Chemistry – The Chemistry of a PhD

July 23, 2019July 23, 2019

Six tips to survive a heatwave working in a chemistry lab

Fiona in lab coat and specs holding a thermometer looking hot and bothered — Feeling hot and bothered

With a heatwave well under way in the south of the UK (which includes Brighton where I’m studying), folks are preparing for some serious heat! As a Scot, I do struggle with the southern climate compared to my baltic homeland. Towards the end of today we clocked on our thermometers it was 29 °C inside our lab while it was a balmy 32 °C outdoors.

The chemistry building I work in is a trusted building, meaning it can’t be altered for the sake of protecting the original architecture. As chemists don’t work with cells and live tissue, we don’t need to keep our labs at optimum temperature for our experiments to behave – if anything, a little heat makes them go a bit faster!

Concertina filter papers on a lab bench — Pre-flutted filter paper, or fans?

We are also required to wear full-length trousers and covered shoes when working in the lab, and this is before donning lab coats etc. At times, I am rather jealous of my friends and colleagues in biology who get to work in temperature-controlled surroundings with a slightly less strict dress code because of the nature of their work.

Over the past couple of years during my PhD, I have learned how to cope with working in a non-air conditioned chemistry laboratory. Here are my tips for keeping cool in a chemistry lab.

1. Get a bigger lab coat (and gloves)

Fiona smiling in a large lab coat — Enjoying my tent of a lab coat

All chemists handling potentially hazardous chemical substances are required to wear a lab coat, safety specs and gloves as part of their prescribed protective equipment (PPE). If you spot a spare coat in a size or two bigger than you’d normally have, why not swap your usual coat for it and enjoy the swish of the cotton about your knees to keep you cool? Similarly, go up a size in gloves if they fit reasonably well and allow you to continue your work.

2. Plan to do all your temperature-sensitive reactions

Dry ice sitting in a container with mysterious fog coming off it — Dry ice, ice, baby

Need to carry out a low-temperature reaction in a heatwave? Excellent! To control the rate of certain reactions, they need to be kept at a low temperature. Sometimes they only need to be cooled to 0-5 °C using iced water but sometimes they need to be as cool as -78 °C using dry ice (solid CO₂) or liquid nitrogen (N₂). Yes, you’ll need to top up your ice bath more often in the heat but at least it’s cold stuff you’re handling!

3. Run endothermic reactions

There are typically two types of chemical reaction in terms of how energy is transferred in the making and breaking of chemical bonds between starting materials and products. Some reactions are “exothermic”, in that they lose energy in order to form the desired chemical products (usually lost in the form of heat energy), or they are endothermic, where they do the opposite and take in energy from their surroundings, typically getting colder, and that energy gets stored up in chemical bonds. Running endothermic reactions means some of the energy around you, is literally being changed into chemical energy and removed from your environment.

4. Hang out in the NMR lab more

Fiona giving a thumbs up in the NMR lab — All the cool chemists hang out in the NMR lab, literally.

NMR stands for nuclear magnetic resonance. It’s an analytical technique that tells chemists about the general magnetic environment their molecules are in. These experiments are usually carried out on NMR instruments which require substances like liquid nitrogen and liquid helium to keep them running, which naturally leads to the NMR lab being a bit cooler. During the summer months, I tend to linger in the NMR lab a bit longer than usual when running my experiments because it is generally a few degrees cooler than my lab or office. Why not bring a paper and wait for your 30-minute experiment to finish running?

5. Bring spare shoes!

Most chemists aren’t spending 100% of their time in the lab. If you happen to have office space ouside of the lab, take the opportunity during your down time between experiments/analysis runs to slip on a more comfortable pair of shoes. I frequently swap my trainers for flip flops if I know I’m going to be sitting at my desk doing NMR analysis for half an hour. Just remember to switch back to your more substantial shoes when you go back into the lab!

