lecture, MO theory is more physically correct than VSEPR or hybridization theory and it can often allow for quantitative energetic analysis, accurate geometry prediction, and other chemical analyses. Based on your answer to the previous question, briefly comment on why, even though MO theory is more fundamentally correct as a model, we still teach, learn, and use VSEPR and hybridization theories all the time.

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