Quantum Mechanics Tools: Glossary

You can use the PsiAPI to run quantum chemistry calculations within the jupyter notebook environment.

During an optimization calculation, the energy flucutates but should generally decrease.

During an optimization calculation, any given bond length may increase or decrease, depending on the stating geometry.

The xyz file is a standard file format for conveying molecular coordinates.

If you constrain the value of a particular intramolecular coordinate, the other coordinates may change their values to reach a new minimum energy structure.

The z-matrix is a way to specify the geometry of a molecule based on connectivity.

It is only correct to perform a frequency calculation if you are at a local energy minimum conformation for your molecule.

The values of molecular properties should converge as you increase the size of the basis set.

The overall redox potential energy should be between -1 and -10 eV.

The free energy of a radical anion should be more negative than the neutral molecule.

Version control keeps a record of every change made to a set of files.

Using version control helps you keep up with changes and merge changes from multiple collaborators.

GitHub maintains text-based files better than more complex file formats like jupyter notebook files.