6. Finally, take it easy

It’s easy to get stressed in warm weather but it’s not really wise (or safe!) to be running around the lab when you’re hot and bothered, trying to do everything at the same pace as when you don’t notice the temperature. Take your time, be careful handling stuff and if your lab is too hot to safely work in, it’s not safe to work in and there’s really nothing you can do about it. I was sent home from a summer placement one day during my undergrad because it was too hot for the fume hoods in the lab to extract chemical fumes properly. The chemistry can usually get done another time so go and take a chill pill – which should probably be in the form of going outside to enjoy the warm weather with an iced coffee!

I hope you found these six tips useful – or amusing at least – as you carry out your work in the warm weather. A huge shout out to those who don’t get a choice about the nature of their work when the weather changes. Keep hydrated, stay cool and protected from the sun as much as you can if working outside.

How do you find warm weather? Can you work in all climates? How do you cope in extreme weather, hot or cold? Let me know in the comments below.

March 31, 2019March 25, 2019

PhD Update: 2019 Q1

This is the last year I’ll be spending in the lab before writing up my PhD next year. I thought it would be useful for me to blog where I am now and what I still need to do in terms of my research about once a quarter. Now that we’re at the end of March it’s time to review the last three months!

A selfie of me looking quite grumpy about some data I'm holding - a printout of a large table with lots of big numbers highlighted in red, orange and yellow

Third year started off with a bit of a rollercoaster. I had received some data back just before Christmas that I had been waiting about six months for. Most of the time I’ve been seeing how good my molecules are at shutting down one or two kinase enzymes. This experiment was slightly different in that it tested my six best molecules against hundreds of them – about 400 of the 518 found in the human body.

When I got the data back I thought it was bad news: the numbers were big for a lot of my kinases and I assumed that was a bad thing. I thought my molecules shut down far too many other kinases in addition to the one I wanted them too. This is typical of a kinase project because kinase enzymes are very similar in their shape.

It wasn’t the end of the world because I was still contributing something new to the field – you can’t drug my particular kinase. I started planning final experiments to make a few more compounds that would nicely round off my thesis to show I had tried all the sensible versions of my compounds as well as some potential new ideas to try and salvage my project.

Unfortunately, it took my collaborator who had organised the experiments a few weeks to get back to my e-mails for him to tell me I had my numbers mixed up! In this particular experiment, big numbers were good news! Very good news in fact! My best molecule only shut down 9/400 kinases.

Fiona looking embarrased with her hand over her mouth realising she made a mistake — Picture caption: Fiona standing in front of a redbrick wall with her hand over her mouth, realising her mistake

It was a huge relief in some ways that my project wasn’t, in fact, dead, but I was annoyed I had wasted a month taking my project in a completely different direction. What encouraged me though was the amount of stuff I had learned over the past couple of years and how I was able to come up with a few options for my project by myself.

Since then I’ve been working on some molecules that will round of ideally two chapters of my thesis, saying goodbye to two sets of compounds I’ve made that haven’t worked quite as well as the others. This has proved quite tricky as I’m trying to make a molecule no one seems to have made before – and as the weeks of failed chemistry go on, I can see why!

Picture caption: A gloved hand holding three sealed glass tubes containing failed reaction mixtures of black goop. Experiment numbers 165/166/167 written on the lids.

Once I get these molecules out the way I can focus on making smaller changes to my best compound to tweak it so that it only hits 1 kinase. That way when biologists use it they can be sure when things happen in the cancer cells they treat with my molecules, they can be relatively sure whatever change they see is due to shutting down that particular kinase.

I’m about to send away a set of compounds that will determine how long my chemistry route is going to be to each compound. At the moment, the best compound requires 9 individual chemical reactions to get to the final compound which is a lot of work for each compound! It’s because of a nitrogen atom present in a particular place that the chemistry is so longwinded.

I was able to make molecules that removed that nitrogen or moved it to another place in my compounds and swapped it for a carbon atom which reduced that chemical route to 3 chemicals steps! I’m hoping the version of the molecule where I’ve moved the nitrogen to a slightly different place will allow me to keep using a shorter chemical route, otherwise, it’s back to the long route I spent ages on in first year!

