The Devil in the Details | A new Lab Class for Computational Chemistry

December 12, 2019
Ideas That MatterJulia Winter

The Devil in the Details – a new lab class for computational chemistry

A podcast with Roberto Peverati

We did a survey in the educational literature and noticed that resources for teaching density functional theory, DFT, were out-of-date and even obsolete. Three years ago, we started to collect and analyze potentially interesting resources that could be used in an educational environment.

Our classes at Florida Tech are small, and the class is dual listed with a mix of 50% undergraduate and 50% graduate students. The smallest class was 5 students and the largest was 12. We are a smaller research university, with 5000 students total. We think the course as designed is scalable to a bigger class, because the examples we chose for the laboratory notebook are not that complicated. Creating a course that can be used by other instructors was one of the goals when we designed the experiments.

We developed a laboratory notebook that consists of 16 experiences, 15 actual labs plus an introductory lecture. These experiences are designed to bring the research and teaching environment closer together.Especially the research from the last 20 years where DFT is the most common method to calculate the electronic structure of molecules.

Though DFT can calculate structures in the 1000s of atoms,our research is more along the lines of 10, 15, maybe 50 atoms. We are chemists, after all, not biochemists. The experiments that we picked for the laboratory notebook are much, much smaller. For example, a very common reaction taught in undergraduate classes is the Diels-Alder reaction.

The students use laptops for the calculations. We are also testing the use of an online server that provides access to small calculations.Some other institutions have provided machines for students, but we have found the easiest approach is to run the experiments on laptops.

We have designed the experiments to be software agnostic. You can use Gaussian, Q-Chem, or Spartan. We use Q-Chem because I am a Q-Chem developer. It could be really any software, for example,open sources like GAMESS or NWChem are very useful because students can download it and not have to pay a license for it.

In our paper we use the analogy of an analytical chemistry lab and manual titrations – even though this is not a modern approach to analysis, it allows students to realize the struggle to get reliable and accurate experimental data. When modern instrumentation is introduced in advanced analytical courses, the students are aware of the limitations of the measurement.

We wanted to give students on the computational side the same kind of experience, so they don’t think that all you have to do is click some buttons on the computer and results come out magically. This is far from what happens on the research side, so this lab class gives students a better view of what happens in a research environment. We wanted to make these resources available, through the publication of the paper and the lab notebook,so that we could bring the educational and research side together and build the computational chemistry community.

The lab experiments are designed so that students are first asked to perform calculations on a very small reaction with as many methods as they want, and all of the methods come up with the same answer. The next set of experiments, they will start to see some problems, where some functionals work and others do not. In the third set of experiments, it gets really complicated,where they can try 10 different functionals and obtain 10 completely different answers. They might not know which is correct, and in fact, there might not be a correct one. This is the point! To show that a research environment is not always nice and the everything works correctly. We want to give the students the freedom to explore and help them grow and build critical thinking skills as they do the research.

Listen to the podcast for more information.  

Read the ChemRXIV pre-print of the paper: The Devil in the Details: What Everybody Should Know when Running DFT Calculations, Pierpaolo Morgante and Roberto Peverati. You can also download the lab notebook and the instructor key from the ChemRXIV site.


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