#RealTimeChem Week 2016 Awards – Tuesday

Tuesday – 1st November

Welcome to the 4th #RealTimeChem Week awards!

 

Just like previous years, I will be offering awards for the best tweets during #RealTimeChem Week. The format has, again, changed a little due to circumstances and budget. This year, after noting that tweets are often quite slim on the weekend portion of #RealTimeChem week, I’ve decided to focus the awards on the 5 days of the working week, with The Great #RealTimeChem Cook off taking up the weekend slot.

 

There are still three different awards available: Ag, Au and Pt. 10 awards will be given each of the five days (6 Ag, 3 Au, 1 Pt). Those winning the coveted Platinum award (5 total) will each win a prize, which is, as usual, a #RealTimeChem mug with this year’s snazzy logo emblazoned on it.

 

So without further ado, onto the 2016 awards.

keep-calm-its-terrific-tuesday

 

Tuesday. Pinch-punch first of the month. Day 2 of #RealTimeChem week moves into November with a much less spooky day of chemistry (unless you are afraid of rubber ducks – in which case, you have been warned). Favourite tweets of the day below!

 

silveraward

Crystals are always a winner and Praveen seems to have cut his off a passing yeti. Or he found them at Donald Trump’s barber. See, I do topical analysis.

David’s stylish shot of “purple” looks great. He also made “green” later. Sequels are never as good as the original. Unless it’s the Empire Strikes Back. Obviously.

Chistine shares the best thing about yellow compounds: easy columns. It’s the little things that matter in chemistry sometimes and this visually pleasing column makes us organic chemists all feel so content with the happy-happy.

Loving the enthusiasm shown in this tweet from Anne, new chemists starting out on their #RealTimeChem journey. *sniff* I’ve got something in my eye.

The folks at “Chemistry: A European Journal” sure do love a good pun. Who can blame them when #chemquackers is about. This isn’t the last time our favourite rubber duck (sorry @chemjobber) will appear today.

I bet Aaron didn’t think his hangover would lead to #RealTimeChem fame did he? Well thanks to Suze, Aaron, your stylish hangover will be immortalised forevermore!  Of course you only get a silver for being late though…

 

goldaward

 

 

The Nortcliffe Group shared a lot of great tweets on Tuesday. This one has to take the award though for encapsulating part of chemistry that we all know so well: the pain. Oh god, the pain. Let’s all give Edward a hug.

Nano dropping with a duck, that’s totally normal right? Fraser had a lot of fun with #chemquackers all day. Many, many tweets, but this is my favourite one.

Nadine shows us a little insight into the mind of most chemists I’ve ever known. First comes Chemistry. Second? Coffee. Sometimes these switch over. 2nd most popular tweet of the day for an inventive use of an old hot plate.

 

 

plataward

 

Tuesday’s overall, most popular tweet, and winner was:

Susan! If the previous tweet by Nadine said something about chemist’s priorities (at least in choice of beverage), I think this tells us something about chemist’s personalities. The most popular tweet of the day was a pun combining two coinciding themed weeks. Good old “Polar” bears. Of course, only chemists could find this hilarious. I love you chemists.

Susan, you win a much coveted #RealTimeChem week mug:

mug-preview

Super shiny.

 

Congratulations to all winners and thanks to everyone for taking part in #RealTimeChem week so far! Wednesday’s award winners will be announced tomorrow.

 

-Doctor Galactic-

 

 

 

 

 

#RealTimeChem Week 2016 – FAQ

rtc-week-2016

Hello everybody,

It’s almost that time again, time for #RealTimeChem Week! For those not in the know, #RealTimeChem Week is a 7 day event to help raise awareness of the #RealTimeChem chemistry community on Twitter and encourage as many chemists to tweet about their chemistry as possible. During the week various events, competitions and prizes are on offer, just to make it all the more fun and exciting.

If you are completely new and want to know more about #RealTimeChem in general, then following this link to the regular FAQ, where you can learn all about the project and the community.

If you don’t use #RealTimeChem all that regularly, this is the week to give it a go. Why not take some time during #RealTimeChem to share some chemistry and connect to other chemists in the world and have some fun while you’re at it?

 

When is it?

31st October-6th November. It runs all day for all 7 days.

 

How do I take part again?

Just tweet about chemistry using the hashtag #RealTimeChem. Simple as that.

 

So whats going on during this years event?

This year has seen the proposed addition of four brand new elements to the periodic table: nihonium, moscovium, tennessine and oganesson (due to be ratified in November). And with these additions the periodic table is now full. Row 7 is done folks! Such a big change doesn’t happen all that often and it’s been just one of a number of big changes that have occurred, and not just in chemistry, in chemistry during 2016.

From a personal perspective, I became a father for the first time this year and while asking about the community for ideas for #RealTimeChem Week this year, a theme that resonated with me was a suggestion from @nadineborduas:

As such, this year’s overall event theme is “New Elements in Chemistry” i.e. #NewElemChem – but this is not just about the periodic table’s new additions, it’s all about you. What new elements have been introduced in your life as a chemist or to your chemistry this year? Perhaps you’ve just started your life as a chemist? Maybe you’ve made some new, ground breaking discoveries? Had to learn new skills? Got new equipment or glass ware?  All the new things.

Of course the event isn’t limited to the theme, but this is just a few suggestions to think upon and will also be the subject of all #RealTimeChem Blog Carnival posts (more on that below).

 

#RealTimeChem Week Advert

Below you can find some banners to help you share the word about #RealTimeChem Week 2016. Designed again by the awesome Andy Brunning of @compoundinterest (www.compoundchem.com)

rtcw-about-poster

Plus in a few different colours:

rtcw-about-poster_bluertcw-about-poster_redrtcw-about-poster_purple

#RealTimeChem Awards 2016 (31st October – 4th November)

Just like previous years, I will be offering awards for the best tweets during #RealTimeChem Week. The format has, again, changed a little due to circumstances and budget. This year, after noting that tweets are often quite slim on the weekend portion of #RealTimeChem week, I’ve decided to focus the awards on the 5 days of the working week, with The Great #RealTimeChem Cook off taking up the weekend slot.

So, all you have to do to potentially win a prize in the awards is tweet using #RealTimeChem on the Monday-Friday. There are three different awards available: Ag, Au and Pt. 10 awards will be given each of the five days (6 Ag, 3 Au, 1 Pt). Those winning the coveted Platinum award (5 total) will each win a prize, which is, as usual, a #RealTimeChem mug with this year’s snazzy logo emblazoned on it:

mug-preview

This years mug prize.

Sadly, due to severe budget restrictions this year, Gold and Silver award winners don’t get a prize unfortunately, except recognition that you are, completely awesome.

 

The Great #RealTimeChem Cook Off (5th– 6th November) 

 

It’s back! Introduced last year, The Great #RealTimeChem Cook Off celebrates the perfect combination that is chemistry and cooking.

This year’s contest is sponsored by @WileyVCH‘s society chemistry journals.* Five winners will receive a ChemPubSoc Europe package containing

A copy of What’s Cooking in Chemistry: How Leading Chemists Succeed in the Kitchen
-An exclusive #chemquackers scientist rubber duck (which you can use for all your #RealTimeChem posts!)
-Other Wiley-VCH goodies!

cpse-realtimechem-whatscooking-2016-prizes

This year’s cook off prizes

The competition only takes place on the weekend of #RealTimeChem Week. Feel free to cook something during the week, but the tweet must be shared on the weekend of November 5th-6th to count.

