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Computational Chemistry Lab

Ten experiments on density functional theory, from basis sets to transition metals

Welcome to the computational lab of Advanced Physical Chemistry. Over ten experiments you will use density functional theory (DFT) the way researchers do: choose a method, run real quantum-chemistry jobs on a shared server, compare your numbers with high-level reference data, and decide which results you can trust. Every experiment comes from real benchmark databases, and every one hides a lesson about where DFT works well and where it doesn’t.

How every experiment works

  1. Warm up. A short concept check (not graded) brings back what you need.
  2. Meet the molecules. Rotate them in 3D, check charge and spin, and download the geometries.
  3. Predict first. Commit to what you think will happen before you compute anything.
  4. Run the jobs in Q-Chem through IQmol. Each page gives you a checklist and a ready-made input for every job.
  5. Enter your results. The page checks your arithmetic, without giving away the answer, and draws the plots.
  6. Explain. Answer the questions using your own tables and plots, and see how your predictions held up.
  7. Submit your file through the Microsoft Form (sign in with your Florida Tech email).

Your work is saved automatically in this browser as you go. To switch computers, download your submission file and load it on the other machine.

Lecture notes

All fifteen lecture handouts in one PDF, with a table of contents and a single bibliography: the textbook for this lab. You can also read each lecture online under Lectures.

⬇ Download the lecture notes (PDF)

Before your first experiment

The experiments

Experiment 1
Basis set incompleteness error
How big must a basis be? The HCl dimer with 6 basis sets.
48 jobs · quick
Experiment 2
Jacob's ladder
Classify 20 functionals by rung. No calculations.
self-check
Experiment 3
Organic chemistry, part A
Rotational barriers, conformers and isomers with 16 methods.
128 jobs
Experiment 4
Organic chemistry, part B
Diels–Alder, alkane isomers and dispersion-bound dimers.
160 jobs · dispersion
Experiment 5
Difficult cases for DFT
Ozone, CaO and atomization energies: when errors stop cancelling.
192 jobs · hard
Experiment 6
Why is B3LYP/6-31G* so successful?
A famous combination and its lucky error cancellation.
64 jobs · basis sets
Experiment 7
Integration grids
The argon dimer and unphysical wiggles.
480 short jobs · curves
Experiment 8
Stability analysis and transition metals
Excitation energies of Fe and Ru⁺.
24 jobs · open shell
Experiment 9
Comparison with experiment
Bond dissociation and atomization energies vs NIST data.
78 jobs · thermochemistry
Experiment 10
Final review
You are the consultant: design the calculation for a Pd complex.
3 jobs · your report

The class comparison for each experiment appears on Class results after the deadline.

NoteWhere these experiments come from

The experiments are adapted from a tutorial review on the often-overlooked details of DFT calculations  [1]. The calculations use Q-Chem  [2] through the free IQmol interface  [3].

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References

[1]
P. Morgante and R. Peverati, The devil in the details: A tutorial review on some undervalued aspects of density functional theory calculations, Int. J. Quantum Chem. 120, e26332 (2020).
[2]
E. Epifanovsky et al., Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package, J. Chem. Phys. 155, 084801 (2021).
[3]
A. T. B. Gilbert, IQmol molecular viewer, (n.d.).