Quantum Mechanics Tools: Glossary

Key Points

Geometry optimization
  • 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.

Intramolecular Potential Energy Surfaces
  • 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.

Intermolecular Potential Energy Surfaces
  • The z-matrix is a way to specify the geometry of a molecule based on connectivity.

Basis set convergence of molecular properties: Geometry and Vibrational Frequency
  • 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.

Computation of standard redox potentials
  • 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 with Git and GitHub
  • 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.

Making Changes to an Existing Code
  • GitHub maintains text-based files better than more complex file formats like jupyter notebook files.