In the middle of March I attended a conference called Mastering Med Chem that was being held at the site of a pharmaceutical company called Eli Lilley based in Surrey, just a couple of hours up the road for me. I went to the conference last year and I was really encouraged coming across familiar faces and having a greater knowledge of the field in the talks I was listening to. To get a special discount I took a research poster with me and hovered beside it during coffee and lunch breaks just in case anyone wanted to talk about my research with me – which a few people did!

Fiona in business attire and wearing a conference lanyard standing in front of her A0-sized research poster summarising her PhD with a mixture of images and text. The poster title says "Design and Synthesis of Novel PRK2 Tools to Probe Cancer" — Picture caption: Fiona in business attire and wearing a conference lanyard standing in front of her A0-sized research poster summarising her PhD with a mixture of images and text. The poster title says “Design and SYnthesis of Novel PRK2 Tools to Probe Cancer”

Across all my channels (Twitter: @fi0n0 and Instagram: @thechemistryofaphd and on this blog) I started my #positperiodictable series where most weeks I post about an element of the periodic table to mark the 150th anniversary of Dmitri Mendeleev presenting his method for organising the elements to the world. I’ve managed to post the first 6 groups so far, 18 plus the f-block of superheavy radioactive metals to go!

I have also been trying to collect all the data for the molecules I made between October and December last year. I just have three more compounds to finish, then I can write up that bit of my thesis. I’m glad I’ve stuck with writing this part of my work up in thesis style, called the experimental section because it will save me a lot of time in the future.

So, in summary, after briefly thinking my PhD project was over, I’ve been trying to make some compounds that will round of large segments of my these I’m nearly there, and I think after the ups and downs of January, I don’t think I’ve been as motivated to be in the lab as much as I could have been but hopefully the next quarter will be better.

In terms of other things that happened this quarter, I enjoyed a short surprise holiday to Vienna with my partner, celebrated my 26^th birthday, played in the Royal Albert Hall and got to do some fun science communication stuff on campus and in the London Science Museum so I’d say it’s been a pretty good few months. Just need to get on with the science I’m supposed to be doing!

Picture caption: Fiona holding a violin sitting on the stage of the Royal Albert Hall with her orchestra desk partner Ouli.

How’s the start of 2019 been for you? Any highlights or challenges? Let me know in the comments below.

March 29, 2019March 25, 2019

What’s on my lab bench?

Most people have a desk as a place of work. I’m lucky enough to have three workspaces as a chemist: my desk, my lab bench, and my fume hood, all for different aspects of chemistry research. Today I’m going to give you a tour around my lab bench!

labelled lab bench.png — Picture caption: Fiona’s busy lab bench with different items labeled, from the sink to the sample vials!

My lab bench is used to carry out low-risk tasks involving my chemical samples. Most of the work I do when handling and manipulating my reactions is carried out in a fume hood to reduce my exposure to them but small analytical tests and sample preparation can b carried out on a bench – unless my sample is particularly smelly which thankfully not many of my compounds are!

I share a sink with another chemist in my lab where we wash up our glassware. We’re a bit like a student flat in that neither of us like putting the glassware away in the cupboards so take stuff directly from the drying rack which can turn into a mountain of conical flasks and beakers sometimes!

While I use an electronic lab book for my final write-ups, I keep a rough note of what I’m doing for each experiment in these blue and while notebooks and transfer it to the ELN at the end of the experiment. If I had to grab one thing in the event of a fire, it would be these notebooks as everything else I do is digitally backed up!

I keep final products in these sample vials before transferring them to smaller ones for archive storage about once a quarter. I draw the chemical structure on the yellow circular labels to help me find samples quickly. I try to keep my samples in chronological order but it doesn’t always happen so you’ll often find me hovering over these boxes trying to find vial such and such.

Although the picture doesn’t show it too well, I have to boxes of glass pipettes on my side of the bench, individual disposable glass droppers. I have a rubber atomiser that I attach to them when I need to transfer small quantities of liquid between flasks etc. and then the glass pipette gets recycled. We have two lengths of pipette and I seem to get through the shorter ones a lot quicker than the longer ones.

The tip-ex isn’t actually for correcting written mistakes in my notebooks – I tend to just scribble. I actually use it to mark sample lids so I can differentiate them as my own from my colleagues when using shared equipment. Our group has to use black lids for our NMR tubes so I found it a simple way to identify my samples from the dozens than go on the NMR instrument carousel.

