17 Jul 2014

Exploring Post-Translational Modification with DFT

In-Class Activity

Submitted by Gerard Rowe, University of South Carolina Aiken
Categories
Description: 

This activity is designed to give students a deeper understanding of what post-translational modification does in a metalloenzyme using nitrile hydratase (NHase) as a model system.  The metallo-active site of NHase contains a cobalt(III) center that is bound to an unusual coodination sphere containing bis-amidate, cysteinate, sulfenate (RSO-), and sulfinate (RSO2-) ligands.  Using density functional theory calculations on a simple model of the coordination environment of the cobalt, students will carry out geometry optimizations on three compounds that have either a sulfide, sulfenate, or sulfinate ligand.  The students will compare the partial atomic charges on sulfur in the three cases and compare them to their predicted atomic charges based on oxidation number.

Learning Goals: 

The student will use their knowledge of oxidation numbers to determine how electron rich a sulfur-containing ligand atom feels

The student will predict ligand binding strength based on electron richness trends

The student will convert a Lewis structure into a 3-dimensional representation in a molecular modeling program

The student will set and run up a geometry optimization using a computational package like Gaussan

The student will tabulate the results of a computational chemisty calculation

The student will compare their predictions of electron richness and donor strength to the calculated atomic charges and bond distances from their calculation

Equipment needs: 

A fairly hefty computer to carry out the calculations (at least 4 core processor system with 8 GB of ram)

A computational package like Gaussian, Spartan, Gamess*, ADF, or Orca*

A 3-D drawing program like GaussView, Spartan, WebMO*, or Avogadro*

* Free!

Implementation Notes: 

This activity takes long enough that it could be used as its lab exercise or as an addition to a synthetic lab.  With a larger class, you will probably need a day or two for all the calculations to finish.  The analysis is very easy, as it is only a few charges and bond angles to jot down.  The charges can also be found as a list in the log file, which can be opened in any text editor.  

If you are pressed for time or have a few students who cannot, for whatever reason, draw the starting structures correctly, Gaussian input files for each of the three compounds are provided.  The structures in each file have already been through several geometry optimization cycles of a successful calculation, so calculations using these files will finish much more quickly  than starting from scratch.

Output files are also available that contain the final data that were used to generate the key.  As an alternative to waiting for everyone's calculations to finish, you can play the "cooking show" game by giving students the completed log files after they successfully create their input files. 

Time Required: 
One 50 minute class + 20 minutes for analysis once calculations are complete (~1.5 h per group)
Evaluation
Evaluation Methods: 

Students will be evaluated based on whether or not they are able to complete the three required calculations with appropriately drawn structures.  They will also be awarded points based on completion of the worksheet and how well they compare their results to their predictions.

A test or quiz question using atomic charges taken from a published calculation on an inorganic would be a nice idea.  

Evaluation Results: 

This activity has not yet been implemented.  Will update when results become available.

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.