Autumn leaves

Autumn is upon us. The rain is coming, the temperature is dropping and the trees are changing from their summery greens into their autumnal reds and golds.

I saw Compound Chem had made a wonderful infographic about the chemicals that produce the brilliant coloured leaves this time of the year and so I sent the link to my Dad, an avid gardener. He then replied to me with a poem, another of his hobbies, that he'd written a few years ago describing the changes to the leaves with a chemical insight.

The colours in the leaves

Once the green of chlorophyll,

Didst verdant scenes on yonder hill,

Fill with glowing hues its summer’s glory,

And leaves shine forth to tell a chemist’s story.

As leaves do turn to feed from moistened light,

And deadly gas from which these leafy leaves will soon take flight.

How silently, as autumn ushers in bright days yet frosty nights,

These many-hued greens give way to other sights.

Other forms usurp the molecular green-maker’s robe,

And from their secret lair these tribes with ear-harsh names do probe.

So chlorophyll succumbs to xanthophyll,

No more such verdant scenes on yonder hill,

And carotene and anthocyanins do hold the day,

And orange, yellow, red and gold do sway.

Yet does not summer green pass to autumn splendour,

And to us cold breezes crispness render. 

Peter Branson 2007

That love-hate supervisor relationship

 
What? I've not even started this blog post yet and you've already got a problem.

Supervisors

A mentor, a role model, a leader, a helping hand. These are all terms that could describe that voice of reason encouraging your next step. But when it came to reports and manuscripts, my supervisor always made me see red. Red pen that is.

Just wait a minute I'll get on to it soon.

 

No, I'm saying what you did. That's the point.

My PhD supervisor kept a certain red pen that he saved especially for colouring in my reports. Don't get me wrong, I was very grateful for all the feedback and insightful comments. Only it was sometimes quite hard to pick out the wise words amongst all the scribbles that appeared in the margins, on the figures and generally in any part of the paper with the smallest bit of blank space available. I spent hours writing up my work and of course felt some pride when presenting good results. All I ever wanted was just the smallest sign of approval, a pat on the back, a simple 'well done'.

Thanks! Finally some approval.

Ok I'll move on.

Corrections

Thanks to comments from my supervisor, I have learnt the proper use of a semicolon and when it is wise to avoid 74 word sentences. I'm sure (I'm almost sure) that he always wanted the best for me, but the criticism sometimes gets hard to take. Yes, he has years more experience than me, but come on, when was the last time he did a real experiment? There's no way he could still actually get in the lab and create the data that I was producing, right?

What! But I think you actually mean "your data are crap"?

 Are you sure? It looks correct to me.

Ok, ok. Maybe I'll scrap it all. I should never have started this blog post in the first place.

I actually had a very good working relationship with my supervisor and he tells me it was only for this reason that he felt able to fully unleash when it came to marking my work. Likewise, I was comfortable taking the criticism, knowing (hoping) that it would only make my writing better in the end.

I wanted to end by pointing out your obvious superiority and how indebted I am for all your help...

Thanks, thought I would just give it a stab and see where it went.

What?!

Elemental errors

Every writer should be prepared to take a step back sometimes, hold their hands up and say "I'm sorry, I was wrong". Some startling information has just come to my attention and I feel compelled to share it. If this misjudgement on my behalf leads to a loss of trust, I understand and I thank those of you who still support me.

Last year I wrote a post about one of my favourite films and how it was almost perfect. Avatar is that film and there was one aspect that saddened me and which I deemed to be a major flaw in the film. This flaw was enough to take away that 5th star from the rating, to knock it off the top of the all time great list. 

Not so ridiculous after all

Therefore now, with much pleasure, I can announce that Avatar has been rerated and is now deemed perfect. Hooray! Yes I know it has giant blue people and floating mountains, but let's move on. Avatar centres on the hunt for unobtainium. That wonderfully named element, that unprecocious and most mature name for an element was previously my focus of distaste. But I now embrace the simplicity and accuracy with which the name came about.

You see, there are already not one but two elements, real elements, that have names as ridiculous as our unobtainium and  I have shamefully only just uncovered this informationfound. These culprits are lanthanum and dysprosium. These two elements, however, escape the derision and ridicule that was focussed on unobtainium simply because they are not English words. Lanthanum comes from the Greek meaning "to be hidden" and dysprosium, also from the Greek, meaning "hard to get".