I use a ruler for drawing straight lines on my TLC plates and for measuring the distance between spots once I’ve run TLC experiments (see my How do I know I’ve made the right molecule post).

The small tubes in the little beaker are how we store samples long term. They’re obviously a lot smaller than the glass vials and we typically have less than 0.1 g of a sample left after using what we need for future chemistry. We also use these tubes for transporting samples because they have individual bar codes on them. These are six compounds that I’ve taken out of archive storage for my colleague in biology to come to get whenever she needs them.

The conical flask on my desk contains empty NMR tubes, long skinny glass tubes used to prepare a sample for a particular type of analysis that investigates the magnetic character of the compounds – again see my previous post for more detail. The tubes are capped with the black lids I cover in Tipex.

I don’t keep many chemicals on my desk but these two are for a public engagement activity I’m doing with schools soon and so because they weren’t bought using the group’s research budget, need to be stored separately from the other chemicals I use, which are typically stored under my fume hood or in one of our several filing cabinets.

A calculator is a chemist’s best friend for double checking sample dilution factors and scaling reactions up to bigger quantities (like doubling a recipe). My electronic lab book does a lot of calculations for me but there are always some that need to be done manually like converting concentrations units from % to molar etc.

I hold on to my NMR samples until I’ve definitely got everything I need to write-up an experiment. Cleaning these tubes out isn’t the most fun job in the world so I tend to wait until I have a lot of tubes to clean before the repetitive task of rinsing them out.

My colleague and I share a number of things on our bench like sample vials and empty plastic columns for purification. We try to keep them topped up for each other.

Every chemist needs gloves for handling chemicals. I try to not get through more than a couple of pairs of gloves a day having mastered the technique of removing them in such a way that they can be worn again if I know I’ve been particularly careful and not got much on them.

My green tray has samples ready for being archived. I got this from a colleague who was leaving and it’s the perfect size for storing out mini sample vials. Scientists are a bit like vultures when they know there’s a free for all during a lab clearout or someone moves job, we become quite territorial about our pieces of lab kit.

My cardboard box has random bits and pieces in it like pencils and stickers for my lab vials.

I also have a mountain of plastic rings for storing round-bottomed flasks – spherical pieces of glassware that as you can tell by the name don’t stand up very well on their own.

Sometimes I get deliveries in the post in boxes that I bring into the lab. This tiny box was the perfect size for storing my TLC plates.

The laminated sheets are for writing the reaction schemes for what’s going on in my hood if I’m leaving a reaction on overnight. It allows colleagues and security to check a reaction is running at the temperature it is supposed to and hasn’t randomly heated up or cooled down overnight.

Lastly comes my vacuum pump which is attached to my rotary evaporator. My rotary evaporator, or “Buchi” as they’re named after one particular brand that makes them, is a bit like a kettle. Attach round-bottomed flasks to it and boil off liquid solvents that I’ve dispersed my reaction in. The vacuum pump allows me to boil te solvents off at much lower temperatures than usual.

You may know about the phenomenon where water boils at a lower temperature at the top of Everest due to the reduced air pressure. My Buchi takes this to the nth degree by creating a vacuum and can actually boil water off at 40 °C! The samples sit in the water bath which is warmed to my desired temperature and rotates to maximise even distribution and mixing of my reaction mixture while also creating a thin film of solvent which then evaporates more easily.

The shelf above my bench contains frequently used chemicals for reaction work-ups/purifications. It includes various acids, bases, substances for removing water, stuff for preparing columns and my NMR solvents. We also have parafilm, a bit like clingfilm, used to seal vials and chemical bottles to stop samples or reagents from going off.

I hope you’ve enjoyed my lab bench tour. Stay tuned for future posts about my desk and fume hood.

What’s your working space like? Let me know in the comment below.

February 22, 2019February 22, 2019

#postitperiodictable Group 2

The second column elements of the periodic table are known as the alkali earth metals. They are like group 1 in that they are relatively soft metals that react with water to produce hydrogen gas however they don’t react as vigorously.

