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A week in my life

Hello! My name is Laura Jane, and I’m a PhD candidate hailing from Stellenbosch, South Africa, here to show you what a week in my #RealTimeChem life entails!

 

One of the things our group is working on is a class of molecules called dithiadiazolyls (see this paper for more). Dithiadiazolyls (or DTDAs) are sulphur- and nitrogen-containing heterocycles that exist as neutral radicals. (It is interesting to note that the SOMO, in which the unpaired electronDTDA resides, is nodal at the carbon of the DTDA ring, so it is possible to alter the nature of the R-group without significantly altering the nature of the DTDA ring.) Thiazyl radicals have been investigated as potential building blocks for the design of molecular materials with interesting and desirable physical properties, such as conductivity and magnetism. Their magnetic and electrical conducting properties relate directly to their solid state structure. Unfortunately, many DTDAs tend to diamerise in the solid state, which results in spin pairing and, consequently, loss of any magnetic or conductive properties. We therefore look into ways to override this diamerisation and direct the structure of these materials in the solid state. My project involves the use of porphyrins as supramolecular scaffolds to create novel materials.

Monday

Monday morning starts like any other, with a cup of tea and `n Ouma beskuit while I read the news, then a breakfast of fresh fruit while I check up on what’s new in the Chemistry world. After checking my email, it’s off to my supervisor’s office, to discuss my plans for the week, but more importantly – to discuss our group’s plans regarding data backups (and storing data off-campus), spurred on by the previous day’s fire at one of our neighbouring buildings. Today ended up being an office day, not a lab day. First, backing up my data. While that’s running (my laptop tends to crash if you try giving it two things to do at once), I head off on a library run. When I return, it’s time to go play catch-up by going through some data from the last two weeks that I collected, but didn’t process, as I had fallen ill.

On Tuesday afternoons I have to demonstrate (“demi”) for an undergraduate practical session. First though, marking a stack of my class’s lab reports (nothing like leaving your marking to the last moment!). By the time that is finally done, there’s only an hour or two to spend in the lab, so I catch up on the always-fun tasks such as cleaning the never-ending pile of dirty glassware, sweeping the floor, taking inventory and so on. After a quick lunch at my desk while I catch up with what’s happening on Twitter, I haul myself and my giant stack of books across the road and around the block to one of the other Chemistry buildings for my demi duty. (The Department of Chemistry and Polymer Science at SU is spread over five buildings). This semester I’m involved in second year Inorganic Chemistry, a fun course to demi for as the pracs involve fundamental concepts and lots of pretty colours! Today’s practical involves introducing the students to the concept of qualitative analysis. South Africa has a very diverse population and consequently has 11 official languages – so language policy is a very important topic. While SU has traditionally been an Afrikaans university, undergraduate programs are now mostly bilingual (with postgraduate programs typically run only in English), so it’s quite a challenge constantly switching between the two languages when explaining to the students if your brain isn’t fully engaged.

Tuesday 

Wednesday arrives and it’s time to hit the lab for some DTDA synthesis! DTDAs are very moisture sensitive, so it’s all about the Schlenk line. I work in a tiny little synthesis lab, where currently only myself and a MSc student are working in the fume hoods.  Today it’s just step one of the DTDA synthesis, first creating LiHMDS in situ (it arrives in an unusable state when purchased as-is), then – no, wait, load shedding has kicked in again. Luckily, our building can get power from back-up generators (otherwise it’s 2.5 hours without power each time), but it’s still a minute of standing around in the dark waiting for electricity to return. Once the lights are back on and the stirrer plate is working again, it’s on adding the desired aromatic nitrile to form a silylated amidine.  While those reactions are stirring away until completed, I turn my attention to my DTDA – metalloporphyrin complexations. These tend to take (what seems like) forever to form diffraction-quality crystals, so there are normally lots of these running in the background. Because of the moisture-sensitive nature of the DTDA radicals, I tend to set up these crystallizations in skinny Schlenk tubes rather than crystallization vials – it turns out that old-school test tube racks are perfect for holding these flasks when there’s only so much room to clamp flasks in your fume hood!

Wednesday

Thursday brings step two, condensation of the silylated amidine with SCl2 to form a dithiadiazolylium chloride salt. SCl2 is another reagent that we have to synthesise ourselves (from powdered sulphur and chlorine gas), and smells just about as lovely as you can guess, so luckily I don’t have many lab-mates to irritate! Once the product has formed, it’s time to filter and wash it – inertly of course. After drying in vacuo, the dithiadiazolylium chloride salt is obtained as a yellow powder. Halfway through the day, there’s a short break from the lab for group meeting. Typically, our group meetings involve one student presenting their current research and another presenting a paper in a relevant field. This week, however, was something a little bit different as our group was hosting Prof. Wais Hosseini (University of Strasbourg), who was given the opportunity to discuss some of his group’s work in molecular tectonics.

Thursday

The last thing to do for Friday is reduce the dithiadiazolylium chloride salt to the dithiadiazolyl radical. There are several ways to do this, but my favourite is a solid-state reduction using triphenylantimony. (Zinc-Copper couple in THF is another option.) If the reaction is successful, a drastic colour change from yellow to purple is observed. Purification is then achieved by means of sublimation to get shiny dark purple crystals, all ready to meet up with some porphyrins next week.

