Chemistry PhD: A Day in the Life

I find people’s routines really interesting. Everybody’s different. Some people are early birds while others are night owls. Some people work long hours and others manage to fit a lot of work into a short period of time. In this post I chat about what a typical day looks like for me and the various things I get involved with both inside and outside of the lab as a PhD student.

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Picture caption: Fiona in a lab coat taking a selfie in the chemistry lab.

Day in the life:

0630: My alarm goes off. More often than not I press the snooze button for a little while.

0630-0700: If I’m sufficiently awake I go for a run then get ready for uni. I’m currently training for the Brighton Half Marathon at the end of February next year.

0815: Get the bus to campus.

0845-0900: Depending on how the buses are, get into the office, check e-mail and RSS feeds.

MORNING: I spend the morning either at my desk doing data analysis or in the lab running experiments.

1200: I eat lunch with colleagues. I usually bring a packed lunch but occasionally I treat myself to lunch at one of the university cafes.

AFTERNOON: I usually have a bit of an energy slump after lunch so I switch to low-brain-power tasks e.g. running TLCs in the lab or writing up analysis.

1600: I usually kick back into gear at this time of the day so I will have a burst of activity in the lab or at my desk.

1800-1830: leave office

Evenings: I don’t tend to do work on my PhD when I’m not on campus. In the evenings I’m either chilling at home, going along to something at my church or going to review something at the theatre.

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This is what a typical day where I have nothing in the calendar looks like. There are other things that pop up throughout the week which mixes things up. I generally prefer days when I have a meeting or two in the calendar. This is because it makes me more productive with my time because in my head I’m thinking “I have to get this done by X because of Y”. Below are some other things that are typical of chemistry PhD life outside of doing experiments:

Cleaning the Lab

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Picture caption: a set of super sensitive scales, known as a balance, reading 0.0000 g.

While everyone in my lab has responsibility for their own lab space, we have a rota for cleaning the communal areas of the lab. This involves checking our balances don’t have residual chemicals on them; cleaning up the TLC plate area; and checking our communal rotary evaporator for removing toxic/smelly substances has been cleaned.

Solvent Run

In a lab capable of up to nine chemists working in it at once, we get through a lot of chemicals, especially solvents! Solvents are the liquids we run our reactions in. Sometimes its water but its usually an organic solvent such as dichloromethane, tetrahydrofuan or an alcohol. We take it in turns to check our communal solvent stocks in the lab and top them up from the school’s central store as needed.

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Picture caption: multiple plastic bottles with different coloured lids containing different solvents.

Supervisor 1-2-1s

About once a week I sit down with my lab supervisor to review the chemistry and other work I’ve done, troubleshoot any problems I’m having and I propose what I plan to do next. About once a month I give a slightly “bigger picture” version of this project update to my main PhD supervisor. This helps me to build up a record of what I do on a weekly/monthly basis and gain input on my project from people with more experience than me.

Teaching

PhD students can undertake casual work with at my university to earn extra money. So far I have demonstrated in undergraduate labs – walk around and make sure everyone is carrying out their experiments safely and helping with any issues they have; invigilated exams; marked exam papers and taught tutorials and workshops for undergraduate chemistry/life science courses.

Attend lectures/seminars

As I am undertaking a research postgraduate degree instead of a taught one I don’t have any mandatory classes as part of my course. That doesn’t mean I can’t take advantage of the learning that’s happening around me on campus. Last year I attended a module called Fundamental Cancer Biology which helped me to consolidate what I’d learned about the biology side of cancer from my own personal reading which I found very helpful.

The life science school puts on a number of seminars that are mainly geared towards postgraduate students and research staff. While the term “seminar” can mean different things, in Sussex’s School of Life Science this session is usually an hour long where an in-house/invited speaker talks for about 45 minutes about their research followed by questions. It tends to be a very applied talk with only general concepts covered in the first few minutes. I enjoy seminars because you get the chance to learn about all kinds of research outside of your own.

Conferences

A few times a year I go to conferences. These are 1-3 day events where researchers in academia/industry meet in a specific location to hear talks about research around a specific area. I’ve been to conferences about medicinal chemistry, genome stability, the specific class of drug target I’m working on, and more! There’s a conference for everyone.

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Picture: Fiona giving a presentation at the RSC Kinase 2018 conference. A single slide summarises my PhD project with diagrams of chemical structures and biological processes.

While I haven’t had the chance to go abroad yet I’ve been to conferences on my own campus and in Glasgow, Cambridge and London so far. I sometimes take a poster summarising my research and am now applying to talk at some conferences now that I’m later on in my PhD. They’re a good opportunity to network and catch-up with people from my field of research.

Public Engagement

It is becoming increasingly common that researchers are required to demonstrate the impact their research has on society by communicating that research to the public. I’ll do a separate post about the various public engagement activities I’ve been involved in another time but very briefly, from time to time I take part in science fairs, schools events at the university and sometimes go into schools to talk about chemistry.

