Shadowing

             My shadowing experience came from Laxman, which occurred on Thursday January 17, 2013. His experiment was dealing with a Diels-Alder reaction. For this experiment he used computational chemistry to predict the transition state of the molecule, which is a different type of method to work with desired products than what I am doing.  I use actual chemicals while he uses a computer program called Gaussian to perform the calculations.

 

 

When I arrived upstairs to where he was working, he was making the structures that he thought how the reactant, product, and transition state was oriented within a molecule. An interesting thing about his experiment is that unless the predicted structure is connecting, the calculation stops. I saw him frequently modeling the reactants, products, and transition state molecules. I even saw him with molecular modeling skit to generate ideas about how he should orient the molecules so that the specific reaction can occur. I found it fascinating when he showed me the animation of how the atoms vibrate within transition state obtained from his calculation.

          Despite the fact that I am doing an experiment procedure to my research, he is modeling a reaction. His entire experiment is basically a mathematical equation where he must know what the equation is when he already has the answer! I like his experiment because he can change the structure as many times as he wants. The software he was using has the entire feature that can add or delete any molecule.  He showed me how such tools are used to model the structure. Another interesting thing that I liked was how he was spending time on making similar models of the molecules such that the reactant, product and transition state would be oriented exactly the same way.

I liked his experiment in a sense that anyone having Gaussian software can model the structure and let the computer perform calculation. However, for my research we should be within a lab and we should follow experimental procedure. In the lab, we should be worrying about the safety measures for my research but for his research there is nothing a person has to worry about when he performs a calculation. The only concern that I thought of was that a person should be careful in saving files and pay attention to what results were obtained before the computer goes on to the next equation/model to work on.

            It feels to me that there is underlying concept of physics on his research which is very tough to understand since I had a lot of difficulty in that class. I imagine that anyone with a strong background in physics and math would have an easier time to understand just how and what the equation should be. One more thing that I would like to add: I chose him to shadow because it dealt with Diels-Alder reactions, my second favorite reaction. It also dealt with a type of chemistry that I was not familiar with: that of math and computation. It was remarkable that a computer did all the work for Laxman. In my case, it would have taken me a long time to do the reactions by hand.