20 Mar 2010

Viewing Molecular Orbital Calculations with GaussView: a Lab for First or Second Year Undergraduate Students.

Lab Experiment

Submitted by Deborah Sunderland, Washington and Jefferson College

This laboratory exercise was developed to compliment several weeks of freshmen or sophomore level quantum chemistry lecture material at our institution. The students meet in a computer lab on campus and use the software package known as GaussView. We focus on molecular orbital calculations for a series of homonuclear diatomic molecules of the second row in the periodic table (Li2, B2, C2, N2, and F2).  The students view and compare pictures of the sigma and pi molecular orbitals so that they can readily observe the overall shapes of the atomic orbital lobes that result in bonding and antibonding interactions between atoms.  The students also look at electrostatic maps of their simple molecules to observe any trends in electron density across the series.

Prior to the computer portion of the lab, the students are also asked to determine electron configuration for the elements Li, B, C, N, and F.  They draw Lewis dot structures for the diatomic molecules Li2, B2, C2, N2, and F2.  Finally, they sketch molecular orbital shapes and diagrams on paper for the simple molecules included in the periodic series.

Learning Goals: 
  • Reinforce some simple molecular orbital theory for freshmen or sophomore undergraduate students
  • Students determine the MOs on paper for simple homonuclear diatomic molecules of the second row in the periodic table
    • Review of electron configuration and Lewis dot structures
  • Students use the software program GaussView to view the outputs of calculated molecular orbital energies and shapes
    • Compare the computational results to their paper sketches
    • Visualize the shapes of the MOs to compare sigma and pi bonds, and bonding and antibonding MOs
  • Students use the software program GaussView to view potentiostatic maps of the homonuclear diatomic molecules in Period 2
    • Detect trends in electronegativities of atoms across a period


Equipment needs: 
  • Computers with GaussView 4.1 molecular modeling software
Implementation Notes: 

Students had no prior experience with using molecular orbital computational software in preparation for this lab exercise.  Selected molecular orbitals were calculated in advance for the students using an appropriate level of theory.  The detailed "MO Lab Instructions" and "GaussView Instructions" sheets are attached.     

The first time for trying this lab exercise was during the fall 2009 semester.  The instructors for each section spent approximately 30 minutes doing a "pre-lab" lecture review of some simple molecular orbital theory.  Prior to viewing the computational outputs from GaussView, students were asked to form small groups and sketch on paper the molecular orbital energy level diagrams and the general shapes of the MOs that should result for the homonuclear diatomic molecules explored in this lab.  They then could compare the calculated surfaces to their paper sketches. 

At Washington & Jefferson College, students take a one semester Introduction to Inorganic Chemistry course in their sophomore year that serves as a General Chemistry course as well.  The text that we used for this past year was University Chemistry by Brian B. Laird.  The students brought their textbook to lab this day so that they could refer to the MO diagrams printed in the book.

Note to Instructors 

 While the visualization of molecular orbitals is instructionally a valuable tool in chemical education, the aim of computation chemistry is to produce accurate results efficiently.  The price of this accuracy is the loss of an intuitive understanding.  In order to maintain the conceptual value of molecular orbital theory, we only use the STO-3G minimal basis set, which limits both the core and valence atomic orbitals to a single basis function. We employed the restricted open-shell Hartree-Fock (ROHF) method. ROHF creates a single molecular orbital for each orbital that is doubly occupied, but it has the freedom to create separate orbitals for unpaired electrons.  The use of doubly occupied molecular orbitals limits the number of orbitals to the familiar set associated with MO theory discussed at the undergraduate level. At the same time, ROHF has the complexity necessary to describe the triplet states of diatomic boron and oxygen.

Time Required: 
3 hours
Evaluation Methods: 

The "post-lab" analysis for this experiment was collected the following week and consisted of answers to the questions included in the attached "MO Lab Instructions" sheet.  

79 students completed the lab activity, and they were split into lab sections of approximately 20 students per section.    The post-lab was worth 50 points, with points split between the Pre-Lab Assignment, and their answers to the procedural directions while they were working on the computers. 

Evaluation Results: 

The majority of the students were able to answer each question well based on the outputs from GaussView.  Many of their paper sketches of the Lewis Dot structures for molecules such as C2 varied from double bonded atoms (with a lone pair of electrons on each C) to triple bonded atoms (with a single electron on each C).  Students had to be reminded while they were working on the computers to sketch into their notebooks the outputs from the screen, and, specifically, to differentiate between the positive and negative portions of the wavefunctions. 

Creative Commons License: 
Creative Commons Licence

The VIPEr community supports respectful and voluntary sharing. Click here for a description of our default Creative Commons license.