So why don't we have hiddenium and hardtogetium on the periodic table? Well, quite frankly it's probably because they are stupid names that everyone would laugh at. But why should we laugh? Those names simply describe a property of the elements. Why do scientists feel the need to use fancy obsolete languages to describe the world? Is the universe not grand enough by itself? What's wrong with plain old English? Maybe if the names were in a more common language then it might make the science a little more informative and a little more accessible to the non-Greek speaking community.

Revamp for the shining dawn

Therefore I have decided to revamp a few other elements that would benefit from a new name. Bromine is the first one, named from the Greek for stench (because it smells bad) and so I will henceforth refer to it simply as stinkium. Another that needs changing is technetium. The name sounds quite futuristic, rather technical and that would be because it is radioactive and is not often found naturally. The man-made version has been around for less than 100 years and the name comes from the Greek for artificial. So this element will now be called fake-ium. Finally, there is gold. Yes gold, that most precious of metals has the chemical symbol Au, which is short for aurum (from Latin this time) meaning "shining dawn". So the next time somebody flashes their new jewellery at you just tell them what a nice piece of shinyum they have.

p.s.
I couldn't end this post without mentioning that sometimes using obscure words and languages can be beneficial to avoid embarrassment. Copper nanotubes really could do with a new name. Although Cu does originally come from the Latin...

Opening lines

My PhD thesis was submitted back in September. Then two months later, after almost forgetting everything I had done in the previous four years, I faced my viva. I felt a combination of a little bit of panic, a little bit of calm, a little bit of self-doubt and a little bit of over confidence. This mix left me feeling happy with what I had produced and only hoped that my examiners would be happy too.

In the end, it turned out to be a surprisingly enjoyable encounter, with compliments from the examiners on my titles and images at the start of each chapter. All those hours spent playing on ChemDraw and Pymol were not wasted after all. I like to go for grand sweeping statements and so my introduction was entitled,
"From the wilds of Nature to the confines of the lab".

The opening few paragraphs of my thesis introduction are shown below. It is pretty general to begin with as I wanted to write it so that anybody would be able to come along and pick up this volume and have a chance at understanding something before their brain started to hurt...

   "Taking a minute to think about the great variety of life on this planet can only leave you with a feeling of awe. The multitude of complex and beautiful forms that have covered our world seem to be innumerable in their differences. On the nanoscale these differences can become even more apparent. Even within a single species many different tissues are present and each may comprise many different types of cell.

   There is structure to everything. On every scale a new level of appreciation can be found, from the straight, solid trunks of huge redwood trees, to the flexible muscle tissue allowing our movement and to the delicate, helical DNA that encodes all existence. The huge variety of natural structures is easy to see around us and on the nanoscale bioarchitecture can be just as impressive.

   It took billions of years for the natural universe to be shaped around us, yet it is only in the last hundred years or so that humans have truly began to understand the fundamental principles that hold this world together. We are starting to better understand the complex mechanisms that govern how all these systems interact and scientists can now use this information to change and add to what nature has already created.

   A central goal of synthetic biology is to learn from nature and take inspiration. This knowledge can then be used to create bioinspired and novel artificial architectures and systems that meet our needs, demands and are limited only by our own imagination."

When checking over this, my supervisor wrote in the margin, "Camera pans out to reveal Tom standing on top of mountain. Roll credits..." Did anybody else try to go for something general or grand or just stick to the technical stuff for their thesis? I didn't hide anything funny in the text, like Labsolutely, but I managed to reference a YouTube video that I'm in and my very first reference was a tweet.

Arrr! A treasure map in Chem. Eur. J.!

Avast, me hearties! If there be one thing true 'bout academic journals, it is that there be not enough pirates involved. But lucky for us landlubbers, Chem. Eur. J. has put that to right with their latest cover. A treasure map! Aye and what a beauty she be.

This here map plots us a route well travelled by many. From the heart of that great land Europe, out to the wilds of the new colonies in the USA. I don't recommend using this depiction for your explorations though, the USA seems to have moved to where Africa traditionally lies. Nevertheless a great adventure it must be and anyway the map was charted by chemists not sailors.

The real excitement, as any good buccaneer knows, is of course in the hunt for treasure. This map takes us from a bislactim-ether, across the daring seas towards the final goal of tRNA. Along the way an unusual array of sea monsters present themselves, no sharks, krakens or even an octacoss, but instead those pesky amino acid intermediates and tRNA precursors. A healthy display of obstacles to overcome that only the bravest should attempt and which make any great journey even more rewarding. I can only hope that this discovery opened up chests full of funding for these fortune hunters...