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Picture caption: Fiona pouring liquid nitrogen onto the floor, creating a large fog, as part of a public engagement show about chemistry at a school

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Juggling these things requires a lot of time management which I have varying levels of success at doing. I like that there’s a lot of variety in my work but primarily the goal of my PhD is to spend time in a lab making molecules. The other things give me a change of scene and enable me to develop other skills that will be useful for whatever job I do after my degree.

What does your typical working day look like? Is there an established routine or is every day different? Let me know in the comments below.

How do I know I’ve made the right molecule?

I spend my days in a chemistry lab making drug-like molecules. A lot of these end up being small quantities (less than 0.1 g!) and usually have the appearance of a white/off-white powder. Occasionally I get a colour which is very exciting.

Picture caption: stacked boxes of sample bottles of ca. 40 different chemical products I’ve made in the last few months

The question a non-chemist might ask is “how do you know you’ve made the product”? Lots of different analytical techniques have been developed over decades to help chemists determine the chemical structure of the products they’ve made.

In this post I will give you an introduction to the seven analytical techniques I carry out on my samples to prove I have made the right molecule. These various bits of data go in my experimental write up which will make up a large chunk of my thesis.

1) LCMS

LCMS stands for Liquid Chromatography Mass Spectrometry. This combines two techniques: liquid chromatography allows to you separate a mixture into its components while mass spectrometry will tell you the molecular weight of each of those components.

Picture caption: A large grey boxed machine on a lab bench. This is our LCMS instrument in the lab.

Ideally the read off of a pure sample will just show that there’s one component in your mixture and the molecular weight from the mass spec will match the calculated weight of your product (i.e. the number you get when you add up the molecular weights of the individual nitrogen, carbon, oxygen, hydrogen etc. atoms).

2) 1H NMR

NMR stands for nuclear magnetic resonance. There are many different “flavours” of NMR. Proton NMR (written as “1H”) looks at the different hydrogen atoms present in a molecule and the different environments they’re in.

Picture caption: The blue door that leads to the NMR lab with safety signs warning about strong magnetic fields. 

For example, some protons will be attached to carbon atoms, while others will be attached to nitrogen atoms. This means they will have a different “magnetic environment” due to the different number of electrons in different atoms and how they’re distributed between different atoms and chemical bonds.

Below is an NMR spectrum for ethanol, the type of alcohol found in alcoholic beverages. There are three different proton environments in the molecule of ethanol: a hydrogen attached to an oxygen (blue); a hydrogen attached to a carbon that’s attached to a carbon and an oxygen (green); and a hydrogen that’s attached to a carbon that’s attached to another carbon (red).

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Picture caption: a graph with three sets of peaks/spikes corresponding to different hydrogen atoms found in ethanol (chemical structure of ethanol also shown).

The appearance of the peaks is affected by the number of nearby protons e.g. the CH3 peak is split into a triplet because there are two protons on the adjacent carbon atom. Undergraduate chemistry degrees have entire modules dedicated to interpreting NMR spectra, so I won’t go into too much detail here.

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LCMS and 1H NMR are usually the minimum pieces of data you need to be sure you’ve made the right compound to move on with other chemistry. The two pieces of data combined give sufficient evidence that you’ve made something that weighs the same as the expected molecular weight; has the expected number of protons in the predicted magnetic environments to be the right products; and gives an indication of the purity of the compound.

For a PhD thesis you usually need to provide “full characterisation” for compounds which involves more analysis than those two techniques. I agreed with my supervisor that I would only get full analysis for final compounds that are to be tested by a biologist or compounds that don’t appear to have been made before by anyone else.

I determine if a compound is new by doing a literature database search and if zero hits come up in the search, I can assume no one has published the synthesis of this molecule before. I need to provide as much information as possible to prove it is the right compound. Below are 5 additional types of analysis I get on samples that fall into the final/unknown category.

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3) HRMS

High resolution mass spectrometry is just a slightly higher quality version of LCMS. Having two mass spectrometry experiments that match up gives more concrete evidence about what the molecular weight of my chemical product is.

Picture caption: blue lab door leading to the mass spectrometry lab, covered in warning signs about high voltage and magnetic fields.

4) 13C NMR

13C NMR is like 1H NMR but it instead looks at the different environments of carbon atoms in a molecule. There are lots of different types of NMR experiment that are used depending on atoms are in your compounds e.g. fluorine, phosphorus. Going back to the ethanol example, I would expect to see two peaks in a 13C NMR spectrum of ethanol because there are two types of carbon atom present in the molecule.

Picture caption: a grey space ship like instrument in the centre of a room. This is one of the university’s NMR instruments that I run 1H and 13C NMR experiments on.

There are also different types of NMR experiment that combine different types of NMR e.g. COSY, NOESY, HSQC, HMBC etc. which I may talk about in another post some time.

5) IR spectroscopy

IR spectroscopy involves firing infrared radiation (IR) at your sample to determine what types of chemical bonds are present. Different chemical bonds have different energies and absorb and emit different levels of IR. An IR spectrum (see below) will tell me if I have C-H/C=O/C-N bonds present in my product, but not how many there are.

