#Chemsummer Carnival – Productive summer in the lab?

I have finally found some inspiration and time to do a #chemsummer post. There have been a few posts already but I imagine there may be a rush of posts today, so do keep an eye on your readers or twitter.

How is anyone ever productive in the summer?

On paper, the summer break should be the most productive time of year with no students around to bother us. In reality though, I find it my least productive time of the year (as this PhD comic shows).


Below are a list of things that I think are good and bad about the summer vacation:


  • No MChems in the lab (which unfortunately is balanced, of course, by the summer students).
  • No NMR queue
  • No teaching commitments
  • Conferences bring the chance to ‘network’ i.e. get sloshed with like-minded people.


  • I returned from my holiday in the US of A and began working back in the lab only to find that half of my glassware, cork rings, pipette teats and marker pens had gone walkies. Thankfully, I have managed to shift the equilibrium back in my favour by using my powerful master key.
  • Whichever member of staff I need is on holiday. They return from vacation to tell you that you actually need to talk to someone else, who it then turns out is also on vacation.
  • When it is 25°C outside, it is 35°C in the office.
  • All my teacher friends stop complaining for the first time all year and repeatedly post photos of themselves enjoying the nice weather.

So, what do you think? Are you more productive over the summer? What problems do you face when trying to get sh*t done? Let me know in the comments or on twitter (@jessthechemist).

Happy (belated) birthday to me!

So BRSM blog just celebrated his two year blog birthday (blog-iversary?) and he reminded me about my recent one year blog-iversary so I thought I would totally steal his idea. Sorry dude!

My blog started out as somewhere where I shared information about how we came about chemistry in everyday life but became a more whimsical place where I dispensed random ideas and thoughts with the world. I had planned to write a post at the end of May about what I have learnt about blogging over the past year blah blah blah but postdoc and real life got in the way. Instead, I have decided to cheat and take a leaf out of young BRSM’s book and share my top three posts of the OTC Year 1 (ish).

1) My top post from the past year was “The Girl with Zero Hangovers. Yes, I have still really never had a hangover. Thanks must go to the @NatureChemistry blogroll for putting this post and my blog on the map!

2) My personal favourite post comes in at number 2: “My Academic Family II“. The tree has since been updated  so do take a look. This was my favourite post because it started out as a small idea and turned in to something huge thanks mainly to Twitter. Just look how many names are now on there! Feel free to continue to send me names to add to the tree. If I had more time on my hands, the tree would be immense, but alas, no one pays me to make pretty pictures for my blog…

3) My third top post was “Identical Twins but not Identical Income” which I posted a few days after my blog-iversary (yes, I am cheating yet again). It has already had massive hits after only twelve days and is well on its way to being my most popular post to date. Thanks must go to CJ for highlighting this post on his own blog.

Thanks to everyone who has contributed to my first year in the blogosphere. Thanks, especially, to all those bloggers who joined in with the #realtimechem week blog carnival. My highlight as a “firsty” was being asked to contribute to the Nature Chemistry blogroll, so heartfelt thanks to all the guys over there.

Here’s to many more years of The Organic Solution. Cheers!


The awesome blogosphere has been joining in on the Blog Party in aid of @BRSM_Blog’s imminent departure from the UK. Here is a round-up of the posts so far. Have you written a post? If so, just share on twitter using the hashtag #brsmblogparty. If you don’t have a blog but want to offer some advice, just post in the comments section.

#BRSMBlogParty posts so far:

@Jessthechemist (me) gives BRSM a list of things to watch out for.

@azaprins implores you to keep blogging!

@Stuartcantrill kicked things off with a list of things that BRSM should know including that “bacon is somewhat limited and sausage is not sausage as you know it”. So true.

@SeeArrOh then posted a wonderful A Poste-docke Limerick with a fabulous ending line – “And never say no to some pub perks”.

@Chemtips talks language barriers and the class system. I particularly like that “all British accents are appreciated, and all can lend authority to your words”.

@MEvans86 advises BRSM to be nice to grad students…and to not be afraid to challenge your advisor.

@V_Saggiomo tells BRSM to run while you still can but since you can’t do that he does advise you to “always close the separatory funnel”.

@KarlDCollins gives some useful tips including to “quickly identify the most helpful/knowledgable PhD students and be as nice to them as possible”.