Picture caption: post-it note showing beryllium, element number 4, is used to make springs in electronics

This is due to the group 2 elements having 2 outer electrons instead of one. This is a slightly more energetically favourable electron configuration, meaning the atoms in group 2 are happier with two electrons whizzing around the nucleus than group 1 metals are with their single electron, who just want to give it away as quickly as possible to form their preferred state as a positive metal ion (M⁺, where M stands for a metal).

Picture caption: post-it note showing magnesium, element number 12, plays an important role in photosynthesis, the process by which plants use light energy to convert carbon dioxide and water into glucose and oxygen gas – the reverse of what our bodies do.

Group 2 metals aren’t precious about their two electrons though. They are also happy to exist as positive metal ions that have lost their negatively charged electrons, but they tend to form M²⁺. If they formed M⁺ they would then have a similar electron configuration to a group 1 element which we know isn’t very stable and would get rid of that second electron as quickly as they can.

Picture caption: post-it note showing calcium, element number 20, which makes up a significant component of our bones

This relatively lower reactivity means that group 2 elements are often used in portable hydrogen generators because they release hydrogen slowly enough that there isn’t sufficient heat energy given out over the course of the reaction to ignite the flammable hydrogen gas – which is what we see when group 1 metals react with water.

Group two metals are shiny and usually silvery-white in colour. Some occur naturally as free elements but are often found as ores (typically metal oxides) in the ground and the metal needs to be extracted from those compound mixtures.

Picture caption: post-it note showing strontium, element number 38, which is used to make fireworks appear red in colour

Much like Group 1 the reactivity of the metals increases going down the group because the outer electrons become further away from the nucleus with the increasing number of electrons moving around the nucleus, making them easier to remove – much like how a paperclip becomes easier to manipulate the further away it is from a magnet.

The metals react with water to form metal oxides but because of their 2-electron valency, they form hydroxides with the general formula M(OH)₂ as hydroxide (OH^–) ions have a single negative charge so two are needed to balance the double positive metal ion (M²⁺). Beryllium is the exception which has a sufficiently protective oxide layer.

Picture caption: post-it note showing barium, element number 56, rarely used but can be found in some paints

They also react with oxygen to form metal oxides and with halogens, such as chlorine, fluorine etc., to form metal halides.

Throughout group 2 we’ve learned about beryllium’s niche role in missiles and rocket parts; the bright light burning magnesium produces which is used in old photography flashes, flares and fireworks; calcium’s key role in forming our bones and teeth and how strontium can be used to mimic calcium to treat osteoporosis; and the lesser used barium and radium which are used for treating digestive disorders and prostate cancer respectively.

Picture caption: post-it note showing radium, element number 88, which used to be used to be painted onto watches to make components glow in the dark

I hope you’ve enjoyed our tour of group 2. Now we move on to the central block of the periodic table, known as the transition elements which spans groups 3 to 10! Keep an eye on the Instagram account for individual posts about each element as well as other content about my life in the chemistry lab.

What’s your favourite element? How are you marking #IYPT2019 ? Let me know in the comments below.

January 14, 2019

What do the numbers on the periodic table mean?

2019 marks the UN’s International Year of the Periodic Table or #IYPT. It’s 150 years since Dmitri Mendeleev presented his organisation of chemical elements to the world. The periodic table is used daily by chemists and other scientists as reference resource for the ingredients of the universe.

dmitri mendeleev statue dmitrimendeleev.com — Picture caption: A statue commemorating Dmitri Mendeleev surrounding by a radial presentation of his periodic table, in source: dmitrimendeleev.com

Ancient Greeks defined “elements” as one of the following four: earth, fire, water and air. They were used to explain how matter worked. Since the elucidation of atomic theory, scientists have broken the universe down into 118 chemical elements.

the four elements learner.org — Picture caption: the four classical elements and the descriptors used to classify them. Source: learner.org