6) Melting Point

We know that ice melts at 0 °C. Similarly, different products will have characteristic temperature at which they change phase. Recording the melting point of a sample will allow a chemist making the same compound in the future to compare their melting point with yours. The melting point also gives an idea of how volatile a compound is i.e. how easily might it boil off into the atmosphere.

7) Rf value

The final type of analysis I get is an Rf value, which stands for retention factor. You may have carried out chromatography at school or a science fair, whereby you separate a mixture into its components by running a liquid through a medium such as filter paper.

I use a slightly more sophisticated version of this technique called thin layer chromatography (TLC) where I run a spot of my product up a silica plate. The Rf value is a ratio of the distance travelled by the spot of product divided by the distance travelled by the liquid.

Picture caption: small white silica plates with run TLC experiments on them. Lines and spots have been drawn on in pencil for samples that are not visible under normal light.

This gives an indication of how clean the product is (I’ll see multiple spots if there are any impurities). It also tells you how well the product dissolves in that particular liquid – it will travel further up the plate if it dissolves really well in the e.g. water that I run my TLC plate in.

There are other types of analysis beyond this set that I could also use but they are either excessive, time consuming or unnecessary for the type of molecules I make. I think of full characterisation as compiling as much evidence as possible to be sure I’ve made the right molecule, fitting various jigsaw puzzle pieces together to build up a concrete picture of what my product is.

Some of the techniques are qualitative rather than quantitative and aren’t necessarily as sophisticated as others e.g. IR just tells me I have a C-N bond present while NMR will tell me if there are protons attached to that nitrogen, how many, and what other protons/carbons they are close to.

Picture caption: a big pile of printed data to analyse on my desk, and an IR spectrum on the computer screen.

These seven types of data I get are the standard ones expected in most theses and journals, but it wasn’t always that way: in the 1960s chemists only had IR and MP techniques available whereas now 1H NMR and mass spectrometry are the standard minimal analytical techniques, with MP and IR as added extras.

Last month a new analytical technique, called micro-electron diffraction, was published and generated a lot of excitement amongst chemists – on my Twitter feed at least! MicroED might save chemists a lot of time analysing compounds in the future by rapidly generating a 3D “X-ray skeleton” of the molecule using electron beams. This would save having to do all these other analyses.

For more information about different types of spectroscopy and analytical techniques used in chemistry, check out the resources below:

Does it surprise you how much analysis is done on one sample? What types of analyses do you use in your work to make sure a job has been done properly? Let me know in the comments below.

Why did I want to do cancer research?

My PhD project involves designing and making “tool molecules” that might lead to new cancer drugs one day. Medicinal chemistry covers a vast range of disease areas and many scientists often have a personal connection to their particular field. In this post I will discuss some of the personal experiences that motivated me to pursue this particular area of research.

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Picture caption: Fiona taking a selfie in a chemistry lab wearing a lab coat and safety glasses

Cancer, a disease involving uncontrolled division of cells in the body, affects many people. CRUK now say 1 in 2 of us will be diagnosed with cancer but more of us will survive it these days. This is due to many factors: we’re living longer; we’re getting better at detecting it; but also the encouraging news that treatments for some cancers are much better than they used to be. My Grandma Rena died of ovarian cancer when I was 7. This was my first close-to-home experience of the disease.

In my last year of high school, a family friend gave birth to a little boy called Oliver. Unfortunately, he was born with a rare and aggressive form of cancer called a Rhabdoid Tumour and he sadly passed away a few months later, on Christmas Day.

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Picture caption: A photo of baby Oliver smiling

Since then his wonderful parents, Andy and Jennifer, have raised over £530,000 through their charity Love Oliver to support families experiencing childhood cancer and have also helped to fund 2 PhD projects at Newcastle University that research the type of cancer Oliver had.

While Oliver was having cancer treatment I was applying to different universities to study chemistry. I chose chemistry because it was one of my favourite subjects at school, having decided not to pursue music and it gave me plenty of career options.

I was drawn to medicinal chemistry/drug discovery courses because of what was happening with Oliver at the time and I loved the idea of helping patients, without necessarily going down the medicine route – I don’t have the stomach to work in a hospital!

Throughout my degree I continued to find myself drawn towards cancer as the area I was interested in researching. While I applied for PhD projects involving antibiotics and for other disease areas, deep down I knew I really wanted to work on a cancer project because of my past experiences. I managed to secure a project and supervisor at Sussex Drug Discovery Centre.

Then, rather ironically, before starting my PhD I actually had treatment for cancer myself. During the final year of my MChem at University of Strathclyde my mum spotted a lump in my throat. After going to the GP they thought it was a lump on my thyroid that should be checked out.

The thyroid is a small butterfly-shaped gland in your neck that makes a hormone called thyroxine which controls processes such as metabolism. I was told at that appointment by my doctor that if it was thyroid cancer, it was one that is very treatable.

