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It is now the end of June, so its time to reflect on the second quarter of the last year of my PhD. Did I achieve everything I set out to do? Read on to find out…

I did manage to send away the set of compounds I was talking about last quarter – the ones that would define the end of two results chapters of my thesis and the chemistry I plan to do for the rest of the year. I’ve received half of the data back about them, and it seems my compounds made by the shorter chemical route seem to work about as well as the ones made by a longer route.

Unfortunately, I don’t have all the data back. I don’t have the information about a potential side effect my drugs might cause. This side effect may be caused by my drug fitting into an enzyme that’s very similar in shape to the one I specifically want to investigate with my drugs. I need that “selectivity” ratio (i.e. how well the drug shuts down one enzyme vs another) to be better than my best compound so far (it’s a 7-fold different at the moment) otherwise I’ll need to go back to my old chemistry which took a lot longer to carry out.

Usually, I get both sets of data at the same time, but my collaborator has been having issues with setting up the “side effect” experiment, which is unfortunate timing, but these things happen. Hopefully, she’ll have managed it before the start of next month. Otherwise, I can either send the compounds to a company to run the same test or make a guess and get on with the faster and easier chemistry in the process. My current “to make” list seems to have a lot of easy-to-make compounds that don’t seem to have been made before, so there is value in making them despite not having all the information I need to justify making them over other compounds.

I mentioned I’ve made some of the compounds that will wind up other chapters of my thesis. There were two on the list that I have been struggling to make for a very long time. It’s got to the point where I’ve put a pin in those for now, so I can focus on trying new things. After several months of trying to make the same compounds, I’ve had enough. It may well be that with current chemistry techniques and reactions, it isn’t possible to make the particular molecules which I have in mind – which is still new to the field.

I have written up these two sections of my project in paper form for the last month or so and once I get some repeat experiments run by my collaborator I should be able to submit those papers to journals and hopefully get that chunk of work out there – even if it wasn’t successful, I’ve still made some brand new compounds that don’t seem to have been made before which someone else could apply to a different project. This is the first time I’ve tried writing papers and the words have come relatively quickly, which I think is thanks to me spending a lot of time writing as a theatre critic/interviewer in my spare time. Keep those hobbies up, you never know where those transferable skills might come in handy.

I also received some bonus good news regarding papers: I found out some compounds I made in 2015/2016 as part of my master’s project are being included in an article so I might get another publication to my name as well! That project shows how long it can take to discover new things in the early stages of drug discovery. I made that compound 3 years ago, and it’s only now that the biologist I made it for has a nice rounded research “story” to share with the world.

In terms of science communication stuff, I really enjoyed taking part in Soapbox Science Brighton. I got to stand on a soapbox on Brighton beach and share the similarities I’ve found between baking and medicinal chemistry. It was a lot of fun to speak about science in such a unique space!

I tried out that talk for the first time at another event called PubhD in Hackey, London and led other drug design workshops at Sussex University and the London Science Museum. I’m doing well at keeping the science communication stuff to weekends or short periods on campus so I can get on with other work – I’m usually far too good at saying yes to distractions.

I visited another conference, a longer one this time in Ghent, Belgium. It was called Bioheterocycles 2019. I got to give a 15-minute talk about my project which seemed to be well received and enjoyed the mixed programme of interesting chemistry talks and social events including a boat tour, banquet and Belgian beer reception.

Non-science stuff included playing in orchestras for some concerts in the Albert Hall in London and the Usher Hall in Edinburgh; I’ve moved to a flat of my own for the last six months of my PhD and I enjoyed a trip to Warner Bros Studios and a little holiday to Centerparcs to celebrate my partner Darren having his birthday and passing his thesis defence – I’m very proud of him and hope to be in the same position as him by this time next year!

Over the next three months I aim to submit those two papers; have a productive couple of months in the lab making some finer tweaks to my best compound to make it even better; as always, get up to date with my data analysis and experimental write-up; do some theatre reviewing at the Edinburgh Fringe in August and attend another conference in Athens in September which I have just secured a grant to attend. This is the beginning of the end!

How have the past few months been for you? Do you have plans over the summer? Let me know in the comments below.

This is the 2nd post in a series of showing how I work. Today I’ll show you around my fume hood. A fume hood is a ventilated cabinet with a retractable hood where I carry out most of my chemistry to reduce my exposure to chemical fumes.

Sometimes you have a to share a fume hood with another chemist if there’s a shortage of space but I’m lucky enough to have whole fume hood to myself in this lab, especially as this one isn’t very big. In my undergraduate studies, I was usually sharing with one or two other chemists in larger hoods – it was a bit of a squeeze! My fume hood on placement ran up to the ceiling so I could actually stand up inside it when I cleaned it at the end of my placement year, which was a rather surreal experience!

On the side of each hood are various taps for various things. One is for water, while others provide a flow of compressed gas or nitrogen gas when I need them. When reactions need to be run under unreactive conditions are stirred under a constant flow of nitrogen gas, or another unreactive/inert gas like argon to stop the usual reactive oxygen and water vapour from reacting with the chemicals.

The brown bottle, or “Winchester” as these 2.5 L glass bottles are known, is a recycled solvent bottle where I put my solvent waste. Liquid chemicals that I am finished with are poured into these bottles and once full, disposed of by our technical services.

Chemical waste in organic labs is typically separated into two classes – halogenated and non-halogenated waste – but this can vary depending on the contract a lab has with a waste disposal company. Halogenated or non-halogenated refers to group 17 of the periodic table, the halogens (chlorine, fluorine, bromine, iodine, etc.) and essentially if the major component of the reaction mixture contains one of these elements, it needs to go in the “halogenated” waste while anything without those elements goes in the “non-halogenous” waste. The reason they are separated is that combination of some halogenated and non-halogenated species, e.g. acetone (CH3COCH3) and dichloromethane (CH2Cl2) results in a chemical reaction! It’s very important to keep your waste separate.