But whatever happened to those great experimentalists of the seven seas, why are they all confined to landlocked labs nowadays? How do you think Blackbeard kept away all the grey hairs for so long? He was one of the first eminent colour chemists. Why do you think pirates were so obsessed with gold? They were all seafaring alchemists. What about the wooden legs and fondness for parrots? Well, some of them liked to branch out into prosthetics and zoology of course.

The Paper: The synthesis of Methylated, Phosphorylated, and Phosphonated 3'-Aminoacyl-tRNA^sec Mimics
Found at: Chem. Eur. J. 2013, 19, 15872-15878

A new synthetic route is mapped out by this transatlantic team. The group wished to probe the enzymatic mechanism for the biosynthesis of selenocysteine (sec), which is the only amino acid to be synthesized on its related transfer RNA (tRNA). They prepared complex tRNA^sec mimics that were methylated, phosphorylated and phosphonated, with an important amide bond from the ribose moiety that is crucially hydrolysis-resistant. The team wanted to develop these stable structures to gain more insight into the catalytic mechanism for the formation of selenocysteine by methods such as X-ray crystallography.

I'm sure much rum was consumed on the way to creating this little gem but the actual paper has absolutely no mention of buried treasure or pirates at all. The only map they use is 4-dimethylaminopyridine (DMAP), very disappointing indeed. Arr!

Conference tweeting

At the recent International Symposium on Macrocyclic and Supramolecular Chemistry conference (ISMSC8) there was a distinct lack of interactions through social media.

Whilst coffee breaks and poster sessions were full of interesting chats and discussions, the internet was almost completely ignored by the attendees. The ISMSC website encouraged the use of the hashtag #ISMSC before the conference began. But in the book of abstracts and throughout the conference there was no mention at all of Twitter, I was disappointed.

There were a couple tweets in the build up before the conference, giving hope of a social (media) bunch of people.

On my way to #ismsc ! I will present the last development of the peptide synthesising molecular machine. See you there.
— Guillaume De Bo (@GuillaumeDebo) July 6, 2013

But during the conference I found myself a little lonely with only Ivan Aprahamian and Guillaume De Bo really contributing. Ivan summed up the twitter experience calling the crowd "technologically challenged".

300+ plus chemists at #ismsc and only ~10 tweets
— Ivan Aprahamian (@aprahamian) July 10, 2013

With sponsorship from Nature Chemistry and the National Science Foundation, both pretty big in Twitterland, you might have expected some input from them. But alas no, it was left to Chem Comm to join us at the end to publicise the poster prize they were sponsoring.

Big congratulations to Brandon Hirsch (Indiana) winner of @ChemCommun grand poster prize - he won a future front cover of ChemComm! #ISMSC
— ChemComm (@ChemCommun) July 11, 2013

Another chemistry conference, ISACS11 is taking place this week with around 50 tweets just from yesterday, although mostly dominated by one Chemistry World journalist. Whilst this is not a huge amount it is still much better than at ISMSC8. Derek Lowe is also present and so he's busy blogging through some of the talks.

But what is going on here? Is it just a generation difference and the young folks need to step up or are some conferences missing a trick? Get the discussions going over some coffee sure, but continue it and spread it further on the internet.

What am I on about?

Seriously, what on earth am I going on about?

When trying to get your point across, have a debate or tell a story it is very important to say the right words. Communication is all about language and used well can be an incredibly powerful tool.

First some common words

I wanted to have a look at the language I've been using on this blog and see if I'm saying the right things or in fact (more likely) saying some very strange things. I thought that a quick trip over to Wordle, a nice website for making fancy word displays, could tell me what I wanted to know. The 75 most frequently used words from my last 10 blog posts are displayed below.

The most obvious and bizarre thing is that I apparently say first an awful lot! I say first more than any other word. Why? I don't see second in the wordle. Maybe I don't think second is important. Maybe I get so distracted with the first thing that I ramble on and then start talking about other questions like oh look questions is pretty big on the picture too.

Science is up there, journal, work, cover (I do talk about covers a lot) but there are other surprising big ones such as one. When do I say one? Am I talking about unique occurrences or again get bored after the first? I'd like to see more superlatives being used. Great is there, but I have much better words than that in my vocabulary. I think science is wonderful and we should use equally wonderful words to describe the amazing world we live in.

There's no point doing ground breaking work and not telling anyone about it and that's where words come in. Language can not only be useful but also fun. Playing around with your split infinitives can allow you to boldly go where no scientist has gone before.

Chemical poetry

This week on Twitter has been all about Real Time Chem, if you've somehow missed it then you are spending too much time in the lab.