Thyroid cancer generally has a 95% survival rate and was described to me as a “good” cancer to get, if such a thing exists. This meant I never really thought about whether I would die or not. Treatment for thyroid cancer is relatively straightforward: it involves a couple of surgeries to remove your thyroid gland and then some radiotherapy.

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Picture caption: Fiona giving a thumbs up in hospital with medical dressings on her neck

I was able to delay starting my PhD for a few months and during the downtime I had between surgeries/radiotherapy, I made a few trips to see friends in Belfast, London, Brighton, Dublin, even Basingstoke! To combat the mental and emotional strain that came with being a cancer patient I did a Couch-2-5K training programme with the aim of being able to run 5K before going back into hospital for my second surgery – which I achieved!

I had radioiodine treatment at the Beatson West of Scotland Cancer Centre in Glasgow. This is a rather unusual treatment but it is highly successful in thyroid cancer patients.  Radioiodine treatment is a targeted therapy: it hits the cancer cells specifically and healthy cells to a much lesser extent, with minimal side effects. This is the sort of treatment that cancer researchers are aiming towards for many types of cancer. Rather ironically I learned about radioiodine during my MChem degree!

Rather than being fired with radiation, I swallowed a tablet of radioactive iodine and was shut in a lead-lined room for three days. Iodine is only used in the body by thyroid cells to make thyroxine. This specific function means the iodine would only be taken up by any remaining thyroid cells in my neck region. After three days of (almost) solitary confinement, a Geiger counter and CTI scan measured my radioactive iodine levels as undetectable and I was allowed to go home.

Nine months later I had a follow-up treatment where I swallowed a much smaller dose of radioiodine just to detect if any thyroid cells had grown back and thus far, every scan I’ve had indicates that hasn’t happened. I’ve now been in remission for 2 years and continue to have check-ups every so often. As I don’t have a thyroid anymore I have to take thyroxine hormone tablets everyday.

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Picture caption: Picture of the Beatson West of Scotland Cancer Centre Building where I had my radioiodine treatment

My relatively mild ordeal of cancer gave me massive insight into how grim aspects of the experience can be. I am extremely thankful that I didn’t have to go through chemotherapy.

It breaks my heart that people still have to undergo such rigorous treatment and experience severe side effects. I find it so frustrating that we know so much more about cancer and yet a lot of cancer cases still become untreatable when secondary cancers occur after treatment or if tumours are identified too late.

When I’m feeling unmotivated in my project (which happens, chemistry is very repeptitive!), reminders of people close to me (and also those I don’t know) who are living with this dreadful disease everyday gives me the kick up the backside I need to get back in the lab and make those compounds, so that one day, there might be better medicines for other types of cancer.

I am acutely aware of how ironic it is that I couldn’t start my cancer-related PhD because I had the disease myself but it certainly gave me more of a subjective understanding of living with the disease over the largely objective way it is taught in university.

It’s important as a researcher to balance being subjective/objective to try to remove yourself from the emotional aspect that the disease inevitably brings because otherwise I’d spend all my time crying at my desk. I hope this post makes it very clear why I am doing my project.

Are you living with cancer? Do you have a close friend/family member dealing with it? Are you a researcher? What inspired you to choose your particular field? Let me know in the comments below.

I was asked by Macmillan Cancer Care to share my cancer story for a Huffington Post article as part of their #LifeWithCancer campaign.

Will I ever use my A-level Chemistry? (Part 2/2)

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Photo by Pixabay on Pexels.com

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?

Will I ever use my A-level Chemistry? (Part 1/2)

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Photo by Tookapic on Pexels.com

Today is A-level results day. The Independent reported that about 46,800 students took A-level chemistry in 2017 – the fourth most popular subject after mathematics, biology and psychology. That’s a lot of people learning about the ingredients of the universe!

While deep in the exam period, you might think the things you are revising are topics you’ll never need to remember in real life circumstances. I’m aware my job as a chemist means I’m much more likely to apply these concepts than the average person but for those of you thinking about pursuing a chemistry career, it’s useful to know what you should learn now to save you re-learning it later in life.

Having gone through the A-level Chemistry syllabus, here’s a list of things from the first module that I use in my day-to-day life as a chemistry PhD student:

