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The Chemistry of a PhD

The Chemistry of a PhD

Ramblings of a Drug Discovery PhD student who should really be in the lab or writing her thesis.

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Posted on 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 …

Continue reading "PhD Update: 2019 Q1"

About me

Hi there! Thank you for visiting my blog. My name is Fiona Scott. I am a PhD student at Sussex Drug Discovery Centre, based at University of Sussex on the south coast of the UK. I enjoy sharing my love of science and the highs and lows of PhD life on this blog – and also on Twitter and Instagram.

 

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🧪#postitreactions Nitro-reduction🧪 Previously I’ve talked about using protecting chemistry to prevent nitrogen atoms from reacting when I don’t want them to. Another way to prevent amino groups (-NH2) from reacting is to turn them into another group of atoms that don’t react in the same way. A close neighbour of the amino functional group (-NH2) is the nitro functional group (-NO2). Functional groups are specific arrangements of atoms that are given a name to describe that particular arrangement. Instead of two hydrogens, there are two oxygen atoms. A nitrogen bound to two oxygens behaves very different to a nitrogen attached to two atoms and is much less reactive generally. I did need that nitrogen to react in a different way later on in my synthesis so once I’d made the necessary reactive transformations to my molecule with the nitro group present, it was time to turn it into a more reactive amino group. I did this via a reduction reaction. You might remember OIL RIG (oxidation is loss, reduction is gain) from high school chemistry if you studied it. Reduction reactions involve an increase in electrons in the system, which can also be described as a reduction in oxidation state. Oxidation doesn’t always need to include oxygen. In very crude terms, it can be related to how many chemical bonds there are to a particular atom. When nitrogen binds to two oxygens in this way and, usually, another carbon, it forms four bonds with other atoms. Normally nitrogen is most happy forming three bonds but with a neatively charged oxygen present, it is happy with this four bond arrangement. Converting the oxygens to hydrogens reduces the number of bonds that the nitrogen forms to three, so it has therefore been reduced. We use various reducing agents to help carry out this reduction reaction and conversely, there are ways to make the reaction go back in the other direction – from amine to nitro – using an oxidising agent. Do you remember OIL RIG from school? What other functional groups do you know about? What else would you like to know about reduction and oxidation?
📄 The Peer-Review Process📄 It's not just my thesis that I'm working on at the moment. I'm also making corrections to my paper that was accepted with revisions at the start of the year. When you submit a paper to a peer-reviewed journal, it is assessed by an editor who, if they deem it suitable, will then send it out to, usually two, anonymous reviewers who are academics in the field that the paper is written for. The reviewers make their own assessment of the work and suggest any changes and ultimately if they think the paper should be published. This is then returned to the editor and then the authors with a decision. This took a couple of months for this particular paper. My reviewers had a few issues about how the experimental section was written so it was given "acceptance with major revisions". Thankfully none of the correction points require me going back into the lab so I just want to get this out of the way ASAP so I can write in my thesis that the article has been published. One reviewer in particular was quite mean with their language so I've been finding it rather hard to work through their suggested changes. People seem to forget there are humans at the other end of an e-mail. I'm definitely learning to thicken my skin a bit more if I'm going to attempt to get two more papers published from my PhD. Peer-review is important though. Your scientific claims need to be able to stand up to criticism if its to be accepted as fact. I'm simultaneously working on the thesis chapter that the paper summarises and I'm quite enjoying having my head in only one section of my project. Have you been through the peer-review process? How do you take criticism?
🧪Protecting Group Chemistry🧪 In a post #postitperiodictable era, I had a square-shaped gap in my life so I’d now like to share with you some of the chemical reactions I carried out during my PhD project. Rather imaginatively, I’ve called this series #postitreactions. First of all, I’d like to talk about protecting group chemistry. At one point in my project I was using this starting material that had two reactive amino (-NH2) groups on it, but I only wanted one of the amines to react, not both of them! To get around this, chemists “protect” reactive species with a variety of “protecting groups” to remove their reactivity. This means they can then use the protected reagent in their reaction and then remove the protecting group later on. One of the protecting groups used to shield nitrogens is called a “Boc” group. The name comes from the arrangement of carbon, hydrogen and oxygen atoms in a tert-ButOxyCarbonyl arrangement. The Boc group contains an ester which draws electrons away from the nitrogen atom, making it less likely to react. To save a step in the lab, I bought in a version of this diamine that was already protected and, after using it in a reaction, I removed the Boc group by stirring my sample in a concentrated acid. Ideally I’d prefer to not have to use protecting chemistry as it usually adds 1-2 steps to the list of reactions you have to do, but in combination with the two reactions I needed to carry out to get to my desired drug molecule, adding a deprotection step at the end wasn’t too much hassle. What else would you like to know about protecting chemistry? Chemists, what other protecting groups do you know about?
#thisiswhatascientistlookslike In light of gaining some new followers and seeing this hashtag doing the rounds I thought I’d reintroduce myself. Hi! I’m Fiona. I’m a PhD researcher working on potential new cancer drugs of the future. I’ve spent most of the last three years wearing a white coat making molecules in a chemistry lab @sussexuni. I’m currently in my last few months of my PhD where I am writing everything up into papers for publication and a massive thesis. But scientists are people. They’re not all about science all the time. If you swipe you can see me in one of my happy places...I’m a huge theatre nut and love escaping from the world for a couple of hours to watch a play or musical. I sometimes review shows and interview performers and creatives for a website called @broadwayworlduk in my spare time. Just because someone isn’t wearing a white coat, doesn’t mean they aren’t a scientist. Anyone who has an idea about how the world works and tests out that idea to see if it holds up is using the scientific method. Scientists are people too and in my field in particular it can be quite disheartening to hear people don’t think we’re working hard enough or are even hiding a cure for all cancers. We’re not. Drug development is very difficult and I wish it was less cumbersome and expensive than it is at the moment but projects like mine repurpose molecules for targeting other processes in order to speed things up. Why not introduce yourself in the comments below. What do you think makes a scientist?

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Recent Posts

  • PhD Update: 2019 Q3 October 7, 2019
  • Six tips to survive a heatwave working in a chemistry lab July 23, 2019
  • PhD Update: 2019 Q2 July 11, 2019
  • What’s In My Fume Hood? May 2, 2019
  • PhD Update: 2019 Q1 March 31, 2019
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