S1E06: Liberia

This is probably the darkest history we’ve researched while doing “80 Days”, including civil war, cannibalism and the Ebola epidemic, but still makes for a fascinating listen in spite of that.

80 Days

Audio: S1E06 Liberia

This week in 80 Days, we looked at Liberia, a small country on the west coast of Africa. Founded by freed American and Caribbean slaves, Liberia is Africa’s oldest republic and takes its name from the the Latin phrase meaning “Land of the Free.” Unfortunately, the country is best known for a long and bloody civil war that look place in the 1990s and 2000s, and more recently for the Ebola epidemic of 2014. The lush, rainforested country is just 700 kilometres or 430 miles north of the equator, and is bordered by Sierra Leone to its west, Guinea to its north and Ivory Coast (Côte d’Ivoire) to its east. Today, the country is home to around 4.5 million inhabitants, although most are native Africans rather than the descendants of freed slaves. It maintains strong ties to America, and even has…

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S1E01: Namibia

S1E01: Namibia

The first episode of my new podcast with Luke and Mark. A particular highlight of researching Namibia for me was the role the Garda Síochána played in helping the transition to democracy.

80 Days

Audio: S1E01 Namibia
In this week’s first episode of 80 Days, we are talking about Namibia, a large African nation, sharing its southern border with South Africa and with an Atlantic coastline of almost 1,000 miles, known as the ‘Skeleton Coast’. Major features include the Namib Desert, considered to be the oldest desert in the world and the famous Fish River Canyon. The country is roughly similar in size to Pakistan bigger than France or Germany and one of the driest places on earth. Its history includes colonisation by Germany and South Africa, with independence coming in the 1990s. Today it is a stable and developing young democracy. Your hosts are Luke Kelly@thelukejkelly, Mark Boyle@markboyle86 and Joe Byrne@anbeirneach, in Hong Kong, the UK and Ireland, respectively. (Music by Thomas O’Boyle)

File:Namibia homelands 78.jpeg

Namibia’s history spans over many many centuries and is defined by the movement of…

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“Captured and put in chains” – new article in Angewandte Chemie

“Captured and put in chains” – new article in Angewandte Chemie

I recently finished working in Trinity College Dublin after five and a half productive years. My final project was completed in the weeks before I left and submitted to the prestigious journal Angewandte Chemie on the 1st April, the day I started in my new position at Universität Bern.

This article has just come out, and I’m rather proud of it, and happy that it is a fitting ending to my time in Dublin. My original goal in Thorri Gunnlaugsson’s research groupwas to form interlocked molecules, such as “catenanes”, but this challenging goal kept moving further down the queue as we discovered new and interesting ways to exploit the “btp” motif (which has been the topic of all my research to date). But finally, and somewhat unexpectedly, we achieved this goal.

Creating these new structures built upon interesting behaviour we reported in our Chemistry – A European Journal article early this year – where we saw that btp molecules could interact with each other, forming pairs through weak hydrogen bonding. We wondered if this could be used to pre-organise molecules together in such a way that they could be ‘clipped’ together into interlocked rings (by “RCM”, as outlined in the Scheme above). This approach has occasionally been reported before for amides,but not for molecules like the ones we describe.

A representation of the formation of catenanes from btp ligands

In fact, this reaction was more successful than expected – and in the first case I tried, we were surprised to find the majority product (50% yield) was the interlocked “catenane”, with independent non-interlocked rings also observed. We were able to fully identify and characterise these molecules using X-ray crystallographic analysis, giving the clear pictures below (thanks to Dr Salvador Blasco).

These were nice structures, but I wanted them to do something more than look pretty! Discussions with my friend Anna Aletti opened up the idea that the cavity in the middle of the structures might be a perfect fit for some negatively charged ion guest, such as chloride, nitrate or sulfate – none of these ions did very much, but phosphate (the tetrahedral H2PO4- ion), on the other hand, caused changes in the “catenane” host, indicating specific interactions between these two molecules. This was exciting. It makes these the first catenanes in the literature to have such interactions with tetrahedral anions.