All you have to do to enter the competition is to tweet your culinary creation (anything cooking, baking or food related) and include #RealTimeChem #whatscooking & @ChemPubSoc_Euro at the end of your tweet. Your tweet should include a picture or video of your creation and ideally have a short description (the description can even talk about the chemistry in your cooking! It’s up to you). Alternatively, you can write/link a recipe for others to try.

Everyone who tweets a cooking-related post using these hashtags will be entered into the competition, and 5 favourites will win a prize.

Hopefully with a bit more notice this time, you’ll all have time to get some ingredients in and post a tweet. I look forward to seeing what you all come up with!


*@ChemEurJ, @ChemistrySelect, @ChemistryOpen, @ChemBioChem, @ChemCatChem, @ChemMedChem@ChemElectroChem, @ChemPhysChem, @ChemPlusChem, @ChemSusChem,@ChemPhotoChem, @EurJIC, and Eur. J. Org. Chem (all journals of @ChemPubSoc_Euro); @ChemAsianJ, @AsianJOrgChem, and @ChemNanoMat (all journals of the Asian Chemical Editorial Society); and @angew_chem (a journal of @GDCh_aktuell).

 

 

The #RealTimeChem Week Blog Carnival – #NewElemChem (31st October-6th November)

rtcw-new-elements

While the primary action for #RealTimeChem Week takes place on Twitter, there is also a blog carnival that runs alongside it. Chemistry bloggers are part of a thriving community and there are some excellent writers out there just waiting for readers.

Last year, #RealTimeChem Week had a “Back to the Future” theme, resulting in some fantastic posts on #OldTimeChem and #FutureTimeChem (highlights from last year are available here at SciTechConnect).

This year the theme is “New elements in chemistry” (#NewElemChem) and here’s the brief:

Write a blog post about the new chemistry in your life or the new life in your chemistry. The key is the “new” part. Our lives in chemistry are made up of many elements, both chemically and non-chemically speaking, and this is your chance to tell the community all about it. What new reactions have you run this year? Have you had fun with new chemicals? Did you learn something mind-bogglingly for the first time? Are you adapting to a new life situation that’s affecting your chemistry? Have you just started your life as a chemist? You can answer any of these questions and more. Write as little or as much as you like and share it during #RealTimeChem Week with #NewElemChem to be part of the blog carnival.

So, if you are a blogger, write a post and share it during the Week on Twitter using the hastag #NewElemChem. The carnival this year is being kindly hosted again by Elseviers SciTechConnect (thanks Katey Birtcher!). They will be looking out for this hashtag and will collect your blog post into a round up each day so they are all in one place for easy access.

Please note, if you don’t use the hashtag, then your post won’t be included in the carnival, so please make sure you remember to add it. I’ll also be retweeting these via @RealTimeChem to draw attention to them during the week. Happy writing!

 

Compound Interest competition

rtcw-chemunicate-competition

Want a graphic made based on your research? For this year’s #RealTimeChem Week, we’re once again after chemistry researchers who want to explain their research in easy-to-understand terms. To enter, all you have to do is write a piece no longer than 500 words, detailing your work and its potential applications. Note that it should be written so it’s understandable for an audience of non-scientists!

From the submitted pieces, three will be chosen to have graphics made based on them, and these graphics will then be featured alongside your written piece on the Compound Interest site during #RealTimeChem Week, which this year runs from 31 October until 6th November.

You can find details on how to enter here.

 

Other events/competitions

There is always room for more chemistry-based fun. If you would like to run an event or competition during #RealTimeChem Week or to sponsor one of the above events, then please get in touch with me via realtimechem@gmail.com and I’ll be happy to chat about the possibilities.

 

-Doctor Galactic-

 

 

  

It’s #Time4Chem

Hello everybody,

First off, apologies for the lack of updates recently. I’ve been rather busy so far this year both at work and at home so haven’t had the time to do much on the blog. I’m hoping to relaunch the major features like #RealTimeChemInFocus soon.

In the meantime, it’s no secret that I work for the Royal Society of Chemistry as a publishing editor. Generally, I’ve kept #RealTimeChem and the RSC apart, but this year I’ll be making a bit of an exception.

175years

The RSC is the world’s oldest chemical society and is celebrating is 175th anniversary in 2016. As such, it’s going all out this year to recognise it’s history and the chemical community.

It’s hoping that everyone will take some time this year to dedicate 175 minutes to chemistry and then share your story with the rest of the community. Obviously, I know a lot of your spend near 24/7 dedicating yourself to chemistry, but this is a good opportunity to try something different that you may not have considered before.

How does this link into #RealTimeChem and social media? Well, you can share your stories via the dedicated hashtag #Time4Chem, which I’ll be keeping an eye out for this year too.

I’d greatly encourage everyone in the #RealTimeChem community to have some fun with this if you have the time this year. It’s only 175 mins (that’s, like, less than 3 hours) The possibilities of what you can do for your 175 minutes are pretty much endless, but here’s a few suggestions:

  • Take part in some education outreach – a lot of Universities have outreach departments
  • Start a chemistry podcast/youtube channel – chat about chemistry, show off some reactions or chemistry concepts, have some fun.
  • Spend some time editing wikipedia – chemistry articles can always be updated and your knowledge may be just what the world’s biggest free encyclopedia needs.
  • Start a chemistry blog – enjoy writing? Enjoy chemistry? Why not combine both together?
  • Contribute to ChemSpider Synthetic Pages (http://cssp.chemspider.com/)

 

There are many more examples on the RSC website:

http://www.rsc.org/about-us/our-history/175-anniversary/

Just don’t forget to let the RSC know by keeping them up-to-date with #Time4Chem.

Now in particular is a great time to start, as this week is the anniversary week and sees the start of the RSC’s 175 faces of Chemistry exhibition at Burlington House in London – so why not spend some of your 175 minutes celebrating diversity in science? It runs from 22nd February to 4th March.

More information at the link:

http://www.rsc.org/diversity/175-faces/

http://www.rsc.org/events/detail/21557/175-faces-of-chemistry-exhibition

 

Ciao for now,

-Doctor Galactic and The Labcoat Cowboy-

Crystals are a girl chemist’s best friend

My name is Anna Ahveninen. Although that surname can try to convince you otherwise, I’m half a year into my PhD at the University of Melbourne, in Australia. The broad scope of my project is the synthesis of metallosupramolecules and their characterization by X-ray crystallography. The finer details? Well, that’s taking a while to figure out.

 

I’ve only been at the University of Melbourne for as long as I have been working on my PhD. I moved to the Abrahams-Robson group from Monash University, where I completed my undergraduate degree with honours. Having fallen in love with transition metal chemistry — the beautiful coloured complexes and their satisfyingly sparkly crystals — and crystallography in my honours year, the transition to my current project was not a difficult one. Kickstarting it has definitely been troublesome, however. In the past six months, I have been chasing a discrete assembly without a grain of success. The last two months saw a change in my focus from discrete assemblies to coordination polymers (with the same coordination motif), and just a few short weeks ago, I finally hit the jackpot. A red, sparkling, reproducible jackpot.

