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

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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:

RealTimeChemInFocus copy

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!

FAQ Banner

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-

Real Time Chem Week: The FAQ (updated!)

RTCBannerSmall

So this week is #RealTimeChem week! This time around rather than a day, the format has been extended out to a week so that more people can participate. As before I have written an FAQ below to answer questions anyone might have about the event and #RealTimeChem in general.

RTC_FAQ

What is #RealTimeChem?

RealTimeChem is a Twitter-based community project designed to encourage chemists to actively engage with one another online, by sharing what they are working on at any given time. Chemistry often gets sidelined when it comes to science media exposure (thanks for that Physics!), so #RealTimeChem is here to celebrate chemistry and give an insight into the real science that chemists do each day.

The fantastic C&EN article on #RealTimeChem

The fantastic C&EN article on #RealTimeChem

As @carmendrahl of C&E News put it “#RealTimeChem is a virtual watercooler that enables chemists to swap stories, start discussions on journal papers or laboratory techniques and generally geek out over pictures of obscure pieces of glassware, vibrantly coloured compounds or pretty crystals. The sky really is the limit (oh okay you can go into space if you want to). #RealTimeChem is what chemists choose to make of it and I will certainly endeavour to keep it running for as long as the community wants it.

So, if you are doing any type of chemistry (teaching, industrial, research, etc) and you want to share it with the rest of the world, then get on twitter and tweet it under the hash tag “#RealTimeChem” and you’ll find many others doing the same (by Feb 24, 2013 there had been over 3,110 tweets containing #RealTimeChem and counting).

If you want to find out what others are doing then search for the #RealTimeChem hash tag and follow @RealTimeChem.

What do I get out of it? Isn’t it all a bit…well… “pointless”?

Firstly, Pointless is just a TV show…

Pointless

It’s got nothing to do with us. Move along, move along.

Secondly, the truth is this is a community driven project, and you get out whatever you put into it. There are a great many people of the opinion that Twitter and other social media (*cough* Facebook *cough*) are a waste of time, but what there is no denying is that they can be powerful networking tools. They are changing the way we get news and the way we interact. Twitter in particular is very instant, far more so than any other form of “normal” chemistry networking. It only takes a few moments and you can tweet any time of the day or night.

What is #RealTimeChem week?

A weeklong event designed to raise awareness of “the project” (which makes it sound far more sinister than it actually is) and encourage as many chemists in the community as possible to join in. It is a follow on to #RealTimeChem Day which took place on the 7th November 2012.

It takes place the week starting 22nd April 2013 and runs for 7 days (that’s Monday 22nd to Sunday 28th all inclusive  we know some of you work on weekends!).

Note: The epic trailer provided above is courtesy of regular (and fantastic) #RealTimeChem contributor @V_Saggiomo

What are “RealTimeChem Awards”?

Something new for this event are the “RealTimeChem awards”, which are designed to recognise the standout contributions of those taking part in  #RealTimeChem week.

I’ll be selecting my top 20 favourite #RealTimeChem tweets everyday of the week (update: Monday-Friday will have top 20’s and Sat/Sun will have a combined one as those days are simply not as busy – Doctor Galactic). Places 20-11 will win a Silver award. Places 9-4 will win a Gold award. The top three will win the soon to be coverted Platinum award (which you can see below).

AgAward                     AuAward                     PtAward

Shiny, right? You know you want one.

Update:

As an additional incentive the winners of platinum awards will also be added to the shortlist for “best tweets of the week“. The top three tweets of the week shall be selected from this shortlist (via an expert judging panel) and the winners will each win a prize, which has been kindly provided by RSC and Chemspider: A Chemspider branded Lab Coat! (see below):

CSPLabCoat1CSPLabCoat2

The Best Tweets of the Week will be announced a week after the event. So stay tuned and make sure you tweet something brilliant.

Some Rules: Note that prizes will only be awarded for “individual” tweets, links to blogs for example, are excluded. Additionally, prizes will not be awarded to organizations only participating individuals.

Who can take part?

Anybody on the planet Earth (sorry alien species) who works in the field we call “chemistry”. This is an all inclusive event no matter what branch of chemistry that you partake in (including biochemistry, geochemistry, astrochemistry, crystallography, organic, inorganic, analytical, industrial etc) or what level of chemistry you are currently participating in (high school, undergraduate, postgraduate, academia, industry, person in shed etc). It also doesn’t matter what part of the world you live in, which is one of the best benefits of the Web of Interconnectedness (a.k.a the Internet).

Please though only join in if you can spare the time. We understand that you’re all busy people – work commitments and getting our chemistry done must take priority over any shenanigans on Twitter and we wouldn’t want to be responsible for anyone getting into trouble.

What should I tweet?

Anything that involves chemistry counts – lab work, journal reading, writing papers, teaching, demonstrating, field work, instrumental work, baking cakes at home etc. It is entirely at your discretion so long as it’s got some link to real chemistry. If you want some good examples, then check out the recent Chemistry & Engineering News piece, which has some really nice ones.

All things that happen over the weeklong period can be tweeted, good or bad. I’m sure the former shall outweigh the latter, but if you are having problems, say with an experiment or finding a piece of literature then someone else might be able to help you out. Also if you see someone tweeting about something you find interesting, or you think you can help with then, please tweet back. Engagement is the name of the game.

I greatly encourage as many of you as possible to include pictures and videos (especially of great looking experiments) in your tweets because they really stand out.

Vine. Grow some chemistry vines.

Vine. Grow some chemistry vines.

Obviously, we aren’t all great directors so I reccommend using the mobile app Vine (@vineapp) which you can download from the app store (if you happened to have an iPhone). Vine enables its users to create and post short videos with a maximum length of six seconds that can be shared on a variety of social networking services, like Twitter. Perfect for capturing snippets of chemistry as it happens (as this example from @ethylove demonstrates).

