Computational Chemistry by Maya M (Continued)

By in2scienceuk Uncategorized

Continued from her previous post, Maya tells us about the rest of her week in a Computational Chemistry research group…

Day 3: I spent the third day drawing more molecules on the computer.  I also began to optimize the molecules that I had drawn. Optimizing a molecule on Molden meant that I had to use the software to run a program which ensured that each atom and bond utilized the space around it properly and that the bond angle between carbon and hydrogen atoms, for example, was correct. I was already used to Molden by this day so I didn’t encounter any problems using it or carrying out the instructions that my supervisor gave me. I also got to know the PhD students in the ICT room in which I was based.

Image: the graphs are the details of the optimization test

Day 4: Two students who had gained a research placement from the Nuffield Science Work Experience program, joined me on my placement. I was really happy because I was able to speak to students who were of a similar age to me and we all shared ideas and thoughts of how to best use Molden. I felt quite proud of myself, as I was able to demonstrate and explain to the students how they should go about using the software and what we were trying to achieve. On this day, my supervisor, Dr Rosta, decided to show me how you would carry a reaction out on the computer. Dr Rosta’s current research is based on Hydroboration,  so she made me draw a cyclic hydrocarbon and a small BH3 molecule. Then we placed them next to each other and ran the program. The program was a bit like a movie, as it show the BH3 molecule moving towards the nearest double bond, an area of high electron density,  and breaking the double bond to form a new bond. I was really impressed when I saw this occur as it was a visual aid to what normally occurs on an atomic level, which our eyes can’t normally see when we carry out experiments in beakers.

Image: The red and white molecule is the BH3 molecule and it is moving towards the blue and white molecule, which is a cyclic hydrocarbon

maya 2

Day 5: This was my final day and I was very sad to leave. I had enjoyed my time at the department and I didn’t want to leave. My supervisor and I decided to talk about her life and how she arrived at the place where she is now. Dr Rosta had started out studying for a chemistry degree when she decided that she wanted to study Maths. She started her Maths degree and had done three years of her degree when she decided to get a PhD in Chemistry. Dr Rosta is now a lecturer at King’s College,  where she teaches third year students Computational Chemistry. She is very intelligent and I was grateful that I was able to learn how her. I also had my picture taken to go in the in2science records, and I had to strive for a casual pose in the picture, but somehow I don’t think I managed that! Overall I had a great time and learnt new skills.  I have even downloaded Molden on my home computer so I can explore some of the features I didn’t use in my placement. I enjoyed myself immensely and I would do it again if I was given the chance.

By Maya M