MODULE 1 PHYSICAL CHEMISTRY

  • Atomic structure – the study of chemistry is based on developing knowledge about the particles that the universe is made up of. In medicinal chemistry we specifically look at the molecules that make up our bodily functions an how we can design molecules that alter these functions for therapeutic benefit.
  • Mass spectroscopy – an analytical technique that tells you the atomic mass of your molecule. I use this type of analysis on a daily basis in my lab to make sure I’ve made the right product – assuming the mass number I’m given matches the one I’m expecting.
  • Relative atomic mass, relative molecular mass – when looking at mass spec data I have to take relative molecular masses into account if e.g. I have a chlorine atom in my molecule (35-Cl and 37-Cl isotopes give me two different product mass peaks). Also, another analytical technique I use called Nuclear Magnetic Resonance relies on the existence of 13-C in 1.1% of all carbon atoms.
  • The mole and Avogrado’s constant – Moles are the typical unit used to describe a quanitity of a chemical substance, like a dozen eggs, you would talk about needing X moles of a chemical. Luckily, I use an electronic lab book that calculates the majority of mole calculations I need to do for all my experiments to work out how much of each chemical I need. I still need to be able to calculate the number of moles of a chemical I need for my reaction to work from time to time if transferring a protocol from a scientific paper to the lab book software, and also to be able to engage with the software and check its calculating the correct number of moles for my reaction.
  • Empirical and Molecular formula – I often express my compounds in empirical formula (just the relative number of carbon, hydrogen. Nitrogen, oxygen etc.) as a way of keeping the chemical structures confidential. When writing up the reagents I use I often use molecular formula shorthand in my lab notebook (e.g. Chloroform = CH3Cl).
  • Percentage yield calculations – again, my lab book software does a lot of these calculations for me. We use % yields a lot to express how efficient a reaction is and is a very quick way of communicating to fellow chemists how well my chemistry is working (a reaction with yield >85% are pretty good, whereas a 5% yielding reaction needs optimising!). Similarly, I still try to check whether the calculated percentage makes sense for the mass of product I have.
  • Balanced equations – while I don’t write out balanced equations in the same format as I did in high school, I need to make sure the ratio of different reagents I use makes sense for the reaction I’m doing.
  • Volume and concentration calculations – sometimes the prescribed concentration of, say ammonia solution, in my protocol doesn’t match what we have in the cupboard. While I can often use the lab book software to calculate how much 2 M solution I need to use in absence of 13 M solution, a solution concentration is sometimes expressed in different units (%, g/L, M etc.) so I like to do these calculations manually to make sure I can still convert between units and have the right amount of reagent.
  • Knowledge of bonding – the different reagents I use in the lab have different types of bonding properties (covalent, ionic, metallic, polar covalent) which affects how they interact. When working out the mechanism of a reaction (i.e. a detailed step by step rationale for how it works) I need this knowledge to explain why a catalyst might co-ordinate to a starting material, or why a particularly strong covalent bond won’t break.
  • Bonding and non-bonding electrons – again, using this knowledge when working through the mechanisms of the reactions I’m carrying out, it’s important I know which pairs of electrons will get involved in my reaction and which won’t.
  • Intermolecular forces – the forces that hold molecules together or repel them (permanent dipole-dipole forces, Van der Waals, dispersion, London forces and hydrogen bonding) are really important for understanding how a drug molecule fits into a protein to shut down a biological function. When I design molecules for my specific project, it’s usually to increase my understanding of these forces and how to utilise them to make a drug that mimics an ATP molecule in the way it binds to a kinase enzyme.
  • Kinetics and thermodynamics – these fundamental concepts are applied to explain why reactions go a certain way depending on different factors. It explains why my reaction needs to be a particular temperature, or why one chemical product is preferentially formed over another.
  • Chemical equilibria – The equilibrium (balance) involved in a reaction can be used to explain why a reaction hasn’t gone particularly well in converting starting material to product and how I might push that reaction to go to completion (i.e. 100% product in an ideal world) by changing the concentration of certain reagents, temperature etc. (applying Le Chatelier’s principle).
  • Oxidation, reduction and redox equations – Oxidation and reduction reactions are some of the transformations I apply to my molecules so being able to write reactions showing which chemical species are being oxidised/reduced is important to remember.
  • Acids and bases – I frequently use acids and bases in various ways during my reactions e.g. one of my reactions involved acetic acid catalysing the formation of a benzimidazole ring system. I also alter the pH of my reaction mixture sometimes in the purification process  – e.g. if a solid dissolves at a certain pH environment but crashes out as a precipitate at a different pH.
  • pKa – the acidity of protons involved in my molecules is a very important aspect of predicting and explaining reactivity. I learned a bunch of pKa values during my undergraduate degree to explain why one region of a molecule is more reactive than another.
  • Buffers – while I don’t personally use buffer solutions in the chemistry I’m currently doing, a lot of chemical reactions require a buffer to maintain the pH of the reaction at a certain level. The biologists I work with run different biochemical assays (tests involving enzymes and cells etc.) use buffers a lot to mimic cellular conditions when testing molecules I make for them.

I was quite surprised by quite how much physical chemistry feeds into my organic chemistry project. It just shows how much chemistry overlaps. Hopefully this shows you how useful this stuff is to know when thinking about becoming a chemist. Check back for a future post that will list the parts of A-level modules 2 and 3 that I still use as part of my PhD.

