Tag Archives: chemistry

I've forgotten to write a blog post this week as I've been busy writing a presentation to deliver to my industrial PhD partners. I've also been playing far too much roller derby (if such a thing exists) for my poor arms to cope with. A new regular feature has therefore been created from my lack of free time and energy - a pictorial run through of my recent happenings in the lab. I hope you enjoy the photos and the insight into my PhD!

Let's start with an old photo to ease us in. I wish my fume cupboard was still this clean and well organised. Unfortunately I am all to used to the perils of working with wood that stains everything it touches!

I wish my fume hood was still this clean and well organised.

These test tubes are from a flash chromatography system. Flash chromatography is faster at separating compounds than gravity chromatography because it uses pressure to push the compounds through the column. Look at the pretty variations in colour!

Look how concentrated some of these are!

You can also separate compounds using a funnel like this one. Here the sugars from my bark extract are creating a circular pattern on top of the liquid.

Filtering my separations

The layers of filter paper resulting from my recent extraction methodology look like a rather pretty brown speckled poppy. Shame it doesn't smell like one too.

Filter paper from my many extractions

Finally, my top success for the week was finding a solvent system that would dissolve 3 very different compounds. This is a photo of one of the failures, as you can see from the undissolved substance on the right.

vials

That's all from me this week - how was your week in or out of the lab?

Meetings with Joss Whedon (Avengers Assemble), Joseph Kosinski (TRON: Legacy) and Ron Howard (Angels & Demons) are something Sean Carroll calls a ‘cool hobby’. Since moving to Los Angeles, his knowledge of theoretical and astrophysics has contributed to keeping the science we see on our screens factually accurate. I had the opportunity to hear him talk on my first day at the Cheltenham Science Festival.

Carroll's passion for the physically possible has extended from keeping the release of antimatter from creating an unlikely explosion from occurring in Angels & Demons, to preventing a movie from pushing characters off the edge of a flat planet to kill them off during a fight scene.

Even Gravity, a film he commends for being scientifically accurate, cannot escape his eye for improvement. If consulted, he would re-make one particular iconic moment - where George Clooney is pulled away from the space station by a mysterious force. In his more dramatically accurate scene, he would have both Clooney and Sandra Bullock float away together and let Clooney push Bullock back towards safety.

I thoroughly enjoyed his interview, where he also talked about his experiences in Hollywood and stories relating science to the real world. A favourite of mine was when a friend of his took a team from The Big Bang Theory around a real Caltech lab, to see lasers blocked by index cards and orders of untidiness recognised by practicing scientists around the world -  creating possibly the most accurate representation of a physics laboratory on television to date!

Carroll offered a final great piece of advice to aspiring Hollywood science advisors - move to Los Angeles. But don’t be under any impression the job pays well, his flirtation with the film and television industry has only earned him a 'rather comfy sweatshirt and a bottle of wine’. Job aside, it’s not bad for a helpful hobby in Hollywood.


Last weekend I took a trip to Greenwich with Charles to see the 'Stars to Satellites' exhibition at the Royal Observatory Greenwich. I used it as an opportunity to test out my new film camera - hopefully good pictures will soon follow when I get the film developed!

Vegan lemon and blueberry cake from Greenwich market. Baked by Rubys of London (Ruby Tuesdays)
Vegan lemon and blueberry cake from Greenwich market. Baked by Rubys of London (Ruby Tuesdays).

Greenwich market is one of my favourite places to buy vegan cake. I was certainly not disappointed with my slice of lemon and blueberry cake, which I paired with a cup of strong, black coffee. Unfortunately it defeated me - I only managed to eat half!

One of the pubs on Southbank quoted science! Win for chemistry.
One of the pubs on Southbank quoted science! Win for chemistry.
The London Coffee Guide was to irresistible not to pick up
The London Coffee Guide was to irresistible not to pick up

We took a stroll down Southbank in the sunshine to work off my cake and make room for more food. The Tate Modern bookshop beckoned for a peruse. I picked out a guide to all of the independent coffee shops in London.

Look at that basil mayo next to that burger, just look at it!
Look at that basil mayo, just look at it!

Dinner at Mildred's shortly followed. I had a huge butter-bean, black olive and pepper burger slathered in basil mayonnaise. The vegan basil mayonnaise itself was delicious - I must learn how to make it immediately.

