From Bern to CERN

It’s always nice to have an opportunity to see behind the curtain, and all the better if you feel like you’re doing it for a good reason. I was fortunate enough to be invited to join the delegation of Irish parliamentarian James Lawless TD on a fact-finding mission to CERN, the particle physics research centre which straddles the Swiss-French border in a way that is a metaphor for how it brings countries together.

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Deputy Lawless, Prof Ronan Nulty, Dr Kevin Byrne (both of UCD, Dublin; School of Physics and School of Medicine, respectively), and myself visited the facility and met with leaders and scientists who make it work. The aim of the trip was for CERN to put the case for Irish membership of the body to us, for us to see what benefits would come to the country via participation in the many exciting ground-breaking projects happening, and for Deputy Lawless, as opposition Science and Technology spokesperson on to bring this back to the relevant Oireachtas committees and lobby for Ireland making room in its 2019 budget for CERN membership.

It was wonderful to tour the sprawling campus of rolling fields which lie no less than 50 metres above the Large Hadron Collider and visit the various experiments set up along its 26.7-km circumference. At ALICE, CMS and LHCb (‘b’ for ‘beauty’, a flavour of quark) we met scientists, enthusiastic to talk about their work in everything from fundamental particle physics, to medicine and data processing. I was particularly interested by some work at ISOLDE using radioactive lanthanide isotopes in medical applications in hospitals near the collider. It was noted that while a few of the staff were Irish, in almost every case they also held another passport, because as a non-member state, our citizens do not have the same access to employment in this project as those from the 22 member states.

What most surprised me, as we looked at Irish-made semiconductors in action, and visited the factory where they design and assemble particle-accelerator parts, was that, while Irish people do make a contribution here, it’s often relying on loopholes or having a unique product that no one else can offer. Membership, however, would ensure us access on an equal footing to all other partners. Importantly this would mean returns to the Irish economy in every sector, allowing Irish firms to tender for contracts in construction, cleaning, catering, office supplies etc. in addition to the obvious high-tech and engineering opportunities. Big optimistic scientific exploration has positive knock-on effects throughout society.

One of the most obvious examples of unexpected by-products of investing in fundamental research is the very technology by which you are reading this post now. The World Wide Web was invented at CERN by Tim Berners-Lee. We were able to visit the office where this revolutionary technology came to life, almost as an afterthought, to share information from this worldwide collaborative research. And even if you don’t think quarks and neutrinos effect your life (they do!), at least the Web is tangible evidence that clever people allowed to create and explore together can do great things!

I’m calling this photo a Bunsen Byrner

Recently I was lucky enough to get an invite to the 11th CaRLa Catalysis Winter School in Heidelberg, and it was an eye-opening and engaging week, meeting with some of the rising talents within the fields of homogenous catalysis (among others) and hearing from speakers like Mats Tilset (check out his recent article on trans-mutation of gold – a pun I really approve of) and Ilan Marek about their contributions to the field. In particular, I enjoyed having a week to spend time discussing posters with the other attendees; normally this is the most rushed part of any conference, as you try to simultaneously stand by your own poster and see as many others as possible. The Winter School invited flash presentations on all the posters, and gave ample time and coffee over which to really get into the details!

I was able to present my on-going research from my Marie Curie Individual Fellowship (GLYCONHC, MSCA-IF 749549), where I investigate the impact of including carbohydrates in the structure of metal-NHC catalysts. The work is progressing well, and I think I benefited from being able to discuss hurdles in the project with catalysis experts and my peers during the week.

CaRLa (The Catalysis Reasearch Laboratory) is an institute at University of Heidelberg, supported by BASF, a giant of the chemical industry. As a result, the research they undertake is very aligned to real economic and market challenges. We were given a tour of the massive site at Ludwigshafen on the river Rhine, and the scale of production in just the one plant we visited was staggering – round-bottom flasks just can’t compete with building-sized reactors!

One interesting historical note about Heidelberg is that it is where Robert Bunsen did much of his pioneering work in 19th century chemistry and – famously – gifting us with the most widely known (and least widely-used nowadays) apparatus of the chemistry lab. I couldn’t walk past his statue without getting a punny selfie- the “Bunsen Byrner”!

CASE 2015 on the Cover of Supramolecular Chemistry

It was great to read a comprehensive write-up of CASE2015 in Supramolecular Chemistry (http://dx.doi.org/10.1080/10610278.2016.1150595). I designed the website for this conference and helped out with logistics. Many of the photos that appear in the article were taken by me – great that they can be used to show the community how productive a few days it was.

Gunnlaugsson Group, Trinity College Dublin

This month’s cover of Supramolecular Chemistry

This month’s issue of the Taylor & Francis journal Supramolecular Chemistry features a review on CASE 2015 by Robert Elmes, with a picture from the conference on the cover. CASE 2015 (Catalysis and Sensing for our Environment) was part-hosted in Trinity College Dublin, and organised by Thorri, along with Aisling Hume (TCD), Donal O’Shea (RCSI), and Robert Elmes (Maynooth).