Atoms can be thought of as small particles that make up everything but even they are made up of smaller components, known as sub-atomic particles, and the number of sub-atomic particles in each atoms defines what element the atom is. The three sub-atomic particles we learn about at school are protons, neutrons and electrons. Protons, neutrons and electrons are made up of even smaller components but as I am not a physicist, I’m not so concerned about looking at matter at that scale.

atomic structure explainthatstuff.com — Picture caption: the structure of an atom – a central nucleus made up of protons and neutrons surrounded by fast moving electrons. Source: explainthatstuff.com

Protons are positively charged, electrons are negatively charged and neutrons, as you might guess from its name, are neutral. The number of protons and electrons in a neutral atom are the same in order to balance the charge. An atom’s structure is made up of a central nucleus made up of protons and neutrons with electrons whizzing around the nucleus.

Because the electrons are on the exterior of the atom they are the particles that are actually involved in chemical reactions. Electrons can be completely transferred from one atom to another – in a process known as ionisation which forms ions, charged atoms – or they can be shared between two atoms to form a chemical bond. The degree of sharing between two atoms dictates what type of chemical bond has formed.

bonding weheartit.com — Picture caption: cartoon depicting the different ways atoms share valence electrons to form chemical bonds. In a covalent bond electrons are share fairly equally between atoms; in metallic bonds the electrons are not associated with specific atoms; in an ionic bond one atom loses an electron for another to gain that electron and a coordinate bond occurs when an atom donated two electrons to another atom. Source: pearlsofrawnerdism.com

Most of an atom is made up of empty space: if an atom were the size of a football stadium the nucleus would probably only take up the space of a marble sitting in the centre of the playing ground!

A standard periodic table will usually have 2 elements associated with each element: the atomic number and relative atomic mass number of that element. The atomic number can be defined as the number of protons present in the central nucleus of the element’s atom while the mass number is the total number of protons and neutrons in the nucleus. The mass number is the larger of the two numbers found associated with an element in the table.

The mass number can be quantified by a constant (a number that is shown to stay the same across numerous calculations) called Avogadro’s number. Avogadro’s number is 6.02 x 10^23. Essentially, what Avogadro’s number describes is the number of atoms you need of a particular element for the weight of your sample to match the mass number in grams.

A single unit of 6.02 x 10^23 atoms is described as a “mole”. It’s a bit like saying you have “a dozen” eggs = 12 eggs. A “mole” of atoms is 6.02 x 10^23 atoms which, if your element is carbon, would equal 12 g because 12 is the mass number of carbon.

moles hinkhousescience.com — Picture caption: a happy cartoon mole placing 6.02*10^23 carbon atoms on a scale to make 12 g of carbon (aka one mole!) credit: hinkhousescience.weebly.com

The number of neutrons does not correlate perfectly with the number of protons, its more to do with the number of neutrons required to allow that number of protons to be in close proximity with each other while maintaining stability – imagine trying to force two magnets together. They repel, much like the positively charged protons do if they get too close together.

The presence of protons in the nucleus makes the nucleus overall positively charged and the electrons whizz around within the proximity of the nucleus because they, as negatively charged particles, are attracted to that positively charged nucleus.

As an element gets bigger – with more and more protons, neutrons and electrons packed into its structure – its properties change. The smaller elements at the top of the periodic table are gases like hydrogen (atomic number 1), helium (atomic number 2) and oxygen (atomic number 6) while the heavier elements towards the bottom of the table are metals like gold (atomic number 79), lead (atomic umber 82) and uranium (atomic number 92).

phases pt periodictable.com — Picture caption: periodic table coloured according to the phase (solid, liquid, gas) an element exists in at room temperature. Most elements are solid, coloured red; some gas (blue) and only two are liquid, bromine and mercury. Source: periodictable.com

Mendeleev chose to arrange the elements by atomic number rather than mass number and very cleverly left gaps because at the time there were only 56 known elements. He was successfully able to predict the properties of the yet undiscovered elements, such as germanium, gallium and scandium.