@ChemJobber tells BRSM to buy a car and explore because in “any direction you drive, there will be something different that is worth seeing”.

@_byronmiller has also joined in the party. He puts the case forward for BRSM to make videos a la Vittorio!

@Chembark has some top tips including this oh so true one: Try to be nice to—or at least respectful of—your colleagues

BRSM Blog Party: Bon Voyage BRSM

Welcome to the BRSM blog party. In a few weeks @BRSM_blog will be heading to the US of A to start his new life as a postdoc. As a goodbye gift, the chemistry blogosphere decided to give him a send off in the form of blog posts.

If you want to join in the party, then just write a blog post (either your own or using the template that I have used below) and share it on twitter using the hashtag #BRSMblogparty or give your advice in the form of comments below.

Here is my entry:

Jess (@jessthechemist), postdoc.

1. What is your message for BRSM?
Have a great time. Work hard but don’t forget to have fun. You are in a beautiful and exciting country. Explore it!

2. What is one postdoc survival tip you would give to BRSM?
Say yes to new opportunities. You never know what you will learn. I wouldn’t have predicted that I would learn how to use a 50 L vessel!

3. Do you have a fun story you could share from your postdoc and/or US academic experience?
Sometimes people give you work to proof read and it is terrible. Be nice and help them out. You were there once, remember.

4. A survival tip for living in the US?

I lived in the US for a year when I was 18. Here are some random tips I picked up along the way:

  • Meals are served in huge portions. Do not eat all your meal or you will come back to the UK obese.
  • Always say yes if you are offered s’mores. They rock.
  • Bagels taste better in NYC.
  • Hazelnut syrup does not belong in coffee.
  • Americans will not recognise where you are from in the UK so you should always just say London.
  • Right turn on red is awesome. Use it.

5. What would you like to see on BRSM blog in the future?

Keep us updated with postdoc life in the US and keep #blogsyn-ing.

6. Anything else?


BRSM Blog Party: Guest post by Freda!

img_mid_39122 (2)

Freda (@azaprins) – PhD student, not a postdoc!

1. What is your message for BRSM?
Have fun, enjoy yourself, and don’t forget us when you’re famous 😉

2. What is one postdoc survival tip you would give to BRSM?
Have a work-life balance if you can?! Carry on mountain biking in your spare time.

3. Do you have a fun story you could share from your postdoc and/or US academic experience?
Well not really, I am not a postdoc so I thought it?d be rather nice to get some tweeps together who are/were postdocs to bestow their advice and blessing on you at this blog party!

4. A survival tip for living in the US? Share an idiom if you’re American!
Do not make any jokes at US border & customs as gaining entry is essential. After that the world is your oyster.

5. What would you like to see on BRSM blog in the future?
How postdoc life is different Stateside, and keep the Woodward Wednesdays going!

6. Anything else?
Always remember that your interest in the history of our subject (quote!) helped to solve an important synthetic problem. I also think that you’re curious, clever and encouraging enough to be a wonderful postdoc, so I wish you all the very best for the future. X

Did I work hard enough?

As many of you will know, @Chemjobber and @Vinylogous are hosting a kind of blog conversation called “Is graduate school in chemistry bad for your mental health?”, with many other bloggers out there also giving their opinion on the matter.

As a Brit, I feel like these posts aren’t really aimed at me so much. Although I found the PhD process somewhat stressful, I can honestly say I enjoyed 99% of it (I even enjoyed my viva!). I had a great boss who knew the important of social activity within and outside of the group. He also encouraged us to pursue sporting achievements, in moderation, which for me, involved competing in national ballroom dancing competitions. We were also allowed to take a few weeks holiday and the odd day off, if required. I loved (and miss) the mad research I was doing and I can say that met some life-long friends as well as my boyfriend of three years.

My experience of the UK system is that we work from around 9am-6pm with the working hours getting longer as the end of the PhD draws near (most PhDs are between 39 and 48 months). I worked weekends but only when I wanted to catch up on reactions or set reactions up for the week ahead. I also found weekends a relaxing time to do columns as my favourite (communal) glass column would be available for use and I could control what radio station was played. I was also, of course, productive during the week, except maybe when the Ashes were on. I spent my time between reactions writing up experimental and planning my next reactions.