Since then, I have been working away at trying to turn that result into more results, hoping that it will propagate into a project and grow, with care and love and hard work, into a thesis. The following is a sample of how I am going about that.

Monday

Mondays are pretty exciting for someone working on a crystallography project. Mondays mean that my reactions will all have had at least two extra days to crystallise! I pick up my rack of vials and carry it with a flourish over to the microscope to check for clean edges and tell-tale sparkling. Since we do not have a microscope with a camera in-built, macroscopic pictures of my sparklers will have to satisfy you (Fig. 1).

Figure 1: Vials full of sparkly crystals, ripe for the X-ray diffractometer.

Figure 1: Vials full of sparkly crystals, ripe for the X-ray diffractometer.

I set about my run-of-the-mill inorganicky business until my group’s favourite time of the day: tea time. Although we have no formal group meetings, we meet with our supervisors every day around 4 pm for tea. It gives us the opportunity to ask questions of our supervisors and bring new results to their attention, while also being a nice break and group bonding activity. The group bonding consists of doing the quiz in the Herald Sun and a game involving Fred Basset. Fred is a little tradition that goes far back enough in the Abrahams-Robson group that its origins are unclear. In this game, one of our group members describes the comic strip (Fig. 2). Our job is then to guess what Fred says in the last frame. Weirder than weird to an outsider, this tradition absolutely grows on you, and has become akin to a religious duty in our group.

Figure 2: Fred Basset in his natural habitat. Fred's home is at gocomics.

Figure 2: Fred Basset in his natural habitat. Fred’s home is at gocomics.

My afternoon comes with the pleasant surprise of overnight time on the X-ray diffractometer. One of our postdocs does all of the diffractometer time allocation to ensure that the time is divided fairly, so it always seems to spring up on me.

The X-ray diffractometer (Fig. 3) has to be my favourite instrument. I get a serious thrill when sorting through crystals on a glass slide under the microscope, picking the one I think looks the most promising, mounting it on the diffractometer, centering it and then shining some X-rays on it. The excitement builds at the initial blank frame, and a few seconds later – boom! Diffraction (Fig. 4)! As is common in science, the usual result is very little diffraction, streaky diffraction, or no diffraction at all. It’s all worth it, though, when that first frame flashes up and the spots are well-defined and single and strong and beautiful.

Figure 3: The University of Melbourne X-ray diffractometer.

Figure 3: The University of Melbourne X-ray diffractometer.

Figure 4: A frame from one of my X-ray diffraction data collections.

Figure 4: A frame from one of my X-ray diffraction data collections.

 

Tuesday

The morning begins with a coffee with my group mates, followed by the weekly inorganic chemistry seminar. This week, it is a group member’s colloquium, wherein he has chosen a field of chemistry outside his project to give a talk on. These talks are very interesting to listen to and are usually very educational, both for the speaker and the audience. The rest of the day is spent trying to make sense of my X-ray diffraction data, since I have had the misfortune to be working with high-symmetry cubic systems with a high degree of disorder.

Late in the afternoon, I stop bashing my head against the crystallography wall and take some of my amorphous and microcrystalline samples to the IR spectrometer in the teaching labs. IR spectrometry is free and easy; it helps give me an idea of whether a reaction that doesn’t want to grow nice crystals is worth pursuing.

Wednesday

Wednesday morning is when I would usually demonstrate for my first year class, but since there are no first year practicals running this week, I get a free morning. I spend my time marking reports from the previous experiment. I turn my attention to the lab afterward, but discover that frantic preparation for powder samples for the Australian Synchrotron from two weeks prior has left my stash of 3 mL plastic syringes precariously low. I get a reaction or two in, and am then forced to find something else to do while I wait for the chemistry store to fill my order.

Mid-afternoon, I meet with my supervisor for a long talk regarding my red, sparkling, reproducible jackpot and where we can take my project from here. An hour of musing, brainstorming and me frantically scribbling down notes later, we break for tea. My spirits are elevated and the future of chemistry is looking good.

Thursday

To my annoyance, I discover that the delivery of 3 mL plastic syringes is excruciatingly slow. Crippled into inability to do my reactions, I spend part of my day backing up my lab notebook. A good method that I learnt from the postdoc in my honours year, is to take pictures of your notebook pages and create an index in Excel to correspond to compound syntheses found on particular pages.

Leafing through my notebook leads to a decision to create a spreadsheet to track the variables of reactions I have been doing. I feel more secure having it available at a glance and organised, as I swear I can feel the details slipping out of my brain. I also spend some time catching up on my journal RSS feed, which I admittedly ignore in favour of doing lab work much more often than I should.

Friday

With the delivery of my plastic syringes, I can get into some serious synthesis action. My ligand, when deprotonated, tends to oxidise easily in air. To combat this, I bubble nitrogen gas through all three layers to drive out as much air as possible before layering my ligand with a layer containing a base, a metal salt and a counter-ion (Figure 5). The third vial contains a buffer layer between the two. I run two reactions parallel, as this saves me time in the long run.

Figure 5: How metallosupramolecular chemists do air-sensitive chemistry.

Figure 5: How metallosupramolecular chemists do air-sensitive chemistry.

In case you are curious, the 3 mL syringes come in during layering. I layer my reactions in the reverse order, starting with the least dense layer. Then, I inject the buffer layer below the initial solution, and finally, the densest layer. The volume of the syringes is important since I don’t like to do more than one injection per layer: for one, the suba seal becomes compromised quicker, and for another, it is easier to mess up the layering with more than one injection. Syringes with a too-high volume are also unwieldy and tend to draw in too much gas. When layered well, the reactions can look pretty spectacular (Figure 6).

Figure 6: Either layered reactions or bottled sunrise.

Figure 6: Either layered reactions or bottled sunrise.

My day, and week, draws to a close with drinks, snacks and a game of Cards Against Humanity with my group mates. What better way to end a week of brain-intensive work than a really inappropriate game with a bunch of really awesome people? It’s evenings like these that remind you that life – and science – are awesome.

Author biography

AnnaBioAnna Ahveninen was born and raised in Finland. She completed her Bachelor of Science with Honours in 2014 at Monash University, Melbourne, Australia. She is currently a PhD student under the supervision of Assoc. Prof. Brendan Abrahams at the University of Melbourne. She tweets under the handle @Lady_Beaker and blogs on Chemistry Intersection.


If you are a blogger interested in writing a guest post for #RealTimeChemInFocus, please get in touch with @RealTimeChem on Twitter.
Also don’t forget about #RealTimeChem Week 2015’s blog carnival, starting 19th October. Find out more here.

Joining the dark side of the Force for a week

Hello! I am Clemens, a postdoc at the University of Cambridge, and in this #RealTimeChemInFocus blog post you will follow me, a chemist, doing some “biology” a.k.a. the dark side of the Force.

 

I know it’s weird. Why would a chemist venture into the world of biology in the first place? Honestly, it just happened! Organic chemistry was my first love as an undergrad, even after my final product of a 9-step carbohydrate synthesis decided to spontaneously decompose! I still try holding on to my first love by attempting to solve the Denksport problems of Dirk Trauner’s group and I still admire elegant total syntheses. However, the dark side of the Force has always been strong in me and over the course of my PhD and postdoc, I gradually moved towards chemical biology. I can’t help it; I am simply fascinated how chemistry can give answers to complex problems by probing or perturbing cellular systems. So, without further ado, this is a typical week in my life.

