Psi4Education: Computational Labs Using Free Software
Computational chemistry is an increasingly important part of modern research, and yet it is often not part of the typical undergraduate or graduate curriculum. Fortunately, the availability of free software like PSI4 and WebMO lowers the barrier to introducing computational chemistry laboratory modules. The labs below were created using only free software and are available for use in your classes.
Installation and Setup Guide Instruction for installing WebMO and PSI4, along with information about creating and administering user accounts.
Tutorial Lab This introductory lab introduces the key features of WebMO and Psi4, including building molecules, setting up calculations, and visualizing results.
About Psi4Education Jupyter Labs Many of the Psi4 functions and features can be directly imported as python functions in any python interpreter. Some of the labs below use these features imported in jupyter notebooks. These labs assume some prerequisite knowledge of python. See this page for an explanation of these prerequisites.
Many instructors wish to save the labs as PDF files to distribute to students or to post on course management websites. When you click on any of the Lab Handout links below, the page will load as a GoogleDoc. You do not have to sign in to Google to view, download, or print the labs. To save the file as a PDF, click File, then Download As, and choose PDF from the file format list. If you wish edit the the file, you can download it as a Microsoft Word file and then open it in Word. If you want to reload the document into your own Google Drive to make changes, then sign into your own Google account (the Sign In link is blue and in the upper right corner of the lab handout page), then click File, Make a copy. The lab will then reopen in a new tab within your own Google Drive and be editable.
What is the radius of an atom? This lab will expose students to the way in which electrons define the size of an atom. It will demonstrate how the difference in nuclear-electronic interactions shift the size the atom for various trends including going across the periodic table for various charge states of a given atom.
What makes a molecule polar or non-polar? This lab will teach students how to use a Lewis structure to determine the electronic geometry and molecular shape of a molecule. The students will use WebMO to calculate the partial charges on atoms in a molecule. From this information they will draw bond dipole vectors. Using WebMO, the students can visualize a 3D representation of the molecule and determine whether the bond dipole vectors cancel or not.
How do we calculate spectroscopic constants from a potential energy surface? This lab uses psi4 functions imported into a Jupyter notebook to calculate the potential energy surfaces for diatomic molecules using psi4. The students will graph the potential energy surfaces, study the affects of anharmonicity, and determine force constants. To download a fillable Jupyter notebook, right click and save. Jupyter notebook To run the jupyter notebook through binder click here.
How do we calculate the most accurate energies for a boron atom? In order to gain a better understanding of how computational chemistry functions and what types of questions it answers, this lab uses the Boron atom as a means of communicating such information to the students. The students will see the patterns that emerge from the usage of basis sets as well as computational methods such as Hartree-Fock (HF/SCF), MP2/MP4, and CCSD/CCSD(T). Electron affinities and spin states are also discussed.
Can we visually predict binding energies? The role that visual depictions play in a student’s understanding of abstract concepts can be quite substantial. This laboratory exercise depicts the density of the electron cloud around various aromatic systems. The students introduce a sodium cation into the system in a place that makes sense based on the location of the most electron density. The students are asked to make a semi-quantitative connection between what they are seeing in the electrostatic potential and the ultimate strength of the cationic binding energy.
When does water become OH + H? (A study in molecular orbitals) Molecular orbitals are the basis for bonding, the very essence of chemistry. In this laboratory, the students will create the water molecule and then begin to dissociate it in order to understand how bonding and molecular orbitals overlap. This lab can be done in conjunction with the PIB Molecular Orbitals lab to make a longer lab on molecular orbitals.
What happens to the orbitals as a one-dimensional box gets longer? (A study in molecular orbitals) The particle-in-a-box model has long been used to explain the electronic absorption of linear carbon chains. This lab invites the student to explore this phenomenon within the realm of the molecular orbitals that allow the transitions to take place. This lab can be done in conjunction with the H2O Molecular Lab to make a longer, more traditional lab assignment. Further questions can be added by the instructor to augment the exercises incorporated herein.
Is C3H+ present in the Horsehead nebula? This is a lab to engage students in the search for a possible carrier of rotational lines observed in the Horsehead Nebula Photodissociation Region (PDR). Since rotational spectroscopy is the most reliable means for the detection of new molecules in the interstellar medium, this lab brings together computational chemistry and astrochemistry in novel ways.
What is symmetry in chemistry? Symmetry is often a difficult concept for chemistry students to grasp without some type of visual or tangible tool. This laboratory aims to give students experience with immediate feedback in order to give them instantaneous and formative assessment of their skills. The students will perform designated tasks of assigning point group symmetries to given molecules as well as the converse where they must provide examples of molecules for certain point group symmetries.
Additional Information for Instructors
Annotated instructors guides, including solutions, are available for all lab activities. If you would like to register with us and receive access to these materials, please contact us with your name, university information, and a list of courses in which you might use the lab activities. Please use the subject line Psi4Education.
Prof. Ashley Ringer McDonald (Cal Poly San Luis Obispo)
Prof. Ryan C. Fortenberry (Georgia Southern University)
Prof. Tricia D. Shepherd (Franklin & Marshall College)
Prof. C. David Sherrill (Georgia Tech)
Matthew Kennedy (Georgia Tech)