Friday

Finally, the week comes to an end and it’s time to enjoy the late afternoon sun with a glass of cold Sauvignon Blanc on the lawns of a wine farm just up the road! Life in Stellenbosch isn’t all too bad!

wine

Author biography:

 

LauraJane

Laura van Laeren is a PhD candidate at Stellenbosch University in South Africa. She is currently investigating novel thiazyl radical – metalloporphyrin complexes under the supervision of Prof Delia Haynes and Dr Katherine de Villiers. Her passions include the written word, scientific education and the Cape Winelands.

Blogs at Whimsical Science (http://www.whimsicalscience.com/) & Whimsy Is Forever (http://www.whimsyisforever.com/)

 

Heads up #RealTimeChemists 

Hello all, 

A rather brief blog post just to let you know that I will be on my honeymoon for a whole week in March from the 15th until the 22nd. This means that I won’t be doing anything #RealTimeChem related during this time. 

However…



…because the @RealTimeChem Twitter feed shall be looked after by the fabulous @JessTheChemist during this time. 

Once I get back I’ll be hoping to finish off some of the remaining new features on the blog and also provide you with an update on #RealTimeChem Week 2015. 

Before I go away, you can also look forward to the 2nd #RealTimeChemInFocus blog post by this month’s guest blogger @laurajane0103, plus the 2nd instalment of The Lab Coat Cowboy comic. 

Catch you later folks! 

-Doctor Galactic- 

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A week in the life of a Radical Chemist

G’day! Welcome to the inaugural #RealTimeChemInFocus post, where I aim to give you a bit of an insight into the world of a radical chemist. Radical in the sense that I work with free radicals (molecules or atoms with an unpaired electron), not my political/social leanings. Read on for an introduction to our work on respiratory disease and atmospheric pollutants as I walk you through a typical week in the life of an organic chemistry PhD student.

The WHO estimates that roughly 7 million deaths per year are caused by exposure to air pollution. It is now well known that living in highly polluted areas makes you more susceptible to maladies such as respiratory disease, allergy, asthma and even death. My PhD aims to work out the underlying chemical processes, or chemical entities, responsible for these biological effects. Using a bottom-up approach, we expose simple biomolecules to pollutant gases and see what kind of havoc they wreak.

The week begins with an outline of the research tasks ahead and, like most, this is one dominated by organic synthesis. For us, this is purely a means to an end. Each peptide we wish to study is carefully designed with respect to amino acid sequence and composition. As we work on gram scale, it is typically more cost effective to synthesise these peptides in-house. That means grunt work and grunt work means coffee, lots and lots of coffee.1

Past me had the foresight to prepare the compound I needed before end of year closure. Present me lacked memory of events before end of year closure.

Past me had the foresight to prepare the compound I needed before end of year closure. Present me lacked memory of events before end of year closure.

 

Synthesising each peptide involves protection of the amino acids, a coupling reaction, followed by extraction/washing and purification. Building up larger peptides, such as tri- or tetra-peptides, also involves deprotection and another coupling/work-up. To work efficiently, I often do two or three reactions simultaneously. Each reaction uses the same solvent, reagents and work-up procedure so this saves a lot of time.

 

 

 

 

A fairly epic prank by Aaron’s group members, who replaced all of the posters in the building the morning of his talk - this is one of about four different versions

A fairly epic prank by Aaron’s group members, who replaced all of the posters in the building the morning of his talk – this is one of about four different versions

The end of the week brings a busy day. Friday means more coffee (#FilterFriday!), our department’s organic chemistry seminar and, today, our group meeting and a couple of  radical reactions. These experiments are the true focus of my PhD – new, original research, delving into the effects atmospheric pollutants may have on our body. That means its time to take those peptides prepared earlier in the week and treat them with some ‘pollution’, today it will be nitrogen dioxide (NO2•).

Huge quantities of nitrogen dioxide are produced in China, where air pollution is now a part of daily life – via NASA (http://www.nasa.gov/topics/earth/features/KnowYourEarth/Air_prt.htm)

Every time you drive your car you are emitting not only carbon dioxide but also nitrogen oxides (collectively referred to as NOx gases) such as NO2•. This is one of the most abundant radicals in our atmosphere and has been implicated in respiratory disease, being toxic by inhalation. Once upon a time we obtained gas cylinders of pure nitrogen dioxide. As Australia does not produce it locally, they were shipped from overseas but sadly the freight costs are exorbitant and it can be surprisingly difficult to convince a ship captain to receive a cylinder of toxic NO2• gas. Tyranny of distance strikes again. We now produce our own nitrogen dioxide in the lab.

While chemistry is famous for beautiful colours, the field of organic chemistry is typically characterised by white solids, colourless oils and clear solutions. Peptide chemistry doubly so. My favourite chemical reaction, for reasons now obvious, is the classic reaction between copper and concentrated nitric acid. Nitric acid is slowly dripped over solid copper metal (such as the copper penny above), producing a brown noxious gas – our pollutant, nitrogen dioxide. The copper is converted from Cu0 to Cu2+, forming a gorgeous, bright blue solution of copper nitrate. Meanwhile, the nitrogen dioxide passes through a drying tube and is condensed as a liquid which allows us to react a known quantity with our peptides.

