Lab #3: Choice of Theoretical Method

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Lab #3: Choice of Theoretical Method These directions assume the user is familiar with the WebMO interface and can build molecules, set up calculations, etc. Exercise 1 - Determine the Proton Affinity for Pyridine Using AM1 Build a molecule of C 5 H 5 N. Clean up the structure by selecting Clean-Up > Comprehensive Mechanics. Choose Mopac as the computational engine. Type in/choose the following: Job Name: C5H5NAM1 Theory: AM1 pyridine Click on New Job Using This Geometry, click Open Editor, and add an H atom to the N atom. Choose the Adjust tool (Arrow 6 th down on left) and click on the H atom you just added. With this H atom highlighted, choose Adjust on the pull-down menu and select Charge. Type in +1, click Apply followed by OK. Job Name: C5H6N(+1)AM1 Theory: AM1 Click on the blue continue arrow. You should now see your job listed. When the calculation Start a New Job, Open the Editor, Click on the Periodic Table, Select H, and click one in the Editor screen. A white H atom should appear. Click the Adjust tool (Arrow, 6 th down on left), click on the H atom to select it. Click on the Adjust pull-down menu, select Charge, and type in +1. Click Apply, followed by OK. Job Name: H(+1)AM1 Theory: AM1 Calculate the r H = PA for: C 5 H 5 N + H + C 5 H 5 NH + N

Using r H = f H(C 5 H 5 NH + ) - [ f H(C 5 H 5 N) + f H(H + )] = kcal mol -1. The literature value is -219.2 ± 1.7 kcal mol -1. Calculate the percent difference =. Using PM3 Build a molecule of C 5 H 5 N. Clean up the structure as before. Choose Mopac as the computational engine. Type in/choose the following: Job Name: C5H5NPM3 Theory: PM3 Click on New Job Using This Geometry, click Open Editor, and add an H atom to the N atom. Choose the Adjust tool (Arrow 6 th down on left) and click on the H atom you just added. With this H atom highlighted, choose Adjust on the pull-down menu and select Charge. Type in +1, click Apply followed by OK. Job Name: C5H6N(+1)PM3 Theory: PM3 Start a New Job, Open the Editor, Click on the Periodic Table, Select H, and click one in the Editor screen. A white H atom should appear. Click the Adjust tool (Arrow, 6 th down on left), click on the H atom to select it. Click on the Adjust pull-down menu, select Charge, and type in +1. Click Apply, followed by OK. Job Name: H(+1)PM3 Theory: PM3 Calculate the r H = PA for: C 5 H 5 N + H + C 5 H 5 NH + Using r H = f H(C 5 H 5 NH + ) - [ f H(C 5 H 5 N) + f H(H + )] = kcal mol -1. Calculate the percent difference from the literature value given above =.

Using B3LYP/6-31G(d) UNOTEU: The calculations in this exercise can each take up to 30 minutes to complete. Build a molecule of C 5 H 5 N. Clean up the structure as before. Choose Gaussian (or GAMESS) as the computational engine. Type in/choose the following: Job Name: C5H5NDFT Theory: DFT DFT Functional: B3LYP Basis Set: Routine 6-31G(d) the R-B3LYP Energy value here: h. (Note: Units are hartrees) Click on New Job Using This Geometry, click Open Editor, and add an H atom to the N atom. Choose the Adjust tool (Arrow 6 th down on left) and click on the H atom you just added. With this H atom highlighted, choose Adjust on the pull-down menu and select Charge. Type in +1, click Apply followed by OK. Job Name: C5H6N(+1)DFT Theory: DFT DFT Functional: B3LYP Basis Set: 6-31G(d) the R-B3LYP Energy value here: h. Given H(H + ) = 1.481 kcal mol -1, calculate the r H = PA for: C 5 H 5 N + H + C 5 H 5 NH + Using r H = [H(C 5 H 5 NH + ) - H(C 5 H 5 N)](627.51 kcal mol -1 /h) + H(H + )] = kcal mol -1. Calculate the percent difference from the literature value given above =. Compare the results for the AM1, PM3 and B3LYP/6-31G(d) calculations. Look at the Time taken for the DFT calculations in the Job Manager window. Was the additional accuracy worth the added expense? Exercise 2 - Structure of Cyclopropane In the WebMO Editor window, build a molecule of cyclopropane (C 3 H 6 ) by making a triangle of C atoms. Choose Clean-Up > Comprehensive-Mechanics. You should now have the basic structure.