What was your favourite thing that you learned during A-level chemistry? Is there anything from your A-level days that you still use in your job today? 

pH and Drug Design

Today’s Google Doodle celebrates the Danish biochemist S.P.L. Sørensen (1868-1939) (Figure 1). He came up with the famous pH scale that is taught to high school chemistry students and is an important property to consider when using chemicals. The Doodle is a game which gets you to guess how acidic or basic some common household items are.

google doodle#
Figure 1 S.P.L. Sørensen Google Doodle1

The pH scale varies from 1-14 (Figure 2). A neutral solution (e.g. water) is considered to have pH 7 and any pH lower than 7 is deemed to be an acidic solution and anything more than 7 a basic/alkaline solution. The pH scale is logarithmic so something with a pH of 6 is 10 times more acidic than something with a pH of 7.

pH scale
Figure 2 The pH scale

The average pH of our body is slightly alkaline at pH 7.4, “physiological pH” but it actually varies across different parts of the body:

  • Mouth: pH 6.5-7.5
  • Stomach: pH 1.5-4
  • Intestines: pH 4-7
  • Blood: pH 7.4

This is important in drug design because as the pH environment changes, a drug molecule may undergo chemical changes because of the acidic/basic solution it is in.

If an environment is too acidic, a drug may become “protonated”. Chemists use the term proton/hydrogen interchangeably because a hydrogen ion is by definition a proton as it has lost its single electron to form H+.

An acid is defined as a proton/hydrogen donor, it loses hydrogen atoms to other species. This means any acid present in an environment, say gastric acid in our stomach, may react with the drug, adding a proton to the molecule (Figure 3). This forms a drug salt.

basic drug and acid
Figure 3 A basic drug reacting with an acid to form a protonated salt

Similarly, if an environment is too basic, a drug may become “deprotonated”. Bases react with acidic protons present on the drug molecule and remove them from the drug molecule, again causing it to become a salt (Figure 4). A drug salt will behave differently to the neutral drug and might not get to where it needs to be in the body.

acidic drug and base
Figure 4 An acidic drug reacting with a base/alkali to form a deprotonated salt

Have you ever tried mixing oil and water? They don’t tend to like mixing together very well (Figure 5). This phenomenon is important for how a drug behaves in the body. The neutral form of the drug will typically be happier dissolved in the oil over the water, whereas the protonated/deprotonated salt form of a drug would be happier dissolved in the water.

clear long stem wine glass with yellow liquid
Figure 5 Oil and water do not mixPhoto by Pixabay on Pexels.com

Our body is made up of a mixture of oily and watery (“aqueous”) environments. For example, the outside of our cells is an oily phospholipid membrane whereas the inside and outside of our cells are water-based. A drug needs to be sufficiently oil soluble to be able to cross the cell membrane to get inside the cell (Figure 6).

If the drug has been chemically altered by the acidic/basic environment around it and is in its salt form, it is highly unlikely to cross the cell membrane to get into cells and have the desired effect. This is because salts are much happier dissolved in water. The non-salt version of the drug may well dissolve in water too but it is more likely to also dissolve in oily substances to cross a cellular membrane.

drug absorption pH
Figure 6 Drug form vs cell permeability (i.e. its ability to cross a cell membrane)

There are a number of different ways of administering a drug to a patient (topical creams, intravenous injections, slow-release patches, inhalers etc.) but the preferred method is oral dosing, that is, a tablet you swallow with water. Each delivery method has its own set of advantages and disadvantages. Regarding oral tablets, the drug then needs to bypass the gastrointestinal tract (GIT) (Figure 7) to get to where it needs to be in the body to have its desired biological effect.

GIT
Figure 7 Gastrointestinal Tract (GIT)2

 

The GIT is made up of the mouth, throat, stomach and upper and lower intestines. When the drug first enters the body by mouth, it is in a neutral environment (pH 6.5-7.4). Some of the drug may be absorbed into the lining of our mouths but most of it travels down our throats to our stomach which is relatively much more acidic (pH 1-4).

If we don’t want the drug to be absorbed into the stomach lining, we design our drug such that it contains groups of atoms that will be protonated to form the salt. This means the drug will be happier in the stomach acid than the oily stomach lining. Similarly, it is important to make sure a drug is sufficiently stable to survive this acidic environment and not be broken down by our body’s metabolism processes.

The drug then moves on to the intestines which are relatively more basic than the stomach (pH 4-7). Usually any protonated parts of the drug will be deprotonated again to give the neutral form of the drug and this is where many drugs travel through the oily intestine lining and into the blood (pH 7.4).

As you can see, knowing about pH and how it can affect molecules is very important in drug design. Sørensen’s pH scale is a helpful way of quantitatively measuring how acidic or basic a chemical environment is. Chemists use this to predict how a drug might behave in that environment.

  1. Google homepage, accessed 29th May 2018
  2. Image used under creative commons license using Bing Image Search software

What is the drug discovery process?

During my undergraduate degree, people would often ask what course I was studying. Usually the response to “Chemistry with Drug Discovery” was “Chemistry with what?”. No, it doesn’t involve hunting around with a magnifying glass looking for paracetamol. The drug discovery process is a huge chain of events involving numerous people that gets a medicine from initial idea to market. This process can take up to 20 years and many projects fail at various points of the journey. Below is a diagram that I will talk through to take you through the drug discovery process (the blue portion).

