Tag Archives: Chemistry

Computational Chemistry by Maya M (Continued)

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

Optimization
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

Attempting to successfully design and synthesise a Benzothiophene antibiotic a third year Chemistry research project, carried out by Umar Warsame

As soon I heard “third year”, I was thinking how intellectually stimulating this placement has already been, but, for me to carry out a high-level project aimed at students who have covered inorganic, organic, physical and analytical Chemistry to great detail – WAY more than myself – made me realise for a brief moment that I wasn’t capable and that I didn’t have the skill to – I was wrong.

Starting the second week of my Chemistry placement and reminiscing about the insightful Chemistry I have learnt: from observations, techniques and methods, theory and mechanisms, and also the things I have learnt from the discussions I had with my supervisor, Dr Barry Marsh, and the PhD students, working with on topics ranging from catalysis to bio sensing. The experience gained from a small framework of time has implemented the idea that I have the ability to successfully synthesise the precursor (finally understand what precursor means, and why “the methylamine keeps flowing”) needed and then from there, start to design my OWN Benzothiophene antibiotic through several intricate steps.

With the whole group behind me and the whole lab open for my use, I put on my safety glasses and lab coat, put on gloves and started reading the instructions intently and began the AWESOME project…

by Umar Warsame

A Computational Chemistry placement at King’s College London, By Maya M

Maya undertook a placement in Computational Chemistry at King’s College London,  supervised by Dr Edina Rosta.  

On Monday the 14th of July,  I arrived at King’s College London to take part in my Computational Chemistry placement. It was a daunting task. As my supervisor showed me my task for the week, I looked on in confusion. My task was to use computer software to display and optimise a chemical reaction. The hardest part was that the software could only be operated through a command-line interface, which was something I had never used before. I was in for an interesting and eye-opening week!

I spent the second day of my placement trying to learn how to use Linux and how to understand coding, as this was a crucial step for me to be able to use the software programs. My supervisor taught me the basic commands I would need to operate the software. However, to ensure that I had complete understanding of the software I watched a YouTube video which highlighted and explained how to draw and optimize chemical molecules. The software I used was called Molden and it is used by people in the Computational Chemistry field to draw software and to run virtual reactions so they can have a visual idea of what would happen if a reaction was to take place (see photo).

compchem

By Maya M