Reflections on second year

shallow focus photography of yellow star lanterns
Photo by 嘉淇 徐 on Pexels.com

This is my last week in the lab of 2018. It’s only really four days because we’re having our group’s Christmas party on Friday (laser quest and pub lunch) and then I’m at a conference on Monday before taking the rest of the week off before Christmas.

Towards the end of first year I wrote this post about how I thought first year had gone and I listed 5 things I wanted to change. In this post I’m going to see how I did with those goals and create 5 new goals for third year.

  1. Read more papers – I managed this one quite well. In first year I sporadically printed and read papers but this year I got organised and set up an RSS feed and have been pretty good at checking in with it most days – perhaps a little too often with my “inbox zero” tendencies. I use Mendeley to save anything I come across that might be useful for my project. I tried #365papers  and failed miserably though, partly due to me losing the spreadsheet I was keeping track of papers on in an IT nightmare but also me just not getting into a habit.
  2. Make more compounds – I certainly achieved this one. First year involved trying a lot of new chemistry and at the start of this year I optimised a lot of that chemistry making it far easier to get final compounds out. For example, one set of molecules I made last year took 8-9 separate reactions to get there and now with a small change to the chemical structure that I’ve learned doesn’t kill the activity of the drug in most cases, I can get to those compounds in 2-3 steps.
  3. Be more selective in the seminars I attend – In first year I felt I had to go to every single seminar to widen my knowledge but as you specialise you learn what interests you and what a good use of your time is. I still go to the odd seminar outside of my research area so I’m not in too much of a rabbit hole, but I certainly feel like I’ve been using my time a bit better when it comes to seminars.
  4. Attend more conferences – having only been to one conference in first year, I went to a few in 2018 – and still have one to go next week! I started the year by attending the Genome Stability Network Meeting in Cambridge in January, in March I went to the RSC-BMCS Mastering MedChem conference at University of Strathclyde in Glasgow, then RSC/SCI Kinase 2018 in May, again in Cambridge, and still have the RSC Biotechnology Group Chemical Tools in Systems Biology in London a week today.
  5. Use this blog more – this one I’ve technically achieved in the last month or so. Most of the year I found myself “procrasti-blogging” sporadically blogging if I was taking part in a science writing course where an assignment involved writing a blog or the Google Doodle of the day was linked to chemistry. Now I’m making a concerted effort to post regularly on here and also on my dedicated Instagram account.

I think I’ve done quite well in meeting all of those goals. They were fairly realistic goals without quantification. Now here are my goals for third year:

  1. Keep using this blog – weekly blog posts, a couple of Instagram stories/posts a week. Over Christmas I’m going to make a longer term plan for content and schedule as many posts as I can so it doesn’t take up too much of my time during term time. Let me know if there’s anything in particular you’d like to see.
  2. Get the desk/bench balance right – I continue to struggle with staying at my desk more often than being in the lab. Often I choose reading, agonising over lab book/write-up and writing off lab tasks to “tomorrow” that could be done today rather than making stuff in the lab. If anyone has any tips about this please let me know in the comments.
  3. Get something published – I have something to show for my research and I really want to get some of it published in a medicinal journal to show alongside my thesis at the end of the PhD. I’m waiting for some long-promised data from a collaborator which will help supplement my work but I’ve agreed with my supervisor that in February I need to start writing papers for publication without that research.
  4. Speak at a conference – similar to above, I have a sufficient story to tell that I would love to give a talk about just once about my research at a conference rather than just standing beside a research poster at said conferences where people may or may not come over to hear about it. I’d also like to go to a conference outside of the UK because travel is one of the perks of being in research.
  5. Finish the practical side of the project well – I plan to spend another year in the lab before writing up. I have until March 2020 technically but I’m leaving those three months as a “backstop” of sorts – #relevant. I have in my head I’d like to get to 100 final compounds for my thesis (I’m about two thirds of the way there so it seems tangible) and I’d also like to spend some time in the biology labs my group have testing some of those compounds.

Hopefully this time next year I’ll be writing a similar post about how well I did in achieving my third year goals. It’s crazy it’s got to my last year in lab already!

Did you make any goals/resolutions for 2018? Did you achieve them? If not, are you going to reattempt them in 2019? Let me know in the comments below.

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.