 

Real Time Chem is a great community project on Twitter using the hashtag #RealTimeChem. Chemists all over the world have been sharing their daily experiences, lab work, cool articles and finding solace in the fact that they are not the only one failing to purify that unknown black mess.

Amongst other things this week, I have been doing some isothermal titration calorimetry (ITC). A wonderful technique (when it works) of measuring the binding enthalpies and association constants for non-covalent interactions. It's one of my favourite pieces of kit to use; it can give great insight into the success (or failure) of synthesised ligands and makes some pretty graphs.

 
After setting the experiment going I had about 30 minutes to procrastinate before the run was finished. So the internet gets fired up and through a strange connection of aimless link clicking, on websites including "Facebook", "Chemistry World" and "Jet2 cheap flights" (possibly not in that order), I came across Nobel prize winner Roald Hoffmann. Whilst obviously being a great scientist, Professor Hoffmann is also the author of a large number of poems. Some of his work focuses on chemistry and I thought what a fantastic medium poetry is for expressing the wonder and excitement of uncovering nature. I'm sure it would work equally well for portraying the torment and anguish at failed reactions, but let's stick to the wonder for now.

Back at the ITC, a flash of inspiration hit me and I came up with a poem all about the technique...


Isothermal Titration Calorimetry

Separate they contemplate their lives alone
But this the only thought they share
Not knowing their worlds are about to collide
Never loneliness will they again bear

One passively waits for an injection of life
Floating in their own little cell
The other poised to mix at the first chance
That stirring sensation will tell

But it takes another to set their paths
One who knows what makes them attract
To turn up the temperature, wait for the calm
Push the right buttons, see them interact

An initial touch, not sure where it will lead
At first you can never quite know
But a second feel, a larger reach
The heat given off starts to show

As if they had always been as one
They're together and will never part
The creator watches his successful work
Plotting their lives as a chart

Their story lives on for others to see
An example for anyone that looks
To find a guest for that elusive host
Written down in the wisest of books

Macro Letters "cool cover"

The relatively new ACS Macro Letters journal has joined Twitter ("finally", I hear you all call out)! Their 3rd ever tweet boldly publicises, "The cool cover for the sample Jan '13 issue". So let's see just how cool it is...

Cool. adjective, 1. moderately cold

The cover image for the first edition of 2013 really does stand out, but is it for being cool? Simple, is maybe the biggest compliment I could give it. Old fashioned, boring, forgettable are perhaps more fitting descriptions. Perhaps the editors had inadvertently left their first paper copy in the fridge and so were just commenting on how it was now at a fairly low temperature. Different journals do often distinguish between articles with catchy names, such as Chemical Science's "edge articles" and Angewandte's "hot papers". Using these definitions does lead to a distinction between papers in the same journal and is in part an (successful?) attempt to bring modern and exciting language into a sometimes dry, emotionless academic world.

But leaving behind this first attempt to reach out into the hip and trendy world of twittering, let's dissect the imagery...

Separated into four pictures, the bright colours and ambiguity of the images at least attracted my curiosity as to what this is all meant to mean. Some nice regular pattern going on at the top left with a close up at bottom right. The always fashionable brown shading, favoured by eccentric physicists, indicating an AFM image. In the top right corner we have a mold pressing in to a surface or perhaps a representation of some complimentary interactions? I'm a big fan of simple cartoons, but a little context would be nice. And finally at the bottom left we have some actual science with a cross-linked polymer structure that can possibly rotate. This piece of the puzzle confirms the polymeric patterning idea, although it would have been good of them to choose slightly nicer ChemDraw settings.

The January issues of ACS Macro Letters are open access, a rare and potentially lucrative way of attracting a new readership. But this also puts more of an emphasis on first impressions and therefore the cover. A great opportunity then to show off some eye-catching, "cool" scientific artwork. Opportunity missed I fear for this year.

Reversible covalent bonds

The paper: Thermally Induced Nanoimprinting of Biodegradable Polycarbonates Using Dynamic Covalent Cross-Links

Found at: ACS Macro Lett., 2013, 2 (1) 19-22

The actual science is not too bad at all. Copolymers are produced with furanyl and maleimido side chains which can undergo a Diels-Alder reaction at an elevated temperature of 130 °C. This process cross-links the polymer, giving it an increased rigidity. They use a nanoimprinting method to put a pattern into the polymer film at the high temperature and then when cooled down the design stays put. The effect is reversible, as when the temperature is increased once more the side chains break apart and, in the absence of a mold, will form new unstructured bonds with no overall shape on the macroscale. A simple and nicely demonstrated idea.