20 May 2019

CompChem 02: Introduction to WebMO

In-Class Activity

Submitted by Joanne Stewart, Hope College
Categories
Description: 

This is the second in a series of exercises used to teach computational chemistry. It has been adapted, with permission, from a Shodor CCCE exercise (http://www.computationalscience.org/ccce).

It was tested on WebMO Version 18 but should work with minimal modification on earlier versions. WebMO is a free web-based interface to computational chemistry packages (www.webmo.net).

The directions assume no prior knowledge of the WebMO interface and provide detailed, click-by-click instructions on building molecules and setting up calculations.

AttachmentSize
File Introduction to WebMO student handout725.64 KB
Learning Goals: 

After completing this exercise, students will be able to:

  1.  Draw a molecule in WebMO
  2.  Rotate, translate, and zoom the molecule
  3.  Choose a theory and basis set for calculations
  4.  Optimize the geometry of a molecule
  5.  Determine the bond lengths, bond angle, and dihedral angles in a molecule in WebMO
  6.  Calculate molecular orbitals in WebMO
  7.  Use the Z-matrix editor and coordinate scans to compare the energies of different molecular geometries
Equipment needs: 

Students need access to a computer, the internet, and WebMO (with Mopac). Other computational engines (Gaussian, GAMESS) can be used.

I initially taught this part of the course in a computer lab, but last year all of the students were able to bring their own laptops. I bring an extra laptop to class just in case.

Implementation Notes: 

I use this as an in-class exercise. The students are able to follow the directions with little difficulty. Many of them have used the WebMO interface briefly in general chemistry and organic chemistry, so this is not their first exposure.

The students need a reminder of what a dihedral angle is.

Time Required: 
50 minutes
Evaluation
Evaluation Methods: 

The students write their answers to the questions directly onto the handout. I collect the handout in the next class and check it for completeness (credit/no credit).

Evaluation Results: 

Because the students completed the exercise in class where they could ask questions, their work is typically complete and correct.

Creative Commons License: 
Creative Commons Licence

Comments

Looks good!  Consider in implementation notes or equipment needs that other engines besides MOPAC could be used.

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