I am aware that the UK has research groups and departments that do expect much longer hours. I know people at these groups and some of them have told me they stay late just because they are expected to and that their productivity in a day is no higher than if they had done an 8 hour day. I know some academics that require their students to put on a certain number of reactions a day. My view is that chemistry just doesn’t work like that. I am also of the opinion that, because I worked somewhat sensible hours, I kept my passion for the subject that I loved and my sanity.

I was recently of the thinking that I should have gone to the States to get the best PhD that I could have done but I now realise staying in the UK allowed me to become a much more impassioned and motivated chemist. I may not be the best in the world or have millions of results, but I can say I still love my subject.

I hope that this post does not appear to you like I am trying to rub it in your face. I just thought I would share my point of view.

** I feel that I should add that there were plenty of days, especially in my second year, that I thought I was a failure, nothing was working etc but I got through it. It seems most people suffer from “second year blues” so I dug deep and persevered.  I am also not a stressed out person generally. I tend to take whatever is thrown at me and deal with it. I have a somewhat easy going temperament which probably would have not been the best personality to have in a huge, cut throat lab elsewhere.

Chem Coach Carnival – I was nearly a banker

So See Arr Oh’s Just Like Cooking is hosting a Chem Coach Carnival. This is in celebration of US National Chemistry Week. Although I am very early in my career I thought I would still share some stories that might help future scientists.

My Current Job

I am a postdoc in organic chemistry doing more abstract synthesis than most chemists I know. I work with physical chemists. I synthesise deuterated analogues and they do some fancy photolysis and get some lovely graphs which should help us determine reaction mechanisms. Working in a collaborative project is great as I get to learn  more than I ever really wanted to know about photolysis and pretty coloured lasers (I only make white solids and colourless oils so anything coloured is like Christmas has come early). It is hard work though. They think the synthesis takes a couple of days from the initial literature search to giving them the purified compound. It does not. Most of the compounds I make have not been made and I have limited ways of putting deuterium into the compounds. It is fun to come up with new syntheses though and adapt procedures from 1929, in some cases. On the other hand, I naively think that flashing a laser at something is easy.

What do I do in a standard work day?

The first thing I do is make a cup of tea. Can you tell I am British? I generally have a plan of the synthesis I am doing in a given week and so I figure out what the days synthesis entails and then get started on that. I also start on work-up/purification of any reactions that have finished. On an average day it is pretty likely I will have a distillation of a stinky amine to do but I am a pro at these now so I don’t actually mind them. As an undergrad I used to be scared of the dreaded vac pump and the stories of liquid oxygen *shudder*.

As well as lab work I have papers to write. I am currently writing a section of a review article and preparing a manuscript on mine and a PhD student’s results. I also proof read theses and reports written by the students in the lab, which I don’t mind doing but can be time consuming. I run a weekly organic chemistry revision session which is good fun and has greatly improved my knowledge in chemistry and teaching but preparing for the sessions always takes longer than expected.

As well as all that I am also in fellowship application writing hell. It seems as soon as you start a postdoc, you have to start planning for the next. Who needs job security hey?

What kind of schooling/training helped me get where I am?

I have a 4 year undergraduate MChem. degree (with the final year spent in a research lab full-time) and a PhD in fluoro-organic chemistry from the same University. Although my schooling was very good I think it was what I did outside of University that has given me the edge. I spent 3 months at a University in Hong Kong in the summer between my 3rd and 4th year of my undergrad. Although I worked in a biology lab, I learnt a lot about the research environment and this really ignited my passion for research. I would highly recommend spending some time in a research environment before choosing to do graduate studies whether that be in industry or at a University.

As part of my PhD, I also had the opportunity to spend 3 months working in a pharma company. I continued my own research but was surrounded by so many interesting scientists. It was a great break from my normal everyday lab, especially as I got to play with lots of fancy machines and have my lunch paid for everyday!

How does chemistry inform my work?

I spend every day doing, teaching, reading or writing about chemistry.

A unique anecdote about my career

I nearly went to University to study economics but I had gap year where I lived and worked in the US. I was an au pair working for some very academic people and they inspired me to study what I enjoyed, not necessarily what I was best at in school. I then applied to my first choice university and got a spot on the 4 year chemistry degree. I found the first two years very intensive but I learnt to love the labs and since then I have never looked back.