Picture1
Drug Discovery and Drug Testing Processes. Image reproduced from http://nmtpharma.com/en/drug-development-stages/
  1. Identify target – Scientists (mainly biologists) work out how they might target a disease. We have many tiny molecular machines in our bodies called proteins which do various jobs and keep us alive. Sometimes those proteins are missing or go rogue and that often causes a disease, so it becomes the drug target.
  2. Identify compounds – Often, the way to treat a disease is to shut down the protein that is causing the symptoms. These are called inhibitor molecules and they do so by binding to the protein, rendering it useless. Think of it like putting a key in a lock that means a door can’t be unlocked from the other side. These compounds can be found using a number of techniques: by doing a screen (chucking hundreds to millions of potential molecules at the desired protein to see what sticks), working on an existing molecule someone else has identified, or using educated guesses based on the shape of the protein. Chemists will then make dozens, if not hundreds, of these molecules and also slight variants of them based on the same general shape to find a brand new drug.
  3. Establish activity – It’s now back to team biology who test the drug compounds the chemists have made to see if they have the desired effect. This is done using a test called an assay where the individual proteins/cells are monitored to see if adding the drug stops the protein from doing its job. The results of these assays can be relayed back to the chemists who can then make more molecules to ask further questions about how the protein is inhibited and improve on their compounds. Many rounds of this exchange can take place (which is what my PhD project largely involves).
  4. Select clinical candidates – Once scientists are concretely sure about how their drug binds to the protein and have found compounds that shut down the protein with high potency (that is, requiring very little drug to carry out this effect), a shortlist of clinical candidate compounds are selected and made ready for testing in live subjects instead of cells.
  5. Test safety – This is the most controversial aspect of the drug discovery process. Before clinical trials, where drugs are tested in increasingly larger groups of humans, they are first tested in other animal models to see what effect the drug has on an entire organism’s system. Such models include rat, mice, dog and primates, with increasing similarity to human anatomy. I am not involved with this work as a chemist but from what I’ve learned such testing is heavily regulated and I personally think it is a vital step before putting drug candidates into humans. I may discuss this further in a future post.

In the rare occurrence that a drug compound makes it through all of the above stages, it is ready to test in humans. This first part of the process can take years. As I said above, my PhD comes in at stages 2/3 of this diagram and that is 3-4 years worth of work on my part in addition to the work done before me by biologists in identifying the protein I am targeting for treating cancer.

As you can see, the drug discovery process is a rigorous and lengthy one. In a future post I will talk about the various phases of clinical trials that take place to make sure a drug is safe before going on the market.

Are there aspects of the drug discovery process that surprise you? Is this how you expected new drugs to come about? Let me know in the comments.

 

Where to find a PhD

Everyone is different. Everyone chooses to do a PhD for a variety of reasons. Everyone wants to get different things out of a PhD project. Below is how I decided which projects to apply for.

Why a PhD?

Before even thinking of applying, you need to be sure you know exactly why you want to apply for a PhD as it is something you will be asked in application forms and interviews. Is it the next natural step in your chosen field? Are you excited to be part of cutting edge research and contributing something new to the scientific narrative? Are you up for a few more years of studying? Can you afford/do you want to live on a stipend for the next few years for the sake of research? Or do you just not know what you want to do next? Speak to people who have done/dropped out of PhDs to find out their motivation and see if you’re on the same wavelength as them.

While I don’t think I want to stay in academia forever, I knew I wanted to contribute something to research into treating cancer and a PhD is a very easy way to do that. I had spent the final year of my MChem in a med chem group and saw what doing a PhD was like and could see myself doing that in the future.

My absolutes

First and foremost, once deciding to do a PhD, I knew I wanted to do a cool project in an interesting place. This took the pressure off the overwhelming number of options to take into account. With those two criteria met, other factors can then be weighed up, such as location, discipline, university credibility etc. After answering yes to the two questions “Is it a cool project? Is it in an interesting place?”, I settled on the following checklist:

  • Medicinal chemistry with a bit of biology
  • Oncology-related project
  • Good university, reputable research group
  • Interesting location – Scotland (not Glasgow, needed a change of scene) or UK (if England, close to London for easy access to theatre etc. and friends who had moved south)
  • Applying to a project, not a Centre for Doctoral Teaching (CDT, will explain below)

Finding PhDs

Now the all important where do I find the things to apply to:

  • FindaPhD.com is where I found most of the PhD projects that I applied for. It has a very useful search function where you can search for projects based on subject, institution, funding grant and even by supervisor.
  • Ask staff at your current institution if they’re looking or can recommend people for the work you’re interested in. Academia is a smaller world than you think.
  • Good old Google. If a particular institution takes your fancy, look up what research is going on, by whom, and contact them directly for any opportunities.
  • Look up industry options – there are a number of industry-based PhD options popping up for chemists (GSK/Strathclyde, AstraZeneca/Cambridge etc.). If you’re not wanting to spend a few more years entirely in an academic environment, looking for PhDs with placements/mostly based in industry might be a good alternative.
  • Attend postgrad fairs – to be honest, I didn’t find this massively helpful as it was geared towards grad schemes but there are universities present. I had to inform the GSK recruitment staff there that they offered a PhD scheme with Strathclyde.
  • Attend Open Days – I only attended one open day (St Andrews) but it was very worthwhile. After the generic morning being shown around the university, my coursemates and I that attended got a chance to speak to academics one-to-one about potential projects. Sadly the funding for a project I agreed to fell through but it was a useful day.