The catenane acts as a selective host for phosphate, as can be seen from changes in the NMR spectrum

Detailed analysis of the formation of these interesting compounds, as well as their adducts with phosphate was important to strengthening these results and making sure we understood what we were seeing. Working closely with Dr Gary Hessman, Technical Officer at TCD, allowed further insight into the systems and their composition.

If any of this sounds interesting, then you should read the article (http://dx.doi.org/10.1002/anie.201603213) or at least look at the pictures! One fun advantage of publishing in Angewandte Chemie is that they translate your abstract into German (which I am currently learning), which means I now know the useful everyday term “Triazolylwasserstoffbrüken“, which – of course – means “triazolyl hydrogen-bonding interactions”. I now use that in the pubs of Bern almost daily!

TG Group travel to Southampton for Supramolecular Symposium

It was nice to catch up with some old colleagues in Southampton and chat molecular logic with my “academic grandfather” AP de Silva, as well as why he enjoyed being educated by Buddhist monks and Catholic nuns at the same time in Sri Lanka!

Gunnlaugsson Group, Trinity College Dublin

Anna Aletti, Samuel Bradberry and Dr. Oxana Kotova of the TG group attended Southampton Supramolecular Chemistry Symposium on the 24th of June 2016.

delegates Southamption Supramolecular Symposium 2016 Delegates

All of them presented posters and, in addition, Samuel gave an excellent talk on “Lanthanide Luminescent Logic – functional organic scaffolds and soft polymers gels as logic gate mimics”.

DSC_0048 Sam giving his talk

DSC_0036 Sam and A P at the poster session

DSC_0043 Oxana with her poster

DSC_0035 Anna presenting her poster

2016-06-24 18.02.36 A P de Silva, Oxana, Anna, Joe and Sam at the drinks reception

Our former group member Dr. Joseph Byrne who is currently a postdoctoral researcher in the University of Bern attended the conference as well and presented a poster on his recent work published in Angew. Chem. Int. Ed. on self-templated btp [2]Catenane.

The meeting included speakers and posters from UK Universities and beyond, including an outstanding lecture from the…

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Surprisin’ horizon 

Now that summer is here, something keeps happening to me on my cycle to work, and it keeps on surprising me. The cloudy sky of spring has lifted, more or less permanently, and so as I round  one particular corner on my route, I see the alpine vista over the train lines. I can’t help but smile stupidly every time. The horizon is beautiful when the sky is blue in contrast to the snow capped peaks. And I consistently forget that I will see this view almost every day. It’s nice to smile on the way to work!  

Shelley-esque weather

Disclaimer: So, I’ve been reading Frankenstein recently in order to fully associate my new Swiss situation (more on that some other time perhaps), and as a result, my view of weather here is a bit skewed.

On Friday, we went for drinks after work because the sun was shining brightly. Summer had finally come to Bern and was to be enjoyed. It was great, getting to know some new people and learning some of the important differences between Hochtdeutsch (standard German) and Bärndutsch (the wonderful and specific dialect of Bern). For example, the past tense in Bern is always the perfect (“I have been in Ireland / Ich bin in Irland gegessen / i bi in Irland g’si “) and never the imperfect (“I was / Ich war“). Good information for someone who wants to be a chameleon!

But I digress. As the sun set, the air got heavy and suddenly out of the corner of my eye, I caught a glimpse of a flash of light. I assumed that someone at the other end of the park was taking a photograph with a very strong flash… I couldn’t have been more wrong, but I didn’t think much more about it.

Over the next half an hour or so, these flashes became more frequent, and soon were accompanied by low rumbles echoing from the sky across the plain on which Bern sits. The forks of lightning were starkly visible, standing out against the dark clouds which rolled in. Drizzle began to fall and our drinking-in-the-sun broke up. One of my new acquaintances asked me how far I had to cycle. I told him it was a twenty minute trip. He chuckled and wished me luck. I’m Irish – what’s a bit of rain? That was my naive thought!