There are other periodic tables that have additional information on them such as the size of atoms, density of elements and melting points. Trends can be seen as you go along the rows and columns of the periodic table, which I may discuss in further detail in a future post. But normally the most basic ones have the atomic and mass numbers of each element on them, as well as the symbol used to abbreviate the element’s name.

desnity pt periodictabloe.com — Picture caption: Graphic showing the increasing density of the elements going down the periodic table and also peaking in the middle of the table going left to right. Source: periodictable.com

On my Instagram and twitter account I will be posting about each element over the course of this year and will summarise each column of the periodic table in a longer blog post here. I hope you enjoy exploring the periodic table with me this year along with everyone else marking #IYPT as we learn about the stuff that makes us and everything around us.

Did you learn about the periodic table at school? Do you have a favourite element? Let me know in the comments below.

January 2, 2019January 4, 2019

Science Conferences I went to in 2018

Over the course of a PhD, students are encouraged to leave the lab from time to time to go to conferences to learn about other kinds of research going on in their field. Science conferences gather researchers from academia and industry. In this post I will talk about the different conferences I went to in the second year of my PhD in 2018 and what I learned from them.

January – Genome Stability Network Meeting, Cambridge

The Genome Stability Network is a group of scientists interested in learning about how the DNA in our cells is damaged and repaired, usually with the aim of utilising these processes to treat cancer. At the start of 2018 I attended the annual meeting of the GSN and heard a lot of talks about different aspects of DNA damage and repair processes.

While I’m pretty sure I was the only chemist in the room – a lot of this work is carried out by biologists establishing the pathways by which these processes take place in cells – it was useful to see what themes emerged across the few talks.

March – Mastering Medicinal Chemistry, Glasgow

Picture caption: A metal sign at the bottom of some stairs pointing the way to the Mastering MedChem conference

I had the opportunity to go back to my old university, University of Strathclyde, where I completed my undergraduate MChem degree for a medicinal chemistry conference aimed at early-career researchers. The talks covered a whole range of disease areas and approaches and I also took a poster summarising my own research to talk to people about during the coffee breaks.

I learned about new unconventional ways of finding starting point molecules (“hits”) to start new drug discovery projects, as well as hear from someone from pharmaceutical company AstraZeneca about a project similar to my own. It was useful to exchange ideas with the speaker to help my own project.

There was also a panel where the speakers were asked about their outlook on the future of the drug discovery industry, which I sadly learned was sounding bleak on all fronts. RxNet asked me to write a more detailed conference report which can be found here.

May – Kinase 2018, Cambridge

Picture caption: Fiona giving a presentation to a group of scientists in front of a slide titled "Designing PRK2 tools to treat cancer". The slide has pictures of enzymes and chemical structures, giving a snapshot of my PhD project — Picture caption: Fiona giving a presentation to a group of scientists in front of a slide titled “Designing PRK2 tools to treat cancer”. The slide has pictures of enzymes and chemical structures, giving a snapshot of my PhD project

The first two conferences were relatively general in their subject matter. In May I returned to chemistry for a much more focused meeting around kinases.

Kinases are signalling proteins (enzymes that tell a cell to do something) and are implicated in many diseases, particularly cancer. There are 516 kinases in humans so there are lots of opportunities to target them in different ways to treat patients.

I learned a lot about the different disease areas kinases are being targeted for as well as what the trendy kinases were that a lot of researchers seem to be looking at just now.

At this conference I got the opportunity to give a 2 minute, single-slide “flash presentation” about the poster I had brought. While having such a small amount of time to sell my research was challenging, I noticed a huge difference between the number of people who came over to my poster to chat to me afterwards.

If you’re attending a conference and are nervous about applying for such a slot I highly recommend it, it’s over in a flash and resulted in many more useful conversations about my work than if I hadn’t done it.

December – Chemical Probes in Systems Biology, London

Picture caption: the entrance to a stately building, Burlington House in London, with "Royal Soc of Chemistry" in gold above the door. There is a Christmas tree and an old lamp post next to the door. — Picture caption: the entrance to a stately building, Burlington House in London, with “Royal Soc of Chemistry” in gold above the door. There is a Christmas tree and an old lamp post next to the door.

At the end of the year I popped up to the Royal Society of Chemistry’s headquarters at Burlington House to attend the smallest of the conferences I have been to. There were roughly 50 people present and was very relevant to my project – the title conference alone would work as a thesis title for my project.

