Undergraduate Worksheet

Here are some exercises to get you started doing research in the Deskins research group. These will teach you the basics of using molecular modeling tools and once you can complete these exercises you can start on some "real" research. You may need to connect to the webmo server on campus. You'll also need your Java to be up-to-date.

Document all your results and provide a written copy of your results (pictures, tables, data) to Prof. Deskins so he can make sure you are on the right track.

1. Login to webmo and build a water molecule. Run "Geometry Optimization" at the B3LYP/Routine level.

2. Run similar calculations for ethane, ethene, and ethyne. Determine the optimized C-C bond lengths. How do they compare with experiment (1.531, 1.339, and 1.203 Å, respectively)?

3. Water is a polar molecule, meaning that it has positive and negative parts. Calculate the atomic charges and dipole moment of water. Also calculate the atomic charges/dipole moments for ammonia, HCl, methane, methanol, and CO. Based on your analysis, rank the polarity of these molecules. The dipole moment and charges will be listed in the output section of webmo.

4. Determine the reaction energies for combustion of octane, butane, methane, ethane, methanol, hexane. Complete combustion has the following reaction stoichiometry: C_xH_y + zO₂ -> xCO₂ + y/2 H₂O. You'll need to calculate the energies (running "Geometry Optimization") for all the species and calculate the reaction energy using the following. ΔH_rxn ≈ Σ(v_i*E_i), where v_i is the stoichiometric coefficient from the balanced reaction equation and E_i is the calculated energy of that species. Energies are given in the output section of webmo.

Note: O₂ is a triplet, meaning it has two unpaired electrons. When you set up the calculation, choose Triplet in the Multiplicity menu.

How do your calculated values compare to experimental combustion energies? Look up heats for formation from the NIST Chemistry WebBook (type the formula in the box to search) to calculate experimental combustion energies. The experimental heats of formation will help you calculate the heat of reaction (combustion): ΔH_rxn = Σ(v_i*H_formation-i).

Report the combustion energies from theory (Webmo) and experiment (NIST). Also report the percentage error in the calculated combustion energies.

This resource may help. Webmo site

5. Calculate the combustion energies of octane, butane, butanol, and ethanol, but add vibrational motion/vibrational energy. Run your jobs as "Optimize+Vib Freq". This time use the Enthalpy values in the output section of webmo, or ΔH_rxn = Σ(v_i*H_i). How do these new values compare?

6. Run "Optimize+Vib Freq" calculations for methanol, ethanol, and benzene to generate vibrational spectrum. Compare your vibrational spectrum with experimental IR spectrum from the NIST database. Here is an example for methanol.

7. Calculate the atomic orbitals of beryllium, manganese, nitrogen and neon. Run a "Molecular Orbitals" calculation. You'll need to click on the individual orbitals to get an image of the orbitals. How do these orbitals compare with what you know from general chemistry (s, p, etc.)?

8. Calculate the molecular orbitals of a simple molecule like water or benzene. Run a "Molecular Orbitals" calculation. You'll need to click on the individual orbitals to get an image of the orbitals. How do these orbitals compare with what you know from general chemistry?

9. Finally, we will compare different modeling methods. Run geometry optimization calculations for cyclopropane using different combinations of Theory and Basis set: Hartree-Fock, B3LYP, AM1, PM3, UFF Mechanics/Minimal, Basic, Routine, Accurate. Make a table of your results comparing geometry information with experimental values. C-C bond distance: 1.501 angstroms. C-H bond distance: 1.083 angstroms. H-C-H angle: 114.5 degrees. Also put calculation time in your table.

Based on your analysis, which method gives best agreement with experiment? Which method gives best trade-off between accuracy and calculation time?

Bonus Problems

1. Learn some background theory (you can do this while working on steps 1-4 above). Read the chapter "The Concept of the Potential Energy Surface" from Computational Chemistry by Lewars (available as an e-book from the WPI library). Also read the following topics on wikipedia: computational chemistry, molecular modeling, density functional theory, quantum mechanics, energy minimization, and any interesting associated links to these articles. There will probably be much you don't understand, but you should try to understand the basics of the modeling methods.

2. Learn linux/unix if necessary (talk to Prof. Deskins). See this page: Linux/Unix.

3. Learn CP2K or VASP (talk to Prof. Deskins) and repeat steps 1-4 using CP2K or VASP. Start here: Getting Started.

4. Read chapters 1-4 of "Density Functional Theory: A Practical Introduction" by Sholl and Steckel. This is available as an e-book from the library.

5. Read any research papers assigned by Prof. Deskins

'6. Start a "real" research problem.