Once we have treated our peptides with this simulated pollution, we go through a painstaking process of identifying each product that is formed. This involves repeated HPLC purifications and characterisation with analytical techniques including HRMS, MS/MS, multi-dimensional NMR and, when I’m lucky, X-ray crystallography. Our results so far show that nitrogen dioxide and ozone are a destructive force, modifying residues or cleaving peptide chains. For a nice article on our latest research check out “Nitrogen dioxide and ozone: a sinister synergy” via Chemistry World or the accompanying paper  published in Organic and Biomolecular Chemistry.

Over the last few years I have taken great pleasure in becoming a part of the online chemistry community. In particular, the burgeoning #RealTimeChem community is extremely welcoming, friendly and engaging. Whether it’s talking about the latest Nature paper, whingeing about that guy who just lined up 6 hours worth of samples on the NMR queue or asking for tips about how to get that postdoc you’ve always wanted – there’s something for chemists of all kinds. A PhD can sometimes be quite a solitary experience and I love having the opportunity to engage with passionate, creative and ambitious people from all around the globe. Get on there, #RealTimeChem and tweet me some time.

 

Thankfully, I live in Melbourne, Australia’s coffee mecca (sorry Sydney), surrounded by multiple coffee roasters.

Author Biography:
lgamon
Luke Gamon is in the final year of his PhD in chemistry at The University of Melbourne, Australia. Under the supervision of A/Prof Uta Wille, he is currently investigating the effects of pollution on biological molecules. Passions include coffee, baking sourdough, photography, sci-comm and board games.
Blogs at A Radical Approach lukegamon.wordpress.com

icon320x320Follow: @lgamon

Announcing #RealTimeChem Hub & new 2015 features

Hello everybody,

It’s taken me a little while and some serious blog maintenance (wordpress sadly doesn’t make that very easy sometimes!), but I can finally announce the launch of the #RealTimeChem Hub page.

From this page you can find links to other parts of the #RealTimeChem universe. So far, these include a link to the #RealTimeChem: FAQ and a few other features. These include:

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New for 2015 are guest blog posts from members of the #RealTimeChem community with the 1st one scheduled for February 2015. To find out more about these posts and how this works, click the picture above to take you to the #RealTimeChemInFocus page.

RTCBanners#RealTimeChemBanners is the new name for the #RealTimeChemBannerChallenge that started at the end of 2014. If you are feeling artistic, why not submit some art and it could be used as the banner for the @RealTimeChem feed on Twitter!

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Finally, the recently announced #RealTimeChemPlaylist, hosted on Spotify. Add your favourite chemistry based tunes and rock out in the laboratory/office/shed.

 

So, that’s it for now. More to come! Any questions, get in touch on Twitter.

 

-Doctor Galactic & The Lab Coat Cowboy-

 

#RealTimeChemBannerChallenge Update!

Hi all,

So the #RealTimeChemBannerChallenge came and went. I had 3 entries from #RealTimeChemists @narf42, @theyakman and @azaprins. All very good ones, so I couldn’t really decide who should win. Then, it hit me that it might be better to run the whole challenge a different way, so…

Here is @narf42's banner, which will be up until the end of December.

Here is @narf42’s banner, which will be up until the end of December.

The #RealTimeChemBannerChallenge is now an all year event! Think of it as #RealTimeChem’s version of cover artwork, just like your favourite chemistry journals (except without any fees, ever.). 

Entries that are chosen to feature will be used as the banner (+ avatar if provided) for the #RealTimeChem feed for a whole month before being replaced with the next chosen artwork.

I will add this up to the all new 2015 FAQ that I am building at some point, but I thought I’d get it out there now.

THE NEW “RULES” OF THE #REALTIMECHEM BANNERCHALLENGE

1. Your image has got to be chemistry related. Pretty obvious I know. It can be from your latest research, something exciting, something funny, one of your most beautiful realtimechem images etc. The sky is the limit really.

2. Along with your banner you can also produce an Avatar Image – all I ask with this one is that it contains Real Time Chem in it, or no one is going to recognize it!

3. The final dimensions for the image should be 1500px (width) X 421px (height) – I’d suggest a resolution of at the very least 300 DPI or greater. In case you need any further guide on the layout you should look at this handy template I found (here).

4. In order to enter the competition please upload your entry to Twitter using the hashtag #RealTimeChemBannerChallenge. Otherwise it won’t be considered. I’m harsh like that.

5. If chosen, your artwork will be assigned to a month of the year, I’ll then let you know which month and you can send your final image to realtimechem@gmail.com.

 

I hope that some of you will chose to take up this challenge and produce some fantastic banner artwork to keep the feed looking fresh and exciting each month.  The running order so far will be as follows:

December 2014 – @narf42

January 2015 – @theyakman

February 2015 – @azaprins

March-December 2015 – Up for grabs!

 

 

-Doctor Galactic & The Lab Coat Cowboy-