Click the blue continue arrow in the lower right side of the Build Molecule window. Choose Gaussian as the computational engine. Click the blue continue arrow (lower right). Type in/choose the following: Job Name: C3H6 STO-3G Theory: Hartree-Fock Basis Set: Minimal STO-3G Click on the blue continue arrow. You should now see your job listed. Click on the hyperlinked name (C3H6 STO-3G) to open the View Job window. Choose the Select arrow (4 th icon down on left). Click on one of the H atoms in the structure (the other atoms and bonds will fade ). Shift and Click the attached C atom (both atoms are now highlighted). The bond length is displayed just below the molecule. Record the value of the C-H bond length in the table on the next page. Check the other C-H bond lengths. Click on one of the C atoms in the structure, then Shift and Click the attached C atom. Record the value of the C-C bond length in the table. Check the other C-C bond lengths. Click on one of the H atoms, then Shift and click the C atom, followed by the other H atom. The bond angle is displayed just below the molecule. Record the value of the H-C-H bond angle in the table. Check the other H-C-H bond angles. Also check the C-C-C bond angles and the C-C-H bond angles. Place representative values in the table. Record the calculation time in the table (located under Summary, left of the molecule display). Item STO-3G B3LYP/6-31G(d) B3LYP 6-311+G(d,p) Experimental C-C distance 1.501Å C-H distance 1.083Å H-C-H angle 114.5 C-C-C angle 60.000 C-C-H angle 117.937 Calc. time

Repeat the entire process, but use the following: Job Name: C3H6 DFT Theory: B3LYP Basis Set: Routine 6-31G(d) Repeat the entire process described above, but use 6-311+G(d,p) as a basis set. Record the results in the above table. Compare the calculated values with the experimental values. Does the choice of basis set affect the bond distances a great deal? Which basis set gives the best bond angles? Look at the three calculation times. Approximately how many times longer did the calculation take to run using B3LYP/6-31G(D) vs. HF/STO-3G? Approximately how many times longer did the calculation take to run using B3LYP/6-311+G(d,p) vs. HF/STO-3G? Is it worth the extra time? Exercise 3 - Bond Length of the H-F Molecule In this exercise you will build H-F and optimize the geometry using Hartree-Fock, Density Functional Theory (B3LYP) or Møller Plesset 4 with several different basis sets. Electron correlation is known to be an important factor in calculating the bond length for this system. The experimental bond length in the H-F molecule is 0.917Å. In the WebMO Editor window, place an atom of fluorine (F) in the workspace. Choose Clean-Up > Comprehensive-Mechanics. You should now have the H-F molecule. Click the blue continue arrow in the lower right side of the Build Molecule window. Choose Gaussian as the computational engine. Click the blue continue arrow (lower right). Type in/choose the following: Job Name: HF HF STO-3G Theory: Hartree-Fock Basis Set: 3-21G Click on the blue continue arrow. You should now see your job listed. Determine the bond length, and place the value in the table below:

U Basis Set HF B3LYP MP 4 3-21G 6-31G(d) 6-311+G(d,p) Repeat the above process using Hartree-Fock and the 6-31G(d) and 6-311+G(d,p) basis sets. Record the bond length values in the table. Repeat the above process using B3LYP and the 3-21G, 6-31G(d), and 6-311+G(d,p) basis sets. Record the bond length values in the table. Repeat the above process using Møller Plesset 4 and the 3-21G, 6-31G(d), and 6-311+G(d,p) basis sets. Record the bond length values in the table. Which basis set and method gave the result closest to the experimental value? Exercise 4 - Geometry Optimization of Malonaldehyde In this exercise you will try several methods to see which is required to give reasonable structural results for the malonaldehyde molecule, pictured below. Experimental bond lengths and angles are listed in the Table below. UNOTE Your atom numbers may be different!! UNOTEU: The calculations in this exercise can each take up to 30 minutes to complete. Try using each of the following methods to do your calculations. Record the results in the Table. 1. MOPAC > PM3 2. Gaussian > HF/6-31G(d) 3. Gaussian > HF/6-311+G(d,p) 4. Gaussian > MP2/6-311+G(d,p) H 8 H 7 C 2 C 3 C 4 H 9 O 1 O 5 H 6 Parameter PM3 B3LYP/6-311+G(d,p) MP2/6-311+G(d,p) Experimental r(o1-h6) 0.969 r(o1-c2) 1.32

r(c4-o5) 1.234 r(o5-h6) 1.68 r(c3-h8) 1.091 ø(h6-o1-c2) 106.3 ø(c2-c3-c4) 119.4 ø(o1-c2-c3) 124.5 ø(c3-c4-o5) 123.0 Calc. time About how many times longer did the MP2 calculation take than the PM3? Do the results justify the added time? Which method was better overall the MP2 or B3LYP?

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