Monday

Although I am not a particular fan of Monday mornings, this Monday morning is one of the toughest of the year! I just came back from an exciting week featuring the ISACS16 conference in Zurich and a 3-day music festival in Austria (Figure 1). It made me realize how similar festivals and conferences are. Long days, short nights, meeting new people and listening to some raw talent all day long.

Figure 1: A tough start to this week after a conference & festival double feature last week.

Figure 1: A tough start to this week after a conference & festival double feature last week.

Don’t get me wrong, I enjoyed it a lot, but it took a lot of energy out of me and getting up for the obligatory Monday morning group meeting at 9 a.m. is tough. I get coffee and arrive on time, a miracle! After the meeting, which is held in the Chemistry department, I postpone my plans to go to the Cancer Research UK (CRUK) Cambridge Institute, where the biology projects of our group happen, for one day and take some time to recover. After all, I missed a lot of science in the last week, as my RSS feed and email client tell me (Figure 2). Even better, I have to analyze some exciting sequencing data, which were generated in my absence. Having multiple, diverse projects running in parallel is one of the great things about being a chemical biologist. As my computer does all the hard work, aligning millions of reads to a reference genome, all I need to do is drink coffee and use the software correctly. The latter is something I am still struggling with (Figure 2). Nevertheless, at the end of the day I get everything analyzed and the results tell me that I am all set for writing my first manuscript as a postdoc! I also managed to catch up with my emails and the RSS feed so it’s time to cycle home and get some much-needed rest!

Figure 2: Clearly, I haven't figured out how to take screenshots on a mac…

Figure 2: Clearly, I haven’t figured out how to take screenshots on a mac…

Tuesday

Another morning and it is time to head to the CRUK Cambridge Institute (Figure 3), where I will spend the rest of my working week.

Figure 3: The CRUK Cambridge institute and yes, we do have the occasional sunshine here in the UK.

Figure 3: The CRUK Cambridge institute and yes, we do have the occasional sunshine here in the UK.

I am not sure how many of you fellow chemists have ever set food in a hardcore biology working environment, so let me give you a short tour. Things here are a lot cleaner and the number of fume hoods is sadly kept to a bare minimum. They are mostly used for “dangerous” phenol-chloroform extractions of nucleic acids. Being thrown into a new working environment, I always look out for things I recognize or can relate to. Lab coats are mandatory and even wearing eye protection is reinforced (Figure 4). You can also spot the occasional TLC chamber (everybody loves TLC chambers), although they are often used for a completely different purpose than analyzing your reactions.

Figure 4: Familiar sights for a chemist in a biology lab.

Figure 4: Familiar sights for a chemist in a biology lab.

Once you are feeling more comfortable in the world of biology, you might even find more similarities to your familiar chemistry lab. For working with tissue cultures, we have special hoods that remind me a lot of glove boxes. Instead of using an airlock you are using ethanol to decontaminate everything before placing it inside the hood. Of course, once you put your thoroughly washed hands inside, your nose starts to itch. Another similarity to the familiar glove box; you have to keep the place spotless as contamination with evil bacteria or yeast will spoil not only your cells, but could affect the cultures of a whole lot of other people (Figure 5). This scenario is especially bothersome, when you have worked for months creating a cell line for a particular disease you’re studying, only to find it contaminated and yourself right back at the start of your project.

Figure 5: Things you do not want find in your mammalian cell cultures! (https://www.microscopyu.com/articles/livecellimaging/livecellmaintenance.html)

Figure 5: Things you do not want find in your mammalian cell cultures! (https://www.microscopyu.com/articles/livecellimaging/livecellmaintenance.html)

Unfortunately for you, I won’t culture any cells this week, so I can’t show of my recently acquired and still embarrassingly clumsy skills, but I encourage anyone who’s curious to give it a go. It is surprisingly simple to culture mammalian cells like HeLa or HEK293 and as a chemist you have enough skills in your repertoire to learn it quickly. Because you have to work carefully and be gentle with the cells, I always picture myself handling tert-BuLi, which freaks me out, but my cells seem to appreciate the gentle treatment.

The plan for the week is to continue with a project I stopped working on before my week abroad. To cut a rather long story short, we identified some potential protein targets in a screen and are now keen on validating these hits. To get an independent confirmation, we need to clone all  28 proteins of interest (P.O.I.) into a transfection vector and express them inside the cell as a tagged version, in order to confirm the interaction by Western blot. That should suffice to give you a rough idea, and the rest of my day is spent planning everything and diluting 56 primers to the right concentrations. By the time night falls, my pipetting thumb has had a good workout!

Wednesday

I spent my PhD in an enzyme-engineering lab, so I did my fair share of cloning and from my experience I can tell you everything starts approximately like this:

Figure 6: Every good cloning starts with a successful PCR. The tricky thing is where to go from there.

Figure 6: Every good cloning starts with a successful PCR. The tricky thing is where to go from there.

For the current task at hand it is a bit trickier. For half of our P.O.I.s we were lucky and could obtain the cDNA – that is the complementary DNA synthesized from the corresponding messenger RNA – in the form of E. coli glycerol stocks that carry a vector containing the cDNA. For these proteins, cloning is easy: isolate the plasmid from the E. coli precultures and simply amplify the cDNA with the correct primers. We use primers that have 5’ and 3’ overhangs, which allow us to subclone the amplified cDNAs into the Gateway cloning system (Figure 7, http://scienceftw.wikia.com/wiki/Gateway_cloning).

Figure 7: Step-by-step workflow of Gateway cloning.

Figure 7: Step-by-step workflow of Gateway cloning.

This method is neat, because it uses a recombinase instead of restriction enzymes and the main objective is to bring your insert into the entry vector for the Gateway system. From there, you can use another recombinase and insert your cDNA into a whole bunch of different vectors that carry appropriate tags and also allows transfecting mammalian cells! Compared to 10 years ago, when I first tackled a cloning problem, this protocol is a piece of cake.

As I started the E. coli precultures from the glycerol stocks before I left yesterday, my day consists of isolating the plasmid, doing the PCR reactions, and purifying the inserts. Sounds like a walk in the park, but it takes time (a lot of pipetting again). By the end of the day, I got 12 out of 28 cDNAs ready to insert them into the entry vector. It was clearly a successful day and I leave the lab happy for my weekly basketball game!

Thursday

Today, I start the cloning of the P.O.I.s we couldn’t obtain from the cDNA in the convenient E. coli glycerol stock form. This cloning is a lot trickier, as we have to prepare our own cDNA. For this, we isolate the total RNA from HeLA cells, which involves a phenol-chloroform extraction (so dangerous!) in a real hood (so happy!). Next, we use a poly dT primer that – at least in theory – is expected to hybridize with all mRNAs in the cell as they carry a complementary poly A tail. Creating an RNA-DNA duplex allows us to reverse transcribe the whole transcriptome and generate our sought-after cDNAs. In principle, we should have our P.O.I. cDNAs in there as well, however there is no easy way of determining the concentration and whether they were fully reverse transcribed in the first place. Nevertheless, we take the crude reaction as a template for some PCR reactions. Given that we are working with a complex mixture, I start a gradient PCR – which probes annealing temperatures between 50 and 70 degrees – and hope for the best. A few hours later, I load the first 48 out of 96 PCR reactions onto an agarose gel (Figure 8), and after size separation take a look at the gel under UV light! Hurray, for 4 of 6 targets we amplified something (Figure 8). I check, whether they have the right size, which they all do, and purify them. The second batch looks equally good, which means that combined with the inserts I amplified yesterday, I got 25 out of 28 constructs ready for the recombination reaction. That’s pretty awesome and I call it a day!

