Welcome to the CAChe Molecular Modeling Tutorials

Department of Chemistry

University of Pittsburgh at Johnstown

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General Chemistry
Ferrocene

Which Theoretical Method Should I Use?

In the last two exercises, you optimized a molecule of cyclohexanol using two different methods: molecular mechanics and a semi-empirical quantum mechanical approach (MOPAC-PM5).  The list of available procedures may seem endless. Now you may be asking yourself:

"What's the difference?"

"How do I know which one to use?"

These are good questions.  There are several considerations you want take into account as you set out to do a calculation.  Some general considerations include:

bulletResources: Software & Computer
bulletExpense: Time & Money
bulletAccuracy

Since these tutorials are written for CAChe, we won't need to worry about the choice of software. Likewise, for our present case, money probably isn't a big consideration. 

Time -- The speed of the computer and the size of the molecule will impact the time needed to complete the calculation. So, time is an an issue. The time requirements of the calculation will determine the computation method we choose.

Accuracy -- This also is worth considering. The method of choice depends to some degree on the property of interest.

In the next two exercises, we'll compare accuracy by two different approaches.

bulletFirst approach: We'll start with the cyclohexanol molecules that you optimized in the last two exercises. You used molecular mechanics (MM3) and a semi-empirical quantum mechanical method (PM5). Now let's superimpose the two molecules. Do the two geometries really differ?

Superimposing molecules is one approach.  But if the molecule is really BIG or very small you can't visualize much of a difference. We might want to try another approach.  

bulletSecond approach: We can compute a property of a molecule (e.g. heat of formation, ΔHf°) and compare the values with the literature value. Earlier we built a molecule of ammonia.  We'll compute the heat of formation (ΔHf°) using two semi empirical methods (MOPAC AM1 and PM5) and an ab initio method (B88-LYP DFT).  This exercise has three parts. Do them in order:
  1. Compute the ΔHf° of ammonia using MOPAC (AM1 and PM5).
  2. Compute the ΔHf°of ammonia using DFT (B88-LYP DFT). 
  3. Compare the different values we obtained with the one in the literature.