On the 2018 A-level results day I posted the first of two blogs about what learning outcomes of A-level Chemistry I still use in my day to day work as a medicinal chemistry PhD student. It was so many that I had to split it into two blog posts! Since it’s the first day of term for many English students today, here’s the second post where I further reflect on what aspects of Modules 2 and 3 of A-level Chemistry I need to remember to help me understand what I’m doing in the lab:
- Module 2: Inorganic chemistry
- Electronegativity – knowing the relative affinity an element has for its electrons helps me to differentiate between different atoms when describing reaction mechanisms and when doing NMR analysis (e.g. the relative position of peaks associated with carbon atoms next to a nitrogen atom vs an oxygen atom)
- Transtion metals – I use a lot of transition metal catalysts (mostly palladium) so my knowledge of metal complexes helps me to understand the structure of the catalysts with their various ligands attached and how they might work better because of those differences in complex structure and subsequent steric/electronic property changes.
- Substitution reactions – knowing the exchanges that may take place between ionic species in my reaction mixture can help me know what side products may also be produced in my reaction mixture and how easy it will be to remove them.
- Formation of coloured ions – a methylation reaction that I’ve carried out many times has a characteristic colour change from yellow to red, indicating the formation of the desired reaction intermediate. Knowledge of changes in the compound and the energies associated with that can be used to explain the colour change and can sometimes (but not always) indicate a reaction has worked.
- Oxidation states in catalysis – understanding how the catalysts I use work at an oxidation level is important for the Suzuki reactions I’m running at the moment.
- Module 3: Organic chemistry
- Organic chemistry nomenclature – I use different formula types to describe the compounds I make and the reagents I use. They come in handy for shorthand notation in my lab notebook (e.g. trethylamine = Et3N). Skeletal formula is the type of formula I use the most when describing the compounds I make – I’ve lost count of how many hexagons I’ve drawn.
- Reaction mechanisms – as I’ve expressed above, I am expected to understand the mechanism of every reaction I’m carrying out and be able to draw curly arrows to show how electrons move to break and form the desired chemical bonds needed to make the product I want.
- Isomerism – knowledge of the two types of stereoisomerism (E and Z) is important for knowing whether a reaction that forms one isomer over the other preferentially is going to make the product I want, or whether I’ve made a side product that I need to remove.
- Organic functional groups and reactivities – knowledge of how alkanes, alkenes, alcohols, aldehydes, ketones, carboxylic acids, esters, acid anhydrides, acyl chlorides, amides, amines and many more functional groups react is central to organic chemistry.
- Nucleophilic substitution and elimination reactions – understanding how these reactions work, not just regarding halogoalkanes and alcohols as taught in A-level, is important as I use these reactions a lot in my project.
- Organic analysis – while I don’t use the qualitative colour change tests such as Fehling’s solution to detect ketones, I use mass spectrometry, infrared spectroscopy, NMR and optical isomerism as analytical tests to prove I’ve made the right molecule, as needed.
- Aromatic chemistry – there are a lot of aromatic rings in drug discovery because our bodies uses these strong and stable ring systems to build lots of things in our bodies. I need to understand the properties of aromatic systems like benzene and how they react to make the molecules I need for my project. I am literally searching how to carry out electrophilic substitutions such as nitrations, chlorinations and acylations on a set of aromatic molecules right now!
- Amino acids, proteins and DNA – while I’m not making amino acids in my project, the protein I am trying to shut down to kill cancer cells is made up of amino acids. I had a lot of fun learning to 20 fundamental ones in our bodies during my undergraduate degree. As eluded to previously, while I am learning to make specific kinds of compounds, I also need an understanding of the biochemical molecules and the processes they are associated with in order to combat disease.
- Chromatography – another form of chemical analysis. I use thin layer chromatography daily in the lab to follow how a reaction is progressing and need to report the Rf of every new final compound I make. I also apply chromatography in a different way by carrying out column chromatography to purify my compounds when needed.
- Organic synthesis – understanding that it often takes multiple reaction steps to get to a desired molecule and how I can design the safest, most cost effective and efficient process is a vital part of being a chemistry PhD student.
So as you can see, organic chemists genuinely do use a lot of the chemistry they use at school. If its a career you’re thinking about, it’s definitely worth putting the work in now and learning this stuff really well to put you in a good position for further study.
A-level chemistry isn’t just used by chemists though. Doctors, pharmacists, chemical engineers, pharmacologists, product designers and many more roles rely on an understanding of chemical matter. Do you use chemistry in your work?