Figure 8: Loading of my agarose gel on the left (hoping), results on the right (celebrating).

Figure 8: Loading of my agarose gel on the left (hoping), results on the right (celebrating).

 

Friday

It’s Friday! And it’s a special Friday, as we are invited to our bosses place for a British “summer” BBQ. I prepared some salmon-spinach roles yesterday night, but they really looked ugly so I didn’t dare taking a picture. With the BBQ coming up later in the afternoon, it will also be a short day in the lab, which suits me, as all I need to do is finishing the first stage of my cloning efforts.

To insert my cDNAs into the Gateway entry vector, all I need to do is mix the vector with my PCR products. I then add the recombinase enzyme that swaps the standard insert – a gene encoding for a toxic protein that prevents growth of false positives – with my cDNAs. After incubating the reaction for an hour at room temperature, I thaw some chemically competent E. coli cells, which I will use for the upcoming transformation. These bacteria are suspended in a buffer-DMSO mixture, conditions that promote plasmid uptake through the cell membrane when heated to 42 degrees Celsius for a short time (about a minute). This procedure is a bit cruel as it kills most of the bacteria; after all they don’t like the DMSO too much. However, some bacteria that took up the plasmid during the heat shock survive and they are allowed to recover at 37 degrees Celsius in a rich medium for half an hour. Next, they are pelleted by centrifugation and resuspended in 100 μL of medium. The E. coli suspension is finally spread onto LB agar plates that have the right antibiotic (kanamycin) in them, which ensures the plasmid is amplified while the bacteria happily divide. Normally, you would incubate at 37 degrees Celsius overnight, which will give you good-sized colonies; however, with the BBQ and the weekend coming up, I just place them on my bench, where they will incubate at room temperature over the weekend, delaying the growth by about two days (Figure 9).

Figure 9: My prize after a week of cloning! Grow E. coli, grow!

Figure 9: My prize after a week of cloning! Grow E. coli, grow!

All there’s left to do: Head home, get the ugly salmon-spinach roles out of the fridge, cycle to my bosses place and enjoy a burger and some beer at the BBQ. Obviously, rain begins to fall as soon as the BBQ starts, but hey, that’s life in the UK after all.

 Figure 10: A proper British “Summer” BBQ in the rain.


Figure 10: A proper British “Summer” BBQ in the rain.

Author biography:

ClemensClemens Mayer is a postdoc, working at the University of Cambridge under the supervision of Prof. Shankar Balasubramanian. He was born in Graz, where he completed his undergrad in 2008. Subsequently, he moved to Zurich to pursue his Ph.D. in the field of enzyme engineering. In 2014 he joined the University of Cambridge, where he is currently investigating the role of RNA structures in biological processes. Passions include coffee, basketball, the accumulation of useless knowledge, being a geek, and dreading the English summer.


If you are interested in writing a guest post for #RealTimeChemInFocus, please get in touch with @RealTimeChem on Twitter.

Chemistry: Lost in Translation (sort of)

I’m Jason Hoshikawa, a 2nd year PhD student in the Kitagawa Lab at Kyoto University in Kyoto, Japan.My main area of focus is polymer synthesis and heterogenous catalysis using porous coordination polymers (PCPs).

The thing about working in the sciences (and maybe the arts too) is that we generally work in a multi-cultural environment. During my undergrad and Masters in the US, I was the native surrounded by foreign students. It was a wonderful experience. Many of the members of that group were from India, specifically from around the Hyderabad area. This turned out nicely for me because Indian food is my favorite food. When I entered my first research lab as an undergrad, I was assigned to work with a woman that makes the most amazing food. She quickly learned the key to motivating me to work hard in the lab. If I worked late enough, she would bring me dinner. I miss those dinners more than you can imagine.

Kyoto University's clocktower. - Image Courtesy of Wikipedia.

Kyoto University’s clock tower – Image Courtesy of Wikipedia.

But, now, I live in Japan where I am the foreign student surrounded by natives. Aside from learning about chemistry, I’ve learned a lot about myself. This is not the first time I’ve lived in Japan, but this time it’s very different from my previous experiences.

More than the simple difference in culture between the US and Japan, the other bit of context that may be important is that the Chemistry Department at my previous university is relatively small compared to our department at Kyoto University. The change in environment was quite significant. Going from a department where everyone basically knows everyone else to a department where there are simply too many people to know hardly anyone outside one’s own research group was rather shocking.

In my research group, all of the students are assigned various jobs. Most students are assigned to manage an instrument or two, and some students, like myself, are assigned to administrative roles. I have two administrative roles, actually. Firstly, I am the lab manager. I’m responsible for the general day-to-day operation of the lab (i.e., the room where experiments are performed). I purchase all the expendables (e.g., gloves, vials, pipette tips, glassware, weigh paper, etc). In a separate (but related) administrative role, I’m also responsible for buying all of the solvents (both regular and deuterated) and common reagents (acids, bases, metal salts, etc). Basically, I buy everything except specific reagents that only one or two people would use, and instrument-specific expendables.

An average day

In our lab, we work Monday through Saturday, and the layout of my day is basically the same, unless there is something special that requires me to leave early.

My alarm is set for 07:00. The actual time that I wake up varies seasonally. I don’t have blackout curtains in my room, and Japan doesn’t observe summer time (which I’m happy about), so right now, the sun rises at around 05:00. During the summer, I wake up often before my alarm, but during the winter, I can usually sleep until my alarm wakes me up.

I like to leave my apartment at 08:45 so that I can get to the bus stop early enough to get a seat on the 09:00 bus. The trip to campus takes about 10 mins. If you’d like to see the area around where I live on the bus ride to campus, watch the video below.

I take breakfast at the bakery on campus. They have a lovely breakfast set for Â¥270, and I usually add to that a donut (Â¥151). While I eat breakfast, I like to look at twitter, reddit or Instagram, while listening to a podcast. My work day starts between 09:30 and 10:00. Everyone usually gets in during this time, and we generally think of 10:00 as the start of our workday. The first work period is 10:00 to 12:30. During this time I like to look over new ASAPs in my RSS reader, and then try to write for an hour, or look up papers. Then at 12:30 we have an hour for lunch. My hearing is not so good, so I tend to eat lunch by myself in the office rather than going to the cafeteria with everyone else. I used to go, but it’s just so noisy that I can’t really hear anyone. So, I sit at my desk and watch the PBS Newshour (@pbsnewshour) on YouTube.

After lunch is the second work period that runs from about 13:30 to 19:30. During this block of time, I like to do heavy synthetic work. I try to start reactions, end reactions, and do work up during this period. If at all possible, I try to do all synthesis related work during that six hours.

Dinner from 19:30 to 20:00. After dinner, I try to focus mainly on characterization. After 20:00, the number of students starts to decrease, and it’s easier to make reservations on the instruments. I can use them in peace and quiet.

