Pyridine, pictured below, is a Lewis base (electron pair donor) due to the lone pair of electrons on the nitrogen atom. It is also a Bronsted Lowry base (proton acceptor) and can use the lone pair of electrons to form a bond with a proton (H + ). The section below use Hess's law to find the enthalpy change (drH) for the protonation reaction:
The calculation will be carried out using two different semiempirical methods (AM1, PM3) and also using density functional theory (dft) to illustrate the relative computational cost and accuracy.

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Using AM1 semiempirical methods
Calculate the Heat of Formation value of C5H5N
1. Use the guest account (username: guest, password: guest) to log in the WebMO demo site.
Click New Job -> Open Editor. A small window opens where you build molecules.

2. Build a molecule of C5H5N. Clean up the structure by selecting CleanUp -> Comprehensive-Mechanics.

3. Choose Gaussian as the computational engine. Type in/Choose the following:
Job Name: C5H5NAM1, Calculation: Geometry Optimization, Theory: AM1, Basis Set: Basic: 3-21G(or accept default), Charge: 0, Multiplicity: Singlet.

4. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the Heat of Formation value here: _____________ kcal mol-1

Calculate the Heat of Formation value of C5H6N(+1)
5. Click on New Job Using This Geometry, click Open Editor, and add an H atom to the N atom. Choose the 'Adjust' tool and click on the H atom you just added. With
this H atom highlighted, choose 'Adjust' on the pulldown menu and select 'Charge'. Type in +1, click Apply followed by OK.

6. Close the Editor, click the blue continue arrow, and Type in/Choose the following:
Job Name: C5H6N(+1)AM1, Calculation: Geometry Optimization, Theory: AM1, Basis Set: Basic: 3-21G(or accept default), Charge: +1, Multiplicity: Singlet.

7. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the Heat of Formation value here: _____________ kcal mol-1

Calculate the Heat of Formation value of H+
8. 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, click on the H atom to select it. Click on the 'Adjust' pulldown menu, select Charge, and type in +1. Click Apply, followed by OK.

9. Close the Editor, click the blue continue arrow, and Type in/Choose the following:
Job Name: H(+1)AM1, Calculation: Geometry Optimization, Theory: AM1, Basis Set: Basic: 3-21G(or accept default), Charge: +1, Multiplicity: Singlet.

10. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the Heat of Formation value here: _____________ kcal mol-1

Calculate the drH = Proton Affinity for: C5H5N + H(+1) -> C5H5NH(+1).
Using drH = dfH(C5H5NH(+1)) - [ dfH(C5H5N) + dfH(H(+1))] = ______________ kcal mol-1.
The literature value is 219.2 +/- 1.7 kcal mol-1. Calculate the percent difference = __________.

Using PM3 semiempirical methods
Calculate the Heat of Formation value of C5H5N
1. Use the guest account (username: guest, password: guest) to log in the WebMO demo site.
Click New Job -> Open Editor. A small window opens where you build molecules.

2. Build a molecule of C5H5N. Clean up the structure by selecting CleanUp -> Comprehensive-Mechanics.

3. Choose Gaussian as the computational engine. Type in/Choose the following:
Job Name: C5H5NPM3, Calculation: Geometry Optimization, Theory: PM3, Basis Set: Basic: 3-21G(or accept default), Charge: 0, Multiplicity: Singlet.

4. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the Heat of Formation value here: _____________ kcal mol-1

Calculate the Heat of Formation value of C5H6N(+1)
5. Click on New Job Using This Geometry, click Open Editor, and add an H atom to the N atom. Choose the 'Adjust' tool and click on the H atom you just added. With
this H atom highlighted, choose 'Adjust' on the pulldown menu and select 'Charge'. Type in +1, click Apply followed by OK.

6. Close the Editor, click the blue continue arrow, and Type in/Choose the following:
Job Name: C5H6N(+1)PM3, Calculation: Geometry Optimization, Theory:PM3, Basis Set: Basic: 3-21G(or accept default), Charge: +1, Multiplicity: Singlet.

7. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the Heat of Formation value here: _____________ kcal mol-1

Calculate the Heat of Formation value of H+
8. 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, click on the H atom to select it. Click on the 'Adjust' pulldown menu, select Charge, and type in +1. Click Apply, followed by OK.

9. Close the Editor, click the blue continue arrow, and Type in/Choose the following:
Job Name: H(+1)PM3, Calculation: Geometry Optimization, Theory: PM3, Basis Set: Basic: 3-21G(or accept default), Charge: +1, Multiplicity: Singlet.

10. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the Heat of Formation value here: _____________ kcal mol-1

Calculate the drH = Proton Affinity for: C5H5N + H(+1) -> C5H5NH(+1).
Using drH = dfH(C5H5NH(+1)) - [ dfH(C5H5N) + dfH(H(+1))] = ______________ kcal mol-1.
Calculate the percent difference from the literature value given above = __________.

Using B3LYP/631G(d) semiempirical methods

NOTE: The calculations in this exercise can each take up to 20 minutes to complete. You may want to set up this calculation to run during meal or break time, or overnight.

Calculate the Heat of Formation value of C5H5N
1. Use the guest account (username: guest, password: guest) to log in the WebMO demo site.
Click New Job -> Open Editor. A small window opens where you build molecules.

2. Build a molecule of C5H5N. Clean up the structure by selecting CleanUp -> Comprehensive-Mechanics.

3. Choose Gaussian as the computational engine. Type in/Choose the following:
Job Name: C5H5NDFT, Calculation: Geometry Optimization, Theory: DFT, DFT Functional: B3LYP, Basis Set: Basic: Routine 631G(d), Charge: 0, Multiplicity: Singlet.

4. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the R-B3LYP Energy value here: ____________________ h. (Note: Units are hartrees)

Calculate the Heat of Formation value of C5H6N(+1)
5. Click on New Job Using This Geometry, click Open Editor, and add an H atom to the N atom. Choose the 'Adjust' tool and click on the H atom you just added. With
this H atom highlighted, choose 'Adjust' on the pulldown menu and select 'Charge'. Type in +1, click Apply followed by OK.

6. Close the Editor, click the blue continue arrow, and Type in/Choose the following:
Job Name: C5H6N(+1)DFT, Calculation: Geometry Optimization, Theory: DFT, DFT Functional: B3LYP, Basis Set: Basic: 631G(d), Charge: +1, Multiplicity: Singlet.

7. Click on the blue continue arrow. You should now see your job listed. When the calculation is finished, click on the filename to open the View Job window.
Scroll down and record the R-B3LYP Energy value here: _____________ h.

Given H(H + ) = 1.481 kcal mol-1, calculate the drH = Proton Affinity for: C5H5N + H(+1) -> C5H5NH(+1).
Using drH = dfH(C5H5NH(+1)) - [ dfH(C5H5N) + dfH(H(+1))] = ______________ kcal mol-1.
Calculate the percent difference from the literature value given above = __________.

Compare the results for the AM1, PM3 and B3LYP/631G(d) calculations. Look at the time taken for the DFT calculations in the Job Manager window. Was the additional accuracy worth the added expense?