If I had have gone down the economics route I would have graduated in 2006 and would have been looking for a job in banking just in time for the recession to hit. Although I may have had more money as an economist/banker-type person, I certainly wouldn’t have as much fun as I do in my current field. Who wouldn’t want a job where you got to play with liquid nitrogen? I also would never have met my PhD chemist boyfriend (soppy, I know).

I am the captain of Team Fluorine

So..I thought it about time I joined in with #ToxicCarnival since I spent 3.5 years of my life playing with oh so scary elemental fluorine for my PhD.

According to gospel Wikipedia “above a concentration of 25 ppm, fluorine causes significant irritation while attacking the eyes, respiratory tract, lungs, liver and kidneys. At a concentration of 100 ppm, human eyes and noses are seriously damaged”. The MSDS of fluorine also states that fluorine gas is corrosive to exposed tissues and to the upper and lower respiratory tracts.  Fluorine penetrates deeply into body tissues and will continue to exert toxic effects unless neutralized.  Workers should have 2.5% calcium gluconate gel on hand before work with fluorine begins. Fluorine also reacts violently and decomposes to hydrofluoric acid (which has previously been described as part of #ToxicCarnival) on contact with moisture.  Fluorine is the most powerful oxidiser known.  It reacts with virtually all inorganic and organic substances.  Fluorine ignites in contact with ammonia, ceramic materials, phosphorus, sulfur, copper wire, acetone and many other organic and inorganic compounds.

As you can tell, it is pretty darn unpleasant. Thankfully, the very pungent odour is detectable at concentrations as low as 20 ppb so you have time to escape, should you come across a fluorine leak.

A little history lesson… Fluorine was isolated successfully over a century ago by Moissan (Ann. Chim. Phys., 1891, 19, 272.) who gained a Nobel Prize in 1906 for his achievement. He produced fluorine by electrolysing a solution of potassium hydrogen difluoride in non-conducting liquid anhydrous HF. The electrolytic cell was constructed from platinum/iridium electrodes in a platinum holder and the apparatus was cooled to -50 °C. Today, fluorine is still manufactured using this electrochemical process.

The first large-scale production of fluorine was actually associated with the Manhattan Project during World War II, where uranium hexafluoride (UF6) was used to allow separation of the 235U and 238U isotopes. The radioactive uranium was used for the construction of the first atomic bombs in 1945 and uranium refining for nuclear energy is still one of the major uses for elemental fluorine.

So..so far you have learnt that fluorine is scary stuff and can be used to make atomic bombs. Now I am going to tell you why we should all love fluorine a little more.

Organo-fluorine compounds are almost non-existent as natural products but these days 20–25 % of pharmaceuticals contain at least one fluorine atom with these drugs treating a huge variety of diseases. One of the earliest synthetic fluorinated drugs was the anti-neoplastic agent 5-fluorouracil, an anti-metabolite first synthesised in 1957 (Nature, 1957, 179, 663-666). It shows high anticancer activity by inhibiting the enzyme thymidylate synthase, thereby preventing the cellular synthesis of thymidine. Since 5-fluorouracil, fluorine substitution is commonly used in med. chem. to improve metabolic stability, bioavailability and protein–ligand interactions amongst other things. An increasing number of related fluorinated anti-tumour agents have now becoming available as cancer treatments, including 5-fluoro-2’- deoxyuridine and its derivatives (Frontiers Biosci., 2004, 9, 2484-2494).

5-Fluorouracil is synthesised by bubbling fluorine through a solution  of uracil in a high di-electric constant solvent. If used correctly and safely fluorine can be a cheap and easy reagent, especially in large scale synthesis. EASY PEASY! Other fluorinating agents (mainly N-F) are seen to be an easier and safer alternative but these reagents can be expensive and wasteful. Using elemental fluorine is really all about knowing how to use it, for example it is best when the reaction is carried out at around -10C as a low concentration mixture in nitrogen. The key is to stop the competing radical reaction and promote the electrophilic process by polarising the F-F bond.

So what have we learnt?

1) fluorine is toxic and smells bad

2) fluorine can be used to make life-saving drugs (cheaply and easily if the infrastructure is in place)

3) I love fluorine a little too much.

If you want to know more about elemental fluorine in synthesis then check out publications by R. D. Chambers, G. Sandford and S. Rozen. All legends in their own right.

If you want to know more about fluorine, then just get in touch. I may or may not know the answer but I will probably be able to point you in the right direction.