Beginning my cycle, all was well, though the streets were markedly empty. The gaps between lightning and thunder became shorter and I counted the seconds with interest; the rain grew heavier. I joined a pack of terrified cyclists, all pelting their way full speed down the long road along the train tracks. Then heaven fell!

The cyclists peeled off one by one, seemingly evaporating into side streets and buildings along the road, leaving me alone to face the wall of water that crashed down without mercy or respite. It was incredible. I was only minutes from home, but my hat and coat were ineffectual. In seconds, I was the wettest I’ve ever been! My jeans darkened three shades and clung to my skin and my shoes were literally full of water. Removing my shoes had the same sound as taking off a wetsuit!

I have gained an appreciation and respect for the changeable weather here. Thunder storms are serious about living up to their maximum potential!

Now I just need to erect a lightning rod on my lab and I can start the project of bringing reanimated monsters to life!

The Gurten – my local “mountain”

I like hiking – or at least, I did in Ireland. A look to the scenery all around me in Switzerland suggests that my understanding of the word “hike” may need an upgrade. The Wicklow “Mountains” where I so often wandered with friends and colleagues are only foothills on the scale of the Alps. The Great Sugarloaf (An Beannach Mór), the pointy quartzite cone visible from anywhere high in Dublin or Wicklow is a mere 500 metres at its summit, and I considered that a considerable day out!

The Great Sugarloaf and me in 2014
The Great Sugarloaf and me in 2014

With nothing else planned for my third Saturday here, my new co-worker was interested in an outdoor activity, so we met at the train station and walked up the Aare River (which I had only seen briefly to date) southwards out of town. It was a decent trek to the base of the mountain, but it was a fine sunny day and I was keen to explore my new home.

Eventually coming to the tram stop where a lazier adventurer would have started, we ignored the cool retro furnicular which climbed the slope of the hill on mechanisms of cogs and rope. I should, of course, say “mountain”. It’s 858 metres at the peak – that beats anything I’ve done before, I think.IMG_7209 IMG_7211

It was a steep climb up the wooded path. We were, however, constantly being passed out by infuriatingly fit old Swiss people zooming up and down the slope. Everyone is fit here – I suppose that’s what they all do on Sundays when the city becomes eerily quiet and empty. If not, they’d all just be hiding indoors. With this scenery on your doorstep, why wouldn’t you be hiking or climbing or skiing? We were treated with occasional glances back up the river to the Old City of Bern which is a UNESCO World Heritage Site.

Altstadt Bern
Altstadt Bern

Anyway, we reached the top of the mountain, turned left and the scene opened out – I looked out over the vista and saw the Alps in the distance, straddling the horizon… so that’s what a mountain looks like! I mean, they’re really big. Still snow-capped into Spring, despite the sun. Jungfrau mountain in the distance (for comparison to our paltry examples) is a whopping 4158 metres high! The peaks were away over the rolling green manicured lawns of the park on top of Gurten.  It’s truly an idyllic scene.

The Bernese Oberland
The Bernese Oberland from the top of Gurten

We strolled around the top, stumbling upon a meadow, full of dandelions and other wildflowers; it was a Sound of Music moment. In the distance, across the valley, the sound of cowbells drifted across on the air as a herd wandered on the far slope. They made quite the noise with only a few cowbells, I can only imagine the din if there were more cowbell [I couldn’t resist].

"What a lovely meadow!"
“What a lovely meadow!”

Suitably put in my place by my new understanding of what “tall” means, we wandered back by the river Aare and saw the local celebrities, the Bernese Bears, just waking up from hibernation. They’ve been moved out of their pit into a very pleasant and spacious environment.

The bear in Bern having a kip
The bear in Bern having a kip

I’m living in a nice country now! Plenty of peaks to attempt, although I may have to be more satisfied with shoulders going forward.