I generally go home on one of the two busses in the 22:00-hour. Once home, I decompress by taking a shower and reading until I fall asleep. With that ideal in mind, here is reality…

An average week

Saturday

I like to think of my week starting on a Saturday. The reason is because that it’s the last day of the research week. I go through and take inventory of the lab in order to figure out what I need to order. It’s not as involved as it may sound. It usually occupies the first work period. I have lists of everything so I can check through quickly, and for most things, I can stand in one spot and just look around the room while marking off my list. The solvents are easy too. I open the cabinet and count the bottles remaining.

I place the orders by writing them into the order notebooks for each of the suppliers. In Japan, representatives from manufactures and suppliers come around several times a day to collect the orders, and then they deliver them directly. Each lab manages its own finances, so as long as one isn’t buying and NMR spectrometer, there is almost no red tape.

Figure 1

Figure 1

On this particular day, I spent most of it cleaning as my workbench was a complete disaster (Figure 1). Also, I didn’t want to start any reactions because the reactions that wanted/needed to do I did not want to leave running unchecked on Sunday.

Sunday

Sunday is the one day a week off that we have. I treasure those days. Getting to sleep in late, and getting to do what I want all day is a luxury I try not to squander. However, there are still practical things that must be done. As if cleaning my workbench wasn’t enough, I clean my apartment and do laundry. I also cook lunch and dinner for the next seven day period. I try to do as much pleasure reading as I can because during the rest of the week, I read mainly research related materials. It’s a nice break.

Monday

I had run out of a ligand that I need to make several of the MOFs that I use. To start the process, I perform a Suzuki-Miyaura coupling reaction. I use the reaction to couple an arylbromide with an arylboronic acid.

Figure 2

Figure 2

Figure 2 shows the progression of the reaction. In the upper left is the start of the reaction. The brown color is from the palladium(II) acetate that I’m using as the catalyst. The upper right shows the reaction mixture right before I stop the reaction. The palladium has formed palladium black over the course of the reaction. During the catalytic cycle, palladium(0) is formed, and in this oxidation state, if two palladium(0) atoms bump into each other, they can begin to form palladium nano particles, which kills the catalyst. Basically, the reaction is over. The lower right shows the result after liquid-liquid extraction. Many people try to get rid of the palladium black, but I find it too much trouble to deal with, plus I always end up with a lower yield. I prefer to just let most of it get clumped onto the magnesium sulfate that I used to dry the organic extract, and if it still persists after filtration, it will be stopped by the column when I purify by chromatography. In the lower right is the nice white powder that I obtain after purification.

Incidentally, I love watching the condenser of the rotavap.

Tuesday

It’s lab clean up day! Every Tuesday morning, everyone gets together and cleans the lab. At my university, every lab is responsible for taking out the trash and the recycling. The cleaning staff are only responsible for common areas. The labs are our responsibility. This is an average load of refuse for a week (Figure 3):

Figure 3

Figure 3

The product from the previous reaction has a methyl group attach to a phenyl ring. This methyl group can be easily oxidized to a carboxylic acid. A synonymous reaction would be that of turning toluene into benzoic acid. The method I prefer is heating the starting material in a hydrothermal vessel in the presence of about 30% nitric acid (Figure 4).

Figure 4

Figure 4

This reaction makes me nervous because it heats nitric acid to 170 ℃. The product of this reaction, aside from the carboxylic acid, is a lot of nitric oxide gas. I made a video showing the opening of the vessel after the reaction.

Wednesday

After the ligand has been purified, it’s time to make the PCPs. The PCPs that I use are made of a mix of ligands. That means I combine more than one ligand to form the framework in the hopes of altering the pore surface functionality. I made two different PCPs on this day. One is a copper(II)-based PCP, and it’s synthesized in two steps.

In the first step, one set of ligands are combined with a copper(II) salt. This is then stirred for two days. The video below shows the mixing of reagents at the beginning of the reaction.

The other MOF is aluminium(III)-based. It’s a one step reaction that performed in a glass vial in the oven at 120 ℃. Unfortunately, that’s all I can say about those projects until they are published!

Thursday

I spent most of this day performing spectroscopy. Of all the spectroscopic techniques, NMR is my favorite. I fell in love with NMR the first day I had ever heard of it.

Figure 5

Figure 5

Our NMR lab (Firgure 5) has three spectrometers, all made by JEOL. In the foreground is the 400 MHz, behind that is the 600 MHz (my workhorse), and in the back on the right side is a 500 MHz. The sample that I was measuring that day was of a polymer that I had synthesized. I was doing a full set of characterization, so I set up a whole set of experiments: 1-D 1H and 13C, COSY, HSQC and I measured relaxation t1 with a double pulse experiment.

Figure 6

Figure 6

The sample (Figrue 6) was dissolved in benzene-d6, and I was was worried that since this sample would be running for 3 or 4 days that the solvent would slowly evaporate, so I sealed it rather than using a cap.

Friday

I realized that I forgot to add the group meeting schedule to my calendar. I’m presenting on Monday of the next week. There’s two things you should know about me. First, I have a terrible memory. If my Google calendar doesn’t remind me about important things like group meetings, I will surely forget them. Of course this isn’t a fail proof system because I have to remember to put these important reminders into the calendar first!

Normally, I do it right when I get the e-mail from the boss with the schedule for the next month. Somehow, I forgot.

The second thing is, I really hate making presentations. I often wish I could pay someone to do it for me. In some ways, I think this might make me a failure as a scientist (Editor’s note: Far from it!) While I love using my computer, I hate being chained to it. That’s how I feel when I have to sit and work on a presentation, or poster, or paper. I would much rather just work in the lab. However, I realize that it doesn’t work that way. My results, success or failure, are meaningless unless I report them.

However true that may be, making presentations is still probably my least favorite thing to do in science. And so, since I forgot, I spent most of the Friday and Saturday compiling data and making figures and putting together a presentation.

Maybe next week won’t be so crazy.

Yeah, that’s what I always tell myself.

Author biography:

wLT3vNAF_400x400Jason Hoshikawa is a 2nd year PhD student working in the Kitagawa Lab at Kyoto University under Assoc. Prof. Takashi Uemura. He was born in Dallas, Texas. After working in the television and radio industry as a high-power transmitter engineer, he started his undergrad education at the University of Hawaii at Manoa, but returned to Texas to finish his BS in Chemistry (2010) and MSc in Organic Chemistry (2012) at the University of North Texas under Prof. Mohammad A Omary. After being awarded a Japanese Government Scholarship for Research Students (2013) he entered the Graduate School of Engineering at Kyoto University to complete his PhD studies.

You can follow Jason on Twitter (@ChemistInJapan), on YouTube (https://www.youtube.com/user/ChemistInJapan), and Instagram (@ChemistInJapan).

The weekly adventures of a jolly chemist

In this world there are two kind of postdocs: some are hired for a specific project and are focused on that, others are jolly helping here and there. I am, ladies and gentleman, a jolly.

I’m Vittorio Saggiomo, a postdoc in the BioNanoTechnology group at the University of Wageningen (in the sunny, sunny Netherlands). As a jolly, I’m working on PDMS microfluidics chips, coacervate micelles and (quite a lot) of devices with chemical sensors for soil, animal food, and recently, malaria vectors.