PhD or CDT?

In the UK there are two approaches to offering PhD scholarships. There is the traditional route where you apply to individual projects with specific supervisors at a specific institution. Increasingly, due to the way funding is being offered, universities are setting up “Centres for Doctoral Training” which focus on offering a number of PhD scholarships dedicated to a specific topic across a number of groups/institutions. Some examples I have come across are listed below.

CDTs typically offer a first year of rotation around different research groups and projects and then you decide on your PhD project and supervisor after that period of training. This strategy is useful for candidates who know which institution or what field they’d like to work in but not neccessarily which project and allows an informed decision. Personally I decided to apply for a specific project and supervisor as there wasn’t a guarantee I’d get a project I was after once joining a CDT but I have ex-coursemates who are largely enjoying the CDT option.

I could say much more about my personal process of finding a PhD as there’s lots to take into account. Please comment below or tweet me (@fi0n0) any other questions you might have if you’re looking into studying for a doctorate.

Reflections on first year

I am coming to the end of my first year at the SDDC and have been thinking a lot about what I’d like to do differently in my second year. I’ve achieved some of the primary aims of my project, but not all of them. This was due to collaborators and things outside my control so I’m not too hung up about that. I made some compounds and some preliminary data showed some of them bind to the protein I want them too and have an inhibitory effect. Win!

Here are 5 things I will do differently next year:

  1. Read more papers. My lit reading is so inconsistent and I’d like to change that. I’ve set up a Feedly account where I receive RS feeds from big papers I read from. I’d also like to attempt the #365papers challenge ad keep track of my reading via twitter.
  2. Make more compounds. My lab skills have accelerated a lot this year and hopefully that means I’ll be able to churn out more compounds.
  3. Be more selective in the seminars I attend. While it’s useful to attend seminars and classes in and outside your field, more often than not I’ve found myself way in over my head in a seminar I perhaps only understand the first 10 minutes of. Perhaps I should just google the speaker, read a bit about their group/institute/work then decide to go.
  4. Attend more conferences. I only attended in-house symposiums in my first year. Illness meant I missed an RSC Chemical Biology conference in June and I was too late to attend a postgrad one next month in Oxford.
  5. Use this blog more. I have been neglecting “the Chemistry of a PhD” and need to recitify that.

Here’s hoping you’ll be hearing from me more often on here.

How did I get here?

How does someone end up designing cancer drugs for their PhD project? Well…

After deciding not to pursue a music career while at high school, I needed to rethink my options. Chemistry had become more interesting once I started studying it as an individual subject. I found breaking the world down into processes and ingredients at a chemical level fascinating. The careers advisor said a science degree would give me plenty options after university. Deciding not to follow my parent’s footsteps into the land of accountancy, and knowing  I had the grades but not the stomach to study medicine, I started looking at chemistry university courses.

While applying to a few of these courses, a family friend gave birth to a son, Oliver, who was sadly born with a rare and aggressive tumour in his arm. Unfortunately he only survived 5 months but since then his parents have been able to raise huge amounts of money for research into childhood cancer, including funding a PhD studentship. When Oliver stopped responding to his treatment, I started to look into how chemistry is used to design new medicines and found myself attracted to chemistry courses with drug discovery streams.

I spent 5 years at University of Strathclyde where I attained a First Class MChem Chemistry with Drug Discovery. This is an integrated masters degree, a year longer than a conventional chemistry degree and includes a year in industry. These types of degree are becoming increasingly common in science subjects. During my placement year I spent time as an R&D intern at Corden Pharma Switzerland. They are a contract manufacturing pharmaceutical firm who make all sorts of different compounds for different customers and I learned a breadth of different types of chemistry while there.

I was um-ing and ah-ing during this placement year over whether to continue my studies, as a PhD was the usual next step in a chemistry career. In the end I realised a PhD would be challenging but would allow me to develop lots of skills and allow me to progress more quickly in a pharmaceutical career, plus there were still many options open to me afterwards.

I decided against a PhD focussing purely on organic chemistry as I was attracted to the idea of making and testing drug compounds I made myself. While this narrowed my choice in PhD options I ended up being offered a project at Sussex Drug Discovery Centre, an interdisciplinary group seeking to discover novel therapeutics for diseases with high unmet medical need.

The title of my project is currently ‘Enabling Drug Discovery in Genome Stability Targets to Target Cancer’. This involves the design and synthesis of novel small molecules which will perhaps in the future allow the design of cancer drugs that stop cancer cells from repairing their own DNA. I spend a lot of my time in a chemistry lab running different reactions to prepare molecules which are then tested by a biologist – but hopefully by me in the future – to see if they stop this process of DNA repair. I also spend time at my desk analysing data, writing up my lab book and various reports, reading journal articles and regularly presenting my findings to my research group.