Obviously, when it comes to what you can Tweet, there are limits. For instance, only take pictures of things you are allowed to show. We understand certain areas of chemistry are shrouded in secrecy, particularly in industry. Don’t tweet anything sensitive and always get permission first. If in doubt, don’t tweet it.

Equally, be nice to others. Just because you’re on the internet doesn’t mean you should forget your manners.

How much should I tweet?

As much or as little as you want. Some participants will tweet their whole day or week, others just brief highlights, but even if it is just one tweet then that is perfectly fine. So long as you remember to include the hash tag #RealTimeChem, so that your tweet can be easily found by other chemists in the community and is recognised as part of the event.

How can I follow the event?

Search for the hashtag #RealTimeChem on Twitter or follow @RealTimeChem for highlights. I’ll be keeping an eye on twitter all week long and re-tweeting the best #RealTimeChem tweets I find (or as many as Twitter will allow me too) and commenting on the fabulous things you are doing.

There is also a Facebook group, which will act as a jumping off point for people and contain useful information like this FAQ! Although only once I sort it out…

Update:

oddt_oddticon

After some recent discussions with @chemconnector and @rkiddr at RSC and some jiggery-pokery by @aclarkxyz you can also follow the #RealTimeChem hashtag via the ODDT (Open Drug Discovery Teams) app for iPad and iPhone, which can be found at the link here. If you wish to learn more about it, this blog post is quite illuminating. Suffice to say it’s rather nifty.

Who invented #RealTimeChem?

Certainly not me. The inventor was @azmanam who was trying to determine what was in Lemishine and happened to tweet his results using the hash tag. @JessTheChemist then produced a storify page to follow all the RealTimeChem that happened. I got involved in this by tweeting about my own experiments in the laboratory. The rest is history as the saying goes.

Who is running RealTimeChem?

Yours truly again who can be found under @doctor_galactic on Twitter and @RealTimeChem. I work as a publishing editor for the RSC. While this project does not have any strict official affiliation with the RSC, it and many other chemistry organisations have helped to support this project. Please note though that I run #RealTimeChem in my spare time. I don’t get paid. This is not a commercial venture.

Can I help to promote/support RealTimeChem?

Yes. A thousand times yes. There are limits of course, but word of mouth is a really important thing when it comes to a grass roots community project like this one. I’m only one person and can only do so much so please pass the word about #RealTimeChem onto any chemists you know. The more chemists we get to tweet, the more interesting chemistry we get to see we get to enjoy!

Below you will eventually find a couple of posters that I have uploaded that you can print out and use (get permission first before you put posters anywhere though). Some have been provided in B&W for easy printing. Banner and badges are provided for use in Twitter avatars/backgrounds, Facebook banners etc, etc.

First Batch Of Posters

RTCNewPostersConicalB&W RTCNewPostersConicalB&YRTCNewPostersRBF_B&WRTCNewPostersRBF_B&Y   RTCNewPostersBeakerB&WRTCNewPostersBeakerB&Y  Keep Calm I want you

Twitter Avatars – add these to the bottom corner of your twitter avatar during the event if you wish.

RTC_TwitterBadgeV2 RTC_TwitterBadgeV_3 copy

Banners – use these for forums, blogs or wherever elese you want to.

UK Date Version

UK Date Version

US Date Version

US Date Version

RTCWeekBannerInternational copy

International Date version

Blogs, blogs, blogs, blogs…I really like blogs, can I write a special one for #RealTimeChem week?

If you write a chemistry-related blog then yes, perhaps you might consider doing a special blog piece for the week.

RealTimeChemCarnival copy

RealTimeChemist, @Jessthechemist has kindly agreed to run a blog carnival for #RealTimeChem week on The Organic Solutio Much like other blog carnivals she will collect together all blog posts relating to #RealTimeChem. In order to take part in this email Jess, via: theorganicsolutionblog@gmail.com or post your blog up on twitter during #RealTimeChem week using the hashtag #RealTimeChemCarnival so that Jess can find your blog post and put it alongside all the others.

If you are struggling to think of something to write for the carnival, Jess has produced an example based on her own work, which you can access here.

What is the future of #RealTimeChem?

To continue to grow into something the chemistry community finds useful. Social media isn’t going away and having a virtual water cooler, seems to be an appealing idea.

#RealTimeChem will continue to be available as a hash tag to use every single day of the year, whenever you feel like tweeting something about chemistry.

I plan to hold a major “event” like this one every year (possibly twice if the demand is there) as they give people something to focus and prepare specifically for. The format might change in the future as more people get involved and there is the potential for actual meet ups and whatnot. We. Shall. See.

Can I have a fancy and somewhat abstract summary of what it’s all about? 

Yes. You’re weird…but yes you can. These are the three key ideas of #RealTimeChem:

Connect.

We are all spending increasing amount of time online, why not spend a little of it connecting with other people in your field? The online world and Chemistry itself can sometimes feel a little isolating, especially if you’re doing a PhD, so this is a chance to be join in and feel part of the wider community.

Discuss.

This is your chemistry, your ideas, your expertise….Your best chemistry jokes. Anything relating to chemistry can be united under the #RealTimeChem banner. Once you’ve shared your chemistry, why not discover someone else’s? If something interests you, spark up a discussion. You never know where it might lead.

Enjoy.

We all love chemistry, that’s a fact. #RealTimeChem is another way to show what chemistry means to you every day. So have fun with it, be playful, have a laugh.

Still got questions?

My, my you’re an inquistive soul. If I have forgotten anything, or anything is unclear. Then sound off in the comments or contact via Twitter. I’ll do my best to find you some answers.

-Doctor Galactic & The Lab Coat Cowboy-