As I tend to swear a lot, in this blogpost I’ve censored myself changing the word f*ck with frak (Doctor Galactic: I’m partial to frell myself).

Vit1

Fig 1. Example of the research going on in my university…

Fig 2. Mosquito farm

Monday starts like all my Mondays: the alarm clock buzzing on my night table, me thinking that it’s Sunday morning and relaxing a little bit more in the bed. Between 10 and 15 minutes later I finally realize that it’s not Sunday and I have to rush to the university. Welcome, first frak of the week.

Our building is probably the only laboratory in the whole of the Netherlands that is uphill (here it’s called “the mountain”) and when I’m late I try to bike as fast as I can. Entering the corridor of the building is like finishing the marathon, with coworkers cheering me up and giving me water. In a chaos of people screaming my name I finally enter my office with only 30/45 minutes of delay. Then I usually need 10/15 minutes to recover from the high speed biking uphill, and to get my heartbeat on a human level and to try to breath again.

Turn on my computer, 20/30 unread email, 10/15 “frak I completely forgot about this” and “oh for frak’s sake” and finally I’m in the lab, my acetone smelling kingdom.

I devote the first two days of the week on synthesis. We are trying to control the core of the coacervate micelle (very huge 100 nm micelles with a soft core of chocolate (ok, maybe not chocolate, but still a soft core) for incorporating and releasing drugs on command (hopefully our command). I put a couple of reactions on the notes of Metallica and/or AC/DC.

I spend the rest of the day supervising (or trying my best to) two master students.

Fig 3. Fairy dust synthesis

Tuesday is purification day. I love column chromatography, I find it extremely zen and relaxing. And it gives me an awesome excuse not to do anything else -“come on dude, I cannot stop my column, I’ll come to you later”-. TLC, rotavap, NMR, and then i can choose between: “fraking hell, why you don’t want to work?”, “what the frak are you?”, “for frak sake, who on earth is doing a 2 h proton NMR?”.

Then I try not to get mad at one master student because he believes that his column didn’t work because the size of the capillaries is wrong. Between a colloquium and a coworker that MUST show you at least 10 youtube videos the day passes quite easily. Tuesday after work is also squash night with my boss. Perfect for stress reliever and for legs related injuries.

Fig 4. The eye of Sauron

Wednesday is PDMS and devices day. Since I came in this lab I have fallen in love with PDMS, an extremely nice polymer for making microfluidics chips, stamps for microcontact printing and bouncing balls. I spend most of the day playing around with PDMS, using different crosslinkers, checking the swelling and the stability, pressure and so on. We are currently applying for a patent on a discovery we made last year and now are waiting to publish it. Usually on a Wednesday I also discuss a little bit with the boss. It happens more or less randomly, but most of the time it is on Wednesday. My boss’ office is between my lab and my office and when I walk from one place to the other I can clearly hear someone screaming my name.

The discussion goes often like this (I’m currently working on many different projects and I’m extremely picky on which new project I can accept):

Boss: Maybe we can do this…

Me: No.

Boss: Yes.

Me: No.

Boss: Yes.

Me: No.

Boss: Yes.

Me: No.

The discussion can go on for hours. The first that lowers his eyes loses.

When I’m finally back in the lab I can start soldering wires, checking resistances and programming Arduino and Raspberry Pi. It’s not chemistry but it’s quite entertaining.

Fig 5. Maybe a pinch more crosslinker.

Fig 6. Maybe even more crosslinker.

 

Fig 7. Pinky microfluidics.

Thursday is terminator day. The day of the machines. Now NMR, now fluorimeter, now AFM. The synthesis of new sensor would be useless without some in-depth characterization. In this day the amount of fraks climbs to the top. Swearing at a random machine is one of my favorite hobbies. When Skynet finally takes control of the world I will be one of the first to be murdered (or enslaved). The time lost in understanding why a machine is not properly working is way more than the time used for the real analysis. Today is also a day of squash with my colleagues. Time for shoulder related injuries.

Fig 8. 8-bit AFM.

Friday is group meeting day. I usually clean a little bit in the lab, write down the stuff I did in the week and program what I’ll do the following week. The group meeting starts after lunch and no one knows when it will end, but usually we finish very, very late. Beer, alcohol and junk food are more than welcome during the discussions. BBQ in summer time. We also use 10 minutes of our time collectively swearing at a random referee number 3.

Fig 9. Group meeting.

Saturday and Sunday I try to read some literature, writing/correcting/rewriting papers,grant, patents and blog posts.

….and from my side, that’s all folks. Feel free to contact me for info, news, fun or just for swearing together.

 

Author biography:

Vit

Dr. Vittorio Saggiomo is a post doc, working at the University of Wageningen under Professor Aldrick Velders. He was born in Naples (Italy) where earning an M.Sc in Organic Chemistry in 2007. He then moved to Kiel (Germany) pursuing a Ph.D. working on Dynamic Combinatorial Chemistry. In 2010 he moved to Groningen for his first post doc in the field of Systems Chemistry, before heading to Wageningen. Find about more about him at: www.vsaggiomo.com/

Blogs at Labsolutely (http://www.labsolutely.org/) & creates videos on Youtube (https://www.youtube.com/user/vsaggiomo)

 

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/)

 

Chemistry stars don’t shine in Science Magazine’s Twitter galaxy.

Hello everyone,

It’s been a while since I last blogged all the way back during #RealTimeChem week. A lot of interesting stuff has happened in the online chemistry world since then, in particular Science Magazine’s much debated and hugely controversial “Top 50 science stars of Twitter“. I’m a little late to write a long winded blog post on how immensely wrong this list was, but suffice to say it mostly boiled down to 1) a lack of women (4 out of 50!) and 2) zero chemists.

A galaxy of science stars. Probably more likely to find Wally than a chemist in here.

Although considering that Science Magazine has tried to rectify their original mistakes by creating a sequel to this list, which adds an extra 50 stars, maybe I’m not so late after all. If at first you don’t succeed and all that jazz. While the new list is something of an improvement in that it adds some more women into the mix, it also adds in a raft of all male economists and Brian May (who may have completed his thesis recently, but I’d hardly consider his stardom due to science).

The excellent Paige Brown Jarreau addressed the lack of women in the original list in some considerable style with her blog post response to Science Magazine’s list. It’s well worth a read, explains the situation far more succinctly than I could and is a fantastic guide to finding some of the many women who tweet about science on a daily basis (you can also check the hashtag #WomenTweetScienceToo). I maintain that a career in science (in all of it’s shapes and forms) should be open to both genders on this planet.  Anyone who disagrees with this… well, here’s a door. Please use it.

No, that white light isn't heaven, it's oblivion.

No, that white light isn’t heaven, it’s oblivion.

With respect to the second point earlier, considering the amount of time I’ve spent on Twitter conversing and interacting with other chemists via #RealTimeChem, I was rather flabbergasted by the omission of every single one of them, especially considering that there are some who are plenty more active than many of the Tweeters on Science Magazine’s so-called “Top 50”.

So, when I was approached by Lauren Wolf to be a member of a panel to choose 20 Chemists Worth Following on Twitter I jumped at the chance. Please check the link if you want to find some cool Chemists to follow. Alternatively, check out Stuart Cantrill’s somewhat larger list as well (you could also follow @RealTimeChem, but hopefully you already know about that one).