The Lego bus stop
The Lego bus stop

There is a bus stop near Hamleys entirely made out of Lego. Lego! The bricks were firmly glued down to stop any of the 100,000+ pieces going missing. The busy tourist shelter was the last stop on our day out before heading to a friends leaving party. I ate the rest of my cake on the train home.

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TweetmyPhd

It's the 100th day of my PhD! How do I know this? I'm tweeting my way through my PhD, one day at a time.

Hashtags are all the rage on Twitter, so I thought I'd jump on board and use one too for my own little project (or big project if you consider it as part of the PhD itself). Documenting my highs and lows in a concise way (oh I love you Twitter) will hopefully give me something to look back on in the future and engage with others who are going through, or have had, the same experiences as me in my PhD.

I'm hoping that grouping all of the relevant tweets together using the #TweetmyPhD hashtag and numbering them by day will keep the tweets easy to find and time line easy to follow. (Although, I've already mixed up the numbering on a few of the days - I usually tweet at the end of the day, when I'm tired and my proof-reading skills slip!)

The numbering follows the simple rule that if I spend a considerable amount of time working or thinking about my PhD, it gets a tweet using the hashtag. Hence I foresee that most weeks will have five #TweetmyPhD tweets (Mon-Fri) and some will extend to six or seven. I'm aiming to stick to working Mon-Fri only, but we will see what happens further into my PhD.

Is anyone else out there tweeting their way through their PhD? I'd love to hear from you! As for celebrating my 100th day, I think I will enjoy a few cocktails later. After all, it is a Friday!

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I should probably be talking about the Higgs boson today, as most people with access to the internet will hopefully now recognise the evidential possibility of its existence according to preliminary data posted by Cern yesterday. That is, if they weren't distracted by the life-changing headlines about Justin Bieber throwing a tantrum. (I won't even honour that mention with a link).

Anyway, instead of thinking about the Higgs boson I've been directing my attention towards my dissertation. The loving memory of my dissertation that I handed in on May 1st this year has sprung back into my life, as I've been asked by my former supervisor to write an essay about my research, in the hope that some lovely people will give me an award for all of my hard work. In a way my dissertation was somewhat like the Higgs boson before today: hard to find (amongst the crates of degree related folders) and difficult to understand (I presented it to my Mother to read and she didn't even understand the title). Hopefully I can remedy the latter by explaining my project, for those of you who are interested - ie. my Mother, in this post.

That drip-drop process: normal-phase column chromatography purification of my 3rd compound.

I spent six months almost solidly in the lab, from October 2011 to March 2012, working on the "Synthesis of  Norlignan Derivatives". What I did during those six months was to spend every free minute of my time (when not in lectures or eating lunch) wearing my lab coat, working out quantities of chemicals to use, mixing chemicals, monitoring reactions, hoping the reactions worked, working out why they didn't work, extracting products, weighing yields, working out which liquid chemicals (solvent systems) I should put together to separate out and purify my products, purifying my products in a long drip-drop process (normal phase column chromatography), washing thousands of vials, working out the structure of the products I had made using fancy instruments (NMR, IR, GC-MS) and finally, writing my dissertation. (Phew - I hope you got all of that!)

I was trying to make a compound with something new stuck on the side of it, that may exhibit greater anti-inflammatory properties than the same compound without that new thing stuck on the side of it (see diagram below). I won't go into too much detail about the chemistry here, but I will say that it took 5 steps and some interesting reactions to get to the end product.

My beautiful compound, or at least, what I was trying to make: (E)-1-(4-carboxyphenyl),3,-(4-hydroxyphenyl)prop-2-en-1-one.

Unfortunately the final reaction failed and I got a slightly different product than I intended. However it could still show good anti-inflammatory properties and I got a chance to show off my theoretical knowledge by explaining why I think it happened. Explaining why things went wrong is possibly my second favourite thing about chemistry experiments, the first being working out the structures of compounds (which is easily fueled by my love of nuclear magnetic resonance).

So that's my final year project dissertation, hopefully explained simply enough that my Mother understands it, but with enough science in it that I can justify posting it here! If you're a science-type and want to know more about my project, I'm always very happy to discuss it in more detail, just get in touch. My project was definitely my favourite thing about final year and probably the best piece of academic writing I've produced so far. Now I just have to explain to my Mother what my placement project was all about...anyone for a slice of zeolite?