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It was great news today to hear the 2016 Nobel Prize in Chemistry was awarded to some pioneers in the field of supramolecular chemistry: Jean-Pierre Sauvage, J Fraser Stoddart and Bernard Feringa. During my PhD studies, I read the work of Sauvage and Stoddart a lot for inspiration; they are constantly producin Sauvage's article in Tetrahedron Letters 1983 g beautiful and elegant structures from discrete molecular units interacting in controlled ways. While most of my PhD ended up focussing on lanthanide-directed self assembly and luminescent compounds, I was always chasing the goal of interlocked structures and remember being fascinated by Sauvage’s early results describing the first metal-directed catenanes (Tetrahedron Letters 1983), mechanically interlocked rings with no chemical bonds between the two molecular components. This article laid the groundwork for the tiny molecular machines for which the trio were given the prestigious award today. Stoddart’s contributions to controlling rotaxane movement and Feringa’s publication of the first ‘molecular motor’ were remarkable breakthroughs, but the elegance of interlocked systems has fascinated me since I first saw them and I was delighted to finally publish some of my own work on catenanes in Angewandte Chemie this year, contributing in a small way to the ever-expanding supramolecular field.

To end this post, I’ll add a quote from my PhD supervisor Prof Thorri Gunnlaugsson (Trinity College Dublin) talking today about Sir JF Stoddart, a man he greatly admires and who received an honorary doctorate from Trinity a few years ago:

Speaking about the significance of the work that led to him sharing the 2016 Nobel Prize, Professor of Chemistry at Trinity, Thorri Gunnlaugsson, said: This is truly a fantastic day for chemists and specially for those of us who are involved in the development of supramolecular and nano-chemistry. The development of molecules that are functional and can carry out actions such as programmed operations, and can mimic macroscopic function on the nanoscale, such as that of machines, has been at the heart of this area of chemistry.”

“Today’s announcement of the Nobel Prize in Chemistry being awarded to Professors Stoddart, Sauvage and Feringa, for their development of molecular machines, acknowledges the major scientific achievement made to date in this important field.”

80 Days featured on Broadsheet.ie

Irish “news source for the bemused” Broadsheet.ie has given a plug to our podcast 80 Days, which – I think – means we’ve definitely made it! I’m a big fan of Broadsheet’s mixture of hard-hitting corruption exposés, parish bulletin-board style notices about lost bikes and things involving Irish people all over the world. It makes for the ideal combination of news and humour for my generation.

Their article focusses on the fact that Luke, Mark and I are all Irish men abroad, using this medium to explore the world and maintain connections around it. I think (and hope) our project will resonate with a lot of people. You can read it by clicking on this link.

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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

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)

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

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Monosaccharide azides – challenges

I am not a carbohydrate chemist by training. I remember as an undergrad being very intimidated by the chair conformations, Fischer projections and the seemingly endless chiral centres, so I filed that knowledge away as “unlikely to use” and focussed on supramolecular chemistry. In recent times however, I couldn’t help but be drawn back to looking at these natural sources of chirality, particularly as a next direction to turn after my investigations to amino-acid derived triazolyl(pyridine) ligands. Sugars seemed a way to get chirality and solubility all in one go with the potential for biological interactions as a bonus.

oac-n3 sugar scheme

So, I began researching how to make various monosaccharide azides of the above form in a selective way, so that I could very the stereochemical properties at will when making families of compounds. It required a lot of searching to find everything I need, so I will present it here for anyone else who might be interested in making (in particular) tetra-acetylated glucose, galactose and mannose with an azide in the anomeric position, either α or β.

For glucose and galactose, buried in the German-language pages of a paper by Paulsen et al. from 1974 is a Lewis acid catalysed reaction, which selectively gives the β-azide derivative directly from reacting the penta-acetylated sugar (with mixed anomeric configuration) with tin(IV) chloride and trimethylsilyl-azide. This reaction has some nasty components and leaves you with a lot of tin-contaminated water to dispose of. I was delighted, therefore to find that the reaction can also be carried out rather straightforwardly from the commercially-available α-bromo tetra-acetylated compounds (for glucose and galactose) by simply heating overnight with sodium azide in a water-acetone mixture, a methodology that comes from that oft-overlooked source: Journal of Chemical Education (Norris and co-workers, 2012).

With mannose, things are a little trickier! It differs from glucose and galactose, by having the C-2 hydroxyl group in the axial position, and since this is adjacent to the reactive anomeric position, this will influence the outcome. Using tin(IV) chloride, as above, for instance, will yield the α-azide. This is a result of the reaction, as above, favour a 1,2-trans geometry. For the purposes of my research, however, I was really interested in using the β-azide to make a compound which differed from the glucose derivative in only one position. After a lot of hunting, I stumbled upon a two-step reaction in an article by Prof Paul Murphy from NUI Galway (Chem. Eur. J. 2013), which had originated with an early study from University of California. This approach generated an α-glycosyl-iodide in situ and reaction with tetrabutylammonium azide gave the desired β-azide product in good yields. Importantly, this gives β-azides in all cases and allowed me access to the building blocks I need to pursue my current project.

“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.

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”.

Sam giving his talk

Sam and A P at the poster session

Oxana with her poster

Anna presenting her poster

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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