With the release of the second longer list and still a lack of any chemists, it does begin to beg the question…where are the social media stars of chemistry? Why doesn’t our branch of science have anyone with enough popularity (judging from the number of followers anyway) to make it on to this list? Why is the most famous modern chemist the average person on the street can name most probably a fictional meth peddler?

He does wear a hat well.

These are difficult questions to answer. Chemistry certainly has a well documented image problem in the wider mainstream media at the moment. An image where chemicals are more often than not instantly labelled as “bad” and big pharma is the equivalent of the stereotypical moustache-twirling evil villain of old black and white movies.

It might be that Chemistry seemingly doesn’t have the same sex appeal as other sciences such as physics, which can pull any number of fancy universe spanning subjects out of its bag of tricks.

Just look at that. Physicists have claimed the universe as their playground.

They’ve also got Professor Brian Cox, super star. A man who is so not a fan of chemistry he’s hopeful that the notion of chemistry will disappear forever to be replaced by his beloved physics.

How can we improve this situation? How can we ensure a chemist is included on any future lists of science’s social media stars?

We work harder. We shout louder. We show the world what chemistry means to us and what it should mean to human kind. We engage. We enthuse. We excite. We amaze.  

Oh… and we should probably all tweet a lot more. 

-The Lab Coat Cowboy-

Could more be done to teach young chemists the right ethics?

Disclaimer: As always this is just my opinion. In fact, this blog post is more of a stream of consciousness that I’ve had today more than a structured argument. Please feel free to discuss this issue with me on Twitter (@doctor_galactic) or in the comments section.

Do young scientists need more guidance on scientific ethics?

Do young scientists need more guidance on scientific ethics?

I imagine that by now most of the chemistry community is aware of the “Dorta affair” that has been recently exposed by ChemBark. In brief, a recently published article in the journal Organometallics contained a rather suspcious note in its supporting information that seemed to suggest that the principal investigator was asking his student to fabricate elemental analysis data (the actual supporting information can be found here).

This line will probably lead to a "meme". Please just don't. Do something with cats instead.

This line will probably lead to a “meme”. Please just don’t. Do something with cats instead.

How this note, which appears on page 12, came to be, what it actually means and how it got through the peer review process are all under investigation. Unsurprisingly, this issue has sparked a huge amount of debate. As for my own two pence on the issue, I’m reserving judgement until all of the facts have been fully revealed. Let’s just say it does not look good, at all. I will say that I hope that everyone stays professional as distinctly dislike “witch hunts” and “personal assassinations”. So far, the authors have not defended themselves and they should have the opportunity to do so. The paper is currently I believe being withdrawn.

All in all though seeing something like this in a published work reminds me of a song by Tim Vine and should sound “Alarm Bells”:

Science in general is receiving an ever increasing amount of scrutiny concerning just how widespread fraud is, be it plagiarism, deception, bribery, sabotage, professorial misconduct or simply making shit up. A lot of this is likely a symptom of the “publish or perish” culture that seems to have a vice-like grip on the scientific world. Research-oriented universities put pressure on scholars, particularly those early in their careers, to publish as much as possible. This can detract from the amount of time that they have to actually teach and train undergraduates and postgraduates. Universities largely don’t seem to hire on teaching/mentoring ability, but rather by apparent research prowess. This approach can be detrimental to creating the next generation of scientists.

Anyway, all of this leads to some questions (and the point of this already rambling blog post); from where do we new chemists learn our scientific ethical compass? And could we do more to teach chemists (and scientists in general) the correct ethics?

PhD comics has a comic covering most things in your PhD and a lot of them are very accurate.

One imagines that the biggest influence on your ethical choices as a student of the sciences are your teachers, lecturers and subsequently your PhD supervisor. Let’s go straight to the example of PhD students. I’ve certainly worked for senior chemists who were ethical and always encouraged the right sort of behaviour. But, what if they hadn’t? What if you do have a supervisor who encourages you to do something that is not ethically correct? Most of us would say that we’d cry foul and say no. However, clearly this is not the case for all of us. It seems that would probably go along what our supervisor suggests, PhD’s are stressful, supervisors often want results all the time, corners may be cut and it may seem all perfectly innocent and reasonable if your supervisor says it’s okay. They are your direct boss. This is the person you work for after all, they are your scientific mentor.

Of course it’s perfectly possible that a supervisor can be ethically perfect and a student can still do things that are not. In which case it is still the supervisors responsiblity to: a) spot this and b) stamp it out.

By the time you get to being a PhD student you should have already developed a strong idea of the ethical rights and wrongs of science. You should feel empowered enough to say no if you are asked to do something that you know is wrong. This empowerment and the ideals should come from the top down at your University (that place of learning that you’re spending a huge amount of money to attend). They should have provided you with ethical guidelines and a structure by which to report any ethical problems that you run into. However, is what you get from your University on this subject adequate?

I posted the following question on Twitter to my chemistry based followers (of which I have quite a few these days!):

The response so far have ranged from PhDs being given full courses (even at the undergraduate level) to practically nothing at all. In my own experience, I don’t recall any formal courses or talks being made at my University on this subject, at least not any that were mandatory or weren’t so perfunctory that I actually could remember them. Like a lot of universities mine ran “doctoral workshops”, but attendance at these was never truly enforced, they are merely suggestions. This can vary wildly from insitution to instuition, and from supervisor to supervisor. Yet, it really shouldn’t. There should be some kind of set standard level of training. The general impression given during a PhD is that your laboratory work comes first and everything else is secondary and should happen off your own back. In part, I feel like this is actually okay sometimes, after all, every PhD students should take responsibility for their own career and personal development.

Take this place. Not that hot on the ethics. At least it’s only a Disney film.

The question becomes, are universities giving PhD students the tools to do this? I have only good things to say about the supervisors I have worked for, but I cannot say the same for the institutions I have worked at. I haven’t written a blog post on my experiences with university administrations (mainly because it brings up bad memories and I think it’s time to let bygones be bygones), but suffice to say that I have generally felt, at times, like those higher up have an “out of sight, out of mind” attitude toward postgraduates.

At my postgraduate university the grand sum of ethics training for PhD student was a handbook to read and a form to sign. It’s all in there of course, in black and white, the “do’s and don’ts” and the consequences and processes, but these are just words on a page. It’s something you read, sign a piece of paper to say that you have read it and then, probably, never read again. That’s it. All ethic’d up for 3-4 years. The same kind of forms and hand books come out again at Post Doctoral stage.

I think that universities should take more responsibility for ensuring that students are adequately equipped to understand and follow the ethical guidelines of science. That students feel empowered enough to take a stand and report unethical behaviour and recognise that a good scientist is an ethical scientist. It is something that should be drilled into those learning science from the moment they enter an institution of higher learning until the day that they leave it (preferably before this). I’d advocate training courses at undergraduate, postgraduate and post doctoral levels, giving case studies, advice and information about the procedures in place at the university to deal with ethical issues.

This should really form only a small part of an all around more adequate training for postgraduate students at all higher education institutions. So that PhD students are better equipped for their future careers. Currently, it’s a complete lottery in terms of the amount and quality of extra training and support that are available to postgraduates and this should not be the case.

Going back to the title of this blog post; could more be done to teach young chemists the right ethics?

Yes.

-The Lab Coat Cowboy-