The efficiency of a reaction can be measured in terms of how much product you get relative to the amount you calculated from the starting material, expressed as a percentage yield, but increasingly, in terms of how much waste is produced per g of material. Some reactions create very little waste but sometimes I can fill a Winchester of waste in a day if I’m running a  lot of purifications which use lots of solvents.

I have a yellow and orange sharps bin for disposing of any sharp needles I use in my reactions. Syringes are frequently used to add precise quantities of a liquid reagent to a reaction mixture.

The metal bars are used to clamp different pieces of glassware in place using all manner of knobs and handles. I like to have a portable clamp stand in my hood because my hood has fewer bars than some of my colleagues.

Any sample vials I have in my hood typically have a final product in them that I’m waiting to dry. The constant extractor fan that’s running makes it useful to transfer chemical products by dissolving them in a volatile solvent that evaporates easily. Once dry I transfer lidded samples to my bench.

Ongoing reactions tend to be in various round-bottomed flasks (RBFs). RBFs, as the name would suggest are spherical pieces of glassware with different fixtures to connect with different lab apparatus. TO hold them upright I use cork rings, made of actual cork or plastic, to store them in the hood. I typically have more than these in my hood but this was my “tidy hood” before Christmas.

When reactions need to be heated I typically use a magnetic hotplate stirrer like these two in my hood. The hotplates work very similarly to the ones used in cooking and have dials to control temperature and extent of stirring. I stir my reactions by adding a little magnetic pellet into the reaction mixture which sits atop a spinning magnet within in the hotplate. The spinning magnet causes the pellet to stir which means I don’t need to stir the reaction by hand – useful when you’re doing multiple reactions at once.

I also have a temperature probe that allows me to set a reaction at a particular temperature and keep it there. Once or twice I’ve forgotten to put the probe in my reaction mixture which causes the hotplate to continue heating up and “nuke” my reaction, which is not a good sight to come back to. Hotplates only going up to 300 °C or so.

My hood also typically contains racks of test tubes from column purifications. These racks are full of mixtures that have been separated into their components by running them through a column of silica gel – the little bags you find in new shoes and bags to absorb moisture. Much of my time is spent rinsing out these test tubes into my waste bottle when I’ve isolated the products from the test tubes I need.

My Thin Layer Chromatography (TLC) tank is where I run larger TLC analytical experiments, otherwise, I use a beaker for plates that aren’t as wide as the one pictured. You may have carried out a separation of pen inks in school using paper chromatography. TLC works by the same principle of allowing a liquid to run up a rectangular plate of silica to see how many components are in a reaction mixture, indicated by the number of spots seen on a plate after it has been run.

Finally, the manner of glass tubes in my hood is known as a Shlenk line and allows me to control the flow of nitrogen gas and vacuum into my hood. I can use the various taps to connect to my reaction mixtures and remove the air form them using the vacuum pump just to the outside of my hood, then flood them with nitrogen, and repeat a few times to make sure I’ve got rid of most of the air.

So there you have it. I hope you’ve enjoyed this tour of my fume hood and how I use everything in it. I’ve spent many hours standing at this hood during my Ph.D. and it helps to contain my spills and mini explosions to keep me safe from chemical harm.

I try to tidy my fume hood at the end of the day, cleaning up any spills, removing all unnecessary glassware as it can get pretty busy with several reactions and multiple flasks on the go at once! I give it a deep clean every so often before I go on holiday when I tend to have less stuff in it.

I hope that’s given you a flavour of what goes on in a fume hood. Usually, a school science classroom will have one for storing certain chemicals but in research, they’re used daily! Stay tuned for future posts about my desk and organisation system.

If you’re a chemist, what’s your fume hood like? Otherwise, what’s your main working space like? Let me know in the comments below.

Every day last week I posted about each element in the first column of the periodic table to mark the International Year of the Periodic Table on my instagram account. Elements are grouped in columns based on their properties and in this post I’ll talk about how the group 1 elements are chemically similar.

On the extreme left of the periodic table lie the alkali metals. Alkali because when they come into contact with water they form alkaline species e.g. lithium forms lithium hydroxide.

Hydrogen is a bit of an anomaly for this group but technically belongs to group 1 because like its fellow members, it only has one outer shell electron, known as a valence electron, available to interact with other atoms.

This single electron is what makes these elements so reactive because atoms prefer to have full stable complements of electrons and they are eager to rid themselves of this electron, which is relatively easy to do, in order to gain a more stable electron configuration.

Aside from hydrogen, alkali metals are soft metals that react with air and water, meaning they are rather fun to through into a lake. When they react with water they release hydrogen gas, some in more violent ways than others.

Their flammability and reactivity increase going down the table. The YouTube channel Periodic Videos have some really nice videos demonstrating these reactions.

Lithium is a slow burner and takes its time converting to its metal hydroxide. Sodium will fizz while potassium bursts into violet flames. Rubidium and caesium explode when they contact water while francium is too radioactive and usually explodes without needing to be hydrated.

Alkali metals also react with oxygen to form metal oxides, or in the case of hydrogen, forms water, one of the key molecules of life. We are made up of 55-60% water.

They also react with halogens (group 7 elements) to form salts such as sodium chloride which we enjoy on all manner of foodstuffs. Lithium powers our laptops and cars, potassium and sodium keep the electronic signals from our brain to our body in check and rubidium and caesium help keep us on time through their use in atomic clocks.

Next we shall move across the periodic table to group 2 to a similar class of elements, known as a the alkali earth metals.

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