I’ve found it encouraging to note over the course of the last couple of years I’ve become familiar with “names” and institutions in my field. The first talk was by someone from the institute I collaborate with on my project and another speaker was someone I had previously applied to do a PhD with.

I had applied to speak at this conference but my application was unsuccessful. I was still able to take a poster and the collaborator I mentioned gave me some useful insight about some data I had been waiting a while for regarding my project.

Hopefully I will get to speak about my PhD at a conference in my third year – and it would be especially nice to get to travel abroad to a conference.

Have you been able to travel anywhere exotic for conferences in your line of work? Were they useful to attend? Have you ever given a flash presentation before? Let me know in the comments below.

Christmas may feel like its over but I have one more day of my #12DaysOfChemistmas that I’ve been sharing on twitter and instagram.

December 24, 2018December 24, 2018

This Molecule Spells “Happy Christmas”!

It’s Christmas Eve! I hope you’re all getting to enjoy the festivities in some way, whether you’re taking a break from research/work with family and friends or taking advantage of it being quiet to get work done – or a special shout out if you’re one of the superheroes that keep the emergency services running over the Christmas/New Year period.

In true chemistry-geek fashion, I’d like to wish you a very Happy Christmas with this molecule!

MERRYCHRISTMASunlabelled — A Christmassy peptide

It might not look like it says much at first but let me explain the structure in a bit more detail. This is a peptide, that is a long chain molecule made up of individual amino acid components. The amino acid “links” are connected by amide bonds.

amide bond formation — An amide bond forms between an amino (NH2) and a carboxylic acid (COOH)

Amino acids are used to build hundreds of thousands of proteins that carry out many jobs in our bodies. There are 20 common amino acids which are typically found in biology and 9 of those are “essential amino acids”, meaning they can only be obtained by our diet and not synthesised by our own bodies.

The 20 amino acids can be categorised by their chemical structure. While all possess an amine (NH2) and a carboxylic acid group (COOH), hence the name “amino acid”, they contain side chains that branch off a central atom between the amine and acid groups.

These side chains can be categorised as to whether they contain a greasy aliphatic group of atoms or something containing an alcohol, sulfur, acidic or basic group. Andy Brunning’s infographic summarises this really nicely.

20 Common Amino Acids Physiological [EDIT].png — Amino Acid summary produced by Andy Brunning of Compound Interest

Because peptides are lengthy sequences of amino acids, its easier to abbreviate the individual amino acid chains with individual letters to succinctly describe the amino acids present within a protein:

H – histidine, a basic amino acid containing an imidazole heterocycle (ring of atoms that isn’t just made up of carbons and hydrogens)

A – alanine, one of the simpler aliphatic amino acids with just a methyl side chain

P – proline, the only amino acid that incorporates the amino acid motif into the side chain.

P – another proline

Y – tyrosine, an aromatic amino acid (contains a hexagonal benzene ring) with an alcoholic phenol OH attached.

C – cysteine, the other sulfur-containing amino acid

H – histidine, another basic amino acid

R – another arginine

I – isoleucine. Leucine is a straight chain of three carbons. Isoleucine is an “isomer” of leucine, meaning those atoms are arranged slightly differently

S – serine, an alcoholic amino group

T – threonine, the third of the three alcohol containing amino acids (serine, threonine and tyrosine). It has a slightly longer carbon chain than serine. The kinase proteins I’m trying to target in my PhD reacts with these kinds of residues in our cells.

M – another methionine

A – another alanine

S – a final alcoholic serine caps the end of our festive molecule

With that, I’d like to thank you all for following my scientific escapades so far and wish you all a Christmas period full of peace and joy and all the best for 2019.

MERRYCHRISTMASLabelled — My labelled festive peptide wishing you a HAPPY CHRISTMAS

How are you celebrating Christmas? Do you have any fun abbreviations in your work? Let me know in the comments below.

November 26, 2018November 26, 2018

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.

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

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.

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.

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.

liquidnitrogenPACA — 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.

November 19, 2018November 19, 2018

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).

ethanolnmr — 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.

***

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.